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Lu K, Zhao Y, Li Y, Fu Z, Chen Y, Kong Y, Li G. IFI16 promotes the progression of clear cell renal cell carcinoma through the IL6/PI3K/AKT axis. J Transl Med 2024; 22:533. [PMID: 38831470 PMCID: PMC11149187 DOI: 10.1186/s12967-024-05354-w] [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: 03/11/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is a common disease in the urinary system, with a high incidence and poor prognosis in advanced stages. Although γ-interferon-inducible protein 16 (IFI16) has been reported to play a role in various tumors, its involvement in ccRCC remains poorly documented, and the molecular mechanisms are not yet clear. METHODS We conducted bioinformatics analysis to study the expression of IFI16 in ccRCC using public databases. Additionally, we analyzed and validated clinical specimens that we collected. Subsequently, we explored the impact of IFI16 on ccRCC cell proliferation, migration, and invasion through in vitro and in vivo experiments. Furthermore, we predicted downstream molecules and pathways using transcriptome analysis and confirmed them through follow-up experimental validation. RESULTS IFI16 was significantly upregulated in ccRCC tissue and correlated with poor patient prognosis. In vitro, IFI16 promoted ccRCC cell proliferation, migration, and invasion, while in vivo, it facilitated subcutaneous tumor growth and the formation of lung metastatic foci. Knocking down IFI16 suppressed its oncogenic function. At the molecular level, IFI16 promoted the transcription and translation of IL6, subsequently activating the PI3K/AKT signaling pathway and inducing epithelial-mesenchymal transition (EMT). CONCLUSION IFI16 induced EMT through the IL6/PI3K/AKT axis, promoting the progression of ccRCC.
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Affiliation(s)
- Ke Lu
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu, China
- Department of Urology, Affiliated Changshu Hospital of Nantong University, Changshu, 215500, Jiangsu, China
| | - Yan Zhao
- Department of Urology, Xuzhou Cancer Hospital, Affiliated Hospital of Jiangsu University, Xuzhou, 221000, Jiangsu, China
| | - Yu Li
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu, China
| | - Zhenyu Fu
- Department of Urology, Affiliated Changshu Hospital of Nantong University, Changshu, 215500, Jiangsu, China
| | - Yongchang Chen
- Department of Urology, Affiliated Changshu Hospital of Nantong University, Changshu, 215500, Jiangsu, China.
| | - Ying Kong
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu, China.
| | - Gang Li
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu, China.
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Lin W, Zhao Z, Du W, Ni Z, Pan C, Fang P, Li J, ZhuGe L, Jin S. Interferon-Gamma-Inducible Protein 16 Inhibits Hepatocellular Carcinoma via Interferon Regulatory Factor 3 on Chemosensitivity. Dig Dis Sci 2024; 69:491-501. [PMID: 38170337 DOI: 10.1007/s10620-023-08175-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/29/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND AND AIM Previous reports have suggested IFI16 as a tumor suppressor in hepatocellular carcinoma (HC). Nonetheless, the biological significance of IFI16 and its mechanism concerning resistance to cisplatin (DDP) in HC requires further exploration. METHODS Samples of tumor and corresponding para-carcinoma tissues were acquired from patients with HC. Furthermore, DDP-resistant cell lines of HC, specifically HCC, Huh7 and Hepatoblastoma, HepG3, were generated by gradually increasing the concentration of DDP. Cell apoptosis and DNA damage were evaluated by utilizing flow cytometry assay and TUNEL staining. The interaction between IFI16 and interferon regulatory factor 3 (IRF3) proteins were analyzed using Co-Immunoprecipitation (Co-IP) assay. In vivo assays were conducted by establishing HC subcutaneous xenograft tumor models. RESULTS The study found a reduction in IFI16 expression in both HC tissues and DDP-resistant HC cell lines. The binding of IFI16 to IRF3 regulated DNA damage-associated markers in vitro. Overexpression of IFI16 heightened the susceptibility of DDP-induced apoptosis and DNA damage, which was counteracted by IRF3 knockdown, while strengthened by IRF3 overexpression. Moreover, overexpression of IFI16 diminished in vivo DDP-resistant HC tumorigenicity. CONCLUSION In summary, our findings suggest that IFI16 serves as a tumor suppressor in HC by promoting DNA damage via its interaction with IRF3, thereby reversing DDP resistance.
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Affiliation(s)
- Wei Lin
- Department of Infectious Diseases, The Second Affiliated Hospital of Wenzhou Medical University, #1111 of Wenzhou Wenzhou Avenue, Longwan District, Wenzhou, Zhejiang, China.
| | - Zhiguang Zhao
- Department of Pathology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Wenjun Du
- Department of Liver Diseases, Shandong Public Health Clinical Center, Shangdong University, Jinan, Shangdong, China
| | - Zhonglin Ni
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chenwei Pan
- Department of Infectious Diseases, The Second Affiliated Hospital of Wenzhou Medical University, #1111 of Wenzhou Wenzhou Avenue, Longwan District, Wenzhou, Zhejiang, China
| | - Peipei Fang
- Department of Infectious Diseases, The Second Affiliated Hospital of Wenzhou Medical University, #1111 of Wenzhou Wenzhou Avenue, Longwan District, Wenzhou, Zhejiang, China
| | - Jie Li
- Department of Infectious Diseases, The Second Affiliated Hospital of Wenzhou Medical University, #1111 of Wenzhou Wenzhou Avenue, Longwan District, Wenzhou, Zhejiang, China
| | - Lu ZhuGe
- Department of Infectious Diseases, The Second Affiliated Hospital of Wenzhou Medical University, #1111 of Wenzhou Wenzhou Avenue, Longwan District, Wenzhou, Zhejiang, China
| | - Shuanghong Jin
- Department of Infectious Diseases, The Second Affiliated Hospital of Wenzhou Medical University, #1111 of Wenzhou Wenzhou Avenue, Longwan District, Wenzhou, Zhejiang, China
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Azumi Y, Koma YI, Tsukamoto S, Kitamura Y, Ishihara N, Yamanaka K, Nakanishi T, Miyako S, Urakami S, Tanigawa K, Kodama T, Nishio M, Shigeoka M, Kakeji Y, Yokozaki H. IFI16 Induced by Direct Interaction between Esophageal Squamous Cell Carcinomas and Macrophages Promotes Tumor Progression via Secretion of IL-1α. Cells 2023; 12:2603. [PMID: 37998338 PMCID: PMC10670642 DOI: 10.3390/cells12222603] [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: 10/13/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Tumor-associated macrophages (TAMs), one of the major components of the tumor microenvironment, contribute to the progression of esophageal squamous cell carcinoma (ESCC). We previously established a direct co-culture system of human ESCC cells and macrophages and reported the promotion of malignant phenotypes, such as survival, growth, and migration, in ESCC cells. These findings suggested that direct interactions between cancer cells and macrophages contribute to the malignancy of ESCC, but its underlying mechanisms remain unclear. In this study, we compared the expression levels of the interferon-induced genes between mono- and co-cultured ESCC cells using a cDNA microarray and found that interferon-inducible protein 16 (IFI16) was most significantly upregulated in co-cultured ESCC cells. IFI16 knockdown suppressed malignant phenotypes and also decreased the secretion of interleukin-1α (IL-1α) from ESCC cells. Additionally, recombinant IL-1α enhanced malignant phenotypes of ESCC cells through the Erk and NF-κB signaling. Immunohistochemistry revealed that high IFI16 expression in human ESCC tissues tended to be associated with disease-free survival and was significantly associated with tumor depth, lymph node metastasis, and macrophage infiltration. The results of this study reveal that IFI16 is involved in ESCC progression via IL-1α and imply the potential of IFI16 as a novel prognostic factor for ESCC.
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Affiliation(s)
- Yuki Azumi
- Division of Pathology, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.A.); (S.T.); (N.I.); (K.Y.); (T.N.); (S.M.); (S.U.); (T.K.); (M.N.); (M.S.); (H.Y.)
- Division of Gastro-Intestinal Surgery, Department of Surgery, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.K.); (K.T.); (Y.K.)
| | - Yu-ichiro Koma
- Division of Pathology, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.A.); (S.T.); (N.I.); (K.Y.); (T.N.); (S.M.); (S.U.); (T.K.); (M.N.); (M.S.); (H.Y.)
| | - Shuichi Tsukamoto
- Division of Pathology, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.A.); (S.T.); (N.I.); (K.Y.); (T.N.); (S.M.); (S.U.); (T.K.); (M.N.); (M.S.); (H.Y.)
| | - Yu Kitamura
- Division of Gastro-Intestinal Surgery, Department of Surgery, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.K.); (K.T.); (Y.K.)
| | - Nobuaki Ishihara
- Division of Pathology, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.A.); (S.T.); (N.I.); (K.Y.); (T.N.); (S.M.); (S.U.); (T.K.); (M.N.); (M.S.); (H.Y.)
- Division of Hepato-Biliary-Pancreatic Surgery, Department of Surgery, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Keitaro Yamanaka
- Division of Pathology, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.A.); (S.T.); (N.I.); (K.Y.); (T.N.); (S.M.); (S.U.); (T.K.); (M.N.); (M.S.); (H.Y.)
- Division of Obstetrics and Gynecology, Department of Surgery Related, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Takashi Nakanishi
- Division of Pathology, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.A.); (S.T.); (N.I.); (K.Y.); (T.N.); (S.M.); (S.U.); (T.K.); (M.N.); (M.S.); (H.Y.)
- Division of Gastro-Intestinal Surgery, Department of Surgery, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.K.); (K.T.); (Y.K.)
| | - Shoji Miyako
- Division of Pathology, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.A.); (S.T.); (N.I.); (K.Y.); (T.N.); (S.M.); (S.U.); (T.K.); (M.N.); (M.S.); (H.Y.)
- Division of Gastro-Intestinal Surgery, Department of Surgery, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.K.); (K.T.); (Y.K.)
| | - Satoshi Urakami
- Division of Pathology, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.A.); (S.T.); (N.I.); (K.Y.); (T.N.); (S.M.); (S.U.); (T.K.); (M.N.); (M.S.); (H.Y.)
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Kohei Tanigawa
- Division of Gastro-Intestinal Surgery, Department of Surgery, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.K.); (K.T.); (Y.K.)
| | - Takayuki Kodama
- Division of Pathology, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.A.); (S.T.); (N.I.); (K.Y.); (T.N.); (S.M.); (S.U.); (T.K.); (M.N.); (M.S.); (H.Y.)
| | - Mari Nishio
- Division of Pathology, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.A.); (S.T.); (N.I.); (K.Y.); (T.N.); (S.M.); (S.U.); (T.K.); (M.N.); (M.S.); (H.Y.)
| | - Manabu Shigeoka
- Division of Pathology, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.A.); (S.T.); (N.I.); (K.Y.); (T.N.); (S.M.); (S.U.); (T.K.); (M.N.); (M.S.); (H.Y.)
| | - Yoshihiro Kakeji
- Division of Gastro-Intestinal Surgery, Department of Surgery, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.K.); (K.T.); (Y.K.)
| | - Hiroshi Yokozaki
- Division of Pathology, Department of Pathology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; (Y.A.); (S.T.); (N.I.); (K.Y.); (T.N.); (S.M.); (S.U.); (T.K.); (M.N.); (M.S.); (H.Y.)
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Park H. Unraveling the Molecular Puzzle: Exploring Gene Networks across Diverse EMT Status of Cell Lines. Int J Mol Sci 2023; 24:12784. [PMID: 37628965 PMCID: PMC10454379 DOI: 10.3390/ijms241612784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Understanding complex disease mechanisms requires a comprehensive understanding of the gene regulatory networks, as complex diseases are often characterized by the dysregulation and dysfunction of molecular networks, rather than abnormalities in single genes. Specifically, the exploration of cell line-specific gene networks can provide essential clues for precision medicine, as this methodology can uncover molecular interplays specific to particular cell line statuses, such as drug sensitivity, cancer progression, etc. In this article, we provide a comprehensive review of computational strategies for cell line-specific gene network analysis: (1) cell line-specific gene regulatory network estimation and analysis of gene networks under varying epithelial-mesenchymal transition (EMT) statuses of cell lines; and (2) an explainable artificial intelligence approach for interpreting the estimated massive multiple EMT-status-specific gene networks. The objective of this review is to help readers grasp the concept of computational network biology, which holds significant implications for precision medicine by offering crucial clues.
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Affiliation(s)
- Heewon Park
- School of Mathematics, Statistics and Data Science, Sungshin Women's University, Seoul 02844, Republic of Korea
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5
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Choubey D. Cytosolic DNA sensor IFI16 proteins: Potential molecular integrators of interactions among the aging hallmarks. Ageing Res Rev 2022; 82:101765. [PMID: 36270606 DOI: 10.1016/j.arr.2022.101765] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/11/2022] [Accepted: 10/16/2022] [Indexed: 01/31/2023]
Abstract
Cellular changes that are linked to aging in humans include genomic instability, telomere attrition, epigenetic alterations, mitochondrial dysfunction, cellular senescence, and altered intercellular communications. The extent of the changes in these aging hallmarks and their interactions with each other are part of the human aging. However, the molecular mechanisms through which the aging hallmarks interact with each other remain unclear. Studies have indicated a potential role for the type I interferon (IFN) and p53-inducible IFI16 proteins in interactions with the aging hallmarks. The IFI16 proteins are members of the PYHIN protein family. Proteins in the family share a DNA-binding domain (the HIN domain) and a protein-protein interaction pyrin domain (PYD). IFI16 proteins are needed for cytosolic DNA-induced activation of the cGAS-STING pathway for type I IFN (IFN-β) expression. The pathway plays an important role in aging-related inflammation (inflammaging). Further, increased levels of the IFI16 proteins potentiate the cell growth inhibitory functions of the p53 and pRb tumor suppressors proteins. Moreover, IFI16 proteins are needed for most aging hallmarks. Therefore, here we discuss how an improved understanding of the role of the IFI16 proteins in integration of the aging hallmarks has potential to improve the human health and lifespan.
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Affiliation(s)
- Divaker Choubey
- Department of Environmental & Public Health Sciences University of Cincinnati, 160 Panzeca Way, P.O. Box 670056, Cincinnati, OH 45267, USA.
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6
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Liu C, Li L, Hou G, Lu Y, Gao M, Zhang L. HERC5/IFI16/p53 signaling mediates breast cancer cell proliferation and migration. Life Sci 2022; 303:120692. [PMID: 35671810 DOI: 10.1016/j.lfs.2022.120692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 12/29/2022]
Abstract
AIMS This study aims to find differentially expressed ubiquitination-related gene(s) and elucidates their biological significance in breast cancer. MAIN METHODS Differentially expressed genes were profiled in MCF-7 and MDA-MB-231 cells by using PCR array method. Abnormal expression of HERC5 was studied in the cells and in breast cancer specimens via Quantitative Real-time PCR and western blot. Cell proliferation and cell migration abilities were evaluated by using cell counting kits, or through colony formation, wound healing and trans-well assays. HERC5 target proteins were investigated via proteomic, co-immunoprecipitation and western blot methods. Down-stream signaling pathways were investigated through gene expression/knockdown methods. KEY FINDINGS Huge increase of HERC5 expression was found in MCF-7 and MDA-MB-231 cells, knockdown of which repressed the cell proliferation and migration. HERC5 interacted with IFI16, mediated IFI16 ISGylation at K274 and facilitated IFI16 proteasomal degradation. IFI16 acted as a tumor suppressor and to some extent mediated the HERC5 function in the breast cancer (BC) cells. HERC5 was negatively correlated with IFI16 protein, while IFI16 was positively correlated to p53 expression at mRNA and protein levels, which indicates a novel signaling pathway - HERC5/IFI16/p53. HERC5 expression was increased in glucose-starved BC cells and in human breast cancer tissues, accompanied with the decrease of IFI16 and P53. SIGNIFICANCE Our work reveals the abnormal expression of HERC5 and its carcinogenic role in breast cancer cells, which is probably mediated by an HERC5/IFI16/p53 signaling pathway. This work also provides potential diagnostic/therapeutic biomarkers for breast cancer diagnosis and treatment.
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Affiliation(s)
- Congcong Liu
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300350, China
| | - Ling Li
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300350, China
| | - Gang Hou
- Department of Pathology, Tai'an City Central Hospital, 29 Longtan Road, Tai'an 271000, China
| | - Ying Lu
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300350, China
| | - Meng Gao
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300350, China
| | - Lianwen Zhang
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300350, China.
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Borucka J, Sterzyńska K, Kaźmierczak D, Świerczewska M, Nowacka M, Wojtowicz K, Klejewski A, Nowicki M, Zabel M, Ramlau R, Januchowski R. The significance of interferon gamma inducible protein 16 (IFI16) expression in drug resistant ovarian cancer cell lines. Biomed Pharmacother 2022; 150:113036. [PMID: 35489285 DOI: 10.1016/j.biopha.2022.113036] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Inherent or developed during treatment drug resistance is the main reason for the low effectiveness of chemotherapy in ovarian cancer. IFI16 is a cytoplasmic/nuclear protein involved in response to virus's infection and cell cycle arrest associated with the cellular senescence. METHODS Here we performed a detailed IFI16 expression analysis in ovarian cancer cell lines sensitive (A2780) and resistant to doxorubicin (DOX) (A2780DR1 and A2780DR2) and paclitaxel (PAC) (A2780PR1). IFI16 mRNA level, protein level in the nuclear and cytoplasmic fraction (Western blot analysis), the protein expression in cancer cells and nuclei (immunofluorescence analysis) and cancer patient lesions (immunohistochemistry) were performed in this study. RESULTS We observed upregulation of IFI16 expression in drug resistant cell lines with dominant cytoplasmic localization in DOX-resistant cell lines and nuclear one in the PAC-resistant cell line. The most abundantly overexpressed isoforms of IFI16 were IFI16A and IFI16C. Finally, an analysis of a histological type of ovarian cancer (immunohistochemistry) showed expression in serous ovarian cancer. CONCLUSIONS Expression of IFI16 in drug-resistant cell lines suggests its role in drug resistance development in ovarian cancer. Expression in serous ovarian cancer suggests its role in the pathogenesis of this histological type.
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Affiliation(s)
- Justyna Borucka
- Department of Oncology, Poznan University of Medical Sciences, Szamarzewskiego 82/84, 60-569 Poznań, Poland
| | - Karolina Sterzyńska
- Department of Histology and Embryology, Poznan University of Medical Sciences, Święcickiego 6 St., 61-781 Poznań, Poland
| | - Dominika Kaźmierczak
- Department of Histology and Embryology, Poznan University of Medical Sciences, Święcickiego 6 St., 61-781 Poznań, Poland
| | - Monika Świerczewska
- Department of Histology and Embryology, Poznan University of Medical Sciences, Święcickiego 6 St., 61-781 Poznań, Poland
| | - Marta Nowacka
- Department of Histology and Embryology, Poznan University of Medical Sciences, Święcickiego 6 St., 61-781 Poznań, Poland
| | - Karolina Wojtowicz
- Department of Histology and Embryology, Poznan University of Medical Sciences, Święcickiego 6 St., 61-781 Poznań, Poland
| | - Andrzej Klejewski
- Department of Nursing, Poznan University of Medical Sciences, Smoluchowskiego 11 St., 60-179 Poznań, Poland; Department of Obstetrics and Women's Diseases, Poznan University of Medical Sciences, Polna 33 St, 60-535 Poznań, Poland
| | - Michał Nowicki
- Department of Histology and Embryology, Poznan University of Medical Sciences, Święcickiego 6 St., 61-781 Poznań, Poland
| | - Maciej Zabel
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, Wroclaw, Poland; Department of Anatomy and Histology, Collegium Medicum, University of Zielona Gora, Zyty 28 St, 65-046 Zielona Gora, Poland
| | - Rodryg Ramlau
- Department of Oncology, Poznan University of Medical Sciences, Szamarzewskiego 82/84, 60-569 Poznań, Poland
| | - Radosław Januchowski
- Department of Anatomy and Histology, Collegium Medicum, University of Zielona Gora, Zyty 28 St, 65-046 Zielona Gora, Poland.
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Khan M, Nur S, Abdulaal W. A study on DNA methylation modifying natural compounds identified EGCG for induction of IFI16 gene expression related to the innate immune response in cancer cells. Oncol Lett 2022; 24:218. [PMID: 35707762 PMCID: PMC9178671 DOI: 10.3892/ol.2022.13339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/25/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Mohammad Khan
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Suza Nur
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Wesam Abdulaal
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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9
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Zou Y, Zhang J, Zhang L, Yan X. Interferon-induced protein 16 expression in colorectal cancer and its correlation with proliferation and immune signature markers. Oncol Lett 2021; 22:687. [PMID: 34434286 PMCID: PMC8335744 DOI: 10.3892/ol.2021.12948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/16/2021] [Indexed: 12/13/2022] Open
Abstract
Interferon-induced protein 16 (IFI16) is important for innate immune recognition of foreign/damaged DNA. Abnormal IFI16 expression is closely related to the occurrence of multiple malignant tumours, but its expression pattern in colorectal cancer (CRC) remains unclear. The present study aimed to investigated IFI16 expression and association with cell proliferation in CRC tissues and adjacent normal tissues. A multiplex immunofluorescence panel of antibodies against IFI16, Ki-67 and phosphorylated (p)-ERK1/2 was applied to assess a tissue microarray (TMA). The TMA included 77 CRC samples and 74 normal adjacent tissue samples which were collected from The First People's Hospital of Yunnan Province (Kunming, China) (3 paracancerous tissues were lost because of repeated cutting). Immunohistochemistry was used to detect CD8+ tumour-infiltrating lymphocyte (TIL) abundance and programmed death-ligand 1 (PD-L1) expression in cancer tissues. The present study demonstrated that IFI16 localized to the nucleus of CRC cells. Although IFI16 was weakly expressed in normal mucosal epithelial cells, absent to strong expression was detectable in different patients with CRC. Typically, IFI16 was not co-localized with Ki-67 within CRC cells. The multiplex immunofluorescence data demonstrated that the proportion of IFI16-/Ki-67+ cells from CRC tissues was 57.13%; however, that of IFI16+/Ki-67+ cells was 1.50%. The IFI16-/Ki-67+ phenotype was significantly positively associated with the tumor-node-metastasis stage and was marginally significantly correlated with lymph node metastasis. p-ERK1/2 protein was primarily localized to the cytoplasm and cell membrane of CRC cells and sometimes to the nucleus. Although, IFI16 demonstrated a strong correlation with p-ERK1/2, IFI16 did not co-localize with p-ERK1/2 and the proportion of IFI16 and p-ERK1/2 double-negative CRC cells was 84.95%. IFI16 expression displayed no significant association with CD8+ TILs or PD-L1. However, a strong positive correlation between CD8+ TILs and PD-L1 was observed. High CD8+ TIL infiltration in CRC tissue was associated with lower lymph node metastasis and tumor-node-metastasis stage. In summary, the results of the present study provided a novel insight for the role of IFI16 in CRC occurrence via the regulation of cancer cell proliferation.
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Affiliation(s)
- Yunlian Zou
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Jinping Zhang
- Institute of Medical Sciences, Yunnan Blood Disease Clinical Medical Center, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, P.R. China
| | - Lichen Zhang
- Medical Faculty, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Xinmin Yan
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
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Park H, Maruhashi K, Yamaguchi R, Imoto S, Miyano S. Global gene network exploration based on explainable artificial intelligence approach. PLoS One 2020; 15:e0241508. [PMID: 33156825 PMCID: PMC7647077 DOI: 10.1371/journal.pone.0241508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/03/2020] [Indexed: 12/26/2022] Open
Abstract
In recent years, personalized gene regulatory networks have received significant attention, and interpretation of the multilayer networks has been a critical issue for a comprehensive understanding of gene regulatory systems. Although several statistical and machine learning approaches have been developed and applied to reveal sample-specific regulatory pathways, integrative understanding of the massive multilayer networks remains a challenge. To resolve this problem, we propose a novel artificial intelligence (AI) strategy for comprehensive gene regulatory network analysis. In our strategy, personalized gene networks corresponding specific clinical characteristic are constructed and the constructed network is considered as a second-order tensor. Then, an explainable AI method based on deep learning is applied to decompose the multilayer networks, thus we can reveal all-encompassing gene regulatory systems characterized by clinical features of patients. To evaluate the proposed methodology, we apply our method to the multilayer gene networks under varying conditions of an epithelial–mesenchymal transition (EMT) process. From the comprehensive analysis of multilayer networks, we identified novel markers, and the biological mechanisms of the identified genes and their reciprocal mechanisms are verified through the literature. Although any biological knowledge about the identified genes was not incorporated in our analysis, our data-driven approach based on AI approach provides biologically reliable results. Furthermore, the results provide crucial evidences to reveal biological mechanism related to various diseases, e.g., keratinocyte proliferation. The use of explainable AI method based on the tensor decomposition enables us to reveal global and novel mechanisms of gene regulatory system from the massive multiple networks, which cannot be demonstrated by existing methods. We expect that the proposed method provides a new insight into network biology and it will be a useful tool to integrative gene network analysis related complex architectures of diseases.
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Affiliation(s)
- Heewon Park
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
- * E-mail:
| | | | - Rui Yamaguchi
- Division of Cancer Systems Biology, Aichi Cancer Center Research Institute, Aichi, Japan
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seiya Imoto
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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11
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Hsa-miR-889-3p promotes the proliferation of osteosarcoma through inhibiting myeloid cell nuclear differentiation antigen expression. Biomed Pharmacother 2019; 114:108819. [DOI: 10.1016/j.biopha.2019.108819] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/23/2019] [Accepted: 03/26/2019] [Indexed: 01/06/2023] Open
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12
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Zhang Z, Wu H, Zhou H, Gu Y, Bai Y, Yu S, An R, Qi J. Identification of potential key genes and high-frequency mutant genes in prostate cancer by using RNA-Seq data. Oncol Lett 2018; 15:4550-4556. [PMID: 29616087 DOI: 10.3892/ol.2018.7846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/22/2017] [Indexed: 01/26/2023] Open
Abstract
The aim of the present study was to identify potential key genes and single nucleotide variations (SNVs) in prostate cancer. RNA sequencing (RNA-seq) data, GSE22260, were downloaded from the Gene Expression Omnibus database, including 4 prostate cancer samples and 4 normal tissues samples. RNA-Seq reads were processed using Tophat and differentially-expressed genes (DEGs) were identified using the Cufflinks package. Gene Ontology enrichment analysis of DEGs was performed. Subsequently, Seqpos was used to identify the potential upstream regulatory elements of DEGs. SNV was analyzed using Genome Analysis Toolkit. In addition, the frequency and risk-level of mutant genes were calculated using VarioWatch. A total of 150 upregulated and 211 downregulated DEGs were selected and 25 upregulated and 17 downregulated potential upstream regulatory elements were identified, respectively. The SNV annotations of somatic mutations revealed that 65% were base transition and 35% were base transversion. At frequencies ≥2, a total of 17 mutation sites were identified. The mutation site with the highest frequency was located in the folate hydrolase 1B (FOLH1B) gene. Furthermore, 20 high-risk mutant genes with high frequency were identified using VarioWatch, including ribosomal protein S4 Y-linked 2 (RPS4Y2), polycystin 1 transient receptor potential channel interacting (PKD1) and FOLH1B. In addition, kallikrein 1 (KLK1) and PKD1 are known tumor suppressor genes. The potential regulatory elements and high-frequency mutant genes (RPS4Y2, KLK1, PKD1 and FOLH1B) may have key functions in prostate cancer. The results of the present study may provide novel information for the understanding of prostate cancer development.
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Affiliation(s)
- Ze Zhang
- Department of Urology Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - He Wu
- Department of Pathology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Hong Zhou
- Department of Respiration, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Yunhe Gu
- Department of Pathology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Yufeng Bai
- Department of Urology Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Shiliang Yu
- Department of Urology Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Ruihua An
- Department of Urology Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Jiping Qi
- Department of Pathology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
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13
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Danziger O, Shai B, Sabo Y, Bacharach E, Ehrlich M. Combined genetic and epigenetic interferences with interferon signaling expose prostate cancer cells to viral infection. Oncotarget 2018; 7:52115-52134. [PMID: 27366948 PMCID: PMC5239539 DOI: 10.18632/oncotarget.10313] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/13/2016] [Indexed: 12/27/2022] Open
Abstract
Interferons (IFNs) induce anti-viral programs, regulate immune responses, and exert anti-proliferative effects. To escape anti-tumorigenic effects of IFNs, malignant cells attenuate JAK/STAT signaling and expression of IFN stimulated genes (ISGs). Such attenuation may enhance the susceptibility of tumor cells to oncolytic virotherapy. Here we studied genetic and epigenetic mechanisms of interference with JAK/STAT signaling and their contribution to susceptibility of prostate cancer cells to viral infection. Bioinformatics analysis of gene-expression in cohorts of prostate cancer patients revealed genetic and epigenetic interference with the IFN program. To correlate lack of IFN signaling and susceptibility to viral infection and oncolysis; we employed LNCaP prostate cancer cells as cellular model, and the human metapneumovirus and the epizootic hemorrhagic disease virus as infectious agents. In LNCaP cells, JAK1 is silenced by bi-allelic inactivating mutations and epigenetic silencing, which also silences ISGs. Chemical inhibition of epigenetic silencing partially restored IFN-sensitivity, induced low levels of expression of selected ISGs and attenuated, but failed to block, viral infection and oncolysis. Since viral infection was not blocked by epigenetic modifiers, and these compounds may independently-induce anti-tumor effects, we propose that epigenetic modifiers and virotherapy are compatible in treatment of prostate tumors defective in JAK1 expression and IFN signaling.
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Affiliation(s)
- Oded Danziger
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ben Shai
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yosef Sabo
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Eran Bacharach
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Marcelo Ehrlich
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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14
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Li Y, Guo H, Jin C, Qiu C, Gao M, Zhang L, Liu Z, Kong B. Spliceosome-associated factor CTNNBL1 promotes proliferation and invasion in ovarian cancer. Exp Cell Res 2017; 357:124-134. [PMID: 28501461 DOI: 10.1016/j.yexcr.2017.05.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 04/28/2017] [Accepted: 05/08/2017] [Indexed: 01/20/2023]
Abstract
Ovarian cancer is the most lethal gynecologic malignancy and the molecular pathogenesis of high-grade serous ovarian carcinoma has not been completely characterized. Numerous studies have shown that altered splicing patterns and splicing factors were found to contribute to tumor development and progression. In this study, we demonstrated that spliceosome-associated factor CTNNBL1 was significantly upregulated in high-grade serous ovarian carcinoma, the elevated level of CTNNBL1 indicates poor prognosis in patients with high-grade serous ovarian carcinoma. Functional characterization revealed that CTNNBL1 promoted the proliferation and invasion of ovarian cancer cells in vitro. Furthermore, through transcriptome analysis, we found CTNNBL1 regulates multiple splicing events and gene expression in ovarian cancer cells. Importantly, we identified IFI16 and FOXM1 splicing was regulated by CTNNBL1. To our knowledge, this is the first study exploring the expression, functional roles and regulated splicing events of CTNNBL1 in ovarian cancer.
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Affiliation(s)
- Yingwei Li
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan 250012, China
| | - Haiyang Guo
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Chengjuan Jin
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan 250012, China
| | - Chunping Qiu
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan 250012, China
| | - Min Gao
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan 250012, China
| | - Lei Zhang
- School of Biological and Chemical Engineering, Zhejiang University of Science & Technology Hangzhou 310023, China
| | - Zhaojian Liu
- Department of Cell Biology, Shandong University School of Medicine, Jinan 250012, China.
| | - Beihua Kong
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan 250012, China.
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15
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Choubey D, Panchanathan R. IFI16, an amplifier of DNA-damage response: Role in cellular senescence and aging-associated inflammatory diseases. Ageing Res Rev 2016; 28:27-36. [PMID: 27063514 DOI: 10.1016/j.arr.2016.04.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 03/30/2016] [Accepted: 04/04/2016] [Indexed: 12/22/2022]
Abstract
DNA-damage induces a DNA-damage response (DDR) in mammalian cells. The response, depending upon the cell-type and the extent of DNA-damage, ultimately results in cell death or cellular senescence. DDR-induced signaling in cells activates the ATM-p53 and ATM-IKKα/β-interferon (IFN)-β signaling pathways, thus leading to an induction of the p53 and IFN-inducible IFI16 gene. Further, upon DNA-damage, DNA accumulates in the cytoplasm, thereby inducing the IFI16 protein and STING-dependent IFN-β production and activation of the IFI16 inflammasome, resulting in the production of proinflammatory cytokines (e.g., IL-1β and IL-18). Increased expression of IFI16 protein in a variety of cell-types promotes cellular senescence. However, reduced expression of IFI16 in cells promotes cell proliferation. Because expression of the IFI16 gene is induced by activation of DNA-damage response in cells and increased levels of IFI16 protein in cells potentiate the p53-mediated transcriptional activation of genes and p53 and pRb-mediated cell cycle arrest, we discuss how an improved understanding of the role of IFI16 protein in cellular senescence and associated inflammatory secretory phenotype is likely to identify the molecular mechanisms that contribute to the development of aging-associated human inflammatory diseases and a failure to cancer therapy.
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Affiliation(s)
- Divaker Choubey
- Cincinnati VA Medical Center, 3200 Vine Street, Cincinnati, OH 45220, United States; Department of Environmental Health, University of Cincinnati, 160 Panzeca Way, P.O. Box-670056, Cincinnati, OH 45267, United States.
| | - Ravichandran Panchanathan
- Cincinnati VA Medical Center, 3200 Vine Street, Cincinnati, OH 45220, United States; Department of Environmental Health, University of Cincinnati, 160 Panzeca Way, P.O. Box-670056, Cincinnati, OH 45267, United States
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16
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IFI16 Expression Is Related to Selected Transcription Factors during B-Cell Differentiation. J Immunol Res 2015; 2015:747645. [PMID: 26185770 PMCID: PMC4491573 DOI: 10.1155/2015/747645] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 04/27/2015] [Accepted: 05/14/2015] [Indexed: 01/21/2023] Open
Abstract
The interferon-inducible DNA sensor IFI16 is involved in the modulation of cellular survival, proliferation, and differentiation. In the hematopoietic system, IFI16 is consistently expressed in the CD34+ stem cells and in peripheral blood lymphocytes; however, little is known regarding its regulation during maturation of B- and T-cells. We explored the role of IFI16 in normal B-cell subsets by analysing its expression and relationship with the major transcription factors involved in germinal center (GC) development and plasma-cell (PC) maturation. IFI16 mRNA was differentially expressed in B-cell subsets with significant decrease in IFI16 mRNA in GC and PCs with respect to naïve and memory subsets. IFI16 mRNA expression is inversely correlated with a few master regulators of B-cell differentiation such as BCL6, XBP1, POU2AF1, and BLIMP1. In contrast, IFI16 expression positively correlated with STAT3, REL, SPIB, RELA, RELB, IRF4, STAT5B, and STAT5A. ARACNE algorithm indicated a direct regulation of IFI16 by BCL6, STAT5B, and RELB, whereas the relationship between IFI16 and the other factors is modulated by intermediate factors. In addition, analysis of the CD40 signaling pathway showed that IFI16 gene expression directly correlated with NF-κB activation, indicating that IFI16 could be considered an upstream modulator of NF-κB in human B-cells.
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17
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Nutlin-3-induced redistribution of chromatin-bound IFI16 in human hepatocellular carcinoma cells in vitro is associated with p53 activation. Acta Pharmacol Sin 2015; 36:252-8. [PMID: 25544361 DOI: 10.1038/aps.2014.106] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 09/01/2014] [Indexed: 12/15/2022] Open
Abstract
AIM Interferon-γ inducible protein 16 (IFI16), a DNA sensor for DNA double-strand break (DSB), is expressed in most human hepatocellular carcinoma cell (HCC) lines. In this study we investigated the re-localization of chromatin-bound IFI16 by Nutlin-3, a DNA damage agent, in HCC cells in vitro, and the potential mechanisms. METHODS Human HCC SMMC-7721 (wild-type TP53), Huh-7 (mutant TP53), Hep3B (null TP53) and normal fetal liver L02 cell lines were examined. DSB damage in HCC cells was detected via γH2AX expression and foci formation assay. The expression of IFI16 and IFNB mRNA was measured using RT-PCR, and subcellular localization and expression of the IFI16 protein were detected using chromatin fractionation, Western blot analysis, and fluorescence microscopy. RESULTS Treatment of SMMC-7721 cells with Nutlin-3 (10 μmol/L) or etoposide (40 μmol/L) induced significant DSB damage. In SMMC-7721 cells, Nutlin-3 significantly increased the expression levels of IFI16 and IFNB mRNA, and partially redistributed chromatin-bound IFI16 protein to the cytoplasm. These effects were blocked by pretreatment with pifithrin-α, a p53 inhibitor. Furthermore, Nutlin-3 did not induce ectopic expression of IFI16 protein in Huh-7 and Hep3B cells. Moreover, the association of IFI16 with chromatin and Nutlin-3-induced changes in localization were not detected in L02 cells. CONCLUSION Nutlin-3 regulates the subcellular localization of IFI16 in HCC cells in vitro in a p53-dependent manner.
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18
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Orvis T, Hepperla A, Walter V, Song S, Simon J, Parker J, Wilkerson MD, Desai N, Major MB, Hayes DN, Davis IJ, Weissman B. BRG1/SMARCA4 inactivation promotes non-small cell lung cancer aggressiveness by altering chromatin organization. Cancer Res 2014; 74:6486-6498. [PMID: 25115300 DOI: 10.1158/0008-5472.can-14-0061] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
SWI/SNF chromatin remodeling complexes regulate critical cellular processes, including cell-cycle control, programmed cell death, differentiation, genomic instability, and DNA repair. Inactivation of this class of chromatin remodeling complex has been associated with a variety of malignancies, including lung, ovarian, renal, liver, and pediatric cancers. In particular, approximately 10% of primary human lung non-small cell lung cancers (NSCLC) display attenuations in the BRG1 ATPase, a core factor in SWI/SNF complexes. To evaluate the role of BRG1 attenuation in NSCLC development, we examined the effect of BRG1 silencing in primary and established human NSCLC cells. BRG1 loss altered cellular morphology and increased tumorigenic potential. Gene expression analyses showed reduced expression of genes known to be associated with progression of human NSCLC. We demonstrated that BRG1 losses in NSCLC cells were associated with variations in chromatin structure, including differences in nucleosome positioning and occupancy surrounding transcriptional start sites of disease-relevant genes. Our results offer direct evidence that BRG1 attenuation contributes to NSCLC aggressiveness by altering nucleosome positioning at a wide range of genes, including key cancer-associated genes.
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Affiliation(s)
- Tess Orvis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina , USA
| | - Austin Hepperla
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina , USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Vonn Walter
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina , USA
| | - Shujie Song
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina , USA.,Cancer Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Jeremy Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina , USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joel Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina , USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina , USA
| | - Matthew D Wilkerson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina , USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina , USA
| | - Nisarg Desai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina , USA
| | - Michael B Major
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina , USA.,Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599
| | - D Neil Hayes
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina , USA.,Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina , USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina , USA.,Department of Pediatrics and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina , USA
| | - Bernard Weissman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina , USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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19
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Shi X, Liu J, Liu Q, Li M. IFI16 mis-localization can be a contributing factor to hepatocellular carcinoma progression. Med Hypotheses 2014; 82:398-400. [PMID: 24491427 DOI: 10.1016/j.mehy.2014.01.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/06/2014] [Accepted: 01/18/2014] [Indexed: 01/05/2023]
Abstract
Hepatocellular carcinoma (HCC) is a highly deadly cancer, with usually drug resistance. However the mechanisms responsible for this phenomenon are poorly understood. Interferon-γ inducible protein 16 (IFI16), a multifunctional protein, has roles in anti-proliferation, autophagy, cell senescence, anti-inflammation, and DNA sensor to trigger innate immunity. IFI16 physiologically absents in adult healthy hepatocyte, but exists in liver cancer cells. Interestingly, increasing evidences suggest that dysregulation or/and loss of IFI16 function have a critical role in drug resistance and tumor progression. Furthermore, interaction with DNA or other protein depends on IFI16 localization. In our study, to our knowledge, we first showed that IFI16 is a chromatin-binding protein in four HCC cell lines with different TP53 genotype, but not in fetal liver cell line, L02 cells. However, the function of IFI16 subcellular localization has not been determined in HCC. Therefore, we present our study and theoretical basis and presume that chromatin-bounding localization of IFI16 is associated with HCC progression. If we are able to acetylate or/and delete NLS of IFI16 with activated-p53 restoration, we may offer an alternative for HCC therapy.
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Affiliation(s)
- Xinli Shi
- Department of Pathobiology and Immunology, Hebei University of Traditional Chinese Medicine, Shijiazhuang, Hebei 050200, China; Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jingli Liu
- Department of Repairing and Servicing Technology of Medical Equipment, Bethune Medical Non-commissioned Officer Academy of PLA, Shijiazhuang, Hebei 050081, China
| | - Qiujun Liu
- Department of Biochemistry, Luzhou Medical College, Luzhou 646000, China
| | - Mingyuan Li
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, China.
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20
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Sun C, Liu C, Dong J, Li D, Li W. Effects of the myeloid cell nuclear differentiation antigen on the proliferation, apoptosis and migration of osteosarcoma cells. Oncol Lett 2014; 7:815-819. [PMID: 24520299 PMCID: PMC3919948 DOI: 10.3892/ol.2014.1811] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 09/25/2013] [Indexed: 11/05/2022] Open
Abstract
Despite improvements over the past two decades, the outcome for patients with advanced osteosarcoma remains poor. Targeted therapies have emerged as promising treatment options for various malignancies. However, effective targeted cancer therapies require the identification of key molecules in the pathogenesis of cancer. The aim of this study was to evaluate the value of the myeloid cell nuclear differentiation antigen (MNDA), a member of the interferon-inducible p200 (IFI-200) family, as a therapeutic target for osteosarcoma by analyzing the baseline expression of MNDA in human osteosarcoma cells and determining the effect of MNDA overexpression on the proliferation and apoptosis profiles and migration/invasion ability in osteosarcoma cells. To this end, MNDA mRNA abundance in wild-type sarcoma osteogenic (Saos-2) cells was analyzed using reverse transcription-polymerase chain reaction, proliferation/apoptosis profiles and migration/invasion capacity in Saos-2 cells overexpressing a green fluorescence protein (GFP)-human MNDA fusion protein. Saos-2 cells found to be overexpressing GFP alone were assessed by 3-(4,5-dimethylthiazol-2-yl-2,5-diphenyltetrazolium bromide (MTT) assay, flow cytometric analysis and Matrigel Transwell migration assay. The results demonstrated that MNDA mRNA was significantly less abundant in wild-type Saos-2 cells compared with human monocyte-like U-937 cells and MNDA overexpression effectively inhibited proliferation, induced apoptosis and reduced migration/invasiveness in Saos-2 cells compared with GFP overexpression alone. Preliminary observations suggested that MNDA potentially serves as a novel therapeutic target for osteosarcoma.
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Affiliation(s)
- Chengliang Sun
- Department of Orthopaedic Surgery, Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250021, P.R. China
| | - Chuanju Liu
- Department of Orthopaedic Surgery and Cell Biology, New York University School of Medicine, New York, NY 10003, USA
| | - Jun Dong
- Department of Orthopaedic Surgery, Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250021, P.R. China
| | - Dong Li
- Department of Orthopaedic Surgery, Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250021, P.R. China
| | - Wei Li
- Department of Orthopaedic Surgery, Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250021, P.R. China
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Kim KY, Cha IH. Possibility of the use of public microarray database for identifying significant genes associated with oral squamous cell carcinoma. Genomics Inform 2012; 10:23-32. [PMID: 23105925 PMCID: PMC3475481 DOI: 10.5808/gi.2012.10.1.23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 02/16/2012] [Accepted: 02/18/2012] [Indexed: 11/20/2022] Open
Abstract
There are lots of studies attempting to identify the expression changes in oral squamous cell carcinoma. Most studies include insufficient samples to apply statistical methods for detecting significant gene sets. This study combined two small microarray datasets from a public database and identified significant genes associated with the progress of oral squamous cell carcinoma. There were different expression scales between the two datasets, even though these datasets were generated under the same platforms - Affymetrix U133A gene chips. We discretized gene expressions of the two datasets by adjusting the differences between the datasets for detecting the more reliable information. From the combination of the two datasets, we detected 51 significant genes that were upregulated in oral squamous cell carcinoma. Most of them were published in previous studies as cancer-related genes. From these selected genes, significant genetic pathways associated with expression changes were identified. By combining several datasets from the public database, sufficient samples can be obtained for detecting reliable information. Most of the selected genes were known as cancer-related genes, including oral squamous cell carcinoma. Several unknown genes can be biologically evaluated in further studies.
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Affiliation(s)
- Ki-Yeol Kim
- Oral Cancer Research Institute, College of Dentistry, Yonsei University, Seoul 120-752, Korea
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22
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Berry A, Matthews L, Jangani M, Plumb J, Farrow S, Buchan N, Wilson PA, Singh D, Ray DW, Donn RP. Interferon-inducible factor 16 is a novel modulator of glucocorticoid action. FASEB J 2010; 24:1700-13. [PMID: 20086048 PMCID: PMC3000051 DOI: 10.1096/fj.09-139998] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Previously, we used cDNA expression profiling to identify genes associated with glucocorticoid (Gc) sensitivity. We now identify which of these directly influence Gc action. Interferon-inducible protein 16 (IFI16), bone morphogenetic protein receptor type II (BMPRII), and regulator of G-protein signaling 14 (RGS14) increased Gc transactivation, whereas sialyltransferase 4B (SIAT4B) had a negative effect. Amyloid β (A4) precursor-protein binding, family B, member 1 (APBB1/Fe65) and neural cell expressed developmentally down-regulated 9 (NEDD9) were without effect. Only IFI16 potentiated Gc repression of NF-κB. In addition, IFI16 affected basal expression, and Gc induction of endogenous target genes. IFI16 did not affect glucocorticoid receptor (GR) expression, ligand-dependent repression of GR expression, or the ligand-dependent induction of GR phosphorylation on Ser-211 or Ser-203. Coimmunoprecipitation revealed an interaction, suggesting that IFI16 modulation of GR function is mediated by protein crosstalk. Transfection analysis with GR mutants showed that the ligand-binding domain of GR binds IFI16 and is the target domain for IFI16 regulation. Analysis of human lung sections identified colocalization of GR and IFI16, suggesting a physiologically relevant interaction. We demonstrate that IFI16 is a novel modulator of GR function and show the importance of analyzing variation in Gc sensitivity in humans, using appropriate technology, to drive discovery.—Berry, A., Matthews, L. Jangani, M., Plumb, J., Farrow, S., Buchan, N., Wilson, P. A., Singh, D., Ray, D., W., Donn, R. P. Interferon-inducible factor 16 is a novel modulator of glucocorticoid action.
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Affiliation(s)
- A Berry
- Arthritis Research Campaign Epidemiology Unit, University of Manchester, Manchester, UK
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In vivo growth inhibition of head and neck squamous cell carcinoma by the Interferon-inducible gene IFI16. Cancer Lett 2010; 287:33-43. [DOI: 10.1016/j.canlet.2009.05.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Revised: 05/14/2009] [Accepted: 05/29/2009] [Indexed: 12/30/2022]
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Mndal, a new interferon-inducible family member, is highly polymorphic, suppresses cell growth, and may modify plasmacytoma susceptibility. Blood 2009; 114:2952-60. [PMID: 19654412 DOI: 10.1182/blood-2009-01-198812] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The human HIN-200 gene cluster and its mouse counterpart, the interferon inducible-200 (Ifi200) family, both on Chr 1, are associated with several diseases, including solid tumors and lupus. Our study was initiated to identify the modifier gene(s) encoded by the Pctm locus, in which mouse B-cell plasmacytomas induced by pristane are associated with heterozygosity of Chr 1 genes near the Ifi200 cluster. A screen for differentially expressed genes in granulomatous tissues induced by pristane in resistant and susceptible strains identified a new Ifi200 member whose expression was 1000-fold higher in the strain carrying the resistant allele of Pctm and was the most highly expressed Ifi200 gene. The gene, designated Mndal (for MNDA-like, myeloid nuclear differentiation antigen-like), was absent in the susceptible genome, as were genomic sequences upstream of Ifi203, the gene adjacent to Mndal. Ectopic expression of MNDAL suppressed cell growth, which, together with the disease susceptibility of heterozygotes at the Pctm locus, suggests that Mndal, perhaps with Ifi203, acts as a tumor suppressor and display(s) haploinsufficiency. Mndal is highly polymorphic among inbred mouse strains, because it is absent in 10 of 24 strains. This polymorphism may have implications for other disease modifiers mapping to the same region.
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Yan H, Dalal K, Hon BK, Youkharibache P, Lau D, Pio F. RPA nucleic acid-binding properties of IFI16-HIN200. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1087-97. [PMID: 18472023 DOI: 10.1016/j.bbapap.2008.04.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Revised: 03/20/2008] [Accepted: 04/03/2008] [Indexed: 02/08/2023]
Abstract
InterFeron-gamma Inducible protein 16 (IFI16) belongs to the interferon inducible HIN200 protein family that contains transcriptional regulators linked to cell cycle regulation and differentiation. All family members contain at most two domains of 200 amino acids, called HIN200, each containing two Oligonucleotide/Oligosaccharide Binding (OB) folds. IFI16 is involved in transcriptional repression and is a component of the DNA repair multi-protein complex known as BASC, which forms after UV-induced DNA damage. In this study, we used fold recognition and biophysical approaches as a tool to infer and validate functions to the HIN200 domain. Since the best template to model IFI16-HIN200 is Replication Protein A (RPA) in complex with single-stranded nucleic acids, we tested six RPA nucleic acid-binding characteristics for IFI16-HIN200. Our results indicate that IFI16-HIN200 is an RPA-like, OB-fold, nucleic acid-binding protein that binds to ssDNA with higher affinity than to dsDNA, recognizes ssDNA in the same orientation as RPA, oligomerizes upon ssDNA binding, wraps and stretches ssDNA, but does not destabilize dsDNA. We finally propose a framework model explaining how the HIN200 domain could prevent ssDNA from re-annealing.
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Affiliation(s)
- Hongyue Yan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada V5A 1S6
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