1
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Phillips D, Noble D. Bubbling beyond the barrier: exosomal RNA as a vehicle for soma-germline communication. J Physiol 2024; 602:2547-2563. [PMID: 37936475 DOI: 10.1113/jp284420] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
'Weismann's barrier' has restricted theories of heredity to the transmission of genomic variation for the better part of a century. However, the discovery and elucidation of epigenetic mechanisms of gene regulation such as DNA methylation and histone modifications has renewed interest in studies on the inheritance of acquired traits and given them mechanistic plausibility. Although it is now clear that these mechanisms allow many environmentally acquired traits to be transmitted to the offspring, how phenotypic information is communicated from the body to its gametes has remained a mystery. Here, we discuss recent evidence that such communication is mediated by somatic RNAs that travel inside extracellular vesicles to the gametes where they reprogram the offspring epigenome and phenotype. How gametes learn about bodily changes has implications not only for the clinic, but also for evolutionary theory by bringing together intra- and intergenerational mechanisms of phenotypic plasticity and adaptation.
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Affiliation(s)
- Daniel Phillips
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Denis Noble
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
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2
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Tang J, Liu J, Nie J, Pei H, Zhou G. YBX1 Underwent Phase Separation into Stress Granules Stimulated by Ionizing Radiation. Radiat Res 2024; 201:215-223. [PMID: 38253057 DOI: 10.1667/rade-23-00113.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
Stress granules (SGs) are formed through liquid-liquid phase separation (LLPS), in response to external stimuli. YBX1, an integral component of SGs, plays a crucial role in tumor progression and cellular stress response. This study aims to elucidate the mechanisms and specific biological implications of YBX1 in SG formation, along with the identification of key regions and interacting proteins. Our observations indicate that YBX1 rapidly undergoes liquid-liquid phase separation, leading to SG formation in response to 8 Gy X-ray irradiation within 1 h, with SGs reverting to their original state after 5 h. There was a potential interaction between ATXN2L and YBX1, persisting YBX1 within the SGs. Our data suggested a potential interaction between ATXN2L and YBX1, and it remained associated with YBX1 within the SGs. Furthermore, our subsequent studies demonstrate that targeting ATXN2L can diminish the recruitment of YBX1 to stress granules (SGs), consequently enhancing the radiosensitivity of HeLa cells.
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Affiliation(s)
- Jiaxin Tang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Suzhou 215123, China
| | - Jiyuan Liu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Suzhou 215123, China
| | - Jing Nie
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Suzhou 215123, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Hailong Pei
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Suzhou 215123, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Guangming Zhou
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Suzhou 215123, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
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3
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Maciak P, Suder A, Wadas J, Aronimo F, Maiuri P, Bochenek M, Pyrc K, Kula-Pacurar A, Pabis M. Dynamic changes in LINC00458/HBL1 lncRNA expression during hiPSC differentiation to cardiomyocytes. Sci Rep 2024; 14:109. [PMID: 38167488 PMCID: PMC10761834 DOI: 10.1038/s41598-023-49753-3] [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: 10/18/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) constitute the largest and most diverse class of non-coding RNAs. They localize to the nucleus, cytoplasm, or both compartments, and regulate gene expression through various mechanisms at multiple levels. LncRNAs tend to evolve faster and present higher tissue- and developmental stage-specific expression than protein-coding genes. Initially considered byproducts of erroneous transcription without biological function, lncRNAs are now recognized for their involvement in numerous biological processes, such as immune response, apoptosis, pluripotency, reprogramming, and differentiation. In this study, we focused on Heart Brake lncRNA 1 (HBL1), a lncRNA recently reported to modulate the process of pluripotent stem cell differentiation toward cardiomyocytes. We employed RT-qPCR and high-resolution RNA FISH to monitor the expression and localization of HBL1 during the differentiation progression. Our findings indicate a significant increase in HBL1 expression during mesodermal and cardiac mesodermal stages, preceding an anticipated decrease in differentiated cells. We detected the RNA in discrete foci in both the nucleus and in the cytoplasm. In the latter compartment, we observed colocalization of HBL1 with Y-box binding protein 1 (YB-1), which likely results from an interaction between the RNA and the protein, as the two were found to be coimmunoprecipitated in RNP-IP experiments. Finally, we provide evidence that HBL1, initially reported as an independent lncRNA gene, is part of the LINC00458 (also known as lncRNA-ES3 or ES3) gene, forming the last exon of some LINC00458 splice isoforms.
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Affiliation(s)
- Patrycja Maciak
- Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
| | - Agnieszka Suder
- Virogenetics Laboratory of Virology, Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11, 30-348, Cracow, Poland
| | - Jakub Wadas
- Virogenetics Laboratory of Virology, Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11, 30-348, Cracow, Poland
| | - Faith Aronimo
- Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
| | - Paolo Maiuri
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Michał Bochenek
- Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland
| | - Anna Kula-Pacurar
- Virogenetics Laboratory of Virology, Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland.
| | - Marta Pabis
- Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Cracow, Poland.
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4
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Peng J, He J, Lin L, Li Y, Xia Y. Neural Stem Cell Extracellular Vesicles Carrying YBX1 Inhibited Neuronal Pyroptosis Through Increasing m6A-modified GPR30 Stability and Expression in Ischemic Stroke. Transl Stroke Res 2023:10.1007/s12975-023-01210-z. [PMID: 37966628 DOI: 10.1007/s12975-023-01210-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 10/12/2023] [Accepted: 10/26/2023] [Indexed: 11/16/2023]
Abstract
Neural stem cell-derived extracellular vesicles (NSC-derived EVs) alleviated ischemic stroke (IS) by suppressing the activation of nucleotide-binding domain leucine-rich repeats family protein 3 (NLRP3) inflammasome and neuronal pyroptosis. However, the specific mechanism needs further investigation. qRT-qPCR, Western blotting, and immunofluorescence detected related gene expression. Immunofluorescent analyzed the expression of Ki-67, βIII-Tubulin (Tuj1), and GFAP. Lactate dehydrogenase (LDH) release and IL-1β and IL-18 levels were analyzed by LDH and ELISA kits. TTC staining evaluated the infarction of brain tissues. Flow cytometric analysis measured caspase-1 activity. M6A methylated RNA immunoprecipitation PCR (MeRIP-PCR) measured methylation levels of G protein-coupled receptor 30 (GPR30). RIP and Co-IP analyzed the interactions of Y box binding protein (YBX1)/GPR30, YBX1/IGF2BP1 and NLRP3/speckle-type POZ protein (SPOP), as well as the ubiquitination levels of NLRP3. NSC-derived EVs inhibited the ischemia-reperfusion (I/R) injury of rats and the neuronal pyroptosis induced by oxygen-glucose deprivation/reoxygenation (OGD/R). Knockdown of EVs carrying YBX1 or GPR30 silencing abolished these inhibiting effects. GPR30 mRNA and IGF2BP1 protein were enriched by YBX1 antibody. YBX1 enhanced the stability of m6A-modified GPR30 by interacting with IGF2BP1 and thus promoting GPR30 expression. Knockdown of IGF2BP1 suppressed the binding between YBX1 and GPR30 mRNA. GPR30 promoted NLRP3 ubiquitination by interacting with SPOP. EVs carrying YBX1 could reduce the infarction of brain tissues and inhibit neuronal pyroptosis in rats with I/R injury. NSC-derived EVs carrying YBX1 increased the stability of m6A-modified GPR30 by interacting with IGF2BP1; the upregulation of GPR30 inhibited the activation of NLRP3 inflammasome through promoting NLRP3 ubiquitination by SPOP, ultimately suppressing the neuronal pyroptosis in IS.
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Affiliation(s)
- Jun Peng
- Department of Neurosurgery, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Hainan Province, Haikou, 570208, People's Republic of China
| | - Jun He
- Department of Neurosurgery, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Hainan Province, Haikou, 570208, People's Republic of China
| | - Long Lin
- Department of Neurosurgery, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Hainan Province, Haikou, 570208, People's Republic of China
| | - You Li
- Department of Neurosurgery, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Hainan Province, Haikou, 570208, People's Republic of China
| | - Ying Xia
- Department of Neurosurgery, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Hainan Province, Haikou, 570208, People's Republic of China.
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5
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Li Y, Tam WW, Yu Y, Zhuo Z, Xue Z, Tsang C, Qiao X, Wang X, Wang W, Li Y, Tu Y, Gao Y. The application of Aptamer in biomarker discovery. Biomark Res 2023; 11:70. [PMID: 37468977 DOI: 10.1186/s40364-023-00510-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/29/2023] [Indexed: 07/21/2023] Open
Abstract
Biomarkers are detectable molecules that can reflect specific physiological states of cells, organs, and organisms and therefore be regarded as indicators for specific diseases. And the discovery of biomarkers plays an essential role in cancer management from the initial diagnosis to the final treatment regime. Practically, reliable clinical biomarkers are still limited, restricted by the suboptimal methods in biomarker discovery. Nucleic acid aptamers nowadays could be used as a powerful tool in the discovery of protein biomarkers. Nucleic acid aptamers are single-strand oligonucleotides that can specifically bind to various targets with high affinity. As artificial ssDNA or RNA, aptamers possess unique advantages compared to conventional antibodies. They can be flexible in design, low immunogenicity, relative chemical/thermos stability, as well as modifying convenience. Several SELEX (Systematic Evolution of Ligands by Exponential Enrichment) based methods have been generated recently to construct aptamers for discovering new biomarkers in different cell locations. Secretome SELEX-based aptamers selection can facilitate the identification of secreted protein biomarkers. The aptamers developed by cell-SELEX can be used to unveil those biomarkers presented on the cell surface. The aptamers from tissue-SELEX could target intracellular biomarkers. And as a multiplexed protein biomarker detection technology, aptamer-based SOMAScan can analyze thousands of proteins in a single run. In this review, we will introduce the principle and workflow of variations of SELEX-based methods, including secretome SELEX, ADAPT, Cell-SELEX and tissue SELEX. Another powerful proteome analyzing tool, SOMAScan, will also be covered. In the second half of this review, how these methods accelerate biomarker discovery in various diseases, including cardiovascular diseases, cancer and neurodegenerative diseases, will be discussed.
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Affiliation(s)
- Yongshu Li
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China.
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, China.
| | - Winnie Wailing Tam
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Yuanyuan Yu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Zhenjian Zhuo
- State Key Laboratory of Chemical Oncogenomic, Peking University Shenzhen Graduate School, Shenzhen, China
- Laboratory Animal Center, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Zhichao Xue
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, China
| | - Chiman Tsang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaoting Qiao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Xiaokang Wang
- Department of Pharmacy, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Weijing Wang
- Shantou University Medical College, Shantou, China
| | - Yongyi Li
- Laboratory Animal Center, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Yanyang Tu
- Research Center, Huizhou Central People's Hospital, Guangdong Medical University, Huizhou City, China.
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China.
- Shenzhen Institute for Technology Innovation, National Institute of Metrology, Shenzhen, China.
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6
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Ni P, Zhou C, Liang S, Jiang Y, Liu D, Shao Z, Noh H, Zhao L, Tian Y, Zhang C, Wei J, Li X, Yu H, Ni R, Yu X, Qi X, Zhang Y, Ma X, Deng W, Guo W, Wang Q, Sham PC, Chung S, Li T. YBX1-Mediated DNA Methylation-Dependent SHANK3 Expression in PBMCs and Developing Cortical Interneurons in Schizophrenia. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300455. [PMID: 37211699 PMCID: PMC10369273 DOI: 10.1002/advs.202300455] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/05/2023] [Indexed: 05/23/2023]
Abstract
Schizophrenia (SCZ) is a severe psychiatric and neurodevelopmental disorder. The pathological process of SCZ starts early during development, way before the first onset of psychotic symptoms. DNA methylation plays an important role in regulating gene expression and dysregulated DNA methylation is involved in the pathogenesis of various diseases. The methylated DNA immunoprecipitation-chip (MeDIP-chip) is performed to investigate genome-wide DNA methylation dysregulation in peripheral blood mononuclear cells (PBMCs) of patients with first-episode SCZ (FES). Results show that the SHANK3 promoter is hypermethylated, and this hypermethylation (HyperM) is negatively correlated with the cortical surface area in the left inferior temporal cortex and positively correlated with the negative symptom subscores in FES. The transcription factor YBX1 is further found to bind to the HyperM region of SHANK3 promoter in induced pluripotent stem cells (iPSCs)-derived cortical interneurons (cINs) but not glutamatergic neurons. Furthermore, a direct and positive regulatory effect of YBX1 on the expression of SHANK3 is confirmed in cINs using shRNAs. In summary, the dysregulated SHANK3 expression in cINs suggests the potential role of DNA methylation in the neuropathological mechanism underlying SCZ. The results also suggest that HyperM of SHANK3 in PBMCs can serve as a potential peripheral biomarker of SCZ.
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Affiliation(s)
- Peiyan Ni
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
- Department of PsychiatryMcLean Hospital/Harvard Medical SchoolBelmontMA02478USA
- Department of Cell Biology and AnatomyNew York Medical CollegeValhallaNY10595USA
| | - Chuqing Zhou
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Sugai Liang
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Youhui Jiang
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Dongxin Liu
- Department of Cell Biology and AnatomyNew York Medical CollegeValhallaNY10595USA
| | - Zhicheng Shao
- Department of PsychiatryMcLean Hospital/Harvard Medical SchoolBelmontMA02478USA
| | - Haneul Noh
- Department of PsychiatryMcLean Hospital/Harvard Medical SchoolBelmontMA02478USA
- Department of Cell Biology and AnatomyNew York Medical CollegeValhallaNY10595USA
| | - Liansheng Zhao
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Yang Tian
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Chengcheng Zhang
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Jinxue Wei
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Xiaojing Li
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Hua Yu
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Rongjun Ni
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Xueli Yu
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- NHC and CAMS Key Laboratory of Medical NeurobiologyMOE Frontier Science Center for Brain Science and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouZhejiang310058China
| | - Xueyu Qi
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- NHC and CAMS Key Laboratory of Medical NeurobiologyMOE Frontier Science Center for Brain Science and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouZhejiang310058China
| | - Yamin Zhang
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Xiaohong Ma
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Wei Deng
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- NHC and CAMS Key Laboratory of Medical NeurobiologyMOE Frontier Science Center for Brain Science and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouZhejiang310058China
| | - Wanjun Guo
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- NHC and CAMS Key Laboratory of Medical NeurobiologyMOE Frontier Science Center for Brain Science and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouZhejiang310058China
| | - Qiang Wang
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Pak C. Sham
- Department of PsychiatryLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong, SAR999077China
- Centre for PanorOmic SciencesThe University of Hong KongHong Kong, SAR999077China
| | - Sangmi Chung
- Department of PsychiatryMcLean Hospital/Harvard Medical SchoolBelmontMA02478USA
- Department of Cell Biology and AnatomyNew York Medical CollegeValhallaNY10595USA
| | - Tao Li
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- NHC and CAMS Key Laboratory of Medical NeurobiologyMOE Frontier Science Center for Brain Science and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouZhejiang310058China
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7
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Shi Q, He Y, He S, Li J, Xia J, Chen T, Huo L, Ling Y, Liu Q, Zang W, Wang Q, Tang C, Wang X. RP11-296E3.2 acts as an important molecular chaperone for YBX1 and promotes colorectal cancer proliferation and metastasis by activating STAT3. J Transl Med 2023; 21:418. [PMID: 37370092 DOI: 10.1186/s12967-023-04267-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND RP11-296E3.2 is a novel long noncoding RNA (lncRNA) associated with colorectal cancer (CRC) metastasis, that was reported in our previous clinical studies. However, the mechanisms of RP11-296E3.2 in colorectal tumorigenesis remain elusive. METHODS RNA sequencing (RNA-seq), Fluorescence in situ hybridization (FISH), Transwell assays and others, were performed to evaluate the function of RP11-296E3.2 for proliferation and metastasis in vitro. In situ and metastatic tumor models were performed to evaluate the function of RP11-296E3.2 for proliferation and metastasis in vivo. RNA-pulldown, RNA-interacting protein immunoprecipitation (RIP), tissue microarray (TMA) assay, a luciferase reporter assay, chromatin immunoprecipitation (ChIP) and others were performed to explore the mechanisms by which RP11-296E3.2 regulates CRC tumorigenesis. RESULTS RP11-296E3.2 was confirmed to be associated with CRC cell proliferation and metastasis in vitro and in vivo. Mechanistically, RP11-296E3.2 directly bound to recombinant Y-Box Binding Protein 1 (YBX1) and enhanced signal transducer and activator of transcription 3 (STAT3) transcription and phosphorylation. YBX1 promoted the CRC cell proliferation and migration, while knockdown of RP11-296E3.2 attenuated the effects of YBX1 on CRC cell proliferation, and metastasis and the expression of several related downstream genes. We are the first to discover and confirm the existence of the YBX1/STAT3 pathway, a pathway dependent on RP11-296E3.2. CONCLUSION Together, these novel findings show that the RP11-296E3.2/YBX1 pathway promotes colorectal tumorigenesis and progression by activating STAT3 transcription and phosphorylation, and suggest that RP11-296E3.2 is a potential diagnostic biomarker and therapeutic target in CRC.
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Affiliation(s)
- Qian Shi
- Key Laboratory for Translational Medicine, First Affiliated Hospital, The First People's Hospital of Huzhou, Huzhou University, Huzhou, 313000, China
| | - Ying He
- Key Laboratory for Translational Medicine, First Affiliated Hospital, The First People's Hospital of Huzhou, Huzhou University, Huzhou, 313000, China
| | - Shouyu He
- Key Laboratory for Translational Medicine, First Affiliated Hospital, The First People's Hospital of Huzhou, Huzhou University, Huzhou, 313000, China
| | - Jingjing Li
- Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Ji Xia
- Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Tianwei Chen
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Lixia Huo
- Key Laboratory for Translational Medicine, First Affiliated Hospital, The First People's Hospital of Huzhou, Huzhou University, Huzhou, 313000, China
| | - Yuhang Ling
- Key Laboratory for Translational Medicine, First Affiliated Hospital, The First People's Hospital of Huzhou, Huzhou University, Huzhou, 313000, China
| | - Qinchen Liu
- Department of General Surgery, Shanghai Fengxian Central Hospital (Affiliated Fengxian Hospital to Southern Medical University), Shanghai, 201499, China
| | - Wei Zang
- Department of General Surgery, Shanghai Fengxian Central Hospital (Affiliated Fengxian Hospital to Southern Medical University), Shanghai, 201499, China
| | - Qiang Wang
- Medical Transformation Research Institute, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, China.
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, China.
| | - Chengwu Tang
- Key Laboratory for Translational Medicine, First Affiliated Hospital, The First People's Hospital of Huzhou, Huzhou University, Huzhou, 313000, China.
| | - Xiang Wang
- Key Laboratory for Translational Medicine, First Affiliated Hospital, The First People's Hospital of Huzhou, Huzhou University, Huzhou, 313000, China.
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
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8
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Yang R, Li L, Hou Y, Li Y, Zhang J, Yang N, Zhang Y, Ji W, Yu T, Lv L, Liang H, Li X, Li T, Shan H. Long non-coding RNA KCND1 protects hearts from hypertrophy by targeting YBX1. Cell Death Dis 2023; 14:344. [PMID: 37253771 DOI: 10.1038/s41419-023-05852-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 04/11/2023] [Accepted: 05/05/2023] [Indexed: 06/01/2023]
Abstract
Cardiac hypertrophy is a common structural remodeling in many cardiovascular diseases. Recently, long non-coding RNAs (LncRNAs) were found to be involved in the physiological and pathological processes of cardiac hypertrophy. In this study, we found that LncRNA KCND1 (LncKCND1) was downregulated in both transverse aortic constriction (TAC)-induced hypertrophic mouse hearts and Angiotensin II (Ang II)-induced neonatal mouse cardiomyocytes. Further analyses showed that the knockdown of LncKCND1 impaired cardiac mitochondrial function and led to hypertrophic changes in cardiomyocytes. In contrast, overexpression of LncKCND1 inhibited Ang II-induced cardiomyocyte hypertrophic changes. Importantly, enhanced expression of LncKCND1 protected the heart from TAC-induced pathological cardiac hypertrophy and improved heart function in TAC mice. Subsequent analyses involving mass spectrometry and RNA immunoprecipitation assays showed that LncKCND1 directly binds to YBX1. Furthermore, overexpression of LncKCND1 upregulated the expression level of YBX1, while silencing LncKCND1 had the opposite effect. Furthermore, YBX1 was downregulated during cardiac hypertrophy, whereas overexpression of YBX1 inhibited Ang II-induced cardiomyocyte hypertrophy. Moreover, silencing YBX1 reversed the effect of LncKCND1 on cardiomyocyte mitochondrial function and its protective role in cardiac hypertrophy, suggesting that YBX1 is a downstream target of LncKCND1 in regulating cardiac hypertrophy. In conclusion, our study provides mechanistic insights into the functioning of LncKCND1 and supports LncKCND1 as a potential therapeutic target for pathological cardiac hypertrophy.
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Affiliation(s)
- Rui Yang
- Shanghai Frontiers Science Research Center for Druggability of Cardiovascular noncoding RNA, Institute for Frontier Medical Technology, Shanghai University of Engineering Science, Shanghai, 201620, China
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
- Department of Pharmacology, School of Basic Medicine, Inner Mongolia Medical University, Hohhot, 010110, China
| | - Liangliang Li
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Yumeng Hou
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Yingnan Li
- Center for Tumor and Immunology, the Precision Medical Institute, Xi'an Jiaotong University, Xi'an, 710115, China
| | - Jing Zhang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Na Yang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Yuhan Zhang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Weihang Ji
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Tong Yu
- Shanghai Frontiers Science Research Center for Druggability of Cardiovascular noncoding RNA, Institute for Frontier Medical Technology, Shanghai University of Engineering Science, Shanghai, 201620, China
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Lifang Lv
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
- Department of Basic Medicine, The Centre of Functional Experiment Teaching, Harbin Medical University, Harbin, 150081, China
| | - Haihai Liang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
- Research Unit of Noninfectious Chronic Diseases in Frigid Zone (2019RU070), Chinese Academy of Medical Sciences, Harbin, 150081, China
| | - Xuelian Li
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Tianyu Li
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China.
| | - Hongli Shan
- Shanghai Frontiers Science Research Center for Druggability of Cardiovascular noncoding RNA, Institute for Frontier Medical Technology, Shanghai University of Engineering Science, Shanghai, 201620, China.
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China.
- Research Unit of Noninfectious Chronic Diseases in Frigid Zone (2019RU070), Chinese Academy of Medical Sciences, Harbin, 150081, China.
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9
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Li X, Chen G, Liu B, Tao Z, Wu Y, Zhang K, Feng Z, Huang Y, Wang H. PLK1 inhibition promotes apoptosis and DNA damage in glioma stem cells by regulating the nuclear translocation of YBX1. Cell Death Discov 2023; 9:68. [PMID: 36805592 PMCID: PMC9938146 DOI: 10.1038/s41420-023-01302-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/12/2022] [Accepted: 01/04/2023] [Indexed: 02/19/2023] Open
Abstract
Glioma stem cells (GSCs) are the important cause of tumorigenesis, recurrence, and chemo(radio)resistance in glioma. Targeting GSCs helps improve the outcomes of glioma treatment. Polo-like kinase 1 (PLK1) is a member of the serine/threonine protein kinase family, which is highly conserved. In recent years, it has been suggested that increased levels of PLK1 and its activity are associated with tumor progression and poor prognosis. We aimed to identify whether PLK1 plays a critical role in stemness maintenance and apoptosis regulation in GSCs. Here we identify that PLK1 inhibition can induce apoptosis and DNA damage of GSCs, we have also delineat the possible underlying molecular mechanisms: PLK1 interacts with YBX1 and directly phosphorylates serine 174 and serine 176 of YBX1. Inhibition of PLK1 reduces the phosphorylation level of YBX1, and decreased phosphorylation of YBX1 prevents its nuclear translocation, thereby inducing apoptosis and DNA damage of GSCs. We confirmed that YBX1 knockdown resulted in the apoptosis and DNA damage of GSCs. These findings uncover that PLK1 inhibition induces cell apoptosis and DNA damage in GSCs through YBX1 phosphorylation, providing new insights into the mechanism by which PLK1 inhibition contributes to the apoptosis of and DNA damage in gliomas.
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Affiliation(s)
- Xuetao Li
- grid.263761.70000 0001 0198 0694Department of Neurosurgery, Dushu Lake Hospital Affiliated of Soochow University, Suzhou, Jiangsu China
| | - Guangliang Chen
- grid.429222.d0000 0004 1798 0228Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu China
| | - Bin Liu
- grid.469564.cDepartment of Neurosurgery, Qinghai Provincial People’s Hospital, Xining, Qinghai 810007 China
| | - Zhennan Tao
- grid.41156.370000 0001 2314 964XDepartment of Neurosurgery, The Affiliated Drum Tower Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Yue Wu
- grid.429222.d0000 0004 1798 0228Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu China
| | - Kai Zhang
- grid.429222.d0000 0004 1798 0228Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu China
| | - Zibin Feng
- grid.429222.d0000 0004 1798 0228Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu China
| | - Yulun Huang
- Department of Neurosurgery, Dushu Lake Hospital Affiliated of Soochow University, Suzhou, Jiangsu, China.
| | - Hao Wang
- Institute of Soochow University, Suzhou, Jiangsu, China.
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10
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Hussain SA, Venkatesh T. YBX1/lncRNA SBF2-AS1 interaction regulates proliferation and tamoxifen sensitivity via PI3K/AKT/MTOR signaling in breast cancer cells. Mol Biol Rep 2023; 50:3413-3428. [PMID: 36754932 DOI: 10.1007/s11033-023-08308-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/26/2023] [Indexed: 02/10/2023]
Abstract
BACKGROUND Y-box binding protein 1 (YBX1) is a multifunctional oncoprotein that can interact with several long non-coding RNAs (lncRNAs) to regulate metastasis in malignancies including breast cancer (BC). In the present study, we demonstrated the association of YBX1 with oncogenic lncRNA SBF2-AS1 (SET-binding factor 2 antisense RNA 1) via PI3K/AKT/mTOR signaling to regulate BC cell proliferation. We further explored the involvement of the YBX1/SBF2-AS1/PI3K/AKT/mTOR axis in the restoration of tamoxifen (TAM) sensitivity. METHODS AND RESULTS YBX1-SBF2-AS1 association was predicted in silico and verified by RNA immunoprecipitation (RIP)-qPCR assay. Transfection experiments, Real-time RT PCR, Western blots, Phospho AKT/mTOR antibody array kit, and cell proliferation/apoptosis assays were employed to detect the YBX1/SBF2-AS1/ PI3K/AKT/mTOR axis and its effects upon TAM treatment in vitro. We identified that the YBX1 protein specifically binds to lncRNA SBF2-AS1. Our transfection experiments in MCF-7 and MDA-MB-468 cells with SBF2-AS1 silenced or overexpressed YBX1 plasmids, and their negative controls revealed that YBX1 regulates the expression of SBF2-AS1 by forming a positive feedback loop for its activation. We further demonstrated YBX1-SBF2-AS1 association exerts its effects on cell proliferation via PI3K/AKT/mTOR signaling pathway. Furthermore, we observed an increase in TAM sensitivity in BC cells after the knockdown of YBX1-SBF2-AS1 marked by decreased cell proliferation through disruption of the PI3K/AKT/mTOR axis. CONCLUSION Our study has identified a novel YBX1/SBF2-AS1/PI3K/AKT/mTOR regulatory axis which may serve as a potential target to improve the effectiveness and efficacy of TAM treatment in BC.
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Affiliation(s)
- Shaharbhanu A Hussain
- Department of Biochemistry and Molecular Biology, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Thejaswini Venkatesh
- Department of Biochemistry and Molecular Biology, Central University of Kerala, Kasaragod, Kerala, 671316, India.
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11
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Wu R, Feng S, Li F, Shu G, Wang L, Gao P, Zhu X, Zhu C, Wang S, Jiang Q. Transcriptional and post-transcriptional control of autophagy and adipogenesis by YBX1. Cell Death Dis 2023; 14:29. [PMID: 36642732 PMCID: PMC9841012 DOI: 10.1038/s41419-023-05564-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/17/2023]
Abstract
Obesity is strongly associated with metabolic diseases, which have become a global health problem. Exploring the underlying mechanism of adipogenesis is crucial for the treatment of excess white fat. Oncogene YBX1 is a multifunctional DNA- and RNA-binding protein that regulates brown adipogenesis. However, the role of YBX1 in white adipogenesis and adipose tissue expansion remains unknown. Here, we showed that YBX1 deficiency inhibited murine and porcine adipocyte differentiation. YBX1 positively regulated adipogenesis through promoting ULK1- and ULK2-mediated autophagy. Mechanistically, we identified YBX1 serves as a 5-methylcytosine (m5C)-binding protein directly targeting m5C-containing Ulk1 mRNA by using RNA immunoprecipitation. RNA decay assay further proved that YBX1 upregulated ULK1 expression though stabilizing its mRNA. Meanwhile, YBX1 promoted Ulk2 transcription and expression as a transcription factor, thereby enhancing autophagy and adipogenesis. Importantly, YBX1 overexpression in white fat enhanced ULK1/ULK2-mediated autophagy and promoted adipose tissue expansion in mice. Collectively, these findings unveil the post-transcriptional and transcriptional mechanism and functional importance of YBX1 in autophagy and adipogenesis regulation, providing an attractive molecular target for therapies of obesity and metabolic diseases.
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Affiliation(s)
- Ruifan Wu
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Shengchun Feng
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Fan Li
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Gang Shu
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Lina Wang
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Ping Gao
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaotong Zhu
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Canjun Zhu
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Songbo Wang
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Qingyan Jiang
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Animal Nutritional Regulation and National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
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12
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Sylvén C, Wärdell E, Månsson-Broberg A, Cingolani E, Ampatzis K, Larsson L, Björklund Å, Giacomello S. High cardiomyocyte diversity in human early prenatal heart development. iScience 2022; 26:105857. [PMID: 36624836 PMCID: PMC9823232 DOI: 10.1016/j.isci.2022.105857] [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: 03/10/2022] [Revised: 07/19/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
Cardiomyocytes play key roles during cardiogenesis, but have poorly understood features, especially in prenatal stages. Here, we characterized human prenatal cardiomyocytes, 6.5-7 weeks post-conception, by integrating single-cell RNA sequencing, spatial transcriptomics, and ligand-receptor interaction information. Using a computational workflow developed to dissect cell type heterogeneity, localize cell types, and explore their molecular interactions, we identified eight types of developing cardiomyocyte, more than double compared to the ones identified in the Human Developmental Cell Atlas. These have high variability in cell cycle activity, mitochondrial content, and connexin gene expression, and are differentially distributed in the ventricles, including outflow tract, and atria, including sinoatrial node. Moreover, cardiomyocyte ligand-receptor crosstalk is mainly with non-cardiomyocyte cell types, encompassing cardiogenesis-related pathways. Thus, early prenatal human cardiomyocytes are highly heterogeneous and develop unique location-dependent properties, with complex ligand-receptor crosstalk. Further elucidation of their developmental dynamics may give rise to new therapies.
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Affiliation(s)
- Christer Sylvén
- Department of Medicine, Karolinska Institute, Huddinge, Sweden,Corresponding author
| | - Eva Wärdell
- Department of Medicine, Karolinska Institute, Huddinge, Sweden
| | | | | | | | - Ludvig Larsson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Åsa Björklund
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Stefania Giacomello
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden,Corresponding author
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13
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Bauer KM, Nelson MC, Tang WW, Chiaro TR, Brown DG, Ghazaryan A, Lee SH, Weis AM, Hill JH, Klag KA, Tran VB, Thompson JW, Ramstead AG, Monts JK, Marvin JE, Alexander M, Voth WP, Stephens WZ, Ward DM, Petrey AC, Round JL, O'Connell RM. CD11c+ myeloid cell exosomes reduce intestinal inflammation during colitis. JCI Insight 2022; 7:159469. [PMID: 36214220 PMCID: PMC9675566 DOI: 10.1172/jci.insight.159469] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/19/2022] [Indexed: 01/25/2023] Open
Abstract
Intercellular communication is critical for homeostasis in mammalian systems, including the gastrointestinal (GI) tract. Exosomes are nanoscale lipid extracellular vesicles that mediate communication between many cell types. Notably, the roles of immune cell exosomes in regulating GI homeostasis and inflammation are largely uncharacterized. By generating mouse strains deficient in cell-specific exosome production, we demonstrate deletion of the small GTPase Rab27A in CD11c+ cells exacerbated murine colitis, which was reversible through administration of DC-derived exosomes. Profiling RNAs within colon exosomes revealed a distinct subset of miRNAs carried by colon- and DC-derived exosomes. Among antiinflammatory exosomal miRNAs, miR-146a was transferred from gut immune cells to myeloid and T cells through a Rab27-dependent mechanism, targeting Traf6, IRAK-1, and NLRP3 in macrophages. Further, we have identified a potentially novel mode of exosome-mediated DC and macrophage crosstalk that is capable of skewing gut macrophages toward an antiinflammatory phenotype. Assessing clinical samples, RAB27A, select miRNAs, and RNA-binding proteins that load exosomal miRNAs were dysregulated in ulcerative colitis patient samples, consistent with our preclinical mouse model findings. Together, our work reveals an exosome-mediated regulatory mechanism underlying gut inflammation and paves the way for potential use of miRNA-containing exosomes as a novel therapeutic for inflammatory bowel disease.
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Affiliation(s)
- Kaylyn M Bauer
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Morgan C Nelson
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - William W Tang
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Tyson R Chiaro
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - D Garrett Brown
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Arevik Ghazaryan
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Soh-Hyun Lee
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Allison M Weis
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Jennifer H Hill
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Kendra A Klag
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Van B Tran
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Jacob W Thompson
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Andrew G Ramstead
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Josh K Monts
- University of Utah Flow Cytometry Core, Salt Lake City, Utah, USA
| | - James E Marvin
- University of Utah Flow Cytometry Core, Salt Lake City, Utah, USA
| | - Margaret Alexander
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Warren P Voth
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - W Zac Stephens
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Diane M Ward
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA
| | - Aaron C Petrey
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA.,Department of Internal Medicine, Division of Gastroenterology, and
| | - June L Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA.,Hunstman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Ryan M O'Connell
- Department of Pathology, Division of Microbiology and Immunology, University of Utah, Salt Lake City, Utah, USA.,Hunstman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
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14
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Zeng X, Xiao J, Bai X, Liu Y, Zhang M, Liu J, Lin Z, Zhang Z. Research progress on the circRNA/lncRNA-miRNA-mRNA axis in gastric cancer. Pathol Res Pract 2022; 238:154030. [PMID: 36116329 DOI: 10.1016/j.prp.2022.154030] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 01/19/2023]
Abstract
Gastric cancer is one of the most common malignant tumours worldwide. Genetic and epigenetic alterations are key factors in gastric carcinogenesis and drug resistance to chemotherapy. Competing endogenous RNA (ceRNA) regulation models have defined circRNA/lncRNA as miRNA sponges that indirectly regulate miRNA downstream target genes. The ceRNA regulatory network is related to the malignant biological behaviour of gastric cancer. The circRNA/lncRNA-miRNA-mRNA axis may be a marker for the early diagnosis and prognosis of gastric cancer and a potential therapeutic target for gastric cancer. Exosomal ncRNAs play an important role in gastric cancer and are expected to be ideal biomarkers for the diagnosis, prognosis, and treatment of gastric cancer. This review summarizes the specific ceRNA regulatory network (circRNA/lncRNA-miRNA-mRNA) discovered in gastric cancer in recent years, which may provide new ideas or strategies for early clinical diagnosis, further development, and application.
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Affiliation(s)
- Xuemei Zeng
- Cancer Research Institute of Hengyang Medical School, University of South China; Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hengyang, Hunan 421001, China
| | - Juan Xiao
- Department of Otorhinolaryngology, The Second Affiliated Hospital, Hengyang Medical School,University of South China, Hengyang 421001, China
| | - Xue Bai
- Cancer Research Institute of Hengyang Medical School, University of South China; Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hengyang, Hunan 421001, China
| | - Yiwen Liu
- Cancer Research Institute of Hengyang Medical School, University of South China; Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hengyang, Hunan 421001, China
| | - Meilan Zhang
- Cancer Research Institute of Hengyang Medical School, University of South China; Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hengyang, Hunan 421001, China
| | - Jiangrong Liu
- Cancer Research Institute of Hengyang Medical School, University of South China; Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hengyang, Hunan 421001, China
| | - Zixuan Lin
- Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Zhiwei Zhang
- Cancer Research Institute of Hengyang Medical School, University of South China; Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hengyang, Hunan 421001, China.
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15
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Chetta M, Tarsitano M, Oro M, Rivieccio M, Bukvic N. An in silico pipeline approach uncovers a potentially intricate network involving spike SARS-CoV-2 RNA, RNA vaccines, host RNA-binding proteins (RBPs), and host miRNAs at the cellular level. J Genet Eng Biotechnol 2022; 20:129. [PMID: 36066672 PMCID: PMC9446605 DOI: 10.1186/s43141-022-00413-5] [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: 03/25/2022] [Accepted: 08/25/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND In the last 2 years, we have been fighting against SARS-CoV-2 viral infection, which continues to claim victims all over the world. The entire scientific community has been mobilized in an attempt to stop and eradicate the infection. A well-known feature of RNA viruses is their high mutational rate, particularly in specific gene regions. The SARS-CoV-2 S protein is also affected by these changes, allowing viruses to adapt and spread more easily. The vaccines developed using mRNA coding protein S undoubtedly contributed to the "fight" against the COVID-19 pandemic even though the presence of new variants in the spike protein could result in protein conformational changes, which could affect vaccine immunogenicity and thus vaccine effectiveness. RESULTS The study presents the findings of an in silico analysis using various bioinformatics tools finding conserved sequences inside SARS-CoV-2 S protein (encoding mRNA) same as in the vaccine RNA sequences that could be targeted by specific host RNA-binding proteins (RBPs). According to the results an interesting scenario emerges involving host RBPs competition and subtraction. The presence of viral RNA in cytoplasm could be a new tool in the virus's armory, allowing it to improve its chances of survival by altering cell gene expression and thus interfering with host cell processes. In silico analysis was used also to evaluate the presence of similar human miRNA sequences within RBPs motifs that can modulate human RNA expression. Increased cytoplasmic availability of exogenous RNA fragments derived from RNA physiological degradation could potentially mimic the effect of host human miRNAs within the cell, causing modulation of the host cell network. CONCLUSIONS Our in silico analysis could aid in shedding light on the potential effects of exogenous RNA (i.e. viruses and vaccines), thereby improving our understanding of the cellular interactions between virus and host biomolecules. Finally, using the computational approach, it is possible to obtain a safety assessment of RNA-based vaccines as well as indications for use in specific clinical conditions.
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Affiliation(s)
- Massimiliano Chetta
- AORN A. Cardarelli-Dipartimento delle Tecnologie Avanzate Diagnostico-Terapeutiche e dei Servizi sanitari-U.O.C. Genetica Medica e di Laboratorio, Via A. Cardarelli 9, 80131, Napoli, Italy.
| | - Marina Tarsitano
- AORN A. Cardarelli-Dipartimento delle Tecnologie Avanzate Diagnostico-Terapeutiche e dei Servizi sanitari-U.O.C. Genetica Medica e di Laboratorio, Via A. Cardarelli 9, 80131, Napoli, Italy
| | - Maria Oro
- AORN A. Cardarelli-Dipartimento delle Tecnologie Avanzate Diagnostico-Terapeutiche e dei Servizi sanitari-U.O.C. Genetica Medica e di Laboratorio, Via A. Cardarelli 9, 80131, Napoli, Italy
| | - Maria Rivieccio
- AORN A. Cardarelli-Dipartimento delle Tecnologie Avanzate Diagnostico-Terapeutiche e dei Servizi sanitari-U.O.C. Genetica Medica e di Laboratorio, Via A. Cardarelli 9, 80131, Napoli, Italy
| | - Nenad Bukvic
- AOUC "Policlinico di Bari"-UOC Lab. di Genetica Medica, Piazza Giulio Cesare 11, 70124, Bari, Italy
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16
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Abstract
Signaling via extracellular regulated kinase 1/2 (ERK1/2) and p90 ribosomal S6 kinase (RSK), a downstream effector, mediates numerous processes. For example, ERK1/2-RSK signaling is essential for estrogen homeostasis in the mammary gland and uterus to maintain physiological responsiveness. This review will focus on the coordination of ERK1/2-RSK2 and estrogen signaling through estrogen receptor alpha (ERα). The interrelationship and the feedback mechanisms between these pathways occurs at the level of transcription, translation, and posttranslational modification. Identifying how ERK1/2-RSK2 and estrogen signaling cooperate in homeostasis and disease may lead to novel therapeutic approaches in estrogen-dependent disorders.
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Affiliation(s)
- Deborah A Lannigan
- Correspondence: Deborah A. Lannigan, PhD, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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17
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Lu X, Xu Q, Tong Y, Zhang Z, Dun G, Feng Y, Tang J, Han D, Mao Y, Deng L, He X, Li Q, Xiang Y, Wang F, Zeng D, Tang B, Mao X. Long non-coding RNA EVADR induced by Fusobacterium nucleatum infection promotes colorectal cancer metastasis. Cell Rep 2022; 40:111127. [PMID: 35858553 DOI: 10.1016/j.celrep.2022.111127] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/10/2022] [Accepted: 06/30/2022] [Indexed: 11/03/2022] Open
Abstract
Both Fusobacterium nucleatum (F. nucleatum) and long non-coding RNA (lncRNA) EVADR are associated with colorectal cancer (CRC), but their relationship with CRC metastasis and the mechanisms by which EVADR promotes CRC metastasis are poorly understood. Here, we report that F. nucleatum promotes colorectal cancer cell metastasis to the liver and lung and that it can be detected in CRC-metastasis colonization in mouse models. Furthermore, F. nucleatum upregulates the expression of EVADR, which can increase the metastatic ability of CRC cells in vivo and in vitro. Mechanistically, elevated EVADR serves as a modular scaffold for the Y-box binding protein 1 (YBX1) to directly enhance the translation of epithelial-mesenchymal transition (EMT)-related factors, such as Snail, Slug, and Zeb1. These findings suggest that EVADR induced by F. nucleatum promotes colorectal cancer metastasis through YBX1-dependent translation. The EVADR-YBX1 axis may be useful for the prevention and treatment of patients with F. nucleatum-associated CRC metastasis.
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Affiliation(s)
- Xiaoxue Lu
- Department of Clinical Microbiology and Immunology, College of Pharmacy and Laboratory Medicine Science, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Qiaolin Xu
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Yanan Tong
- Department of Clinical Microbiology and Immunology, College of Pharmacy and Laboratory Medicine Science, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Zhujun Zhang
- Department of Hospital Infection Control, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Guodong Dun
- Department of Clinical Microbiology and Immunology, College of Pharmacy and Laboratory Medicine Science, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yuyang Feng
- Department of Clinical Microbiology and Immunology, College of Pharmacy and Laboratory Medicine Science, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Jie Tang
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Dan Han
- Department of Clinical Microbiology and Immunology, College of Pharmacy and Laboratory Medicine Science, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yilan Mao
- Class of 2021 Undergraduate, Nursing College of Chongqing Medical University, Chongqing 400016, China
| | - Ling Deng
- Department of Clinical Microbiology and Immunology, College of Pharmacy and Laboratory Medicine Science, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xiaoyi He
- Department of Clinical Microbiology and Immunology, College of Pharmacy and Laboratory Medicine Science, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Qian Li
- Department of Clinical Microbiology and Immunology, College of Pharmacy and Laboratory Medicine Science, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yang Xiang
- Department of Clinical Microbiology and Immunology, College of Pharmacy and Laboratory Medicine Science, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - FengChao Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Dongzhu Zeng
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China.
| | - Bin Tang
- Department of General Surgery, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China.
| | - Xuhu Mao
- Department of Clinical Microbiology and Immunology, College of Pharmacy and Laboratory Medicine Science, Third Military Medical University (Army Medical University), Chongqing 400038, China.
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Liu C, Kuang J, Wang Y, Duan T, Min L, Lu C, Zhang T, Chen R, Wu Y, Zhu L. A functional reference map of the RNF8 interactome in cancer. Biol Direct 2022; 17:17. [PMID: 35831895 PMCID: PMC9277853 DOI: 10.1186/s13062-022-00331-z] [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] [Received: 03/14/2022] [Accepted: 06/20/2022] [Indexed: 12/02/2022] Open
Abstract
Background RNF8 is an E3 ligase identified as a critical DNA damage-responsive protein. Recently, multiple reports have shown that RNF8 could be used as an important therapeutic target for cancer chemo/radiotherapy. However, the understanding of RNF8 remains limited due to the lack of its interactome reference map and comprehensive analysis of RNF8 in diverse cancers, which underscores the need to map the interactome of RNF8 via high-throughput methods. Results A two-way identification method based on LC–MS was designed for the identification of the RNF8 interactome with high-specificity. By in silico analysis and in vitro validation, we identified a new reference map of the RNF8 interactome network containing many new targets, such as YBX1, DNMT1, and HDCA1, new biological functions and the gene-disease associations of RNF8. Our results revealed a close relationship between RNF8 and neurodegenerative diseases or tumor-infiltrating immune cells using bulk RNA-seq and scRNA-seq datasets. As a proof of concept of our interactome map, we validated the direct binding between RNF8 and YBX1 and showed that RNF8 catalyzed the ubiquitination of YBX1. These results demonstrated that RNF8 might be a crucial regulator of YBX1. Conclusions Our work provides a unique framework for researchers and clinicians who seek to better explore or understand RNF8-regulated biological functions in cancers. This study will hopefully facilitate the rational design and further development of anti-RNF8 therapy in cancers. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13062-022-00331-z.
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Affiliation(s)
- Chuanyang Liu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Jingyu Kuang
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China.
| | - Yuxuan Wang
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Ting Duan
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Lu Min
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Chenyu Lu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Tianyi Zhang
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Ruifen Chen
- Joint Logistic Support Force 921th Hospital, Changsha, 410073, Hunan, China
| | - Ying Wu
- Department of Critical Care Medicine, Second Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China.
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19
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Panachan J, Rojsirikulchai N, Pongsakul N, Khowawisetsut L, Pongphitcha P, Siriboonpiputtana T, Chareonsirisuthigul T, Phornsarayuth P, Klinkulab N, Jinawath N, Chiangjong W, Anurathapan U, Pattanapanyasat K, Hongeng S, Chutipongtanate S. Extracellular Vesicle-Based Method for Detecting MYCN Amplification Status of Pediatric Neuroblastoma. Cancers (Basel) 2022; 14:cancers14112627. [PMID: 35681607 PMCID: PMC9179557 DOI: 10.3390/cancers14112627] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 01/02/2023] Open
Abstract
Simple Summary MYCN gene amplification, the strongest prognostic marker of aggressive neuroblastoma, is detected on invasive biopsy tissues. This study aimed to establish a less invasive method to detect MYCN status based on MYCN mRNA contents in large extracellular vesicles or microvesicles. MYCN mRNA-containing microvesicles were detectable in three distinct MYCN-amplified neuroblastoma cell lines but absent in three neuroblastoma cells with MYCN-non-amplification. The feasibility of this EV-based workflow was successfully demonstrated by using the simulated samples (prepared by pulsing neuroblastoma MVs into the normal human serum) and bone marrow plasma specimens obtained from nine patients at various disease stages. Taken together, this study established the novel EV-based method for detecting MYCN status in pediatric neuroblastoma. Abstract MYCN amplification is the strongest predictor of high-risk neuroblastoma (NB). The standard procedure to detect MYCN status requires invasive procedures. Extracellular vesicles (EVs) contain molecular signatures of originated cells, present in biofluids, and serve as an invaluable source for cancer liquid biopsies. This study aimed to establish an EV-based method to detect the MYCN status of NB. Two EV subtypes, i.e., microvesicles (MVs) and exosomes, were sequentially isolated from the culture supernatant by step-wise centrifugation, ultrafiltration, and size-exclusion chromatography. Quantitative RT-PCR was performed to detect MYCN mRNA. As a result, MYCN mRNA was detectable in the MVs, but not exosomes, of MYCN-amplified NB cells. MYCN mRNA-containing MVs (MYCN-MV) were successfully detected in three distinct MYCN-amplified NB cell lines but absent in three MYCN non-amplification cells. The simulated samples were prepared by pulsing MVs into human serum. MYCN–MV detection in the simulated samples showed a less interfering effect from the human blood matrix. Validation using clinical specimens (2 mL bone marrow plasma) obtained from patients at various disease stages showed a promising result. Five out of six specimens of MYCN-amplified patients showed positive results, while there were no false positives in four plasma samples of the MYCN non-amplification group. This study communicated a novel EV-based method for detecting the MYCN status of pediatric NB based on MYCN mRNA contents in MVs. Future studies should be pursued in a prospective cohort to determine its true diagnostic performance.
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Affiliation(s)
- Jirawan Panachan
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (J.P.); (P.P.); (U.A.)
| | - Napat Rojsirikulchai
- Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.P.); (W.C.)
| | - Nutkridta Pongsakul
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.P.); (W.C.)
| | - Ladawan Khowawisetsut
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Pongpak Pongphitcha
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (J.P.); (P.P.); (U.A.)
| | - Teerapong Siriboonpiputtana
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.S.); (T.C.); (P.P.); (N.K.)
| | - Takol Chareonsirisuthigul
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.S.); (T.C.); (P.P.); (N.K.)
| | - Pitichai Phornsarayuth
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.S.); (T.C.); (P.P.); (N.K.)
| | - Nisakorn Klinkulab
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.S.); (T.C.); (P.P.); (N.K.)
| | - Natini Jinawath
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Bangkok 10700, Thailand;
| | - Wararat Chiangjong
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.P.); (W.C.)
| | - Usanarat Anurathapan
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (J.P.); (P.P.); (U.A.)
| | - Kovit Pattanapanyasat
- Center of Excellence for Microparticle and Exosome in Diseases, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Suradej Hongeng
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (J.P.); (P.P.); (U.A.)
- Correspondence: (S.H.); or (S.C.)
| | - Somchai Chutipongtanate
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.P.); (W.C.)
- Department of Environmental and Public Health Sciences, Division of Epidemiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Correspondence: (S.H.); or (S.C.)
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20
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Liu J, Huang T, Chen W, Ding C, Zhao T, Zhao X, Cai B, Zhang Y, Li S, Zhang L, Xue M, He X, Ge W, Zhou C, Xu Y, Zhang R. Developmental mRNA m 5C landscape and regulatory innovations of massive m 5C modification of maternal mRNAs in animals. Nat Commun 2022; 13:2484. [PMID: 35513466 PMCID: PMC9072368 DOI: 10.1038/s41467-022-30210-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 04/06/2022] [Indexed: 11/09/2022] Open
Abstract
m5C is one of the longest-known RNA modifications, however, its developmental dynamics, functions, and evolution in mRNAs remain largely unknown. Here, we generate quantitative mRNA m5C maps at different stages of development in 6 vertebrate and invertebrate species and find convergent and unexpected massive methylation of maternal mRNAs mediated by NSUN2 and NSUN6. Using Drosophila as a model, we reveal that embryos lacking maternal mRNA m5C undergo cell cycle delays and fail to timely initiate maternal-to-zygotic transition, implying the functional importance of maternal mRNA m5C. From invertebrates to the lineage leading to humans, two waves of m5C regulatory innovations are observed: higher animals gain cis-directed NSUN2-mediated m5C sites at the 5' end of the mRNAs, accompanied by the emergence of more structured 5'UTR regions; humans gain thousands of trans-directed NSUN6-mediated m5C sites enriched in genes regulating the mitotic cell cycle. Collectively, our studies highlight the existence and regulatory innovations of a mechanism of early embryonic development and provide key resources for elucidating the role of mRNA m5C in biology and disease. mRNAs are known to be decorated with m5C at a low-to-medium level. Here, the authors generate atlases of mRNA m5C during animal development in 6 species and identify convergent and unexpected massive methylation of maternal mRNAs by NSUN2 and NSUN6.
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Affiliation(s)
- Jianheng Liu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Tao Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Wanying Chen
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Chenhui Ding
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Tianxuan Zhao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Xueni Zhao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Bing Cai
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Yusen Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Song Li
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Ling Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Maoguang Xue
- Division of Human Reproduction and Developmental Genetics, Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Xiuju He
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Wanzhong Ge
- Division of Human Reproduction and Developmental Genetics, Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China. .,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China. .,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Canquan Zhou
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China.
| | - Yanwen Xu
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China.
| | - Rui Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China.
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Zhong X, Wang T, Zhang W, Wang M, Xie Y, Dai L, He X, Madhusudhan T, Zeng H, Wang H. ERK/RSK-mediated phosphorylation of Y-box binding protein-1 aggravates diabetic cardiomyopathy by suppressing its interaction with deubiquitinase OTUB1. J Biol Chem 2022; 298:101989. [PMID: 35490780 PMCID: PMC9163515 DOI: 10.1016/j.jbc.2022.101989] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 12/22/2022] Open
Abstract
Diabetic cardiomyopathy (DCM) is a major complication of diabetes, but its underlying mechanisms still remain unclear. The multifunctional protein Y-box binding protein-1 (YB-1) plays an important role in cardiac pathogenesis by regulating cardiac apoptosis, cardiac fibrosis, and pathological remodeling, whereas its role in chronic DCM requires further investigation. Here, we report that the phosphorylation of YB-1 at serine102 (S102) was markedly elevated in streptozotocin-induced diabetic mouse hearts and in high glucose-treated cardiomyocytes, whereas total YB-1 protein levels were significantly reduced. Coimmunoprecipitation experiments showed that YB-1 interacts with the deubiquitinase otubain-1, but hyperglycemia-induced phosphorylation of YB-1 at S102 diminished this homeostatic interaction, resulting in ubiquitination and degradation of YB-1. Mechanistically, the high glucose-induced phosphorylation of YB-1 at S102 is dependent on the upstream extracellular signal-regulated kinase (ERK)/Ras/mitogen-activated protein kinase (p90 ribosomal S6 kinase [RSK]) signaling pathway. Accordingly, pharmacological inhibition of the ERK pathway using the upstream kinase inhibitor U0126 ameliorated features of DCM compared with vehicle-treated diabetic mice. We demonstrate that ERK inhibition with U0126 also suppressed the phosphorylation of the downstream RSK and YB-1 (S102), which stabilized the interaction between YB-1 and otubain-1 and thereby preserved YB-1 protein expression in diabetic hearts. Taken together, we propose that targeting the ERK/RSK/YB-1 pathway could be a potential therapeutic approach for treating DCM.
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Affiliation(s)
- Xiaodan Zhong
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, PR China
| | - Tao Wang
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China; Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, PR China
| | - Wenjun Zhang
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, PR China
| | - Mengwen Wang
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, PR China
| | - Yang Xie
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, PR China
| | - Lei Dai
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, PR China
| | - Xingwei He
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, PR China
| | - Thati Madhusudhan
- Center for Thrombosis and Hemostasis, University Medical Center Mainz, Mainz, Germany
| | - Hesong Zeng
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, PR China.
| | - Hongjie Wang
- Division of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, PR China.
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22
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Deng M, Chen B, Liu Z, Wan Y, Li D, Yang Y, Wang F. YBX1 mediates alternative splicing and maternal mRNA decay during pre-implantation development. Cell Biosci 2022; 12:12. [PMID: 35109938 PMCID: PMC8812265 DOI: 10.1186/s13578-022-00743-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 01/03/2022] [Indexed: 11/28/2022] Open
Abstract
Background In mammals, maternal gene products decay and zygotic genome activation (ZGA) during maternal to zygotic transition (MZT) is critical for the early embryogenesis. Y-box binding protein YBX1 plays vital roles in RNA stabilization and transcriptional regulation, but its roles remain to be elucidated during pre-implantation development. Methods In the present study, we re-analyzed transcriptional level of YBX1 in mice, human, bovine, and goat embryos using public RNA-seq datasets. We further performed siRNA microinjection to knock down the expression of YBX1, and RNA sequencing of the 8-cell stage embryos in the control and YBX1 knockdown group. To reveal the regulation mechanisms of YBX1, we conducted differentially expression analysis, alternative splicing (AS) analysis, enrichment analysis, and 5-EU staining using DESeq2, rMATs, clusterProfiler, and immunofluorescence technique, respectively. Results The expression of YBX1 was increased during MZT in goat, bovine, human, and mice, but significantly decreased in YBX1 knockdown embryos compared with the controls, suggesting successfully knockdown of YBX1. The percentage of blastocyst was decreased, while embryos blocked at the 2- and 4-cell stage were increased in YBX1 knockdown embryos compared to the controls. Using RNA-seq, we identified 1623 up-regulated and 3531 down-regulated genes in the 8-cell stage YBX1 knockdown embryos. Of note, the down-regulated genes were enriched in regulation of RNA/mRNA stability and spliceosome, suggesting that YBX1 might medicate RNA stability and AS. To this end, we identified 3284 differential AS events and 1322 differentially expressed maternal mRNAs at the 8-cell stage YBX1 knockdown embryos. Meanwhile, the splicing factors and mRNA decay-related genes showed aberrant expression, and the transcriptional activity during ZGA in goat and mice was compromised when YBX1 was knocked down. Conclusion YBX1 serves an important role in maternal mRNA decay, alternative splicing, and the transcriptional activity required for early embryogenesis, which will broaden the current understanding of YBX1 functions during the stochastic reprogramming events. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-022-00743-4.
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Affiliation(s)
- Mingtian Deng
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Baobao Chen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zifei Liu
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yongjie Wan
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dongxu Li
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yingnan Yang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Wang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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Lin Y, Zhang J, Li Y, Guo W, Chen L, Chen M, Chen X, Zhang W, Jin X, Jiang M, Xiao H, Wang C, Song C, Fu F. CTPS1 promotes malignant progression of triple-negative breast cancer with transcriptional activation by YBX1. J Transl Med 2022; 20:17. [PMID: 34991621 PMCID: PMC8734240 DOI: 10.1186/s12967-021-03206-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/17/2021] [Indexed: 01/18/2023] Open
Abstract
Background Cytidine nucleotide triphosphate synthase 1 (CTPS1) is a CTP synthase which play critical roles in DNA synthesis. However, its biological regulation and mechanism in triple-negative breast cancer (TNBC) has not been reported yet. Methods The expression of CTPS1 in TNBC tissues was determined by GEO, TCGA databases and immunohistochemistry (IHC). The effect of CTPS1 on TNBC cell proliferation, migration, invasion, apoptosis and tumorigenesis were explored in vivo and in vitro. In addition, the transcription factor Y-box binding protein 1 (YBX1) was identified by bioinformatics methods, dual luciferase reporter and chromatin immunoprecipitation (CHIP) assays. Pearson correlation analysis was utilized to assess the association between YBX1 and CTPS1 expression. Results CTPS1 expression was significantly upregulated in TNBC tissues and cell lines. Higher CTPS1 expression was correlated with a poorer disease-free survival (DFS) and overall survival (OS) in TNBC patients. Silencing of CTPS1 dramatically inhibited the proliferation, migration, invasion ability and induced apoptosis of MDA-MB-231 and HCC1937 cells. Xenograft tumor model also indicated that CTPS1 knockdown remarkably reduced tumor growth in mice. Mechanically, YBX1 could bind to the promoter of CTPS1 to promote its transcription. Furthermore, the expression of YBX1 was positively correlated with CTPS1 in TNBC tissues. Rescue experiments confirmed that the enhanced cell proliferation and invasion ability induced by YBX1 overexpression could be reversed by CTPS1 knockdown. Conclusion Our data demonstrate that YBX1/CTPS1 axis plays an important role in the progression of TNBC. CTPS1 might be a promising prognosis biomarker and potential therapeutic target for patients with triple-negative breast cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03206-5.
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Affiliation(s)
- Yuxiang Lin
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Jie Zhang
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Yan Li
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Wenhui Guo
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Lili Chen
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Minyan Chen
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Xiaobin Chen
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Wenzhe Zhang
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Xuan Jin
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China
| | - Meichen Jiang
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China
| | - Han Xiao
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China
| | - Chuan Wang
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China. .,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China. .,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China.
| | - Chuangui Song
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China. .,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China. .,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China.
| | - Fangmeng Fu
- Department of Breast Surgery, Fujian Medical University Union Hospital, No.29, Xin Quan Road, Gulou District, Fuzhou, 350001, Fujian, China. .,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian, China. .,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian, China.
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Chen Q, Wang H, Li Z, Li F, Liang L, Zou Y, Shen H, Li J, Xia Y, Cheng Z, Yang T, Wang K, Shen F. Circular RNA ACTN4 promotes intrahepatic cholangiocarcinoma progression by recruiting YBX1 to initiate FZD7 transcription. J Hepatol 2022; 76:135-147. [PMID: 34509526 DOI: 10.1016/j.jhep.2021.08.027] [Citation(s) in RCA: 116] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Intrahepatic cholangiocarcinoma (ICC) is a primary liver cancer with high aggressiveness and extremely poor prognosis. The role of circular RNAs (circRNAs) in ICC carcinogenesis and progression remains to be determined. METHODS CircRNA microarray was performed to screen significantly upregulated circRNAs in paired ICC and non-tumor tissues. Colony formation, transwell, and xenograft models were used to examine the role of circRNAs in ICC proliferation and metastasis. RNA pulldown, mass spectrometry, chromatin immunoprecipitation, RNA-binding protein immunoprecipitation, chromatin isolation by RNA purification, electrophoretic mobility shift assay, and luciferase reporter assays were used to explore the molecular sponge role of the circRNA (via miRNA binding), and the interaction between circRNA and RNA-binding proteins. RESULTS Hsa_circ_0050898, which originated from exon 1 to exon 20 of the ACTN4 gene (named circACTN4), was significantly upregulated in ICC. High circACTN4 expression was associated with enhanced tumor proliferation and metastasis in vitro and in vivo, as well as a worse prognosis following ICC resection. In addition, circACTN4 upregulated Yes-associated protein 1 (YAP1) expression by sponging miR-424-5p. More importantly, circACTN4 also recruited Y-box binding protein 1 (YBX1) to stimulate Frizzled-7 (FZD7) transcription. Furthermore, circACTN4 overexpression in ICC cells enhanced the interaction between YAP1 and β-catenin, which are the core components of the Hippo and Wnt signaling pathways, respectively. CONCLUSIONS CircACTN4 was upregulated in ICC and promoted ICC proliferation and metastasis by acting as a molecular sponge of miR-424-5p, as well as by interacting with YBX1 to transcriptionally activate FZD7. These results suggest that circACTN4 is a potential prognostic marker and therapeutic target for ICC. LAY SUMMARY Intrahepatic cholangiocarcinoma is a primary liver cancer associated with aggressiveness and extremely poor prognosis. It is essential for therapeutic development that we uncover relevant pathogenic pathways. Herein, we showed that a circular RNA (circACTN4) was highly expressed in intrahepatic cholangiocarcinoma and was positively associated with tumor growth and metastasis through key developmental signaling pathways. Thus, circACTN4 could be a prognostic biomarker and therapeutic target for intrahepatic cholangiocarcinoma.
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Affiliation(s)
- Qinjunjie Chen
- Department of Hepatic Surgery IV, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Haibo Wang
- Department of Hepatic Surgery IV, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Zheng Li
- Department of Hepatic Surgery IV, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Fengwei Li
- Department of Hepatic Surgery IV, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China; Department of Hepatic Surgery II, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Leilei Liang
- Department of Gynecological Oncology, Chinese Academy of Medical Sciences Cancer Institute and Hospital: Cancer Hospital Chinese Academy of Medical Sciences, Beijing, China
| | - Yiran Zou
- Department of Hepatic Surgery IV, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Hao Shen
- Department of Hepatobiliary Surgery, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Jun Li
- Department of Hepatic Surgery IV, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Yong Xia
- Department of Hepatic Surgery IV, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Zhangjun Cheng
- Hepato-Pancreato-Biliary Center, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Tian Yang
- Department of Hepatobiliary Surgery, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Kui Wang
- Department of Hepatic Surgery II, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Feng Shen
- Department of Hepatic Surgery IV, the Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China.
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25
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Shen J, She W, Zhang F, Guo J, Jia R. YBX1 Promotes the Inclusion of RUNX2 Alternative Exon 5 in Dental Pulp Stem Cells. Int J Stem Cells 2021; 15:301-310. [PMID: 34965997 PMCID: PMC9396021 DOI: 10.15283/ijsc21035] [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: 02/21/2021] [Revised: 09/03/2021] [Accepted: 10/25/2021] [Indexed: 11/09/2022] Open
Abstract
Background and Objectives RUNX2 plays an essential role during the odontoblast differentiation of dental pulp stem cells (DPSCs). RUNX2 Exon 5 is an alternative exon and essential for RUNX2 transcriptional activity. This study aimed to investigate the regulatory mechanisms of RUNX2 exon 5 alternative splicing in human DPSCs. Methods and Results The regulatory motifs of RUNX2 exon 5 were analyzed using the online SpliceAid program. The alternative splicing of RUNX2 exon 5 in DPSCs during mineralization-induced differentiation was analyzed by RT-PCR. To explore the effect of splicing factor YBX1 on exon 5 alternative splicing, gaining or losing function of YBX1 was performed by transfection of YBX1 overexpression plasmid or anti-YBX1 siRNA in DPSCs. Human RUNX2 exon 5 is evolutionarily conserved and alternatively spliced in DPSCs. There are three potential YBX1 binding motifs in RUNX2 exon 5. The inclusion of RUNX2 exon 5 and YBX1 expression level increased significantly during mineralization- induced differentiation in DPSCs. Overexpression of YBX1 significantly increased the inclusion of RUNX2 exon 5 in DPSCs. In contrast, silence of YBX1 significantly reduced the inclusion of exon 5 and the corresponding RUNX2 protein expression level. Knockdown of YBX1 reduced the expression of alkaline phosphatase (ALP) and osteocalcin (OC) and the mineralization ability of DPSCs, while overexpression of YBX1 increased the expression of ALP and OC and the mineralization ability of DPSCs. Conclusions Human RUNX2 exon 5 is conserved evolutionarily and alternatively spliced in DPSCs. Splicing factor YBX1 promotes the inclusion of RUNX2 exon 5 and improves the mineralization ability of DPSCs.
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Affiliation(s)
- Jiaoxiang Shen
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China.,Department of Orthodontics, Stomatological Hospital of Xiamen Medical College, Xiamen, China
| | - Wenting She
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China.,Department of Stomatology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Fengxia Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jihua Guo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China.,Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
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26
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Gross DA, Cheng HS, Zhuang R, McCoy MG, Pérez-Cremades D, Salyers Z, Wara AKMK, Haemmig S, Ryan TE, Feinberg MW. Deficiency of lncRNA SNHG12 impairs ischemic limb neovascularization by altering an endothelial cell cycle pathway. JCI Insight 2021; 7:150761. [PMID: 34793334 PMCID: PMC8765056 DOI: 10.1172/jci.insight.150761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 11/17/2021] [Indexed: 01/10/2023] Open
Abstract
SNHG12, a long noncoding RNA (lncRNA) dysregulated in atherosclerosis, is known to be a key regulator of vascular senescence in endothelial cells (ECs). However, its role in angiogenesis and peripheral artery disease has not been elucidated. Hind-limb ischemia studies using femoral artery ligation (FAL) in mice showed that SNHG12 expression falls readily in the acute phase of the response to limb ischemia in gastrocnemius muscle and recovers to normal when blood flow recovery is restored to ischemic muscle, indicating that it likely plays a role in the angiogenic response to ischemia. Gain- and loss-of-function studies demonstrated that SNHG12 regulated angiogenesis — SNHG12 deficiency reduced cell proliferation, migration, and endothelial sprouting, whereas overexpression promoted these angiogenic functions. We identified SNHG12 binding partners by proteomics that may contribute to its role in angiogenesis, including IGF-2 mRNA–binding protein 3 (IGF2BP3, also known as IMP3). RNA-Seq profiling of SNHG12-deficient ECs showed effects on angiogenesis pathways and identified a strong effect on cell cycle regulation, which may be modulated by IMP3. Knockdown of SNHG12 in mice undergoing FAL using injected gapmeRs) decreased angiogenesis, an effect that was more pronounced in a model of insulin-resistant db/db mice. RNA-Seq profiling of the EC and non-EC compartments in these mice revealed a likely role of SNHG12 knockdown on Wnt, Notch, and angiopoietin signaling pathways. Together, these findings indicate that SNHG12 plays an important role in the angiogenic EC response to ischemia.
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Affiliation(s)
- David A Gross
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
| | - Henry S Cheng
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
| | - Rulin Zhuang
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
| | - Michael G McCoy
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
| | - Daniel Pérez-Cremades
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
| | - Zachary Salyers
- Department of Applied Physiology and Kinesiology, University of Florida, Gainesville, United States of America
| | - A K M Khyrul Wara
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
| | - Stefan Haemmig
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
| | - Terence E Ryan
- Department of Applied Physiology and Kinesiology, University of Florida, Gainesville, United States of America
| | - Mark W Feinberg
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
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27
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Li Y, Gao Y, Niu X, Tang M, Li J, Song B, Guan X. LncRNA BASP1-AS1 interacts with YBX1 to regulate Notch transcription and drives the malignancy of melanoma. Cancer Sci 2021; 112:4526-4542. [PMID: 34533860 PMCID: PMC8586662 DOI: 10.1111/cas.15140] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/08/2021] [Accepted: 09/12/2021] [Indexed: 12/14/2022] Open
Abstract
Melanoma is a fatal skin malignant tumor with a poor prognosis. We found that long noncoding RNA BASP1-AS1 is essential for the development and prognosis of melanoma. The methylation, RNA sequencing, copy number variation, mutation data, and sample follow-up information of melanoma from The Cancer Genome Atlas (TCGA) were analyzed using weighted gene co-expression network analysis and 366 samples common to the three omics were selected for multigroup clustering analysis. A four-gene prognostic model (BASP1-AS1, LOC100506098, ARHGAP27P1, and LINC01532) was constructed in the TCGA cohort and validated using the GSE65904 series. The expression of BASP1-AS1 was upregulated in melanoma tissues and various melanoma cell lines. Functionally, the ectopic expression of BASP1-AS1 promoted cell proliferation, migration, and invasion in both A375 and SK-MEL-2 cells. Mechanically, BASP1-AS1 interacted with YBX1 and recruited it to the promoter of NOTCH3, initiating its transcription process. The activation of the Notch signaling then resulted in the transcription of multiple oncogenes, including c-MYC, PCNA, and CDK4, which contributed to melanoma progression. Thus, BASP1-AS1 could act as a potential biomarker for cutaneous malignant melanoma.
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Affiliation(s)
- YaLing Li
- Department of DermatologyThe First Hospital of China Medical University and National Joint Engineering Research Center for Theranostics of Immunological Skin DiseasesThe First Hospital of China Medical University and Key Laboratory of ImmunodermatologyMinistry of Health and Ministry of EducationShenyangChina
| | - YaLi Gao
- Department of DermatologyThe First Afflicated Hospital of Sun Yat‐sen UniversityGuangzhouChina
| | - XueLi Niu
- Department of DermatologyThe First Hospital of China Medical University and National Joint Engineering Research Center for Theranostics of Immunological Skin DiseasesThe First Hospital of China Medical University and Key Laboratory of ImmunodermatologyMinistry of Health and Ministry of EducationShenyangChina
| | - MingSui Tang
- Department of DermatologyThe First Hospital of China Medical University and National Joint Engineering Research Center for Theranostics of Immunological Skin DiseasesThe First Hospital of China Medical University and Key Laboratory of ImmunodermatologyMinistry of Health and Ministry of EducationShenyangChina
| | - JingYi Li
- Department of DermatologyThe First Hospital of China Medical University and National Joint Engineering Research Center for Theranostics of Immunological Skin DiseasesThe First Hospital of China Medical University and Key Laboratory of ImmunodermatologyMinistry of Health and Ministry of EducationShenyangChina
| | - Bing Song
- Department of DermatologyThe First Hospital of China Medical University and National Joint Engineering Research Center for Theranostics of Immunological Skin DiseasesThe First Hospital of China Medical University and Key Laboratory of ImmunodermatologyMinistry of Health and Ministry of EducationShenyangChina
- School of DentistryCardiff UniversityCardiffUK
| | - XiuHao Guan
- Department of DermatologyThe First Hospital of China Medical University and National Joint Engineering Research Center for Theranostics of Immunological Skin DiseasesThe First Hospital of China Medical University and Key Laboratory of ImmunodermatologyMinistry of Health and Ministry of EducationShenyangChina
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28
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Zhao Z, He R, Chu P, Cai H, Shen H, Zhao Z, Feng S, Cao D, Liao M, Gan G, Ye H, Chen Z, Qiu W, Deng J, Ming F, Ma M, Jia J, Wu J, Huang H, Sun C, Li J, Zhang L. YBX has functional roles in CpG-ODN against cold stress and bacterial infection of Misgurnus anguillicaudatus. FISH & SHELLFISH IMMUNOLOGY 2021; 118:72-84. [PMID: 34474150 DOI: 10.1016/j.fsi.2021.08.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Misgurnus anguillicaudatus (M. anguillicaudatus) is a widely cultivated fish. However, in M. anguillicaudatus breeding, the frequent cold stress during daily breeding could induce immune suppression and increase the risk of infection, causing serious economic loss. Based on existing findings, CpG Oligonucleotides (CpG-ODNs) may be an ideal protective agent for low temperature fish breeding, performing anti-infective when faced with cold stress with cold shock proteins Y box binding proteins (YBX). Although YBX has pleiotropic functions, its roles in CpG-ODNs-mediated immunity (especially under cold situations) remain largely unexplored. To clarify the relationship among them, we identified the YBX1/YBX2 in M. anguillicaudatus and analyzed using a series of bioinformatics methods. After that, we immunized the fish with 3 types of CpG-ODNs and challenged with Aeromonas hydrophila (A. hydrophila). Here we showed that the best anti-bacterial effect of CpG-B was accompanied by the significant upregulation of YBX1. And the detection of the YBX1 downstream effectors confirmed that CpG-B induced the YBX1-mediated Th1 oriented responses to A. hydrophila by regulation of the NLRP3 (Caspase-A/-B), IL-1β, IL-12 and IFN-γ. Afterwards, we found that under cold stress, CpG-B can activate the NLRP3 and NF-κB pathways through YBX1, a key mediator of anti-A. hydrophila in CpG-B immunization. In this study, we demonstrated CpG-B protection against infection in low temperature, and its interaction with YBX1, expanded the research of CpG-ODN under cold stress, and provided a new CpG-ODN application for low temperature fish farming.
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Affiliation(s)
- Zengjue Zhao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Rongxiao He
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Pinpin Chu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Haiming Cai
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Haokun Shen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Zitong Zhao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Saixiang Feng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Ding Cao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Ming Liao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Guanhua Gan
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Hejia Ye
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Zhiyang Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Weihong Qiu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jinbo Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Feiping Ming
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Miaopeng Ma
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Junhao Jia
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jiahui Wu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Haobin Huang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Chongjun Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jiayi Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Linghua Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
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Long non-coding RNA MIR200CHG promotes breast cancer proliferation, invasion, and drug resistance by interacting with and stabilizing YB-1. NPJ Breast Cancer 2021; 7:94. [PMID: 34272387 PMCID: PMC8285504 DOI: 10.1038/s41523-021-00293-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 06/09/2021] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNA) have been identified as key regulators of tumorigenesis and development. We aim to explore the biological functions and molecular mechanisms of lncRNA MIR200CHG in breast cancer. We found that MIR200CHG is highly expressed in breast cancer tissues and is related to the tumor size and histopathological grade. In vitro and in vivo experiments confirmed that MIR200CHG can promote breast cancer proliferation, invasion, and drug resistance. MIR200CHG directly binds to the transcription factor Y-box binding protein-1 (YB-1), and inhibits its ubiquitination and degradation. MIR200CHG regulates YB-1 phosphorylation at serine 102, thereby affecting the expression of genes related to tumor cell proliferation, apoptosis, invasion, and drug resistance. Additionally, MIR200CHG partially affects the expression of miR-200c/141-3p encoded by its intron region. Therefore, MIR200CHG can promote the proliferation, invasion, and drug resistance of breast cancer by interacting with and stabilizing YB-1, and has the potential to become a target for breast cancer treatment.
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Kong X, Li J, Li Y, Duan W, Qi Q, Wang T, Yang Q, Du L, Mao H, Wang C. A novel long non-coding RNA AC073352.1 promotes metastasis and angiogenesis via interacting with YBX1 in breast cancer. Cell Death Dis 2021; 12:670. [PMID: 34218256 PMCID: PMC8254808 DOI: 10.1038/s41419-021-03943-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/23/2022]
Abstract
Breast cancer is the major cause of cancer death worldwide in women. Patients with metastasis have poor prognosis and the mechanisms of breast cancer metastasis are not completely understood. Long non-coding RNAs (lncRNAs) have been shown to have crucial roles in breast cancer development and progression. However, the underlying mechanisms by which lncRNA-driven breast cancer metastasis are unknown. The main objective of this paper is to explore a functional lncRNA and its mechanisms in breast cancer. Here we identified a novel lncRNA AC073352.1 that was significantly upregulated in breast cancer tissues and was associated with advanced TNM stages and poor prognosis in breast cancer patients. In addition, AC073352.1 was found to promote the migration and invasion of breast cancer cells in vitro and enhance breast cancer metastasis in vivo. Mechanistically, we elucidated that AC073352.1 interacted with YBX1 and stabilized its protein expression. Knock down of YBX1 reduced breast cancer cell migration and invasion and could partially reverse the stimulative effects of AC073352.1 overexpressed on breast cancer metastasis. Moreover, AC073352.1 might be packaged into exosomes by binding to YBX1 in breast cancer cells resulting in angiogenesis. Collectively, our results demonstrated that AC073352.1 promoted breast cancer metastasis and angiogenesis via binding YBX1, and it could serve as a promising, novel biomarker for prognosis and a therapeutic target in breast cancer.
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Affiliation(s)
- Xue Kong
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, 250012, Jinan, Shandong, China
| | - Juan Li
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, 250012, Jinan, Shandong, China
| | - Yanru Li
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, 250012, Jinan, Shandong, China
| | - Weili Duan
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, 250012, Jinan, Shandong, China
| | - Qiuchen Qi
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, 250012, Jinan, Shandong, China
| | - Tiantian Wang
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, 250012, Jinan, Shandong, China
| | - Qifeng Yang
- Department of Breast Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 250012, Jinan, Shandong, China.,Pathology Tissue Bank, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 250012, Jinan, Shandong, China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, 250012, Jinan, Shandong, China.,Tumor Marker Detection Engineering Technology Research Center of Shandong Province, Jinan, Shandong, China
| | - Haiting Mao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, 250012, Jinan, Shandong, China.
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, 250012, Jinan, Shandong, China. .,Tumor Marker Detection Engineering Laboratory of Shandong Province, Jinan, Shandong, China. .,The Clinical Research Center of Shandong Province for Clinical Laboratory, Jinan, Shandong, China.
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Y-Box Binding Protein 1 Regulates Angiogenesis in Bladder Cancer via miR-29b-3p-VEGFA Pathway. JOURNAL OF ONCOLOGY 2021; 2021:9913015. [PMID: 34306080 PMCID: PMC8270724 DOI: 10.1155/2021/9913015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 06/23/2021] [Indexed: 12/26/2022]
Abstract
Angiogenesis plays a vital role in the development of bladder cancer (BC). The Y-box-binding protein 1 (YB-1) is a well-known oncoprotein which is closely related to angiogenesis of tumors, but the relationship and mechanism of YB-1 and angiogenesis in BC remain unclear. Based on 56 clinical BC specimens, this study found that high expression of YB-1 samples demonstrated a higher expression of vascular endothelial growth factor A (VEGFA) than those of YB-1 low expression. Subsequently, the expression of YB-1 and miR-29b-3p was regulated in the BC cell lines where we noted that YB-1 promoted VEGFA expression by downregulating the expression of miR- 29b-3p. The ability of BC cells to induce angiogenesis decreased after YB-1 was knocked down. Moreover, the in vivo study further confirmed that YB-1 promotes angiogenesis in BC. Our findings enhance the understanding of how YB-1 promotes angiogenesis in BC and provide evidence for YB-1 as a therapeutic target of BC. Moreover, this may provide new inspiration for miRNAs replacement therapies.
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Georgiadou D, Boussata S, Keijser R, Janssen DAM, Afink GB, van Dijk M. Knockdown of Splicing Complex Protein PCBP2 Reduces Extravillous Trophoblast Differentiation Through Transcript Switching. Front Cell Dev Biol 2021; 9:671806. [PMID: 34095140 PMCID: PMC8172583 DOI: 10.3389/fcell.2021.671806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/06/2021] [Indexed: 12/13/2022] Open
Abstract
Mutations in the LINC-HELLP non-coding RNA (HELLPAR) have been associated with familial forms of the pregnancy-specific HELLP syndrome. These mutations negatively affect extravillous trophoblast (EVT) differentiation from a proliferative to an invasive state and disturb the binding of RNA splicing complex proteins PCBP1, PCBP2, and YBX1 to LINC-HELLP. In this study, by using both in vitro and ex vivo experiments, we investigate if these proteins are involved in the regulation of EVT invasion during placentation. Additionally, we study if this regulation is due to alternative mRNA splicing. HTR-8/SVneo extravillous trophoblasts and human first trimester placental explants were used to investigate the effect of siRNA-mediated downregulation of PCBP1, PCBP2, and YBX1 genes on the differentiation of EVTs. Transwell invasion assays and proliferation assays indicated that upon knockdown of PCBP2 and, to a lesser extent, YBX1 and PCBP1, EVTs fail to differentiate toward an invasive phenotype. The same pattern was observed in placental explants where PCBP2 knockdown led to approximately 80% reduction in the number of explants showing any EVT outgrowth. Of the ones that still did show EVT outgrowth, the percentage of proliferating EVTs was significantly higher compared to explants transfected with non-targeting control siRNAs. To further investigate this effect of PCBP2 silencing on EVTs, we performed whole transcriptome sequencing (RNA-seq) on HTR-8/SVneo cells after PCBP2 knockdown. PCBP2 knockdown was found to have minimal effect on mRNA expression levels. In contrast, PCBP2 silencing led to a switch in splicing for a large number of genes with predominant functions in cellular assembly and organization, cellular function and maintenance, and cellular growth and proliferation and the cell cycle. EVTs, upon differentiation, alter their function to be able to invade the decidua of the mother by changing their cellular assembly and their proliferative activity by exiting the cell cycle. PCBP2 appears to be a paramount regulator of these differentiation mechanisms, where its disturbed binding to LINC-HELLP could contribute to dysfunctional placental development as seen in the HELLP syndrome.
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Affiliation(s)
- Danai Georgiadou
- Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Souad Boussata
- Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Remco Keijser
- Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Dianta A M Janssen
- Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Gijs B Afink
- Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Marie van Dijk
- Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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Ban Y, Tan Y, Li X, Li X, Zeng Z, Xiong W, Li G, Xiang B, Yi M. RNA-binding protein YBX1 promotes cell proliferation and invasiveness of nasopharyngeal carcinoma cells via binding to AURKA mRNA. J Cancer 2021; 12:3315-3324. [PMID: 33976741 PMCID: PMC8100805 DOI: 10.7150/jca.56262] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 03/27/2021] [Indexed: 01/02/2023] Open
Abstract
Background: RNA-binding proteins (RBPs) play essential roles in post-transcriptional control of gene expression. Dysregulation of RBPs is intensively implicated in development and progression of human diseases, including cancers. However, the roles of RBPs in nasopharyngeal carcinoma (NPC), which is a distinct subtype of head and neck cancer, remain elusive. Methods: NPC-related RBPs were explored by analyzing GEO database and high-throughput proteomic data obtained from crosslinking immunoprecipitation. The expression levels of Y box binding protein 1 (YBX1) protein in NPC samples were measured by immunohistochemistry (IHC) staining. The association of YBX1 protein levels with prognosis of NPC patients was analyzed by Kaplan-Meier Plotter. The expression levels of YBX1 in NPC cells were inhibited by RNA interference. Cell growth was measured by CCK-8 assay. Cell mobility and invasiveness were measured by transwell assays. Tumorigenicity was measured by using a xenograft tumor assay. The expression levels of mRNAs or proteins were determined by qPCR or western blot assays, respectively. The mRNAs binding to YBX1 were determined by RNA immunoprecipitation (RIP) and qPCR. The effect of YBX1 on mRNA translation was measured by luciferase reporter assay. Results: In the present study, we demonstrated a differentially expressed RBPs profile between NPC and its normal counterpart. Among these aberrantly expressed RBPs, YBX1 was overexpressed in NPC. We found that YBX1 is mainly localized in the cytoplasm of NPC cells. Loss of YBX1 led to reduced cell proliferation, migration and invasiveness in vitro, and reduced tumorigenicity in vivo. Overexpression of YBX1 associates with high expression of cell cycle G2/M checkpoint modulators. In addition, YBX1 promotes AURKA protein expression by directly binding to its mRNA. Loss of YBX1 leads to reduction of AURKA protein level. Forced expression of AURKA rescues cell proliferation and invasiveness in YBX1-silenced NPC cell. Conclusions: The current study indicated that YBX1 promotes NPC cell proliferation and invasiveness through enhancing protein synthesis of AURKA.
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Affiliation(s)
- Yuanyuan Ban
- Hunan Key Laboratory of Cancer Metabolism, Hunan Provincial Cancer Hospital and Cancer Hospital Affiliated to Xiangya Medical School, Central South University, Changsha 410013, Hunan, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha 410078, Hunan, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Yixin Tan
- Department of Dermatology, The Second Xiangya Hospital, The Central South University, Changsha 410011, Hunan, China
| | - Xiaoling Li
- Hunan Key Laboratory of Cancer Metabolism, Hunan Provincial Cancer Hospital and Cancer Hospital Affiliated to Xiangya Medical School, Central South University, Changsha 410013, Hunan, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha 410078, Hunan, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Xiayu Li
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Zhaoyang Zeng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Provincial Cancer Hospital and Cancer Hospital Affiliated to Xiangya Medical School, Central South University, Changsha 410013, Hunan, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha 410078, Hunan, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Wei Xiong
- Hunan Key Laboratory of Cancer Metabolism, Hunan Provincial Cancer Hospital and Cancer Hospital Affiliated to Xiangya Medical School, Central South University, Changsha 410013, Hunan, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha 410078, Hunan, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Guiyuan Li
- Hunan Key Laboratory of Cancer Metabolism, Hunan Provincial Cancer Hospital and Cancer Hospital Affiliated to Xiangya Medical School, Central South University, Changsha 410013, Hunan, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha 410078, Hunan, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Bo Xiang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Provincial Cancer Hospital and Cancer Hospital Affiliated to Xiangya Medical School, Central South University, Changsha 410013, Hunan, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha 410078, Hunan, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan, China
| | - Mei Yi
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.,Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
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Wu QN, Luo XJ, Liu J, Lu YX, Wang Y, Qi J, Liu ZX, Huang QT, Liu ZK, Lu JB, Jin Y, Pu HY, Hu PS, Zheng JB, Zeng ZL, Ju HQ, Xie D, Zhao Q, Xu R. MYC-Activated LncRNA MNX1-AS1 Promotes the Progression of Colorectal Cancer by Stabilizing YB1. Cancer Res 2021; 81:2636-2650. [PMID: 33782099 DOI: 10.1158/0008-5472.can-20-3747] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/20/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022]
Abstract
Long noncoding RNAs (lncRNA) are involved in tumorigenesis and drug resistance. However, the roles and underlying mechanisms of lncRNAs in colorectal cancer are still unknown. In this work, through transcriptomic profiling analysis of 21 paired tumor and normal samples, we identified a novel colorectal cancer-related lncRNA, MNX1-AS1. MNX1-AS1 expression was significantly upregulated in colorectal cancer and associated with poor prognosis. In vitro and in vivo gain- and loss-of-function experiments showed that MNX1-AS1 promotes the proliferation of colorectal cancer cells. MNX1-AS1 bound to and activated Y-box-binding protein 1 (YB1), a multifunctional RNA/DNA-binding protein, and prevented its ubiquitination and degradation. A marked overlap between genes that are differentially expressed in MNX1-AS1 knockdown cells and transcriptional targets of YB1 was observed. YB1 knockdown mimicked the loss of viability phenotype observed upon depletion of MNX1-AS1. In addition, MYC bound the promoter of the MNX1-AS1 locus and activated its transcription. In vivo experiments showed that ASO inhibited MNX1-AS1, which suppressed the proliferation of colorectal cancer cells in both cell-based and patient-derived xenograft models. Collectively, these findings suggest that the MYC-MNX1-AS1-YB1 axis might serve as a potential biomarker and therapeutic target in colorectal cancer. SIGNIFICANCE: This study highlights the discovery of a novel colorectal cancer biomarker and therapeutic target, MNX1-AS1, a long noncoding RNA that drives proliferation via a MYC/MNX1-AS1/YB1 signaling pathway. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/10/2636/F1.large.jpg.
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Affiliation(s)
- Qi-Nian Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiao-Jing Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jia Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yun-Xin Lu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yun Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jingjing Qi
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ze-Xian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qi-Tao Huang
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ze-Kun Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jia-Bin Lu
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ying Jin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Heng-Ying Pu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Pei-Shan Hu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital (Guangdong Gastrointestinal and Anal Hospital), Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jia-Bo Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhao-Lei Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Huai-Qiang Ju
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dan Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qi Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Ruihua Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China. .,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, China
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35
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Huang C, Zhu B, Leng D, Ge W, Zhang XD. Long noncoding RNAs implicated in embryonic development in Ybx1 knockout zebrafish. FEBS Open Bio 2021; 11:1259-1276. [PMID: 33278865 PMCID: PMC8016120 DOI: 10.1002/2211-5463.13057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022] Open
Abstract
Y-box-binding protein 1 (Ybx1, YB-1), also known as Y-box transcription factor, is involved in a variety of biological processes (BPs) and pathways, including embryogenesis, reproduction and development in vertebrates. Several noncoding RNAs regulate Ybx1 signaling. However, the role of long noncoding RNAs (lncRNAs) in embryogenesis remains incompletely understood. Here, we investigated the possible involvement of lncRNAs in Ybx1-mediated regulation of vertebrate development by performing systematic transcriptome analysis of RNA sequencing data derived from ybx1 homozygous mutant zebrafish on day 5 (day5_ybx1-/- ) and wild-type zebrafish on days 5 and 6 (day5_ybx1+/+ and day6_ybx1+/+ ). We identified several lncRNAs affected by ybx1 disruption that may target reduction-oxidation-related genes, such as duox (NADPH oxidase) and noxo1a (NADPH oxidase organizer). Knockdown of three selected lncRNAs led to morphological deformation of larvae, implying an involvement of these lncRNAs in zebrafish embryo development. In summary, our study provides new insights into the lncRNA-mediated mechanisms underlying development in Ybx1-deficient zebrafish larvae.
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Affiliation(s)
- Chen Huang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, China
| | - Bo Zhu
- Faculty of Health Sciences, University of Macau, Taipa, China
| | - Dongliang Leng
- Faculty of Health Sciences, University of Macau, Taipa, China
| | - Wei Ge
- Faculty of Health Sciences, University of Macau, Taipa, China
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36
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Chen YS, Yang WL, Zhao YL, Yang YG. Dynamic transcriptomic m 5 C and its regulatory role in RNA processing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1639. [PMID: 33438329 DOI: 10.1002/wrna.1639] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 11/30/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022]
Abstract
RNA 5-methylcytosine (m5 C) is a prevalent RNA modification in multiple RNA species, including messenger RNAs (mRNAs), transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), and noncoding RNAs (ncRNAs), and broadly distributed from archaea, prokaryotes to eukaryotes. The multiple detecting techniques of m5 C have been developed, such as m5 C-RIP-seq, miCLIP-seq, AZA-IP-seq, RNA-BisSeq, TAWO-seq, and Nanopore sequencing. These high-throughput techniques, combined with corresponding analysis pipeline, provide a precise m5 C landscape contributing to the deciphering of its biological functions. The m5 C modification is distributed along with mRNA and enriched around 5'UTR and 3'UTR, and conserved in tRNAs and rRNAs. It is dynamically regulated by its related enzymes, including methyltransferases (NSUN, DNMT, and TRDMT family members), demethylases (TET families and ALKBH1), and binding proteins (ALYREF and YBX1). So far, accumulative studies have revealed that m5 C participates in a variety of RNA metabolism, including mRNA export, RNA stability, and translation. Depletion of m5 C modification in the organism could cause dysfunction of mitochondria, drawback of stress response, frustration of gametogenesis and embryogenesis, abnormality of neuro and brain development, and has been implicated in cell migration and tumorigenesis. In this review, we provide a comprehensive summary of dynamic regulatory elements of RNA m5 C, including methyltransferases (writers), demethylases (erasers), and binding proteins (readers). We also summarized the related detecting technologies and biological functions of the RNA 5-methylcytosine, and provided future perspectives in m5 C research. This article is categorized under: RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Yu-Sheng Chen
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center For Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Lan Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center For Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Yong-Liang Zhao
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center For Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yun-Gui Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center For Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
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37
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Single-cell RNA sequencing in vision research: Insights into human retinal health and disease. Prog Retin Eye Res 2020; 83:100934. [PMID: 33383180 DOI: 10.1016/j.preteyeres.2020.100934] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 01/03/2023]
Abstract
Gene expression provides valuable insight into cell function. As such, vision researchers have frequently employed gene expression studies to better understand retinal physiology and disease. With the advent of single-cell RNA sequencing, expression experiments provide an unparalleled resolution of information. Instead of studying aggregated gene expression across all cells in a heterogenous tissue, single-cell technology maps RNA to an individual cell, which facilitates grouping of retinal and choroidal cell types for further study. Single-cell RNA sequencing has been quickly adopted by both basic and translational vision researchers, and single-cell level gene expression has been studied in the visual systems of animal models, retinal organoids, and primary human retina, RPE, and choroid. These experiments have generated detailed atlases of gene expression and identified new retinal cell types. Likewise, single-cell RNA sequencing investigations have characterized how gene expression changes in the setting of many retinal diseases, including how choroidal endothelial cells are altered in age-related macular degeneration. In addition, this technology has allowed vision researchers to discover drivers of retinal development and model rare retinal diseases with induced pluripotent stem cells. In this review, we will overview the growing number of single-cell RNA sequencing studies in the field of vision research. We will summarize experimental considerations for designing single-cell RNA sequencing experiments and highlight important advancements in retinal, RPE, choroidal, and retinal organoid biology driven by this technology. Finally, we generalize these findings to genes involved in retinal degeneration and outline the future of single-cell expression experiments in studying retinal disease.
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38
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Rabiee A, Plucińska K, Isidor MS, Brown EL, Tozzi M, Sidoli S, Petersen PSS, Agueda-Oyarzabal M, Torsetnes SB, Chehabi GN, Lundh M, Altıntaş A, Barrès R, Jensen ON, Gerhart-Hines Z, Emanuelli B. White adipose remodeling during browning in mice involves YBX1 to drive thermogenic commitment. Mol Metab 2020; 44:101137. [PMID: 33285300 PMCID: PMC7779825 DOI: 10.1016/j.molmet.2020.101137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/16/2020] [Accepted: 12/02/2020] [Indexed: 02/07/2023] Open
Abstract
Objective Increasing adaptive thermogenesis by stimulating browning in white adipose tissue is a promising method of improving metabolic health. However, the molecular mechanisms underlying this transition remain elusive. Our study examined the molecular determinants driving the differentiation of precursor cells into thermogenic adipocytes. Methods In this study, we conducted temporal high-resolution proteomic analysis of subcutaneous white adipose tissue (scWAT) after cold exposure in mice. This was followed by loss- and gain-of-function experiments using siRNA-mediated knockdown and CRISPRa-mediated induction of gene expression, respectively, to evaluate the function of the transcriptional regulator Y box-binding protein 1 (YBX1) during adipogenesis of brown pre-adipocytes and mesenchymal stem cells. Transcriptomic analysis of mesenchymal stem cells following induction of endogenous Ybx1 expression was conducted to elucidate transcriptomic events controlled by YBX1 during adipogenesis. Results Our proteomics analysis uncovered 509 proteins differentially regulated by cold in a time-dependent manner. Overall, 44 transcriptional regulators were acutely upregulated following cold exposure, among which included the cold-shock domain containing protein YBX1, peaking after 24 h. Cold-induced upregulation of YBX1 also occurred in brown adipose tissue, but not in visceral white adipose tissue, suggesting a role of YBX1 in thermogenesis. This role was confirmed by Ybx1 knockdown in brown and brite preadipocytes, which significantly impaired their thermogenic potential. Conversely, inducing Ybx1 expression in mesenchymal stem cells during adipogenesis promoted browning concurrent with an increased expression of thermogenic markers and enhanced mitochondrial respiration. At a molecular level, our transcriptomic analysis showed that YBX1 regulates a subset of genes, including the histone H3K9 demethylase Jmjd1c, to promote thermogenic adipocyte differentiation. Conclusion Our study mapped the dynamic proteomic changes of murine scWAT during browning and identified YBX1 as a novel factor coordinating the genomic mechanisms by which preadipocytes commit to brite/beige lineage. Dynamic proteome remodeling occurs in mouse subcutaneous white fat with cold. YBX1 acutely increases in response to cold in thermogenic adipose tissues. YBX1 is required for the optimal implementation of the early thermogenic program. YBX1 promotes metabolic and thermogenic programs and enhances mitochondrial respiration.
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Affiliation(s)
- Atefeh Rabiee
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kaja Plucińska
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marie Sophie Isidor
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Erin Louise Brown
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marco Tozzi
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, Denmark
| | - Patricia Stephanie S Petersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marina Agueda-Oyarzabal
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Silje Bøen Torsetnes
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Galal Nazih Chehabi
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Lundh
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ali Altıntaş
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Nørregaard Jensen
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Zachary Gerhart-Hines
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Brice Emanuelli
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Fabbiano F, Corsi J, Gurrieri E, Trevisan C, Notarangelo M, D'Agostino VG. RNA packaging into extracellular vesicles: An orchestra of RNA-binding proteins? J Extracell Vesicles 2020; 10:e12043. [PMID: 33391635 PMCID: PMC7769857 DOI: 10.1002/jev2.12043] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/17/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Extracellular vesicles (EVs) are heterogeneous membranous particles released from the cells through different biogenetic and secretory mechanisms. We now conceive EVs as shuttles mediating cellular communication, carrying a variety of molecules resulting from intracellular homeostatic mechanisms. The RNA is a widely detected cargo and, impressively, a recognized functional intermediate that elects EVs as modulators of cancer cell phenotypes, determinants of disease spreading, cell surrogates in regenerative medicine, and a source for non-invasive molecular diagnostics. The mechanistic elucidation of the intracellular events responsible for the engagement of RNA into EVs will significantly improve the comprehension and possibly the prediction of EV "quality" in association with cell physiology. Interestingly, the application of multidisciplinary approaches, including biochemical as well as cell-based and computational strategies, is increasingly revealing an active RNA-packaging process implicating RNA-binding proteins (RBPs) in the sorting of coding and non-coding RNAs. In this review, we provide a comprehensive view of RBPs recently emerging as part of the EV biology, considering the scenarios where: (i) individual RBPs were detected in EVs along with their RNA substrates, (ii) RBPs were detected in EVs with inferred RNA targets, and (iii) EV-transcripts were found to harbour sequence motifs mirroring the activity of RBPs. Proteins so far identified are members of the hnRNP family (hnRNPA2B1, hnRNPC1, hnRNPG, hnRNPH1, hnRNPK, and hnRNPQ), as well as YBX1, HuR, AGO2, IGF2BP1, MEX3C, ANXA2, ALIX, NCL, FUS, TDP-43, MVP, LIN28, SRP9/14, QKI, and TERT. We describe the RBPs based on protein domain features, current knowledge on the association with human diseases, recognition of RNA consensus motifs, and the need to clarify the functional significance in different cellular contexts. We also summarize data on previously identified RBP inhibitor small molecules that could also be introduced in EV research as potential modulators of vesicular RNA sorting.
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Affiliation(s)
- Fabrizio Fabbiano
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Jessica Corsi
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Elena Gurrieri
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Caterina Trevisan
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Michela Notarangelo
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Vito G. D'Agostino
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
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40
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Wang BG, Yan LR, Xu Q, Zhong XP. The role of Transfer RNA-Derived Small RNAs (tsRNAs) in Digestive System Tumors. J Cancer 2020; 11:7237-7245. [PMID: 33193887 PMCID: PMC7646161 DOI: 10.7150/jca.46055] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/30/2020] [Indexed: 12/29/2022] Open
Abstract
Transfer RNA-derived small RNA(tsRNA) is a type of non-coding tRNA undergoing cleavage by specific nucleases such as Dicer. TsRNAs comprise of tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs). Based on the splicing site within the tRNA, tRFs can be classified into tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF. TiRNAs can be classified into 5′-tiRNA and 3′-tiRNA. Both tRFs and tiRNAs have important roles in carcinogenesis, especially cancer of digestive system. TRFs and tiRNAs can promote cell proliferation and cell cycle progression by regulating the expression of oncogenes, combining with RNA binding proteins such as Y-box binding protein 1 (YBX1) to prevent transcription. Despite many reviews on the basic biological function of tRFs and tiRNAs, few have described their correlation with tumors especially gastrointestinal tumor. This review focused on the relationship of tRFs and tiRNAs with the biological behavior, clinicopathological characteristics, diagnosis, treatment and prognosis of digestive system tumors, and would provide novel insights for the early detection and treatment of digestive system tumors.
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Affiliation(s)
- Ben-Gang Wang
- Department 1 of General Surgery, the First Hospital of China Medical University, Shenyang 110001, China
| | - Li-Rong Yan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Affiliated Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Qian Xu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Affiliated Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Xin-Ping Zhong
- Department 1 of General Surgery, the First Hospital of China Medical University, Shenyang 110001, China
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Moghiman T, Barghchi B, Esmaeili SA, Shabestari MM, Tabaee SS, Momtazi-Borojeni AA. Therapeutic angiogenesis with exosomal microRNAs: an effectual approach for the treatment of myocardial ischemia. Heart Fail Rev 2020; 26:205-213. [PMID: 32632768 DOI: 10.1007/s10741-020-10001-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Therapeutic angiogenesis presents a potential approach for treating ischemic heart diseases especially in patients who are not appropriate candidates for traditional approaches of revascularization. This approach acts through inducing the neovascularization or maturation of pre-existing collateral vessels into functional arteries to bypass the blocked arteries and restore perfusion to ischemic myocardium. Successful stimulation of local angiogenesis can be established by the cross talk between stem cells, endothelial cells, and cardiomyocytes, which is mainly mediated by paracrine communication accompanied by secreted exosomes. Exosomes are extracellular vesicles carrying a complex of signaling molecules, such as microRNAs (miRs) that can modulate the function of recipient cells. Such particles have been indicated to exert cardioprotective role through providing signaling cues for angiogenesis, an effect ascribed mainly to their miRs content. Exosomal miRs-mediated therapeutic angiogenesis has been under drastic preclinical and clinical studies. In the current review, it was aimed to summarize pro-angiogenic exosomal miRs released by various cell types mediating angiogenesis, including stem cells, endothelial cells, and cardiomyocytes, which appear to exert a therapeutic effect on the myocardial ischemia. In brief, secreted exosomal miRs including miR-210, miR-23a-3p, miR-424, let-7f, miR-30b, miR-30c, miR-126, miR-21, miR-132, miR-130a-3p, miR-214, miR-378, miR-126, miR-133, and let-7b-5p could protect against myocardial ischemia through inducing cardiac angiogenesis and vascular regeneration resulting in the increase blood flow to ischemic myocardium.
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Affiliation(s)
- Toktam Moghiman
- Atherosclerosis Prevention Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Bita Barghchi
- Medical School, Islamic Azad University, Tehran Branch, Tehran, Iran
| | - Seyed-Alireza Esmaeili
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Immunology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Seyedeh Samaneh Tabaee
- Cardiology Noncommunicable Disease Research Center, Neyshabur University of Medical Sciences, Neyshabur, Iran.
| | - Amir Abbas Momtazi-Borojeni
- Halal Research center of IRI, FDA, Tehran, Iran.
- Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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Rigo R, Bazin J, Romero‐Barrios N, Moison M, Lucero L, Christ A, Benhamed M, Blein T, Huguet S, Charon C, Crespi M, Ariel F. The Arabidopsis lncRNA ASCO modulates the transcriptome through interaction with splicing factors. EMBO Rep 2020; 21:e48977. [PMID: 32285620 PMCID: PMC7202219 DOI: 10.15252/embr.201948977] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 12/31/2022] Open
Abstract
Alternative splicing (AS) is a major source of transcriptome diversity. Long noncoding RNAs (lncRNAs) have emerged as regulators of AS through different molecular mechanisms. In Arabidopsis thaliana, the AS regulators NSRs interact with the ALTERNATIVE SPLICING COMPETITOR (ASCO) lncRNA. Here, we analyze the effect of the knock-down and overexpression of ASCO at the genome-wide level and find a large number of deregulated and differentially spliced genes related to flagellin responses and biotic stress. In agreement, ASCO-silenced plants are more sensitive to flagellin. However, only a minor subset of deregulated genes overlaps with the AS defects of the nsra/b double mutant, suggesting an alternative way of action for ASCO. Using biotin-labeled oligonucleotides for RNA-mediated ribonucleoprotein purification, we show that ASCO binds to the highly conserved spliceosome component PRP8a. ASCO overaccumulation impairs the recognition of specific flagellin-related transcripts by PRP8a. We further show that ASCO also binds to another spliceosome component, SmD1b, indicating that it interacts with multiple splicing factors. Hence, lncRNAs may integrate a dynamic network including spliceosome core proteins, to modulate transcriptome reprogramming in eukaryotes.
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Affiliation(s)
- Richard Rigo
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Jérémie Bazin
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Natali Romero‐Barrios
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Michaël Moison
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCBUniversidad Nacional del LitoralSanta FeArgentina
| | - Leandro Lucero
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCBUniversidad Nacional del LitoralSanta FeArgentina
| | - Aurélie Christ
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Moussa Benhamed
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Thomas Blein
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Stéphanie Huguet
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Céline Charon
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Martin Crespi
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCBUniversidad Nacional del LitoralSanta FeArgentina
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Ban Y, Tan P, Cai J, Li J, Hu M, Zhou Y, Mei Y, Tan Y, Li X, Zeng Z, Xiong W, Li G, Li X, Yi M, Xiang B. LNCAROD is stabilized by m6A methylation and promotes cancer progression via forming a ternary complex with HSPA1A and YBX1 in head and neck squamous cell carcinoma. Mol Oncol 2020; 14:1282-1296. [PMID: 32216017 PMCID: PMC7266281 DOI: 10.1002/1878-0261.12676] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/02/2020] [Accepted: 03/18/2020] [Indexed: 12/24/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) constitute approximately 4% of all cancers worldwide. In this study, we analyzed the expression profile of the long noncoding RNA (lncRNA) of 502 HNSCC patients from The Cancer Genome Atlas database. Among the differentially expressed lncRNAs between HNSCC and normal samples, LNCAROD is overexpressed in HNSCC and associated with advanced T stage and shortened overall survival. The N6‐methyladenosine (m6A) modification mediated by METTL3 and METTL14 enhanced the stability of LNCAROD in HNSCC cells. Depletion of LNCAROD attenuated cell proliferation, mobility in vitro, and tumorigenicity in vivo, whereas overexpression of LNCAROD exerted opposite effects. LNCAROD is mainly distributed in nucleus and binds with YBX1 and HSPA1A proteins. Silencing either YBX1 or HSPA1A did not affect the level of LNCAROD. However, loss of LNCAROD led to shortened half‐life of YBX1 protein. Mechanistically, LNCAROD protected YBX1 from proteasomal degradation by facilitating YBX1‐HSPA1A protein–protein interaction. Depletion of HSPA1A in LNCAROD‐overexpressing cells resulted in accelerated proteasomal degradation of YBX1 protein. Moreover, re‐expression of Flag‐YBX1 in LNCAROD‐silenced cells rescued malignant behavior of HNSCC cells. Our study indicates that LNCAROD is an oncogenic lncRNA and dysregulation of m6A modification might account for aberrant expression of LNCAROD in HNSCC. LNCAROD acts as a scaffold for the interaction between YBX1 and HSPA1A, preventing proteasomal degradation of YBX1 in HNSCC cells.
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Affiliation(s)
- Yuanyuan Ban
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
| | - Pingqing Tan
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Jing Cai
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
| | - Junjun Li
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
| | - Meng Hu
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
| | - Ying Zhou
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
| | - Yan Mei
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
| | - Yixin Tan
- Department of Dermatology, The Second Xiangya Hospital, The Central South University, Changsha, China
| | - Xiaoling Li
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
| | - Xiayu Li
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Mei Yi
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China.,Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, China
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Bauersachs S, Mermillod P, Almiñana C. The Oviductal Extracellular Vesicles' RNA Cargo Regulates the Bovine Embryonic Transcriptome. Int J Mol Sci 2020; 21:ijms21041303. [PMID: 32075098 PMCID: PMC7072903 DOI: 10.3390/ijms21041303] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 12/11/2022] Open
Abstract
Oviductal extracellular vesicles (oEVs) are emerging as key players in the gamete/embryo–oviduct interactions that contribute to successful pregnancy. Various positive effects of oEVs on gametes and early embryos have been found in vitro. To determine whether these effects are associated with changes of embryonic gene expression, the transcriptomes of embryos supplemented with bovine fresh (FeEVs) or frozen (FoEVs) oEVs during in vitro culture compared to controls without oEVs were analyzed by low-input RNA sequencing. Analysis of RNA-seq data revealed 221 differentially expressed genes (DEGs) between FoEV treatment and control, 67 DEGs for FeEV and FoEV treatments, and minor differences between FeEV treatment and control (28 DEGs). An integrative analysis of mRNAs and miRNAs contained in oEVs obtained in a previous study with embryonic mRNA alterations pointed to direct effects of oEV cargo on embryos (1) by increasing the concentration of delivered transcripts; (2) by translating delivered mRNAs to proteins that regulate embryonic gene expression; and (3) by oEV-derived miRNAs which downregulate embryonic mRNAs or modify gene expression in other ways. Our study provided the first high-throughput analysis of the embryonic transcriptome regulated by oEVs, increasing our knowledge on the impact of oEVs on the embryo and revealing the oEV RNA components that potentially regulate embryonic development.
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Affiliation(s)
- Stefan Bauersachs
- Genetics and Functional Genomics, VetSuisse Faculty Zurich, University of Zurich, 8315 Lindau (ZH), Switzerland;
| | - Pascal Mermillod
- UMR85 PRC, INRA, CNRS 7247, Université de Tours, IFCE, 37380 Nouzilly, France;
| | - Carmen Almiñana
- Genetics and Functional Genomics, VetSuisse Faculty Zurich, University of Zurich, 8315 Lindau (ZH), Switzerland;
- UMR85 PRC, INRA, CNRS 7247, Université de Tours, IFCE, 37380 Nouzilly, France;
- Correspondence:
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Leidal AM, Debnath J. Unraveling the mechanisms that specify molecules for secretion in extracellular vesicles. Methods 2020; 177:15-26. [PMID: 31978536 DOI: 10.1016/j.ymeth.2020.01.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/19/2019] [Accepted: 01/16/2020] [Indexed: 12/15/2022] Open
Abstract
Extracellular vesicles (EVs) are small membrane-bound organelles naturally released from cells and potentially function as vehicles of intercellular communication. Cells release numerous sub-species of EVs, including exosomes and microvesicles, which are formed via distinct cellular pathways and molecular machineries and contain specific proteins, RNAs and lipids. Accumulating evidence indicates that the repertoire of molecules packaged into EVs is shaped by both the physiological state of the cell and the EV biogenesis pathway involved. Although these observations intimate that precisely regulated pathways sort molecules into EVs, the underlying molecular mechanisms that direct molecules for secretion remain poorly defined. Recently, with the advancement of mass spectrometry, next-generation sequencing techniques and molecular biology tools, several mechanisms contributing to EV cargo selection are beginning to be unraveled. This review examines strategies employed to reveal how specific proteins, RNAs and lipids are directed for secretion via EVs.
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Affiliation(s)
- Andrew M Leidal
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Jayanta Debnath
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA
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Architecture of The Human Ape1 Interactome Defines Novel Cancers Signatures. Sci Rep 2020; 10:28. [PMID: 31913336 PMCID: PMC6949240 DOI: 10.1038/s41598-019-56981-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022] Open
Abstract
APE1 is essential in cancer cells due to its central role in the Base Excision Repair pathway of DNA lesions and in the transcriptional regulation of genes involved in tumor progression/chemoresistance. Indeed, APE1 overexpression correlates with chemoresistance in more aggressive cancers, and APE1 protein-protein interactions (PPIs) specifically modulate different protein functions in cancer cells. Although important, a detailed investigation on the nature and function of protein interactors regulating APE1 role in tumor progression and chemoresistance is still lacking. The present work was aimed at analyzing the APE1-PPI network with the goal of defining bad prognosis signatures through systematic bioinformatics analysis. By using a well-characterized HeLa cell model stably expressing a flagged APE1 form, which was subjected to extensive proteomics analyses for immunocaptured complexes from different subcellular compartments, we here demonstrate that APE1 is a central hub connecting different subnetworks largely composed of proteins belonging to cancer-associated communities and/or involved in RNA- and DNA-metabolism. When we performed survival analysis in real cancer datasets, we observed that more than 80% of these APE1-PPI network elements is associated with bad prognosis. Our findings, which are hypothesis generating, strongly support the possibility to infer APE1-interactomic signatures associated with bad prognosis of different cancers; they will be of general interest for the future definition of novel predictive disease biomarkers. Future studies will be needed to assess the function of APE1 in the protein complexes we discovered. Data are available via ProteomeXchange with identifier PXD013368.
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Inhibition of Transcription Induces Phosphorylation of YB-1 at Ser102 and Its Accumulation in the Nucleus. Cells 2019; 9:cells9010104. [PMID: 31906126 PMCID: PMC7016903 DOI: 10.3390/cells9010104] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/26/2019] [Accepted: 12/30/2019] [Indexed: 02/04/2023] Open
Abstract
The Y-box binding protein 1 (YB-1) is an RNA/DNA-binding protein regulating gene expression in the cytoplasm and the nucleus. Although mostly cytoplasmic, YB-1 accumulates in the nucleus under stress conditions. Its nuclear localization is associated with aggressiveness and multidrug resistance of cancer cells, which makes the understanding of the regulatory mechanisms of YB-1 subcellular distribution essential. Here, we report that inhibition of RNA polymerase II (RNAPII) activity results in the nuclear accumulation of YB-1 accompanied by its phosphorylation at Ser102. The inhibition of kinase activity reduces YB-1 phosphorylation and its accumulation in the nucleus. The presence of RNA in the nucleus is shown to be required for the nuclear retention of YB-1. Thus, the subcellular localization of YB-1 depends on its post-translational modifications (PTMs) and intracellular RNA distribution.
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Johnson TG, Schelch K, Mehta S, Burgess A, Reid G. Why Be One Protein When You Can Affect Many? The Multiple Roles of YB-1 in Lung Cancer and Mesothelioma. Front Cell Dev Biol 2019; 7:221. [PMID: 31632972 PMCID: PMC6781797 DOI: 10.3389/fcell.2019.00221] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/18/2019] [Indexed: 12/14/2022] Open
Abstract
Lung cancers and malignant pleural mesothelioma (MPM) have some of the worst 5-year survival rates of all cancer types, primarily due to a lack of effective treatment options for most patients. Targeted therapies have shown some promise in thoracic cancers, although efficacy is limited only to patients harboring specific mutations or target expression. Although a number of actionable mutations have now been identified, a large population of thoracic cancer patients have no therapeutic options outside of first-line chemotherapy. It is therefore crucial to identify alternative targets that might lead to the development of new ways of treating patients diagnosed with these diseases. The multifunctional oncoprotein Y-box binding protein-1 (YB-1) could serve as one such target. Recent studies also link this protein to many inherent behaviors of thoracic cancer cells such as proliferation, invasion, metastasis and involvement in cancer stem-like cells. Here, we review the regulation of YB-1 at the transcriptional, translational, post-translational and sub-cellular levels in thoracic cancer and discuss its potential use as a biomarker and therapeutic target.
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Affiliation(s)
- Thomas G Johnson
- Asbestos Diseases Research Institute, Sydney, NSW, Australia.,Cell Division Laboratory, The ANZAC Research Institute, Sydney, NSW, Australia.,School of Medicine, The University of Sydney, Sydney, NSW, Australia.,Sydney Catalyst Translational Cancer Research Centre, The University of Sydney, Sydney, NSW, Australia
| | - Karin Schelch
- Institute of Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Sunali Mehta
- Department of Pathology, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre, University of Otago, Dunedin, New Zealand
| | - Andrew Burgess
- Cell Division Laboratory, The ANZAC Research Institute, Sydney, NSW, Australia.,School of Medicine, The University of Sydney, Sydney, NSW, Australia
| | - Glen Reid
- Department of Pathology, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre, University of Otago, Dunedin, New Zealand
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Wang Y, Su J, Wang Y, Fu D, Ideozu JE, Geng H, Cui Q, Wang C, Chen R, Yu Y, Niu Y, Yue D. The interaction of YBX1 with G3BP1 promotes renal cell carcinoma cell metastasis via YBX1/G3BP1-SPP1- NF-κB signaling axis. J Exp Clin Cancer Res 2019; 38:386. [PMID: 31481087 PMCID: PMC6720408 DOI: 10.1186/s13046-019-1347-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/25/2019] [Indexed: 12/24/2022] Open
Abstract
Background Renal cell carcinoma (RCC) is a deadly urological tumor that remains largely incurable. Our limited understanding of key molecular mechanisms underlying RCC invasion and metastasis has hampered efforts to identify molecular drivers with therapeutic potential. With evidence from our previous study revealing that nuclear overexpression of YBX1 is associated with RCC T stage and metastasis, we investigated the effects of YBX1 in RCC migration, invasion, and adhesion, and then characterized its interaction with RCC-associated proteins G3BP1 and SPP1. Methods Renal cancer cell lines, human embryonic kidney cells, and clinical samples were analyzed to investigate the functional role of YBX1 in RCC metastasis. YBX1 knockdown cells were established via lentiviral infection and subjected to adhesion, transwell migration, and invasion assay. Microarray, immunoprecipitation, dual-luciferase reporter assay, and classical biochemical assays were applied to characterize the mechanism of YBX1 interaction with RCC-associated proteins G3BP1 and SPP1. Results Knockdown of YBX1 in RCC cells dramatically inhibited cell adhesion, migration, and invasion. Mechanistic investigations revealed that YBX1 interaction with G3BP1 upregulated their downstream target SPP1 in vitro and in vivo, which led to an activated NF-κB signaling pathway. Meanwhile, knockdown of SPP1 rescued the YBX1/G3BP1-mediated activation of NF-κB signaling pathway, and RCC cell migration and invasion. We further showed that YBX1 expression was positively correlated with G3BP1 and SPP1 expression levels in clinical RCC samples. Conclusions YBX1 interacts with G3BP1 to promote metastasis of RCC by activating the YBX1/G3BP1–SPP1–NF-κB signaling axis. Electronic supplementary material The online version of this article (10.1186/s13046-019-1347-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yong Wang
- The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology and School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China
| | - Jing Su
- The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology and School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China.,Department of Laboratory Medicine, Children's Hospital of Hebei Province, Shijiazhuang, 050031, China
| | - Yiting Wang
- The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology and School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China
| | - Donghe Fu
- Department of Clinical Laboratory, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, 300052, China
| | - Justin E Ideozu
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA.,Human Molecular Genetics Program, Stanley Manne Children's Research Institute, Chicago, IL, 60614, USA.,Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Hua Geng
- Center for Intestinal and Liver Inflammation Research, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA.,Department of Pediatrics, Feinberg School of Medicine at Northwestern University Chicago, Chicago, IL, 60611, USA
| | - Qiqi Cui
- The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology and School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China
| | - Chao Wang
- The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology and School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China
| | - Ruibing Chen
- Department of Genetics, School of Basic Medical Sciences, School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China
| | - Yixi Yu
- The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology and School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China
| | - Yuanjie Niu
- The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology and School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China
| | - Dan Yue
- The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology and School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China. .,Department of Microbiology, School of Medical Laboratory, Tianjin Medical University, Tianjin, 300070, China.
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50
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Lin F, Zeng Z, Song Y, Li L, Wu Z, Zhang X, Li Z, Ke X, Hu X. YBX-1 mediated sorting of miR-133 into hypoxia/reoxygenation-induced EPC-derived exosomes to increase fibroblast angiogenesis and MEndoT. Stem Cell Res Ther 2019; 10:263. [PMID: 31443679 PMCID: PMC6708233 DOI: 10.1186/s13287-019-1377-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/24/2019] [Accepted: 08/07/2019] [Indexed: 11/16/2022] Open
Abstract
Background Myocardial fibrosis is a common pathophysiological change in cardiovascular disease, which can cause cardiac dysfunction and even sudden death. Excessively activated fibroblasts proliferate and secret excessive extracellular matrix (ECM) components, resulting in normal cardiac structural damage and cardiac fibrosis. We previously found that human endothelial progenitor cell (EPC)-derived exosomes, after hypoxia/reoxygenation (H/R) induction, could significantly increase the mesenchymal-endothelial transition (MEndoT) compared to normal culture EPC-derived exosomes. Exosomes have been shown to carry different nucleic acids, including microRNAs. However, the effects of microRNAs in EPC-derived exosomes on MEndoT and myocardial fibrosis remain unknown. Methods EPCs were isolated from human peripheral blood, and fibroblasts were isolated from rat hearts, then transfected with miR-133 inhibitor, si-YBX-1, and ov-YBX-1 into EPCs. After H/R induction for 48 h, isolation and characterization of exosomes derived from human EPCs were performed. Finally, fibroblasts were treated by exosome at 48 h. The expression of miR-133 was measured by qRT-PCR; YBX-1 expression was measured by qRT-PCR and western blot. Angiopoiesis was measured by tube formation assay. Endothelial markers and fibrosis markers were measured by western blot. Results H/R treatment promoted miR-133 expression in EPCs and EPC-derived exosomes. miR-133 could be incorporated into exosomes and transmitted to cardiac fibroblasts, increasing the angiogenesis and MEndoT of cardiac fibroblasts. miR-133 silencing in H/R-induced EPCs could inhibit miR-133 expression in EPCs and EPCs-derived exosomes. miR-133 silencing in H/R-induced EPCs could inhibit the angiogenesis and MEndoT of cardiac fibroblasts and reverse the effect of H/R treatment. Additionally, miR-133 was specially sorted into H/R-induced EPC-derived exosomes via YBX-1. YBX-1 silencing inhibited miR-133 transfer and reduced fibroblast angiogenesis and MEndoT. Conclusion miR-133 was specially sorted into H/R-induced EPC-derived exosomes via YBX-1 to increase fibroblast angiogenesis and MEndoT.
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Affiliation(s)
- Fengxia Lin
- Department of Cardiology, Shenzhen Bao'an Traditional Chinese Medicine Hospital Group, The Affiliated Hospital of Guangzhou University of Chinese Medicine, Shenzhen, 518133, China
| | - Zhicong Zeng
- Department of Cardiology, Shenzhen Bao'an Traditional Chinese Medicine Hospital Group, The Affiliated Hospital of Guangzhou University of Chinese Medicine, Shenzhen, 518133, China
| | - Yinzhi Song
- Department of Cardiology, Shenzhen Bao'an Traditional Chinese Medicine Hospital Group, The Affiliated Hospital of Guangzhou University of Chinese Medicine, Shenzhen, 518133, China
| | - Liang Li
- Department of Cardiology, Shenzhen Bao'an Traditional Chinese Medicine Hospital Group, The Affiliated Hospital of Guangzhou University of Chinese Medicine, Shenzhen, 518133, China.,Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Zijun Wu
- Department of Cardiology, Shenzhen Bao'an Traditional Chinese Medicine Hospital Group, The Affiliated Hospital of Guangzhou University of Chinese Medicine, Shenzhen, 518133, China
| | - Xiaoduo Zhang
- Department of Cardiology, Shenzhen Bao'an Traditional Chinese Medicine Hospital Group, The Affiliated Hospital of Guangzhou University of Chinese Medicine, Shenzhen, 518133, China
| | - Zhiwen Li
- Department of Cardiology, Shenzhen Bao'an Traditional Chinese Medicine Hospital Group, The Affiliated Hospital of Guangzhou University of Chinese Medicine, Shenzhen, 518133, China
| | - Xiao Ke
- Department of Cardiology, Fuwai Hospital, Chinese Academy of Medical Sciences, Shenzhen, 518057, Guangdong, China. .,Shenzhen University School of Medicine & Shenzhen University Health Science Center, No. 12, Langshan Road, Nanshan District, Shenzhen, 518057, Guangdong, China.
| | - Xun Hu
- Department of Cardiology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China. .,Key Laboratory on Assisted Circulation, Ministry of Health, Guangzhou, 510080, Guangdong, China.
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