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Xiao F, Shen J, Zhou L, Fang Z, Weng Y, Zhang C, Zhang L, Huang X, Zhan R. ZNF395 facilitates macrophage polarization and impacts the prognosis of glioma. Am J Cancer Res 2022; 12:4312-4325. [PMID: 36225626 PMCID: PMC9548007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/03/2022] [Indexed: 06/16/2023] Open
Abstract
The immune microenvironment of glioma attributes to the initiation and development of glioma; however, the underlying mechanisms of tumor microenvironment formation have not been fully understood. In this study, we revealed that Zinc Finger Protein 395 (ZNF395), a member of the Kruppel C2H2-type zinc-finger protein family and also known as a common transcription factor, was aberrantly overexpressed in glioma and positively associated with the poor clinicopathological features and the prognosis of patients with glioma based on the analyses of TCGA, CGGA and other datasets. Further in vitro experimental data demonstrated that the upregulation of ZNF395 promoted the proliferation of glioma cells. In addition, functional enrichment analysis showed that ZNF395 was involved in immune processes and correlated with macrophage infiltration and polarization. Moreover, C-C Motif Chemokine Ligand 20 (CCL20), one of the ZNF395 co-expressed genes, was validated as the downstream factor under the transcriptional regulation of ZNF395. Importantly, cell co-culture experiments confirmed that ZNF395 upregulated both the intracellular and secreted CCL20 level of glioma cells and induced M2 macrophage polarization which is known to promote the malignant progression of glioma. Taken together, our findings suggested that ZNF395 might play an essential role in glioma development, and inhibition of ZNF395 might be a plausible strategy for glioma therapy.
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Affiliation(s)
- Feng Xiao
- Department of Neurosurgery, The 1st Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Jie Shen
- Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Lihui Zhou
- Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Zebin Fang
- Department of Neurosurgery, The 1st Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Yuxiang Weng
- Department of Neurosurgery, The 1st Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Chao Zhang
- Department of Neurosurgery, The 1st Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Luyuan Zhang
- Department of Neurosurgery, The 1st Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Xin Huang
- Department of Neurosurgery, The 1st Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
| | - Renya Zhan
- Department of Neurosurgery, The 1st Affiliated Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang, China
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MEOX2 Regulates the Growth and Survival of Glioblastoma Stem Cells by Modulating Genes of the Glycolytic Pathway and Response to Hypoxia. Cancers (Basel) 2022; 14:cancers14092304. [PMID: 35565433 PMCID: PMC9099809 DOI: 10.3390/cancers14092304] [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] [Received: 01/28/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Glioblastoma is the most common incurable primary brain tumor in adults, typically leading to death within 15 months of diagnosis. Although there is an ongoing debate in the scientific community about the precise cellular origin of this tumor, glioblastoma stem cells (GSCs), which are able to self-renew, yield a full tumor mass, and determine chemo- and radio-resistance, are recognized to have a pivotal role. Our research aims to understand the role of the mesenchyme homeobox 2 (MEOX2) transcription factor in GSCs where it is strongly and specifically expressed. We have found that MEOX2 is indeed important for the survival of these cells. In fact, when we reduce its expression in two different GSC lines, they undergo a massive death accompanied by the inhibition of key genes of the glycolytic metabolism, the main source of energy for these cells. Our results reveal a novel function for MEOX2 in glioblastoma and suggest a mechanism through which GSCs may survive even in unfavorable conditions. Abstract The most widely accepted hypothesis for the development of glioblastoma suggests that glioblastoma stem-like cells (GSCs) are crucially involved in tumor initiation and recurrence as well as in the occurrence of chemo- and radio-resistance. Mesenchyme homeobox 2 (MEOX2) is a transcription factor overexpressed in glioblastoma, whose expression is negatively correlated with patient survival. Starting from our observation that MEOX2 expression is strongly enhanced in six GSC lines, we performed shRNA-mediated knock-down experiments in two different GSC lines and found that MEOX2 depletion resulted in the inhibition of cell growth and sphere-forming ability and an increase in apoptotic cell death. By a deep transcriptome analysis, we identified a core group of genes modulated in response to MEOX2 knock-down. Among these genes, the repressed ones are largely enriched in genes involved in the hypoxic response and glycolytic pathway, two strictly related pathways that contribute to the resistance of high-grade gliomas to therapies. An in silico study of the regulatory regions of genes differentially expressed by MEOX2 knock-down revealed that they mainly consisted of GC-rich regions enriched for Sp1 and Klf4 binding motifs, two main regulators of metabolism in glioblastoma. Our results show, for the first time, the involvement of MEOX2 in the regulation of genes of GSC metabolism, which is essential for the survival and growth of these cells.
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Chen C, Zhou H, Liu Z, Ma X. Dysregulation of Zinc Finger Protein 395 Contributes to the Pathogenesis of Chondrosarcoma. Onco Targets Ther 2021; 14:3545-3553. [PMID: 34113121 PMCID: PMC8183675 DOI: 10.2147/ott.s310164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/12/2021] [Indexed: 12/26/2022] Open
Abstract
Introduction The transcription factor zinc finger protein 395 (ZNF395) is involved in several cellular responses and tumorigenesis. However, the potential role and clinical significance of ZNF395 in chondrosarcoma are not well investigated. This study determines the expression profile, prognostic value and biological function of ZNF395 in human chondrosarcoma. Methods The mRNA and protein expressions of ZNF395 in fresh chondrosarcomas and the matched adjacent non-tumor tissues were assessed using real-time PCR and immunoblotting, respectively. The protein expression of ZNF395 in chondrosarcoma specimens was evaluated by immunohistochemistry, and the relationships among its protein level, clinicopathological parameters and prognosis were further detected. Cell viability, colony formation, migration, invasion and apoptosis assay were evaluated in chondrosarcoma cells with depletion of ZNF395. Results The mRNA and protein expressions of ZNF395 in chondrosarcoma tissues were significantly higher than those in the matched adjacent non-tumor tissues and benign cartilage tumors. Clinical analysis displayed that ZNF395 was expressed at higher levels in chondrosarcoma patients with higher histological grade and advanced MSTS stage. Furthermore, we demonstrated that high expression of ZNF395 correlated with a worse overall survival of chondrosarcoma patients. Multivariate Cox regression analysis indicated that ZNF395 was an independent prognostic marker in chondrosarcoma patients. Functional studies revealed that depletion of ZNF395 markedly inhibited cell viability, colony formation, migration and invasion, and promoted apoptosis in chondrosarcoma. Conclusion These findings suggest that dysregulation of ZNF395 contributes to chondrosarcoma development, and ZNF395 may act as a potent oncogene and serve as a independently prognostic factor, highlight the potential of ZNF395 as a novel biomarker and therapeutic target for chondrosarcoma.
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Affiliation(s)
- Changbao Chen
- Department of Spinal Surgery, Tianjin Hospital, Tianjin, 300211, People's Republic of China
| | - Hua Zhou
- Department of Orthopaedic Surgery, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Zhongjun Liu
- Department of Orthopaedic Surgery, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Xinlong Ma
- Department of Spinal Surgery, Tianjin Hospital, Tianjin, 300211, People's Republic of China
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Diniz WJS, Crouse MS, Cushman RA, McLean KJ, Caton JS, Dahlen CR, Reynolds LP, Ward AK. Cerebrum, liver, and muscle regulatory networks uncover maternal nutrition effects in developmental programming of beef cattle during early pregnancy. Sci Rep 2021; 11:2771. [PMID: 33531552 PMCID: PMC7854659 DOI: 10.1038/s41598-021-82156-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/13/2021] [Indexed: 01/30/2023] Open
Abstract
The molecular basis underlying fetal programming in response to maternal nutrition remains unclear. Herein, we investigated the regulatory relationships between genes in fetal cerebrum, liver, and muscle tissues to shed light on the putative mechanisms that underlie the effects of early maternal nutrient restriction on bovine developmental programming. To this end, cerebrum, liver, and muscle gene expression were measured with RNA-Seq in 14 fetuses collected on day 50 of gestation from dams fed a diet initiated at breeding to either achieve 60% (RES, n = 7) or 100% (CON, n = 7) of energy requirements. To build a tissue-to-tissue gene network, we prioritized tissue-specific genes, transcription factors, and differentially expressed genes. Furthermore, we built condition-specific networks to identify differentially co-expressed or connected genes. Nutrient restriction led to differential tissue regulation between the treatments. Myogenic factors differentially regulated by ZBTB33 and ZNF131 may negatively affect myogenesis. Additionally, nutrient-sensing pathways, such as mTOR and PI3K/Akt, were affected by gene expression changes in response to nutrient restriction. By unveiling the network properties, we identified major regulators driving gene expression. However, further research is still needed to determine the impact of early maternal nutrition and strategic supplementation on pre- and post-natal performance.
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Affiliation(s)
- Wellison J. S. Diniz
- grid.261055.50000 0001 2293 4611Department of Animal Sciences, Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND USA
| | - Matthew S. Crouse
- grid.463419.d0000 0001 0946 3608USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - Robert A. Cushman
- grid.463419.d0000 0001 0946 3608USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - Kyle J. McLean
- grid.411461.70000 0001 2315 1184Department of Animal Science, University of Tennessee, Knoxville, TN USA
| | - Joel S. Caton
- grid.261055.50000 0001 2293 4611Department of Animal Sciences, Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND USA
| | - Carl R. Dahlen
- grid.261055.50000 0001 2293 4611Department of Animal Sciences, Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND USA
| | - Lawrence P. Reynolds
- grid.261055.50000 0001 2293 4611Department of Animal Sciences, Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND USA
| | - Alison K. Ward
- grid.261055.50000 0001 2293 4611Department of Animal Sciences, Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND USA
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Korbecki J, Kojder K, Kapczuk P, Kupnicka P, Gawrońska-Szklarz B, Gutowska I, Chlubek D, Baranowska-Bosiacka I. The Effect of Hypoxia on the Expression of CXC Chemokines and CXC Chemokine Receptors-A Review of Literature. Int J Mol Sci 2021; 22:ijms22020843. [PMID: 33467722 PMCID: PMC7830156 DOI: 10.3390/ijms22020843] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 12/26/2022] Open
Abstract
Hypoxia is an integral component of the tumor microenvironment. Either as chronic or cycling hypoxia, it exerts a similar effect on cancer processes by activating hypoxia-inducible factor-1 (HIF-1) and nuclear factor (NF-κB), with cycling hypoxia showing a stronger proinflammatory influence. One of the systems affected by hypoxia is the CXC chemokine system. This paper reviews all available information on hypoxia-induced changes in the expression of all CXC chemokines (CXCL1, CXCL2, CXCL3, CXCL4, CXCL5, CXCL6, CXCL7, CXCL8 (IL-8), CXCL9, CXCL10, CXCL11, CXCL12 (SDF-1), CXCL13, CXCL14, CXCL15, CXCL16, CXCL17) as well as CXC chemokine receptors—CXCR1, CXCR2, CXCR3, CXCR4, CXCR5, CXCR6, CXCR7 and CXCR8. First, we present basic information on the effect of these chemoattractant cytokines on cancer processes. We then discuss the effect of hypoxia-induced changes on CXC chemokine expression on the angiogenesis, lymphangiogenesis and recruitment of various cells to the tumor niche, including myeloid-derived suppressor cells (MDSCs), tumor-associated macrophages (TAMs), tumor-associated neutrophils (TANs), regulatory T cells (Tregs) and tumor-infiltrating lymphocytes (TILs). Finally, the review summarizes data on the use of drugs targeting the CXC chemokine system in cancer therapies.
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Affiliation(s)
- Jan Korbecki
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72 Av., 70-111 Szczecin, Poland; (J.K.); (P.K.); (P.K.); (D.C.)
| | - Klaudyna Kojder
- Department of Anaesthesiology and Intensive Care, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-281 Szczecin, Poland;
| | - Patrycja Kapczuk
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72 Av., 70-111 Szczecin, Poland; (J.K.); (P.K.); (P.K.); (D.C.)
| | - Patrycja Kupnicka
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72 Av., 70-111 Szczecin, Poland; (J.K.); (P.K.); (P.K.); (D.C.)
| | - Barbara Gawrońska-Szklarz
- Department of Pharmacokinetics and Therapeutic Drug Monitoring, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72 Av., 70-111 Szczecin, Poland;
| | - Izabela Gutowska
- Department of Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72 Av., 70-111 Szczecin, Poland;
| | - Dariusz Chlubek
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72 Av., 70-111 Szczecin, Poland; (J.K.); (P.K.); (P.K.); (D.C.)
| | - Irena Baranowska-Bosiacka
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72 Av., 70-111 Szczecin, Poland; (J.K.); (P.K.); (P.K.); (D.C.)
- Correspondence: ; Tel.: +48-914661515
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Korbecki J, Kojder K, Barczak K, Simińska D, Gutowska I, Chlubek D, Baranowska-Bosiacka I. Hypoxia Alters the Expression of CC Chemokines and CC Chemokine Receptors in a Tumor-A Literature Review. Int J Mol Sci 2020; 21:ijms21165647. [PMID: 32781743 PMCID: PMC7460668 DOI: 10.3390/ijms21165647] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023] Open
Abstract
Hypoxia, i.e., oxygen deficiency condition, is one of the most important factors promoting the growth of tumors. Since its effect on the chemokine system is crucial in understanding the changes in the recruitment of cells to a tumor niche, in this review we have gathered all the available data about the impact of hypoxia on β chemokines. In the introduction, we present the chronic (continuous, non-interrupted) and cycling (intermittent, transient) hypoxia together with the mechanisms of activation of hypoxia inducible factors (HIF-1 and HIF-2) and NF-κB. Then we describe the effect of hypoxia on the expression of chemokines with the CC motif: CCL1, CCL2, CCL3, CCL4, CCL5, CCL7, CCL8, CCL11, CCL13, CCL15, CCL16, CCL17, CCL18, CCL19, CCL20, CCL21, CCL22, CCL24, CCL25, CCL26, CCL27, CCL28 together with CC chemokine receptors: CCR1, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CCR9, and CCR10. To better understand the effect of hypoxia on neoplastic processes and changes in the expression of the described proteins, we summarize the available data in a table which shows the effect of individual chemokines on angiogenesis, lymphangiogenesis, and recruitment of eosinophils, myeloid-derived suppressor cells (MDSC), regulatory T cells (Treg), and tumor-associated macrophages (TAM) to a tumor niche.
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Affiliation(s)
- Jan Korbecki
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland; (J.K.); (D.S.); (D.C.)
| | - Klaudyna Kojder
- Department of Anaesthesiology and Intensive Care, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-281 Szczecin, Poland;
| | - Katarzyna Barczak
- Department of Conservative Dentistry and Endodontics, Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland;
| | - Donata Simińska
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland; (J.K.); (D.S.); (D.C.)
| | - Izabela Gutowska
- Department of Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland;
| | - Dariusz Chlubek
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland; (J.K.); (D.S.); (D.C.)
| | - Irena Baranowska-Bosiacka
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland; (J.K.); (D.S.); (D.C.)
- Correspondence: ; Tel.: +48-914661515; Fax: +48-914661516
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Belrose JL, Prasad A, Sammons MA, Gibbs KM, Szaro BG. Comparative gene expression profiling between optic nerve and spinal cord injury in Xenopus laevis reveals a core set of genes inherent in successful regeneration of vertebrate central nervous system axons. BMC Genomics 2020; 21:540. [PMID: 32758133 PMCID: PMC7430912 DOI: 10.1186/s12864-020-06954-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 07/27/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The South African claw-toed frog, Xenopus laevis, is uniquely suited for studying differences between regenerative and non-regenerative responses to CNS injury within the same organism, because some CNS neurons (e.g., retinal ganglion cells after optic nerve crush (ONC)) regenerate axons throughout life, whereas others (e.g., hindbrain neurons after spinal cord injury (SCI)) lose this capacity as tadpoles metamorphose into frogs. Tissues from these CNS regions (frog ONC eye, tadpole SCI hindbrain, frog SCI hindbrain) were used in a three-way RNA-seq study of axotomized CNS axons to identify potential core gene expression programs for successful CNS axon regeneration. RESULTS Despite tissue-specific changes in expression dominating the injury responses of each tissue, injury-induced changes in gene expression were nonetheless shared between the two axon-regenerative CNS regions that were not shared with the non-regenerative region. These included similar temporal patterns of gene expression and over 300 injury-responsive genes. Many of these genes and their associated cellular functions had previously been associated with injury responses of multiple tissues, both neural and non-neural, from different species, thereby demonstrating deep phylogenetically conserved commonalities between successful CNS axon regeneration and tissue regeneration in general. Further analyses implicated the KEGG adipocytokine signaling pathway, which links leptin with metabolic and gene regulatory pathways, and a novel gene regulatory network with genes regulating chromatin accessibility at its core, as important hubs in the larger network of injury response genes involved in successful CNS axon regeneration. CONCLUSIONS This study identifies deep, phylogenetically conserved commonalities between CNS axon regeneration and other examples of successful tissue regeneration and provides new targets for studying the molecular underpinnings of successful CNS axon regeneration, as well as a guide for distinguishing pro-regenerative injury-induced changes in gene expression from detrimental ones in mammals.
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Affiliation(s)
- Jamie L Belrose
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Aparna Prasad
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Morgan A Sammons
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Kurt M Gibbs
- Department of Biology and Chemistry, Morehead State University, Morehead, KY, 40351, USA
| | - Ben G Szaro
- Department of Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.
- Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.
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Sun G, Zhou H, Chen K, Zeng J, Zhang Y, Yan L, Yao W, Hu J, Wang T, Xing J, Xiao K, Wu L, Ye Z, Xu H. HnRNP A1 - mediated alternative splicing of CCDC50 contributes to cancer progression of clear cell renal cell carcinoma via ZNF395. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:116. [PMID: 32560659 PMCID: PMC7304168 DOI: 10.1186/s13046-020-01606-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/28/2020] [Indexed: 01/26/2023]
Abstract
BACKGROUND Aberrant alternative splicing events play critical roles in carcinogenesis and progression of many cancers, while sparse studies regarding to alternative splicing are available for clear cell renal cell carcinoma (ccRCC). We identified that alternative splicing of coiled-coil domain containing 50 (CCDC50) was dysregulated in ccRCC, whereas the clinical significance of this splicing event and its splicing regulation mechanisms were still elusive. METHODS Bioinformatic algorithm was utilized to identify significant exon skipping events in ccRCC via exon sequencing data from The Cancer Genome Atlas. Semi-quantitative real-time polymerase chain reaction and western blot were used to validate the aberrant expression of different transcripts in renal cancer tissues, cell lines and corresponding noncancerous controls. Short hairpin RNA targeting CCDC50 and overexpressing plasmids for each transcript were introduced into ccRCC cell lines, followed by a series of in vitro and in vivo functional experiments. Moreover, a panel of splicing factors were identified and their roles on splicing regulation of CCDC50 precursor mRNA (pre-mRNA) were studied. Furthermore, RNAseq data were analyzed to elucidate downstream molecules of CCDC50. Two-way analysis of variance and unpaired Student t test were used in statistical analysis. RESULTS Pre-mRNA of CCDC50 generated two transcripts, full-length transcript (CCDC50-FL) and truncated transcript (CCDC50-S) with exon 6 skipped. CCDC50-S was overexpressed in ccRCC tissues and cell lines compared to noncancerous counterparts, but CCDC50-FL was only detected in noncancerous tissues and normal renal epithelial cells. Higher percent spliced-in index was associated with better survival in ccRCC patients. In vitro and in vivo functional experiments indicated that CCDC50-S transcript promoted the proliferation, migration, invasion and tumorigenesis of ccRCC, while CCDC50-FL exerted opposite tumor suppressive functions. Besides, we identified that heterogeneous nuclear ribonucleoprotein A1 (HnRNP A1) could promote the skipping of exon 6, which resulted in higher portion of CCDC50-S and oncogenic transformation. Moreover, zinc finger protein 395 (ZNF395) was identified as a downstream protein of CCDC50-S, and the interaction initiated oncogenic pathways which were involved in ccRCC progression. CONCLUSIONS Aberrant alternative splicing of CCDC50 is regulated by HnRNP A1 in ccRCC. This splicing event contributes to cancer progression through the downstream pathway involving ZNF395.
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Affiliation(s)
- Guoliang Sun
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Hui Zhou
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Ke Chen
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Jin Zeng
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Yangjun Zhang
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Libin Yan
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Weimin Yao
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Junhui Hu
- Hubei Institute of Urology, Wuhan, 430030 P.R. China ,grid.19006.3e0000 0000 9632 6718Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095 USA
| | - Tao Wang
- grid.412625.6Department of Urology, The First Affiliated Hospital of Xiamen University, Xiamen, 361000 P.R. China
| | - Jinchun Xing
- grid.412625.6Department of Urology, The First Affiliated Hospital of Xiamen University, Xiamen, 361000 P.R. China
| | - Kefeng Xiao
- Department of Urology, The People’s Hospital of Shenzhen City, Shenzhen, 518000 P.R. China
| | - Lily Wu
- grid.19006.3e0000 0000 9632 6718Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095 USA
| | - Zhangqun Ye
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P.R. China. .,Hubei Institute of Urology, Wuhan, 430030, P.R. China.
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Skibiel AL, Peñagaricano F, Amorín R, Ahmed BM, Dahl GE, Laporta J. In Utero Heat Stress Alters the Offspring Epigenome. Sci Rep 2018; 8:14609. [PMID: 30279561 PMCID: PMC6168509 DOI: 10.1038/s41598-018-32975-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/19/2018] [Indexed: 12/20/2022] Open
Abstract
Exposure to intrauterine heat stress during late gestation affects offspring performance into adulthood. However, underlying mechanistic links between thermal insult in fetal life and postnatal outcomes are not completely understood. We examined morphology, DNA methylation, and gene expression of liver and mammary gland for bull calves and heifers that were gestated under maternal conditions of heat stress or cooling (i.e. in utero heat stressed vs. in utero cooled calves). Mammary tissue was harvested from dairy heifers during their first lactation and liver from bull calves at birth. The liver of in utero heat stressed bull calves contained more cells and the mammary glands of in utero heat stressed heifers were comprised of smaller alveoli. We identified more than 1,500 CpG sites differently methylated between maternal treatment groups. These CpGs were associated with approximately 400 genes, which play a role in processes, such as development, innate immune defense, cell signaling, and transcription and translation. We also identified over 100 differentially expressed genes in the mammary gland with similar functions. Interestingly, fifty differentially methylated genes were shared by both bull calf liver and heifer mammary gland. Intrauterine heat stress alters the methylation profile of liver and mammary DNA and programs their morphology in postnatal life, which may contribute to the poorer performance of in utero heat stressed calves.
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Affiliation(s)
- A L Skibiel
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - F Peñagaricano
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - R Amorín
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - B M Ahmed
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - G E Dahl
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA.
| | - J Laporta
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA.
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Mosedale M, Kim Y, Brock WJ, Roth SE, Wiltshire T, Eaddy JS, Keele GR, Corty RW, Xie Y, Valdar W, Watkins PB. Editor's Highlight: Candidate Risk Factors and Mechanisms for Tolvaptan-Induced Liver Injury Are Identified Using a Collaborative Cross Approach. Toxicol Sci 2018; 156:438-454. [PMID: 28115652 DOI: 10.1093/toxsci/kfw269] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Clinical trials of tolvaptan showed it to be a promising candidate for the treatment of Autosomal Dominant Polycystic Kidney Disease (ADPKD) but also revealed potential for idiosyncratic drug-induced liver injury (DILI) in this patient population. To identify risk factors and mechanisms underlying tolvaptan DILI, 8 mice in each of 45 strains of the genetically diverse Collaborative Cross (CC) mouse population were treated with a single oral dose of either tolvaptan or vehicle. Significant elevations in plasma alanine aminotransferase (ALT) were observed in tolvaptan-treated animals in 3 of the 45 strains. Genetic mapping coupled with transcriptomic analysis in the liver was used to identify several candidate susceptibility genes including epoxide hydrolase 2, interferon regulatory factor 3, and mitochondrial fission factor. Gene pathway analysis revealed that oxidative stress and immune response pathways were activated in response to tolvaptan treatment across all strains, but genes involved in regulation of bile acid homeostasis were most associated with tolvaptan-induced elevations in ALT. Secretory leukocyte peptidase inhibitor (Slpi) mRNA was also induced in the susceptible strains and was associated with increased plasma levels of Slpi protein, suggesting a potential serum marker for DILI susceptibility. In summary, tolvaptan induced signs of oxidative stress, mitochondrial dysfunction, and innate immune response in all strains, but variation in bile acid homeostasis was most associated with susceptibility to the liver response. This CC study has indicated potential mechanisms underlying tolvaptan DILI and biomarkers of susceptibility that may be useful in managing the risk of DILI in ADPKD patients.
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Affiliation(s)
- Merrie Mosedale
- Institute for Drug Safety Sciences, University of North Carolina at Chapel Hill, Research Triangle Park, North Carolina 27709.,Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina 27599
| | - Yunjung Kim
- Institute for Drug Safety Sciences, University of North Carolina at Chapel Hill, Research Triangle Park, North Carolina 27709.,Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina 27599
| | - William J Brock
- Otsuka Pharmaceutical Development and Commercialization, Inc., Rockville, Maryland 20850.,Brock Scientific Consulting, Montgomery Village, Maryland 20886
| | - Sharin E Roth
- Otsuka Pharmaceutical Development and Commercialization, Inc., Rockville, Maryland 20850
| | - Tim Wiltshire
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina 27599.,Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina 27599
| | - J Scott Eaddy
- Institute for Drug Safety Sciences, University of North Carolina at Chapel Hill, Research Triangle Park, North Carolina 27709.,Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina 27599
| | - Gregory R Keele
- Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina 27599
| | - Robert W Corty
- Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina 27599
| | - Yuying Xie
- Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina 27599
| | - William Valdar
- Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina 27599.,Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina 27599
| | - Paul B Watkins
- Institute for Drug Safety Sciences, University of North Carolina at Chapel Hill, Research Triangle Park, North Carolina 27709.,Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina 27599
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Yao X, Tan J, Lim KJ, Koh J, Ooi WF, Li Z, Huang D, Xing M, Chan YS, Qu JZ, Tay ST, Wijaya G, Lam YN, Hong JH, Lee-Lim AP, Guan P, Ng MSW, He CZ, Lin JS, Nandi T, Qamra A, Xu C, Myint SS, Davies JOJ, Goh JY, Loh G, Tan BC, Rozen SG, Yu Q, Tan IBH, Cheng CWS, Li S, Chang KTE, Tan PH, Silver DL, Lezhava A, Steger G, Hughes JR, Teh BT, Tan P. VHL Deficiency Drives Enhancer Activation of Oncogenes in Clear Cell Renal Cell Carcinoma. Cancer Discov 2017; 7:1284-1305. [DOI: 10.1158/2159-8290.cd-17-0375] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 07/19/2017] [Accepted: 08/25/2017] [Indexed: 11/16/2022]
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12
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ZNF395 Is an Activator of a Subset of IFN-Stimulated Genes. Mediators Inflamm 2017; 2017:1248201. [PMID: 28316371 PMCID: PMC5339479 DOI: 10.1155/2017/1248201] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/05/2017] [Indexed: 11/17/2022] Open
Abstract
Activation of the interferon (IFN) pathway in response to infection with pathogens results in the induction of IFN-stimulated genes (ISGs) including proinflammatory cytokines, which mount the proper antiviral immune response. However, aberrant expression of these genes is pathogenic to the host. In addition to IFN-induced transcription factors non-IFN-regulated factors contribute to the transcriptional control of ISGs. Here, we show by genome wide expression analysis, siRNA-mediated suppression and Doxycycline-induced overexpression that the cellular transcription factor ZNF395 activates a subset of ISGs including the chemokines CXCL10 and CXCL11 in keratinocytes. We found that ZNF395 acts independently of IFN but enhances the IFN-induced expression of CXCL10 and CXCL11. Luciferase reporter assays revealed a requirement of intact NFκB-binding sites for ZNF395 to stimulate the CXCL10 promoter. The transcriptional activation of CXCL10 and CXCL11 by ZNF395 was abolished after inhibition of IKK by BMS-345541, which increased the stability of ZNF395. ZNF395 encodes at least two motifs that mediate the enhanced degradation of ZNF395 in response to IKK activation. Thus, IKK is required for ZNF395-mediated activation of transcription and enhances its turn-over to keep the activity of ZNF395 low. Our results support a previously unrecognized role of ZNF395 in the innate immune response and inflammation.
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Rhie SK, Guo Y, Tak YG, Yao L, Shen H, Coetzee GA, Laird PW, Farnham PJ. Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits. Epigenetics Chromatin 2016; 9:50. [PMID: 27833659 PMCID: PMC5103450 DOI: 10.1186/s13072-016-0102-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/28/2016] [Indexed: 12/22/2022] Open
Abstract
Background Although technological advances now allow increased tumor profiling, a detailed understanding of the mechanisms leading to the development of different cancers remains elusive. Our approach toward understanding the molecular events that lead to cancer is to characterize changes in transcriptional regulatory networks between normal and tumor tissue. Because enhancer activity is thought to be critical in regulating cell fate decisions, we have focused our studies on distal regulatory elements and transcription factors that bind to these elements. Results Using DNA methylation data, we identified more than 25,000 enhancers that are differentially activated in breast, prostate, and kidney tumor tissues, as compared to normal tissues. We then developed an analytical approach called Tracing Enhancer Networks using Epigenetic Traits that correlates DNA methylation levels at enhancers with gene expression to identify more than 800,000 genome-wide links from enhancers to genes and from genes to enhancers. We found more than 1200 transcription factors to be involved in these tumor-specific enhancer networks. We further characterized several transcription factors linked to a large number of enhancers in each tumor type, including GATA3 in non-basal breast tumors, HOXC6 and DLX1 in prostate tumors, and ZNF395 in kidney tumors. We showed that HOXC6 and DLX1 are associated with different clusters of prostate tumor-specific enhancers and confer distinct transcriptomic changes upon knockdown in C42B prostate cancer cells. We also discovered de novo motifs enriched in enhancers linked to ZNF395 in kidney tumors. Conclusions Our studies characterized tumor-specific enhancers and revealed key transcription factors involved in enhancer networks for specific tumor types and subgroups. Our findings, which include a large set of identified enhancers and transcription factors linked to those enhancers in breast, prostate, and kidney cancers, will facilitate understanding of enhancer networks and mechanisms leading to the development of these cancers. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0102-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Suhn Kyong Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT G511B, Los Angeles, CA 90089-9601 USA
| | - Yu Guo
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT G511B, Los Angeles, CA 90089-9601 USA
| | - Yu Gyoung Tak
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT G511B, Los Angeles, CA 90089-9601 USA
| | - Lijing Yao
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT G511B, Los Angeles, CA 90089-9601 USA
| | - Hui Shen
- Van Andel Research Institute, Grand Rapids, MI 49503 USA
| | | | - Peter W Laird
- Van Andel Research Institute, Grand Rapids, MI 49503 USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT G511B, Los Angeles, CA 90089-9601 USA
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Vela L, Caballero I, Fang L, Liu Q, Ramón F, Díez E, de Los Frailes M. Discovery of Enhancers of the Secretion of Leukemia Inhibitory Factor for the Treatment of Multiple Sclerosis. ACTA ACUST UNITED AC 2016; 21:437-45. [PMID: 26984928 DOI: 10.1177/1087057116638821] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/17/2016] [Indexed: 11/17/2022]
Abstract
Multiple sclerosis (MS) is an autoimmune neurodegenerative disease that involves activation of T cells, microglia, and astrocytes. There is a clear unmet medical need for MS, as current therapies reduce the relapse rate, but are unable to prevent the neurological deterioration. Leukemia inhibitory factor (LIF) is a proinflammatory cytokine that can also positively modulate the immune response, by inducing the inhibition of myelin-reactive TH17 differentiation, and by promoting oligodendrocyte-mediated myelination. The aim of this project was to find central nervous system (CNS)-permeable and orally available small molecules that upregulate production of endogenous LIF. We describe here the development of a phenotypic assay and screening of 1.7 million compounds to identify LIF enhancers using U87 MG cells. Five chemically tractable series of compounds and a few singletons were selected for further progression. Some of them were also active in a different LIF-expressing cell line and in primary rat astrocytes. Although further studies would be required to deconvolute the targets involved in LIF induction and to confirm activity of hits in more disease-relevant assays, our results have demonstrated the potential of the phenotypic approach to identify specific and chemically tractable small molecules that trigger the production of LIF in relevant cell lines.
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Affiliation(s)
- Laura Vela
- Centro de Investigación Básica, GSK, Tres Cantos, Madrid, Spain
| | - Iván Caballero
- Centro de Investigación Básica, GSK, Tres Cantos, Madrid, Spain
| | - Leiping Fang
- GSK (China) R&D Company Limited, Pudong, Shanghai, China
| | - Qin Liu
- GSK (China) R&D Company Limited, Pudong, Shanghai, China
| | - Fernando Ramón
- Centro de Investigación Básica, GSK, Tres Cantos, Madrid, Spain
| | - Emilio Díez
- Centro de Investigación Básica, GSK, Tres Cantos, Madrid, Spain
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