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Yucel-Polat A, Campos-Melo D, Alikhah A, Strong MJ. Dynamic Localization of Paraspeckle Components under Osmotic Stress. Noncoding RNA 2024; 10:23. [PMID: 38668381 PMCID: PMC11053584 DOI: 10.3390/ncrna10020023] [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: 03/11/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024] Open
Abstract
Paraspeckles are nuclear condensates formed by NEAT1_2 lncRNA and different RNA-binding proteins. In general, these membraneless organelles function in the regulation of gene expression and translation and in miRNA processing, and in doing this, they regulate cellular homeostasis and mediate pro-survival in the cell. Despite evidence showing the importance of paraspeckles in the stress response, the dynamics of paraspeckles and their components under conditions of osmotic stress remain unknown. We exposed HEK293T cells to sorbitol and examined NEAT1_2 expression using real-time PCR. Localization and quantification of the main paraspeckle components, NEAT1_2, PSPC1, NONO, and SFPQ, in different cellular compartments was performed using smFISH and immunofluorescence. Our findings showed a significant decrease in total NEAT1_2 expression in cells after osmotic stress. Sorbitol shifted the subcellular localization of NEAT1_2, PSPC1, NONO, and SFPQ from the nucleus to the cytoplasm and decreased the number and size of NEAT1_2 foci in the nucleus. PSPC1 formed immunoreactive cytoplasmic fibrils under conditions of osmotic stress, which slowly disassembled under recovery. Our study deepens the paraspeckle dynamics in response to stress, suggesting a novel role for NEAT1_2 in the cytoplasm in osmotic stress and physiological conditions.
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Affiliation(s)
- Aysegul Yucel-Polat
- Molecular Medicine Group, Schulich School of Medicine & Dentistry, Robarts Research Institute, Western University, London, ON N6A 3K7, Canada; (A.Y.-P.); (A.A.)
| | - Danae Campos-Melo
- Molecular Medicine Group, Schulich School of Medicine & Dentistry, Robarts Research Institute, Western University, London, ON N6A 3K7, Canada; (A.Y.-P.); (A.A.)
| | - Asieh Alikhah
- Molecular Medicine Group, Schulich School of Medicine & Dentistry, Robarts Research Institute, Western University, London, ON N6A 3K7, Canada; (A.Y.-P.); (A.A.)
| | - Michael J. Strong
- Molecular Medicine Group, Schulich School of Medicine & Dentistry, Robarts Research Institute, Western University, London, ON N6A 3K7, Canada; (A.Y.-P.); (A.A.)
- Department of Clinical Neurological Sciences, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada
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2
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Li H, Jiao W, Song J, Wang J, Chen G, Li D, Wang X, Bao B, Du X, Cheng Y, Yang C, Tong Q, Zheng L. circ-hnRNPU inhibits NONO-mediated c-Myc transactivation and mRNA stabilization essential for glycosylation and cancer progression. J Exp Clin Cancer Res 2023; 42:313. [PMID: 37993881 PMCID: PMC10666356 DOI: 10.1186/s13046-023-02898-5] [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: 07/28/2023] [Accepted: 11/12/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Recent evidence reveals the emerging functions of circular RNA (circRNA) and protein glycosylation in cancer progression. However, the roles of circRNA in regulating glycosyltransferase expression in gastric cancer remain to be determined. METHODS Circular RNAs (circRNAs) were validated by Sanger sequencing. Co-immunoprecipitation, mass spectrometry, and RNA sequencing assays were applied to explore protein interaction and target genes. Gene expression regulation was observed by chromatin immunoprecipitation, RNA immunoprecipitation, dual-luciferase reporter, real-time quantitative RT-PCR, and western blot assays. Gain- and loss-of-function studies were performed to observe the impacts of circRNA and its partners on the glycosylation, growth, invasion, and metastasis of gastric cancer cells. RESULTS Circ-hnRNPU, an exonic circRNA derived from heterogenous nuclear ribonuclear protein U (hnRNPU), was identified to exert tumor suppressive roles in protein glycosylation and progression of gastric cancer. Mechanistically, circ-hnRNPU physically interacted with non-POU domain containing octamer binding (NONO) protein to induce its cytoplasmic retention, resulting in down-regulation of glycosyltransferases (GALNT2, GALNT6, MGAT1) and parental gene hnRNPU via repression of nuclear NONO-mediated c-Myc transactivation or cytoplasmic NONO-facilitated mRNA stability. Rescue studies indicated that circ-hnRNPU inhibited the N- and O-glycosylation, growth, invasion, and metastasis of gastric cancer cells via interacting with NONO protein. Pre-clinically, administration of lentivirus carrying circ-hnRNPU suppressed the protein glycosylation, tumorigenesis, and aggressiveness of gastric cancer xenografts. In clinical cases, low circ-hnRNPU levels and high NONO or c-Myc expression were associated with poor survival outcome of gastric cancer patients. CONCLUSIONS These findings indicate that circ-hnRNPU inhibits NONO-mediated c-Myc transactivation and mRNA stabilization essential for glycosylation and cancer progression.
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Affiliation(s)
- Hongjun Li
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, P. R. China
| | - Wanju Jiao
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, P. R. China
| | - Jiyu Song
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, P. R. China
| | - Jianqun Wang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, P. R. China
| | - Guo Chen
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, P. R. China
| | - Dan Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, P. R. China
| | - Xiaojing Wang
- Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, P. R. China
| | - Banghe Bao
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, P. R. China
| | - Xinyi Du
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, P. R. China
| | - Yang Cheng
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, P. R. China
| | - Chunhui Yang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, P. R. China
| | - Qiangsong Tong
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, P. R. China.
| | - Liduan Zheng
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, P. R. China.
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3
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Longitudinal single-cell profiling of chemotherapy response in acute myeloid leukemia. Nat Commun 2023; 14:1285. [PMID: 36890137 PMCID: PMC9995364 DOI: 10.1038/s41467-023-36969-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/22/2023] [Indexed: 03/10/2023] Open
Abstract
Acute myeloid leukemia may be characterized by a fraction of leukemia stem cells (LSCs) that sustain disease propagation eventually leading to relapse. Yet, the contribution of LSCs to early therapy resistance and AML regeneration remains controversial. We prospectively identify LSCs in AML patients and xenografts by single-cell RNA sequencing coupled with functional validation by a microRNA-126 reporter enriching for LSCs. Through nucleophosmin 1 (NPM1) mutation calling or chromosomal monosomy detection in single-cell transcriptomes, we discriminate LSCs from regenerating hematopoiesis, and assess their longitudinal response to chemotherapy. Chemotherapy induced a generalized inflammatory and senescence-associated response. Moreover, we observe heterogeneity within progenitor AML cells, some of which proliferate and differentiate with expression of oxidative-phosphorylation (OxPhos) signatures, while others are OxPhos (low) miR-126 (high) and display enforced stemness and quiescence features. miR-126 (high) LSCs are enriched at diagnosis in chemotherapy-refractory AML and at relapse, and their transcriptional signature robustly stratifies patients for survival in large AML cohorts.
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4
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Reddy D, Bhattacharya S, Levy M, Zhang Y, Gogol M, Li H, Florens L, Workman JL. Paraspeckles interact with SWI/SNF subunit ARID1B to regulate transcription and splicing. EMBO Rep 2023; 24:e55345. [PMID: 36354291 PMCID: PMC9827562 DOI: 10.15252/embr.202255345] [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: 05/03/2022] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 11/12/2022] Open
Abstract
Paraspeckles are subnuclear RNA-protein structures that are implicated in important processes including cellular stress response, differentiation, and cancer progression. However, it is unclear how paraspeckles impart their physiological effect at the molecular level. Through biochemical analyses, we show that paraspeckles interact with the SWI/SNF chromatin-remodeling complex. This is specifically mediated by the direct interaction of the long-non-coding RNA NEAT1 of the paraspeckles with ARID1B of the cBAF-type SWI/SNF complex. Strikingly, ARID1B depletion, in addition to resulting in loss of interaction with the SWI/SNF complex, decreases the binding of paraspeckle proteins to chromatin modifiers, transcription factors, and histones. Functionally, the loss of ARID1B and NEAT1 influences the transcription and the alternative splicing of a common set of genes. Our findings reveal that dynamic granules such as the paraspeckles may leverage the specificity of epigenetic modifiers to impart their regulatory effect, thus providing a molecular basis for their function.
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Affiliation(s)
- Divya Reddy
- Stowers Institute for Medical ResearchKansas CityMOUSA
| | | | | | - Ying Zhang
- Stowers Institute for Medical ResearchKansas CityMOUSA
| | | | - Hua Li
- Stowers Institute for Medical ResearchKansas CityMOUSA
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5
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Zhang Z, Sun J. The Origin of Clonal Hematopoiesis and Its Implication in Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1442:65-83. [PMID: 38228959 DOI: 10.1007/978-981-99-7471-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Clonal expansion of hematopoietic cells is first observed in hematological malignancies where all the leukemic cells can be traced back to a single cell carrying oncogenic alterations. Interestingly, expansion of hematopoietic clones with defined genomic alterations, including single nucleotide variants (SNVs), small insertions and deletions (indels), and large structural chromosomal alterations (CAs), is also found in the healthy population. These genomic changes often affect leukemia driver genes. As a result, healthy individuals bearing such clonal hematopoiesis (CH) are at a higher risk of hematological malignancies. In addition to blood cancers, SNV/indel-related CH has been found associated with elevated cardiovascular and all-cause mortality, indicating adverse impacts of abnormalities in the blood on the normal functions of non-hematological tissues. In the past decade, much effort has been invested in understanding the origins of CH and its causal relationship with diseases in hematological and non-hematological tissues. Here, we review recent progress in these areas and discuss future directions that can be pursued to translate the acquired knowledge into better management of CH-related diseases.
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Affiliation(s)
- Zhen Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jianlong Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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6
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Yang Y, Li M, Ma Y, Ye W, Si Y, Zheng X, Liu H, Cheng L, Zhang L, Zhang H, Zhang X, Lei Y, Shen L, Zhang F, Ma H. LncRNA NEAT1 Potentiates SREBP2 Activity to Promote Inflammatory Macrophage Activation and Limit Hantaan Virus Propagation. Front Microbiol 2022; 13:849020. [PMID: 35495674 PMCID: PMC9044491 DOI: 10.3389/fmicb.2022.849020] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/10/2022] [Indexed: 11/17/2022] Open
Abstract
As the global prototypical zoonotic hantavirus, Hantaan virus (HTNV) is prevalent in Asia and is the leading causative agent of severe hemorrhagic fever with renal syndrome (HFRS), which has profound morbidity and mortality. Macrophages are crucial components of the host innate immune system and serve as the first line of defense against HTNV infection. Previous studies indicated that the viral replication efficiency in macrophages determines hantavirus pathogenicity, but it remains unknown which factor manipulates the macrophage activation pattern and the virus-host interaction process. Here, we performed the transcriptomic analysis of HTNV-infected mouse bone marrow-derived macrophages and identified the long noncoding RNA (lncRNA) nuclear enriched abundant transcript 1 (NEAT1), especially the isoform NEAT1-2, as one of the lncRNAs that is differentially expressed at the early phase. Based on coculture experiments, we revealed that silencing NEAT1-2 hinders inflammatory macrophage activation and facilitates HTNV propagation, while enhancing NEAT1-2 transcription effectively restrains viral replication. Furthermore, sterol response element binding factor-2 (SREBP2), which controls the cholesterol metabolism process, was found to stimulate macrophages by promoting the production of multiple inflammatory cytokines upon HTNV infection. NEAT1-2 could potentiate SREBP2 activity by upregulating Srebf1 expression and interacting with SREBP2, thus stimulating inflammatory macrophages and limiting HTNV propagation. More importantly, we demonstrated that the NEAT1-2 expression level in patient monocytes was negatively correlated with viral load and HFRS disease progression. Our results identified a function and mechanism of action for the lncRNA NEAT1 in heightening SREBP2-mediated macrophage activation to restrain hantaviral propagation and revealed the association of NEAT1 with HFRS severity.
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Affiliation(s)
- Yongheng Yang
- College of Life Sciences, Northwest University, Xi'an, China.,Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Mengyun Li
- College of Life Sciences, Northwest University, Xi'an, China.,Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Yongtao Ma
- Department of Emergency, Children's Hospital of Kaifeng City, Kaifeng, China
| | - Wei Ye
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Yue Si
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Xuyang Zheng
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China.,Department of Infectious Diseases, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - He Liu
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Linfeng Cheng
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Liang Zhang
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Hui Zhang
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Xijing Zhang
- Department of Anesthesiology and Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Yingfeng Lei
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Lixin Shen
- College of Life Sciences, Northwest University, Xi'an, China
| | - Fanglin Zhang
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Hongwei Ma
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China.,Department of Anesthesiology and Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
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7
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Binder M, Carr RM, Lasho TL, Finke CM, Mangaonkar AA, Pin CL, Berger KR, Mazzone A, Potluri S, Ordog T, Robertson KD, Marks DL, Fernandez-Zapico ME, Gaspar-Maia A, Patnaik MM. Oncogenic gene expression and epigenetic remodeling of cis-regulatory elements in ASXL1-mutant chronic myelomonocytic leukemia. Nat Commun 2022; 13:1434. [PMID: 35301312 PMCID: PMC8931048 DOI: 10.1038/s41467-022-29142-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/24/2022] [Indexed: 12/14/2022] Open
Abstract
Myeloid neoplasms are clonal hematopoietic stem cell disorders driven by the sequential acquisition of recurrent genetic lesions. Truncating mutations in the chromatin remodeler ASXL1 (ASXL1MT) are associated with a high-risk disease phenotype with increased proliferation, epigenetic therapeutic resistance, and poor survival outcomes. We performed a multi-omics interrogation to define gene expression and chromatin remodeling associated with ASXL1MT in chronic myelomonocytic leukemia (CMML). ASXL1MT are associated with a loss of repressive histone methylation and increase in permissive histone methylation and acetylation in promoter regions. ASXL1MT are further associated with de novo accessibility of distal enhancers binding ETS transcription factors, targeting important leukemogenic driver genes. Chromatin remodeling of promoters and enhancers is strongly associated with gene expression and heterogenous among overexpressed genes. These results provide a comprehensive map of the transcriptome and chromatin landscape of ASXL1MT CMML, forming an important framework for the development of novel therapeutic strategies targeting oncogenic cis interactions.
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Affiliation(s)
- Moritz Binder
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ryan M Carr
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Terra L Lasho
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Christopher L Pin
- Lawson Health Research Institute, University of Western Ontario, London, ON, Canada
| | - Kurt R Berger
- Lawson Health Research Institute, University of Western Ontario, London, ON, Canada
| | - Amelia Mazzone
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sandeep Potluri
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Tamas Ordog
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Keith D Robertson
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - David L Marks
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, MN, USA
| | - Martin E Fernandez-Zapico
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, MN, USA
| | - Alexandre Gaspar-Maia
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| | - Mrinal M Patnaik
- Division of Hematology, Mayo Clinic, Rochester, MN, USA.
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
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8
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Exploring New Functional Aspects of HTLV-1 RNA-Binding Protein Rex: How Does Rex Control Viral Replication? Viruses 2022; 14:v14020407. [PMID: 35216000 PMCID: PMC8877913 DOI: 10.3390/v14020407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 01/27/2023] Open
Abstract
After integration to the human genome as a provirus, human T-cell leukemia virus type 1 (HTLV-1) utilizes host T cell gene expression machinery for viral replication. The viral RNA-binding protein, Rex, is known to transport unspliced/incompletely spliced viral mRNAs encoding viral structural proteins out of the nucleus to enhance virus particle formation. However, the detailed mechanism of how Rex avoids extra splicing of unspliced/incompletely spliced viral mRNAs and stabilizes them for effective translation is still unclear. To elucidate the underlying molecular mechanism of Rex function, we comprehensively analyzed the changes in gene expression and splicing patterns in Rex-overexpressing T cells. In addition, we identified 81 human proteins interacting with Rex, involved in transcription, splicing, translation, and mRNA quality control. In particular, Rex interacts with NONO and SFPQ, which play important roles in the regulation of transcription and splicing. Accordingly, expression profiles and splicing patterns of a wide variety of genes are significantly changed in Rex-expressing T cells. Especially, the level of vPD-L1 mRNA that lacks the part of exon 4, thus encodes soluble PD-L1 was significantly increased in Rex-expressing cells. Overall, by integrated analysis of these three datasets, we showed for the first time that Rex intervenes the host gene expression machinery throughout the pathway, probably to escort viral unstable mRNAs from transcription (start) to translation (end). Upon exerting its function, Rex may alter the expression level and splicing patterns of various genes, thus influencing the phenotype of the host cell.
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9
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Liu X, Sato N, Shimosato Y, Wang TW, Denda T, Chang YH, Yabushita T, Fujino T, Asada S, Tanaka Y, Fukuyama T, Enomoto Y, Ota Y, Sakamoto T, Kitamura T, Goyama S. CHIP-associated mutant ASXL1 in blood cells promotes solid tumor progression. Cancer Sci 2022; 113:1182-1194. [PMID: 35133065 PMCID: PMC8990791 DOI: 10.1111/cas.15294] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/23/2022] [Accepted: 01/28/2022] [Indexed: 11/30/2022] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is an age‐associated phenomenon characterized by clonal expansion of blood cells harboring somatic mutations in hematopoietic genes, including DNMT3A, TET2, and ASXL1. Clinical evidence suggests that CHIP is highly prevalent and associated with poor prognosis in solid‐tumor patients. However, whether blood cells with CHIP mutations play a causal role in promoting the development of solid tumors remained unclear. Using conditional knock‐in mice that express CHIP‐associated mutant Asxl1 (Asxl1‐MT), we showed that expression of Asxl1‐MT in T cells, but not in myeloid cells, promoted solid‐tumor progression in syngeneic transplantation models. We also demonstrated that Asxl1‐MT–expressing blood cells accelerated the development of spontaneous mammary tumors induced by MMTV‐PyMT. Intratumor analysis of the mammary tumors revealed the reduced T‐cell infiltration at tumor sites and programmed death receptor‐1 (PD‐1) upregulation in CD8+ T cells in MMTV‐PyMT/Asxl1‐MT mice. In addition, we found that Asxl1‐MT induced T‐cell dysregulation, including aberrant intrathymic T‐cell development, decreased CD4/CD8 ratio, and naïve‐memory imbalance in peripheral T cells. These results indicate that Asxl1‐MT perturbs T‐cell development and function, which contributes to creating a protumor microenvironment for solid tumors. Thus, our findings raise the possibility that ASXL1‐mutated blood cells exacerbate solid‐tumor progression in ASXL1‐CHIP carriers.
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Affiliation(s)
- Xiaoxiao Liu
- Division of Molecular Oncology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Naru Sato
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuko Shimosato
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Teh-Wei Wang
- Division of Cancer Cell Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tamami Denda
- Department of Pathology, The Institute of Medical Science Research Hospital, The University of Tokyo, Tokyo, Japan
| | - Yu-Hsuan Chang
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tomohiro Yabushita
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takeshi Fujino
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shuhei Asada
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,The Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo, Japan
| | - Yosuke Tanaka
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tomofusa Fukuyama
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yutaka Enomoto
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasunori Ota
- Department of Pathology, The Institute of Medical Science Research Hospital, The University of Tokyo, Tokyo, Japan
| | - Takeharu Sakamoto
- Department of Cancer Biology, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan
| | - Toshio Kitamura
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Susumu Goyama
- Division of Molecular Oncology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
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10
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Abstract
The development of therapies to eliminate the latent HIV-1 reservoir is hampered by our incomplete understanding of the biomolecular mechanism governing HIV-1 latency. To further complicate matters, recent single cell RNA-seq studies reported extensive heterogeneity between latently HIV-1-infected primary T cells, implying that latent HIV-1 infection can persist in greatly differing host cell environments. We here show that transcriptomic heterogeneity is also found between latently infected T cell lines, which allowed us to study the underlying mechanisms of intercell heterogeneity at high signal resolution. Latently infected T cells exhibited a de-differentiated phenotype, characterized by the loss of T cell-specific markers and gene regulation profiles reminiscent of hematopoietic stem cells (HSC). These changes had functional consequences. As reported for stem cells, latently HIV-1 infected T cells efficiently forced lentiviral superinfections into a latent state and favored glycolysis. As a result, metabolic reprogramming or cell re-differentiation destabilized latent infection. Guided by these findings, data-mining of single cell RNA-seq data of latently HIV-1 infected primary T cells from patients revealed the presence of similar dedifferentiation motifs. >20% of the highly detectable genes that were differentially regulated in latently infected cells were associated with hematopoietic lineage development (e.g. HUWE1, IRF4, PRDM1, BATF3, TOX, ID2, IKZF3, CDK6) or were hematopoietic markers (SRGN; hematopoietic proteoglycan core protein). The data add to evidence that the biomolecular phenotype of latently HIV-1 infected cells differs from normal T cells and strategies to address their differential phenotype need to be considered in the design of therapeutic cure interventions. IMPORTANCE HIV-1 persists in a latent reservoir in memory CD4 T cells for the lifetime of a patient. Understanding the biomolecular mechanisms used by the host cells to suppress viral expression will provide essential insights required to develop curative therapeutic interventions. Unfortunately, our current understanding of these control mechanisms is still limited. By studying gene expression profiles, we demonstrated that latently HIV-1-infected T cells have a de-differentiated T cell phenotype. Software-based data integration allowed for the identification of drug targets that would re-differentiate viral host cells and, in extension, destabilize latent HIV-1 infection events. The importance of the presented data lies within the clear demonstration that HIV-1 latency is a host cell phenomenon. As such, therapeutic strategies must first restore proper host cell functionality to accomplish efficient HIV-1 reactivation.
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Abstract
Advances in population-scale genomic sequencing have greatly expanded the understanding of the inherited basis of cardiovascular disease (CVD). Reanalysis of these genomic datasets identified an unexpected risk factor for CVD, somatically acquired DNA mutations. In this review, we provide an overview of somatic mutations and their contributions to CVD. We focus on the most common and well-described manifestation, clonal hematopoiesis of indeterminate potential. We also review the currently available data regarding how somatic mutations lead to tissue mosaicism in various forms of CVD, including atrial fibrillation and aortic aneurism associated with Marfan Syndrome. Finally, we highlight future research directions given current knowledge gaps and consider how technological advances will enhance the discovery of somatic mutations in CVD and management of patients with somatic mutations.
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Affiliation(s)
- J. Brett Heimlich
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center
| | - Alexander G. Bick
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center
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Godet AC, Roussel E, David F, Hantelys F, Morfoisse F, Alves J, Pujol F, Ader I, Bertrand E, Burlet-Schiltz O, Froment C, Henras AK, Vitali P, Lacazette E, Tatin F, Garmy-Susini B, Prats AC. Long non-coding RNA Neat1 and paraspeckle components are translational regulators in hypoxia. eLife 2022; 11:69162. [PMID: 36546462 PMCID: PMC9799981 DOI: 10.7554/elife.69162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
Internal ribosome entry sites (IRESs) drive translation initiation during stress. In response to hypoxia, (lymph)angiogenic factors responsible for tissue revascularization in ischemic diseases are induced by the IRES-dependent mechanism. Here, we searched for IRES trans-acting factors (ITAFs) active in early hypoxia in mouse cardiomyocytes. Using knock-down and proteomics approaches, we show a link between a stressed-induced nuclear body, the paraspeckle, and IRES-dependent translation. Furthermore, smiFISH experiments demonstrate the recruitment of IRES-containing mRNA into paraspeckle during hypoxia. Our data reveal that the long non-coding RNA Neat1, an essential paraspeckle component, is a key translational regulator, active on IRESs of (lymph)angiogenic and cardioprotective factor mRNAs. In addition, paraspeckle proteins p54nrb and PSPC1 as well as nucleolin and RPS2, two p54nrb-interacting proteins identified by mass spectrometry, are ITAFs for IRES subgroups. Paraspeckle thus appears as a platform to recruit IRES-containing mRNAs and possibly host IRESome assembly. Polysome PCR array shows that Neat1 isoforms regulate IRES-dependent translation and, more widely, translation of mRNAs involved in stress response.
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Affiliation(s)
| | - Emilie Roussel
- UMR 1297-I2MC, Inserm, Université de ToulouseToulouseFrance
| | - Florian David
- UMR 1297-I2MC, Inserm, Université de ToulouseToulouseFrance
| | | | | | - Joffrey Alves
- UMR 1297-I2MC, Inserm, Université de ToulouseToulouseFrance
| | | | - Isabelle Ader
- UMR 1301-RESTORE, Inserm, CNRS 5070, Etablissement Français du Sang-Occitanie (EFS), National Veterinary School of Toulouse (ENVT), Université de ToulouseToulouseFrance
| | | | - Odile Burlet-Schiltz
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRSToulouseFrance
| | - Carine Froment
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRSToulouseFrance
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de ToulouseToulouseFrance
| | - Patrice Vitali
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de ToulouseToulouseFrance
| | - Eric Lacazette
- UMR 1297-I2MC, Inserm, Université de ToulouseToulouseFrance
| | - Florence Tatin
- UMR 1297-I2MC, Inserm, Université de ToulouseToulouseFrance
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Suzuki HI, Onimaru K. Biomolecular condensates in cancer biology. Cancer Sci 2021; 113:382-391. [PMID: 34865286 PMCID: PMC8819300 DOI: 10.1111/cas.15232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022] Open
Abstract
Understanding the characteristics of cancer cells is essential for the development of improved diagnosis and therapeutics. From a gene regulation perspective, the super‐enhancer concept has been introduced to systematically understand the molecular mechanisms underlying the identities of various cell types and has been extended to the analysis of cancer cells and cancer genome alterations. In addition, several characteristic features of super‐enhancers have led to the recognition of the link between gene regulation and biomolecular condensates, which is often mediated by liquid‐liquid phase separation. Several lines of evidence have suggested molecular and biophysical principles and their alterations in cancer cells, which are particularly associated with gene regulation and cell signaling (“ transcriptional” and “signaling” condensates). These findings collectively suggest that the modification of biomolecular condensates represents an important mechanism by which cancer cells acquire various cancer hallmark traits and establish functional innovation for cancer initiation and progression. The condensate model also provides the molecular basis of the vulnerability of cancer cells to transcriptional perturbation and further suggests the possibility of therapeutic targeting of condensates. This review summarizes recent findings regarding the relationships between super‐enhancers and biomolecular condensate models, multiple scenarios of condensate alterations in cancers, and the potential of the condensate model for therapeutic development.
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Affiliation(s)
- Hiroshi I Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
| | - Koh Onimaru
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.,RIKEN Center for Biosystems Dynamics Research, Wako, Japan
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