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Li Y, Xun Z, Long J, Sun H, Yang X, Wang Y, Wang Y, Xue J, Zhang N, Zhang J, Bian J, Shi J, Yang X, Wang H, Zhao H. Immunosuppression and phenotypic plasticity in an atlas of human hepatocholangiocarcinoma. Hepatobiliary Surg Nutr 2024; 13:586-603. [PMID: 39175731 PMCID: PMC11336540 DOI: 10.21037/hbsn-23-400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/30/2023] [Indexed: 08/24/2024]
Abstract
Background Hepatocholangiocarcinoma (H-ChC) has the clinicopathological features of both hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA) and is a more aggressive subtype of primary hepatic carcinoma than HCC or iCCA. Methods We sequenced 91,112 single-cell transcriptomes from 16 human samples to elucidate the molecular mechanisms underlying the coexistence of HCC and iCCA components in H-ChC. Results We observed two molecular subtypes of H-ChC at the whole-transcriptome level (CHP and CIP), where a metabolically active tumour cell subpopulation enriched in CHP was characterized by a cellular pre-differentiation property. To define the heterogeneity of tumours and their associated microenvironments, we observe greater tumour diversity in H-ChC than HCC and iCCA. H-ChC exhibits weaker immune cell infiltration and greater CD8+ exhausted T cell (Tex) dysfunction than HCC and iCCA. Then we defined two broad cell states of 6,852 CD8+ Tex cells: GZMK+ CD8+ Tex cells and terminal CD8+ Tex cells. GZMK+ CD8+ Tex cells exhibited higher infiltration of after treatment in H-ChC, the effector scores and expression of the immune checkpoints of them greatly increased after immunotherapy, which indicated that H-ChC might be more sensitive than HCC or iCCA to immunotherapy. Conclusions In this paper, H-ChC was explored, hoping to contribute to the study of mixed tumours in other cancers.
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Affiliation(s)
- Yiran Li
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Ziyu Xun
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Junyu Long
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Huishan Sun
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xu Yang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Yanyu Wang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Yunchao Wang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Jingnan Xue
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Nan Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Junwei Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Jin Bian
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Jie Shi
- Division of Pulmonary and Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xiaobo Yang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Hanping Wang
- Division of Pulmonary and Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Haitao Zhao
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
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Viet-Nhi NK, Minh Quan T, Cong Truc V, Anh Bich T, Hoang Nam P, Le NQK, Chen PY, Hung SH. Multi-Omics Analysis Reveals the IFI6 Gene as a Prognostic Indicator and Therapeutic Target in Esophageal Cancer. Int J Mol Sci 2024; 25:2691. [PMID: 38473938 DOI: 10.3390/ijms25052691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
The role of the IFI6 gene has been described in several cancers, but its involvement in esophageal cancer (ESCA) remains unclear. This study aimed to identify novel prognostic indicators for ESCA-targeted therapy by investigating IFI6's expression, epigenetic mechanisms, and signaling activities. We utilized public data from the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA) to analyze IFI6's expression, clinical characteristics, gene function, pathways, and correlation with different immune cells in ESCA. The TIMER2.0 database was employed to assess the pan-cancer expression of IFI6, while UALCAN was used to examine its expression across tumor stages and histology subtypes. Additionally, the KEGG database helped identify related pathways. Our findings revealed 95 genes positively correlated and 15 genes negatively correlated with IFI6 in ESCA. IFI6 was over-expressed in ESCA and other cancers, impacting patient survival and showing higher expression in tumor tissues than normal tissues. IFI6 was also correlated with CD4+ T cells and B cell receptors (BCRs), both essential in immune response. GO Biological Process (GO BP) enrichment analysis indicated that IFI6 was primarily associated with the Type I interferon signaling pathway and the defense response to viruses. Intriguingly, KEGG pathway analysis demonstrated that IFI6 and its positively correlated genes in ESCA were mostly linked to the Cytosolic DNA-sensing pathway, which plays a crucial role in innate immunity and viral defense, and the RIG-I-like receptor (RLR) signaling pathway, which detects viral infections and activates immune responses. Pathways related to various viral infections were also identified. It is important to note that our study relied on online databases. Given that ESCA consists of two distinct subgroups (ESCC and EAC), most databases combine them into a single category. Future research should focus on evaluating IFI6 expression and its impact on each subgroup to gain more specific insights. In conclusion, inhibiting IFI6 using targeted therapy could be an effective strategy for treating ESCA considering its potential as a biomarker and correlation with immune cell factors.
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Affiliation(s)
- Nguyen-Kieu Viet-Nhi
- International Master/Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Tran Minh Quan
- Department of Thoracic Surgery, Cho Ray Hospital, Ho Chi Minh City 700000, Vietnam
| | - Vu Cong Truc
- Department of Otolaryngology, Faculty of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam
| | - Tran Anh Bich
- Department of Otolaryngology, Cho Ray Hospital, Ho Chi Minh City 700000, Vietnam
| | - Pham Hoang Nam
- Department of Otolaryngology, Cho Ray Hospital, Ho Chi Minh City 700000, Vietnam
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- AIBioMed Research Group, Taipei Medical University, Taipei 110, Taiwan
- Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei 110, Taiwan
- Translational Imaging Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Po-Yueh Chen
- Department of Otolaryngology, Wan Fang Hospital, Taipei Medical University, Taipei 110, Taiwan
- Department of Otolaryngology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Shih-Han Hung
- International Master/Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Department of Otolaryngology, Wan Fang Hospital, Taipei Medical University, Taipei 110, Taiwan
- Department of Otolaryngology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
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Wan L, Wang S, Xie Z, Ren H, Xie L, Luo S, Li M, Xie Z, Fan Q, Zeng T, Zhang Y, Zhang M, Huang J, Wei Y. Chicken IFI6 inhibits avian reovirus replication and affects related innate immune signaling pathways. Front Microbiol 2023; 14:1237438. [PMID: 38033564 PMCID: PMC10687481 DOI: 10.3389/fmicb.2023.1237438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Interferon-alpha inducible protein 6 (IFI6) is an important interferon-stimulated gene. To date, research on IFI6 has mainly focused on human malignant tumors, virus-related diseases and autoimmune diseases. Previous studies have shown that IFI6 plays an important role in antiviral, antiapoptotic and tumor-promoting cellular functions, but few studies have focused on the structure or function of avian IFI6. Avian reovirus (ARV) is an important virus that can exert immunosuppressive effects on poultry. Preliminary studies have shown that IFI6 expression is upregulated in various tissues and organs of specific-pathogen-free chickens infected with ARV, suggesting that IFI6 plays an important role in ARV infection. To analyze the function of avian IFI6, particularly in ARV infection, the chicken IFI6 gene was cloned, a bioinformatics analysis was conducted, and the roles of IFI6 in ARV replication and the innate immune response were investigated after the overexpression or knockdown of IFI6 in vitro. The results indicated that the molecular weight of the chicken IFI6 protein was approximately 11 kDa and that its structure was similar to that of the human IFI27L1 protein. A phylogenetic tree analysis of the IFI6 amino acid sequence revealed that the evolution of mammals and birds was clearly divided into two branches. The evolutionary history and homology of chickens are similar to those of other birds. Avian IFI6 localized to the cytoplasm and was abundantly expressed in the chicken lung, intestine, pancreas, liver, spleen, glandular stomach, thymus, bursa of Fabricius and trachea. Further studies demonstrated that IFI6 overexpression in DF-1 cells inhibited ARV replication and that the inhibition of IFI6 expression promoted ARV replication. After ARV infection, IFI6 modulated the expression of various innate immunity-related factors. Notably, the expression patterns of MAVS and IFI6 were similar, and the expression patterns of IRF1 and IFN-β were opposite to those of IFI6. The results of this study further advance the research on avian IFI6 and provide a theoretical basis for further research on the role of IFI6 in avian virus infection and innate immunity.
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Affiliation(s)
- Lijun Wan
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, Guangxi, China
| | - Sheng Wang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, Guangxi, China
| | - Zhixun Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, Guangxi, China
| | - Hongyu Ren
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, Guangxi, China
| | - Liji Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, Guangxi, China
| | - Sisi Luo
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, Guangxi, China
| | - Meng Li
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, Guangxi, China
| | - Zhiqin Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, Guangxi, China
| | - Qing Fan
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, Guangxi, China
| | - Tingting Zeng
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, Guangxi, China
| | - Yanfang Zhang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, Guangxi, China
| | - Minxiu Zhang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, Guangxi, China
| | - Jiaoling Huang
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, Guangxi, China
| | - You Wei
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Nanning, Guangxi, China
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Davenport AM, Morris M, Sabti F, Sabti S, Shakya D, Hynds DL, Cheriyath V. G1P3/IFI6, an interferon stimulated protein, promotes the association of RAB5 + endosomes with mitochondria in breast cancer cells. Cell Biol Int 2023; 47:1868-1879. [PMID: 37598317 DOI: 10.1002/cbin.12079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/31/2023] [Accepted: 08/05/2023] [Indexed: 08/21/2023]
Abstract
G1P3/IFI6 is an interferon stimulated gene with antiapoptotic, prometastatic, and antiviral functions. Despite its pleiotropic functions, subcellular localization of G1P3 remains unclear. Using biochemical- and confocal microscopic approaches, this study identified the localization of G1P3 in organelles of the endomembrane system and in the mitochondria of breast cancer cells. In cell fractionation studies, both interferon-induced endogenous- and stably expressed G1P3 cofractionated with affinity-isolated mitochondria. Results of the protease protection assay have suggested that ~24% of mitochondrial G1P3 resides within the mitochondria. Conforming to this, confocal microscopy studies of cells stably expressing epitope-tagged G1P3 (MCF-7/G1P3-FLAG), identified its localization in mitochondria (~38%) as well as in ER, trans-Golgi network (TGN), lysosomes, and in RAB5 positive (RAB5+ ) endosomes. These results suggested the trafficking of G1P3 from TGN into endolysosomes. Both G1P3 and RAB5 were known to confer apoptosis resistance through mitochondrial stabilization. Therefore, the effects of G1P3 on the localization of RAB5 in mitochondria were tested. Compared to vector control, the co-occurrence of RAB5 with the mitochondria was increased by 1.5-fold in MCF-7/G1P3-FLAG expressing cells (p ≤ .005). Taken together, our results demonstrate a role for G1P3 to promote the association of RAB5+ endosomes with mitochondria and provide insight into yet another mechanism of G1P3-induced cancer cell survival.
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Affiliation(s)
- Anne M Davenport
- Department of Biological and Environmental Sciences, Texas A&M University-Commerce, Commerce, Texas, USA
- Department of Biology, Texas Woman's University, Denton, Texas, USA
| | - Madeleine Morris
- Department of Biological and Environmental Sciences, Texas A&M University-Commerce, Commerce, Texas, USA
| | - Fatima Sabti
- Department of Biological and Environmental Sciences, Texas A&M University-Commerce, Commerce, Texas, USA
| | - Sarah Sabti
- Department of Biological and Environmental Sciences, Texas A&M University-Commerce, Commerce, Texas, USA
| | - Diksha Shakya
- Department of Biological and Environmental Sciences, Texas A&M University-Commerce, Commerce, Texas, USA
| | - DiAnna L Hynds
- Department of Biology, Texas Woman's University, Denton, Texas, USA
| | - Venugopalan Cheriyath
- Department of Biological and Environmental Sciences, Texas A&M University-Commerce, Commerce, Texas, USA
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5
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Pan C, Hu T, Liu P, Ma D, Cao S, Shang Q, Zhang L, Chen Q, Fang Q, Wang J. BM-MSCs display altered gene expression profiles in B-cell acute lymphoblastic leukemia niches and exert pro-proliferative effects via overexpression of IFI6. J Transl Med 2023; 21:593. [PMID: 37670388 PMCID: PMC10478283 DOI: 10.1186/s12967-023-04464-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/22/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND The tumor microenvironment (TME) is a supportive environment responsible for promoting the growth and proliferation of tumor cells. Current studies have revealed that the bone marrow mesenchymal stem cells (BM-MSCs), a type of crucial stromal cells in the TME, can promote the malignant progression of tumors. However, in the adult B-cell acute lymphoblastic leukemia (B-ALL) microenvironment, it is still uncertain what changes in BM-MSCs are induced by leukemia cells. METHODS In this study, we mimicked the leukemia microenvironment by constructing a BM-MSC-leukemia cell co-culture system. In vitro cell experiments, in vivo mouse model experiments, lentiviral transfection and transcriptome sequencing analysis were used to investigate the possible change of BM-MSCs in the leukemia niche and the potential factors in BM-MSCs that promote the progression of leukemia. RESULTS In the leukemia niche, the leukemia cells reduced the MSCs' capacity to differentiate towards adipogenic and osteogenic subtypes, which also promoted the senescence and cell cycle arrest of the MSCs. Meanwhile, compared to the mono-cultured MSCs, the gene expression profiles of MSCs in the leukemia niche changed significantly. These differential genes were enriched for cell cycle, cell differentiation, DNA replication, as well as some tumor-promoting biofunctions including protein phosphorylation, cell migration and angiogenesis. Further, interferon alpha-inducible protein 6 (IFI6), as a gene activated by interferon, was highly expressed in leukemia niche MSCs. The leukemia cell multiplication was facilitated evidently by IFI6 both in vitro and in vivo. Mechanistically, IFI6 might promote leukemia cell proliferation by stimulating SDF-1/CXCR4 axis, which leads to the initiation of downstream ERK signaling pathway. As suggested by further RNA sequencing analysis, the high IFI6 level in MSCs somewhat influenced the gene expression profile and biological functions of leukemia cells. CONCLUSIONS BM-MSCs in the leukemia niche have varying degrees of changes in biological characteristics and gene expression profiles. Overexpression of IFI6 in BM-MSCs could be a key factor in promoting the proliferation of B-ALL cells, and this effect might be exerted through the SDF-1/CXCR4/ERK signal stimulation. Targeting IFI6 or related signaling pathways might be an important measure to reduce the leukemia cell proliferation.
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Affiliation(s)
- Chengyun Pan
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, 28 Guiyi St., Yunyan District, Guiyang, 550004, Guizhou, China
- School of Basic Medical Sciences, Guizhou Medical University, Guizhou, China
- Hematological Institute of Guizhou Province, Guizhou, China
| | - Tianzhen Hu
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, 28 Guiyi St., Yunyan District, Guiyang, 550004, Guizhou, China
- Hematological Institute of Guizhou Province, Guizhou, China
- Guizhou Province Hematopoietic Stem Cell Transplantation Centre and Key Laboratory of Hematological Disease Diagnostic and Treatment Centre, Guizhou, China
| | - Ping Liu
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, 28 Guiyi St., Yunyan District, Guiyang, 550004, Guizhou, China
- Hematological Institute of Guizhou Province, Guizhou, China
| | - Dan Ma
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, 28 Guiyi St., Yunyan District, Guiyang, 550004, Guizhou, China
- Hematological Institute of Guizhou Province, Guizhou, China
- Guizhou Province Hematopoietic Stem Cell Transplantation Centre and Key Laboratory of Hematological Disease Diagnostic and Treatment Centre, Guizhou, China
| | - Shuyun Cao
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, 28 Guiyi St., Yunyan District, Guiyang, 550004, Guizhou, China
- Hematological Institute of Guizhou Province, Guizhou, China
| | - Qin Shang
- Department of Pharmacy, Affiliated Hospital of Guizhou Medical University, 28 Guiyi St., Yunyan District, Guiyang, 550004, Guizhou, China
| | - Luxin Zhang
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, 28 Guiyi St., Yunyan District, Guiyang, 550004, Guizhou, China
- Hematological Institute of Guizhou Province, Guizhou, China
| | - Qingzhen Chen
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, 28 Guiyi St., Yunyan District, Guiyang, 550004, Guizhou, China
- Hematological Institute of Guizhou Province, Guizhou, China
| | - Qin Fang
- Department of Pharmacy, Affiliated Hospital of Guizhou Medical University, 28 Guiyi St., Yunyan District, Guiyang, 550004, Guizhou, China
| | - Jishi Wang
- Department of Hematology, Affiliated Hospital of Guizhou Medical University, 28 Guiyi St., Yunyan District, Guiyang, 550004, Guizhou, China.
- School of Basic Medical Sciences, Guizhou Medical University, Guizhou, China.
- Hematological Institute of Guizhou Province, Guizhou, China.
- Guizhou Province Hematopoietic Stem Cell Transplantation Centre and Key Laboratory of Hematological Disease Diagnostic and Treatment Centre, Guizhou, China.
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Qin L, Fan W, Zheng F, Chen H, Qian P, Li X. Swine IFI6 confers antiviral effects against Japanese encephalitis virus in vitro and in vivo. J Gen Virol 2023; 104. [PMID: 37097881 DOI: 10.1099/jgv.0.001847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Swine are considered to be an important intermediate host in the cycle of Japanese encephalitis virus (JEV) infection. Most existing antiviral studies of JEV mainly focus on the host factor of the dead-end hosts. However, little research has addressed this in swine. Here, we found that swine interferon alpha-inducible protein 6 (sIFI6) possessed antiviral activity against JEV. In vitro studies showed that overexpression of sIFI6 inhibited the infection of JEV, while sIFI6 knockdown enhanced the infection of JEV in PK-15 cells. In addition, we also found that the structural integrity of sIFI6 was required by anti-JEV activity and that sIFI6 interacted with JEV nonstructural protein 4A (NS4A), an integral membrane protein with a pivotal function in replication complex during JEV replication. The interaction domain was mapped to the fourth transmembrane domain (TMD), also known as the 2K peptide of NS4A. The antiviral activity of sIFI6 was regulated by endoplasmic reticulum (ER) stress-related protein, Bip. In vivo studies revealed that sIFI6 alleviated symptoms of JEV infection in C57BL/6 mice. In addition, the antiviral spectrum of sIFI6 showed that sIFI6 specifically inhibited JEV infection. In conclusion, this study identified sIFI6 as a host factor against JEV infection for the first time. Our findings provide a potential drug target against JEV infection.
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Affiliation(s)
- Liuxing Qin
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Wenchun Fan
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Feiteng Zheng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Wuhan 430070, PR China
- Key Laboratory of Prevention and Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, PR China
| | - Ping Qian
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Wuhan 430070, PR China
- Key Laboratory of Prevention and Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, PR China
| | - Xiangmin Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Wuhan 430070, PR China
- Key Laboratory of Prevention and Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, PR China
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7
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Park JW, Ndimukaga M, So J, Kim S, Truong AD, Tran HTT, Dang HV, Song KD. Molecular analysis of chicken interferon-alpha inducible protein 6 gene and transcriptional regulation. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2023; 65:183-196. [PMID: 37093904 PMCID: PMC10119460 DOI: 10.5187/jast.2022.e101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/23/2022] [Accepted: 11/02/2022] [Indexed: 01/19/2023]
Abstract
Interferon-alpha inducible protein 6 (IFI6) is an interferon-stimulated gene (ISG), belonging to the FAM14 family of proteins and is localized in the mitochondrial membrane, where it plays a role in apoptosis. Transcriptional regulation of this gene is poorly understood in the context of inflammation by intracellular nucleic acid-sensing receptors and pathological conditions caused by viral infection. In this study, chicken IFI6 (chIFI6) was identified and studied for its molecular features and transcriptional regulation in chicken cells and tissues, i.e., lungs, spleens, and tracheas from highly pathogenic avian influenza virus (HPAIV)-infected chickens. The chIFI6-coding sequences contained 1638 nucleotides encoding 107 amino acids in three exons, whereas the duck IFI6-coding sequences contained 495 nucleotides encoding 107 amino acids. IFI6 proteins from chickens, ducks, and quail contain an IF6/IF27-like superfamily domain. Expression of chIFI6 was higher in HPAIV-infected White Leghorn chicken lungs, spleens, and tracheas than in mock-infected controls. TLR3 signals regulate the transcription of chIFI6 in chicken DF-1 cells via the NF-κB and JNK signaling pathways, indicating that multiple signaling pathways differentially contribute to the transcription of chIFI6. Further research is needed to unravel the molecular mechanisms underlying IFI6 transcription, as well as the involvement of chIFI6 in the pathogenesis of HPAIV in chickens.
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Affiliation(s)
- Jeong-Woong Park
- Department of Animal Biotechnology,
Jeonbuk National University, Jeonju 54896, Korea
| | - Marc Ndimukaga
- Department of Animal Biotechnology,
Jeonbuk National University, Jeonju 54896, Korea
| | - Jaerung So
- Department of Animal Biotechnology,
Jeonbuk National University, Jeonju 54896, Korea
| | - Sujung Kim
- Department of Animal Biotechnology,
Jeonbuk National University, Jeonju 54896, Korea
| | - Anh Duc Truong
- Vietnam National Institute of Veterinary
Research, Ha Noi 100000, Viet Nam
| | - Ha Thi Thanh Tran
- Vietnam National Institute of Veterinary
Research, Ha Noi 100000, Viet Nam
| | - Hoang Vu Dang
- Vietnam National Institute of Veterinary
Research, Ha Noi 100000, Viet Nam
| | - Ki-Duk Song
- Department of Animal Biotechnology,
Jeonbuk National University, Jeonju 54896, Korea
- Department of Agricultural Convergence
Technology, Jeonbuk National University, Jeonju 54896,
Korea
- The Animal Molecular Genetics and Breeding
Center, Jeonbuk National University, Jeonju 54896, Korea
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8
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Ujvari D, Malyukova A, Zovko A, Yektaei-Karin E, Madapura HS, Keszei M, Nagy N, Lotfi K, Björn N, Wallvik J, Stenke L, Salamon D. IFNγ directly counteracts imatinib-induced apoptosis of primary human CD34+ CML stem/progenitor cells potentially through the upregulation of multiple key survival factors. Oncoimmunology 2022; 11:2109861. [PMID: 35979386 PMCID: PMC9377247 DOI: 10.1080/2162402x.2022.2109861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Tyrosine kinase inhibitors (TKIs) have dramatically improved the survival in chronic myeloid leukemia (CML), but residual disease typically persists even after prolonged treatment. Several lines of evidence suggest that TKIs administered to CML patients upregulate interferon γ (IFNγ) production, which may counteract the anti-tumorigenic effects of the therapy. We now show that activated T cell-conditioned medium (TCM) enhanced proliferation and counteracted imatinib-induced apoptosis of CML cells, and addition of a neutralizing anti-IFNγ antibody at least partially inhibited the anti-apoptotic effect. Likewise, recombinant IFNγ also reduced imatinib-induced apoptosis of CML cells. This anti-apoptotic effect of IFNγ was independent of alternative IFNγ signaling pathways, but could be notably diminished by STAT1-knockdown. Furthermore, IFNγ upregulated the expression of several anti-apoptotic proteins, including MCL1, PARP9, and PARP14, both in untreated and imatinib-treated primary human CD34+ CML stem/progenitor cells. Our results suggest that activated T cells in imatinib-treated CML patients can directly rescue CML cells from imatinib-induced apoptosis at least partially through the secretion of IFNγ, which exerts a rapid, STAT1-dependent anti-apoptotic effect potentially through the simultaneous upregulation of several key hematopoietic survival factors. These mechanisms may have a major clinical impact, when targeting residual leukemic stem/progenitor cells in CML.
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Affiliation(s)
- Dorina Ujvari
- Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
- National Pandemic Center, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alena Malyukova
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Ana Zovko
- Division of Hematology, Karolinska University Hospital Solna, Stockholm, Sweden
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Elham Yektaei-Karin
- Division of Hematology, Karolinska University Hospital Solna, Stockholm, Sweden
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Harsha S Madapura
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Marton Keszei
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Noemi Nagy
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Kourosh Lotfi
- Department of Hematology, Linköping University Hospital, Linköping, Sweden
- Department of Medical and Health Sciences, Linköping University, Linköping, Sweden
| | - Niclas Björn
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Jonas Wallvik
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Leif Stenke
- Division of Hematology, Karolinska University Hospital Solna, Stockholm, Sweden
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Daniel Salamon
- Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
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9
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Janesick AS, Scheibinger M, Benkafadar N, Kirti S, Heller S. Avian auditory hair cell regeneration is accompanied by JAK/STAT-dependent expression of immune-related genes in supporting cells. Development 2022; 149:dev200113. [PMID: 35420675 PMCID: PMC10656459 DOI: 10.1242/dev.200113] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 03/31/2022] [Indexed: 11/20/2023]
Abstract
The avian hearing organ is the basilar papilla that, in sharp contrast to the mammalian cochlea, can regenerate sensory hair cells and thereby recover from deafness within weeks. The mechanisms that trigger, sustain and terminate the regenerative response in vivo are largely unknown. Here, we profile the changes in gene expression in the chicken basilar papilla after aminoglycoside antibiotic-induced hair cell loss using RNA-sequencing. We identified changes in gene expression of a group of immune-related genes and confirmed with single-cell RNA-sequencing that these changes occur in supporting cells. In situ hybridization was used to further validate these findings. We determined that the JAK/STAT signaling pathway is essential for upregulation of the damage-response genes in supporting cells during the second day after induction of hair cell loss. Four days after ototoxic damage, we identified newly regenerated, nascent auditory hair cells that express genes linked to termination of the JAK/STAT signaling response. The robust, transient expression of immune-related genes in supporting cells suggests a potential functional involvement of JAK/STAT signaling in sensory hair cell regeneration.
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Affiliation(s)
- Amanda S. Janesick
- Department of Otolaryngology – Head & Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Mirko Scheibinger
- Department of Otolaryngology – Head & Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Nesrine Benkafadar
- Department of Otolaryngology – Head & Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Sakin Kirti
- Department of Otolaryngology – Head & Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Stefan Heller
- Department of Otolaryngology – Head & Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Palo Alto, CA 94305, USA
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10
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Lee H, Jeong SH, Lee H, Kim C, Nam YJ, Kang JY, Song MO, Choi JY, Kim J, Park EK, Baek YW, Lee JH. Analysis of lung cancer-related genetic changes in long-term and low-dose polyhexamethylene guanidine phosphate (PHMG-p) treated human pulmonary alveolar epithelial cells. BMC Pharmacol Toxicol 2022; 23:19. [PMID: 35354498 PMCID: PMC8969249 DOI: 10.1186/s40360-022-00559-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 03/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lung injury elicited by respiratory exposure to humidifier disinfectants (HDs) is known as HD-associated lung injury (HDLI). Current elucidation of the molecular mechanisms related to HDLI is mostly restricted to fibrotic and inflammatory lung diseases. In our previous report, we found that lung tumors were caused by intratracheal instillation of polyhexamethylene guanidine phosphate (PHMG-p) in a rat model. However, the lung cancer-related genetic changes concomitant with the development of these lung tumors have not yet been fully defined. We aimed to discover the effect of long-term exposure of PHMG-p on normal human lung alveolar cells. METHODS We investigated whether PHMG-p could increase distorted homeostasis of oncogenes and tumor-suppressor genes, with long-term and low-dose treatment, in human pulmonary alveolar epithelial cells (HPAEpiCs). Total RNA sequencing was performed with cells continuously treated with PHMG-p and harvested after 35 days. RESULTS After PHMG-p treatment, genes with transcriptional expression changes of more than 2.0-fold or less than 0.5-fold were identified. Within 10 days of exposure, 2 protein-coding and 5 non-coding genes were selected, whereas in the group treated for 27-35 days, 24 protein-coding and 5 non-coding genes were identified. Furthermore, in the long-term treatment group, 11 of the 15 upregulated genes and 9 of the 14 downregulated genes were reported as oncogenes and tumor suppressor genes in lung cancer, respectively. We also found that 10 genes of the selected 24 protein-coding genes were clinically significant in lung adenocarcinoma patients. CONCLUSIONS Our findings demonstrate that long-term exposure of human pulmonary normal alveolar cells to low-dose PHMG-p caused genetic changes, mainly in lung cancer-associated genes, in a time-dependent manner.
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Affiliation(s)
- Hong Lee
- Medical Science Research Center, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Sang Hoon Jeong
- Medical Science Research Center, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Hyejin Lee
- Medical Science Research Center, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Cherry Kim
- Department of Radiology, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Yoon Jeong Nam
- Medical Science Research Center, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Ja Young Kang
- Medical Science Research Center, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Myeong Ok Song
- Medical Science Research Center, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Jin Young Choi
- Medical Science Research Center, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Jaeyoung Kim
- Medical Science Research Center, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Eun-Kee Park
- Department of Medical Humanities and Social Medicine, College of Medicine, Kosin University, Busan, Republic of Korea
| | - Yong-Wook Baek
- Environmental Health Research Department, Humidifier Disinfectant Health Center, National Institute of Environmental Research, Incheon, Republic of Korea
| | - Ju-Han Lee
- Department of Pathology, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea.
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11
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Zou L, Liu Z, Li X, Liu L, Zhu Y. Knockdown of G1P3 inhibits cell proliferation and enhances the cytotoxicity of dexamethasone in acute lymphoblastic leukemia. Open Life Sci 2022. [DOI: 10.1515/biol-2022-0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Drug resistance contributes to treatment failure and relapse in acute lymphoblastic leukemia (ALL). G1P3 (also known as IFI6, interferon, alpha-inducible protein 6) has been regarded as an antiapoptotic protein in myeloma cells and contributes to chemoresistance in breast cancer. However, the role of G1P3 in the proliferation and chemosensitivity of ALL is largely unknown. Data from colony formation and bromo-deoxyuridine (BrdU) incorporation assays showed that siRNA-mediated downregulation of G1P3 repressed cell proliferation of glucocorticoids-resistant human leukemic cells (CEM-C1), while overexpression of G1P3 promoted the cell proliferation. Cell apoptosis of CEM-C1 was suppressed by G1P3 overexpression accompanied by a decrease in cleaved caspase-3 and caspase-9. Knockdown of G1P3 increased protein expression of cleaved caspase-3 and caspase-9 to promote the cell apoptosis of CEM-C1. Moreover, silencing of G1P3 reduced cell viability and promoted cell apoptosis of CEM-C1 exposed to dexamethasone. The proapoptotic protein B-cell lymphoma 2 interacting mediator of cell death (Bim) was enhanced by the interference of G1P3 in CEM-C1. Silencing of Bim attenuated G1P3 interference-induced decrease in cell viability and increase in cell apoptosis in CEM-C1 exposed to dexamethasone. Conclusively, knockdown of G1P3 inhibited cell proliferation of ALL and sensitized glucocorticoid-resistant ALL cells to dexamethasone through upregulation of Bim-mediated cell apoptosis.
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Affiliation(s)
- Liping Zou
- Department of Blood Transfusion, First Affiliated Hospital of Gannan Medical University , Zhanggong District , Ganzhou , Jiangxi Province, 341000 , China
| | - Zhirui Liu
- Human Aging Research Institute (HARI), Nanchang University , Nanchang , Jiangxi Province, 330031 , China
| | - Xueer Li
- Human Aging Research Institute (HARI), Nanchang University , Nanchang , Jiangxi Province, 330031 , China
| | - Liping Liu
- Department of Hematology, First Affiliated Hospital of Gannan Medical University , Ganzhou , Jiangxi Province, 341000 , China
| | - Ying Zhu
- Department of Blood Transfusion, First Affiliated Hospital of Gannan Medical University , Zhanggong District , Ganzhou , Jiangxi Province, 341000 , China
- Human Aging Research Institute (HARI), School of Life Science, Nanchang University , Nanchang , Jiangxi Province, 330031 , China
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12
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Kirby EN, Shue B, Thomas PQ, Beard MR. CRISPR Tackles Emerging Viral Pathogens. Viruses 2021; 13:2157. [PMID: 34834963 PMCID: PMC8624524 DOI: 10.3390/v13112157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/16/2021] [Accepted: 10/19/2021] [Indexed: 12/17/2022] Open
Abstract
Understanding the dynamic relationship between viral pathogens and cellular host factors is critical to furthering our knowledge of viral replication, disease mechanisms and development of anti-viral therapeutics. CRISPR genome editing technology has enhanced this understanding, by allowing identification of pro-viral and anti-viral cellular host factors for a wide range of viruses, most recently the cause of the COVID-19 pandemic, SARS-CoV-2. This review will discuss how CRISPR knockout and CRISPR activation genome-wide screening methods are a robust tool to investigate the viral life cycle and how other class 2 CRISPR systems are being repurposed for diagnostics.
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Affiliation(s)
- Emily N. Kirby
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia; (E.N.K.); (B.S.)
| | - Byron Shue
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia; (E.N.K.); (B.S.)
| | - Paul Q. Thomas
- Adelaide Medical School, The University of Adelaide, Adelaide 5000, Australia;
- Robinson Research Institute, The University of Adelaide, Adelaide 5006, Australia
- Genome Editing Program, South Australian Health & Medical Research Institute, North Terrace, Adelaide 5000, Australia
| | - Michael R. Beard
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia; (E.N.K.); (B.S.)
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13
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Yi F, Hu J, Zhu X, Wang Y, Yu Q, Deng J, Huang X, Ma Y, Xie Y. Transcriptional Profiling of Human Peripheral Blood Mononuclear Cells Stimulated by Mycobacterium tuberculosis PPE57 Identifies Characteristic Genes Associated With Type I Interferon Signaling. Front Cell Infect Microbiol 2021; 11:716809. [PMID: 34490145 PMCID: PMC8416891 DOI: 10.3389/fcimb.2021.716809] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/30/2021] [Indexed: 02/05/2023] Open
Abstract
Proline-glutamic acid (PE)- and proline-proline-glutamic acid (PPE)-containing proteins are exclusive to Mycobacterium tuberculosis (MTB), the leading cause of tuberculosis (TB). In this study, we performed global transcriptome sequencing (RNA-Seq) on PPE57-stimulated peripheral blood mononuclear cells (PBMCs) and control samples to quantitatively measure the expression level of key transcripts of interest. A total of 1367 differentially expressed genes (DEGs) were observed in response to a 6 h exposure to PPE57, with 685 being up-regulated and 682 down-regulated. Immune-related gene functions and pathways associated with these genes were evaluated, revealing that the type I IFN signaling pathway was the most significantly enriched pathway in our RNA-seq dataset, with 14 DEGs identified therein including ISG15, MX2, IRF9, IFIT3, IFIT2, OAS3, IFIT1, IFI6, OAS2, OASL, RSAD2, OAS1, IRF7, and MX1. These PPE57-related transcriptomic profiles have implications for a better understanding of host global immune mechanisms underlying MTB infection outcomes. However, more studies regarding these DEGs and type I IFN signaling in this infectious context are necessary to more fully clarify the underlying mechanisms that arise in response to PPE57 during MTB infection.
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Affiliation(s)
- Fanli Yi
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Hu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoyan Zhu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yue Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Qiuju Yu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Deng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Xuedong Huang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Ying Ma
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Xie
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
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14
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Yin X, Yang J, Chen J, Ni R, Zhou Y, Song H, Jin L, Tang T, Pan Y. LncRNA CTD-3252C9.4 modulates pancreatic cancer cell survival and apoptosis through regulating IFI6 transcription. Cancer Cell Int 2021; 21:433. [PMID: 34399768 PMCID: PMC8365976 DOI: 10.1186/s12935-021-02142-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/10/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Pancreatic cancer (PC) is one of the most lethal cancer types with high degree of malignancy and poor prognosis. Recent studies have shown that long non-coding RNAs (lncRNAs) were associated with the initiation and progression of pancreatic cancer. In the current study, we have investigated the expression, biological function and mechanism of a lncRNA CTD-3252C9.4 in pancreatic cancer. METHODS The expression of CTD-3252C9.4 in pancreatic cancer cells and tissues was measured by qRT-PCR. In vitro and in vivo functional experiments assays were implemented for identifying CTD-3252C9.4 function in pancreatic cancer. Molecular relationships among CTD-3252C9.4, IRF1 and IFI6 were investigated via luciferase reporter assay, pulldown assay and ChIP assays. RESULTS CTD-3252C9.4 was found remarkably decreased in pancreatic cancer cells and tissues. Overexpression of CTD-3252C9.4 suppressed migration, invasion and proliferation, yet facilitated apoptosis of pancreatic cancer cells both in vitro and in vivo. Then, IFI6 was identified as a downstream target that could be down-regulated by CTD-3252C9.4 and IFI6 overexpression could counteract the effects of CTD-3252C9.4 upregulation on the survival and apoptosis of pancreatic cancer cells. Furthermore, mechanism experiments revealed that IRF1 was a transcriptional factor of IFI6 that can be blocked by CTD-3252C9.4 to inhibit IFI6 transcription. CONCLUSION Our data indicated that CTD-3252C9.4 could promote pancreatic cancer cell apoptosis and restrain cell growth via binding IRF1 and preventing the transcription of IFI6, which may become a potential therapeutic target for pancreatic cancer.
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Affiliation(s)
- Xin Yin
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital, 46 Heping Road, Xuzhou, Jiangsu, China
| | - Jingyan Yang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang Avenue, Nanjing, Jiangsu, China
| | - Jintian Chen
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang Avenue, Nanjing, Jiangsu, China
| | - Ruiqi Ni
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang Avenue, Nanjing, Jiangsu, China
| | - Yanhao Zhou
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang Avenue, Nanjing, Jiangsu, China
| | - Hao Song
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang Avenue, Nanjing, Jiangsu, China
| | - Liang Jin
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang Avenue, Nanjing, Jiangsu, China.
| | - Tingting Tang
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, Jiangsu, China.
| | - Yi Pan
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang Avenue, Nanjing, Jiangsu, China.
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15
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Survival-Based Biomarker Module Identification Associated with Oral Squamous Cell Carcinoma (OSCC). BIOLOGY 2021; 10:biology10080760. [PMID: 34439992 PMCID: PMC8389591 DOI: 10.3390/biology10080760] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 12/28/2022]
Abstract
Simple Summary In this study, four OSCC-specific hub genes were identified using high-throughput RNA-Seq data from TCGA cohort. The significant genes within tumor and normal samples were used for weighted PPI network construction based on survival of patients along with their expression profiles. The analysis revealed the most significant module in the training and test datasets. The genes from this module were used for pathway enrichment analysis followed by hub gene selection. These novel biomarkers might have clinical utility for diagnosis and prognosis prediction in OSCC, providing diagnosis at a very early stage. Moreover, a combination of all these biomarkers might distinguish the OSCC patients with low risk and high risk for cancer progression and recurrence, which will provide useful guidance for personalized and precision therapy. However, the results in the present study were obtained by integrative theoretical analysis, and the findings remain to be confirmed by further experimental validations. Abstract Head and neck squamous cell carcinoma (HNSC) is one of the most common malignant tumors worldwide with a high rate of morbidity and mortality, with 90% of predilections occurring for oral squamous cell carcinoma (OSCC). Cancers of the mouth account for 40% of head and neck cancers, including squamous cell carcinomas of the tongue, floor of the mouth, buccal mucosa, lips, hard and soft palate, and gingival. OSCC is the most devastating and commonly occurring oral malignancy, with a mortality rate of 500,000 deaths per year. This has imposed a strong necessity to discover driver genes responsible for its progression and malignancy. In the present study we filtered oral squamous cell carcinoma tissue samples from TCGA-HNSC cohort, which we followed by constructing a weighted PPI network based on the survival of patients and the expression profiles of samples collected from them. We found a total of 46 modules, with 18 modules having more than five edges. The KM and ME analyses revealed a single module (with 12 genes) as significant in the training and test datasets. The genes from this significant module were subjected to pathway enrichment analysis for identification of significant pathways and involved genes. Finally, the overlapping genes between gene sets ranked on the basis of weighted PPI module centralities (i.e., degree and eigenvector), significant pathway genes, and DEGs from a microarray OSCC dataset were considered as OSCC-specific hub genes. These hub genes were clinically validated using the IHC images available from the Human Protein Atlas (HPA) database.
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16
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Drzewiecka EM, Kozlowska W, Paukszto L, Zmijewska A, Wydorski PJ, Jastrzebski JP, Franczak A. Effect of the Electromagnetic Field (EMF) Radiation on Transcriptomic Profile of Pig Myometrium during the Peri-Implantation Period-An In Vitro Study. Int J Mol Sci 2021; 22:7322. [PMID: 34298942 PMCID: PMC8305477 DOI: 10.3390/ijms22147322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 12/13/2022] Open
Abstract
The electromagnetic field (EMF) affects the physiological processes in mammals, but the molecular background of the observed alterations remains not well established. In this study was tested the effect of short duration (2 h) of the EMF treatment (50 Hz, 8 mT) on global transcriptomic alterations in the myometrium of pigs during the peri-implantation period using next-generation sequencing. As a result, the EMF treatment affected the expression of 215 transcript active regions (TARs), and among them, the assigned gene protein-coding biotype possessed 90 ones (differentially expressed genes, DEGs), categorized mostly to gene ontology terms connected with defense and immune responses, and secretion and export. Evaluated DEGs enrich the KEGG TNF signaling pathway, and regulation of IFNA signaling and interferon-alpha/beta signaling REACTOME pathways. There were evaluated 12 differentially expressed long non-coding RNAs (DE-lnc-RNAs) and 182 predicted single nucleotide variants (SNVs) substitutions within RNA editing sites. In conclusion, the EMF treatment in the myometrium collected during the peri-implantation period affects the expression of genes involved in defense and immune responses. The study also gives new insight into the mechanisms of the EMF action in the regulation of the transcriptomic profile through lnc-RNAs and SNVs.
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Affiliation(s)
- Ewa Monika Drzewiecka
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (E.M.D.); (W.K.); (A.Z.); (P.J.W.)
| | - Wiktoria Kozlowska
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (E.M.D.); (W.K.); (A.Z.); (P.J.W.)
| | - Lukasz Paukszto
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (L.P.); (J.P.J.)
| | - Agata Zmijewska
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (E.M.D.); (W.K.); (A.Z.); (P.J.W.)
| | - Pawel Jozef Wydorski
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (E.M.D.); (W.K.); (A.Z.); (P.J.W.)
| | - Jan Pawel Jastrzebski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (L.P.); (J.P.J.)
| | - Anita Franczak
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (E.M.D.); (W.K.); (A.Z.); (P.J.W.)
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17
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Riera Romo M. Cell death as part of innate immunity: Cause or consequence? Immunology 2021; 163:399-415. [PMID: 33682112 DOI: 10.1111/imm.13325] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/11/2021] [Accepted: 02/25/2021] [Indexed: 12/13/2022] Open
Abstract
Regulated or programmed cell death plays a critical role in the development and tissue organization and function. In addition, it is intrinsically connected with immunity and host defence. An increasing cellular and molecular findings cause a change in the concept of cell death, revealing an expanding network of regulated cell death modalities and their biochemical programmes. Likewise, recent evidences demonstrate the interconnection between cell death pathways and how they are involved in different immune mechanisms. This work provides an overview of the main cell death programmes and their implication in innate immunity not only as an immunogenic/inflammatory process, but also as an active defence strategy during immune response and at the same time as a regulatory mechanism.
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Affiliation(s)
- Mario Riera Romo
- Radiology Department, Leiden University Medical Center, Leiden, The Netherlands
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18
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Xu L, Zu T, Li T, Li M, Mi J, Bai F, Liu G, Wen J, Li H, Brakebusch C, Wang X, Wu X. ATF3 downmodulates its new targets IFI6 and IFI27 to suppress the growth and migration of tongue squamous cell carcinoma cells. PLoS Genet 2021; 17:e1009283. [PMID: 33539340 PMCID: PMC7888615 DOI: 10.1371/journal.pgen.1009283] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 02/17/2021] [Accepted: 11/18/2020] [Indexed: 01/16/2023] Open
Abstract
Activating transcription factor 3 (ATF3) is a key transcription factor involved in regulating cellular stress responses, with different expression levels and functions in different tissues. ATF3 has also been shown to play crucial roles in regulating tumor development and progression, however its potential role in oral squamous cell carcinomas has not been fully explored. In this study, we examined biopsies of tongue squamous cell carcinomas (TSCCs) and found that the nuclear expression level of ATF3 correlated negatively with the differentiation status of TSCCs, which was validated by analysis of the ATGC database. By using gain- or loss- of function analyses of ATF3 in four different TSCC cell lines, we demonstrated that ATF3 negatively regulates the growth and migration of human TSCC cells in vitro. RNA-seq analysis identified two new downstream targets of ATF3, interferon alpha inducible proteins 6 (IFI6) and 27 (IFI27), which were upregulated in ATF3-deleted cells and were downregulated in ATF3-overexpressing cells. Chromatin immunoprecipitation assays showed that ATF3 binds the promoter regions of the IFI6 and IFI27 genes. Both IFI6 and IFI27 were highly expressed in TSCC biopsies and knockdown of either IFI6 or IFI27 in TSCC cells blocked the cell growth and migration induced by the deletion of ATF3. Conversely, overexpression of either IFI6 or IFI27 counteracted the inhibition of TSCC cell growth and migration induced by the overexpression of ATF3. Finally, an in vivo study in mice confirmed those in vitro findings. Our study suggests that ATF3 plays an anti-tumor function in TSCCs through the negative regulation of its downstream targets, IFI6 and IFI27. Activating transcription factor 3 (ATF3), a stress response gene, has been shown to play either tumor promoting or tumor suppressing functions depending on the type of tumor cell and the stromal context. Here we discovered that ATF3 plays an anti-tumor role in tongue squamous cell carcinoma (TSCC) cells through the transcriptional suppression of its new downstream targets interferon alpha inducible proteins 6 (IFI6) and 27 (IFI27). This finding contributes to understanding how ATF3, a transcriptional repressor, can target specific downstream genes in different tumor cells to play anti-tumor or pro-tumor functions. A thorough understanding of ATF3 functions and its downstream signaling pathways provides a potential approach to develop new therapeutics for the treatment of tumors such as TSCCs.
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Affiliation(s)
- Lin Xu
- Department of Tissue Engineering and Regeneration, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Shandong, China
- Department of Orthodontics, Liaocheng People’s Hospital, Liaocheng, Shandong, China
- Precision Biomedical Key Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Tingjian Zu
- Department of Tissue Engineering and Regeneration, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China
- School of Stomatology, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai’an, Shandong, China
| | - Tao Li
- Department of Tissue Engineering and Regeneration, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Shandong, China
| | - Min Li
- Precision Biomedical Key Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Jun Mi
- Department of Tissue Engineering and Regeneration, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China
| | - Fuxiang Bai
- Department of Tissue Engineering and Regeneration, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China
| | - Guanyi Liu
- Department of Tissue Engineering and Regeneration, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China
| | - Jie Wen
- Department of Tissue Engineering and Regeneration, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China
| | - Hui Li
- Department of Hematology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Cord Brakebusch
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, Denmark
| | - Xuxia Wang
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Shandong, China
- * E-mail: (XW); (XW)
| | - Xunwei Wu
- Department of Tissue Engineering and Regeneration, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration and Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, China
- * E-mail: (XW); (XW)
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19
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Kohsaka S, Hirata M, Ikegami M, Ueno T, Kojima S, Sakai T, Ito K, Naka N, Ogura K, Kawai A, Iwata S, Okuma T, Yonemoto T, Kobayashi H, Suehara Y, Hiraga H, Kawamoto T, Motoi T, Oda Y, Matsubara D, Matsuda K, Nishida Y, Mano H. Comprehensive molecular and clinicopathological profiling of desmoid tumours. Eur J Cancer 2021; 145:109-120. [PMID: 33444924 DOI: 10.1016/j.ejca.2020.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 12/02/2020] [Indexed: 10/22/2022]
Abstract
Previous studies have not clearly identified a prognostic factor for desmoid tumours (DT). Whole-exome sequencing (WES) and/or RNA sequencing (RNA-seq) were performed in 64 cases of DT to investigate the molecular profiles in combination with the clinicopathological characteristics. CTNNB1 mutations with specific hotspots were identified in 56 cases (87.5%). A copy number loss in chromosome 6 (chr6) was identified in 14 cases (21.9%). Clustering based on the mRNA expression profiles was predictive of the patients' prognoses. The risk score generated by the expression of a three-gene set (IFI6, LGMN, and CKLF) was a strong prognostic marker for recurrence-free survival (RFS) in our cohort. In risk groups stratified by the expression of IFI6, the hazard ratio for recurrence-free survival in the high-risk group relative to the low-risk group was 12.12 (95% confidence interval: 1.56-94.2; p = 8.0 × 106). In conclusion, CTNNB1 mutations and a chr6 copy number loss are likely the causative mutations underlying the tumorigenesis of DT while the gene expression profiles may help to differentiate patients who would be good candidates for wait-and-see management and those who might benefit from additional systemic or radiation therapies.
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Affiliation(s)
- Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Makoto Hirata
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Masachika Ikegami
- Division of Cellular Signaling, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Shinya Kojima
- Division of Cellular Signaling, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Tomohisa Sakai
- Department of Orthopaedic Surgery, Nagoya University Hospital, Nagoya, 466-8550, Japan
| | - Kan Ito
- Department of Orthopaedic Surgery, Nagoya University Hospital, Nagoya, 466-8550, Japan
| | - Norifumi Naka
- Musculoskeletal Oncology Service, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Koichi Ogura
- Department of Musculoskeletal Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Akira Kawai
- Department of Musculoskeletal Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Shintaro Iwata
- Department of Musculoskeletal Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan; Division of Orthopaedic Surgery, Chiba Cancer Center, Chiba, 260-8717, Japan
| | - Tomotake Okuma
- Department of Muscloskeletal Oncology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, 113-0021, Japan
| | - Tsukasa Yonemoto
- Division of Orthopaedic Surgery, Chiba Cancer Center, Chiba, 260-8717, Japan
| | - Hiroshi Kobayashi
- Department of Orthopaedic Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yoshiyuki Suehara
- Department of Orthopedic Surgery, Juntendo University, Graduate School of Medicine, Tokyo, 113-8431, Japan
| | - Hiroaki Hiraga
- Department of Orthopaedic Surgery, Hokkaido Cancer Center, Sapporo, 003-0804, Japan
| | - Teruya Kawamoto
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine, Kobe, 650-0017, Japan
| | - Toru Motoi
- Department of Pathology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, 113-0021, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Daisuke Matsubara
- Division of Integrative Pathology, Jichi Medical University, Shimotsuke, 329-0498, Japan
| | - Koichi Matsuda
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Yoshihiro Nishida
- Department of Orthopaedic Surgery, Nagoya University Hospital, Nagoya, 466-8550, Japan.
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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20
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Jia H, Mo W, Hong M, Jiang S, Zhang YY, He D, Yu D, Shi Y, Cao J, Xu X, Zhang S. Interferon-α inducible protein 6 (IFI6) confers protection against ionizing radiation in skin cells. J Dermatol Sci 2020; 100:139-147. [PMID: 33059972 DOI: 10.1016/j.jdermsci.2020.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/03/2020] [Accepted: 09/13/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND Radiation-induced skin injury is one of the main adverse effects and a dose-limiting factor of radiotherapy without feasible treatment. The underlying mechanism of this disease is still limited. OBJECTIVE To investigate the potential molecular pathways and mechanisms of radiation-induced skin injury. METHODS mRNA expression profiles were determined by Affymetrix Human HTA2.0 microarray.IFI6 overexpression and knockdown were mediated by lentivirus. The functional changes of skin cells were measured by flow cytometry, ROS probe and Edu probe. Protein distribution was detected by immunofluorescence experiment, and IFI6-interacting proteins were detected by immunoprecipitation (IP) combined with mass spectrometry. The global gene changes in IFI6-overexpressed skin cells after irradiation were detected by RNA-seq. RESULTS mRNA expression profiling showed 50 upregulated and 13 down regulated genes and interferon alpha inducible protein 6 (IFI6) was top upregulated. Overexpression of IFI6 promoted cell proliferation and reduced cell apoptosis as well as ROS production following radiation, and conversely, increased the radiosensitivity of HaCaT and human skin fibroblast (WS1). IFI6 was translocated into nucleus in irradiated skin cells and the interacting relationship with mitochondrial single-stranded DNA-binding protein 1 (SSBP1), which could enhance the transcriptional activity of heat shock transcription factor 1 (HSF1).IFI6 augmented HSF1 activity following radiation in HaCaT and WS1 cells. RNA-seq analysis showed IFI6 modulated virus infection and cellular response to stress pathways, which may help to further explore how IFI6 regulate the transcriptional activity of HSF1. CONCLUSION This study reveals that IFI6 is induced by ionizing radiation and confers radioprotection in skin cells.
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Affiliation(s)
- Huimin Jia
- State Key Lab of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Wei Mo
- State Key Lab of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Min Hong
- State Key Lab of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Sheng Jiang
- Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Yuan-Yuan Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Dan He
- Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Daojiang Yu
- Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Yuhong Shi
- Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Jianping Cao
- State Key Lab of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Xiaohui Xu
- Department of General Surgery, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Taicang, China.
| | - Shuyu Zhang
- Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China; West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
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21
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Liu Z, Gu S, Lu T, Wu K, Li L, Dong C, Zhou Y. IFI6 depletion inhibits esophageal squamous cell carcinoma progression through reactive oxygen species accumulation via mitochondrial dysfunction and endoplasmic reticulum stress. J Exp Clin Cancer Res 2020; 39:144. [PMID: 32727517 PMCID: PMC7388476 DOI: 10.1186/s13046-020-01646-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 07/17/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is one of the most lethal forms of adult cancer with poor prognosis. Substantial evidence indicates that reactive oxygen species (ROS) are important modulators of aggressive cancer behavior. However, the mechanism by which ESCC cells integrate redox signals to modulate carcinoma progression remains elusive. METHODS The expression of interferon alpha inducible protein 6 (IFI6) in clinical ESCC tissues and cell lines was detected by RT-PCR and Western blotting. The correlation between IFI6 expression levels and aggressive ESCC disease stage was examined by immunohistochemistry. Bioinformatic analysis was conducted to explore the potential function of IFI6 in ESCC. ESCC cell lines stably depleted of IFI6 and ectopically expressing IFI6 were established using lentiviruses expressing shRNAs and an IFI6 expression plasmid, respectively. The effects of IFI6 on ESCC cells were determined by cell-based analyses, including EdU assay, apoptotic assay, cellular and mitochondria-specific ROS detection, seahorse extracellular flux, and mitochondrial calcium flux assays. Blue native-polyacrylamide gel electrophoresis was used to determine mitochondrial supercomplex assembly. Transcriptional activation of NADPH oxidase 4 (NOX4) via ATF3 was confirmed by dual luciferase assay. In vivo tumor growth was determined in mouse xenograft models. RESULTS We find that the expression of IFI6, an IFN-stimulated gene localized in the inner mitochondrial membrane, is markedly elevated in ESCC patients and a panel of ESCC cell lines. High IFI6 expression correlates with aggressive disease phenotype and poor prognosis in ESCC patients. IFI6 depletion suppresses proliferation and induces apoptosis by increasing ROS accumulation. Mechanistically, IFI6 ablation induces mitochondrial calcium overload by activating mitochondrial Ca2+ uniporter and subsequently ROS production. Following IFI6 ablation, mitochondrial ROS accumulation is also induced by mitochondrial supercomplex assembly suppression and oxidative phosphorylation dysfunction, while IFI6 overexpression produces the opposite effects. Furthermore, energy starvation induced by IFI6 inhibition drives endoplasmic reticulum stress through disrupting endoplasmic reticulum calcium uptake, which upregulates NOX4-derived ROS production in an ATF3-dependent manner. Finally, the results in xenograft models of ESCC further corroborate the in vitro findings. CONCLUSION Our study unveils a novel redox homeostasis signaling pathway that regulates ESCC pathobiology and identifies IFI6 as a potential druggable target in ESCC.
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Affiliation(s)
- Zhenchuan Liu
- Department of Thoracic Surgery, Shanghai Tongji Hospital Affiliated with Tongji University, Shanghai, 200065, P. R. China
| | - Shaorui Gu
- Department of Thoracic Surgery, Shanghai Tongji Hospital Affiliated with Tongji University, Shanghai, 200065, P. R. China
| | - Tiancheng Lu
- Department of Thoracic Surgery, Shanghai Tongji Hospital Affiliated with Tongji University, Shanghai, 200065, P. R. China
| | - Kaiqing Wu
- Department of Thoracic Surgery, Shanghai Tongji Hospital Affiliated with Tongji University, Shanghai, 200065, P. R. China
| | - Lei Li
- Department of Thoracic Surgery, Shanghai Tongji Hospital Affiliated with Tongji University, Shanghai, 200065, P. R. China
| | - Chenglai Dong
- Department of Thoracic Surgery, Shanghai Tongji Hospital Affiliated with Tongji University, Shanghai, 200065, P. R. China
| | - Yongxin Zhou
- Department of Thoracic Surgery, Shanghai Tongji Hospital Affiliated with Tongji University, Shanghai, 200065, P. R. China.
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22
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Warthi G, Fournier PE, Seligmann H. Identification of Noncanonical Transcripts Produced by Systematic Nucleotide Exchanges in HIV-Associated Centroblastic Lymphoma. DNA Cell Biol 2019; 39:1444-1448. [PMID: 31750730 DOI: 10.1089/dna.2019.5066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Noncanonical transcriptions include transcriptions that systematically exchange nucleotides, also called bijective transformations or swinger transformations. Swinger transformation A↔T+C↔G recovers identities of 8 among 9 unknown RNAs differentially expressed in centroblastic lymphoma, a human immunodeficiency virus (HIV)-associated non-Hodgkin's lymphoma. The identified RNAs align with human genes with known anti-HIV1 or oncogenic activities. Function disruption through swinger-transformed transcription potentially enables avoiding antiviral responses and contributes to cancer induction.
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Affiliation(s)
- Ganesh Warthi
- IRD, APHM, Aix Marseille Univ, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Pierre-Edouard Fournier
- IRD, APHM, Aix Marseille Univ, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
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23
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A CRISPR Activation Screen Identifies Genes That Protect against Zika Virus Infection. J Virol 2019; 93:JVI.00211-19. [PMID: 31142663 DOI: 10.1128/jvi.00211-19] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/22/2019] [Indexed: 02/05/2023] Open
Abstract
Zika virus (ZIKV) is an arthropod-borne emerging pathogen causing febrile illness. ZIKV is associated Guillain-Barré syndrome and other neurological complications. Infection during pregnancy is associated with pregnancy complications and developmental and neurological abnormalities collectively defined as congenital Zika syndrome. There is still no vaccine or specific treatment for ZIKV infection. To identify host factors that can rescue cells from ZIKV infection, we used a genome-scale CRISPR activation screen. Our highly ranking hits included a short list of interferon-stimulated genes (ISGs) previously reported to have antiviral activity. Validation of the screen results highlighted interferon lambda 2 (IFN-λ2) and interferon alpha-inducible protein 6 (IFI6) as genes providing high levels of protection from ZIKV. Activation of these genes had an effect on an early stage in viral infection. In addition, infected cells expressing single guide RNAs (sgRNAs) for both of these genes displayed lower levels of cell death than did the controls. Furthermore, the identified genes were significantly induced in ZIKV-infected placenta explants. Thus, these results highlight a set of ISGs directly relevant for rescuing cells from ZIKV infection or its associated cell death and substantiate CRISPR activation screens as a tool to identify host factors impeding pathogen infection.IMPORTANCE Zika virus (ZIKV) is an emerging vector-borne pathogen causing a febrile disease. ZIKV infection might also trigger Guillain-Barré syndrome, neuropathy, and myelitis. Vertical transmission of ZIKV can cause fetus demise, stillbirth, or severe congenital abnormalities and neurological complications. There is no vaccine or specific antiviral treatment against ZIKV. We used a genome-wide CRISPR activation screen, where genes are activated from their native promoters to identify host cell factors that protect cells from ZIKV infection or associated cell death. The results provide a better understanding of key host factors that protect cells from ZIKV infection and might assist in identifying novel antiviral targets.
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24
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Emran AA, Marzese DM, Menon DR, Hammerlindl H, Ahmed F, Richtig E, Duijf P, Hoon DS, Schaider H. Commonly integrated epigenetic modifications of differentially expressed genes lead to adaptive resistance in cancer. Epigenomics 2019; 11:732-737. [PMID: 31070054 PMCID: PMC6595545 DOI: 10.2217/epi-2018-0173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Aim: To investigate the integrated epigenetic regulation of acquired drug resistance in cancer. Materials & methods: Our gene expression data of five induced drug-tolerant cell models, one resistant cell line and one publicly available drug-resistant dataset were integrated to identify common differentially expressed genes and pathways. ChIP-seq and DNA methylation by HM450K beadchip were used to study the epigenetic profile of differential expressed genes. Results & conclusion: Integrated transcriptomic analysis identified a common ‘viral mimicry’ related gene signature in induced drug-tolerant cells and the resistant state. Analysis of the epigenetic regulation revealed a common set of down-regulated genes, which are marked and regulated by a concomitant loss of H3K4me3, gain of H3K9me3 and increment of regional DNA methylation levels associated with tumor suppressor genes and apoptotic signaling.
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Affiliation(s)
- Abdullah Al Emran
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia.,Centenary Institute of Cancer Medicine & Cell Biology, University of Sydney, Camperdown, NSW, Australia
| | - Diego M Marzese
- Department of Translational Molecular Medicine, John Wayne Cancer Institute, 2200 Santa Monica Boulevard, Santa Monica, CA 90404, USA
| | - Dinoop R Menon
- Department of Translational Molecular Medicine, John Wayne Cancer Institute, 2200 Santa Monica Boulevard, Santa Monica, CA 90404, USA
| | - Heinz Hammerlindl
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Farzana Ahmed
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Erika Richtig
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - Pascal Duijf
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Dave Sb Hoon
- Centenary Institute of Cancer Medicine & Cell Biology, University of Sydney, Camperdown, NSW, Australia
| | - Helmut Schaider
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia.,Department of Dermatology, The Townsville Hospital, Douglas, QLD, Australia
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25
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Richardson RB, Ohlson MB, Eitson JL, Kumar A, McDougal MB, Boys IN, Mar KB, De La Cruz-Rivera PC, Douglas C, Konopka G, Xing C, Schoggins JW. A CRISPR screen identifies IFI6 as an ER-resident interferon effector that blocks flavivirus replication. Nat Microbiol 2018; 3:1214-1223. [PMID: 30224801 PMCID: PMC6202210 DOI: 10.1038/s41564-018-0244-1] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 08/13/2018] [Indexed: 11/24/2022]
Abstract
The endoplasmic reticulum (ER) is an architecturally diverse organelle that serves as a membrane source for the replication of multiple viruses. Flaviviruses, including yellow fever virus, West Nile virus, dengue virus and Zika virus, induce unique single-membrane ER invaginations that house the viral replication machinery1. Whether this virus-induced ER remodelling is vulnerable to antiviral pathways is unknown. Here, we show that flavivirus replication at the ER is targeted by the interferon (IFN) response. Through genome-scale CRISPR screening, we uncovered an antiviral mechanism mediated by a functional gene pairing between IFI6 (encoding IFN-α-inducible protein 6), an IFN-stimulated gene cloned over 30 years ago2, and HSPA5, which encodes the ER-resident heat shock protein 70 chaperone BiP. We reveal that IFI6 is an ER-localized integral membrane effector that is stabilized through interactions with BiP. Mechanistically, IFI6 prophylactically protects uninfected cells by preventing the formation of virus-induced ER membrane invaginations. Notably, IFI6 has little effect on other mammalian RNA viruses, including the related Flaviviridae family member hepatitis C virus, which replicates in double-membrane vesicles that protrude outwards from the ER. These findings support a model in which the IFN response is armed with a membrane-targeted effector that discriminately blocks the establishment of virus-specific ER microenvironments that are required for replication. Flavivirus replication at the endoplasmic reticulum (ER) is targeted by the interferon response through blocking of the formation of virus-induced ER membrane invaginations by the interferon-stimulated gene IFI6, encoding an ER-localized integral membrane effector.
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Affiliation(s)
- R Blake Richardson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Maikke B Ohlson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jennifer L Eitson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ashwani Kumar
- Bioinformatics Core, McDermott Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Matthew B McDougal
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ian N Boys
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Katrina B Mar
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Connor Douglas
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chao Xing
- Bioinformatics Core, McDermott Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Cheriyath V, Kaur J, Davenport A, Khalel A, Chowdhury N, Gaddipati L. G1P3 (IFI6), a mitochondrial localised antiapoptotic protein, promotes metastatic potential of breast cancer cells through mtROS. Br J Cancer 2018; 119:52-64. [PMID: 29899394 PMCID: PMC6035266 DOI: 10.1038/s41416-018-0137-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 04/27/2018] [Accepted: 05/09/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Redox deregulations are ubiquitous in cancer cells. However, the role of mitochondrial redox deregulation in metastasis remains unclear. In breast cancer, upregulation of mitochondrial antiapoptotic protein G1P3 (IFI6) was associated with poor distance metastasis-free survival (DMFS). Therefore, we tested the hypothesis that G1P3-induced mitochondrial redox deregulation confers metastatic potentials in breast cancer cells. METHODS Cell migration and invasion assays; confocal and immunofluorescence microscopy; and Illumina HumanHT-12 BeadChip to assess gene expression. RESULTS Consequent to its localisation on inner-mitochondrial membrane, mtROS were higher in G1P3-expressing cells (MCF-7G1P3). G1P3-overexpressing cells migrated and invaded faster than the vector controls with increased number of filopodia and F-actin bundles (p ≤ 0.05). mtROS suppression with H2O2 scavengers and mitochondrial-specific antioxidants significantly decreased migratory structures and reversed G1P3-induced migration and invasion (p ≤ 0.05). Knocking down G1P3 decreased both migration and migratory structures in MCF-7G1P3 cells. Moreover, gene networks involved in redox regulation, metastasis and actin remodelling were upregulated in MCF-7G1P3 cells. CONCLUSIONS G1P3-induced mtROS have a direct role in migratory structure formation and nuclear gene expression to promote breast cancer cell metastasis. Therefore, interrupting mitochondrial functions of G1P3 may improve clinical outcomes in breast cancer patients.
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Affiliation(s)
- Venugopalan Cheriyath
- Department of Biological and Environmental Sciences, Texas A&M University-Commerce, Commerce, TX, 75429, USA.
| | - Jaspreet Kaur
- Department of Biological and Environmental Sciences, Texas A&M University-Commerce, Commerce, TX, 75429, USA
| | - Anne Davenport
- Department of Biological and Environmental Sciences, Texas A&M University-Commerce, Commerce, TX, 75429, USA.,Department of Biology, Texas Woman's University, Denton, TX, 76204, USA
| | - Ashjan Khalel
- Department of Biological and Environmental Sciences, Texas A&M University-Commerce, Commerce, TX, 75429, USA
| | - Nobel Chowdhury
- Department of Biological and Environmental Sciences, Texas A&M University-Commerce, Commerce, TX, 75429, USA
| | - Lalitha Gaddipati
- Department of Biological and Environmental Sciences, Texas A&M University-Commerce, Commerce, TX, 75429, USA
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27
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Voels B, Wang L, Sens DA, Garrett SH, Zhang K, Somji S. The unique C- and N-terminal sequences of Metallothionein isoform 3 mediate growth inhibition and Vectorial active transport in MCF-7 cells. BMC Cancer 2017; 17:369. [PMID: 28545470 PMCID: PMC5445401 DOI: 10.1186/s12885-017-3355-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 05/15/2017] [Indexed: 12/28/2022] Open
Abstract
Background The 3rd isoform of the metallothionein (MT3) gene family has been shown to be overexpressed in most ductal breast cancers. A previous study has shown that the stable transfection of MCF-7 cells with the MT3 gene inhibits cell growth. The goal of the present study was to determine the role of the unique C-terminal and N-terminal sequences of MT3 on phenotypic properties and gene expression profiles of MCF-7 cells. Methods MCF-7 cells were transfected with various metallothionein gene constructs which contain the insertion or the removal of the unique MT3 C- and N-terminal domains. Global gene expression analysis was performed on the MCF-7 cells containing the various constructs and the expression of the unique C- and N- terminal domains of MT3 was correlated to phenotypic properties of the cells. Results The results of the present study demonstrate that the C-terminal sequence of MT3, in the absence of the N-terminal sequence, induces dome formation in MCF-7 cells, which in cell cultures is the phenotypic manifestation of a cell’s ability to perform vectorial active transport. Global gene expression analysis demonstrated that the increased expression of the GAGE gene family correlated with dome formation. Expression of the C-terminal domain induced GAGE gene expression, whereas the N-terminal domain inhibited GAGE gene expression and that the effect of the N-terminal domain inhibition was dominant over the C-terminal domain of MT3. Transfection with the metallothionein 1E gene increased the expression of GAGE genes. In addition, both the C- and the N-terminal sequences of the MT3 gene had growth inhibitory properties, which correlated to an increased expression of the interferon alpha-inducible protein 6. Conclusions Our study shows that the C-terminal domain of MT3 confers dome formation in MCF-7 cells and the presence of this domain induces expression of the GAGE family of genes. The differential effects of MT3 and metallothionein 1E on the expression of GAGE genes suggests unique roles of these genes in the development and progression of breast cancer. The finding that interferon alpha-inducible protein 6 expression is associated with the ability of MT3 to inhibit growth needs further investigation. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3355-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Brent Voels
- Department of Pathology, University of North Dakota, School of Medicine and Health Sciences, 1301 N. Columbia Road, Stop 9037, Grand Forks, ND, 58202, USA.,Departments of Science, Cankdeska Cikana Community College, 214 1st Avenue, Fort Totten, ND, 58335, USA
| | - Liping Wang
- Department of Pathology, University of North Dakota, School of Medicine and Health Sciences, 1301 N. Columbia Road, Stop 9037, Grand Forks, ND, 58202, USA.,Present address: Department of Medical Ultrasound, Tongji Hospital, Tongji Medical College, Huangzhong University of Science and Techology, Wuhan, 430030, People's Republic of China
| | - Donald A Sens
- Department of Pathology, University of North Dakota, School of Medicine and Health Sciences, 1301 N. Columbia Road, Stop 9037, Grand Forks, ND, 58202, USA
| | - Scott H Garrett
- Department of Pathology, University of North Dakota, School of Medicine and Health Sciences, 1301 N. Columbia Road, Stop 9037, Grand Forks, ND, 58202, USA
| | - Ke Zhang
- Department of Pathology, University of North Dakota, School of Medicine and Health Sciences, 1301 N. Columbia Road, Stop 9037, Grand Forks, ND, 58202, USA
| | - Seema Somji
- Department of Pathology, University of North Dakota, School of Medicine and Health Sciences, 1301 N. Columbia Road, Stop 9037, Grand Forks, ND, 58202, USA.
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Systematic identification of anti-interferon function on hepatitis C virus genome reveals p7 as an immune evasion protein. Proc Natl Acad Sci U S A 2017; 114:2018-2023. [PMID: 28159892 DOI: 10.1073/pnas.1614623114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Hepatitis C virus (HCV) encodes mechanisms to evade the multilayered antiviral actions of the host immune system. Great progress has been made in elucidating the strategies HCV employs to down-regulate interferon (IFN) production, impede IFN signaling transduction, and impair IFN-stimulated gene (ISG) expression. However, there is a limited understanding of the mechanisms governing how viral proteins counteract the antiviral functions of downstream IFN effectors due to the lack of an efficient approach to identify such interactions systematically. To study the mechanisms by which HCV antagonizes the IFN responses, we have developed a high-throughput profiling platform that enables mapping of HCV sequences critical for anti-IFN function at high resolution. Genome-wide profiling performed with a 15-nt insertion mutant library of HCV showed that mutations in the p7 region conferred high levels of IFN sensitivity, which could be alleviated by the expression of WT p7 protein. This finding suggests that p7 protein of HCV has an immune evasion function. By screening a liver-specific ISG library, we identified that IFI6-16 significantly inhibits the replication of p7 mutant viruses without affecting WT virus replication. In contrast, knockout of IFI6-16 reversed the IFN hypersensitivity of p7 mutant virus. In addition, p7 was found to be coimmunoprecipitated with IFI6-16 and to counteract the function of IFI6-16 by depolarizing the mitochondria potential. Our data suggest that p7 is a critical immune evasion protein that suppresses the antiviral IFN function by counteracting the function of IFI6-16.
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Gytz H, Hansen MF, Skovbjerg S, Kristensen ACM, Hørlyck S, Jensen MB, Fredborg M, Markert LD, McMillan NA, Christensen EI, Martensen PM. Apoptotic properties of the type 1 interferon induced family of human mitochondrial membrane ISG12 proteins. Biol Cell 2016; 109:94-112. [DOI: 10.1111/boc.201600034] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Heidi Gytz
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus 8000 Denmark
| | - Mariann F. Hansen
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus 8000 Denmark
| | - Signe Skovbjerg
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus 8000 Denmark
| | | | - Sofie Hørlyck
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus 8000 Denmark
| | - Mette B. Jensen
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus 8000 Denmark
| | - Marlene Fredborg
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus 8000 Denmark
| | - Lotte D. Markert
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus 8000 Denmark
| | - Nigel A. McMillan
- Centre of Immunological and Cancer Research; Queensland University; Brisbane Australia
| | | | - Pia M. Martensen
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus 8000 Denmark
- Centre of Immunological and Cancer Research; Queensland University; Brisbane Australia
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30
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Tiffen JC, Gallagher SJ, Tseng HY, Filipp FV, Fazekas de St. Groth B, Hersey P. EZH2 as a mediator of treatment resistance in melanoma. Pigment Cell Melanoma Res 2016; 29:500-7. [PMID: 27063195 PMCID: PMC5021620 DOI: 10.1111/pcmr.12481] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 03/24/2016] [Indexed: 12/27/2022]
Abstract
Direct treatments of cancer such as chemotherapy, radiotherapy and targeted therapy have been shown to depend on recruitment of the immune system for their effectiveness. Recent studies have shown that development of resistance to direct therapies such as BRAF inhibitors in melanoma is associated with suppression of immune responses. We point to emerging data that implicate activation of the polycomb repressive complex 2 (PRC2) and its catalytic component-enhancer of zeste homolog 2 (EZH2)-in progression of melanoma and suppression of immune responses. EZH2 appears to have an important role in differentiation of CD4 T cells and particularly in the function of T regulatory cells, which suppress immune responses to melanoma. We review mechanisms of EZH2 activation at the genomic level and from activation of the MAP kinase, E2F or NF-kB2 pathways. These studies are consistent with activation of EZH2 as a common mechanism for induction of immune suppression in patients failing direct therapies and suggest EZH2 inhibitors may have a role in combination with immunotherapy and targeted therapies to prevent development of immunosuppression.
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Affiliation(s)
- Jessamy C Tiffen
- Melanoma Immunology and Oncology Group, The Centenary Institute, University of Sydney, Camperdown, NSW, Australia
| | - Stuart J Gallagher
- Melanoma Immunology and Oncology Group, The Centenary Institute, University of Sydney, Camperdown, NSW, Australia
| | - Hsin-Yi Tseng
- Melanoma Immunology and Oncology Group, The Centenary Institute, University of Sydney, Camperdown, NSW, Australia
| | - Fabian V Filipp
- Systems Biology and Cancer Metabolism, Program for Quantitative Systems Biology, University of California Merced, Merced, CA, USA
| | | | - Peter Hersey
- Melanoma Immunology and Oncology Group, The Centenary Institute, University of Sydney, Camperdown, NSW, Australia.
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31
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Leisner TM, Freeman TC, Black JL, Parise LV. CIB1: a small protein with big ambitions. FASEB J 2016; 30:2640-50. [PMID: 27118676 DOI: 10.1096/fj.201500073r] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/05/2016] [Indexed: 12/11/2022]
Abstract
Calcium- and integrin-binding protein 1 (CIB1) is a small, ubiquitously expressed protein that was first identified as an intracellular binding partner of a platelet-specific α-integrin cytoplasmic tail. Although early studies revealed a role for CIB1 in regulating platelet integrin activity, recent studies have indicated a more diverse role for CIB1 in many different cell types and processes, including calcium signaling, migration, adhesion, proliferation, and survival. Increasing evidence also points to a novel role for CIB1 in cancer and cardiovascular disease. In addition, an array of CIB1 binding partners has been identified that provide important insight into how CIB1 may regulate these processes. Some of these binding partners include the serine/threonine kinases, p21-activated kinase 1 (PAK1), apoptosis signal-regulating kinase 1 (ASK1), and polo-like kinase 3 (PLK3). Structural and mutational studies indicate that CIB1 binds most or all of its partners via a well-defined hydrophobic cleft. Although CIB1 itself lacks known enzymatic activity, it supports the PI3K/AKT and MEK/ERK oncogenic signaling pathways, in part, by directly modulating enzymes in these pathways. In this review, we discuss our current understanding of CIB1 and key questions regarding structure and function and how this seemingly diminutive protein impacts important signaling pathways and cellular processes in human health and disease.-Leisner, T. M., Freeman, T. C., Black, J. L., Parise, L. V. CIB1: a small protein with big ambitions.
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Affiliation(s)
- Tina M Leisner
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Thomas C Freeman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Justin L Black
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Leslie V Parise
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, North Carolina, USA; and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
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32
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Széll M, Danis J, Bata-Csörgő Z, Kemény L. PRINS, a primate-specific long non-coding RNA, plays a role in the keratinocyte stress response and psoriasis pathogenesis. Pflugers Arch 2016; 468:935-43. [PMID: 26935426 PMCID: PMC4893059 DOI: 10.1007/s00424-016-1803-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/23/2016] [Indexed: 12/30/2022]
Abstract
In the last few years with the recent emergence of high-throughput technologies, thousands of long non-coding RNAs (lncRNAs) have been identified in the human genome. However, assigning functional annotation and determining cellular contexts for these RNAs are still in its infancy. As information gained about lncRNA structure, interacting partners, and roles in human diseases may be helpful in the characterization of novel lncRNAs, we review our knowledge on a selected group of lncRNAs that were identified serendipitously years ago by large-scale gene expression methods used to study human diseases. In particular, we focus on the Psoriasis-susceptibility-Related RNA Gene Induced by Stress (PRINS) lncRNA, first identified by our research group as a transcript highest expressed in psoriatic non-lesional epidermis. Results gathered for PRINS in the last 10 years indicate that it is conserved in primates and plays a role in keratinocyte stress response. Elevated levels of PRINS expression in psoriatic non-lesional keratinocytes alter the stress response of non-lesional epidermis and contribute to disease pathogenesis. Finally, we propose a categorization for the PRINS lncRNA based on a recently elaborated system for lncRNA classification.
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Affiliation(s)
- Márta Széll
- Department of Medical Genetics, Faculty of Medicine, University of Szeged, Szeged, Somogyi B. u. 4, 6720, Hungary. .,MTA-SZTE Dermatological Research Group, Szeged, Korányi fasor 6, 6720, Hungary.
| | - Judit Danis
- Department of Dermatology and Allergology, Faculty of Medicine, University of Szeged, Szeged, Korányi fasor 6, 6720, Hungary
| | - Zsuzsanna Bata-Csörgő
- MTA-SZTE Dermatological Research Group, Szeged, Korányi fasor 6, 6720, Hungary.,Department of Dermatology and Allergology, Faculty of Medicine, University of Szeged, Szeged, Korányi fasor 6, 6720, Hungary
| | - Lajos Kemény
- MTA-SZTE Dermatological Research Group, Szeged, Korányi fasor 6, 6720, Hungary.,Department of Dermatology and Allergology, Faculty of Medicine, University of Szeged, Szeged, Korányi fasor 6, 6720, Hungary
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33
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Chen S, Li S, Chen L. Interferon-inducible Protein 6-16 (IFI-6-16, ISG16) promotes Hepatitis C virus replication in vitro. J Med Virol 2015; 88:109-14. [DOI: 10.1002/jmv.24302] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Shan Chen
- Institute of Blood Transfusion; Chinese Academy of Medical Sciences and Peking Union Medical College; Chengdu China
| | - Shilin Li
- Institute of Blood Transfusion; Chinese Academy of Medical Sciences and Peking Union Medical College; Chengdu China
| | - Limin Chen
- Institute of Blood Transfusion; Chinese Academy of Medical Sciences and Peking Union Medical College; Chengdu China
- Toronto General Research Institute; University of Toronto; Toronto Ontario Canada
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34
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Qi Y, Li Y, Zhang Y, Zhang L, Wang Z, Zhang X, Gui L, Huang J. IFI6 Inhibits Apoptosis via Mitochondrial-Dependent Pathway in Dengue Virus 2 Infected Vascular Endothelial Cells. PLoS One 2015; 10:e0132743. [PMID: 26244642 PMCID: PMC4526556 DOI: 10.1371/journal.pone.0132743] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/17/2015] [Indexed: 12/03/2022] Open
Abstract
Dengue hemorrhagic fever (DHF)/Dengue shock syndrome (DSS) is a fatal infectious disease that demands an effective treatment. Interferon (IFN)-stimulated genes (ISGs) induced by dengue virus (DENV) exert antiviral effects. Among ISGs, IFN-α inducible gene 6 (IFI6) was increased in DENV infected human umbilical vascular endothelial cells (HUVECs) by microarray analysis in our previous study. However, its function is incompletely understood. In this study, we confirmed that IFI6 was markedly induced in DENV infection of both primary HUVECs and EA.hy926 cell lines. Recombinant EA.hy926 cell lines in which IFI6 was either over-expressed (IFI6+/+) or knocked-down (IFI6-/-) were generated. The activation of caspase-3 and intrinsic apoptosis-related protein caspase-9 were down-regulated in IFI6+/+ but up-regulated in IFI6-/- cells at 24–48 hrs post-infection. After incubation with DENV for 48 hrs, the mitochondrial membrane potential (Δψ(m)) was more stable in IFI6+/+ cells but reduced in IFI6-/- cells, as assayed by fluorescence staining with JC-1. We observed that Bcl-2 expression was increased in IFI6+/+ and decreased in IFI6-/- cells. By contrast, Bax expression was decreased in IFI6+/+ and increased in IFI6-/- cells. It is presumed that the anti-apoptotic function of IFI6 is expressed by regulating the rheostatic balance between bcl-2/bax expression and inhibition of Δψ(m) depolarization during DENV infection of vascular endothelial cells(VECs). In addition, the pro-apoptotic protein X-linked Inhibitor of Apoptosis (XIAP)-Associated Factor 1(XAF1) expression had been reported to be up-regulated and led to the induction of apoptosis in DENV2-infected VECs,but the relationship between XAF1 and IFI6 dengue virus-induced apoptosis in VECs warrants further study.
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Affiliation(s)
- Yiming Qi
- Institute of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
- Key Laboratory of Tropical Diseases Control, Ministry of Education, Guangzhou, PR China
| | - Ying Li
- Institute of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
- Key Laboratory of Tropical Diseases Control, Ministry of Education, Guangzhou, PR China
| | - Yingke Zhang
- Institute of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
- Key Laboratory of Tropical Diseases Control, Ministry of Education, Guangzhou, PR China
| | - Lin Zhang
- Institute of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
- Key Laboratory of Tropical Diseases Control, Ministry of Education, Guangzhou, PR China
| | - Zilian Wang
- First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xuzhi Zhang
- Institute of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
- Key Laboratory of Tropical Diseases Control, Ministry of Education, Guangzhou, PR China
| | - Lian Gui
- Institute of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
- Key Laboratory of Tropical Diseases Control, Ministry of Education, Guangzhou, PR China
| | - Junqi Huang
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, PR China
- First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Institute of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
- Key Laboratory of Tropical Diseases Control, Ministry of Education, Guangzhou, PR China
- * E-mail:
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35
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Meyer K, Kwon YC, Liu S, Hagedorn CH, Ray RB, Ray R. Interferon-α inducible protein 6 impairs EGFR activation by CD81 and inhibits hepatitis C virus infection. Sci Rep 2015; 5:9012. [PMID: 25757571 PMCID: PMC4355636 DOI: 10.1038/srep09012] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 02/16/2015] [Indexed: 02/06/2023] Open
Abstract
Viral entry requires co-operative interactions of several host cell factors. Interferon (IFN) and the IFN-stimulated genes (ISGs) play a central role in antiviral responses against hepatitis C virus (HCV) infection. We examined the effect of interferon-α inducible protein 6 (IFI6) against HCV infection in human hepatoma cells. HCV RNA level or infectious foci were inhibited significantly by ectopic expression of IFI6. IFI6 impaired CD81 co-localization with claudin-1 (CLDN1) upon HCV infection or CD81 cross-linking by specific antibody. Activation of epidermal growth factor receptor (EGFR), a co-factor involved in CD81/CLDN1 interactions, was reduced in IFI6 expressing cells in response to HCV infection or CD81 cross linking by antibody, but not by treatment with EGF. Taken together, the results from our study support a model where IFI6 inhibits HCV entry by impairing EGFR mediated CD81/CLDN1 interactions. This may be relevant to other virus entry processes employing EGFR.
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Affiliation(s)
- Keith Meyer
- Department of Internal Medicine, Saint Louis University
| | | | - Shuanghu Liu
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah
| | - Curt H Hagedorn
- 1] Department of Medicine and Genetics, University of Arkansas for Medical Sciences [2] The Central Arkansas Veterans Healthcare System
| | - Ratna B Ray
- 1] Department of Internal Medicine, Saint Louis University [2] Department of Pathology, Saint Louis University
| | - Ranjit Ray
- 1] Department of Internal Medicine, Saint Louis University [2] Department of Molecular Microbiology &Immunology, Saint Louis University
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36
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Swan AL, Stekel DJ, Hodgman C, Allaway D, Alqahtani MH, Mobasheri A, Bacardit J. A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data. BMC Genomics 2015; 16 Suppl 1:S2. [PMID: 25923811 PMCID: PMC4315157 DOI: 10.1186/1471-2164-16-s1-s2] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Investigations into novel biomarkers using omics techniques generate large amounts of data. Due to their size and numbers of attributes, these data are suitable for analysis with machine learning methods. A key component of typical machine learning pipelines for omics data is feature selection, which is used to reduce the raw high-dimensional data into a tractable number of features. Feature selection needs to balance the objective of using as few features as possible, while maintaining high predictive power. This balance is crucial when the goal of data analysis is the identification of highly accurate but small panels of biomarkers with potential clinical utility. In this paper we propose a heuristic for the selection of very small feature subsets, via an iterative feature elimination process that is guided by rule-based machine learning, called RGIFE (Rule-guided Iterative Feature Elimination). We use this heuristic to identify putative biomarkers of osteoarthritis (OA), articular cartilage degradation and synovial inflammation, using both proteomic and transcriptomic datasets. RESULTS AND DISCUSSION Our RGIFE heuristic increased the classification accuracies achieved for all datasets when no feature selection is used, and performed well in a comparison with other feature selection methods. Using this method the datasets were reduced to a smaller number of genes or proteins, including those known to be relevant to OA, cartilage degradation and joint inflammation. The results have shown the RGIFE feature reduction method to be suitable for analysing both proteomic and transcriptomics data. Methods that generate large 'omics' datasets are increasingly being used in the area of rheumatology. CONCLUSIONS Feature reduction methods are advantageous for the analysis of omics data in the field of rheumatology, as the applications of such techniques are likely to result in improvements in diagnosis, treatment and drug discovery.
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Affiliation(s)
- Anna L Swan
- School of Biosciences, Faculty of Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, United Kingdom
| | - Dov J Stekel
- School of Biosciences, Faculty of Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, United Kingdom
| | - Charlie Hodgman
- School of Biosciences, Faculty of Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, United Kingdom
- The D-BOARD European Consortium for Biomarker Discovery, The Universities of Surrey, Nottingham and Newcastle, United Kingdom
| | - David Allaway
- WALTHAM® Centre for Pet Nutrition, Waltham-on-the-Wolds, Melton Mowbray, Leicestershire, LE14 4RT, United Kingdom
| | - Mohammed H Alqahtani
- Center of Excellence in Genomic Medicine Research (CEGMR), King AbdulAziz University, Jeddah, 21589, Kingdom of Saudi Arabia
| | - Ali Mobasheri
- The D-BOARD European Consortium for Biomarker Discovery, The Universities of Surrey, Nottingham and Newcastle, United Kingdom
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Duke of Kent Building, Guildford, Surrey, GU2 7XH, United Kingdom
- Center of Excellence in Genomic Medicine Research (CEGMR), King AbdulAziz University, Jeddah, 21589, Kingdom of Saudi Arabia
- Arthritis Research UK Centre for Sport, Exercise, and Osteoarthritis, Arthritis Research UK Pain Centre, Medical Research Council-Arthritis Research UK Centre for Musculoskeletal Ageing Research, Faculty of Medicine and Health Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Jaume Bacardit
- The D-BOARD European Consortium for Biomarker Discovery, The Universities of Surrey, Nottingham and Newcastle, United Kingdom
- The Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Claremont Tower, Newcastle-upon-Tyne, NE1 7RU, United Kingdom
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Shift in monocyte apoptosis with increasing viral load and change in apoptosis-related ISG/Bcl2 family gene expression in chronically HIV-1-infected subjects. J Virol 2014; 89:799-810. [PMID: 25355877 DOI: 10.1128/jvi.02382-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
UNLABELLED Although monocytes and macrophages are targets of HIV-1-mediated immunopathology, the impact of high viremia on activation-induced monocyte apoptosis relative to monocyte and macrophage activation changes remains undetermined. In this study, we determined constitutive and oxidative stress-induced monocyte apoptosis in uninfected and HIV(+) individuals across a spectrum of viral loads (n = 35; range, 2,243 to 1,355,998 HIV-1 RNA copies/ml) and CD4 counts (range, 26 to 801 cells/mm(3)). Both constitutive apoptosis and oxidative stress-induced apoptosis were positively associated with viral load and negatively associated with CD4, with an elevation in apoptosis occurring in patients with more than 40,000 (4.6 log) copies/ml. As expected, expression of Rb1 and interferon-stimulated genes (ISGs), plasma soluble CD163 (sCD163) concentration, and the proportion of CD14(++) CD16(+) intermediate monocytes were elevated in viremic patients compared to those in uninfected controls. Although CD14(++) CD16(+) frequencies, sCD14, sCD163, and most ISG expression were not directly associated with a change in apoptosis, sCD14 and ISG expression showed an association with increasing viral load. Multivariable analysis of clinical values and monocyte gene expression identified changes in IFI27, IFITM2, Rb1, and Bcl2 expression as determinants of constitutive apoptosis (P = 3.77 × 10(-5); adjusted R(2) = 0.5983), while changes in viral load, IFITM2, Rb1, and Bax expression were determinants of oxidative stress-induced apoptosis (P = 5.59 × 10(-5); adjusted R(2) = 0.5996). Our data demonstrate differential activation states in monocytes between levels of viremia in association with differences in apoptosis that may contribute to greater monocyte turnover with high viremia. IMPORTANCE This study characterized differential monocyte activation, apoptosis, and apoptosis-related gene expression in low- versus high-level viremic HIV-1 patients, suggesting a shift in apoptosis regulation that may be associated with disease state. Using single and multivariable analysis of monocyte activation parameters and gene expression, we supported the hypothesis that monocyte apoptosis in HIV disease is a reflection of viremia and activation state with contributions from gene expression changes within the ISG and Bcl2 gene families. Understanding monocyte apoptosis response may inform HIV immunopathogenesis, retention of infected macrophages, and monocyte turnover in low- or high-viral-load states.
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Zhang F, Qi Y, Harrison TJ, Luo B, Zhou Y, Li X, Song A, Huang W, Wang Y. Hepatitis E genotype 4 virus from feces of monkeys infected experimentally can be cultured in PLC/PRF/5 cells and upregulate host interferon-inducible genes. J Med Virol 2014; 86:1736-44. [PMID: 25042677 DOI: 10.1002/jmv.24014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2014] [Indexed: 12/15/2022]
Abstract
The understanding of the interaction between hepatitis E virus (HEV) and its host cells has been impeded greatly by the absence of a cell culture system. In this study, an efficient cultivation method was developed in PLC/PRF/5 cells for HEV genotype 4 from the feces of monkeys infected experimentally. Compared to minimal essential medium (MEM), mixed Dulbecco's Modified Eagle's Medium (DMEM)/M199 improved the infection efficiency of HEV in PLC/PRF/5 cells. The incubation time and temperature were set at 6 hr and 40°C, respectively. Compared to a 100% ELISA positive ratio (EPR) of 1 × 10(6) copies/ml HEV inoculated flasks, the ELISA positive ratio was 100%, 75%, 37.5%, and 100% for flasks inoculated with HEV incubated for 30 min under the conditions of pH 3.0, pH 11.0, 56°C and delipidation treatment, respectively. Gene expression profiles of HEV inoculated and control PLC/PRF/5 cells were assayed using a microarray. Four interferon-inducible genes, IFI27, IFI6, Mx1, and CMPK2, were up-regulated during HEV-infection. Furthermore, the replication of HEV was inhibited at 3-14 days after treatment with 500 IU/ml IFN-α2b.
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Affiliation(s)
- Feng Zhang
- Graduate School of Peking Union Medical College, Beijing, China; Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control, Beijing, China
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Wang X, Lu C, He X, Hu S, Sun A, Hu M, Chen WR. WITHDRAWN: CIB1 acts as a partner protein of CD38 in cADPR synthesis. Biochem Biophys Res Commun 2014:S0006-291X(14)01139-5. [PMID: 24967876 DOI: 10.1016/j.bbrc.2014.06.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Xianwang Wang
- Functional Laboratory, School of Medicine, Yangtze University, Jingzhou 434023, China.
| | - Chengbiao Lu
- Functional Laboratory, School of Medicine, Yangtze University, Jingzhou 434023, China
| | - Xiaobing He
- Functional Laboratory, School of Medicine, Yangtze University, Jingzhou 434023, China
| | - Shujuan Hu
- Institute of Physical Education, Yangtze University, Jingzhou 434023, China
| | - Anbang Sun
- Functional Laboratory, School of Medicine, Yangtze University, Jingzhou 434023, China
| | - Menglong Hu
- Department of Physiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Wei R Chen
- Biophotonics Research Laboratory, Center for Interdisciplinary Biomedical Education and Research, University of Central Oklahoma, Edmond, OK 73034, USA.
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Saben J, Zhong Y, McKelvey S, Dajani NK, Andres A, Badger TM, Gomez-Acevedo H, Shankar K. A comprehensive analysis of the human placenta transcriptome. Placenta 2013; 35:125-31. [PMID: 24333048 DOI: 10.1016/j.placenta.2013.11.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/25/2013] [Accepted: 11/13/2013] [Indexed: 01/16/2023]
Abstract
As the conduit for nutrients and growth signals, the placenta is critical to establishing an environment sufficient for fetal growth and development. To better understand the mechanisms regulating placental development and gene expression, we characterized the transcriptome of term placenta from 20 healthy women with uncomplicated pregnancies using RNA-seq. To identify genes that were highly expressed and unique to the placenta we compared placental RNA-seq data to data from 7 other tissues (adipose, breast, hear, kidney, liver, lung, and smooth muscle) and identified several genes novel to placental biology (QSOX1, DLG5, and SEMA7A). Semi-quantitative RT-PCR confirmed the RNA-seq results and immunohistochemistry indicated these proteins were highly expressed in the placental syncytium. Additionally, we mined our RNA-seq data to map the relative expression of key developmental gene families (Fox, Sox, Gata, Tead, and Wnt) within the placenta. We identified FOXO4, GATA3, and WNT7A to be amongst the highest expressed members of these families. Overall, these findings provide a new reference for understanding of placental transcriptome and can aid in the identification of novel pathways regulating placenta physiology that may be dysregulated in placental disease.
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Affiliation(s)
- J Saben
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Y Zhong
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - S McKelvey
- Department of Obstetrics and Gynecology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - N K Dajani
- Department of Obstetrics and Gynecology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - A Andres
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - T M Badger
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - H Gomez-Acevedo
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - K Shankar
- Arkansas Children's Nutrition Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
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Swindell WR, Johnston A, Xing X, Voorhees JJ, Elder JT, Gudjonsson JE. Modulation of epidermal transcription circuits in psoriasis: new links between inflammation and hyperproliferation. PLoS One 2013; 8:e79253. [PMID: 24260178 PMCID: PMC3829857 DOI: 10.1371/journal.pone.0079253] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/19/2013] [Indexed: 12/16/2022] Open
Abstract
Background Whole-genome expression profiling has been used to characterize molecular-level differences between psoriasis lesions and normal skin. Pathway analysis, however, is complicated by the fact that expression profiles have been derived from bulk skin biopsies with RNA derived from multiple cell types. Results We analyzed gene expression across a large sample of psoriatic (PP) and uninvolved/normal (PN) skin biopsies (n = 215 patients). We identified 1975 differentially expressed genes, including 8 associated with psoriasis susceptibility loci. To facilitate pathway analysis, PP versus PN differences in gene expression were analyzed with respect to 235 gene modules, each containing genes with a similar expression pattern in keratinocytes and epidermis. We identified 30 differentially expressed modules (DEMs) biased towards PP-increased or PP-decreased expression. These DEMs were associated with regulatory axes involving cytokines (e.g., IFN-γ, IL-17A, TNF-α), transcription factors (e.g., STAT1, NF-κB, E2F, RUNX1) and chromatin modifiers (SETDB1). We identified an interferon-induced DEM with genes encoding anti-viral proteins (designated “STAT1-57”), which was activated in psoriatic epidermis but repressed following biologic therapy. Genes within this DEM shared a motif near the transcription start site resembling the interferon-stimulated response element (ISRE). Conclusions We analyzed a large patient cohort and developed a new approach for delineating epidermis-specific pathways and regulatory mechanisms that underlie altered gene expression in psoriasis. Our findings highlight previously unrecognized “transcription circuits” that can provide targets for development of non-systemic therapies.
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Affiliation(s)
- William R. Swindell
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
- * E-mail:
| | - Andrew Johnston
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Xianying Xing
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - John J. Voorhees
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - James T. Elder
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Johann E. Gudjonsson
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
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Kotredes KP, Gamero AM. Interferons as inducers of apoptosis in malignant cells. J Interferon Cytokine Res 2013; 33:162-70. [PMID: 23570382 DOI: 10.1089/jir.2012.0110] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Discovered as antiviral cytokines, interferons (IFNs) are now also recognized for their capacity to inhibit the growth of malignant cells via activation of programmed cell death, better known as apoptosis. In this review, we will cover recent advances made in this field, as it pertains to the various proposed mechanisms of IFN-induced apoptosis and the characterization of IFN-responsive genes not previously known to have apoptotic function. Also mentioned here is a description of the activation and crosstalk of survival signaling pathways as a mode of IFN resistance that remains a persistent clinical adversary to overcome and the future of IFNs as antitumor agents.
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Affiliation(s)
- Kevin P Kotredes
- Department of Biochemistry, Temple University School of Medicine , Philadelphia, PA 19140, USA
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Zapata JC, Carrion R, Patterson JL, Crasta O, Zhang Y, Mani S, Jett M, Poonia B, Djavani M, White DM, Lukashevich IS, Salvato MS. Transcriptome analysis of human peripheral blood mononuclear cells exposed to Lassa virus and to the attenuated Mopeia/Lassa reassortant 29 (ML29), a vaccine candidate. PLoS Negl Trop Dis 2013; 7:e2406. [PMID: 24069471 PMCID: PMC3772037 DOI: 10.1371/journal.pntd.0002406] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 07/24/2013] [Indexed: 12/22/2022] Open
Abstract
Lassa virus (LASV) is the causative agent of Lassa Fever and is responsible for several hundred thousand infections and thousands of deaths annually in West Africa. LASV and the non-pathogenic Mopeia virus (MOPV) are both rodent-borne African arenaviruses. A live attenuated reassortant of MOPV and LASV, designated ML29, protects rodents and primates from LASV challenge and appears to be more attenuated than MOPV. To gain better insight into LASV-induced pathology and mechanism of attenuation we performed gene expression profiling in human peripheral blood mononuclear cells (PBMC) exposed to LASV and the vaccine candidate ML29. PBMC from healthy human subjects were exposed to either LASV or ML29. Although most PBMC are non-permissive for virus replication, they remain susceptible to signal transduction by virus particles. Total RNA was extracted and global gene expression was evaluated during the first 24 hours using high-density microarrays. Results were validated using RT-PCR, flow cytometry and ELISA. LASV and ML29 elicited differential expression of interferon-stimulated genes (ISG), as well as genes involved in apoptosis, NF-kB signaling and the coagulation pathways. These genes could eventually serve as biomarkers to predict disease outcomes. The remarkable differential expression of thrombomodulin, a key regulator of inflammation and coagulation, suggests its involvement with vascular abnormalities and mortality in Lassa fever disease. The virulent Lassa fever virus (LASV) and the non-pathogenic Mopeia virus (MOPV) infect rodents and, incidentally, people in West Africa. The mechanism of LASV damage in human beings is unclear. There is no licensed Lassa fever vaccine and therapeutic intervention is usually too late. The ML29 vaccine candidate derived from Lassa and Mopeia viruses protects rodents and primates from Lassa fever disease. Peripheral blood mononuclear cells from healthy human subjects were exposed to either LASV or ML29 in order to identify early cellular responses that could be attributed to the difference in virulence between the two viruses. Differential expression of interferon-stimulated genes as well as coagulation-related genes could lead to an explanation for Lassa fever pathogenesis and indicate protective treatments for Lassa fever disease.
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Affiliation(s)
- Juan Carlos Zapata
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
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Aspirin enhances IFN-α-induced growth inhibition and apoptosis of hepatocellular carcinoma via JAK1/STAT1 pathway. Cancer Gene Ther 2013; 20:366-74. [PMID: 23703473 DOI: 10.1038/cgt.2013.29] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
STAT1 has a key role in exerting the antiproliferative and proapoptotic effects of interferon (IFN)-α on tumors, and its defects in expression is associated with IFN-α resistance. In this study we want to investigate whether aspirin can improve the antitumor efficiency of IFN-α on hepatocellular carcinoma (HCC) through the activation of STAT1. We found that aspirin not only significantly enhanced IFN-α-induced antiproliferation and apoptosis of HCC in vitro study but also enhanced tumor growth inhibition in nude mice. Although IFN-α alone resulted in significant phosphorylation of both STAT1 and STAT3, aspirin only prompted the IFN-α-induced phosphorylation of STAT1. Further study revealed that aspirin-prompted phosphorylation of STAT1 was activated through phosphorylation of JAK1. Furthermore, aspirin-activated STAT1 upregulated the transcription of proapoptotic IFN-stimulated gene (ISG) of X-linked inhibitor of apoptosis-associated factor-1 and downregulated the transcription of antiapoptotic ISG of G1P3, which in turn promoted the expression of Bax and activation of caspase-9 and caspase-3, thereby sensitizing HCC cells to IFN-α-induced apoptosis. Taken together, our findings suggest a novel strategy of using aspirin to overcome tumor resistance and enhance the effectiveness of IFN-α in HCC treatment through activating STAT1 gene, and have potential implications for improving future IFN-α protein and gene therapy.
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Park GH, Kim KY, Cho SW, Cheong JY, Yu GI, Shin DH, Kwack KB. Association between Interferon-Inducible Protein 6 (IFI6) Polymorphisms and Hepatitis B Virus Clearance. Genomics Inform 2013; 11:15-23. [PMID: 23613678 PMCID: PMC3630380 DOI: 10.5808/gi.2013.11.1.15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 02/08/2013] [Accepted: 02/14/2013] [Indexed: 01/28/2023] Open
Abstract
CD8+ T cells are key factors mediating hepatitis B virus (HBV) clearance. However, these cells are killed through HBV-induced apoptosis during the antigen-presenting period in HBV-induced chronic liver disease (CLD) patients. Interferon-inducible protein 6 (IFI6) delays type I interferon-induced apoptosis in cells. We hypothesized that single nucleotide polymorphisms (SNPs) in the IFI6 could affect the chronicity of CLD. The present study included a discovery stage, in which 195 CLD patients, including chronic hepatitis B (HEP) and cirrhosis patients and 107 spontaneous recovery (SR) controls, were analyzed. The genotype distributions of rs2808426 (C > T) and rs10902662 (C > T) were significantly different between the SR and HEP groups (odds ratio [OR], 6.60; 95% confidence interval [CI], 1.64 to 26.52, p = 0.008 for both SNPs) and between the SR and CLD groups (OR, 4.38; 95% CI, 1.25 to 15.26; p = 0.021 and OR, 4.12; 95% CI, 1.18 to 14.44; p = 0.027, respectively). The distribution of diplotypes that contained these SNPs was significantly different between the SR and HEP groups (OR, 6.58; 95% CI, 1.63 to 25.59; p = 0.008 and OR, 0.15; 95% CI, 0.04 to 0.61; p = 0.008, respectively) and between the SR and CLD groups (OR, 4.38; 95% CI, 1.25 to 15.26; p = 0.021 and OR, 4.12; 95% CI, 1.18 to 14.44; p = 0.027, respectively). We were unable to replicate the association shown by secondary enrolled samples. A large-scale validation study should be performed to confirm the association between IFI6 and HBV clearance.
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Affiliation(s)
- Geun-Hee Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 463-836, Korea
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Cheriyath V, Kuhns MA, Jacobs BS, Evangelista P, Elson P, Downs-Kelly E, Tubbs R, Borden EC. G1P3, an interferon- and estrogen-induced survival protein contributes to hyperplasia, tamoxifen resistance and poor outcomes in breast cancer. Oncogene 2012; 31:2222-36. [PMID: 21996729 DOI: 10.1038/onc.2011.393] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2010] [Revised: 06/26/2011] [Accepted: 08/04/2011] [Indexed: 02/06/2023]
Abstract
Hormonally regulated survival factors can have an important role in breast cancer. Here we elucidate G1P3, a survival protein induced by interferons (IFNs), as a target of estrogen signaling and a contributor to poor outcomes in estrogen receptor-positive (ER(+)) breast cancer. Compared with normal breast tissue, G1P3 was upregulated in the malignant epithelium (50 × higher) and was induced by estrogen ex vivo. In accord with its overexpression in early stages of breast cancer (hyperplasia and ductal carcinoma in situ), in morphogenesis assays G1P3 enhanced the survival of MCF10A acinar luminal cells causing hyperplasia by suppressing detachment-induced loss of mitochondrial potential and apoptosis (anoikis). In cells undergoing anoikis, G1P3 attenuated the induction of Bim protein, a proapoptotic member of the Bcl-2 family and reversed the downmodulation of Bcl-2 protein. Downregulation of G1P3 induced spontaneous apoptosis in BT-549 breast cancer cells and significantly reduced the growth of ER(+) breast cancer cell MCF7 (P≤0.01), further suggesting its prosurvival activity. In agreement with its induction by estrogen, G1P3 antagonized tamoxifen, an inhibitor of ER in MCF7 cells. More importantly, elevated expression of G1P3 was significantly associated with decreased relapse-free and overall survival in ER(+) breast cancer patients (P≤0.01). Our studies suggest that elevated expression of G1P3 may perturb canonical tumor-suppressing activity of IFNs partly by affecting the balance of pro- and antiapoptotic members of Bcl-2 family proteins, leading to breast cancer development and resistance to therapies.
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Affiliation(s)
- V Cheriyath
- Translational Hematology and Oncology Research, Taussig Cancer Institute, The Cleveland Clinic, Cleveland, OH 44195, USA.
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Search for specific biomarkers of IFNβ bioactivity in patients with multiple sclerosis. PLoS One 2011; 6:e23634. [PMID: 21886806 PMCID: PMC3160307 DOI: 10.1371/journal.pone.0023634] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Accepted: 07/21/2011] [Indexed: 11/19/2022] Open
Abstract
Myxovirus A (MxA), a protein encoded by the MX1 gene with antiviral activity, has proven to be a sensitive measure of IFNβ bioactivity in multiple sclerosis (MS). However, the use of MxA as a biomarker of IFNβ bioactivity has been criticized for the lack of evidence of its role on disease pathogenesis and the clinical response to IFNβ. Here, we aimed to identify specific biomarkers of IFNβ bioactivity in order to compare their gene expression induction by type I IFNs with the MxA, and to investigate their potential role in MS pathogenesis. Gene expression microarrays were performed in PBMC from MS patients who developed neutralizing antibodies (NAB) to IFNβ at 12 and/or 24 months of treatment and patients who remained NAB negative. Nine genes followed patterns in gene expression over time similar to the MX1, which was considered the gold standard gene, and were selected for further experiments: IFI6, IFI27, IFI44L, IFIT1, HERC5, LY6E, RSAD2, SIGLEC1, and USP18. In vitro experiments in PBMC from healthy controls revealed specific induction of selected biomarkers by IFNβ but not IFNγ, and several markers, in particular USP18 and HERC5, were shown to be significantly induced at lower IFNβ concentrations and more selective than the MX1 as biomarkers of IFNβ bioactivity. In addition, USP18 expression was deficient in MS patients compared with healthy controls (p = 0.0004). We propose specific biomarkers that may be considered in addition to the MxA to evaluate IFNβ bioactivity, and to further explore their implication in MS pathogenesis.
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Absent in Melanoma 2 (AIM2) is an important mediator of interferon-dependent and -independent HLA-DRA and HLA-DRB gene expression in colorectal cancers. Oncogene 2011; 31:1242-53. [PMID: 21804607 PMCID: PMC3307062 DOI: 10.1038/onc.2011.320] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Absent in Melanoma 2 (AIM2) is a member of the HIN-200 family of hematopoietic, IFN-inducible, nuclear proteins, associated with both, infection defense and tumor pathology. Recently, AIM2 was found to act as a DNA sensor in innate immunity. In addition, we and others have previously demonstrated a high frequency of AIM2-alterations in microsatellite unstable (MSI-H) tumors. To further elucidate AIM2 function in colorectal tumors, we here addressed AIM2-responsive target genes by microarray based gene expression profiling of 22 244 human genes. A total of 111 transcripts were significantly upregulated, whereas 80 transcripts turned out to be significantly downregulated in HCT116 cells, constitutively expressing AIM2, compared with AIM2-negative cells. Among the upregulated genes that were validated by quantitative PCR and western blotting we recognized several interferon-stimulated genes (ISGs: IFIT1, IFIT2, IFIT3, IFI6, IRF7, ISG15, HLA-DRA, HLA-DRB, TLR3 and CIITA), as well as genes involved in intercellular adhesion and matrix remodeling. Expression of ISGs correlated with expression of AIM2 in 10 different IFN-γ treated colorectal cancer cell lines. Moreover, small interfering RNA-mediated knock-down of AIM2 resulted in reduced expression of HLA-DRA, HLA-DRB and CIITA in IFN-γ-treated cells. IFN-γ independent induction of HLA-DR genes and their encoded proteins was also demonstrated upon doxycyclin-regulated transient induction of AIM2. Luciferase reporter assays revealed induction of the HLA-DR promoter upon AIM2 transfection in different cell lines. STAT-signaling was not involved in IFN-γ independent induction of ISGs, arguing against participation of cytokines released in an autostimulating manner. Our data indicate that AIM2 mediates both IFN-γ dependent and independent induction of several ISGs, including genes encoding the major histocompatibility complex (MHC) class II antigens HLA-DR-α and -β. This suggests a novel role of the IFN/AIM2/ISG cascade likewise in cancer cells.
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Deletion of Kaposi's sarcoma-associated herpesvirus FLICE inhibitory protein, vFLIP, from the viral genome compromises the activation of STAT1-responsive cellular genes and spindle cell formation in endothelial cells. J Virol 2011; 85:10375-88. [PMID: 21795355 DOI: 10.1128/jvi.00226-11] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Kaposi's sarcoma herpesvirus (KSHV) Fas-associated death domain (FADD)-like interleukin-1 beta-converting enzyme (FLICE)-inhibitory protein, vFLIP, has antiapoptotic properties, is a potent activator of the NF-κB pathway, and induces the formation of endothelial spindle cells, the hallmark of Kaposi's sarcoma, when overexpressed in primary endothelial cells. We used a reverse genetics approach to study several functions of KSHV vFLIP in the context of the whole viral genome. Deletion of the gene encoding vFLIP from a KSHV genome cloned in a bacterial artificial chromosome (BAC) reduced the ability of the virus to persist and induce spindle cell formation in primary human umbilical vein endothelial cells (HUVECs). Only a few, mainly interferon (IFN)-responsive, genes were expressed in wild-type KSHV (KSHV-wt)-infected endothelial cells at levels higher than those in KSHV-ΔFLIP-infected endothelial cells, in contrast to the plethora of cellular genes induced by overexpressed vFLIP. In keeping with this observation, vFLIP induces the phosphorylation of STAT1 and STAT2 in an NF-κB-dependent manner in endothelial cells. vFLIP-dependent phosphorylation of STAT1 and STAT2 could be demonstrated after endothelial cells were infected with KSHV-wt, KSHV-ΔFLIP, and a KSHV-vFLIP revertant virus. These findings document the impact of KSHV vFLIP on the transcriptome of primary endothelial cells during viral persistence and highlight the role of vFLIP in the activation of STAT1/STAT2 and STAT-responsive cellular genes by KSHV.
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Lu MY, Liao F. Interferon-stimulated gene ISG12b2 is localized to the inner mitochondrial membrane and mediates virus-induced cell death. Cell Death Differ 2011; 18:925-36. [PMID: 21151029 PMCID: PMC3131945 DOI: 10.1038/cdd.2010.160] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 10/29/2010] [Accepted: 11/08/2010] [Indexed: 12/11/2022] Open
Abstract
Interferons (IFNs) are crucial for host defence against viruses. Many IFN-stimulated genes (ISGs) induced by viral infection exert antiviral effects. Microarray analysis of gene expression induced in liver tissues of mice on dengue virus (DENV) infection has led to identification of the ISG gene ISG12b2. ISG12b2 is also dramatically induced on DENV infection of Hepa 1-6 cells (mouse hepatoma cell line). Here, we performed biochemical and functional analyses of ISG12b2. We demonstrate that ISG12b2 is an inner mitochondrial membrane (IMM) protein containing a cleavable mitochondrial targeting sequence and multiple transmembrane segments. Overexpression of ISG12b2 in Hepa 1-6 induced release of cytochrome c from mitochondria, disruption of the mitochondrial membrane potential, and activation of caspase-9, caspase-3, and caspase-8. Treatment of ISG12b2-overexpressing Hepa 1-6 with inhibitors of pan-caspase, caspase-9, or caspase-3, but not caspase-8, reduced apoptotic cell death, suggesting that ISG12b2 activates the intrinsic apoptotic pathway. Of particular interest, we further demonstrated that ISG12b2 formed oligomers, and that ISG12b2 was able to mediate apoptosis through both Bax/Bak-dependent and Bax/Bak-independent pathways. Our study demonstrates that the ISG12b2 is a novel IMM protein induced by IFNs and regulates mitochondria-mediated apoptosis during viral infection.
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Affiliation(s)
- M-Y Lu
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - F Liao
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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