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Ren R, Ding S, Ma K, Jiang Y, Wang Y, Chen J, Wang Y, Kou Y, Fan X, Zhu X, Qin L, Qiu C, Simons M, Wei X, Yu L. SUMOylation Fine-Tunes Endothelial HEY1 in the Regulation of Angiogenesis. Circ Res 2024; 134:203-222. [PMID: 38166414 PMCID: PMC10872267 DOI: 10.1161/circresaha.123.323398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 12/15/2023] [Indexed: 01/04/2024]
Abstract
BACKGROUND Angiogenesis, which plays a critical role in embryonic development and tissue repair, is controlled by a set of angiogenic signaling pathways. As a TF (transcription factor) belonging to the basic helix-loop-helix family, HEY (hairy/enhancer of split related with YRPW motif)-1 (YRPW motif, abbreviation of 4 highly conserved amino acids in the motif) has been identified as a key player in developmental angiogenesis. However, the precise mechanisms underlying HEY1's actions in angiogenesis remain largely unknown. Our previous studies have suggested a potential role for posttranslational SUMOylation in the dynamic regulation of vascular development and organization. METHODS Immunoprecipitation, mass spectrometry, and bioinformatics analysis were used to determine the biochemical characteristics of HEY1 SUMOylation. The promoter-binding capability of HEY1 was determined by chromatin immunoprecipitation, dual luciferase, and electrophoretic mobility shift assays. The dimerization pattern of HEY1 was determined by coimmunoprecipitation. The angiogenic capabilities of endothelial cells were assessed by CCK-8 (cell counting kit-8), 5-ethynyl-2-deoxyuridine staining, wound healing, transwell, and sprouting assays. Embryonic and postnatal vascular growth in mouse tissues, matrigel plug assay, cutaneous wound healing model, oxygen-induced retinopathy model, and tumor angiogenesis model were used to investigate the angiogenesis in vivo. RESULTS We identified intrinsic endothelial HEY1 SUMOylation at conserved lysines by TRIM28 (tripartite motif containing 28) as the unique E3 ligase. Functionally, SUMOylation facilitated HEY1-mediated suppression of angiogenic RTK (receptor tyrosine kinase) signaling and angiogenesis in primary human endothelial cells and mice with endothelial cell-specific expression of wild-type HEY1 or a SUMOylation-deficient HEY1 mutant. Mechanistically, SUMOylation facilitates HEY1 homodimer formation, which in turn preserves HEY1's DNA-binding capability via recognition of E-box promoter elements. Therefore, SUMOylation maintains HEY1's function as a repressive TF controlling numerous angiogenic genes, including RTKs and Notch pathway components. Proangiogenic stimuli induce HEY1 deSUMOylation, leading to heterodimerization of HEY1 with HES (hairy and enhancer of split)-1, which results in ineffective DNA binding and loss of HEY1's angiogenesis-suppressive activity. CONCLUSIONS Our findings demonstrate that reversible HEY1 SUMOylation is a molecular mechanism that coordinates endothelial angiogenic signaling and angiogenesis, both in physiological and pathological milieus, by fine-tuning the transcriptional activity of HEY1. Specifically, SUMOylation facilitates the formation of the HEY1 transcriptional complex and enhances its DNA-binding capability in endothelial cells.
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Affiliation(s)
- Ruizhe Ren
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province of Sir Run Run Shaw Hospital, MOE Laboratory of Biosystems Homeostasis & Protection of College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center and Joint Research Centre for Engineering Biology, Zhejiang University, Zhejiang, China
| | - Sha Ding
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province of Sir Run Run Shaw Hospital, MOE Laboratory of Biosystems Homeostasis & Protection of College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center and Joint Research Centre for Engineering Biology, Zhejiang University, Zhejiang, China
| | - Kefan Ma
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province of Sir Run Run Shaw Hospital, MOE Laboratory of Biosystems Homeostasis & Protection of College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center and Joint Research Centre for Engineering Biology, Zhejiang University, Zhejiang, China
| | - Yuanqing Jiang
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province of Sir Run Run Shaw Hospital, MOE Laboratory of Biosystems Homeostasis & Protection of College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center and Joint Research Centre for Engineering Biology, Zhejiang University, Zhejiang, China
| | - Yiran Wang
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province of Sir Run Run Shaw Hospital, MOE Laboratory of Biosystems Homeostasis & Protection of College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center and Joint Research Centre for Engineering Biology, Zhejiang University, Zhejiang, China
| | - Junbo Chen
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province of Sir Run Run Shaw Hospital, MOE Laboratory of Biosystems Homeostasis & Protection of College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center and Joint Research Centre for Engineering Biology, Zhejiang University, Zhejiang, China
| | - Yunyun Wang
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province of Sir Run Run Shaw Hospital, MOE Laboratory of Biosystems Homeostasis & Protection of College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center and Joint Research Centre for Engineering Biology, Zhejiang University, Zhejiang, China
| | - Yaohui Kou
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province of Sir Run Run Shaw Hospital, MOE Laboratory of Biosystems Homeostasis & Protection of College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center and Joint Research Centre for Engineering Biology, Zhejiang University, Zhejiang, China
| | - Xiao Fan
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province of Sir Run Run Shaw Hospital, MOE Laboratory of Biosystems Homeostasis & Protection of College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaolong Zhu
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province of Sir Run Run Shaw Hospital, MOE Laboratory of Biosystems Homeostasis & Protection of College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center and Joint Research Centre for Engineering Biology, Zhejiang University, Zhejiang, China
| | - Lingfeng Qin
- Department of Surgery, Program in Vascular Biology and Therapeutics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Cong Qiu
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province of Sir Run Run Shaw Hospital, MOE Laboratory of Biosystems Homeostasis & Protection of College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center and Joint Research Centre for Engineering Biology, Zhejiang University, Zhejiang, China
| | - Michael Simons
- Yale Cardiovascular Research Center, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Xiyang Wei
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province of Sir Run Run Shaw Hospital, MOE Laboratory of Biosystems Homeostasis & Protection of College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Luyang Yu
- Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province of Sir Run Run Shaw Hospital, MOE Laboratory of Biosystems Homeostasis & Protection of College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center and Joint Research Centre for Engineering Biology, Zhejiang University, Zhejiang, China
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Patton BK, Madadi S, Briley SM, Ahmed AA, Pangas SA. Sumoylation regulates functional properties of the oocyte transcription factors SOHLH1 and NOBOX. FASEB J 2023; 37:e22747. [PMID: 36607631 PMCID: PMC10129296 DOI: 10.1096/fj.202201481r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/02/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023]
Abstract
SOHLH1 and NOBOX are oocyte-expressed transcription factors with critical roles in ovary development and fertility. In mice, Sohlh1 and Nobox are essential for fertility through their regulation of the oocyte transcriptional network and cross-talk to somatic cells. Sumoylation is a posttranslational modification that regulates transcription factor function, and we previously showed that mouse oocytes deficient for sumoylation had an altered transcriptional landscape that included significant changes in NOBOX target genes. Here, we show that mouse SOHLH1 is modified by SUMO2/3 at lysine 345 and mutation of this residue alters SOHLH1 nuclear to cytoplasmic localization. In NOBOX, we identify a non-consensus SUMO site, K97, that eliminates NOBOX mono-SUMO2/3 conjugation, while a point mutation at K125 had no effect on NOBOX sumoylation. However, NOBOXK97R/K125R double mutants showed loss of mono-SUMO2/3 and altered higher molecular weight modifications, suggesting cooperation between these lysine's. NOBOXK97R and NOBOXK97R/K125R differentially regulated NOBOX promoter targets, with increased activity on the Gdf9 promoter, but no effect on the Pou5f1 promoter. These data implicate sumoylation as a novel regulatory mechanism for SOHLH1 and NOBOX, which may prove useful in refining their roles during oogenesis as well as their function during reprogramming to generate de novo germ cells.
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Affiliation(s)
- Bethany K. Patton
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Surabhi Madadi
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030
- Rice University, Houston, TX 77005
| | - Shawn M. Briley
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Avery A. Ahmed
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, TX 77030
| | - Stephanie A. Pangas
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX 77030
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3
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Tang J, Baba M. MiT/TFE Family Renal Cell Carcinoma. Genes (Basel) 2023; 14:genes14010151. [PMID: 36672892 PMCID: PMC9859458 DOI: 10.3390/genes14010151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
The microphthalmia-associated transcription factor/transcription factor E (MiT/TFE) family of transcription factors are evolutionarily conserved, basic helix-loop-helix leucine zipper (bHLH-Zip) transcription factors, consisting of MITF, TFEB, TFE3, and TFEC. MiT/TFE proteins, with the exception of TFEC, are involved in the development of renal cell carcinoma (RCC). Most of the MiT/TFE transcription factor alterations seen in sporadic RCC cases of MiT family translocation renal cell carcinoma (tRCC) are chimeric proteins generated by chromosomal rearrangements. These chimeric MiT/TFE proteins retain the bHLH-Zip structures and act as oncogenic transcription factors. The germline variant of MITF p.E318K has been reported as a risk factor for RCC. E 318 is present at the SUMOylation consensus site of MITF. The p.E318K variant abrogates SUMOylation on K 316, which results in alteration of MITF transcriptional activity. Only a few cases of MITF p.E318K RCC have been reported, and their clinical features have not yet been fully described. It would be important for clinicians to recognize MITF p.E318K RCC and consider MITF germline testing for undiagnosed familial RCC cases. This review outlines the involvement of the MiT/TFE transcription factors in RCC, both in sporadic and hereditary cases. Further elucidation of the molecular function of the MiT/TFE family is necessary for better diagnosis and treatment of these rare diseases.
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Wang K, Xiong J, Lu Y, Wang L, Tian T. SENP1-KLF4 signalling regulates LPS-induced macrophage M1 polarization. FEBS J 2023; 290:209-224. [PMID: 35942612 DOI: 10.1111/febs.16589] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 03/19/2022] [Accepted: 08/08/2022] [Indexed: 01/14/2023]
Abstract
Macrophages are very important immune cells and play critical roles in tumour immunity. Macrophage subtypes can be divided into classical polarization (M1 macrophages) and alternative polarization (M2 macrophages) under different microenvironments. Krüppel-like factor 4 (KLF4) is an essential transcription factor for macrophage polarization. Our previous study has shown that KLF4 SUMOylation plays an important role in macrophage M2 polarization. In the present study, small ubiquitin-like modifier (SUMO) specific peptidase (SENP)1 was identified as a specific protease for KLF4 de-SUMOylation, with the SENP1-KLF4 axis playing a vital role in M1 macrophage polarization by affecting the nuclear factor kappa B signalling pathway. Additionally, the activity of tumour cells was weakened by KLF4 SUMOylation deficient macrophages. Hence, the SENP1-KLF4 axis is considered to play a crucial role in regulating lipopolysaccharide-induced macrophage M1 polarization, thereby affecting the activity of tumour cells. Therefore, the SENP1-KLF4 axis has therapeutic potential as a target in cancer therapy.
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Affiliation(s)
- Kezhou Wang
- Department of Pathology, Xinhua Hospital, Affiliated to Medicine School of Shanghai Jiaotong University, Shanghai, China
| | - Jie Xiong
- Department of Gastroenterology and Hepatology, Tongji Hospital, Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Yiwen Lu
- Department of Laboratory Medicine, Xinhua Hospital, Affiliated to Medicine School of Shanghai Jiaotong University, Shanghai, China
| | - Lifeng Wang
- Department of Pathology, Xinhua Hospital, Affiliated to Medicine School of Shanghai Jiaotong University, Shanghai, China
| | - Tian Tian
- Department of Ophthalmology, Xinhua Hospital, Affiliated to Medicine School of Shanghai Jiaotong University, Shanghai, China
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5
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Hegde S, Sreejan A, Gadgil CJ, Ratnaparkhi GS. SUMOylation of Dorsal attenuates Toll/NF-κB signaling. Genetics 2022; 221:iyac081. [PMID: 35567478 PMCID: PMC9252280 DOI: 10.1093/genetics/iyac081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/03/2022] [Indexed: 11/29/2022] Open
Abstract
In Drosophila, Toll/NF-κB signaling plays key roles in both animal development and in host defense. The activation, intensity, and kinetics of Toll signaling are regulated by posttranslational modifications such as phosphorylation, SUMOylation, or ubiquitination that target multiple proteins in the Toll/NF-κB cascade. Here, we have generated a CRISPR-Cas9 edited Dorsal (DL) variant that is SUMO conjugation resistant. Intriguingly, embryos laid by dlSCR mothers overcome dl haploinsufficiency and complete the developmental program. This ability appears to be a result of higher transcriptional activation by DLSCR. In contrast, SUMOylation dampens DL transcriptional activation, ultimately conferring robustness to the dorso-ventral program. In the larval immune response, dlSCR animals show an increase in crystal cell numbers, stronger activation of humoral defense genes, and high cactus levels. A mathematical model that evaluates the contribution of the small fraction of SUMOylated DL (1-5%) suggests that it acts to block transcriptional activation, which is driven primarily by DL that is not SUMO conjugated. Our findings define SUMO conjugation as an important regulator of the Toll signaling cascade, in both development and host defense. Our results broadly suggest that SUMO attenuates DL at the level of transcriptional activation. Furthermore, we hypothesize that SUMO conjugation of DL may be part of a Ubc9-dependent mechanism that restrains Toll/NF-κB signaling.
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Affiliation(s)
- Sushmitha Hegde
- Biology, Indian Institute of Science Education & Research, Pune 411008, India
| | - Ashley Sreejan
- Chemical Engineering and Process Development Division, CSIR—National Chemical Laboratory, Pune 411008, India
| | - Chetan J Gadgil
- Chemical Engineering and Process Development Division, CSIR—National Chemical Laboratory, Pune 411008, India
- CSIR—Institute of Genomics and Integrative Biology, New Delhi 110020, India
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Hua D, Wu X. Small-molecule inhibitors targeting small ubiquitin-like modifier pathway for the treatment of cancers and other diseases. Eur J Med Chem 2022; 233:114227. [PMID: 35247754 DOI: 10.1016/j.ejmech.2022.114227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/12/2022] [Accepted: 02/21/2022] [Indexed: 02/07/2023]
Abstract
SUMOylation is a key post-translational modification that involves the covalent attachment of small ubiquitin-like modifier (SUMO) to the lysine residues of target proteins. The well-balanced SUMOylation is essential for normal cellular behaviors, while disturbance of SUMOylation is associated with various cancers and other diseases. Herein, we summarize the structures and biological functions of proteins involved in the SUMOylation process, their dysregulation in human diseases, and the discovery of small-molecular inhibitors targeting this pathway. In addition, we highlight the emerging trends in this field.
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Affiliation(s)
- Dexiang Hua
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Xiaoxing Wu
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
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7
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Baig MS, Dou Y, Bergey BG, Bahar R, Burgener JM, Moallem M, McNeil JB, Akhter A, Burke GL, Sri Theivakadadcham VS, Richard P, D’Amours D, Rosonina E. Dynamic sumoylation of promoter-bound general transcription factors facilitates transcription by RNA polymerase II. PLoS Genet 2021; 17:e1009828. [PMID: 34587155 PMCID: PMC8505008 DOI: 10.1371/journal.pgen.1009828] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/11/2021] [Accepted: 09/15/2021] [Indexed: 11/18/2022] Open
Abstract
Transcription-related proteins are frequently identified as targets of sumoylation, including multiple subunits of the RNA polymerase II (RNAPII) general transcription factors (GTFs). However, it is not known how sumoylation affects GTFs or whether they are sumoylated when they assemble at promoters to facilitate RNAPII recruitment and transcription initiation. To explore how sumoylation can regulate transcription genome-wide, we performed SUMO ChIP-seq in yeast and found, in agreement with others, that most chromatin-associated sumoylated proteins are detected at genes encoding tRNAs and ribosomal proteins (RPGs). However, we also detected 147 robust SUMO peaks at promoters of non-ribosomal protein-coding genes (non-RPGs), indicating that sumoylation also regulates this gene class. Importantly, SUMO peaks at non-RPGs align specifically with binding sites of GTFs, but not other promoter-associated proteins, indicating that it is GTFs specifically that are sumoylated there. Predominantly, non-RPGs with SUMO peaks are among the most highly transcribed, have high levels of TFIIF, and show reduced RNAPII levels when cellular sumoylation is impaired, linking sumoylation with elevated transcription. However, detection of promoter-associated SUMO by ChIP might be limited to sites with high levels of substrate GTFs, and promoter-associated sumoylation at non-RPGs may actually be far more widespread than we detected. Among GTFs, we found that TFIIF is a major target of sumoylation, specifically at lysines 60/61 of its Tfg1 subunit, and elevating Tfg1 sumoylation resulted in decreased interaction of TFIIF with RNAPII. Interestingly, both reducing promoter-associated sumoylation, in a sumoylation-deficient Tfg1-K60/61R mutant strain, and elevating promoter-associated SUMO levels, by constitutively tethering SUMO to Tfg1, resulted in reduced RNAPII occupancy at non-RPGs. This implies that dynamic GTF sumoylation at non-RPG promoters, not simply the presence or absence of SUMO, is important for maintaining elevated transcription. Together, our findings reveal a novel mechanism of regulating the basal transcription machinery through sumoylation of promoter-bound GTFs. Six general transcription factors (GTFs) assemble at promoters of protein-coding genes to enable recruitment of RNA polymerase II (RNAPII) and facilitate transcription initiation, but little is known about how they are regulated once promoter-bound. Here, we demonstrate that, in budding yeast, some components of GTFs are post-translationally modified by the SUMO peptide specifically when they are assembled at promoters. We determined that the large subunit of TFIIF, Tgf1, is the major target of sumoylation among GTFs and that increasing Tfg1 sumoylation reduces the interaction of TFIIF with RNAPII. Consistent with this, we found that increasing levels of SUMO at promoters of some protein-coding genes, by permanently attaching SUMO to Tfg1, resulted in reduced RNAPII levels associated with those genes. On the other hand, reducing promoter-associated sumoylation, by mutating SUMO-modified residues on Tfg1, also reduced RNAPII occupancy levels. Explaining these apparently contradictory findings, we propose that dynamic sumoylation of promoter-bound GTFs, not merely the presence or absence of SUMO, is important for facilitating rearrangements of promoter-bound GTF components that enhance transcription. Together, our data reveal a novel level of regulating the basal transcription machinery through SUMO modification at promoters of protein-coding genes.
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Affiliation(s)
- Mohammad S. Baig
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Yimo Dou
- Department of Biology, York University, Toronto, Ontario, Canada
| | | | - Russell Bahar
- Department of Biology, York University, Toronto, Ontario, Canada
| | | | - Marjan Moallem
- Department of Biology, York University, Toronto, Ontario, Canada
| | - James B. McNeil
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Akhi Akhter
- Department of Biology, York University, Toronto, Ontario, Canada
| | | | | | - Patricia Richard
- Stellate Therapeutics, New York, New York, United States of America
| | - Damien D’Amours
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Emanuel Rosonina
- Department of Biology, York University, Toronto, Ontario, Canada
- * E-mail:
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Paakinaho V, Lempiäinen JK, Sigismondo G, Niskanen EA, Malinen M, Jääskeläinen T, Varjosalo M, Krijgsveld J, Palvimo J. SUMOylation regulates the protein network and chromatin accessibility at glucocorticoid receptor-binding sites. Nucleic Acids Res 2021; 49:1951-1971. [PMID: 33524141 PMCID: PMC7913686 DOI: 10.1093/nar/gkab032] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 12/13/2022] Open
Abstract
Glucocorticoid receptor (GR) is an essential transcription factor (TF), controlling metabolism, development and immune responses. SUMOylation regulates chromatin occupancy and target gene expression of GR in a locus-selective manner, but the mechanism of regulation has remained elusive. Here, we identify the protein network around chromatin-bound GR by using selective isolation of chromatin-associated proteins and show that the network is affected by receptor SUMOylation, with several nuclear receptor coregulators and chromatin modifiers preferring interaction with SUMOylation-deficient GR and proteins implicated in transcriptional repression preferring interaction with SUMOylation-competent GR. This difference is reflected in our chromatin binding, chromatin accessibility and gene expression data, showing that the SUMOylation-deficient GR is more potent in binding and opening chromatin at glucocorticoid-regulated enhancers and inducing expression of target loci. Blockage of SUMOylation by a SUMO-activating enzyme inhibitor (ML-792) phenocopied to a large extent the consequences of GR SUMOylation deficiency on chromatin binding and target gene expression. Our results thus show that SUMOylation modulates the specificity of GR by regulating its chromatin protein network and accessibility at GR-bound enhancers. We speculate that many other SUMOylated TFs utilize a similar regulatory mechanism.
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Affiliation(s)
- Ville Paakinaho
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | | | | | - Einari A Niskanen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Marjo Malinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Tiina Jääskeläinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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Boulanger M, Chakraborty M, Tempé D, Piechaczyk M, Bossis G. SUMO and Transcriptional Regulation: The Lessons of Large-Scale Proteomic, Modifomic and Genomic Studies. Molecules 2021; 26:molecules26040828. [PMID: 33562565 PMCID: PMC7915335 DOI: 10.3390/molecules26040828] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
One major role of the eukaryotic peptidic post-translational modifier SUMO in the cell is transcriptional control. This occurs via modification of virtually all classes of transcriptional actors, which include transcription factors, transcriptional coregulators, diverse chromatin components, as well as Pol I-, Pol II- and Pol III transcriptional machineries and their regulators. For many years, the role of SUMOylation has essentially been studied on individual proteins, or small groups of proteins, principally dealing with Pol II-mediated transcription. This provided only a fragmentary view of how SUMOylation controls transcription. The recent advent of large-scale proteomic, modifomic and genomic studies has however considerably refined our perception of the part played by SUMO in gene expression control. We review here these developments and the new concepts they are at the origin of, together with the limitations of our knowledge. How they illuminate the SUMO-dependent transcriptional mechanisms that have been characterized thus far and how they impact our view of SUMO-dependent chromatin organization are also considered.
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Affiliation(s)
- Mathias Boulanger
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Mehuli Chakraborty
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Denis Tempé
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Marc Piechaczyk
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
| | - Guillaume Bossis
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
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Kmiecik SW, Drzewicka K, Melchior F, Mayer MP. Heat shock transcription factor 1 is SUMOylated in the activated trimeric state. J Biol Chem 2021; 296:100324. [PMID: 33493517 PMCID: PMC7949154 DOI: 10.1016/j.jbc.2021.100324] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/23/2020] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
The heat shock response is a transcriptional program of organisms to counteract an imbalance in protein homeostasis. It is orchestrated in all eukaryotic cells by heat shock transcription factor 1 (Hsf1). Despite very intensive research, the intricacies of the Hsf1 activation-attenuation cycle remain elusive at a molecular level. Post-translational modifications belong to one of the key mechanisms proposed to adapt the Hsf1 activity to the needs of individual cells, and phosphorylation of Hsf1 at multiple sites has attracted much attention. According to cell biological and proteomics data, Hsf1 is also modified by small ubiquitin-like modifier (SUMO) at several sites. How SUMOylation affects Hsf1 activity at a molecular level is still unclear. Here, we analyzed Hsf1 SUMOylation in vitro with purified components to address questions that could not be answered in cell culture models. In vitro Hsf1 is primarily conjugated at lysine 298 with a single SUMO, though we did detect low-level SUMOylation at other sites. Different SUMO E3 ligases such as protein inhibitor of activated STAT 4 enhanced the efficiency of in vitro modification but did not alter SUMO site preferences. We provide evidence that Hsf1 trimerization and phosphorylation at serines 303 and 307 increases SUMOylation efficiency, suggesting that Hsf1 is SUMOylated in its activated state. Hsf1 can be SUMOylated when DNA bound, and SUMOylation of Hsf1 does neither alter DNA-binding affinity nor affects heat shock cognate 71kDa protein (HSPA8)+DnaJ homolog subfamily B member 1-mediated monomerization of Hsf1 trimers and concomitant dislocation from DNA. We propose that SUMOylation acts at the transcription level of the heat shock response.
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Affiliation(s)
- Szymon W Kmiecik
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, Heidelberg, Germany
| | - Katarzyna Drzewicka
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, Heidelberg, Germany
| | - Frauke Melchior
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, Heidelberg, Germany
| | - Matthias P Mayer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, Heidelberg, Germany.
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11
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Barysch SV, Stankovic-Valentin N, Miedema T, Karaca S, Doppel J, Nait Achour T, Vasudeva A, Wolf L, Sticht C, Urlaub H, Melchior F. Transient deSUMOylation of IRF2BP proteins controls early transcription in EGFR signaling. EMBO Rep 2021; 22:e49651. [PMID: 33480129 PMCID: PMC7926235 DOI: 10.15252/embr.201949651] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/30/2022] Open
Abstract
Molecular switches are essential modules in signaling networks and transcriptional reprogramming. Here, we describe a role for small ubiquitin‐related modifier SUMO as a molecular switch in epidermal growth factor receptor (EGFR) signaling. Using quantitative mass spectrometry, we compare the endogenous SUMO proteomes of HeLa cells before and after EGF stimulation. Thereby, we identify a small group of transcriptional coregulators including IRF2BP1, IRF2BP2, and IRF2BPL as novel players in EGFR signaling. Comparison of cells expressing wild type or SUMOylation‐deficient IRF2BP1 indicates that transient deSUMOylation of IRF2BP proteins is important for appropriate expression of immediate early genes including dual specificity phosphatase 1 (DUSP1, MKP‐1) and the transcription factor ATF3. We find that IRF2BP1 is a repressor, whose transient deSUMOylation on the DUSP1 promoter allows—and whose timely reSUMOylation restricts—DUSP1 transcription. Our work thus provides a paradigm how comparative SUMO proteome analyses serve to reveal novel regulators in signal transduction and transcription.
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Affiliation(s)
- Sina V Barysch
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg University, Heidelberg, Germany
| | - Nicolas Stankovic-Valentin
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg University, Heidelberg, Germany
| | - Tim Miedema
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg University, Heidelberg, Germany
| | - Samir Karaca
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Judith Doppel
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg University, Heidelberg, Germany
| | - Thiziri Nait Achour
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg University, Heidelberg, Germany
| | - Aarushi Vasudeva
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg University, Heidelberg, Germany
| | - Lucie Wolf
- German Cancer Research Center (DKFZ), Division of Signalling and Functional Genomics, Heidelberg, Germany.,BioQuant & Department for Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Carsten Sticht
- Center of Medical Research, Bioinformatic and Statistic, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Frauke Melchior
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg University, Heidelberg, Germany
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12
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Kroonen JS, Vertegaal ACO. Targeting SUMO Signaling to Wrestle Cancer. Trends Cancer 2020; 7:496-510. [PMID: 33353838 DOI: 10.1016/j.trecan.2020.11.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 01/16/2023]
Abstract
The small ubiquitin-like modifier (SUMO) signaling cascade is critical for gene expression, genome integrity, and cell cycle progression. In this review, we discuss the important role SUMO may play in cancer and how to target SUMO signaling. Recently developed small molecule inhibitors enable therapeutic targeting of the SUMOylation pathway. Blocking SUMOylation not only leads to reduced cancer cell proliferation but also to an increased antitumor immune response by stimulating interferon (IFN) signaling, indicating that SUMOylation inhibitors have a dual mode of action that can be employed in the fight against cancer. The search for tumor types that can be treated with SUMOylation inhibitors is ongoing. Employing SUMO conjugation inhibitory drugs in the years to come has potential as a new therapeutic strategy.
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Affiliation(s)
- Jessie S Kroonen
- Department of Cell and Chemical Biology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands.
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13
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Wang D, Ruan X, Liu X, Xue Y, Shao L, Yang C, Zhu L, Yang Y, Li Z, Yu B, Feng T, Liu Y. SUMOylation of PUM2 promotes the vasculogenic mimicry of glioma cells via regulating CEBPD. Clin Transl Med 2020; 10:e168. [PMID: 32997416 PMCID: PMC7507322 DOI: 10.1002/ctm2.168] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/30/2020] [Accepted: 08/20/2020] [Indexed: 02/05/2023] Open
Abstract
Glioma is the most common form of primary central nervous malignant tumors. Vasculogenic mimicry (VM) is a blood supply channel that is different from endothelial blood vessels in glioma. VM is related to tumor invasion and metastasis. Therefore, it plays an important role to target therapy for glioma VM. Our experimental results showed abnormal expression of UBE2I, PUM2, CEBPD, and DSG2 in glioma cells. The Co-IP and Immunofluorescence staining were used to detect that PUM2 can be modified by SUMO2/3. The interaction between PUM2 and CEBPD mRNA was detected by the RIP assays. The interaction between transcription factor CEBPD and promoter region of DSG2 was detected by the ChIP assays and luciferase assays. The capacity for migration in glioma cells was observed by the laser holographic microscope. The capacity for invasion in glioma cells was detected by Transwell method. The VM in glioma cells was detected by three-dimensional cell culture method. The experimental results found that the upregulation of UBE2I in glioma tissues and cells promotes the SUMOylation of PUM2, which decreases not only the stability of PUM2 protein but also decreases the inhibitory effect of PUM2 on CEBPD mRNA. The upregulation of CEBPD promotes the binding to the upstream promoter region of DSG2 gene, further upregulates the expression of DSG2, and finally promotes the development of glioma VM. In conclusion, this study found that the UBE2I/PUM2/CEBPD/DSG2 played crucial roles in regulating glioma VM. It also provides potential targets and alternative strategies for combined treatment of glioma.
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Affiliation(s)
- Di Wang
- Department of NeurosurgeryShengjing Hospital of China Medical UniversityShenyangChina
- Liaoning Clinical Medical Research Center in Nervous System DiseaseShenyangChina
- Key Laboratory of Neuro‐oncology in Liaoning ProvinceShenyangChina
| | - Xuelei Ruan
- Department of Neurobiology, School of life SciencesChina Medical UniversityShenyangChina
- Key Laboratory of Cell Biology, Ministry of Public Health of ChinaChina Medical UniversityShenyangChina
- Key Laboratory of Medical Cell Biology, Ministry of Education of ChinaChina Medical UniversityShenyangChina
| | - Xiaobai Liu
- Department of NeurosurgeryShengjing Hospital of China Medical UniversityShenyangChina
- Liaoning Clinical Medical Research Center in Nervous System DiseaseShenyangChina
- Key Laboratory of Neuro‐oncology in Liaoning ProvinceShenyangChina
| | - Yixue Xue
- Department of Neurobiology, School of life SciencesChina Medical UniversityShenyangChina
- Key Laboratory of Cell Biology, Ministry of Public Health of ChinaChina Medical UniversityShenyangChina
- Key Laboratory of Medical Cell Biology, Ministry of Education of ChinaChina Medical UniversityShenyangChina
| | - Lianqi Shao
- Department of Neurobiology, School of life SciencesChina Medical UniversityShenyangChina
- Key Laboratory of Cell Biology, Ministry of Public Health of ChinaChina Medical UniversityShenyangChina
- Key Laboratory of Medical Cell Biology, Ministry of Education of ChinaChina Medical UniversityShenyangChina
| | - Chunqing Yang
- Department of NeurosurgeryShengjing Hospital of China Medical UniversityShenyangChina
- Liaoning Clinical Medical Research Center in Nervous System DiseaseShenyangChina
- Key Laboratory of Neuro‐oncology in Liaoning ProvinceShenyangChina
| | - Lu Zhu
- Department of Neurobiology, School of life SciencesChina Medical UniversityShenyangChina
- Key Laboratory of Cell Biology, Ministry of Public Health of ChinaChina Medical UniversityShenyangChina
- Key Laboratory of Medical Cell Biology, Ministry of Education of ChinaChina Medical UniversityShenyangChina
| | - Yang Yang
- Department of NeurosurgeryShengjing Hospital of China Medical UniversityShenyangChina
- Liaoning Clinical Medical Research Center in Nervous System DiseaseShenyangChina
- Key Laboratory of Neuro‐oncology in Liaoning ProvinceShenyangChina
| | - Zhen Li
- Department of NeurosurgeryShengjing Hospital of China Medical UniversityShenyangChina
- Liaoning Clinical Medical Research Center in Nervous System DiseaseShenyangChina
- Key Laboratory of Neuro‐oncology in Liaoning ProvinceShenyangChina
| | - Bo Yu
- Department of NeurosurgeryShengjing Hospital of China Medical UniversityShenyangChina
- Liaoning Clinical Medical Research Center in Nervous System DiseaseShenyangChina
- Key Laboratory of Neuro‐oncology in Liaoning ProvinceShenyangChina
| | - Tianda Feng
- Department of NeurosurgeryShengjing Hospital of China Medical UniversityShenyangChina
- Liaoning Clinical Medical Research Center in Nervous System DiseaseShenyangChina
- Key Laboratory of Neuro‐oncology in Liaoning ProvinceShenyangChina
| | - Yunhui Liu
- Department of NeurosurgeryShengjing Hospital of China Medical UniversityShenyangChina
- Liaoning Clinical Medical Research Center in Nervous System DiseaseShenyangChina
- Key Laboratory of Neuro‐oncology in Liaoning ProvinceShenyangChina
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14
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Saik NO, Park N, Ptak C, Adames N, Aitchison JD, Wozniak RW. Recruitment of an Activated Gene to the Yeast Nuclear Pore Complex Requires Sumoylation. Front Genet 2020; 11:174. [PMID: 32211027 PMCID: PMC7067905 DOI: 10.3389/fgene.2020.00174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/13/2020] [Indexed: 01/10/2023] Open
Abstract
In addition to their role in regulating transport across the nuclear envelope, increasing evidence suggests nuclear pore complexes (NPCs) function in regulating gene expression. For example, the induction of certain genes (e.g., yeast INO1) is accompanied by their movement from the nuclear interior to NPCs. As sumoylation has been linked to the regulation of chromatin spatial organization and transcriptional activity, we investigated the role of sumoylation in the expression and NPC recruitment of the INO1 gene. We observed that induction of INO1 is accompanied by both increased and decreased sumoylation of proteins associated with specific regions along the INO1 locus. Furthermore, we show that the E3 ligase Siz2/Nfi1 is required for targeting the INO1 locus to the NPC where it interacts with the SUMO isopeptidase Ulp1. Our data suggest that this interaction is required for both the association of INO1 with the NPC and for its normal expression. These results imply that sumoylation is a key regulator of INO1 targeting to the NPC, and a cycle of sumoylation and NPC-associated desumoylation events contribute to the regulation of INO1 expression.
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Affiliation(s)
- Natasha O Saik
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Nogi Park
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada.,Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
| | - Christopher Ptak
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Neil Adames
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada.,New Culture, San Francisco, CA, United States
| | - John D Aitchison
- Seattle Children's Research Institute, Seattle, WA, United States
| | - Richard W Wozniak
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
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