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Siwo GH, Singal AG, Waljee AK. Pan-cancer molecular signatures connecting aspartate transaminase (AST) to cancer prognosis, metabolic and immune signatures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582939. [PMID: 38496547 PMCID: PMC10942358 DOI: 10.1101/2024.03.01.582939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Background Serum aspartate transaminase (sAST) level is used routinely in conjunction with other clinical assays to assess liver health and disease. Increasing evidence suggests that sAST is associated with all-cause mortality and has prognostic value in several cancers, including gastrointestinal and urothelial cancers. Here, we undertake a systems approach to unravel molecular connections between AST and cancer prognosis, metabolism, and immune signatures at the transcriptomic and proteomic levels. Methods We mined public gene expression data across multiple normal and cancerous tissues using the Genotype Tissue Expression (GTEX) resource and The Cancer Genome Atlas (TCGA) to assess the expression of genes encoding AST isoenzymes (GOT1 and GOT2) and their association with disease prognosis and immune infiltration signatures across multiple tumors. We examined the associations between AST and previously reported pan-cancer molecular subtypes characterized by distinct metabolic and immune signatures. We analyzed human protein-protein interaction networks for interactions between GOT1 and GOT2 with cancer-associated proteins. Using public databases and protein-protein interaction networks, we determined whether the subset of proteins that interact with AST (GOT1 and GOT2 interactomes) are enriched with proteins associated with specific diseases, miRNAs and transcription factors. Results We show that AST transcript isoforms (GOT1 and GOT2) are expressed across a wide range of normal tissues. AST isoforms are upregulated in tumors of the breast, lung, uterus, and thymus relative to normal tissues but downregulated in tumors of the liver, colon, brain, kidney and skeletal sarcomas. At the proteomic level, we find that the expression of AST is associated with distinct pan-cancer molecular subtypes with an enrichment of specific metabolic and immune signatures. Based on human protein-protein interaction data, AST physically interacts with multiple proteins involved in tumor initiation, suppression, progression, and treatment. We find enrichments in the AST interactomes for proteins associated with liver and lung cancer and dermatologic diseases. At the regulatory level, the GOT1 interactome is enriched with the targets of cancer-associated miRNAs, specifically mir34a - a promising cancer therapeutic, while the GOT2 interactome is enriched with proteins that interact with cancer-associated transcription factors. Conclusions Our findings suggest that perturbations in the levels of AST within specific tissues reflect pathophysiological changes beyond tissue damage and have implications for cancer metabolism, immune infiltration, prognosis, and treatment personalization.
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Affiliation(s)
| | - Amit G. Singal
- Department of Learning Health Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas TX
- Center for Global Health Equity, University of Michigan, Ann Arbor, MI, USA
| | - Akbar K. Waljee
- Department of Learning Health Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas TX
- Center for Global Health Equity, University of Michigan, Ann Arbor, MI, USA
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2
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Fu D, Si Q, Yu C, Han Z, Zang L. USF1-mediated ALKBH5 stabilizes FLII mRNA in an m6A-YTHDF2-dependent manner to repress glycolytic activity in prostate adenocarcinoma. Mol Carcinog 2023; 62:1700-1716. [PMID: 37493109 DOI: 10.1002/mc.23609] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023]
Abstract
Upstream-stimulating factor 1 (USF1) is a ubiquitously expressed transcription factor implicated in multiple cellular processes, including metabolism and proliferation. This study focused on the function of USF1 in glycolysis and the malignant development of prostate adenocarcinoma (PRAD). Bioinformatics predictions suggested that USF1 is poorly expressed in PRAD. The clinical PRAD samples revealed a low level of USF1, which was correlated with an unfavorable prognosis. Artificial upregulation of USF1 significantly repressed glycolytic activity in PRAD cells and reduced cell growth and metastasis in vitro and in vivo. Potential downstream genes of USF1 were probed by integrated bioinformatics analyses. The chromatin immunoprecipitation and luciferase assays indicated that USF1 bound to the α-ketoglutarate-dependent dioxygenase alkB homolog 5 (ALKBH5) promoter for transcription activation. Flightless I (FLII) was identified as the gene showing the highest degree of correlation with ALKBH5. As an m6A demethylase, ALKBH5 enhanced FLII mRNA stability by inducing m6A demethylation in an m6A-YTH N6-methyladenosine RNA-binding protein F2 (YTHDF2)-dependent manner. Either silencing of ALKBH5 or FLII blocked the role of USF1 in PARD cells and restored glycolysis, cell proliferation, and invasion. This study demonstrates that USF1 activates ALKBH5 to stabilize FLII mRNA in an m6A-YTHDF2-dependent manner, thereby repressing glycolysis processes and the progression of PRAD.
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Affiliation(s)
- Dewang Fu
- Department of Urology Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, P.R. China
| | - Qingyue Si
- Department of Urology Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, P.R. China
| | - Chenxi Yu
- Department of Urology Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, P.R. China
| | - Zhifu Han
- Department of Urology Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, P.R. China
| | - Li'e Zang
- Department of Neurology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, P.R. China
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3
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Kang T, Moore EC, Kopania EEK, King CD, Schilling B, Campisi J, Good JM, Brem RB. A natural variation-based screen in mouse cells reveals USF2 as a regulator of the DNA damage response and cellular senescence. G3 (BETHESDA, MD.) 2023; 13:jkad091. [PMID: 37097016 PMCID: PMC10320765 DOI: 10.1093/g3journal/jkad091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 04/26/2023]
Abstract
Cellular senescence is a program of cell cycle arrest, apoptosis resistance, and cytokine release induced by stress exposure in metazoan cells. Landmark studies in laboratory mice have characterized a number of master senescence regulators, including p16INK4a, p21, NF-κB, p53, and C/EBPβ. To discover other molecular players in senescence, we developed a screening approach to harness the evolutionary divergence between mouse species. We found that primary cells from the Mediterranean mouse Mus spretus, when treated with DNA damage to induce senescence, produced less cytokine and had less-active lysosomes than cells from laboratory Mus musculus. We used allele-specific expression profiling to catalog senescence-dependent cis-regulatory variation between the species at thousands of genes. We then tested for correlation between these expression changes and interspecies sequence variants in the binding sites of transcription factors. Among the emergent candidate senescence regulators, we chose a little-studied cell cycle factor, upstream stimulatory factor 2 (USF2), for molecular validation. In acute irradiation experiments, cells lacking USF2 had compromised DNA damage repair and response. Longer-term senescent cultures without USF2 mounted an exaggerated senescence regulatory program-shutting down cell cycle and DNA repair pathways, and turning up cytokine expression, more avidly than wild-type. We interpret these findings under a model of pro-repair, anti-senescence regulatory function by USF2. Our study affords new insights into the mechanisms by which cells commit to senescence, and serves as a validated proof of concept for natural variation-based regulator screens.
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Affiliation(s)
- Taekyu Kang
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Emily C Moore
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Emily E K Kopania
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | | | | | - Judith Campisi
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Rachel B Brem
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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4
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Liu W, Xie A, Xiong J, Li S, Yang L, Liu W. WDR3 promotes stem cell-like properties in prostate cancer by inhibiting USF2-mediated transcription of RASSF1A. J Gene Med 2023; 25:e3498. [PMID: 36905106 DOI: 10.1002/jgm.3498] [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: 08/08/2022] [Revised: 02/01/2023] [Accepted: 03/04/2023] [Indexed: 03/12/2023] Open
Abstract
BACKGROUND WD repeat domain 3 (WDR3) is involved in tumor growth and proliferation, but its role in the pathological mechanism of prostate cancer (PCa) is still unclear. METHODS WDR3 gene expression levels were obtained by analyzing databases and our clinical specimens. The expression levels of genes and proteins were determined by a real-time polymerase chain reaction, western blotting and immunohistochemistry, respectively. Cell-counting kit-8 assays were used to measure the proliferation of PCa cells. Cell transfection was used to investigate the role of WDR3 and USF2 in PCa. Fluorescence reporter and chromatin immunoprecipitation assays were used to detect USF2 binding to the promoter region of RASSF1A. Mouse experiments were used to confirm the mechanism in vivo. RESULTS By analyzing the database and our clinical specimens, we found that WDR3 expression was significantly increased in PCa tissues. Overexpression of WDR3 enhanced PCa cell proliferation, decreased cell apoptosis rate, increased spherical cell number and increased indicators of stem cell-like properties. However, these effects were reversed by WDR3 knockdown. WDR3 was negatively correlated with USF2, which was degraded by promoting ubiquitination of USF2, and USF2 interacted with promoter region-binding elements of RASSF1A to depress PCa stemness and growth. In vivo studies showed that WDR3 knockdown reduced tumor size and weight, reduced cell proliferation and enhanced cell apoptosis. CONCLUSIONS WDR3 ubiquitinated USF2 and inhibited its stability, whereas USF2 interacted with promoter region-binding elements of RASSF1A. USF2 transcriptionally activated RASSF1A, which inhibited the carcinogenic effect of WDR3 overexpression.
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Affiliation(s)
- Weijing Liu
- Department of Reproductive Medicine, Hexian Memorial Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - An Xie
- Jiangxi Institute of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jing Xiong
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Sheng Li
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Lin Yang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Weipeng Liu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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Andalib KMS, Rahman MH, Habib A. Bioinformatics and cheminformatics approaches to identify pathways, molecular mechanisms and drug substances related to genetic basis of cervical cancer. J Biomol Struct Dyn 2023; 41:14232-14247. [PMID: 36852684 DOI: 10.1080/07391102.2023.2179542] [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: 10/17/2022] [Accepted: 02/07/2023] [Indexed: 03/01/2023]
Abstract
Cervical cancer (CC) is a global threat to women and our knowledge is frighteningly little about its underlying genomic contributors. Our research aimed to understand the underlying molecular and genetic mechanisms of CC by integrating bioinformatics and network-based study. Transcriptomic analyses of three microarray datasets identified 218 common differentially expressed genes (DEGs) within control samples and CC specimens. KEGG pathway analysis revealed pathways in cell cycle, drug metabolism, DNA replication and the significant GO terms were cornification, proteolysis, cell division and DNA replication. Protein-protein interaction (PPI) network analysis identified 20 hub genes and survival analyses validated CDC45, MCM2, PCNA and TOP2A as CC biomarkers. Subsequently, 10 transcriptional factors (TFs) and 10 post-transcriptional regulators were detected through TFs-DEGs and miRNAs-DEGs regulatory network assessment. Finally, the CC biomarkers were subjected to a drug-gene relationship analysis to find the best target inhibitors. Standard cheminformatics method including in silico ADMET and molecular docking study substantiated PD0325901 and Selumetinib as the most potent candidate-drug for CC treatment. Overall, this meticulous study holds promises for further in vitro and in vivo research on CC diagnosis, prognosis and therapies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- K M Salim Andalib
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia, Bangladesh
- Center for Advanced Bioinformatics and Artificial Intelligent Research, Islamic University, Kushtia, Bangladesh
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
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USF2-mediated upregulation of TXNRD1 contributes to hepatocellular carcinoma progression by activating Akt/mTOR signaling. Cell Death Dis 2022; 13:917. [PMID: 36319631 PMCID: PMC9626593 DOI: 10.1038/s41419-022-05363-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022]
Abstract
Thioredoxin reductase 1 (TXNRD1) is one of the major redox regulators in mammalian cells, which has been reported to be involved in tumorigenesis. However, its roles and regulatory mechanism underlying the progression of HCC remains poorly understood. In this study, we demonstrated that TXNRD1 was significantly upregulated in HCC tumor tissues and correlated with poor survival in HCC patients. Functional studies indicated TXNRD1 knockdown substantially suppressed HCC cell proliferation and metastasis both in vitro and in vivo, and its overexpression showed opposite effects. Mechanistically, TXNRD1 attenuated the interaction between Trx1 and PTEN which resulting in acceleration of PTEN degradation, thereby activated Akt/mTOR signaling and its target genes which conferred to elevated HCC cell mobility and metastasis. Moreover, USF2 was identified as a transcriptional suppressor of TXNRD1, which directly interacted with two E-box sites in TXNRD1 promoter. USF2 functioned as tumor suppressor through the downstream repression of TXNRD1. Further clinical data revealed negative co-expression correlations between USF2 and TXNRD1. In conclusion, our findings reveal that USF2-mediated upregulation of TXNRD1 contributes to hepatocellular carcinoma progression by activating Akt/mTOR signaling.
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Chen M, Li X, Du B, Chen S, Li Y. Upstream stimulatory factor 2 inhibits erastin-induced ferroptosis in pancreatic cancer through transcriptional regulation of pyruvate kinase M2. Biochem Pharmacol 2022; 205:115255. [DOI: 10.1016/j.bcp.2022.115255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/28/2022] [Accepted: 09/13/2022] [Indexed: 11/25/2022]
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8
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Gao S, Zhang Z, Wang X, Ma Y, Li C, Liu H, Jing C, Li L, Guo X. hsa-miR-875-5p inhibits tumorigenesis and suppresses TGF-β signalling by targeting USF2 in gastric cancer. J Transl Med 2022; 20:115. [PMID: 35255935 PMCID: PMC8900418 DOI: 10.1186/s12967-022-03253-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 01/15/2022] [Indexed: 12/19/2022] Open
Abstract
Abstract
Background
Gastric cancer (GC) is one of the most common malignancies, and an increasing number of studies have shown that its pathogenesis is regulated by various miRNAs. In this study, we investigated the role of miR-875-5p in GC.
Methods
The expression of miR-875-5p was detected in human GC specimens and cell lines by miRNA qRT–PCR. The effect of miR-875-5p on GC proliferation was determined by Cell Counting Kit-8 (CCK-8) proliferation and 5-ethynyl-2′-deoxyuridine (EdU) assays. Migration and invasion were examined by transwell migration and invasion assays as well as wound healing assays. The interaction between miR-875-5p and its target gene upstream stimulatory factor 2(USF2) was verified by dual luciferase reporter assays. The effects of miR-875-5p in vivo were studied in xenograft nude mouse models. Related proteins were detected by western blot.
Results
The results showed that miR-875-5p inhibited the proliferation, migration and invasion of GC cells in vitro and inhibited tumorigenesis in vivo. USF2 was proved to be a direct target of miR-875-5p. Knockdown of USF2 partially counteracted the effects of miR-875-5p inhibitor. Overexpression of miR-875-5p could inhibit proliferation, migration and invasion and suppress the TGF-β signalling pathway by downregulating USF2.
Conclusions
MiR-875-5p can inhibit the progression of GC by directly targeting USF2. And in the future, miR-875-5p is expected to be a potential target for GC diagnosis and treatment.
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9
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Gupta S, Ahmed MM. Targeting radiation-induced upstream stimulatory factor-1 by histone deacetylase inhibitors to reverse radioresistance in prostate cancer. Cancer Rep (Hoboken) 2021; 5:e1553. [PMID: 34533293 PMCID: PMC9780427 DOI: 10.1002/cnr2.1553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 08/11/2021] [Accepted: 08/23/2021] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Ionizing radiation (IR) is a standard modality for the management of solid tumors. Apart from its killing effects, IR can induce pro-survival factors leading to radioresistance of cancer. Mechanistic understanding of radiation resistance is warranted to overcome the pro-survival effects of IR. AIM The aim of this study was to investigate the role of upstream stimulatory factor-1 (USF-1) in the induction of radioresistance in prostate cancer and its targeting by histone deacetylase (HDAC) inhibitors to reverse resistance. METHODS AND RESULTS This study reports here that USF-1 is a marker for radioresistance in PC-3 cells. Using protein-DNA array analysis, it was documented that DNA binding activity of USF-1 was elevated following IR in PC-3 cells. Novel HDAC inhibitors downregulated USF-1 binding either alone or in combination with IR. A 5 Gy dose of IR induced the expression of target genes of USF-1 (human telomerase reverse transcriptase [hTERT], IGF2R, CyclinB1, and Cdk1), however, HDAC inhibitors alone or in combination with IR reduced their expression as measured by real time RT PCR analysis. Furthermore, immunofluorescence analysis revealed that while USF-1 localized primarily in the nucleus following IR, it localized in the cytoplasm when treated with HDAC inhibitors/combination. Maximum effects of modulation of USF-1 expression (overexpression or suppression) were observed on hTERT activity as determined by dual-luciferase reporter assay. To further confirm the role of USF-1 in radioresistance, cell growth was analyzed using the real-time cell electronic sensing (RT-CES) system. This study found that USF-1-transfected cells proliferated faster than the vector-transfected cells with or without treatments with HDAC inhibitors/IR/combination. Colony forming assay also confirmed that USF-1 overexpression led to increased survival following IR. Importantly, colony-forming assay demonstrated that HDAC inhibitors reversed the radioresistance in both PC-3 and DU-145 cells. CONCLUSION These studies demonstrate that HDAC inhibitors reverse the radioresistance in prostate cancer through down-modulation of USF-1-mediated transactivation of target genes involved in cell proliferation and cell cycle.
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Affiliation(s)
- Seema Gupta
- Department of Radiation OncologyUniversity of MiamiMiamiFloridaUSA,Present address:
The Loop Immuno‐Oncology Laboratory, Lombardi Comprehensive Cancer CenterGeorgetown University Medical CenterWashington, DCUSA
| | - Mansoor M. Ahmed
- Department of Radiation OncologyUniversity of MiamiMiamiFloridaUSA,Present address:
Radiation Research Program (RRP), Division of Cancer Treatment and Diagnosis (DCTD)National Cancer Institute/National Institutes of HealthRockvilleMarylandUSA
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Ajit K, Murphy BD, Banerjee A. Elucidating evolutionarily conserved mechanisms of diapause regulation using an in silico approach. FEBS Lett 2021; 595:1350-1374. [PMID: 33650678 DOI: 10.1002/1873-3468.14064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/02/2021] [Accepted: 02/19/2021] [Indexed: 11/11/2022]
Abstract
Embryonic diapause is an enigmatic phenomenon that appears in diverse species. Although regulatory mechanisms have been established, there is much to be discovered. Herein, we have made the first comprehensive attempt to elucidate diapause regulatory mechanisms using a computational approach. We found transcription factors unique to promoters of genes in diapause species. From pathway analysis and STRING PPI networks, the signaling pathways regulated by these unique transcription factors were identified. The pathways were then consolidated into a model to combine various known mechanisms of diapause regulation. This work also highlighted certain transcription factors that may act as 'master transcription factors' to regulate the phenomenon. Promoter analysis further suggested evidence for independent evolution for some of regulatory elements involved in diapause.
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Affiliation(s)
- Kamal Ajit
- Department of Biological Sciences, BITS Pilani KK Birla Goa Campus, Goa, India
| | - Bruce D Murphy
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médicine Vétérinaire, Université Montréal, St-Hyacinthe, QC, Canada
| | - Arnab Banerjee
- Department of Biological Sciences, BITS Pilani KK Birla Goa Campus, Goa, India
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Li S, Zhang J, Qian S, Wu X, Sun L, Ling T, Jin Y, Li W, Sun L, Lai M, Xu F. S100A8 promotes epithelial-mesenchymal transition and metastasis under TGF-β/USF2 axis in colorectal cancer. Cancer Commun (Lond) 2021; 41:154-170. [PMID: 33389821 PMCID: PMC7896751 DOI: 10.1002/cac2.12130] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/25/2020] [Accepted: 12/20/2020] [Indexed: 12/12/2022] Open
Abstract
Background The transforming growth factor‐β (TGF‐β) pathway plays a pivotal role in inducing epithelial‐mesenchymal transition (EMT), which is a key step in cancer invasion and metastasis. However, the regulatory mechanism of TGF‐β in inducing EMT in colorectal cancer (CRC) has not been fully elucidated. In previous studies, it was found that S100A8 may regulate EMT. This study aimed to clarify the role of S100A8 in TGF‐β‐induced EMT and explore the underlying mechanism in CRC. Methods S100A8 and upstream transcription factor 2 (USF2) expression was detected by immunohistochemistry in 412 CRC tissues. Kaplan‐Meier survival analysis was performed. In vitro, Western blot, and migration and invasion assays were performed to investigate the effects of S100A8 and USF2 on TGF‐β‐induced EMT. Mouse metastasis models were used to determine in vivo metastasis ability. Luciferase reporter and chromatin immunoprecipitation assay were used to explore the role of USF2 on S100A8 transcription. Results During TGF‐β‐induced EMT in CRC cells, S100A8 and the transcription factor USF2 were upregulated. S100A8 promoted cell migration and invasion and EMT. USF2 transcriptionally regulated S100A8 expression by directly binding to its promoter region. Furthermore, TGF‐β enhanced the USF2/S100A8 signaling axis of CRC cells whereas extracellular S100A8 inhibited the USF2/S100A8 axis of CRC cells. S100A8 expression in tumor cells was associated with poor overall survival in CRC. USF2 expression was positively related to S100A8 expression in tumor cells but negatively related to S100A8‐positive stromal cells. Conclusions TGF‐β was found to promote EMT and metastasis through the USF2/S100A8 axis in CRC while extracellular S100A8 suppressed the USF2/S100A8 axis. USF2 was identified as an important switch on the intracellular and extracellular S100A8 feedback loop.
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Affiliation(s)
- Si Li
- Department of Pathology and Pathophysiology, and Department of General Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P. R. China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P. R. China
| | - Jun Zhang
- Department of Pathology and Pathophysiology, and Department of General Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P. R. China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P. R. China
| | - Senmi Qian
- Department of Pathology and Pathophysiology, and Department of General Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P. R. China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P. R. China
| | - Xuesong Wu
- Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P. R. China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P. R. China
| | - Liang Sun
- Department of Pathology and Pathophysiology, and Department of General Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P. R. China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P. R. China
| | - Tianyi Ling
- Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P. R. China
| | - Yao Jin
- Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P. R. China
| | - Wenxiao Li
- Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P. R. China
| | - Lichao Sun
- State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, P. R. China
| | - Maode Lai
- Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P. R. China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P. R. China
| | - Fangying Xu
- Department of Pathology and Pathophysiology, and Department of General Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P. R. China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, P. R. China
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12
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Chi TF, Khoder-Agha F, Mennerich D, Kellokumpu S, Miinalainen II, Kietzmann T, Dimova EY. Loss of USF2 promotes proliferation, migration and mitophagy in a redox-dependent manner. Redox Biol 2020; 37:101750. [PMID: 33059314 PMCID: PMC7566946 DOI: 10.1016/j.redox.2020.101750] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/02/2020] [Accepted: 10/04/2020] [Indexed: 12/15/2022] Open
Abstract
The upstream stimulatory factor 2 (USF2) is a transcription factor implicated in several cellular processes and among them, tumor development seems to stand out. However, the data with respect to the role of USF2 in tumor development are conflicting suggesting that it acts either as tumor promoter or suppressor. Here we show that absence of USF2 promotes proliferation and migration. Thereby, we reveal a previously unknown function of USF2 in mitochondrial homeostasis. Mechanistically, we demonstrate that deficiency of USF2 promotes survival by inducing mitophagy in a ROS-sensitive manner by activating both ERK1/2 and AKT. Altogether, this study supports USF2′s function as tumor suppressor and highlights its novel role for mitochondrial function and energy homeostasis thereby linking USF2 to conditions such as insulin resistance, type-2 diabetes mellitus, and the metabolic syndrome.
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Affiliation(s)
- Tabughang Franklin Chi
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Fawzi Khoder-Agha
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Daniela Mennerich
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - IIkka Miinalainen
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Elitsa Y Dimova
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.
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13
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Costa L, Corre S, Michel V, Le Luel K, Fernandes J, Ziveri J, Jouvion G, Danckaert A, Mouchet N, Da Silva Barreira D, Torres J, Camorlinga M, D'Elios MM, Fiette L, De Reuse H, Galibert MD, Touati E. USF1 defect drives p53 degradation during Helicobacter pylori infection and accelerates gastric carcinogenesis. Gut 2020; 69:1582-1591. [PMID: 31822580 PMCID: PMC7456735 DOI: 10.1136/gutjnl-2019-318640] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 10/24/2019] [Accepted: 11/24/2019] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Helicobacter pylori (Hp) is a major risk factor for gastric cancer (GC). Hp promotes DNA damage and proteasomal degradation of p53, the guardian of genome stability. Hp reduces the expression of the transcription factor USF1 shown to stabilise p53 in response to genotoxic stress. We investigated whether Hp-mediated USF1 deregulation impacts p53-response and consequently genetic instability. We also explored in vivo the role of USF1 in gastric carcinogenesis. DESIGN Human gastric epithelial cell lines were infected with Hp7.13, exposed or not to a DNA-damaging agent camptothecin (CPT), to mimic a genetic instability context. We quantified the expression of USF1, p53 and their target genes, we determined their subcellular localisation by immunofluorescence and examined USF1/p53 interaction. Usf1-/- and INS-GAS mice were used to strengthen the findings in vivo and patient data examined for clinical relevance. RESULTS In vivo we revealed the dominant role of USF1 in protecting gastric cells against Hp-induced carcinogenesis and its impact on p53 levels. In vitro, Hp delocalises USF1 into foci close to cell membranes. Hp prevents USF1/p53 nuclear built up and relocates these complexes in the cytoplasm, thereby impairing their transcriptional function. Hp also inhibits CPT-induced USF1/p53 nuclear complexes, exacerbating CPT-dependent DNA damaging effects. CONCLUSION Our data reveal that the depletion of USF1 and its de-localisation in the vicinity of cell membranes are essential events associated to the genotoxic activity of Hp infection, thus promoting gastric carcinogenesis. These findings are also of clinical relevance, supporting USF1 expression as a potential marker of GC susceptibility.
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Affiliation(s)
- Lionel Costa
- Unit of Helicobacter Pathogenesis, Department of Microbiology, CNRS ERL6002, Institut Pasteur, Paris, France,INSERM U1016, CNRS UMR 8104, Institut Cochin, Paris, France,Université Paris Diderot, Sorbone Paris Cité, Paris, France
| | - Sébastien Corre
- Institut de Génétique et Développement, Université de Rennes 1, Rennes, France
| | - Valérie Michel
- Unit of Helicobacter Pathogenesis, Department of Microbiology, CNRS ERL6002, Institut Pasteur, Paris, France
| | - Krysten Le Luel
- Unit of Helicobacter Pathogenesis, Department of Microbiology, CNRS ERL6002, Institut Pasteur, Paris, France,Université Paris Diderot, Sorbone Paris Cité, Paris, France
| | - Julien Fernandes
- Unit of Helicobacter Pathogenesis, Department of Microbiology, CNRS ERL6002, Institut Pasteur, Paris, France,UtechS PBI-C2RT, Institut Pasteur, Paris, France
| | - Jason Ziveri
- Unit of Helicobacter Pathogenesis, Department of Microbiology, CNRS ERL6002, Institut Pasteur, Paris, France,Pathogenesis of Systemic Infection, Institut Fédératif de Recherche Necker-Enfants Malades, Paris, France
| | - Gregory Jouvion
- Unit of Experimental Neuropathology, Department of Global Health, Institut Pasteur, Paris, France
| | | | - Nicolas Mouchet
- Institut de Génétique et Développement, Université de Rennes 1, Rennes, France
| | - David Da Silva Barreira
- Unit of Helicobacter Pathogenesis, Department of Microbiology, CNRS ERL6002, Institut Pasteur, Paris, France,AgroSup, Laboratoire PAM UMR A 02.102, Université de Bourgogne, Dijon, France
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatria, Instituto Mexicano del Seguro Social (IMSS), México city, Mexico
| | - Margarita Camorlinga
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatria, Instituto Mexicano del Seguro Social (IMSS), México city, Mexico
| | - Mario Milco D'Elios
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Laurence Fiette
- Unit of Experimental Neuropathology, Department of Global Health, Institut Pasteur, Paris, France,Institut Mutualiste Montsouris, Paris, France
| | - Hilde De Reuse
- Unit of Helicobacter Pathogenesis, Department of Microbiology, CNRS ERL6002, Institut Pasteur, Paris, France
| | - Marie-Dominique Galibert
- Institut de Génétique et Développement, Université de Rennes 1, Rennes, France,CHU, Department of Molecular Genetics and Genomics, Université de Rennes 1, Rennes, France
| | - Eliette Touati
- Unit of Helicobacter Pathogenesis, Department of Microbiology, CNRS ERL6002, Institut Pasteur, Paris, France
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Chi TF, Horbach T, Götz C, Kietzmann T, Dimova EY. Cyclin-Dependent Kinase 5 (CDK5)-Mediated Phosphorylation of Upstream Stimulatory Factor 2 (USF2) Contributes to Carcinogenesis. Cancers (Basel) 2019; 11:cancers11040523. [PMID: 31013770 PMCID: PMC6521020 DOI: 10.3390/cancers11040523] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 03/30/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022] Open
Abstract
The transcription factor USF2 is supposed to have an important role in tumor development. However, the regulatory mechanisms contributing to the function of USF2 are largely unknown. Cyclin-dependent kinase 5 (CDK5) seems to be of importance since high levels of CDK5 were found in different cancers associated with high USF2 expression. Here, we identified USF2 as a phosphorylation target of CDK5. USF2 is phosphorylated by CDK5 at two serine residues, serine 155 and serine 222. Further, phosphorylation of USF2 at these residues was shown to stabilize the protein and to regulate cellular growth and migration. Altogether, these results delineate the importance of the CDK5-USF2 interplay in cancer cells.
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Affiliation(s)
- Tabughang Franklin Chi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland; (T.F.C.); (T.K.)
| | - Tina Horbach
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland; (T.F.C.); (T.K.)
| | - Claudia Götz
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany;
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland; (T.F.C.); (T.K.)
| | - Elitsa Y. Dimova
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland; (T.F.C.); (T.K.)
- Correspondence: ; Tel.: +358-0-294-485-785; Fax: +358-8-553-114
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15
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Tan Y, Chen Y, Du M, Peng Z, Xie P. USF2 inhibits the transcriptional activity of Smurf1 and Smurf2 to promote breast cancer tumorigenesis. Cell Signal 2018; 53:49-58. [PMID: 30244169 DOI: 10.1016/j.cellsig.2018.09.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 09/16/2018] [Accepted: 09/19/2018] [Indexed: 10/28/2022]
Abstract
Smurf1 (Smad ubiquitylation regulatory factor 1) and Smurf2 are negative regulators of the TGF-β (transforming growth factor-β) pathway. The protein stability and ubiquitin E3 activity regulation of Smurfs have been well studied. However, the mechanism of Smurfs expression at the transcriptional level remains uncharacterized. Here, we reported that USF2 (upstream stimulatory factor 2), a basic helix-loop-helix-leucine-zip transcription factor, is necessary for the transcriptional activity of Smurf1 and Smurf2. The 5'-flanking sequences of the Smurfs gene have more than one E-box motifs, and USF2 bounds the Smurfs promoter in vitro and in vivo. Over-expression USF2 inhibited the transcriptional activity of the Smurfs, and Smurfs mRNA was markedly decreased. Therefore, the activity of TGF-β was distinctly enhanced. Furthermore, in human breast cancers, USF2 was abnormally high expressed and correlated with cancer progression. USF2 was specifically inversely correlated with Smurfs in Luminal A subtype breast cancer patients. These findings suggest the mechanism regulation of Smurfs transcriptional activity, and shed new light on the cancer-promoting role of USF2.
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Affiliation(s)
- Yawen Tan
- Department of Breast and Thyroid Surgery, The Second People's Hospital of Shenzhen, Guangdong 518035, China
| | - Yujiao Chen
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory for Cancer Invasion and Metastasis Research, Capital Medical University, Beijing 100069, China
| | - Mengge Du
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory for Cancer Invasion and Metastasis Research, Capital Medical University, Beijing 100069, China
| | - Zhiqiang Peng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center of Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
| | - Ping Xie
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory for Cancer Invasion and Metastasis Research, Capital Medical University, Beijing 100069, China.
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16
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Kim KC, Yun J, Son DJ, Kim JY, Jung JK, Choi JS, Kim YR, Song JK, Kim SY, Kang SK, Shin DH, Roh YS, Han SB, Hong JT. Suppression of metastasis through inhibition of chitinase 3-like 1 expression by miR-125a-3p-mediated up-regulation of USF1. Am J Cancer Res 2018; 8:4409-4428. [PMID: 30214629 PMCID: PMC6134921 DOI: 10.7150/thno.26467] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/15/2018] [Indexed: 12/30/2022] Open
Abstract
Rationale: Chitinase 3-like 1 (Chi3L1) protein is up-regulated in various diseases including solid cancers. According to Genome-Wide Association Study (GWAS)/Online Mendelian Inheritance in Man (OMIM)/Differentially Expressed Gene (DEG) analyses, Chi3L1 is associated with 38 cancers, and more highly associated with cancer compared to other oncogenes such as EGFR, TNFα, etc. However, the mechanisms and pathways by which Chi3L1 is associated with cancer are not clear. In current study, we investigated the role of Chi3L1 in lung metastasis. Methods: We performed the differentially expressed gene analysis to explore the genes which are associated with Chi3L1 using the web-based platform from Biomart. We investigated the metastases in lung tissues of C57BL/6 mice injected with B16F10 melanoma following treatment with Ad-shChi3L1. We also investigated the expression of USF1 and Chi3L1 in Chi3L1 KD mice lung tissues by Western blotting and IHC. We also analyzed lung cancer cells metastases induced by Chi3L1 using migration and cell proliferation assay in human lung cancer cell lines. The involvement of miR-125a-3p in Chi3L1 regulation was determined by miRNA qPCR and luciferase reporter assay. Results: We showed that melanoma metastasis in lung tissues was significantly reduced in Chi3L1 knock-down mice, accompanied by down-regulation of MMP-9, MMP-13, VEGF, and PCNA in Chi3L1 knock-down mice lung tissue, as well as in human lung cancer cell lines. We also found that USF1 was conversely expressed against Chi3L1. USF1 was increased by knock-down of Chi3L1 in mice lung tissues, as well as in human lung cancer cell lines. In addition, knock-down of USF1 increased Chi3L1 levels in addition to augmenting metastasis cell migration and proliferation in mice model, as well as in human cancer cell lines. Moreover, in human lung tumor tissues, the expression of Chi3L1 was increased but USF1 was decreased in a stage-dependent manner. Finally, Chi3L1 expression was strongly regulated by the indirect translational suppressing activity of USF1 through induction of miR-125a-3p, a target of Chi3L1. Conclusion: Metastases in mice lung tissues and human lung cancer cell lines were decreased by KD of Chi3L1. USF1 bound to the Chi3L1 promoter, however, Chi3L1 expression was decreased by USF1, despite USF1 enhancing the transcriptional activity of Chi3L1. We found that USF1 induced miR-125a-3p levels which suppressed Chi3L1 expression. Ultimately, our results suggest that lung metastasis is suppressed by knock-down of Chi3L1 through miR-125a-3p-mediated up-regulation of USF1.
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17
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Castro J, Araya G, Inostroza P, Hidalgo P, González-Ramos R, Sovino H, Boric MA, Fuentes A, Johnson MC. Differential expression of upstream stimulatory factor (USF) 2 variants in eutopic endometria from women with endometriosis: estradiol regulation. Biol Res 2015; 48:56. [PMID: 26453052 PMCID: PMC4600330 DOI: 10.1186/s40659-015-0047-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 09/30/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Endometriosis, pro-inflammatory and invasive benign disease estrogen dependent, abnormally express in endometria the enzyme P450Arom, positively regulated by steroid factor-1 (SF-1). Our objective was to study the nuclear protein contents of upstream stimulating factor 2 (USF2a and USF2b), a positive regulator of SF-1, throughout the menstrual cycle in eutopic endometria from women with and without (control) endometriosis and the involvement of nuclear estrogen receptors (ER) and G-coupled protein estrogen receptor (GPER)-1. RESULTS Upstream stimulating factor 2 protein contents were higher in mid (USF2b) and late (USF2a and USF2b) secretory phase in eutopic endometria from endometriosis than control (p < 0.05). In isolated control epithelial cells incubated with E2 and PGE2, to resemble the endometriosis condition, the data showed: (a) significant increase of USF2a and USF2b nuclear protein contents when treated with E2, PPT (specific agonist for ERα) or G1 (specific agonist for GPER1); (b) no increase in USF2 binding to SF-1 E-Box/DNA consensus sequence in E2-treated cells; (c) USF2 variants protein contents were not modified by PGE2; (d) SF-1 nuclear protein content was significantly higher than basal when treated with PGE2, E2 or G1, stimulation unaffected by ICI (nuclear ER antagonist); and (e) increased (p < 0.05) cytosolic protein contents of P450Arom when treated with PGE2, E2, PPT or G1 compared to basal, effect that was additive with E2 + PGE2 together. Nevertheless, in endometriosis cells, the high USF2, SF-1 and P450Arom protein contents in basal condition were unmodified. CONCLUSION These data strongly suggest that USF2 variants and P450Arom are regulated by E2 through ERα and GPER1, whereas SF-1 through GPER1, visualized by the response of the cells obtained from control endometria, being unaffected the endogenously stimulated cells from endometriosis origin. The lack of E2 stimulation on USF2/SF-1 E-Box/DNA-sequence binding and the absence of PGE2 effect on USF2 variants opposite to the strong induction that they exert on SF1 and P450 proteins suggest different mechanisms and indirect regulations. The sustained USF2 variants protein expression during the secretory phase in eutopic endometria from women with endometriosis may participate in the pathophysiology of this disease strongly associated with infertility and its characteristic endometrial invasion to ectopic sites in the pelvic cavity.
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Affiliation(s)
- Jazmin Castro
- Faculty of Medicine, Institute of Maternal and Child Research, University of Chile, P.O. Box 226-3, Santiago, Chile.
| | - Germán Araya
- Faculty of Medicine, Institute of Maternal and Child Research, University of Chile, P.O. Box 226-3, Santiago, Chile.
| | - Pamela Inostroza
- Faculty of Medicine, Institute of Maternal and Child Research, University of Chile, P.O. Box 226-3, Santiago, Chile.
| | - Paulina Hidalgo
- Faculty of Medicine, Institute of Maternal and Child Research, University of Chile, P.O. Box 226-3, Santiago, Chile.
| | - Reinaldo González-Ramos
- Faculty of Medicine, Institute of Maternal and Child Research, University of Chile, P.O. Box 226-3, Santiago, Chile.
- San Borja-Arriarán Clinical Hospital, Santiago, Chile.
| | - Hugo Sovino
- Faculty of Medicine, Institute of Maternal and Child Research, University of Chile, P.O. Box 226-3, Santiago, Chile.
- San Borja-Arriarán Clinical Hospital, Santiago, Chile.
| | - M Angélica Boric
- Faculty of Medicine, Institute of Maternal and Child Research, University of Chile, P.O. Box 226-3, Santiago, Chile.
| | - Ariel Fuentes
- Faculty of Medicine, Institute of Maternal and Child Research, University of Chile, P.O. Box 226-3, Santiago, Chile.
- San Borja-Arriarán Clinical Hospital, Santiago, Chile.
| | - M Cecilia Johnson
- Faculty of Medicine, Institute of Maternal and Child Research, University of Chile, P.O. Box 226-3, Santiago, Chile.
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18
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Horbach T, Götz C, Kietzmann T, Dimova EY. Protein kinases as switches for the function of upstream stimulatory factors: implications for tissue injury and cancer. Front Pharmacol 2015; 6:3. [PMID: 25741280 PMCID: PMC4332324 DOI: 10.3389/fphar.2015.00003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/07/2015] [Indexed: 01/30/2023] Open
Abstract
The upstream stimulatory factors (USFs) are regulators of important cellular processes. Both USF1 and USF2 are supposed to have major roles in metabolism, tissue protection and tumor development. However, the knowledge about the mechanisms that control the function of USFs, in particular in tissue protection and cancer, is limited. Phosphorylation is a versatile tool to regulate protein functions. Thereby, phosphorylation can positively or negatively affect different aspects of transcription factor function including protein stability, protein-protein interaction, cellular localization, or DNA binding. The present review aims to summarize the current knowledge about the regulation of USFs by direct phosphorylation and the consequences for USF functions in tissue protection and cancer.
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Affiliation(s)
- Tina Horbach
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu , Oulu, Finland ; Department of Chemistry, University of Kaiserslautern , Kaiserslautern, Germany
| | - Claudia Götz
- Medical Biochemistry and Molecular Biology, Saarland University , Homburg, Germany
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu , Oulu, Finland
| | - Elitsa Y Dimova
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu , Oulu, Finland
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19
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Horbach T, Chi TF, Götz C, Sharma S, Juffer AH, Dimova EY, Kietzmann T. GSK3β-dependent phosphorylation alters DNA binding, transactivity and half-life of the transcription factor USF2. PLoS One 2014; 9:e107914. [PMID: 25238393 PMCID: PMC4169611 DOI: 10.1371/journal.pone.0107914] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/21/2014] [Indexed: 12/13/2022] Open
Abstract
The upstream stimulatory factor 2 (USF2) is a regulator of important cellular processes and is supposed to have also a role during tumor development. However, the knowledge about the mechanisms that control the function of USF2 is limited. The data of the current study show that USF2 function is regulated by phosphorylation and identified GSK3β as an USF2-phosphorylating kinase. The phosphorylation sites within USF2 could be mapped to serine 155 and threonine 230. In silico analyses of the 3-dimensional structure revealed that phosphorylation of USF2 by GSK3β converts it to a more open conformation which may influence transactivity, DNA binding and target gene expression. Indeed, experiments with GSK-3β-deficient cells revealed that USF2 transactivity, DNA binding and target gene expression were reduced upon lack of GSK3β. Further, experiments with USF2 variants mimicking GSK3β phosphorylated USF2 in GSK3β-deficient cells showed that phosphorylation of USF2 by GSK3β did not affect cell proliferation but increased cell migration. Together, this study reports a new mechanism by which USF2 may contribute to cancerogenesis.
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Affiliation(s)
- Tina Horbach
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Chemistry, University of Kaiserslautern, Kaiserslautern, Germany
| | - Tabughang Franklin Chi
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Claudia Götz
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Satyan Sharma
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - André H. Juffer
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Elitsa Y. Dimova
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
- * E-mail:
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20
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Zeng L, Sun Y, Xie L, Wei L, Ren Y, Zhao J, Qin W, Mitchelson K, Cheng J. Construction of a novel oligonucleotide array-based transcription factor interaction assay platform and its uses for profiling STAT1 cofactors in mouse fibroblast cells. Proteomics 2013; 13:2377-85. [PMID: 23749757 DOI: 10.1002/pmic.201200521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 03/14/2013] [Accepted: 05/11/2013] [Indexed: 01/12/2023]
Abstract
Here, we describe a novel oligonucleotide array-based transcription factor (TF) interaction assay platform that can directly identify cointeracting TF complexes following binding to their regulatory DNA elements. This platform that combines immuno-coprecipitation technology with our previously reported oligonucleotide array-based TF assay (OATFA), is named targeted immuno-coprecipitation OATFA (TIC-OATFA). We illustrate use of the system to identify interaction partners of STAT1 (signal transducer and activator of transcription proteins 1) in mouse fibroblasts. Several previously known partners of STAT1, as well as new partners, were identified by TIC-OATFA, including the upstream stimulatory factors 1 and 2 (USF1, USF2), nuclear factor of activated T cells, TATA box-binding protein, nuclear factor erythroid-derived 2, nuclear factor-kappa B, and nuclear factor 1. Both USF1 and nuclear factor-kappa B are well known to interact with STAT1, but the other five TFs are previously unreported STAT1 interaction partners. We examined interactions between one new TF, USF2, and STAT1 in detail. USF2 belongs to the group of bHLH-zip transcription factors, which in a number of diseases including cancers, has enhanced activity. In summary, a novel oligonucleotide array-based assay platform was developed and used to study interactions between STAT1 and functional TF binding partners, revealing that USF2 and potentially four other new TFs are partners of STAT1 in an IFN-γ stimulated mouse fibroblast cell line.
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Affiliation(s)
- Lingqin Zeng
- Department of Biomedical Engineering, Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing, China
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Bier C, Knauer SK, Klapthor A, Schweitzer A, Rekik A, Krämer OH, Marschalek R, Stauber RH. Cell-based analysis of structure-function activity of threonine aspartase 1. J Biol Chem 2011; 286:3007-17. [PMID: 21084304 PMCID: PMC3024795 DOI: 10.1074/jbc.m110.161646] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 10/22/2010] [Indexed: 12/24/2022] Open
Abstract
Taspase1 is a threonine protease responsible for cleaving intracellular substrates. As such, (de)regulated Taspase1 function is expected not only to be vital for ordered development but may also be relevant for disease. However, the full repertoires of Taspase1 targets as well as the exact biochemical requirements for its efficient and substrate-specific cleavage are not yet resolved. Also, no cellular assays for this protease are currently available, hampering the exploitation of the (patho)biological relevance of Taspase1. Here, we developed highly efficient cell-based translocation biosensor assays to probe Taspase1 trans-cleavage in vivo. These modular sensors harbor variations of Taspase1 cleavage sites and localize to the cytoplasm. Expression of Taspase1 but not of inactive Taspase1 mutants or of unrelated proteases triggers proteolytic cleavage and nuclear accumulation of the biosensors. Employing our assay combined with scanning mutagenesis, we identified the sequence and spatial requirements for efficient Taspase1 processing in liquid and solid tumor cell lines. Collectively, our results defined an improved Taspase1 consensus recognition sequence, Q(3)(F/I/L/V)(2)D(1)↓G(1)'X(2)'D(3)'D(4)', allowing the first genome-wide bioinformatic identification of the human Taspase1 degradome. Among the 27 most likely Taspase1 targets are cytoplasmic but also nuclear proteins, such as the upstream stimulatory factor 2 (USF2) or the nuclear RNA export factors 2/5 (NXF2/5). Cleavage site recognition and proteolytic processing of selected targets were verified in the context of the biosensor and for the full-length proteins. We provide novel mechanistic insights into the function and bona fide targets of Taspase1 allowing for a focused investigation of the (patho)biological relevance of this type 2 asparaginase.
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Affiliation(s)
- Carolin Bier
- From the Molecular and Cellular Oncology/Mainzer Screening Center, University Hospital of Mainz, Langenbeckstrasse 1, 55101 Mainz
| | - Shirley K. Knauer
- the Institute for Molecular Biology, Centre for Medical Biotechnology, University Duisburg-Essen, Universitätsstrasse, 45117 Essen
| | - Alexander Klapthor
- From the Molecular and Cellular Oncology/Mainzer Screening Center, University Hospital of Mainz, Langenbeckstrasse 1, 55101 Mainz
| | - Andrea Schweitzer
- From the Molecular and Cellular Oncology/Mainzer Screening Center, University Hospital of Mainz, Langenbeckstrasse 1, 55101 Mainz
| | - Alexander Rekik
- From the Molecular and Cellular Oncology/Mainzer Screening Center, University Hospital of Mainz, Langenbeckstrasse 1, 55101 Mainz
| | - Oliver H. Krämer
- the Institute for Biochemistry and Biophysics/Centre for Molecular Biomedicine, Friedrich-Schiller-University Jena, Hans-Knöll-Strasse 2, 07745 Jena, and
| | - Rolf Marschalek
- the Institute for Pharmaceutical Biology/ZAFES, Goethe-University, Max-von Laue-Strasse 9, 60438 Frankfurt/Main, Germany
| | - Roland H. Stauber
- From the Molecular and Cellular Oncology/Mainzer Screening Center, University Hospital of Mainz, Langenbeckstrasse 1, 55101 Mainz
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22
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Bussière FI, Michel V, Mémet S, Avé P, Vivas JR, Huerre M, Touati E. H. pylori-induced promoter hypermethylation downregulates USF1 and USF2 transcription factor gene expression. Cell Microbiol 2010; 12:1124-33. [PMID: 20180799 DOI: 10.1111/j.1462-5822.2010.01457.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Helicobacter pylori infection is associated with the development of gastric adenocarcinoma. Upstream stimulatory factors USF1 and USF2 regulate the transcription of genes related to immune response, cell cycle and cell proliferation. A decrease in their expression is observed in human gastric epithelial cells infected with H. pylori, associated to a lower binding to their DNA E-box recognition site as shown by electrophoretic mobility shift assay. DNA methylation leads to gene silencing. The treatment of cells with 5'-azacytidine, an inhibitor of DNA methylation, restored the USF1 and USF2 gene expression in the presence of infection. Using promoter PCR methylation assay, a DNA hypermethylation was shown in the promoter region of USF1 and USF2 genes, in infected cells. The inhibition of USF1 and USF2 expression by H. pylori and the DNA hypermethylation in their gene promoter region was confirmed in gastric tissues isolated from 12 to 18 months infected mice. Our study demonstrated the involvement of USF1 and USF2 as molecular targets of H. pylori and the key role of DNA methylation in their regulation. These mechanisms occurred in the context of metaplastic lesions, suggesting that alteration of USF1 and USF2 levels could participate in the promotion of neoplastic process during H. pylori infection.
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Schmeier S, MacPherson CR, Essack M, Kaur M, Schaefer U, Suzuki H, Hayashizaki Y, Bajic VB. Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation. BMC Genomics 2009; 10:595. [PMID: 20003307 PMCID: PMC2797535 DOI: 10.1186/1471-2164-10-595] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 12/10/2009] [Indexed: 12/19/2022] Open
Abstract
Background Macrophages are immune cells involved in various biological processes including host defence, homeostasis, differentiation, and organogenesis. Disruption of macrophage biology has been linked to increased pathogen infection, inflammation and malignant diseases. Differential gene expression observed in monocytic differentiation is primarily regulated by interacting transcription factors (TFs). Current research suggests that microRNAs (miRNAs) degrade and repress translation of mRNA, but also may target genes involved in differentiation. We focus on getting insights into the transcriptional circuitry regulating miRNA genes expressed during monocytic differentiation. Results We computationally analysed the transcriptional circuitry of miRNA genes during monocytic differentiation using in vitro time-course expression data for TFs and miRNAs. A set of TF→miRNA associations was derived from predicted TF binding sites in promoter regions of miRNA genes. Time-lagged expression correlation analysis was utilised to evaluate the TF→miRNA associations. Our analysis identified 12 TFs that potentially play a central role in regulating miRNAs throughout the differentiation process. Six of these 12 TFs (ATF2, E2F3, HOXA4, NFE2L1, SP3, and YY1) have not previously been described to be important for monocytic differentiation. The remaining six TFs are CEBPB, CREB1, ELK1, NFE2L2, RUNX1, and USF2. For several miRNAs (miR-21, miR-155, miR-424, and miR-17-92), we show how their inferred transcriptional regulation impacts monocytic differentiation. Conclusions The study demonstrates that miRNAs and their transcriptional regulatory control are integral molecular mechanisms during differentiation. Furthermore, it is the first study to decipher on a large-scale, how miRNAs are controlled by TFs during human monocytic differentiation. Subsequently, we have identified 12 candidate key controllers of miRNAs during this differentiation process.
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Affiliation(s)
- Sebastian Schmeier
- South African National Bioinformatics Institute, University of the Western Cape, Modderdam Road, Bellville, South Africa.
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Sun Q, Yu X, Degraff DJ, Matusik RJ. Upstream stimulatory factor 2, a novel FoxA1-interacting protein, is involved in prostate-specific gene expression. Mol Endocrinol 2009; 23:2038-47. [PMID: 19846536 DOI: 10.1210/me.2009-0092] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The forkhead protein A1 (FoxA1) is critical for the androgenic regulation of prostate-specific promoters. Prostate tissue rescued from FoxA1 knockout mice exhibits abnormal prostate development, typified by the absence of expression of differentiation markers and inability to engage in secretion. Chromatin immunoprecipitation and coimmunoprecipitation studies revealed that FoxA1 is one of the earliest transcription factors that binds to prostate-specific promoters, and that a direct protein-protein interaction occurs between FoxA1 and androgen receptor. Interestingly, evidence of the interaction of FoxA1 with other transcription factors is lacking. The upstream stimulatory factor 2 (USF2), an E-box-binding transcription factor of the basic-helix-loop-helix-leucine-zipper family, binds to a consensus DNA sequence similar to FoxA1. Our in vitro and in vivo studies demonstrate the binding of USF2 to prostate-specific gene promoters including the probasin promoter, spermine-binding protein promoter, and prostate-specific antigen core enhancer. Furthermore, we show a direct physical interaction between FoxA1 and USF2 through the use of immunoprecipitation and glutathione-S-transferase pull-down assays. This interaction is mediated via the forkhead DNA-binding domain of FoxA1 and the DNA-binding domain of USF2. In summary, these data indicate that USF2 is one of the components of the FoxA1/androgen receptor transcriptional protein complex that contributes to the expression of androgen-regulated and prostate-specific genes.
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Affiliation(s)
- Qian Sun
- Department of Cancer Biology, The Vanderbilt Prostate Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, USA.
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Samoylenko A, Dimova EY, Horbach T, Teplyuk N, Immenschuh S, Kietzmann T. Opposite expression of the antioxidant heme oxygenase-1 in primary cells and tumor cells: regulation by interaction of USF-2 and Fra-1. Antioxid Redox Signal 2008; 10:1163-74. [PMID: 18331200 DOI: 10.1089/ars.2007.1968] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Heme oxygenase-1 is the rate-limiting enzyme for the degradation of the prooxidant heme. Previously, we showed that an E-box within the HO-1 promoter is crucial for the regulation of HO-1 expression in primary hepatocytes. Further to investigate the importance of this E-box, we determined the regulatory capacity of the E-box-binding factor USF-2 in primary cells in comparison with transformed cell lines. We found that HO-1 expression was inhibited by USF-2 in primary cells, whereas it was induced in tumor cell lines. Mutation of either the E-box or the AP-1 site within the HO-1 promoter only partially affected the USF-dependent regulation. However, this regulation was dramatically reduced in tumor cells and completely abolished in primary cells transfected with an HO-1 promoter construct containing mutations in both the E-box and the AP-1 site, suggesting that AP-1 factors and USF-2 may act in a cooperative manner. Indeed, protein-protein interaction studies revealed that USF proteins interacted with Fra-1. Further, the USF-dependent HO-1 promoter activity was not detectable with an USF-2 mutant lacking residues of the USF-specific region (USR) or the transactivation domain encoded by exon 4. Together, these data suggest that USF-2 has opposite regulatory roles for HO-1 gene expression in primary cells and tumor cell lines.
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Affiliation(s)
- Anatoly Samoylenko
- Department of Biochemistry, University of Kaiserslautern, Kaiserslautern, Germany
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Paquette J, Bessette B, Ledru E, Deal C. Identification of upstream stimulatory factor binding sites in the human IGFBP3 promoter and potential implication of adjacent single-nucleotide polymorphisms and responsiveness to insulin. Endocrinology 2007; 148:6007-18. [PMID: 17823260 DOI: 10.1210/en.2006-1729] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The actions of IGFs are regulated at various levels. One mechanism involves binding to IGF-binding protein-3 (IGFBP-3) for transport, thus governing bioavailability. IGFBP3 transcription is modulated by many hormones and agents that stimulate or inhibit growth. We have previously shown in pediatric and adult cohorts a correlation between IGFBP-3 serum levels and two single-nucleotide polymorphisms (SNPs) located within the minimal promoter (-202 A/C and -185 C/T). Functionality of these SNPs was further explored in hepatic adenocarcinoma-derived SK-HEP-1 cells using transient transfections of luciferase constructs driven by different haplotypes of the IGFBP3 promoter. Basal luciferase activity revealed a significant haplotype-dependent transcriptional activity (at nucleotides -202 and -185, AC > CC, P < 0.001; AC > CT, P < 0.001; AC > AT, P < 0.001). Insulin treatment produced a similar haplotype dependence of luciferase activity (AC > CC, P = 0.002; AC > CT, P < 0.001; AC > AT, P = 0.011). However, induction ratios (insulin/control) for CC and AT were significantly higher compared with AC and CT (CC > AC, P = 0.03; CC > CT, P = 0.03; AT > AC, P = 0.03; AT > CT, P = 0.04). Gel retardation assays were used to identify upstream stimulatory factor (USF-1 and USF-2) methylation-dependent binding to E-box motifs located between the SNPs. Mutation of the USF binding site resulted in a significant loss of insulin stimulation of luciferase activity in the transfection assay. Chromatin immunoprecipitation with anti-USF-1/-2 showed an enrichment of IGFBP3 promoter in insulin-treated cells compared with unstimulated cells. Bisulfite sequencing of genomic DNA revealed that CpG methylation in the region of USF binding was haplotype dependent. In summary, we report a methylation-dependent USF binding site influencing the basal and insulin-stimulated transcriptional activity of the IGFBP3 promoter.
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Affiliation(s)
- Jean Paquette
- Endocrine Service, Department of Pediatrics, Ste-Justine Hospital, 3175 Côte Ste-Catherine, Montreal, Quebec, Canada
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Jeffery IB, Madden SF, McGettigan PA, Perrière G, Culhane AC, Higgins DG. Integrating transcription factor binding site information with gene expression datasets. Bioinformatics 2006; 23:298-305. [PMID: 17127681 DOI: 10.1093/bioinformatics/btl597] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Microarrays are widely used to measure gene expression differences between sets of biological samples. Many of these differences will be due to differences in the activities of transcription factors. In principle, these differences can be detected by associating motifs in promoters with differences in gene expression levels between the groups. In practice, this is hard to do. RESULTS We combine correspondence analysis, between group analysis and co-inertia analysis to determine which motifs, from a database of promoter motifs, are strongly associated with differences in gene expression levels. Given a database of motifs and gene expression levels from a set of arrays, the method produces a ranked list of motifs associated with any specified split in the arrays. We give an example using the Gene Atlas compendium of gene expression levels for human tissues where we search for motifs that are associated with expression in central nervous system (CNS) or muscle tissues. Most of the motifs that we find are known from previous work to be strongly associated with expression in CNS or muscle. We give a second example using a published prostate cancer dataset where we can simply and clearly find which transcriptional pathways are associated with differences between benign and metastatic samples. AVAILABILITY The source code is freely available upon request from the authors.
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Affiliation(s)
- Ian B Jeffery
- UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
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