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Liu S, Liu Y, Qiu X, Suhail Y, Kshitiz. Tissue-of-origin for cancers determines HIF-1 activation induced phenotypic heterogeneity. Mol Carcinog 2024; 63:834-848. [PMID: 38372346 PMCID: PMC11013563 DOI: 10.1002/mc.23691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 01/02/2024] [Accepted: 01/16/2024] [Indexed: 02/20/2024]
Abstract
Hypoxia-inducible factor-1 (HIF-1) is the master regulator of cellular response to hypoxia, and is activated in many cancers contributing to many steps in the metastatic cascade by acting as a key transcription co-regulator for a large number of downstream genes. Presence of hypoxia within a tumor is spatially nonuniform, and can also by dynamic. Further, although HIF-1 is primarily stabilized and activated by lack of molecular O2, its stability is also affected by other factors present in the tumor microenvironment. HIF-1 also crosstalks with other transcription factors in co-regulating gene expression. Consequently, it is nontrivial to predict the gene expression patterns in cells in response to hypoxia, or HIF-1 activation. Additionally, cancers originating from tissue origins with different basal level of partial oxygen tension may activate HIF-1 at different threshold of hypoxia. We analyzed large published single cell RNAseq data for colorectal, lung, and pancreatic cancers to investigate the phenotypic outcome of HIF-1 activation in cancer cells. We found that cancers from tissues with different partial O2 tension levels exhibit HIF-1 activation at different stages of metastasis, and phenotypically respond differently to HIF-1 activation, likely by contextual co-option of different transcription factors. We experimentally confirmed these predictions by using cell lines representative of colorectal, lung, and pancreatic cancers, finding that while hypoxia enhances growth of colorectal cancer, it induces increased invasion of lung, and pancreatic cancers. Our analysis suggest that HIF-1 activation may act as a rheostat regulating downstream gene expression towards phenotypic outcomes differently in various cancers.
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Affiliation(s)
- Shaofei Liu
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, Connecticut, USA
| | - Yamin Liu
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, Connecticut, USA
| | - Xihua Qiu
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, Connecticut, USA
| | - Yasir Suhail
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, Connecticut, USA
| | - Kshitiz
- Department of Biomedical Engineering, University of Connecticut Health, Farmington, Connecticut, USA
- Center for Cell Analysis and Modeling, University of Connecticut Health, Farmington, Connecticut, USA
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Foxler DE, Bridge KS, Foster JG, Grevitt P, Curry S, Shah KM, Davidson KM, Nagano A, Gadaleta E, Rhys HI, Kennedy PT, Hermida MA, Chang TY, Shaw PE, Reynolds LE, McKay TR, Wang HW, Ribeiro PS, Plevin MJ, Lagos D, Lemoine NR, Rajan P, Graham TA, Chelala C, Hodivala-Dilke KM, Spendlove I, Sharp TV. A HIF-LIMD1 negative feedback mechanism mitigates the pro-tumorigenic effects of hypoxia. EMBO Mol Med 2018; 10:e8304. [PMID: 29930174 PMCID: PMC6079541 DOI: 10.15252/emmm.201708304] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 05/23/2018] [Accepted: 05/28/2018] [Indexed: 12/23/2022] Open
Abstract
The adaptive cellular response to low oxygen tensions is mediated by the hypoxia-inducible factors (HIFs), a family of heterodimeric transcription factors composed of HIF-α and HIF-β subunits. Prolonged HIF expression is a key contributor to cellular transformation, tumorigenesis and metastasis. As such, HIF degradation under hypoxic conditions is an essential homeostatic and tumour-suppressive mechanism. LIMD1 complexes with PHD2 and VHL in physiological oxygen levels (normoxia) to facilitate proteasomal degradation of the HIF-α subunit. Here, we identify LIMD1 as a HIF-1 target gene, which mediates a previously uncharacterised, negative regulatory feedback mechanism for hypoxic HIF-α degradation by modulating PHD2-LIMD1-VHL complex formation. Hypoxic induction of LIMD1 expression results in increased HIF-α protein degradation, inhibiting HIF-1 target gene expression, tumour growth and vascularisation. Furthermore, we report that copy number variation at the LIMD1 locus occurs in 47.1% of lung adenocarcinoma patients, correlates with enhanced expression of a HIF target gene signature and is a negative prognostic indicator. Taken together, our data open a new field of research into the aetiology, diagnosis and prognosis of LIMD1-negative lung cancers.
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Affiliation(s)
- Daniel E Foxler
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Katherine S Bridge
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - John G Foster
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Paul Grevitt
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Sean Curry
- Faculty of Medicine and Life Sciences, University of Nottingham, Nottingham, UK
| | - Kunal M Shah
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Kathryn M Davidson
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Ai Nagano
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Emanuela Gadaleta
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Paul T Kennedy
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Miguel A Hermida
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Ting-Yu Chang
- Institute of Microbiology and Immunology, National Yang Ming University, Taipei City, Taiwan
| | - Peter E Shaw
- Faculty of Medicine and Life Sciences, University of Nottingham, Nottingham, UK
| | - Louise E Reynolds
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Tristan R McKay
- School of Healthcare Science, Manchester Metropolitan University, Manchester, UK
| | - Hsei-Wei Wang
- Institute of Microbiology and Immunology, National Yang Ming University, Taipei City, Taiwan
| | - Paulo S Ribeiro
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Dimitris Lagos
- Centre for Immunology and Infection, Hull York Medical School and Department of Biology, University of York, York, UK
| | - Nicholas R Lemoine
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Prabhakar Rajan
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Trevor A Graham
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Claude Chelala
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Ian Spendlove
- Faculty of Medicine and Life Sciences, University of Nottingham, Nottingham, UK
| | - Tyson V Sharp
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
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Mimura I, Hirakawa Y, Kanki Y, Kushida N, Nakaki R, Suzuki Y, Tanaka T, Aburatani H, Nangaku M. Novel lnc RNA regulated by HIF-1 inhibits apoptotic cell death in the renal tubular epithelial cells under hypoxia. Physiol Rep 2018; 5:5/8/e13203. [PMID: 28420760 PMCID: PMC5408278 DOI: 10.14814/phy2.13203] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 02/15/2017] [Indexed: 12/22/2022] Open
Abstract
Chronic tubulointerstitial hypoxia plays an important role as the final common pathway to end-stage renal disease. HIF-1 (hypoxia-inducible factor-1) is a master transcriptional factor under hypoxia, regulating downstream target genes. Genome-wide analysis of HIF-1 binding sites using high-throughput sequencers has clarified various kinds of downstream targets and made it possible to demonstrate the novel roles of HIF-1. Our aim of this study is to identify novel HIF-1 downstream epigenetic targets which may play important roles in the kidney. Immortalized tubular cell lines (HK2; human kidney-2) and primary cultured cells (RPTEC; renal proximal tubular cell lines) were exposed to 1% hypoxia for 24-72 h. We performed RNA-seq to clarify the expression of mRNA and long non-coding RNA (lncRNA). We also examined ChIP-seq to identify HIF-1 binding sites under hypoxia. RNA-seq identified 44 lncRNAs which are up-regulated under hypoxic condition in both cells. ChIP-seq analysis demonstrated that HIF-1 also binds to the lncRNAs under hypoxia. The expression of novel lncRNA, DARS-AS1 (aspartyl-tRNA synthetase anti-sense 1), is up-regulated only under hypoxia and HIF-1 binds to its promoter region, which includes two hypoxia-responsive elements. Its expression is also up-regulated with cobalt chloride exposure, while it is not under hypoxia when HIF-1 is knocked down by siRNA To clarify the biological roles of DARS-AS1, we measured the activity of caspase 3/7 using anti-sense oligo of DARS-AS1. Knockdown of DARS-AS1 deteriorated apoptotic cell death. In conclusion, we identified the novel lncRNAs regulated by HIF-1 under hypoxia and clarified that DARS-AS1 plays an important role in inhibiting apoptotic cell death in renal tubular cells.
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Affiliation(s)
- Imari Mimura
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yosuke Hirakawa
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuharu Kanki
- Isotope Science Center, The University of Tokyo., Tokyo, Japan
| | - Natsuki Kushida
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryo Nakaki
- Division of GenomeScience, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Tetsuhiro Tanaka
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Division of GenomeScience, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Yang SJ, Park YS, Cho JH, Moon B, An HJ, Lee JY, Xie Z, Wang Y, Pocalyko D, Lee DC, Sohn HA, Kang M, Kim JY, Kim E, Park KC, Kim JA, Yeom YI. Regulation of hypoxia responses by flavin adenine dinucleotide-dependent modulation of HIF-1α protein stability. EMBO J 2017; 36:1011-1028. [PMID: 28279976 DOI: 10.15252/embj.201694408] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 01/24/2017] [Accepted: 01/26/2017] [Indexed: 01/04/2023] Open
Abstract
Oxygen deprivation induces a range of cellular adaptive responses that enable to drive cancer progression. Here, we report that lysine-specific demethylase 1 (LSD1) upregulates hypoxia responses by demethylating RACK1 protein, a component of hypoxia-inducible factor (HIF) ubiquitination machinery, and consequently suppressing the oxygen-independent degradation of HIF-1α. This ability of LSD1 is attenuated during prolonged hypoxia, with a decrease in the cellular level of flavin adenine dinucleotide (FAD), a metabolic cofactor of LSD1, causing HIF-1α downregulation in later stages of hypoxia. Exogenously provided FAD restores HIF-1α stability, indicating a rate-limiting role for FAD in LSD1-mediated HIF-1α regulation. Transcriptomic analyses of patient tissues show that the HIF-1 signature is highly correlated with the expression of LSD1 target genes as well as the enzymes of FAD biosynthetic pathway in triple-negative breast cancers, reflecting the significance of FAD-dependent LSD1 activity in cancer progression. Together, our findings provide a new insight into HIF-mediated hypoxia response regulation by coupling the FAD dependence of LSD1 activity to the regulation of HIF-1α stability.
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Affiliation(s)
- Suk-Jin Yang
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Young Soo Park
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, South Korea
| | - Jung Hee Cho
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Byul Moon
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, South Korea
| | - Hyun-Jung An
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Ju Yeon Lee
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, South Korea
| | - Zhi Xie
- Pfizer Global Research and Development, San Diego, CA, USA
| | - Yuli Wang
- Pfizer Global Research and Development, San Diego, CA, USA
| | - David Pocalyko
- Pfizer Global Research and Development, San Diego, CA, USA
| | - Dong Chul Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Hyun Ahm Sohn
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Minho Kang
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jin Young Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, South Korea
| | - Eunhee Kim
- Department of Bioscience and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Kyung Chan Park
- Department of Functional Genomics, University of Science and Technology, Daejeon, South Korea .,Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jung-Ae Kim
- Department of Functional Genomics, University of Science and Technology, Daejeon, South Korea .,Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Young Il Yeom
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea .,Department of Functional Genomics, University of Science and Technology, Daejeon, South Korea
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