1
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Kovalenko TF, Yadav B, Anufrieva KS, Larionova TD, Aksinina TE, Latyshev YA, Bastola S, Shakhparonov MI, Pandey AK, Pavlyukov MS. PTEN regulates expression of its pseudogene in glioblastoma cells in DNA methylation-dependent manner. Biochimie 2024; 219:74-83. [PMID: 37619809 DOI: 10.1016/j.biochi.2023.08.010] [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: 12/23/2022] [Revised: 06/08/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
Glioblastoma (GBM) is the most aggressive and frequent type of primary brain cancer in adult patients. One of the key molecular features associated with GBM pathogenesis is the dysfunction of PTEN oncosuppressor. In addition to PTEN gene, humans and several primates possess processed PTEN pseudogene (PTENP1) that gives rise to long non-coding RNA lncPTENP1-S. Regulation and functions of PTEN and PTENP1 are highly interconnected, however, the exact molecular mechanism of how these two genes affect each other remains unclear. Here, we analyzed the methylation level of the CpG islands (CpGIs) in the promoter regions of PTEN and PTENP1 in patient-derived GBM neurospheres. We found that increased PTEN methylation corelates with decreased PTEN mRNA level. Unexpectedly, we showed the opposite trend for PTENP1. Using targeted methylation and demethylation of PTENP1 CpGI, we demonstrated that DNA methylation increases lncPTENP1-S expression in the presence of wild type PTEN protein but decreases lncPTENP1-S expression if PTEN protein is absent. Further experiments revealed that PTEN protein binds to PTENP1 promoter region and inhibits lncPTENP1-S expression if its CpGI is demethylated. Interestingly, we did not detect any effect of lncPTENP1-S on the level of PTEN mRNA, indicating that in GBM cells PTENP1 is a downstream target of PTEN rather than its upstream regulator. Finally, we studied the functions of lncPTENP1-S and demonstrated that it plays a pro-oncogenic role in GBM cells by upregulating the expression of cancer stem cell markers and decreasing cell adhesion.
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Affiliation(s)
| | - Bhupender Yadav
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana, India
| | - Ksenia S Anufrieva
- Laboratory of System Biology, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | | | | | - Yaroslav A Latyshev
- Federal State Autonomous Institution, N.N. Burdenko National Medical Research Center of Neurosurgery, Moscow, Russia
| | - Soniya Bastola
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Amit Kumar Pandey
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana, India; National Institute of Pharmaceutical Education and Research, Palaj, Gandhinagar, Gujarat, India
| | - Marat S Pavlyukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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Szulzewsky F, Thirimanne HN, Holland EC. Meningioma: current updates on genetics, classification, and mouse modeling. Ups J Med Sci 2024; 129:10579. [PMID: 38571886 PMCID: PMC10989216 DOI: 10.48101/ujms.v129.10579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 04/05/2024] Open
Abstract
Meningiomas, the most common primary brain tumors in adults, are often benign and curable by surgical resection. However, a subset is of higher grade, shows aggressive growth behavior as well as brain invasion, and often recurs even after several rounds of surgery. Increasing evidence suggests that tumor classification and grading primarily based on histopathology do not always accurately predict tumor aggressiveness and recurrence behavior. The underlying biology of aggressive treatment-resistant meningiomas and the impact of specific genetic aberrations present in these high-grade tumors is still only insufficiently understood. Therefore, an in-depth research into the biology of this tumor type is warranted. More recent studies based on large-scale molecular data such as whole exome/genome sequencing, DNA methylation sequencing, and RNA sequencing have provided new insights into the biology of meningiomas and have revealed new risk factors and prognostic subtypes. The most common genetic aberration in meningiomas is functional loss of NF2 and occurs in both low- and high-grade meningiomas, whereas NF2-wildtype meningiomas are enriched for recurrent mutations in TRAF7, KLF4, AKT1, PI3KCA, and SMO and are more frequently benign. Most meningioma mouse models are based on patient-derived xenografts and only recently have new genetically engineered mouse models of meningioma been developed that will aid in the systematic evaluation of specific mutations found in meningioma and their impact on tumor behavior. In this article, we review recent advances in the understanding of meningioma biology and classification and highlight the most common genetic mutations, as well as discuss new genetically engineered mouse models of meningioma.
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Affiliation(s)
- Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Eric C. Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Seattle Translational Tumor Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
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3
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Dumelie JG, Chen Q, Miller D, Attarwala N, Gross SS, Jaffrey SR. Biomolecular condensates create phospholipid-enriched microenvironments. Nat Chem Biol 2024; 20:302-313. [PMID: 37973889 PMCID: PMC10922641 DOI: 10.1038/s41589-023-01474-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/08/2023] [Indexed: 11/19/2023]
Abstract
Proteins and RNA can phase separate from the aqueous cellular environment to form subcellular compartments called condensates. This process results in a protein-RNA mixture that is chemically different from the surrounding aqueous phase. Here, we use mass spectrometry to characterize the metabolomes of condensates. To test this, we prepared mixtures of phase-separated proteins and extracts of cellular metabolites and identified metabolites enriched in the condensate phase. Among the most condensate-enriched metabolites were phospholipids, due primarily to the hydrophobicity of their fatty acyl moieties. We found that phospholipids can alter the number and size of phase-separated condensates and in some cases alter their morphology. Finally, we found that phospholipids partition into a diverse set of endogenous condensates as well as artificial condensates expressed in cells. Overall, these data show that many condensates are protein-RNA-lipid mixtures with chemical microenvironments that are ideally suited to facilitate phospholipid biology and signaling.
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Affiliation(s)
- Jason G Dumelie
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Qiuying Chen
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Dawson Miller
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Nabeel Attarwala
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Steven S Gross
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA.
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4
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Chakraborty S, Karmakar S, Basu M, Kal S, Ghosh MK. The E3 ubiquitin ligase CHIP drives monoubiquitylation-mediated nuclear import of the tumor suppressor PTEN. J Cell Sci 2023; 136:jcs260950. [PMID: 37676120 DOI: 10.1242/jcs.260950] [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: 01/10/2023] [Accepted: 08/04/2023] [Indexed: 09/08/2023] Open
Abstract
Monoubiquitylation is a principal mechanism driving nuclear translocation of the protein PTEN (phosphatase and tensin homolog deleted on chromosome ten). In this study, we describe a novel mechanism wherein the protein CHIP (C-terminus of Hsc70-interacting protein) mediates PTEN monoubiquitylation, leading to its nuclear import. Western blot analysis revealed a rise in both nuclear and total cellular PTEN levels under monoubiquitylation-promoting conditions, an effect that was abrogated by silencing CHIP expression. We established time-point kinetics of CHIP-mediated nuclear translocation of PTEN using immunocytochemistry and identified a role of karyopherin α1 (KPNA1) in facilitating nuclear transport of monoubiquitylated PTEN. We further established a direct interaction between CHIP and PTEN inside the nucleus, with CHIP participating in either polyubiquitylation or monoubiquitylation of nuclear PTEN. Finally, we showed that oxidative stress enhanced CHIP-mediated nuclear import of PTEN, which resulted in increased apoptosis, and decreased cell viability and proliferation, whereas CHIP knockdown counteracted these effects. To the best of our knowledge, this is the first report elucidating non-canonical roles for CHIP on PTEN, which we establish here as a nuclear interacting partner of CHIP.
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Affiliation(s)
- Shrabastee Chakraborty
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata 700091 and 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Subhajit Karmakar
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata 700091 and 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Malini Basu
- Department of Microbiology, Dhruba Chand Halder College, Dakshin Barasat, South 24 Parganas 743372, India
| | - Satadeepa Kal
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata 700091 and 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Mrinal K Ghosh
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata 700091 and 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Kumar A, Schwab M, Laborit Labrada B, Silveira MAD, Goudreault M, Fournier É, Bellmann K, Beauchemin N, Gingras AC, Bilodeau S, Laplante M, Marette A. SHP-1 phosphatase acts as a coactivator of PCK1 transcription to control gluconeogenesis. J Biol Chem 2023; 299:105164. [PMID: 37595871 PMCID: PMC10504565 DOI: 10.1016/j.jbc.2023.105164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/20/2023] Open
Abstract
We previously reported that the protein-tyrosine phosphatase SHP-1 (PTPN6) negatively regulates insulin signaling, but its impact on hepatic glucose metabolism and systemic glucose control remains poorly understood. Here, we use co-immunoprecipitation assays, chromatin immunoprecipitation sequencing, in silico methods, and gluconeogenesis assay, and found a new mechanism whereby SHP-1 acts as a coactivator for transcription of the phosphoenolpyruvate carboxykinase 1 (PCK1) gene to increase liver gluconeogenesis. SHP-1 is recruited to the regulatory regions of the PCK1 gene and interacts with RNA polymerase II. The recruitment of SHP-1 to chromatin is dependent on its association with the transcription factor signal transducer and activator of transcription 5 (STAT5). Loss of SHP-1 as well as STAT5 decrease RNA polymerase II recruitment to the PCK1 promoter and consequently PCK1 mRNA levels leading to blunted gluconeogenesis. This work highlights a novel nuclear role of SHP-1 as a key transcriptional regulator of hepatic gluconeogenesis adding a new mechanism to the repertoire of SHP-1 functions in metabolic control.
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Affiliation(s)
- Amit Kumar
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada
| | - Michael Schwab
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada
| | - Beisy Laborit Labrada
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada
| | - Maruhen Amir Datsch Silveira
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de Recherche sur le Cancer de l'Université Laval, Québec, Quebec, Canada; Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de Médecine, Université Laval, Québec, Quebec, Canada
| | - Marilyn Goudreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada
| | - Éric Fournier
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de Recherche sur le Cancer de l'Université Laval, Québec, Quebec, Canada; Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de Médecine, Université Laval, Québec, Quebec, Canada; Centre de recherche en données massives de l'Université Laval, Québec, Quebec, Canada
| | - Kerstin Bellmann
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada
| | - Nicole Beauchemin
- Department of Oncology, Medicine and Biochemistry, Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Steve Bilodeau
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de Recherche sur le Cancer de l'Université Laval, Québec, Quebec, Canada; Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de Médecine, Université Laval, Québec, Quebec, Canada; Centre de recherche en données massives de l'Université Laval, Québec, Quebec, Canada
| | - Mathieu Laplante
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada; Centre de Recherche sur le Cancer de l'Université Laval, Québec, Quebec, Canada
| | - André Marette
- Faculté de Médecine, Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Université Laval, Québec, Quebec, Canada; Institute of Nutrition and Functional Foods, Laval University, Québec, Quebec, Canada.
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6
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Yang Y, Zhang Z, Li W, Si Y, Li L, Du W. αKG-driven RNA polymerase II transcription of cyclin D1 licenses malic enzyme 2 to promote cell-cycle progression. Cell Rep 2023; 42:112770. [PMID: 37422761 DOI: 10.1016/j.celrep.2023.112770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/28/2023] [Accepted: 06/22/2023] [Indexed: 07/11/2023] Open
Abstract
Increased metabolic activity usually provides energy and nutrients for biomass synthesis and is indispensable for the progression of the cell cycle. Here, we find a role for α-ketoglutarate (αKG) generation in regulating cell-cycle gene transcription. A reduction in cellular αKG levels triggered by malic enzyme 2 (ME2) or isocitrate dehydrogenase 1 (IDH1) depletion leads to a pronounced arrest in G1 phase, while αKG supplementation promotes cell-cycle progression. Mechanistically, αKG directly binds to RNA polymerase II (RNAPII) and increases the level of RNAPII binding to the cyclin D1 gene promoter via promoting pre-initiation complex (PIC) assembly, consequently enhancing cyclin D1 transcription. Notably, αKG addition is sufficient to restore cyclin D1 expression in ME2- or IDH1-depleted cells, facilitating cell-cycle progression and proliferation in these cells. Therefore, our findings indicate a function of αKG in gene transcriptional regulation and cell-cycle control.
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Affiliation(s)
- Yanting Yang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Zhenxi Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Wei Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Yufan Si
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Li Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Wenjing Du
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China.
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7
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Long Q, Zhou Y, Guo J, Wu H, Liu X. Multi-phase separation in mitochondrial nucleoids and eukaryotic nuclei. BIOPHYSICS REPORTS 2023; 9:113-119. [PMID: 38028151 PMCID: PMC10648231 DOI: 10.52601/bpr.2023.220018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 02/10/2023] [Indexed: 03/28/2023] Open
Abstract
In mammalian cells, besides nuclei, mitochondria are the only semi-autonomous organelles possessing own DNA organized in the form of nucleoids. While eukaryotic nuclear DNA compaction, chromatin compartmentalization and transcription are regulated by phase separation, our recent work proposed a model of mitochondrial nucleoid self-assembly and transcriptional regulation by multi-phase separation. Herein, we summarized the phase separation both in the nucleus and mitochondrial nucleoids, and did a comparison of the organization and activity regulating, which would provide new insight into the understanding of both architecture and genetics of nucleus and mitochondrial nucleoids.
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Affiliation(s)
- Qi Long
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yanshuang Zhou
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jingyi Guo
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Hao Wu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xingguo Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
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8
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Cahuzac KM, Lubin A, Bosch K, Stokes N, Shoenfeld SM, Zhou R, Lemon H, Asara J, Parsons RE. AKT activation because of PTEN loss upregulates xCT via GSK3β/NRF2, leading to inhibition of ferroptosis in PTEN-mutant tumor cells. Cell Rep 2023; 42:112536. [PMID: 37210723 PMCID: PMC10558134 DOI: 10.1016/j.celrep.2023.112536] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 01/25/2023] [Accepted: 05/03/2023] [Indexed: 05/23/2023] Open
Abstract
Here, we show that the tumor suppressor phosphatase and tensin homolog deleted from chromosome 10 (PTEN) sensitizes cells to ferroptosis, an iron-dependent form of cell death, by restraining the expression and activity of the cystine/glutamate antiporter system Xc- (xCT). Loss of PTEN activates AKT kinase to inhibit GSK3β, increasing NF-E2 p45-related factor 2 (NRF2) along with transcription of one of its known target genes encoding xCT. Elevated xCT in Pten-null mouse embryonic fibroblasts increases the flux of cystine transport and synthesis of glutathione, which enhances the steady-state levels of these metabolites. A pan-cancer analysis finds that loss of PTEN shows evidence of increased xCT, and PTEN-mutant cells are resistant to ferroptosis as a consequence of elevated xCT. These findings suggest that selection of PTEN mutation during tumor development may be due to its ability to confer resistance to ferroptosis in the setting of metabolic and oxidative stress that occurs during tumor initiation and progression.
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Affiliation(s)
- Kaitlyn M Cahuzac
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Abigail Lubin
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kaitlyn Bosch
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicole Stokes
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Royce Zhou
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Haddy Lemon
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Ramon E Parsons
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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9
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Hameed J S F, Devarajan A, M S DP, Bhattacharyya A, Shirude MB, Dutta D, Karmakar P, Mukherjee A. PTEN-negative endometrial cancer cells protect their genome through enhanced DDB2 expression associated with augmented nucleotide excision repair. BMC Cancer 2023; 23:399. [PMID: 37142958 PMCID: PMC10157935 DOI: 10.1186/s12885-023-10892-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 04/26/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Endometrial cancer (EC) arises from uterine endometrium tissue and is the most prevalent cancer of the female reproductive tract in developed countries. It has been predicted that the global prevalence of EC will increase in part because of its positive association with economic growth and lifestyle. The majority of EC presented with endometrioid histology and mutations in the tumor suppressor gene PTEN, resulting in its loss of function. PTEN negatively regulates the PI3K/Akt/mTOR axis of cell proliferation and thus serves as a tumorigenesis gatekeeper. Through its chromatin functions, PTEN is also implicated in genome maintenance procedures. However, our comprehension of how DNA repair occurs in the absence of PTEN function in EC is inadequate. METHODS We utilized The Cancer Genome Atlas (TCGA) data analysis to establish a correlation between PTEN and DNA damage response genes in EC, followed by a series of cellular and biochemical assays to elucidate a molecular mechanism utilizing the AN3CA cell line model for EC. RESULTS The TCGA analyses demonstrated an inverse correlation between the expression of the damage sensor protein of nucleotide excision repair (NER), DDB2, and PTEN in EC. The transcriptional activation of DDB2 is mediated by the recruitment of active RNA polymerase II to the DDB2 promoter in the PTEN-null EC cells, revealing a correlation between increased DDB2 expression and augmented NER activity in the absence of PTEN. CONCLUSION Our study indicated a causal relationship between NER and EC that may be exploited in disease management.
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Affiliation(s)
- Fathima Hameed J S
- Rajiv Gandhi Centre for Biotechnology, Cancer Research Program, Thycaud, Poojappura, Thiruvananthapuram, Kerala, 695014, India
- Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Anjali Devarajan
- Rajiv Gandhi Centre for Biotechnology, Cancer Research Program, Thycaud, Poojappura, Thiruvananthapuram, Kerala, 695014, India
| | - Devu Priya M S
- Rajiv Gandhi Centre for Biotechnology, Cancer Research Program, Thycaud, Poojappura, Thiruvananthapuram, Kerala, 695014, India
| | - Ahel Bhattacharyya
- Rajiv Gandhi Centre for Biotechnology, Cancer Research Program, Thycaud, Poojappura, Thiruvananthapuram, Kerala, 695014, India
| | - Mayur Balkrishna Shirude
- Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
- Rajiv Gandhi Centre for Biotechnology, Regenerative Biology Program, Thycaud, Poojappura, Thiruvananthapuram, Kerala, 695014, India
| | - Debasree Dutta
- Rajiv Gandhi Centre for Biotechnology, Regenerative Biology Program, Thycaud, Poojappura, Thiruvananthapuram, Kerala, 695014, India
| | - Parimal Karmakar
- Department of Life Science and Biotechnology, Jadavpur University, 188, Raja S.C. Mullick Road, Kolkata, West Bengal, 700 032, India
| | - Ananda Mukherjee
- Rajiv Gandhi Centre for Biotechnology, Cancer Research Program, Thycaud, Poojappura, Thiruvananthapuram, Kerala, 695014, India.
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10
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Iwase R, Dempsey DR, Whedon SD, Jiang H, Palanski BA, Deng B, Cole PA. Semisynthetic Approach to the Analysis of Tumor Suppressor PTEN Ubiquitination. J Am Chem Soc 2023; 145:6039-6044. [PMID: 36897111 PMCID: PMC10071500 DOI: 10.1021/jacs.2c13871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Phosphatase and tensin homologue (PTEN) tumor suppressor protein is a PIP3 lipid phosphatase that is subject to multifaceted post-translational modifications. One such modification is the monoubiquitination of Lys13 that may alter its cellular localization but is also positioned in a manner that could influence several of its cellular functions. To explore the regulatory influence of ubiquitin on PTEN's biochemical properties and its interaction with ubiquitin ligases and a deubiquitinase, the generation of a site-specifically and stoichiometrically ubiquitinated protein could be beneficial. Here, we describe a semisynthetic method that relies upon sequential expressed protein ligation steps to install ubiquitin at a Lys13 mimic in near full-length PTEN. This approach permits the concurrent installation of C-terminal modifications in PTEN, thereby facilitating an analysis of the interplay between N-terminal ubiquitination and C-terminal phosphorylation. We find that the N-terminal ubiquitination of PTEN inhibits its enzymatic function, reduces its binding to lipid vesicles, modulates its processing by NEDD4-1 E3 ligase, and is efficiently cleaved by the deubiquitinase, USP7. Our ligation approach should motivate related efforts for uncovering the effects of ubiquitination of complex proteins.
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Affiliation(s)
- Reina Iwase
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Daniel R. Dempsey
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Dermatology and Pharmacology & Experimental Therapeutics, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Samuel D. Whedon
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Hanjie Jiang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Brad A. Palanski
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Bedphiny Deng
- Dana-Farber/Harvard Cancer Center, Boston, Massachusetts 02115, United States
- College of Natural Sciences, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Philip A. Cole
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
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11
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Langdon CG. Nuclear PTEN's Functions in Suppressing Tumorigenesis: Implications for Rare Cancers. Biomolecules 2023; 13:biom13020259. [PMID: 36830628 PMCID: PMC9953540 DOI: 10.3390/biom13020259] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/25/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
Phosphatase and tensin homolog (PTEN) encodes a tumor-suppressive phosphatase with both lipid and protein phosphatase activity. The tumor-suppressive functions of PTEN are lost through a variety of mechanisms across a wide spectrum of human malignancies, including several rare cancers that affect pediatric and adult populations. Originally discovered and characterized as a negative regulator of the cytoplasmic, pro-oncogenic phosphoinositide-3-kinase (PI3K) pathway, PTEN is also localized to the nucleus where it can exert tumor-suppressive functions in a PI3K pathway-independent manner. Cancers can usurp the tumor-suppressive functions of PTEN to promote oncogenesis by disrupting homeostatic subcellular PTEN localization. The objective of this review is to describe the changes seen in PTEN subcellular localization during tumorigenesis, how PTEN enters the nucleus, and the spectrum of impacts and consequences arising from disrupted PTEN nuclear localization on tumor promotion. This review will highlight the immediate need in understanding not only the cytoplasmic but also the nuclear functions of PTEN to gain more complete insights into how important PTEN is in preventing human cancers.
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Affiliation(s)
- Casey G. Langdon
- Department of Pediatrics, Darby Children’s Research Institute, Medical University of South Carolina, Charleston, SC 29425, USA; ; Tel.: +1-(843)-792-9289
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
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12
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PTEN phosphatase inhibits metastasis by negatively regulating the Entpd5/IGF1R pathway through ATF6. iScience 2023; 26:106070. [PMID: 36824269 PMCID: PMC9942123 DOI: 10.1016/j.isci.2023.106070] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/01/2022] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
PTEN encodes a tumor suppressor with lipid and protein phosphatase activities whose dysfunction has been implicated in melanomagenesis; less is known about how its phosphatases regulate melanoma metastasis. We demonstrate that PTEN expression negatively correlates with metastatic progression in human melanoma samples and a PTEN-deficient mouse melanoma model. Wildtype PTEN expression inhibited melanoma cell invasiveness and metastasis in a dose-dependent manner, behaviors that specifically required PTEN protein phosphatase activity. PTEN phosphatase activity regulated metastasis through Entpd5. Entpd5 knockdown reduced metastasis and IGF1R levels while promoting ER stress. In contrast, Entpd5 overexpression promoted metastasis and enhanced IGF1R levels while reducing ER stress. Moreover, Entpd5 expression was regulated by the ER stress sensor ATF6. Altogether, our data indicate that PTEN phosphatase activity inhibits metastasis by negatively regulating the Entpd5/IGF1R pathway through ATF6, thereby identifying novel candidate therapeutic targets for the treatment of PTEN mutant melanoma.
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13
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van der Noord VE, van de Water B, Le Dévédec SE. Targeting the Heterogeneous Genomic Landscape in Triple-Negative Breast Cancer through Inhibitors of the Transcriptional Machinery. Cancers (Basel) 2022; 14:4353. [PMID: 36139513 PMCID: PMC9496798 DOI: 10.3390/cancers14184353] [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: 08/10/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer defined by lack of the estrogen, progesterone and human epidermal growth factor receptor 2. Although TNBC tumors contain a wide variety of oncogenic mutations and copy number alterations, the direct targeting of these alterations has failed to substantially improve therapeutic efficacy. This efficacy is strongly limited by interpatient and intratumor heterogeneity, and thereby a lack in uniformity of targetable drivers. Most of these genetic abnormalities eventually drive specific transcriptional programs, which may be a general underlying vulnerability. Currently, there are multiple selective inhibitors, which target the transcriptional machinery through transcriptional cyclin-dependent kinases (CDKs) 7, 8, 9, 12 and 13 and bromodomain extra-terminal motif (BET) proteins, including BRD4. In this review, we discuss how inhibitors of the transcriptional machinery can effectively target genetic abnormalities in TNBC, and how these abnormalities can influence sensitivity to these inhibitors. These inhibitors target the genomic landscape in TNBC by specifically suppressing MYC-driven transcription, inducing further DNA damage, improving anti-cancer immunity, and preventing drug resistance against MAPK and PI3K-targeted therapies. Because the transcriptional machinery enables transcription and propagation of multiple cancer drivers, it may be a promising target for (combination) treatment, especially of heterogeneous malignancies, including TNBC.
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Affiliation(s)
| | | | - Sylvia E. Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
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14
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Xin R, Shen B, Jiang YJ, Liu JB, Li S, Hou LK, Wu W, Jia CY, Wu CY, Fu D, Ma YS, Jiang GX. Comprehensive analysis to identify a novel PTEN-associated ceRNA regulatory network as a prognostic biomarker for lung adenocarcinoma. Front Oncol 2022; 12:923026. [PMID: 36091160 PMCID: PMC9449356 DOI: 10.3389/fonc.2022.923026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is one of the most prevalent forms of lung cancer. Competitive endogenous RNA (ceRNA) plays an important role in the pathogenesis of lung cancer. Phosphatase and tensin homolog (PTEN) is one of the most frequently deleted tumour suppressor genes in LUAD. The present study aimed to identify a novel PTEN-associated-ceRNA regulatory network and identify potential prognostic markers associated with LUAD. Transcriptome sequencing profiles of 533 patients with LUAD were obtained from TCGA database, and differentially expressed genes (DEGs) were screened in LUAD samples with PTEN high- (PTENhigh) and low- (PTENlow) expression. Eventually, an important PTEN-related marker was identified, namely, the LINC00460/miR-150-3p axis. Furthermore, the predicted target genes (EME1/HNRNPAB/PLAUR/SEMA3A) were closely related to overall survival and prognosis. The LINC00460/miR-150-3p axis was identified as a clinical prognostic factor through Cox regression analysis. Methylation analyses suggested that abnormal regulation of the predicted target genes might be caused by hypomethylation. Furthermore, immune infiltration analysis showed that the LINC00460/miR-150-3p axis could alter the levels of immune infiltration in the tumour immune microenvironment, and promote the clinical progression of LUAD. To specifically induce PTEN deletion in the lungs, we constructed an STP mouse model (SFTPC-rtTA/tetO-cre/Ptenflox/+). Quantitative PCR (qPCR) and immunohistochemical (IHC) analysis were used to detect predicted target genes. Therefore, we revealed that the PTEN-related LINC00460/miR-150-3p axis based on ceRNA mechanism plays an important role in the development of LUAD and provides a new direction and theoretical basis for its targeted therapy.
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Affiliation(s)
- Rui Xin
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Biao Shen
- Department of Thoracic Surgery, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Ying-Jie Jiang
- Department of Pathology, Navy Military Medical University Affiliated Changhai Hospital, Shanghai, China
| | - Ji-Bin Liu
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Sha Li
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Li-Kun Hou
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Wu
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Cheng-You Jia
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chun-Yan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Da Fu
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- *Correspondence: Geng-Xi Jiang, ; Yu-Shui Ma, ; Da Fu,
| | - Yu-Shui Ma
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Geng-Xi Jiang, ; Yu-Shui Ma, ; Da Fu,
| | - Geng-Xi Jiang
- Department of Thoracic Surgery, Navy Military Medical University Affiliated Changhai Hospital, Shanghai, China
- *Correspondence: Geng-Xi Jiang, ; Yu-Shui Ma, ; Da Fu,
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15
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Luo D, Liu Y, Li Z, Zhu H, Yu X. NR2F1-AS1 Promotes Pancreatic Ductal Adenocarcinoma Progression Through Competing Endogenous RNA Regulatory Network Constructed by Sponging miRNA-146a-5p/miRNA-877-5p. Front Cell Dev Biol 2021; 9:736980. [PMID: 34650983 PMCID: PMC8505696 DOI: 10.3389/fcell.2021.736980] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/02/2021] [Indexed: 12/28/2022] Open
Abstract
The role of NR2F1-AS1 in pancreatic ductal adenocarcinoma (PDAC) remains unknown. Therefore, we aimed to investigate the biological mechanism of NR2F1-AS1 in PDAC. The expression of NR2F1-AS1 was measured by using microarray data and real-time PCR. The effects of NR2F1-AS1 knockdown on proliferation, cell cycle progression, invasion in vitro and tumorigenesis in vivo were investigated. The mechanism of competitive endogenous RNAs was determined from bioinformatics analyses and validated by a dual-luciferase reporter gene assay. Potential target mRNAs from TargetScan 7.2 were selected for subsequent bioinformatics analysis. Key target mRNAs were further identified by screening hub genes and coexpressed protein-coding genes (CEGs) of NR2F1-AS1. NR2F1-AS1 was highly expressed in PDAC, and the overexpression of NR2F1-AS1 was associated with overall survival and disease-free survival. The knockdown of NR2F1-AS1 impaired PDAC cell proliferation, migration, invasion and tumorigenesis. NR2F1-AS1 competitively sponged miR-146a-5p and miR-877-5p, and low expression of the two miRNAs was associated with a poor prognosis. An integrative expression and survival analysis of the hub genes and CEGs demonstrated that the NR2F1-AS1–miR-146a-5p/miR-877-5p–GALNT10/ZNF532/SLC39A1/PGK1/LCO3A1/NRP2/LPCAT2/PSMA4 and CLTC ceRNA networks were linked to the prognosis of PDAC. In conclusion, NR2F1-AS1 overexpression was significantly associated with poor prognosis. NR2F1-AS1 functions as an endogenous RNA to construct a novel ceRNA network by competitively binding to miR-146a-5p/miR-877-5p, which may contribute to PDAC pathogenesis and could represent a promising diagnostic biomarker or potential novel therapeutic target in PDAC.
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Affiliation(s)
- Dong Luo
- Department of Hepatopancreatobiliary Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Yunfei Liu
- Department of Hepatopancreatobiliary Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhiqiang Li
- Department of Hepatopancreatobiliary Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Hongwei Zhu
- Department of Hepatopancreatobiliary Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiao Yu
- Department of Hepatopancreatobiliary Surgery, Third Xiangya Hospital, Central South University, Changsha, China
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16
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Langdon CG, Gadek KE, Garcia MR, Evans MK, Reed KB, Bush M, Hanna JA, Drummond CJ, Maguire MC, Leavey PJ, Finkelstein D, Jin H, Schreiner PA, Rehg JE, Hatley ME. Synthetic essentiality between PTEN and core dependency factor PAX7 dictates rhabdomyosarcoma identity. Nat Commun 2021; 12:5520. [PMID: 34535684 PMCID: PMC8448747 DOI: 10.1038/s41467-021-25829-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 09/01/2021] [Indexed: 02/08/2023] Open
Abstract
PTEN promoter hypermethylation is nearly universal and PTEN copy number loss occurs in ~25% of fusion-negative rhabdomyosarcoma (FN-RMS). Here we show Pten deletion in a mouse model of FN-RMS results in less differentiated tumors more closely resembling human embryonal RMS. PTEN loss activated the PI3K pathway but did not increase mTOR activity. In wild-type tumors, PTEN was expressed in the nucleus suggesting loss of nuclear PTEN functions could account for these phenotypes. Pten deleted tumors had increased expression of transcription factors important in neural and skeletal muscle development including Dbx1 and Pax7. Pax7 deletion completely rescued the effects of Pten loss. Strikingly, these Pten;Pax7 deleted tumors were no longer FN-RMS but displayed smooth muscle differentiation similar to leiomyosarcoma. These data highlight how Pten loss in FN-RMS is connected to a PAX7 lineage-specific transcriptional output that creates a dependency or synthetic essentiality on the transcription factor PAX7 to maintain tumor identity.
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Affiliation(s)
- Casey G Langdon
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Katherine E Gadek
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Matthew R Garcia
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Myron K Evans
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kristin B Reed
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Rhodes College, Memphis, TN, 38112, USA
| | - Madeline Bush
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Jason A Hanna
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Purdue Center for Cancer Research, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Catherine J Drummond
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pathology, University of Otago, Dunedin, Otago, New Zealand
| | - Matthew C Maguire
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Patrick J Leavey
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Patrick A Schreiner
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jerold E Rehg
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Mark E Hatley
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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17
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Abbas A, Padmanabhan R, Eng C. Metabolic stress regulates genome-wide transcription in a PTEN-dependent manner. Hum Mol Genet 2021; 29:2736-2745. [PMID: 32744308 DOI: 10.1093/hmg/ddaa168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/19/2020] [Accepted: 07/27/2020] [Indexed: 12/31/2022] Open
Abstract
PTEN is implicated in a wide variety of pathophysiological conditions and traditionally studied in the context of the PIK3-AKT-mTOR axis. Recent studies from our group and others have reported a novel role of PTEN in the regulation of transcription at the genome-wide scale. This emerging role of PTEN on global transcriptional regulation is providing a better understanding of various diseases, including cancer. Because cancer progression is an energy-demanding process and PTEN is known to regulate metabolic processes, we sought to understand the role of PTEN in transcriptional regulation under metabolic stress, a condition often developing in the tumor microenvironment. In the present study, we demonstrate that PTEN modulates genome-wide RNA Polymerase II occupancy in cells undergoing glucose deprivation. The glucose-deprived PTEN null cells were found to continue global gene transcription, which may activate a survival mode. However, cells with constitutive PTEN expression slow transcription, an evolutionary mechanism that may save cellular energy and activate programmed cell death pathways, in the absence of glucose. Interestingly, alternative exon usage by PTEN null cells is increased under metabolic stress in contrast to PTEN-expressing cells. Overall, our study demonstrates distinct mechanisms involved in PTEN-dependent genome-wide transcriptional control under metabolic stress. Our findings provide a new insight in understanding tumor pathology and how PTEN loss of function, whether by genetic or non-genetic mechanisms, can contribute to a favorable transcriptional program employed by tumor cells to escape apoptosis, hence developing more aggressive and metastatic phenotypes.
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Affiliation(s)
- Ata Abbas
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.,Developmental Therapeutics Program, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44116, USA
| | - Roshan Padmanabhan
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA.,Department of Genetics and Genome Sciences.,Germline High Risk Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44116, USA
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18
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Fry AL, Webster AK, Burnett J, Chitrakar R, Baugh LR, Hubbard EJA. DAF-18/PTEN inhibits germline zygotic gene activation during primordial germ cell quiescence. PLoS Genet 2021; 17:e1009650. [PMID: 34288923 PMCID: PMC8294487 DOI: 10.1371/journal.pgen.1009650] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Quiescence, an actively-maintained reversible state of cell cycle arrest, is not well understood. PTEN is one of the most frequently lost tumor suppressors in human cancers and regulates quiescence of stem cells and cancer cells. The sole PTEN ortholog in Caenorhabditis elegans is daf-18. In a C. elegans loss-of-function mutant for daf-18, primordial germ cells (PGCs) divide inappropriately in L1 larvae hatched into starvation conditions, in a TOR-dependent manner. Here, we further investigated the role of daf-18 in maintaining PGC quiescence in L1 starvation. We found that maternal or zygotic daf-18 is sufficient to maintain cell cycle quiescence, that daf-18 acts in the germ line and soma, and that daf-18 affects timing of PGC divisions in fed animals. Importantly, our results also implicate daf-18 in repression of germline zygotic gene activation, though not in germline fate specification. However, TOR is less important to germline zygotic gene expression, suggesting that in the absence of food, daf-18/PTEN prevents inappropriate germline zygotic gene activation and cell division by distinct mechanisms.
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Affiliation(s)
- Amanda L. Fry
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Amy K. Webster
- Department of Biology, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Julia Burnett
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Rojin Chitrakar
- Department of Biology, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - L. Ryan Baugh
- Department of Biology, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - E. Jane Albert Hubbard
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Grossman School of Medicine, New York, New York, United States of America
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19
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Liu X, Liu P, Chernock RD, Yang Z, Lang Kuhs KA, Lewis JS, Luo J, Li H, Gay HA, Thorstad WL, Wang X. A MicroRNA Expression Signature as Prognostic Marker for Oropharyngeal Squamous Cell Carcinoma. J Natl Cancer Inst 2021; 113:752-759. [PMID: 33057626 PMCID: PMC8168274 DOI: 10.1093/jnci/djaa161] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/05/2020] [Accepted: 09/28/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Improved prognostication of oropharyngeal squamous cell carcinoma (OPSCC) may facilitate individualized patient management. The goal of this study was to develop and validate a prognostic signature based on microRNA sequencing (miRNA-seq) analysis. METHODS We collected tumor specimens for miRNA-seq analysis from OPSCC patients treated at Washington University in St Louis (n = 324) and Vanderbilt University (n = 130). OPSCC patients (n = 79) from The Cancer Genome Atlas Program were also included for independent validation. Univariate and multivariable Cox regression analyses were performed to identify miRNAs associated with disease outcomes. All statistical tests were 2-sided. RESULTS By miRNA-seq profiling analysis, we identified a 26-miRNA signature. Based on computed risk scores of the signature, we classified the patients into low- and high-risk groups. In the training cohort, the high-risk group had much shorter overall survival compared with the low-risk group (hazard ratio [HR] = 3.80, 95% confidence interval [CI] = 2.37 to 6.10, P < .001). Subgroup analysis further revealed that the signature was prognostic for HPV-positive OPSCCs (HR = 3.07, 95% CI = 1.65 to 5.71, P < .001). Multivariable analysis indicated that the signature was independent of common clinicopathologic factors for OPSCCs. Importantly, the miRNA signature was a statistically significant predictor of overall survival in independent validation cohorts (The Cancer Genome Atlas Program cohort: HR = 6.05, 95% CI = 2.10 to 17.37, P < .001; Vanderbilt cohort: HR = 7.98, 95% CI = 3.99 to 15.97, P < .001; Vanderbilt HPV-positive cohort: HR = 8.71, 95% CI = 2.70 to 28.14, P < .001). CONCLUSIONS The miRNA signature is a robust and independent prognostic tool for risk stratification of OPSCCs including HPV-positive OPSCCs.
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Affiliation(s)
- Xinyi Liu
- Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO, USA
| | - Ping Liu
- Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO, USA
| | - Rebecca D Chernock
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Zhenming Yang
- Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO, USA
| | - Krystle A Lang Kuhs
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James S. Lewis
- Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jingqin Luo
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Hua Li
- Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO, USA
| | - Hiram A Gay
- Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO, USA
| | - Wade L Thorstad
- Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO, USA
| | - Xiaowei Wang
- Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO, USA
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20
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Cossa G, Parua PK, Eilers M, Fisher RP. Protein phosphatases in the RNAPII transcription cycle: erasers, sculptors, gatekeepers, and potential drug targets. Genes Dev 2021; 35:658-676. [PMID: 33888562 PMCID: PMC8091971 DOI: 10.1101/gad.348315.121] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this review, Cossa et al. discuss the current knowledge and outstanding questions about phosphatases in the context of the RNAPII transcription cycle. The transcription cycle of RNA polymerase II (RNAPII) is governed at multiple points by opposing actions of cyclin-dependent kinases (CDKs) and protein phosphatases, in a process with similarities to the cell division cycle. While important roles of the kinases have been established, phosphatases have emerged more slowly as key players in transcription, and large gaps remain in understanding of their precise functions and targets. Much of the earlier work focused on the roles and regulation of sui generis and often atypical phosphatases—FCP1, Rtr1/RPAP2, and SSU72—with seemingly dedicated functions in RNAPII transcription. Decisive roles in the transcription cycle have now been uncovered for members of the major phosphoprotein phosphatase (PPP) family, including PP1, PP2A, and PP4—abundant enzymes with pleiotropic roles in cellular signaling pathways. These phosphatases appear to act principally at the transitions between transcription cycle phases, ensuring fine control of elongation and termination. Much is still unknown, however, about the division of labor among the PPP family members, and their possible regulation by or of the transcriptional kinases. CDKs active in transcription have recently drawn attention as potential therapeutic targets in cancer and other diseases, raising the prospect that the phosphatases might also present opportunities for new drug development. Here we review the current knowledge and outstanding questions about phosphatases in the context of the RNAPII transcription cycle.
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Affiliation(s)
- Giacomo Cossa
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Pabitra K Parua
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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21
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Abstract
In over two decades since the discovery of phosphatase and tensin homologue deleted on chromosome 10 (PTEN), nearly 18,000 publications have attempted to elucidate its functions and roles in normal physiology and disease. The frequent disruption of PTEN in cancer cells was a strong indication that it had critical roles in tumour suppression. Germline PTEN mutations have been identified in patients with heterogeneous tumour syndromic diseases, known as PTEN hamartoma tumour syndrome (PHTS), and in some individuals with autism spectrum disorders (ASD). Today we know that by limiting oncogenic signalling through the phosphoinositide 3-kinase (PI3K) pathway, PTEN governs a number of processes including survival, proliferation, energy metabolism, and cellular architecture. Some of the most exciting recent advances in the understanding of PTEN biology and signalling have revisited its unappreciated roles as a protein phosphatase, identified non-enzymatic scaffold functions, and unravelled its nuclear function. These discoveries are certain to provide a new perspective on its full tumour suppressor potential, and knowledge from this work will lead to new anti-cancer strategies that exploit PTEN biology. In this review, we will highlight some outstanding questions and some of the very latest advances in the understanding of the tumour suppressor PTEN.
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Affiliation(s)
- Jonathan Tak-Sum Chow
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Leonardo Salmena
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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22
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Katagi H, Takata N, Aoi Y, Zhang Y, Rendleman EJ, Blyth GT, Eckerdt FD, Tomita Y, Sasaki T, Saratsis AM, Kondo A, Goldman S, Becher OJ, Smith E, Zou L, Shilatifard A, Hashizume R. Therapeutic targeting of transcriptional elongation in diffuse intrinsic pontine glioma. Neuro Oncol 2021; 23:1348-1359. [PMID: 33471107 PMCID: PMC8328031 DOI: 10.1093/neuonc/noab009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Diffuse intrinsic pontine glioma (DIPG) is associated with transcriptional dysregulation driven by H3K27 mutation. The super elongation complex (SEC) is required for transcriptional elongation through release of RNA polymerase II (Pol II). Inhibition of transcription elongation by SEC disruption can be an effective therapeutic strategy of H3K27M-mutant DIPG. Here, we tested the effect of pharmacological disruption of the SEC in H3K27M-mutant DIPG to advance understanding of the molecular mechanism and as a new therapeutic strategy for DIPG. METHODS Short hairpin RNAs (shRNAs) were used to suppress the expression of AF4/FMR2 4 (AFF4), a central SEC component, in H3K27M-mutant DIPG cells. A peptidomimetic lead compound KL-1 was used to disrupt a functional component of SEC. Cell viability assay, colony formation assay, and apoptosis assay were utilized to analyze the effects of KL-1 treatment. RNA- and ChIP-sequencing were used to determine the effects of KL-1 on gene expression and chromatin occupancy. We treated mice bearing H3K27M-mutant DIPG patient-derived xenografts (PDXs) with KL-1. Intracranial tumor growth was monitored by bioluminescence image and therapeutic response was evaluated by animal survival. RESULTS Depletion of AFF4 significantly reduced the cell growth of H3K27M-mutant DIPG. KL-1 increased genome-wide Pol II occupancy and suppressed transcription involving multiple cellular processes that promote cell proliferation and differentiation of DIPG. KL-1 treatment suppressed DIPG cell growth, increased apoptosis, and prolonged animal survival with H3K27M-mutant DIPG PDXs. CONCLUSIONS SEC disruption by KL-1 increased therapeutic benefit in vitro and in vivo, supporting a potential therapeutic activity of KL-1 in H3K27M-mutant DIPG.
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Affiliation(s)
- Hiroaki Katagi
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Department of Neurological Surgery, Juntendo University, Tokyo, Japan
| | - Nozomu Takata
- Center for Vascular and Developmental Biology, Feinberg Cardiovascular and Renal Research Institute (FCVRRI), Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Yuki Aoi
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Yongzhan Zhang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Emily J Rendleman
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Gavin T Blyth
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Frank D Eckerdt
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Yusuke Tomita
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Division of Hematology, Oncology, Neuro-Oncology and Stem Cell Transplantation, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois
| | - Takahiro Sasaki
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Amanda M Saratsis
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois,Department of Surgery, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois
| | - Akihide Kondo
- Department of Neurological Surgery, Juntendo University, Tokyo, Japan
| | - Stewart Goldman
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Division of Hematology, Oncology, Neuro-Oncology and Stem Cell Transplantation, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois
| | - Oren J Becher
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Division of Hematology, Oncology, Neuro-Oncology and Stem Cell Transplantation, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois
| | - Edwin Smith
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Lihua Zou
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Rintaro Hashizume
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,Division of Hematology, Oncology, Neuro-Oncology and Stem Cell Transplantation, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois,Corresponding Author: Rintaro Hashizume, MD, PhD, Department of Pediatrics, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Simpson Querrey 4-514, Chicago, IL 60611, USA (, )
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23
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A review on kinases phosphorylating the carboxyl-terminal domain of RNA polymerase II-Biological functions and inhibitors. Bioorg Chem 2020; 104:104318. [PMID: 33142427 DOI: 10.1016/j.bioorg.2020.104318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/18/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
Abstract
RNA polymerase II (RNA Pol II) plays a major role in gene transcription for eukaryote. One of the major modes of regulation in eukaryotes is the phosphorylation of the carboxyl-terminal domain (CTD) of RNA Pol II. The current study found that the phosphorylation of Ser2, Ser5, Ser7, Thr4 and Tyr1 among the heptapeptide repeats of CTD plays a key role in the transcription process. We therefore review the biological functions and inhibitors of kinases that phosphorylate these amino acid residues including transcriptional cyclin-dependent protein kinases (CDKs), bromodomain-containing protein 4 (BRD4), Polo-like kinases 3 (Plk3) and Abelson murine leukemia viral oncogene 1 and 2 (c-Abl1/2).
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24
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Strand KA, Lu S, Mutryn MF, Li L, Zhou Q, Enyart BT, Jolly AJ, Dubner AM, Moulton KS, Nemenoff RA, Koch KA, LaBarbera DV, Weiser-Evans MCM. High Throughput Screen Identifies the DNMT1 (DNA Methyltransferase-1) Inhibitor, 5-Azacytidine, as a Potent Inducer of PTEN (Phosphatase and Tensin Homolog): Central Role for PTEN in 5-Azacytidine Protection Against Pathological Vascular Remodeling. Arterioscler Thromb Vasc Biol 2020; 40:1854-1869. [PMID: 32580634 DOI: 10.1161/atvbaha.120.314458] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Our recent work demonstrates that PTEN (phosphatase and tensin homolog) is an important regulator of smooth muscle cell (SMC) phenotype. SMC-specific PTEN deletion promotes spontaneous vascular remodeling and PTEN loss correlates with increased atherosclerotic lesion severity in human coronary arteries. In mice, PTEN overexpression reduces plaque area and preserves SMC contractile protein expression in atherosclerosis and blunts Ang II (angiotensin II)-induced pathological vascular remodeling, suggesting that pharmacological PTEN upregulation could be a novel therapeutic approach to treat vascular disease. Approach and Results: To identify novel PTEN activators, we conducted a high-throughput screen using a fluorescence based PTEN promoter-reporter assay. After screening ≈3400 compounds, 11 hit compounds were chosen based on level of activity and mechanism of action. Following in vitro confirmation, we focused on 5-azacytidine, a DNMT1 (DNA methyltransferase-1) inhibitor, for further analysis. In addition to PTEN upregulation, 5-azacytidine treatment increased expression of genes associated with a differentiated SMC phenotype. 5-Azacytidine treatment also maintained contractile gene expression and reduced inflammatory cytokine expression after PDGF (platelet-derived growth factor) stimulation, suggesting 5-azacytidine blocks PDGF-induced SMC de-differentiation. However, these protective effects were lost in PTEN-deficient SMCs. These findings were confirmed in vivo using carotid ligation in SMC-specific PTEN knockout mice treated with 5-azacytidine. In wild type controls, 5-azacytidine reduced neointimal formation and inflammation while maintaining contractile protein expression. In contrast, 5-azacytidine was ineffective in PTEN knockout mice, indicating that the protective effects of 5-azacytidine are mediated through SMC PTEN upregulation. CONCLUSIONS Our data indicates 5-azacytidine upregulates PTEN expression in SMCs, promoting maintenance of SMC differentiation and reducing pathological vascular remodeling in a PTEN-dependent manner.
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Affiliation(s)
- Keith A Strand
- From the Division of Renal Diseases and Hypertension, Department of Medicine (K.A.S., S.L., M.F.M., A.J.J., A.M.D., R.A.N., M.C.M.W.-E.), University of Colorado, Anschutz Medical Campus, Aurora
| | - Sizhao Lu
- From the Division of Renal Diseases and Hypertension, Department of Medicine (K.A.S., S.L., M.F.M., A.J.J., A.M.D., R.A.N., M.C.M.W.-E.), University of Colorado, Anschutz Medical Campus, Aurora
| | - Marie F Mutryn
- From the Division of Renal Diseases and Hypertension, Department of Medicine (K.A.S., S.L., M.F.M., A.J.J., A.M.D., R.A.N., M.C.M.W.-E.), University of Colorado, Anschutz Medical Campus, Aurora
| | - Linfeng Li
- School of Pharmacy and Pharmaceutical Sciences (L.L., Q.Z., D.V.L.), University of Colorado, Anschutz Medical Campus, Aurora
| | - Qiong Zhou
- School of Pharmacy and Pharmaceutical Sciences (L.L., Q.Z., D.V.L.), University of Colorado, Anschutz Medical Campus, Aurora
| | - Blake T Enyart
- School of Medicine, Consortium for Fibrosis Research & Translation (B.T.E., K.S.M., R.A.N., K.A.K., M.C.M.W.-E.), University of Colorado, Anschutz Medical Campus, Aurora.,Division of Cardiology, Department of Medicine (B.T.E., K.S.M., K.A.K.), University of Colorado, Anschutz Medical Campus, Aurora
| | - Austin J Jolly
- From the Division of Renal Diseases and Hypertension, Department of Medicine (K.A.S., S.L., M.F.M., A.J.J., A.M.D., R.A.N., M.C.M.W.-E.), University of Colorado, Anschutz Medical Campus, Aurora
| | - Allison M Dubner
- From the Division of Renal Diseases and Hypertension, Department of Medicine (K.A.S., S.L., M.F.M., A.J.J., A.M.D., R.A.N., M.C.M.W.-E.), University of Colorado, Anschutz Medical Campus, Aurora
| | - Karen S Moulton
- School of Medicine, Consortium for Fibrosis Research & Translation (B.T.E., K.S.M., R.A.N., K.A.K., M.C.M.W.-E.), University of Colorado, Anschutz Medical Campus, Aurora.,Division of Cardiology, Department of Medicine (B.T.E., K.S.M., K.A.K.), University of Colorado, Anschutz Medical Campus, Aurora
| | - Raphael A Nemenoff
- From the Division of Renal Diseases and Hypertension, Department of Medicine (K.A.S., S.L., M.F.M., A.J.J., A.M.D., R.A.N., M.C.M.W.-E.), University of Colorado, Anschutz Medical Campus, Aurora.,School of Medicine, Consortium for Fibrosis Research & Translation (B.T.E., K.S.M., R.A.N., K.A.K., M.C.M.W.-E.), University of Colorado, Anschutz Medical Campus, Aurora
| | - Keith A Koch
- School of Medicine, Consortium for Fibrosis Research & Translation (B.T.E., K.S.M., R.A.N., K.A.K., M.C.M.W.-E.), University of Colorado, Anschutz Medical Campus, Aurora.,Division of Cardiology, Department of Medicine (B.T.E., K.S.M., K.A.K.), University of Colorado, Anschutz Medical Campus, Aurora
| | - Daniel V LaBarbera
- School of Pharmacy and Pharmaceutical Sciences (L.L., Q.Z., D.V.L.), University of Colorado, Anschutz Medical Campus, Aurora
| | - Mary C M Weiser-Evans
- From the Division of Renal Diseases and Hypertension, Department of Medicine (K.A.S., S.L., M.F.M., A.J.J., A.M.D., R.A.N., M.C.M.W.-E.), University of Colorado, Anschutz Medical Campus, Aurora.,School of Medicine, Consortium for Fibrosis Research & Translation (B.T.E., K.S.M., R.A.N., K.A.K., M.C.M.W.-E.), University of Colorado, Anschutz Medical Campus, Aurora
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25
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Abbas A, Romigh T, Eng C. PTEN interacts with RNA polymerase II to dephosphorylate polymerase II C-terminal domain. Oncotarget 2019; 10:4951-4959. [PMID: 31452836 PMCID: PMC6697640 DOI: 10.18632/oncotarget.27128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 07/17/2019] [Indexed: 11/25/2022] Open
Abstract
Gene transcription is a highly complex and strictly regulated process. RNA polymerase II (Pol II) C-terminal domain (CTD) undergoes massive cycles of phosphorylation and dephosphorylation during the process of gene transcription. These post-translational modifications of CTD provide an interactive platform for various factors required for transcription initiation, elongation, termination, and co-transcriptional RNA processing. Pol II CTD kinases and phosphatases are key regulators and any deviation may cause genome-wide transcriptional dysregulation leading to various pathological conditions including cancer. PTEN, a well known tumor suppressor, is one of the most commonly somatically altered in diverse malignancies. When mutated in the germline, PTEN causes cancer predisposition. Numerous studies have demonstrated that PTEN regulates the expression of hundreds of genes, however, no mechanism is known so far. PTEN is a dual specificity phosphatase, using both lipid and protein as substrates. In the present study, we demonstrate that PTEN interacts with the RNA Pol II and that PTEN expression is inversely correlated with global phosphorylation of Pol II CTD. Furthermore, PTEN dephosphorylates Pol II CTD in vitro with a significant specificity for Ser5p. Interestingly, ChIP-seq data analysis revealed that PTEN globally binds to promoter proximal regions, and PTEN loss increases genome-wide Pol II Ser5p occupancy, suggest that PTEN is a Pol II CTD phosphatase. Our observations demonstrate an unexplored function of PTEN with the potential of global transcriptional regulation, adding a new dimension to somatic carcinogenesis and germline cancer predisposition.
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Affiliation(s)
- Ata Abbas
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, 44195 OH, USA.,Present address: Division of Hematology Oncology, Department of Medicine, Case Western Reserve University, Cleveland, 44106 OH, USA
| | - Todd Romigh
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, 44195 OH, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, 44195 OH, USA.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, 44195 OH, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, 44116 OH, USA.,Germline High Risk Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, 44116 OH, USA
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