1
|
Zago Baltazar R, Claerhout S, Vander Borght S, Spans L, Sciot R, Schöffski P, Hompes D, Sinnaeve F, Wafa H, Renard M, van den Hout MFCM, Vernemmen A, Libbrecht L, De Roo A, Mazzeo F, van Marcke C, Deraedt K, Bourgain C, Vanden Bempt I. Recurrent and novel fusions detected by targeted RNA sequencing as part of the diagnostic workflow of soft tissue and bone tumours. J Pathol Clin Res 2024; 10:e12376. [PMID: 38738521 PMCID: PMC11089496 DOI: 10.1002/2056-4538.12376] [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: 12/04/2023] [Revised: 03/16/2024] [Accepted: 04/15/2024] [Indexed: 05/14/2024]
Abstract
The identification of gene fusions has become an integral part of soft tissue and bone tumour diagnosis. We investigated the added value of targeted RNA-based sequencing (targeted RNA-seq, Archer FusionPlex) to our current molecular diagnostic workflow of these tumours, which is based on fluorescence in situ hybridisation (FISH) for the detection of gene fusions using 25 probes. In a series of 131 diagnostic samples targeted RNA-seq identified a gene fusion, BCOR internal tandem duplication or ALK deletion in 47 cases (35.9%). For 74 cases, encompassing 137 FISH analyses, concordance between FISH and targeted RNA-seq was evaluated. A positive or negative FISH result was confirmed by targeted RNA-seq in 27 out of 49 (55.1%) and 81 out of 88 (92.0%) analyses, respectively. While negative concordance was high, targeted RNA-seq identified a canonical gene fusion in seven cases despite a negative FISH result. The 22 discordant FISH-positive analyses showed a lower percentage of rearrangement-positive nuclei (range 15-41%) compared to the concordant FISH-positive analyses (>41% of nuclei in 88.9% of cases). Six FISH analyses (in four cases) were finally considered false positive based on histological and targeted RNA-seq findings. For the EWSR1 FISH probe, we observed a gene-dependent disparity (p = 0.0020), with 8 out of 35 cases showing a discordance between FISH and targeted RNA-seq (22.9%). This study demonstrates an added value of targeted RNA-seq to our current diagnostic workflow of soft tissue and bone tumours in 19 out of 131 cases (14.5%), which we categorised as altered diagnosis (3 cases), added precision (6 cases), or augmented spectrum (10 cases). In the latter subgroup, four novel fusion transcripts were found for which the clinical relevance remains unclear: NAB2::NCOA2, YAP1::NUTM2B, HSPA8::BRAF, and PDE2A::PLAG1. Overall, targeted RNA-seq has proven extremely valuable in the diagnostic workflow of soft tissue and bone tumours.
Collapse
Affiliation(s)
| | - Sofie Claerhout
- Department of Human GeneticsUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Sara Vander Borght
- Department of Human GeneticsUniversity Hospitals KU LeuvenLeuvenBelgium
- Department of PathologyUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Lien Spans
- Department of Human GeneticsUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Raphael Sciot
- Department of PathologyUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Patrick Schöffski
- Department of General Medical OncologyUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Daphne Hompes
- Department of Surgical OncologyUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Friedl Sinnaeve
- Department of Orthopaedic SurgeryUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Hazem Wafa
- Department of Orthopaedic SurgeryUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Marleen Renard
- Department of Paediatric Hemato‐OncologyUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Mari FCM van den Hout
- Department of PathologyMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Astrid Vernemmen
- Department of PathologyMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Louis Libbrecht
- Department of PathologyCliniques Universitaires Saint‐LucBrusselsBelgium
- Department of PathologyAZ GroeningeKortrijkBelgium
| | - An‐Katrien De Roo
- Department of PathologyCliniques Universitaires Saint‐LucBrusselsBelgium
- Institute of Experimental and Clinical ResearchUCLouvainBrusselsBelgium
| | - Filomena Mazzeo
- Institute of Experimental and Clinical ResearchUCLouvainBrusselsBelgium
- Breast ClinicKing Albert II Cancer Institute, Cliniques Universitaires Saint‐LucBrusselsBelgium
- Department of Medical OncologyKing Albert II Cancer Institute, Cliniques Universitaires Saint‐LucBrusselsBelgium
| | - Cédric van Marcke
- Institute of Experimental and Clinical ResearchUCLouvainBrusselsBelgium
- Breast ClinicKing Albert II Cancer Institute, Cliniques Universitaires Saint‐LucBrusselsBelgium
- Department of Medical OncologyKing Albert II Cancer Institute, Cliniques Universitaires Saint‐LucBrusselsBelgium
| | - Karen Deraedt
- Department of PathologyZiekenhuis Oost‐LimburgGenkBelgium
| | | | | |
Collapse
|
2
|
Damayanti NP, Cordova RA, Rupert C, Delle Fontane I, Shen L, Orsi S, Klunk AJ, Linehan WM, Staschke KA, Hollenhorst PC, Heppner DE, Pili R. TFE3-Splicing Factor Fusions Represent Functional Drivers and Druggable Targets in Translocation Renal Cell Carcinoma. Cancer Res 2024; 84:1286-1302. [PMID: 38266162 DOI: 10.1158/0008-5472.can-23-1789] [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: 07/10/2023] [Revised: 12/05/2023] [Accepted: 01/22/2024] [Indexed: 01/26/2024]
Abstract
TFE3 is a member of the basic helix-loop-helix leucine zipper MiT transcription factor family, and its chimeric proteins are associated with translocation renal cell carcinoma (tRCC). Despite the variety of gene fusions, most TFE3 fusion partner genes are related to spliceosome machinery. Dissecting the function of TFE3 fused to spliceosome machinery factors (TFE3-SF) could direct the development of effective therapies for this lethal disease, which is refractory to standard treatments for kidney cancer. Here, by using a combination of in silico structure prediction, transcriptome profiling, molecular characterization, and high-throughput high-content screening (HTHCS), we interrogated a number of oncogenic mechanisms of TFE3-SF fusions. TFE3-SF fusions drove the transformation of kidney cells and promoted distinct oncogenic phenotypes in a fusion partner-dependent manner, differentially altering the transcriptome and RNA splicing landscape and activating different oncogenic pathways. Inhibiting TFE3-SF dimerization reversed its oncogenic activity and represented a potential target for therapeutic intervention. Screening the FDA-approved drugs library LOPAC and a small-molecule library (Microsource) using HTHCS combined with FRET technology identified compounds that inhibit TFE3-SF dimerization. Hit compounds were validated in 2D and 3D patient-derived xenograft models expressing TFE3-SF. The antihistamine terfenadine decreased cell proliferation and reduced in vivo tumor growth of tRCC. Overall, these results unmask therapeutic strategies to target TFE3-SF dimerization for treating patients with tRCC. SIGNIFICANCE TFE3-splicing factor fusions possess both transcription and splicing factor functions that remodel the transcriptome and spliceosome and can be targeted with dimerization inhibitors to suppress the growth of translocation renal cell carcinoma.
Collapse
Affiliation(s)
- Nur P Damayanti
- Genitourinary Program, Division of Hematology & Oncology, Indiana University, Indianapolis, Indiana
- Department of Neurosurgery, Division of Neuro-Oncology, Indiana University, Indianapolis, Indiana
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
| | - Ricardo A Cordova
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, Indiana
| | - Christopher Rupert
- Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Ilaria Delle Fontane
- Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Li Shen
- Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Sabrina Orsi
- Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Angela J Klunk
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, Indiana
| | - W Marston Linehan
- Urological Oncology Branch, National Cancer Institute, Bethesda, Maryland
| | - Kirk A Staschke
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, Indiana
| | - Peter C Hollenhorst
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | - David E Heppner
- Department of Chemistry, University at Buffalo, Buffalo, New York
| | - Roberto Pili
- Genitourinary Program, Division of Hematology & Oncology, Indiana University, Indianapolis, Indiana
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
- Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| |
Collapse
|
3
|
Almalki WH. NEAT1 in inflammatory infectious diseases: An integrated perspective on molecular modulation. Pathol Res Pract 2024; 254:154956. [PMID: 38218038 DOI: 10.1016/j.prp.2023.154956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 01/15/2024]
Abstract
The long non-coding RNA (lncRNA), NEAT1, has emerged as a central figure in the intricate network of molecular regulators in inflammatory infectious diseases (IIDs). The review initiates a comprehensive exploration of NEAT1's multifaceted roles and molecular interactions in the context of these complex diseases. The study begins by acknowledging the global health burden of IIDs, underscoring the urgency for innovative insights into their pathogenesis and therapeutic avenues. NEAT1 is introduced as a pivotal lncRNA with growing relevance in immune responses and inflammatory processes. The core of this review unravels the NEAT1 landscape, elucidating its involvement in the modulation of immune signalling pathways, regulation of inflammatory cytokines, and interactions with various immune cells during infection. It explores NEAT1's role in orchestrating immune responses and balancing host defence mechanisms with the risk of immunopathology. Furthermore, the review underscores the clinical significance of NEAT1 in infectious diseases, discussing its associations with disease severity, prognosis, and potential as a diagnostic and therapeutic target. It provides insights into ongoing research endeavours aimed at harnessing NEAT1 for innovative disease management strategies, including developing RNA-based therapeutics. Concluding on a forward-looking note, the review highlights the broader implications of NEAT1 in the context of emerging infectious diseases and the possibility for precision medicine approaches that leverage NEAT1's regulatory capacities. In summary, this review illuminates the pivotal role of NEAT1 in IIDs by navigating its complex landscape, offering profound insights into its implications for disease pathogenesis and the development of targeted therapies.
Collapse
Affiliation(s)
- Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.
| |
Collapse
|
4
|
Chen D, Wang J, Li Y, Xu C, Fanzheng M, Zhang P, Liu L. LncRNA NEAT1 suppresses cellular senescence in hepatocellular carcinoma via KIF11-dependent repression of CDKN2A. Clin Transl Med 2023; 13:e1418. [PMID: 37752791 PMCID: PMC10522973 DOI: 10.1002/ctm2.1418] [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: 04/18/2023] [Revised: 09/02/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related deaths worldwide. Therapeutic options for advanced HCC are limited, which is due to a lack of full understanding of pathogenesis. Cellular senescence is a state of cell cycle arrest, which plays important roles in the pathogenesis of HCC. Mechanisms underlying hepatocellular senescence are not fully understood. LncRNA NEAT1 acts as an oncogene and contributes to the development of HCC. Whether NEAT1 modulates hepatocellular senescence in HCC is unknown. METHODS The role of NEAT1 and KIF11 in cellular senescence and tumor growth in HCC was assessed both in vitro and in vivo. RNA pulldown, mass spectrometry, Chromatin immunoprecipitation (ChIP), luciferase reporter assays, RNA FISH and immunofluorescence (IF) staining were used to explore the detailed molecular mechanism of NEAT1 and KIF11 in cellular senescence of HCC. RESULTS We found that NEAT1 was upregulated in tumor tissues and hepatoma cells, which negatively correlated with a senescence biomarker CDKN2A encoding p16INK4a and p14ARF proteins. NEAT1 was reduced in senescent hepatoma cells induced by doxorubicin (DOXO) or serum starvation. Furthermore, NEAT1 deficiency caused senescence in cultured hepatoma cells, and protected against the progression of HCC in a mouse model. During senescence, NEAT1 translocated into cytosol and interacted with a motor protein KIF11, resulting in KIF11 protein degradation and subsequent increased expression of CDKN2A in cultured hepatoma cells. Furthermore, KIF11 knockdown caused senescence in cultured hepatoma cells. Genetic deletion of Kif11 in hepatocytes inhibited the development of HCC in a mouse model. CONCLUSIONS Conclusively, NEAT1 overexpression reduces senescence and promotes tumor progression in HCC tissues and hepatoma cells, whereas NEAT1 deficiency causes senescence and inhibits tumor progression in HCC. This is associated with KIF11-dependent repression of CDKN2A. These findings lay the foundation to develop potential therapies for HCC by inhibiting NEAT1 and KIF11 or inducing senescence.
Collapse
Affiliation(s)
- Danlei Chen
- Department of Hepatobiliary SurgeryThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhuiChina
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhuiChina
| | - Jinghao Wang
- Zhejiang Cancer HospitalHangzhou Institute of MedicineChinese Academy of SciencesHangzhouZhejiangChina
| | - Yang Li
- Zhejiang Cancer HospitalHangzhou Institute of MedicineChinese Academy of SciencesHangzhouZhejiangChina
| | - Chenglin Xu
- Department of Hepatobiliary SurgeryThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
| | - Meng Fanzheng
- Department of Hepatobiliary SurgeryThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhuiChina
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhuiChina
| | - Pengfei Zhang
- Department of Hepatobiliary SurgeryThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
- Zhejiang Cancer HospitalHangzhou Institute of MedicineChinese Academy of SciencesHangzhouZhejiangChina
| | - Lianxin Liu
- Department of Hepatobiliary SurgeryThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhuiChina
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhuiChina
| |
Collapse
|
5
|
Hamilton DJ, Hein AE, Wuttke DS, Batey RT. The DNA binding high mobility group box protein family functionally binds RNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1778. [PMID: 36646476 PMCID: PMC10349909 DOI: 10.1002/wrna.1778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/18/2023]
Abstract
Nucleic acid binding proteins regulate transcription, splicing, RNA stability, RNA localization, and translation, together tailoring gene expression in response to stimuli. Upon discovery, these proteins are typically classified as either DNA or RNA binding as defined by their in vivo functions; however, recent evidence suggests dual DNA and RNA binding by many of these proteins. High mobility group box (HMGB) proteins have a DNA binding HMGB domain, act as transcription factors and chromatin remodeling proteins, and are increasingly understood to interact with RNA as means to regulate gene expression. Herein, multiple layers of evidence that the HMGB family are dual DNA and RNA binding proteins is comprehensively reviewed. For example, HMGB proteins directly interact with RNA in vitro and in vivo, are localized to RNP granules involved in RNA processing, and their protein interactors are enriched in RNA binding proteins involved in RNA metabolism. Importantly, in cell-based systems, HMGB-RNA interactions facilitate protein-protein interactions, impact splicing outcomes, and modify HMGB protein genomic or cellular localization. Misregulation of these HMGB-RNA interactions are also likely involved in human disease. This review brings to light that as a family, HMGB proteins are likely to bind RNA which is essential to HMGB protein biology. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
|
6
|
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.
Collapse
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
| | | | | |
Collapse
|
7
|
Nalavade R, Singh M. Intracellular Compartmentalization: A Key Determinant of MicroRNA Functions. Microrna 2023; 12:114-130. [PMID: 37638608 DOI: 10.2174/2211536612666230330184006] [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: 11/24/2022] [Revised: 12/26/2022] [Accepted: 01/19/2023] [Indexed: 08/29/2023]
Abstract
Being an integral part of the eukaryotic transcriptome, miRNAs are regarded as vital regulators of diverse developmental and physiological processes. Clearly, miRNA activity is kept in check by various regulatory mechanisms that control their biogenesis and decay pathways. With the increasing technical depth of RNA profiling technologies, novel insights have unravelled the spatial diversity exhibited by miRNAs inside a cell. Compartmentalization of miRNAs adds complexity to the regulatory circuits of miRNA expression, thereby providing superior control over the miRNA function. This review provides a bird's eye view of miRNAs expressed in different subcellular locations, thus affecting the gene regulatory pathways therein. Occurrence of miRNAs in diverse intracellular locales also reveals various unconventional roles played by miRNAs in different cellular organelles and expands the scope of miRNA functions beyond their traditionally known repressive activities.
Collapse
Affiliation(s)
- Rohit Nalavade
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Mohini Singh
- Department of Life Sciences, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, India
| |
Collapse
|
8
|
Rothzerg E, Feng W, Song D, Li H, Wei Q, Fox A, Wood D, Xu J, Liu Y. Single-Cell Transcriptome Analysis Reveals Paraspeckles Expression in Osteosarcoma Tissues. Cancer Inform 2022; 21:11769351221140101. [PMID: 36507075 PMCID: PMC9730017 DOI: 10.1177/11769351221140101] [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: 08/03/2022] [Accepted: 10/30/2022] [Indexed: 12/12/2022] Open
Abstract
Nuclear paraspeckles are subnuclear bodies contracted by nuclear-enriched abundant transcript 1 (NEAT1) long non-coding RNA, localised in the interchromatin space of mammalian cell nuclei. Paraspeckles have been critically involved in tumour progression, metastasis and chemoresistance. To this date, there are limited findings to suggest that paraspeckles, NEAT1 and heterogeneous nuclear ribonucleoproteins (hnRNPs) directly or indirectly play roles in osteosarcoma progression. Herein, we analysed NEAT1, paraspeckle proteins (SFPQ, PSPC1 and NONO) and hnRNP members (HNRNPK, HNRNPM, HNRNPR and HNRNPD) gene expression in 6 osteosarcoma tumour tissues using the single-cell RNA-sequencing method. The normalised data highlighted that the paraspeckles transcripts were highly abundant in osteoblastic OS cells, except NEAT1, which was highly expressed in myeloid cell 1 and 2 subpopulations.
Collapse
Affiliation(s)
- Emel Rothzerg
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia,Perron Institute for Neurological and Translational Science, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia
| | - Wenyu Feng
- Department of Orthopaedics, Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Dezhi Song
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia,Department of Orthopaedics, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Hengyuan Li
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia,Department of Orthopedics, Centre for Orthopedic Research, Second Affiliated Hospital, School of Medicine, Orthopedics Research Institute, Zhejiang University, Hangzhou, China
| | - Qingjun Wei
- Department of Orthopaedics, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Archa Fox
- School of Human Sciences and Molecular Sciences, The University of Western Australia and Harry Perkins Institute of Medical Research, Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
| | - David Wood
- Medical School, The University of Western Australia, Perth, WA, Australia
| | - Jiake Xu
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia,Jiake Xu, School of Biomedical Sciences, The University of Western Australia, 35 Stirling Hwy, Perth, WA 6009, Australia.
| | - Yun Liu
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia,Department of Orthopaedics, First Affiliated Hospital of Guangxi Medical University, Nanning, China,Yun Liu, School of Biomedical Sciences, The University of Western Australia, 35 Stirling Hwy, Perth, WA 6009, Australia.
| |
Collapse
|
9
|
Mitrea DM, Mittasch M, Gomes BF, Klein IA, Murcko MA. Modulating biomolecular condensates: a novel approach to drug discovery. Nat Rev Drug Discov 2022; 21:841-862. [PMID: 35974095 PMCID: PMC9380678 DOI: 10.1038/s41573-022-00505-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2022] [Indexed: 12/12/2022]
Abstract
In the past decade, membraneless assemblies known as biomolecular condensates have been reported to play key roles in many cellular functions by compartmentalizing specific proteins and nucleic acids in subcellular environments with distinct properties. Furthermore, growing evidence supports the view that biomolecular condensates often form by phase separation, in which a single-phase system demixes into a two-phase system consisting of a condensed phase and a dilute phase of particular biomolecules. Emerging understanding of condensate function in normal and aberrant cellular states, and of the mechanisms of condensate formation, is providing new insights into human disease and revealing novel therapeutic opportunities. In this Perspective, we propose that such insights could enable a previously unexplored drug discovery approach based on identifying condensate-modifying therapeutics (c-mods), and we discuss the strategies, techniques and challenges involved.
Collapse
|
10
|
Wang Y, Xiang M, Zhang H, Lu Y. Decreased complement 4d increases poor prognosis in patients with non‑small cell lung cancer combined with gastrointestinal lymph node metastasis. Exp Ther Med 2022; 24:560. [PMID: 35978919 PMCID: PMC9366274 DOI: 10.3892/etm.2022.11497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/23/2022] [Indexed: 11/18/2022] Open
Abstract
Lung cancer is a common malignancy that is difficult to treat and has a high risk of mortality. Although gastrointestinal lymph node metastasis has long been known to exert major impact on the prognosis of lung cancer, the mechanism of its occurrence and potential biological markers remain elusive. Therefore, the present study retrospectively analyzed data from 132 patients with non-small cell lung cancer (NSCLC) combined with lymph node metastasis between February 2010 and April 2019 from the First Affiliated Hospital of Soochow University (Suzhou, China) and Sichuan Cancer Hospital (Chengdu, China). Overall survival was assessed using Kaplan-Meier analysis and Cox logistic regression model. In addition, a prediction model was constructed based on immune indicators such as complement C3b and C4d (measured by ELISA), before the accuracy of this model was validated using calibration curves for 5-year OS. Among the 132 included patients, a total of 92 (70.0%) succumbed to the disease within 5 years. Multifactorial analysis revealed that complement C3b deficiency increased the risk of mortality by nearly two-fold [hazard ratio (HR)=2.23; 95% CI=1.20-4.14; P=0.017], whilst complement C4d deficiency similarly increased the risk of mortality by two-fold (HR=2.14; 95% CI=1.14-4.00; P=0.012). The variables were subsequently screened using Cox model to construct a prediction model based on complement C3b and C4d levels before a Nomogram plotted. By internal validation for the 132 patients, the Nomogram accurately estimated the risk of mortality, with a corrected C-index of 0.810. External validation of the model in another 50 patients from Sichuan Cancer Hospital revealed an accuracy of 77.0%. Overall, this mortality risk prediction model constructed based on complement levels showed accuracy in assessing the prognosis of patients with metastatic NSCLC. Therefore, complement C3b and C4d have potential for use as biomarkers to predict the risk of mortality in such patients.
Collapse
Affiliation(s)
- Yan Wang
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, P.R. China
| | - Mengqi Xiang
- Department of Medical Oncology, Sichuan Cancer Hospital, Medical School of University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, P.R. China
| | - Huachuan Zhang
- Department of Thoracic Surgery, Sichuan Cancer Hospital, Medical School of University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, P.R. China
| | - Yongda Lu
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, P.R. China
| |
Collapse
|
11
|
Belmont AS. Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture. Cold Spring Harb Perspect Biol 2022; 14:a041268. [PMID: 34400557 PMCID: PMC9248822 DOI: 10.1101/cshperspect.a041268] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This work reviews nuclear compartments, defined broadly to include distinct nuclear structures, bodies, and chromosome domains. It first summarizes original cytological observations before comparing concepts of nuclear compartments emerging from microscopy versus genomic approaches and then introducing new multiplexed imaging approaches that promise in the future to meld both approaches. I discuss how previous models of radial distribution of chromosomes or the binary division of the genome into A and B compartments are now being refined by the recognition of more complex nuclear compartmentalization. The poorly understood question of how these nuclear compartments are established and maintained is then discussed, including through the modern perspective of phase separation, before moving on to address possible functions of nuclear compartments, using the possible role of nuclear speckles in modulating gene expression as an example. Finally, the review concludes with a discussion of future questions for this field.
Collapse
Affiliation(s)
- Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
| |
Collapse
|
12
|
Chen S, Zheng J, Zhang B, Tang X, Cun Y, Wu T, Xu Y, Ma T, Cheng J, Yu Z, Wang H. Identification and characterization of virus-encoded circular RNAs in host cells. Microb Genom 2022; 8. [PMID: 35731570 PMCID: PMC9455708 DOI: 10.1099/mgen.0.000848] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Emerging evidence has identified viral circular RNAs (circRNAs) in human cells infected by viruses, interfering with the immune system and inducing diseases including human cancer. However, the biogenesis and regulatory mechanisms of virus-encoded circRNAs in host cells remain unknown. In this study, we used the circRNA detection tool CIRI2 to systematically determine the virus-encoded circRNAs in virus-infected cancer cell lines and cancer patients, by analysing RNA-Seq datasets derived from RNase R-treated samples. Based on the thousands of viral circRNAs we identified, the biological characteristics and potential roles of viral circRNAs in regulating host cell function were determined. In addition, we developed a Viral-circRNA Database (http://www.hywanglab.cn/vcRNAdb/), which is open to all users to search, browse and download information on circRNAs encoded by viruses upon infection.
Collapse
Affiliation(s)
- Shuting Chen
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
| | - Jie Zheng
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
| | - Bingyue Zhang
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
| | - Xinyue Tang
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
| | - Yewei Cun
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
| | - Tao Wu
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
| | - Yue Xu
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
| | - Ting Ma
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
| | - Jingxin Cheng
- Department of Obstetrics and Gynecology, Shanghai East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai 200120, PR China
| | - Zuoren Yu
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai 200120, PR China
| | - Haiyun Wang
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China
| |
Collapse
|
13
|
Sur S, Ray RB. Emerging role of lncRNA ELDR in development and cancer. FEBS J 2022; 289:3011-3023. [PMID: 33860640 DOI: 10.1111/febs.15876] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/31/2021] [Accepted: 04/12/2021] [Indexed: 02/06/2023]
Abstract
Whole-genome sequencing and transcriptome analysis revealed more than 90% of the human genome transcribes noncoding RNAs including lncRNAs. From the beginning of the 21st century, lncRNAs have gained widespread attention as a new layer of regulation in biological processes. lncRNAs are > 200 nucleotides in size, transcribed by RNA polymerase II, and share many similarities with mRNAs. lncRNA interacts with DNA, RNA, protein, and miRNAs, thereby regulating many biological processes. In this review, we have focused mainly on LINC01156 [also known as the EGFR long non-coding downstream RNA (ELDR) or Fabl] and its biological importance. ELDR is a newly identified lncRNA and first reported in a mouse model, but it has a human homolog. The human ELDR gene is closely localized downstream of epidermal growth factor receptor (EGFR) gene at chromosome 7 on the opposite strand. ELDR is highly expressed in neuronal stem cells and associated with neuronal differentiation and mouse brain development. ELDR is upregulated in head and neck cancer, suggesting its role as an oncogene and its importance in prognosis and therapy. Publicly available RNA-seq data further support its oncogenic potential in different cancers. Here, we summarize all the aspects of ELDR in development and cancer, highlighting its future perspectives in the context of mechanism.
Collapse
Affiliation(s)
- Subhayan Sur
- Department of Pathology, Saint Louis University, MO, USA
| | - Ratna B Ray
- Department of Pathology, Saint Louis University, MO, USA.,Cancer Center, Saint Louis University, MO, USA
| |
Collapse
|
14
|
Inadvertent Transfer of Murine VL30 Retrotransposons to CAR-T Cells. ADVANCES IN CELL AND GENE THERAPY 2022; 2022. [PMID: 36081760 PMCID: PMC9450689 DOI: 10.1155/2022/6435077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
For more than a decade, genetically engineered autologous T-cells have been successfully employed as immunotherapy drugs for patients with incurable blood cancers. The active components in some of these game-changing medicines are autologous T-cells that express viral vector-delivered chimeric antigen receptors (CARs), which specifically target proteins that are preferentially expressed on cancer cells. Some of these therapeutic CAR expressing T-cells (CAR-Ts) are engineered via transduction with
-retroviral vectors (
-RVVs) produced in a stable producer cell line that was derived from murine PG13 packaging cells (ATCC CRL-10686). Earlier studies reported on the copackaging of murine virus-like 30S RNA (VL30) genomes with
-retroviral vectors generated in murine stable packaging cells. In an earlier study, VL30 mRNA was found to enhance the metastatic potential of human melanoma cells. These findings raise biosafety concerns regarding the possibility that therapeutic CAR-Ts have been inadvertently contaminated with potentially oncogenic VL30 retrotransposons. In this study, we demonstrated the presence of infectious VL30 particles in PG13 cell-conditioned media and observed the ability of these particles to deliver transcriptionally active VL30 genomes to human cells. Notably, VL30 genomes packaged by HIV-1-based vector particles transduced naïve human cells in culture. Furthermore, we detected the transfer and expression of VL30 genomes in clinical-grade CAR-T cells generated by transduction with PG13 cell-derived
-retroviral vectors. Our findings raise biosafety concerns regarding the use of murine packaging cell lines in ongoing clinical applications.
Collapse
|
15
|
Zhao J, Xie W, Yang Z, Zhao M, Ke T, Xu C, Li H, Chen Q, Wang QK. Identification and characterization of a special type of subnuclear structure: AGGF1-coated paraspeckles. FASEB J 2022; 36:e22366. [PMID: 35608889 DOI: 10.1096/fj.202101690rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 11/11/2022]
Abstract
AGGF1 is an angiogenic factor with G-Patch and FHA domains 1 described by our group. Gain-of-function mutations in AGGF1 cause Klippel-Trenaunay syndrome, whereas somatic loss-of-function mutations cause cancer. Paraspeckles are small membraneless subnuclear structures with a diameter of 0.5-1 μm, and composed of lncRNA NEAT1 as the scaffold and three core RNA-binding proteins NONO, PSPC1, and PSF. Here, we show that AGGF1 is a key regulatory and structural component of paraspeckles that induces paraspeckle formation, forms an outside rim of paraspeckles, wraps around the NONO/PSF/PSPC1/NEAT1 core, and regulates the size and number of paraspeckles. AGGF1-paraspeckles are larger (>1 μm) than conventional paraspeckles. RNA-FISH in combination with immunostaining shows that AGGF1, NONO, and NEAT1_2 co-localize in 20.58% of NEAT1_2-positive paraspeckles. Mechanistically, AGGF1 interacts with NONO, PSF, and HNRNPK, and upregulates NEAT1_2, a longer, 23 kb NEAT1 transcript with a key role in regulation of paraspeckle size and number. RNA-immunoprecipitation shows that AGGF1 interacts with NEAT1, which may be another possible mechanism underlying the formation of AGGF1-paraspeckles. NEAT1_2 knockdown reduces the number and size of AGGF1-paraspeckles. Functionally, AGGF1 regulates alternative RNA splicing as it decreases the exon skipping/inclusion ratio in a CD44 model. AGGF1 is also localized in some nuclear foci without NEAT1 or NONO, suggesting that AGGF1 is an important liquid-liquid phase separation (LLPS) driver for other types of AGGF1-positive nuclear condensates (referred to as AGGF1-bodies). Our results identify a special type of AGGF1-coated paraspeckles and provide important insights into the formation, structure, and function of paraspeckles.
Collapse
Affiliation(s)
- Jinyan Zhao
- Center for Human Genome Research, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Wen Xie
- Center for Human Genome Research, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Zhongcheng Yang
- Center for Human Genome Research, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Miao Zhao
- Center for Human Genome Research, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Tie Ke
- Center for Human Genome Research, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Chengqi Xu
- Center for Human Genome Research, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Hui Li
- Center for Human Genome Research, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Qiuyun Chen
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Qing K Wang
- Center for Human Genome Research, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
| |
Collapse
|
16
|
Ma ZL, Ding YL, Jing J, Du LN, Zhang XY, Liu HM, He PX. ATRA promotes PD-L1 expression to control gastric cancer immune surveillance. Eur J Pharmacol 2022; 920:174822. [DOI: 10.1016/j.ejphar.2022.174822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/31/2022] [Accepted: 02/09/2022] [Indexed: 11/03/2022]
|
17
|
Petit FG, Jamin SP, Kernanec PY, Becker E, Halet G, Primig M. EXOSC10/Rrp6 is essential for the eight-cell embryo/morula transition. Dev Biol 2021; 483:58-65. [PMID: 34965385 DOI: 10.1016/j.ydbio.2021.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/16/2021] [Accepted: 12/21/2021] [Indexed: 11/03/2022]
Abstract
The conserved 3'-5' exoribonuclease EXOSC10/Rrp6 is required for gametogenesis, brain development, erythropoiesis and blood cell enhancer function. The human ortholog is essential for mitosis in cultured cancer cells. Little is known, however, about the role of Exosc10 during embryo development and organogenesis. We generated an Exosc10 knockout model and find that Exosc10-/- mice show an embryonic lethal phenotype. We demonstrate that Exosc10 maternal wild type mRNA is present in mutant oocytes and that the gene is expressed during all stages of early embryogenesis. Furthermore, we observe that EXOSC10 early on localizes to the periphery of nucleolus precursor bodies in blastomeres, which is in keeping with the protein's role in rRNA processing and may indicate a function in the establishment of chromatin domains during initial stages of embryogenesis. Finally, we infer from genotyping data for embryonic days e7.5, e6.5 and e4.5 and embryos cultured in vitro that Exosc10-/- mutants arrest at the eight-cell embryo/morula transition. Our results demonstrate a novel essential role for Exosc10 during early embryogenesis, and they are consistent with earlier work showing that impaired ribosome biogenesis causes a developmental arrest at the morula stage.
Collapse
Affiliation(s)
- Fabrice G Petit
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France.
| | - Soazik P Jamin
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France
| | - Pierre-Yves Kernanec
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France
| | | | - Guillaume Halet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes), UMR 6290, F-35000, Rennes, France
| | - Michael Primig
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000, Rennes, France.
| |
Collapse
|
18
|
Cao RZ, Min L, Liu S, Tian RY, Jiang HY, Liu J, Shao LL, Cheng R, Zhu ST, Guo SL, Li P. Rictor Activates Cav 1 Through the Akt Signaling Pathway to Inhibit the Apoptosis of Gastric Cancer Cells. Front Oncol 2021; 11:641453. [PMID: 34540654 PMCID: PMC8442624 DOI: 10.3389/fonc.2021.641453] [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: 12/14/2020] [Accepted: 03/08/2021] [Indexed: 01/01/2023] Open
Abstract
Background Rapamycin-insensitive companion of mammalian target of rapamycin (Rictor) protein is a core subunit of mammalian target of rapamycin complex 2, and is associated with cancer progression. However, the biological function of Rictor in cancer, particularly its clinical relevance in gastric cancer (GC) remains largely unknown. Methods Rictor expression and its association with clinicopathologic characteristics in GC were analyzed by immunohistochemistry. Effect of Rictor and Caveolin-1 (Cav 1) on GC cells apoptosis was evaluated via overexpression experiment in vitro. Mechanisms of Rictor and Cav 1 in GC were explored through overexpression and knockdown, by immunofluorescence and western blot analyses. Results Rictor was upregulated in GC, and mainly located in the cytoplasm of cancer cells. Moreover, higher Rictor levels were associated with worse prognosis. Rictor could inhibit GC cell apoptosis and promote cell growth in vitro. The results of immunofluorescence revealed that Cav 1 localized in GC cell membrane but did not co-localize with Rictor. Further, Rictor regulated apoptosis-related proteins, long non-coding RNAs and also activated cellular signaling, thereby positively regulating Cav 1 expression. This effect was attenuated by the Akt inhibitor ly294002. Cav 1 did not significantly affect the ability of Rictor to inhibit tumor cell apoptosis. Conclusions Rictor is upregulated in GC and associated with worse prognosis. It inhibits tumor apoptosis and activates Cav 1 through the Akt signaling pathway to inhibit the apoptosis of GC cells. Rictor is, therefore, a promising prognostic biomarker and possible therapeutic target in GC patients.
Collapse
Affiliation(s)
- Rui-Zhen Cao
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China.,Department of Gastroenterology, Ordos Central Hospital, National Clinical Research Center for Digestive Disease-Ordos Subcenter, Ordos, China
| | - Li Min
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Si Liu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Ru-Yue Tian
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Hai-Yan Jiang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China.,Department of Gastroenterology, Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, China
| | - Juan Liu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China.,Department of Gastroenterology, Shanxi Province Cancer Hospital, Shanxi Medical University, Taiyuan, China
| | - Lin-Lin Shao
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Rui Cheng
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Sheng-Tao Zhu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Shui-Long Guo
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Peng Li
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| |
Collapse
|
19
|
The periphilin 1-like BFAR isoform 3 is highly expressed in transcriptionally silent oocytes and involved in RNA metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119086. [PMID: 34175335 DOI: 10.1016/j.bbamcr.2021.119086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 05/22/2021] [Accepted: 06/19/2021] [Indexed: 11/22/2022]
Abstract
The mouse 3110001I22Rik gene located in the first intron of Bfar is considered as a Bfar variant coding for the BFARv3 protein. However, it differs from other BFAR isoforms and resembles periphilin 1 (PPHLN1) due to its two (Lge1 and serine-rich) conserved domains. We identified the BFARv3/EGFP-interacting proteins by co-immunoprecipitation coupled to mass spectrometry, which revealed 40S ribosomal proteins (RPS3, RPS14, RPS19, RPS25, RPS27), histones (H1.2, H1.4, H3.3C), proteins involved in RNA processing and splicing (SFPQ, SNRPA1, HNRNPA3, NONO, KHDRBS3), calcium signaling (HPCAL1, PTK2B), as well as HSD17B4, GRB14, POSTN, and MYO10. Co-immunoprecipitation revealed that both Lge1 and Ser-rich domains of BFARv3 were necessary for binding to RNA-interacting factors NONO and SFPQ, known to be components of paraspeckles. Reciprocal co-immunoprecipitation and the proximity ligation assay confirmed that both BFARv3 and PPHLN1 could interact with NONO and SFPQ, suggesting a new function for PPHLN1 as well. BFARv3 and its Lge1 or Ser-rich-deficient mutants preferentially localize in the nucleus. We found an accumulation of BFARv3/EGFP (but not its mutated forms) in the nuclear granules, which was enhanced in response to arsenite treatment and ionizing radiation. Although Bfar v3 is expressed ubiquitously in mouse tissues, its expression is the highest in metaphase II oocytes. The BFARv3 interactome suggests its role in RNA metabolism, which is critical for the transcriptionally silent MII oocyte. Mouse BFARv3 has no ortholog in the human genome, thus it may contribute to the differences between these two species observed in oocyte maturation and early embryonic development.
Collapse
|
20
|
Fan XJ, Wang YL, Zhao WW, Bai SM, Ma Y, Yin XK, Feng LL, Feng WX, Wang YN, Liu Q, Hung MC, Wan XB. NONO phase separation enhances DNA damage repair by accelerating nuclear EGFR-induced DNA-PK activation. Am J Cancer Res 2021; 11:2838-2852. [PMID: 34249431 PMCID: PMC8263645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/25/2021] [Indexed: 06/13/2023] Open
Abstract
Radioresistance is one of the main causes of cancer treatment failure, which leads to relapse and inferior survival outcome of cancer patients. Liquid-liquid phase separation (LLPS) of proteins is known to be involved in various biological processes, whereas its role in the regulation of radiosensitivity remains largely unknown. In this study, we characterized NONO, an RNA/DNA binding protein with LLPS capacity, as an essential regulator of tumor radioresistance. In vitro assay showed that NONO involved in DNA repair via non-homologous end joining (NHEJ) manner. NONO knockout significantly reduced DNA damage repair and sensitized tumor cells to irradiation in vitro and in vivo. NONO overexpression was correlated with an inferior survival outcome in cancer patients. Mechanically, NONO was associated with nuclear EGFR (nEGFR). Both irradiation and EGF treatment induced nEGFR accumulation, thereby increased the association between NONO and nEGFR. However, NONO was not a substrate of EGFR kinase. Furthermore, NONO promoted DNA damage-induced DNA-PK phosphorylation at T2609 by enhancing the interaction between EGFR and DNA-PK. Importantly, NONO protein formed high concentration LLPS droplets in vitro, and recruited EGFR and DNA-PK. Disruption of NONO droplets with LLPS inhibitor significantly reduced the interaction between EGFR and DNA-PK, and suppressed DNA damage-induced phosphorylation of T2609-DNA-PK. Taken together, LLPS of NONO recruits nuclear EGFR and DNA-PK and enhances their interaction, further increases DNA damage-activated pT2609-DNA-PK and promotes NHEJ-mediated DNA repair, finally leads to tumor radioresistance. NONO phase separation-mediated radioresistance may serve as a novel molecular target to sensitize tumor cell to radiotherapy.
Collapse
Affiliation(s)
- Xin-Juan Fan
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510655, Guangdong, P. R. China
- Department of Pathology, The Sixth Affiliated Hospital of Sun Yat-sen UniversityGuangzhou 510655, Guangdong, P. R. China
| | - Yun-Long Wang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510655, Guangdong, P. R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510655, Guangdong, P. R. China
| | - Wan-Wen Zhao
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510655, Guangdong, P. R. China
| | - Shao-Mei Bai
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510655, Guangdong, P. R. China
| | - Yan Ma
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510655, Guangdong, P. R. China
| | - Xin-Ke Yin
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510655, Guangdong, P. R. China
| | - Li-Li Feng
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510655, Guangdong, P. R. China
| | - Wei-Xing Feng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510655, Guangdong, P. R. China
| | - Ying-Nai Wang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer CenterHouston 77030, Texas, USA
| | - Quentin Liu
- Institute of Cancer Stem Cell, Dalian Medical UniversityDalian 116044, Liaoning, P. R. China
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen UniversityGuangzhou 510060, Guangdong, P. R. China
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer CenterHouston 77030, Texas, USA
- Graduate Institute of Biomedical Sciences and Research Centers for Cancer Biology and Molecular Medicine, China Medical UniversityTaichung 404, Taiwan
- Department of Biotechnology, Asia UniversityTaichung 413, Taiwan
| | - Xiang-Bo Wan
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510655, Guangdong, P. R. China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510655, Guangdong, P. R. China
- Department of Medical Engineering, The Sixth Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510655, Guangdong, P. R. China
| |
Collapse
|
21
|
Escalante LE, Gasch AP. The role of stress-activated RNA-protein granules in surviving adversity. RNA (NEW YORK, N.Y.) 2021; 27:rna.078738.121. [PMID: 33931500 PMCID: PMC8208049 DOI: 10.1261/rna.078738.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/28/2021] [Indexed: 05/17/2023]
Abstract
Severe environmental stress can trigger a plethora of physiological changes and, in the process, significant cytoplasmic reorganization. Stress-activated RNA-protein granules have been implicated in this cellular overhaul by sequestering pre-existing mRNAs and influencing their fates during and after stress acclimation. While the composition and dynamics of stress-activated granule formation has been well studied, their function and impact on RNA-cargo has remained murky. Several recent studies challenge the view that these granules degrade and silence mRNAs present at the onset of stress and instead suggest new roles for these structures in mRNA storage, transit, and inheritance. Here we discuss recent evidence for revised models of stress-activated granule functions and the role of these granules in stress survival and recovery.
Collapse
|
22
|
Fernandes N, Buchan JR. RNAs as Regulators of Cellular Matchmaking. Front Mol Biosci 2021; 8:634146. [PMID: 33898516 PMCID: PMC8062979 DOI: 10.3389/fmolb.2021.634146] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/22/2021] [Indexed: 12/30/2022] Open
Abstract
RNA molecules are increasingly being identified as facilitating or impeding the interaction of proteins and nucleic acids, serving as so-called scaffolds or decoys. Long non-coding RNAs have been commonly implicated in such roles, particularly in the regulation of nuclear processes including chromosome topology, regulation of chromatin state and gene transcription, and assembly of nuclear biomolecular condensates such as paraspeckles. Recently, an increased awareness of cytoplasmic RNA scaffolds and decoys has begun to emerge, including the identification of non-coding regions of mRNAs that can also function in a scaffold-like manner to regulate interactions of nascently translated proteins. Collectively, cytoplasmic RNA scaffolds and decoys are now implicated in processes such as mRNA translation, decay, protein localization, protein degradation and assembly of cytoplasmic biomolecular condensates such as P-bodies. Here, we review examples of RNA scaffolds and decoys in both the nucleus and cytoplasm, illustrating common themes, the suitability of RNA to such roles, and future challenges in identifying and better understanding RNA scaffolding and decoy functions.
Collapse
Affiliation(s)
| | - J. Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, United States
| |
Collapse
|
23
|
Song Z, Lin J, Li Z, Huang C. The nuclear functions of long noncoding RNAs come into focus. Noncoding RNA Res 2021; 6:70-79. [PMID: 33898883 PMCID: PMC8053782 DOI: 10.1016/j.ncrna.2021.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/16/2022] Open
Abstract
Long noncoding RNAs (lncRNAs), defined as untranslated and tightly-regulated transcripts with a length exceeding 200 nt, are common outputs of the eukaryotic genome. It is becoming increasingly apparent that many lncRNAs likely serve as important regulators in a variety of biological processes. In particular, some of them accumulate in the nucleus and function in diverse nuclear events, including chromatin remodeling, transcriptional regulation, RNA processing, DNA damage repair, etc. Here, we unite recent progresses on the functions of nuclear lncRNAs and provide insights into the future research directions of this field.
Collapse
Affiliation(s)
- Zhenxing Song
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Jiamei Lin
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
- Corresponding author. School of Life Sciences, Chongqing University, Chongqing, 401331, China.
| |
Collapse
|
24
|
Sas-Nowosielska H, Magalska A. Long Noncoding RNAs-Crucial Players Organizing the Landscape of the Neuronal Nucleus. Int J Mol Sci 2021; 22:ijms22073478. [PMID: 33801737 PMCID: PMC8037058 DOI: 10.3390/ijms22073478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/25/2022] Open
Abstract
The ability to regulate chromatin organization is particularly important in neurons, which dynamically respond to external stimuli. Accumulating evidence shows that lncRNAs play important architectural roles in organizing different nuclear domains like inactive chromosome X, splicing speckles, paraspeckles, and Gomafu nuclear bodies. LncRNAs are abundantly expressed in the nervous system where they may play important roles in compartmentalization of the cell nucleus. In this review we will describe the architectural role of lncRNAs in the nuclei of neuronal cells.
Collapse
|
25
|
Kim W, Kim DY, Lee KH. RNA-Binding Proteins and the Complex Pathophysiology of ALS. Int J Mol Sci 2021; 22:ijms22052598. [PMID: 33807542 PMCID: PMC7961459 DOI: 10.3390/ijms22052598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/21/2022] Open
Abstract
Genetic analyses of patients with amyotrophic lateral sclerosis (ALS) have identified disease-causing mutations and accelerated the unveiling of complex molecular pathogenic mechanisms, which may be important for understanding the disease and developing therapeutic strategies. Many disease-related genes encode RNA-binding proteins, and most of the disease-causing RNA or proteins encoded by these genes form aggregates and disrupt cellular function related to RNA metabolism. Disease-related RNA or proteins interact or sequester other RNA-binding proteins. Eventually, many disease-causing mutations lead to the dysregulation of nucleocytoplasmic shuttling, the dysfunction of stress granules, and the altered dynamic function of the nucleolus as well as other membrane-less organelles. As RNA-binding proteins are usually components of several RNA-binding protein complexes that have other roles, the dysregulation of RNA-binding proteins tends to cause diverse forms of cellular dysfunction. Therefore, understanding the role of RNA-binding proteins will help elucidate the complex pathophysiology of ALS. Here, we summarize the current knowledge regarding the function of disease-associated RNA-binding proteins and their role in the dysfunction of membrane-less organelles.
Collapse
Affiliation(s)
- Wanil Kim
- Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea;
| | - Do-Yeon Kim
- Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu 41940, Korea
- Correspondence: (D.-Y.K.); (K.-H.L.); Tel.: +82-53-660-6880 (D.-Y.K.); +82-53-819-7743 (K.-H.L.)
| | - Kyung-Ha Lee
- Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea;
- Correspondence: (D.-Y.K.); (K.-H.L.); Tel.: +82-53-660-6880 (D.-Y.K.); +82-53-819-7743 (K.-H.L.)
| |
Collapse
|
26
|
Zan J, Zhao X, Deng X, Ding H, Wang B, Lu M, Wei Z, Huang Z, Wang S. Paraspeckle Promotes Hepatocellular Carcinoma Immune Escape by Sequestering IFNGR1 mRNA. Cell Mol Gastroenterol Hepatol 2021; 12:465-487. [PMID: 33667716 PMCID: PMC8255817 DOI: 10.1016/j.jcmgh.2021.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Hepatocellular carcinoma (HCC) is the most common type of hepatic malignancies, with poor prognosis and low survival rate. Paraspeckles, which are unique subnuclear structures, are recently found to be involved in the development of various tumors, including HCC, and are related to induction in chemoresistance of HCC. This study aimed to investigate the possibility of paraspeckle in HCC cells participating in immune escape and its underlying mechanism in vitro and in vivo. METHODS Expression of NEAT1_2, the framework of paraspeckle, in HCC cells and tissues was detected by qRT-PCR and RNA-FISH. mRNAs interacted with NEAT1_2 were pull-downed and sequenced in C-terminal S1-aptamer-tagged NEAT1_2 endogenously expressed HCC cells constructed using CRISPR-CAS9 knock-in technology. The effects of paraspeckle on HCC sensitivity to T-cell-mediated cytolysis were detected by T-cell mediated tumor cell killing assay. The roles of NEAT1_2 or NONO on IFNGR1 expression and IFN-γ signaling by applying gene function loss analysis in HCC cells were detected by qRT-PCR, RNA immunoprecipitation, Western blotting, and ELISA. The role of paraspeckle during adoptive T-cell transfer therapy for HCC in vivo was performed with a subcutaneous xenograft mouse. RESULTS Paraspeckle in HCC cells is negatively related to T-cell-mediated cytolysis. Destruction of paraspeckle in HCC cells by knockdown of NEAT1_2 or NONO significantly improved the sensibility of resistant HCC cells to T-cell killing effects. Furthermore, IFNGR1 mRNA, which is sequestered by NEAT1_2 and NONO, is abundant in paraspeckle of T-cell killing-resistant HCC cells. Incapable IFN-γ-IFNGR1 signaling accounts for paraspeckle mediated-adoptive T-cell therapy resistance. Moreover, NEAT1_2 expression negatively correlates with IFNGR1 expression in clinical HCC tissues. CONCLUSIONS Paraspeckle in HCC cells helps tumor cells escape from immunosurveillance through sequestering IFNGR1 mRNA to inhibiting IFN-γ-IFNGR1 signaling, thereby avoiding T-cell killing effects. Collectively, our results hint that NEAT1_2 highly expressed HCC patient is more resistant to T-cell therapy in clinic, and NEAT1_2 may be potential target for HCC immunotherapy.
Collapse
Affiliation(s)
- Jie Zan
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou
| | - Xuya Zhao
- Department of Interventional Radiology, Affiliated Cancer Hospital of Guizhou Medical University, Guiyang
| | - Xiya Deng
- School of Life Sciences, Westlake University, Hangzhou
| | - Hongda Ding
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Bi Wang
- School of Basic Medical Science, Guizhou Medical University, Guiyang, China
| | - Minyi Lu
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou
| | - Zijing Wei
- Department of interventional radiology, the Affiliated Hosptial of Guizhou Medical University, Guiyang, China
| | - Zhi Huang
- Department of interventional radiology, the Affiliated Hosptial of Guizhou Medical University, Guiyang, China; School of Basic Medical Science, Guizhou Medical University, Guiyang, China.
| | - Shuai Wang
- School of Life Sciences, Westlake University, Hangzhou.
| |
Collapse
|
27
|
Li J, Cao Z, Mi L, Xu Z, Wu X. Complement sC5b-9 and CH50 increase the risk of cancer-related mortality in patients with non-small cell lung cancer. J Cancer 2020; 11:7157-7165. [PMID: 33193878 PMCID: PMC7646172 DOI: 10.7150/jca.46721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 10/08/2020] [Indexed: 12/29/2022] Open
Abstract
Objectives: Immunologic dysfunction occurred in most of patients with non-small cell lung cancer (NSCLC), which worsened the overall survival (OS) of patients. Complement activation plays a significant role in abnormal activation of immune system. However, the prognostic value of complement components such as CH50 and sC5b-9 in NSCLC patients remains unclear. This study evaluated the risk factors of NSCLC and created a prediction model. Methods: A real-world study was conducted including data from 928 patients with NSCLC between April 1, 2005 and June 1, 2015. CH50 and sC5b-9 were recorded during the admission. Cox proportional hazard model was applied for survival analyses and for assessing risk factors of cancer-related mortality and to create a nomogram for prediction. The accuracy of the model was evaluated by C-index and calibration curve. Results: In this study, the mortality in group with high CH50 level (≥ 480.56 umol/L) was 92.0%. Based on univariate analysis, we put factors (P <0.05) into a multivariate regression model, patients with high CH50 level (P <0.001, HR=1.59) and sC5b-9 >1422.18 μmol/L (P <0.001, HR=2.28) remained statistically factors for worsened OS and regarded as independent risk factors. These independently associated risk factors were applied to establish an OS estimation nomogram. Nomogram revealed good accuracy in estimating the risk, with a bootstrap-corrected C index of 0.741. Conclusion: sC5b-9 and CH50 increased the risk of cancer-related mortality in patients with NSCLC. Nomogram based on multivariate analysis demonstrated good accuracy in estimating the risk of overall mortality.
Collapse
Affiliation(s)
- Jing Li
- Department of Medicine, Respiratory, Emergency and Intensive Care Medicine, The Affiliated Dushu Lake Hospital of Soochow University, Suzhou, China
| | - Zhijun Cao
- Department of Urology, The Ninth People's Hospital of Suzhou, Suzhou, China
| | - Lijie Mi
- Department of Cardiovascular, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhihua Xu
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiangmei Wu
- Department of Endocrinology, Suzhou Xiangcheng People's Hospital, Suzhou, China
| |
Collapse
|
28
|
NEAT1 and Paraspeckles in Cancer Development and Chemoresistance. Noncoding RNA 2020; 6:ncrna6040043. [PMID: 33143162 PMCID: PMC7712271 DOI: 10.3390/ncrna6040043] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 09/21/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
Non-coding RNA were previously thought to be biologically useless molecules arising from simple transcriptional noise. These are now known to be an integral part of cellular biology and pathology. The wide range of RNA molecules have a diverse range of structures, functions, and mechanisms of action. However, structural long non-coding RNAs (lncRNAs) are a particular class of ncRNA that are proving themselves more and more important in cellular biology, as the exact structures that such RNAs form and stabilise become more understood. Nuclear Enriched Abundant Transcript 1 (NEAT1) is a specific structural RNA emerging as a critical component in the progress and development of cancer. NEAT1 forms part of multiple biological pathways, acting through a diverse group of mechanisms. The most important of these is the formation of the paraspeckle, through which it can influence the stability of a tumour to develop resistance to drugs. This review will thus cover the range of effects by which NEAT1 interacts with cancer progression in order to describe the various roles of NEAT1 in chemoresistance, as well as to identify drug targets that protein research alone could not provide.
Collapse
|
29
|
Bian W, Chen W, Jiang X, Qu H, Jiang J, Yang J, Liang X, Zhao B, Sun Y, Zhang C. Downregulation of Long Non-coding RNA Nuclear Paraspeckle Assembly Transcript 1 Inhibits MEG-01 Differentiation and Platelet-Like Particles Activity. Front Genet 2020; 11:571467. [PMID: 33193674 PMCID: PMC7596361 DOI: 10.3389/fgene.2020.571467] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/22/2020] [Indexed: 01/22/2023] Open
Abstract
Platelets are derived from megakaryocytes and play an important role in blood coagulation. By using high throughput sequencing, we have found that the long non-coding RNA (lncRNA) nuclear paraspeckle assembly transcript 1 (NEAT1) is abundant in platelets (GEO ID: 200097348). However, little is known about its role in regulating megakaryocyte differentiation and platelet activity. This study aims to clarify the effect of NEAT1 on MEG-01 differentiation and platelet-like particle (PLP) activity. NEAT1 in MEG-01 cells was knocked down by siRNA transfection. The adhesion of MEG-01 and PLP to collagen-coated coverslips was observed under a fluorescence microscope. Flow cytometry was used to investigate cell apoptosis, cell cycle, the levels of D41/CD42b on MEG-01 cells and CD62P on PLPs. Quantitative real-time polymerase chain reaction was used to detect NEAT1 and IL-8 expression levels. Western blot was used to measure the protein levels of Bcl-2, Bax, cleaved caspase-3, and IL-8. RNA-binding protein immunoprecipitation was used to detect the interaction of NEAT1 and splicing factor proline/glutamine-rich (SFPQ). Results showed that NEAT1 knockdown decreased the adhesion ability of thrombin-stimulated MEG-01 and PLP. The expression of CD62P on PLPs and CD41/CD42b on MEG-01 cells was inhibited by NEAT1 knockdown. In addition, NEAT1 knockdown inhibited cell apoptosis with increased Bcl2/Bax ratio and decreased cleaved caspase-3, and reduced the percentage of cells in the G0/G1 phase. Meanwhile, NEAT1 knockdown inhibited the expression of IL-8. A strong interaction of NEAT1 and SFPQ, a transcriptional repressor of IL-8, was identified. NEAT1 knockdown reduced the interaction between SFPQ and NEAT1.The results suggest that lncRNA NEAT1 knockdown decreases MEG-01 differentiation, PLP activity, and IL-8 level. The results also indicate that the regulation of NEAT1 on IL-8 may be realized via a direct interaction between NEAT1 and SFPQ.
Collapse
Affiliation(s)
- Weihua Bian
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Wangping Chen
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiaoli Jiang
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Huiqing Qu
- Department of Blood Transfusion, Affiliated Hospital of Binzhou Medical University, Binzhou, China
| | - Jing Jiang
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Jinfu Yang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xinyue Liang
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Bingrui Zhao
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Yeying Sun
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Chunxiang Zhang
- School of Pharmacy, Binzhou Medical University, Yantai, China
| |
Collapse
|
30
|
Razin SV, Gavrilov AA, Iarovaia OV. Modification of Nuclear Compartments and the 3D Genome in the Course of a Viral Infection. Acta Naturae 2020; 12:34-46. [PMID: 33456976 PMCID: PMC7800604 DOI: 10.32607/actanaturae.11041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/07/2020] [Indexed: 12/17/2022] Open
Abstract
The review addresses the question of how the structural and functional compartmentalization of the cell nucleus and the 3D organization of the cellular genome are modified during the infection of cells with various viruses. Particular attention is paid to the role of the introduced changes in the implementation of the viral strategy to evade the antiviral defense systems and provide conditions for viral replication. The discussion focuses on viruses replicating in the cell nucleus. Cytoplasmic viruses are mentioned in cases when a significant reorganization of the nuclear compartments or the 3D genome structure occurs during an infection with these viruses.
Collapse
Affiliation(s)
- S. V. Razin
- Institute of Gene Biology Russian Academy of Sciences
| | | | | |
Collapse
|