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D’Amico M, De Amicis F. Challenges of Regulated Cell Death: Implications for Therapy Resistance in Cancer. Cells 2024; 13:1083. [PMID: 38994937 PMCID: PMC11240625 DOI: 10.3390/cells13131083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 07/13/2024] Open
Abstract
Regulated cell death, a regulatory form of cell demise, has been extensively studied in multicellular organisms. It plays a pivotal role in maintaining organismal homeostasis under normal and pathological conditions. Although alterations in various regulated cell death modes are hallmark features of tumorigenesis, they can have divergent effects on cancer cells. Consequently, there is a growing interest in targeting these mechanisms using small-molecule compounds for therapeutic purposes, with substantial progress observed across various human cancers. This review focuses on summarizing key signaling pathways associated with apoptotic and autophagy-dependent cell death. Additionally, it explores crucial pathways related to other regulated cell death modes in the context of cancer. The discussion delves into the current understanding of these processes and their implications in cancer treatment, aiming to illuminate novel strategies to combat therapy resistance and enhance overall cancer therapy.
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Affiliation(s)
- Maria D’Amico
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Francesca De Amicis
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
- Health Center, University of Calabria, 87036 Rende, Italy
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2
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Dowaidar M. Guidelines for the role of autophagy in drug delivery vectors uptake pathways. Heliyon 2024; 10:e30238. [PMID: 38707383 PMCID: PMC11066435 DOI: 10.1016/j.heliyon.2024.e30238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/22/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024] Open
Abstract
The process of autophagy refers to the intracellular absorption of cytoplasm (such as proteins, nucleic acids, tiny molecules, complete organelles, and so on) into the lysosome, followed by the breakdown of that cytoplasm. The majority of cellular proteins are degraded by a process called autophagy, which is both a naturally occurring activity and one that may be induced by cellular stress. Autophagy is a system that can save cells' integrity in stressful situations by restoring metabolic basics and getting rid of subcellular junk. This happens as a component of an endurance response. This mechanism may have an effect on disease, in addition to its contribution to the homeostasis of individual cells and tissues as well as the control of development in higher species. The main aim of this study is to discuss the guidelines for the role of autophagy in drug delivery vector uptake pathways. In this paper, we discuss the meaning and concept of autophagy, the mechanism of autophagy, the role of autophagy in drug delivery vectors, autophagy-modulating drugs, nanostructures for delivery systems of autophagy modulators, etc. Later in this paper, we talk about how to deliver chemotherapeutics, siRNA, and autophagy inducers and inhibitors. We also talk about how hard it is to make a drug delivery system that takes nanocarriers' roles as autophagy modulators into account.
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Affiliation(s)
- Moataz Dowaidar
- Bioengineering Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, 31261, Saudi Arabia
- Interdisciplinary Research Center for Hydrogen Technologies and Carbon Management, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, 31261, Saudi Arabia
- Biosystems and Machines Research Center, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, 31261, Saudi Arabia
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3
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Du J, Liu F, Liu X, Zhao D, Wang D, Sun H, Yan C, Zhao Y. Lysosomal dysfunction and overload of nucleosides in thymidine phosphorylase deficiency of MNGIE. J Transl Med 2024; 22:449. [PMID: 38741129 PMCID: PMC11089807 DOI: 10.1186/s12967-024-05275-8] [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: 02/20/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024] Open
Abstract
Inherited deficiency of thymidine phosphorylase (TP), encoded by TYMP, leads to a rare disease with multiple mitochondrial DNA (mtDNA) abnormalities, mitochondrial neurogastrointestinal encephalomyopathy (MNGIE). However, the impact of TP deficiency on lysosomes remains unclear, which are important for mitochondrial quality control and nucleic acid metabolism. Muscle biopsy tissue and skin fibroblasts from MNGIE patients, patients with m.3243 A > G mitochondrial encephalopathy, lactic acidosis and stroke-like episodes (MELAS) and healthy controls (HC) were collected to perform mitochondrial and lysosomal functional analyses. In addition to mtDNA abnormalities, compared to controls distinctively reduced expression of LAMP1 and increased mitochondrial content were detected in the muscle tissue of MNGIE patients. Skin fibroblasts from MNGIE patients showed decreased expression of LAMP2, lowered lysosomal acidity, reduced enzyme activity and impaired protein degradation ability. TYMP knockout or TP inhibition in cells can also induce the similar lysosomal dysfunction. Using lysosome immunoprecipitation (Lyso- IP), increased mitochondrial proteins, decreased vesicular proteins and V-ATPase enzymes, and accumulation of various nucleosides were detected in lysosomes with TP deficiency. Treatment of cells with high concentrations of dThd and dUrd also triggers lysosomal dysfunction and disruption of mitochondrial homeostasis. Therefore, the results provided evidence that TP deficiency leads to nucleoside accumulation in lysosomes and lysosomal dysfunction, revealing the widespread disruption of organelles underlying MNGIE.
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Affiliation(s)
- Jixiang Du
- Department of Rheumatology and Immunology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
- Research Institute of Neuromuscular and Neurodegenerative Disease, Department of Neurology, Cheeloo College of Medicine, Qilu Hospital, Shandong University, West Wenhua Street No.107, Jinan, 250012, Shandong, China
- Department of Rheumatology and Immunology, Cheeloo College of Medicine, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Fuchen Liu
- Research Institute of Neuromuscular and Neurodegenerative Disease, Department of Neurology, Cheeloo College of Medicine, Qilu Hospital, Shandong University, West Wenhua Street No.107, Jinan, 250012, Shandong, China
| | - Xihan Liu
- Key Laboratory of Experimental Teratology, Ministry of Education, School of Basic Medical Science, Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China
| | - Dandan Zhao
- Research Institute of Neuromuscular and Neurodegenerative Disease, Department of Neurology, Cheeloo College of Medicine, Qilu Hospital, Shandong University, West Wenhua Street No.107, Jinan, 250012, Shandong, China
| | - Dongdong Wang
- Research Institute of Neuromuscular and Neurodegenerative Disease, Department of Neurology, Cheeloo College of Medicine, Qilu Hospital, Shandong University, West Wenhua Street No.107, Jinan, 250012, Shandong, China
| | - Hongsheng Sun
- Department of Rheumatology and Immunology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
- Department of Rheumatology and Immunology, Cheeloo College of Medicine, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Chuanzhu Yan
- Research Institute of Neuromuscular and Neurodegenerative Disease, Department of Neurology, Cheeloo College of Medicine, Qilu Hospital, Shandong University, West Wenhua Street No.107, Jinan, 250012, Shandong, China.
- Mitochondrial Medicine Laboratory, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, 266000, Shandong, China.
- Brain Science Research Institute, Shandong University, Jinan, 250012, Shandong, China.
| | - Yuying Zhao
- Research Institute of Neuromuscular and Neurodegenerative Disease, Department of Neurology, Cheeloo College of Medicine, Qilu Hospital, Shandong University, West Wenhua Street No.107, Jinan, 250012, Shandong, China.
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4
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Sedaghatmehr M, Balazadeh S. Autophagy: a key player in the recovery of plants from heat stress. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2246-2255. [PMID: 38236036 PMCID: PMC11016841 DOI: 10.1093/jxb/erae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/15/2024] [Indexed: 01/19/2024]
Abstract
Plants can be primed to withstand otherwise lethal heat stress (HS) through exposure to a preceding temporary and mild HS, commonly known as the 'thermopriming stimulus'. Plants have also evolved mechanisms to establish 'memories' of a previous stress encounter, or to reset their physiology to the original cellular state once the stress has ended. The priming stimulus triggers a widespread change of transcripts, proteins, and metabolites, which is crucial for maintaining the memory state but may not be required for growth and development under optimal conditions or may even be harmful. In such a scenario, recycling mechanisms such as autophagy are crucial for re-establishing cellular homeostasis and optimizing resource use for post-stress growth. While pivotal for eliminating heat-induced protein aggregates and protecting plants from the harmful impact of HS, recent evidence implies that autophagy also breaks down heat-induced protective macromolecules, including heat shock proteins, functioning as a resetting mechanism during the recovery from mild HS. This review provides an overview of the latest advances in understanding the multifaceted functions of autophagy in HS responses, with a specific emphasis on its roles in recovery from mild HS, and the modulation of HS memory.
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Affiliation(s)
- Mastoureh Sedaghatmehr
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Salma Balazadeh
- Leiden University, PO Box 9500, 2300 RA, Leiden, The Netherlands
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Lopes RM, Souza ACS, Otręba M, Rzepecka-Stojko A, Tersariol ILS, Rodrigues T. Targeting autophagy by antipsychotic phenothiazines: potential drug repurposing for cancer therapy. Biochem Pharmacol 2024; 222:116075. [PMID: 38395266 DOI: 10.1016/j.bcp.2024.116075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 01/14/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
Cancer is recognized as the major cause of death worldwide and the most challenging public health issues. Tumor cells exhibit molecular adaptations and metabolic reprograming to sustain their high proliferative rate and autophagy plays a pivotal role to supply the high demand for metabolic substrates and for recycling cellular components, which has attracted the attention of the researchers. The modulation of the autophagic process sensitizes tumor cells to chemotherapy-induced cell death and reverts drug resistance. In this regard, many in vitro and in vivo studies having shown the anticancer activity of phenothiazine (PTZ) derivatives due to their potent cytotoxicity in tumor cells. Interestingly, PTZ have been used as antiemetics in antitumor chemotherapy-induced vomiting, maybe exerting a combined antitumor effect. Among the mechanisms of cytotoxicity, the modulation of autophagy by these drugs has been highlighted. Therefore, the use of PTZ derivatives can be considered as a repurposing strategy in antitumor chemotherapy. Here, we provided an overview of the effects of antipsychotic PTZ on autophagy in tumor cells, evidencing the molecular targets and discussing the underlying mechanisms. The modulation of autophagy by PTZ in tumor cells have been consistently related to their cytotoxic action. These effects depend on the derivative, their concentration, and also the type of cancer. Most data have shown the impairment of autophagic flux by PTZ, probably due to the blockade of lysosome-autophagosome fusion, but some studies have also suggested the induction of autophagy. These data highlight the therapeutic potential of targeting autophagy by PTZ in cancer chemotherapy.
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Affiliation(s)
- Rayssa M Lopes
- Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), Santo Andre, SP, Brazil.
| | - Ana Carolina S Souza
- Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), Santo Andre, SP, Brazil.
| | - Michał Otręba
- Department of Drug and Cosmetics Technology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Poland.
| | - Anna Rzepecka-Stojko
- Department of Drug and Cosmetics Technology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Poland.
| | - Ivarne L S Tersariol
- Departament of Molecular Biology, Federal University of São Paulo (UNIFESP), Sao Paulo, SP, Brazil
| | - Tiago Rodrigues
- Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), Santo Andre, SP, Brazil.
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Wu Y, Huang J, Liu C, Wang F. Autophagy Proteins and clinical data reveal the prognosis of polycystic ovary syndrome. BMC Pregnancy Childbirth 2024; 24:152. [PMID: 38383330 PMCID: PMC10880238 DOI: 10.1186/s12884-024-06273-w] [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: 05/09/2023] [Accepted: 01/14/2024] [Indexed: 02/23/2024] Open
Abstract
OBJECTIVE We aimed to investigate the significance of autophagy proteins and their association with clinical data on pregnancy loss in polycystic ovary syndrome (PCOS), while also constructing predictive models. METHODS This study was a secondary analysis. we collected endometrial samples from 33 patients with polycystic ovary syndrome (PCOS) and 7 patients with successful pregnancy control women at the Reproductive Center of the Second Hospital of Lanzhou University between September 2019 and September 2020. Liquid chromatography tandem mass spectrometry was employed to identify expressed proteins in the endometrium of 40 patients. R was use to identify differential expression proteins(DEPs). Subsequently, Metascape was utilized for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Multivariate Cox analysis was performed to analyze autophagy proteins associated with reproductive outcomes, while logistic regression was used for analyzing clinical data. Linear correlation analysis was conducted to examine the relationship between autophagy proteins and clinical data. We established prognostic models and constructed the nomograms based on proteome data and clinical data respectively. The performance of the prognostic model was evaluated by the receiver operating characteristic curve (ROC) and decision curve analysis (DCA). RESULTS A total of 5331 proteins were identified, with 450 proteins exhibiting significant differential expression between the PCOS and control groups. A prognostic model for autophagy protein was developed based on three autophagy proteins (ARSA, ITGB1, and GABARAPL2). Additionally, another prognostic model for clinical data was established using insulin, TSH, TPOAB, and VD3. Our findings revealed a significant positive correlation between insulin and ARSA (R = 0.49), as well as ITGB1 (R = 0.3). Conversely, TSH exhibited a negative correlation with both ARSA (-0.33) and ITGB1 (R = -0.26). CONCLUSION Our research could effectively predict the occurrence of pregnancy loss in PCOS patients and provide a basis for subsequent research.
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Affiliation(s)
- Yuanyuan Wu
- Gansu University of Chinese Medicine, Lanzhou, 730030, China
| | - Jinge Huang
- Gansu University of Chinese Medicine, Lanzhou, 730030, China
| | - Cai Liu
- Department of Reproductive Medicine, Lanzhou University Second Hospital Lanzhou, Lanzhou, 730030, China
| | - Fang Wang
- Department of Reproductive Medicine, Lanzhou University Second Hospital Lanzhou, Lanzhou, 730030, China.
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7
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Kolapalli SP, Nielsen TM, Frankel LB. Post-transcriptional dynamics and RNA homeostasis in autophagy and cancer. Cell Death Differ 2023:10.1038/s41418-023-01201-5. [PMID: 37558732 DOI: 10.1038/s41418-023-01201-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/22/2023] [Accepted: 08/01/2023] [Indexed: 08/11/2023] Open
Abstract
Autophagy is an essential recycling and quality control pathway which preserves cellular and organismal homeostasis. As a catabolic process, autophagy degrades damaged and aged intracellular components in response to conditions of stress, including nutrient deprivation, oxidative and genotoxic stress. Autophagy is a highly adaptive and dynamic process which requires an intricately coordinated molecular control. Here we provide an overview of how autophagy is regulated post-transcriptionally, through RNA processing events, epitranscriptomic modifications and non-coding RNAs. We further discuss newly revealed RNA-binding properties of core autophagy machinery proteins and review recent indications of autophagy's ability to impact cellular RNA homeostasis. From a physiological perspective, we examine the biological implications of these emerging regulatory layers of autophagy, particularly in the context of nutrient deprivation and tumorigenesis.
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Affiliation(s)
| | | | - Lisa B Frankel
- Danish Cancer Institute, Copenhagen, Denmark.
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
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Feng J, Wang M, Du GS, Peng K, Li LQ, Li XS. Crosstalk between autophagy and bladder transitional cell carcinoma by autophagy-related lncRNAs. Medicine (Baltimore) 2023; 102:e34130. [PMID: 37390250 PMCID: PMC10313302 DOI: 10.1097/md.0000000000034130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/07/2023] [Indexed: 07/02/2023] Open
Abstract
The aim of this study was to investigate the crosstalk between autophagy and bladder transitional cell carcinoma (TCC) by autophagy-related long noncoding RNAs (lncRNAs). A total of 400 TCC patients from The Cancer Genome Atlas were enrolled in this study. We identified the autophagy-related lncRNA expression profile of the TCC patients and then constructed a prognostic signature using the least absolute shrinkage and selection operation and Cox regression. Risk, survival, and independent prognostic analyses were carried out. Receiver operating characteristic curve, nomogram, and calibration curves were explored. Gene Set Enrichment Analysis was employed to verify the enhanced autophagy-related functions. Finally, we compared the signature with several other lncRNA-based signatures. A 9-autophagy-related lncRNA signature was established by least absolute shrinkage and selection operation-Cox regression that was significantly associated with overall survival in TCC. Among them, 8 of the 9 lncRNAs were protective factors while the remaining was a risk factor. The risk scores calculated by the signature showed significant prognostic value in survival analysis between the high- or low-risk groups. The 5-year survival rate for the high-risk group was 26.0% while the rate for the low-risk group was 56.0% (P < .05). Risk score was the only significant risk factor in the multivariate Cox regression survival analysis (P < .001). A nomogram connecting this signature with clinicopathologic characteristics was assembled. To assess the performance of the nomogram, a C-index (0.71) was calculated, which showed great convergence with an ideal model. The Gene Set Enrichment Analysis results demonstrated 2 major autophagy-related pathways were significantly enhanced in TCC. And this signature performed a similar predictive effect as other publications. The crosstalk between autophagy and TCC is significant, and this 9 autophagy-related lncRNA signature is a great predictor of TCC.
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Affiliation(s)
- Jie Feng
- Special Medical Department, Chongqing General Hospital, Chongqing PR China
| | - Min Wang
- Special Medical Department, Chongqing General Hospital, Chongqing PR China
| | - Guang-Sheng Du
- Department of General Surgery, Xinqiao Hospital, Army Medical University, Chongqing, PR China
| | - Ke Peng
- Department of General Surgery, Xinqiao Hospital, Army Medical University, Chongqing, PR China
| | - Li-Qi Li
- Department of General Surgery, Xinqiao Hospital, Army Medical University, Chongqing, PR China
| | - Xiang-Sheng Li
- Department of General Surgery, Xinqiao Hospital, Army Medical University, Chongqing, PR China
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9
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Zhang Q, Tian B. The emerging theme of 3'UTR mRNA isoform regulation in reprogramming of cell metabolism. Biochem Soc Trans 2023; 51:1111-1119. [PMID: 37171086 PMCID: PMC10771799 DOI: 10.1042/bst20221128] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/26/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
The 3' untranslated region (3'UTR) of mRNA plays a key role in the post-transcriptional regulation of gene expression. Most eukaryotic protein-coding genes express 3'UTR isoforms owing to alternative cleavage and polyadenylation (APA). The 3'UTR isoform expression profile of a cell changes in cell proliferation, differentiation, and stress conditions. Here, we review the emerging theme of regulation of 3'UTR isoforms in cell metabolic reprogramming, focusing on cell growth and autophagy responses through the mTOR pathway. We discuss regulatory events that converge on the Cleavage Factor I complex, a master regulator of APA in 3'UTRs, and recent understandings of isoform-specific m6A modification and endomembrane association in determining differential metabolic fates of 3'UTR isoforms.
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Affiliation(s)
- Qiang Zhang
- Gene Expression and Regulation Program and Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA 19104, U.S.A
| | - Bin Tian
- Gene Expression and Regulation Program and Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA 19104, U.S.A
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10
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Gyurkovska V, Murtazina R, Zhao SF, Shikano S, Okamoto Y, Segev N. Dual function of Rab1A in secretion and autophagy: hypervariable domain dependence. Life Sci Alliance 2023; 6:e202201810. [PMID: 36781179 PMCID: PMC9939007 DOI: 10.26508/lsa.202201810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/15/2023] Open
Abstract
We currently understand how the different intracellular pathways, secretion, endocytosis, and autophagy are regulated by small GTPases. In contrast, it is unclear how these pathways are coordinated to ensure efficient cellular response to stress. Rab GTPases localize to specific organelles through their hypervariable domain (HVD) to regulate discrete steps of individual pathways. Here, we explored the dual role of Rab1A/B (92% identity) in secretion and autophagy. We show that although either Rab1A or Rab1B is required for secretion, Rab1A, but not Rab1B, localizes to autophagosomes and is required early in stress-induced autophagy. Moreover, replacing the HVD of Rab1B with that of Rab1A enables Rab1B to localize to autophagosomes and regulate autophagy. Therefore, Rab1A-HVD is required for the dual functionality of a single Rab in two different pathways: secretion and autophagy. In addition to this mechanistic insight, these findings are relevant to human health because both the pathways and Rab1A/B were implicated in diseases ranging from cancer to neurodegeneration.
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Affiliation(s)
- Valeriya Gyurkovska
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Rakhilya Murtazina
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Sarah F Zhao
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Sojin Shikano
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Yukari Okamoto
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Nava Segev
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
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Zhu YD, Liu HY, Lei XM, Peng XQ. Long non-coding RNA PVT1 induces proliferation, inhibits apoptosis, and induces autophagy by up-regulating Atg5 in rectal cancer cells. Shijie Huaren Xiaohua Zazhi 2023; 31:307-315. [DOI: 10.11569/wcjd.v31.i8.307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND As a long noncoding RNA (lncRNA), PVT1 has been proved to play a role in promoting cancer in many tumors, but there are few reports on its impact on the biological behavior of rectal cancer. Therefore, this study investigated the expression of lncRNA PVT1 in rectal cancer and its relationship with prognosis, as well as its effect on rectal cancer cell autophagy, proliferation, and apoptosis, so as to provide a reliable target for treatment of rectal cancer.
AIM To investigate the expression of lncRNA PVT1 in rectal cancer and its effects on autophagy and proliferation of rectal cancer cells.
METHODS The expression data of lncRNA PVT1 in 92 rectal cancer samples and 318 healthy control samples were obtained from the GEPIA database, and the expression levels of lncRNA PVT1 in rectal cancer cell lines SW837, HR8348, SW1463, and FHC were detected by quantitative real-time PCR. The relationship between the expression level of lncRNA PVT1 and the prognosis of rectal cancer was analyzed using the R packages (survival and survminer) based on the TCGA database. Overexpression of lncRNA PVT1 was then induced in SW837 and HR8348 cells. Transwell assay, CCK-8 assay, and flow cytometry were used to analyze the changes of cell invasion, proliferation, and apoptosis. Western blot analysis was performed to detect the expression of LC3-II/LC3-I, immunofluorescence was used to analyze the change of LC3 expression, and transmission electron microscopy was used to determine the change of autophagosomes. After co-transfection with si-Atg5, the changes of rectal cancer cell autophagy were analyzed.
RESULTS The expression of lncRNA PVT1 in rectal cancer tissues and cells increased significantly. The expression of lncRNA PVT1 was related to the prognosis of rectal cancer. Overexpression of lncRNA PVT1 activated autophagy of rectal cancer cells and induced tumor cell proliferation, invasion, and apoptosis inhibition (P < 0.05).
CONCLUSION LncRNA PVT1 is highly expressed in rectal cancer tissues and cells, and is significantly related to the prognosis of rectal cancer. Overexpression of lncRNA PVT1 induces rectal cancer cell proliferation and invasion, and inhibits their apoptosis. LncRNA PVT1 participates in the regulation of rectal cancer cell autophagy by regulating the expression of Atg5, which may be involved in the occurrence and development of rectal cancer.
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12
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Borniego ML, Innes RW. Extracellular RNA: mechanisms of secretion and potential functions. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2389-2404. [PMID: 36609873 PMCID: PMC10082932 DOI: 10.1093/jxb/erac512] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/21/2022] [Indexed: 06/06/2023]
Abstract
Extracellular RNA (exRNA) has long been considered as cellular waste that plants can degrade and utilize to recycle nutrients. However, recent findings highlight the need to reconsider the biological significance of RNAs found outside of plant cells. A handful of studies suggest that the exRNA repertoire, which turns out to be an extremely heterogenous group of non-coding RNAs, comprises species as small as a dozen nucleotides to hundreds of nucleotides long. They are found mostly in free form or associated with RNA-binding proteins, while very few are found inside extracellular vesicles (EVs). Despite their low abundance, small RNAs associated with EVs have been a focus of exRNA research due to their putative role in mediating trans-kingdom RNAi. Therefore, non-vesicular exRNAs have remained completely under the radar until very recently. Here we summarize our current knowledge of the RNA species that constitute the extracellular RNAome and discuss mechanisms that could explain the diversity of exRNAs, focusing not only on the potential mechanisms involved in RNA secretion but also on post-release processing of exRNAs. We will also share our thoughts on the putative roles of vesicular and extravesicular exRNAs in plant-pathogen interactions, intercellular communication, and other physiological processes in plants.
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Affiliation(s)
- M Lucía Borniego
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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13
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A Cuproptosis-Related lncRNAs Signature Could Accurately Predict Prognosis in Patients with Clear Cell Renal Cell Carcinoma. Anal Cell Pathol (Amst) 2022; 2022:4673514. [PMID: 36588797 PMCID: PMC9800904 DOI: 10.1155/2022/4673514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 12/24/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney cancers. As cuproptosis, a new cell death mechanism proposed recently, differs from all other known mechanisms regulating cell death, we aimed to create prognostic markers using cuproptosis-related long non-coding ribonucleic acids (RNAs; lncRNAs) and elucidate the molecular mechanism. Methods Data from transcriptome RNA sequencing of ccRCC samples and the relevant clinical data were downloaded from The Cancer Genome Atlas, and Pearson's correlation analysis was implemented to obtain the cuproptosis-related lncRNAs. Then, univariate Cox, multivariate Cox, and Least Absolute Shrinkage and Selection Operator Cox analyses were performed to construct the risk signatures. The cuproptosis-related lncRNAs predictive signature was evaluated with receiver operating characteristic curves and subgroup analysis. Finally, Gene Set Enrichment Analysis (GSEA), single-sample GSEA (ssGSEA), tumor immune microenvironment (TIME), and immune checkpoints were performed to explore the relationship between immunity and patient prognosis. Results Five cuproptosis-related lncRNAs, including FOXD2-AS1, LINC00460, AC091212.1, AC007365.1, and AC026401.3, were used to construct the signature. In the training and test sets, low-risk groups (as identified by a risk score lower than the median) demonstrated a better prognosis with an area under the curve for 1-, 3-, and 5-year survival being 0.793, 0.716, and 0.719, respectively. GSEA analysis suggested significant enrichment of the tricarboxylic acid cycle and metabolism-related pathways in the low-risk group. Besides, both ssGSEA and TIME suggested that the high-risk group exhibited more active immune infiltration. Conclusion We proposed a cuproptosis-related lncRNAs signature, which had the potential for prognoses and prediction. Our findings might contribute to elucidating potential genomic biomarkers and targets for future therapies in the cuproptosis-related signaling pathways.
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Autophagy and polyphenol intervention strategy in aging. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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15
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An anti-influenza combined therapy assessed by single cell RNA-sequencing. Commun Biol 2022; 5:1075. [PMID: 36216966 PMCID: PMC9549038 DOI: 10.1038/s42003-022-04013-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 09/20/2022] [Indexed: 11/08/2022] Open
Abstract
Influenza makes millions of people ill every year, placing a large burden on the healthcare system and the economy. To develop a treatment against influenza, we combined virucidal sialylated cyclodextrins with interferon lambda and demonstrated, in human airway epithelia, that the two compounds inhibit the replication of a clinical H1N1 strain more efficiently when administered together rather than alone. We investigated the mechanism of action of the combined treatment by single cell RNA-sequencing analysis and found that both the single and combined treatments impair viral replication to different extents across distinct epithelial cell types. We showed that each cell type comprises multiple sub-types, whose proportions are altered by H1N1 infection, and assessed the ability of the treatments to restore them. To the best of our knowledge this is the first study investigating the effectiveness of an antiviral therapy against influenza virus by single cell transcriptomic studies. When combined with interferon lambda, virucidal sialylated cyclodextrins inhibit the replication of a clinical H1N1 influenza strain in ex vivo human airway epithelia more efficiently than when delivered alone.
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Duan L, Xia Y, Li C, Lan N, Hou X. Identification of Autophagy-Related LncRNA to Predict the Prognosis of Colorectal Cancer. Front Genet 2022; 13:906900. [PMID: 36035142 PMCID: PMC9403719 DOI: 10.3389/fgene.2022.906900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/17/2022] [Indexed: 11/18/2022] Open
Abstract
Objective: To establish a prediction model based on autophagy-related lncRNAs and investigate the functional enrichment of autophagy-related lncRNAs in colorectal cancer. Methods: TCGA database was used to extract the transcriptome data and clinical features of colorectal cancer patients. HADb was used to obtain autophagy-related genes. Pearson correlation analysis was performed to identify autophagy-related lncRNAs. The autophagy-related lncRNAs with prognostic values were selected. Based on the selected lncRNAs, the risk score model and nomogram were constructed, respectively. Calibration curve, concordance index, and ROC curve were performed to evaluate the predictive efficacy of the prediction model. GSEA was performed to figure out the functional enrichment of autophagy-related lncRNAs. Results: A total of 13413 lncRNAs and 938 autophagy-related genes were obtained. A total of 709 autophagy-related genes were identified in colon cancer tissues, and 11 autophagy-related lncRNAs (AL138756.1, LINC01063, CD27-AS1, LINC00957, EIF3J-DT, LINC02474, SNHG16, AC105219.1, AC068580.3, LINC02381, and LINC01011) were finally selected and set as prognosis-related lncRNAs. According to the risk score, patients were divided into the high-risk and low-risk groups, respectively. The survival K–M (Kaplan–Meier) curve showed the low-risk group exhibits better overall survival than the high-risk group. The AUCs under the ROC curves were 0.72, 0.814, and 0.83 at 1, 3, and 5 years, respectively. The C-index (concordance index) of the model was 0.814. The calibration curves at 1, 3, and 5 years showed the predicting values were consistent with the actual values. Functional enrichment analysis showed that autophagy-related lncRNAs were enriched in several pathways. Conclusions: A total of 11 specific autophagy-related lncRNAs were identified to own prognostic value in colon cancer. The predicting model based on the lncRNAs and clinical features can effectively predict the OS. Furthermore, functional enrichment analysis showed that autophagy-related genes were enriched in various biological pathways.
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Affiliation(s)
- Ling Duan
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, China
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Yang Xia
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
- Department of Oncology, The First People’s Hospital of Lanzhou, Lanzhou, China
| | - Chunmei Li
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, China
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Ning Lan
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Xiaoming Hou
- Department of Oncology, The First Hospital of Lanzhou University, Lanzhou, China
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
- *Correspondence: Xiaoming Hou,
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Yao Q, Zhang X, Chen D. The emerging potentials of lncRNA DRAIC in human cancers. Front Oncol 2022; 12:867670. [PMID: 35992823 PMCID: PMC9386314 DOI: 10.3389/fonc.2022.867670] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/11/2022] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNA (lncRNA) is a subtype of noncoding RNA that has more than 200 nucleotides. Numerous studies have confirmed that lncRNA is relevant during multiple biological processes through the regulation of various genes, thus affecting disease progression. The lncRNA DRAIC, a newly discovered lncRNA, has been found to be abnormally expressed in a variety of diseases, particularly cancer. Indeed, the dysregulation of DRAIC expression is closely related to clinicopathological features. It was also reported that DRAIC is key to biological functions such as cell proliferation, autophagy, migration, and invasion. Furthermore, DRAIC is of great clinical significance in human disease. In this review, we discuss the expression signature, clinical characteristics, biological functions, relevant mechanisms, and potential clinical applications of DRAIC in several human diseases.
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Affiliation(s)
- Qinfan Yao
- Kidney Disease Center, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, China
- National Key Clinical Department of Kidney Diseases, Institute of Nephrology, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
| | - Xiuyuan Zhang
- Kidney Disease Center, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, China
- National Key Clinical Department of Kidney Diseases, Institute of Nephrology, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
| | - Dajin Chen
- Kidney Disease Center, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, China
- National Key Clinical Department of Kidney Diseases, Institute of Nephrology, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
- *Correspondence: Dajin Chen,
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Establishment and Analysis of a Prognostic Model of Autophagy-Related lncRNAs in ESCA. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9265088. [PMID: 35928921 PMCID: PMC9345713 DOI: 10.1155/2022/9265088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 07/07/2022] [Indexed: 12/05/2022]
Abstract
Esophageal cancer (ESCA) is a malignant tumor of the upper gastrointestinal tract, with a high mortality rate and poor prognosis. Long noncoding RNAs (lncRNAs) play a role in the malignant progression of tumors by regulating autophagy. This study is aimed at establishing a prognostic model of autophagy-related lncRNAs in ESCA and provide a theoretical basis to determine potential therapeutic targets for ESCA. The transcriptome expression profiles were downloaded from The Cancer Genome Atlas (TCGA). We identified autophagy-related mRNAs and lncRNAs in ESCA using differential expression analysis and the Human Autophagy Database (HADb). Four differentially expressed autophagy-related lncRNAs with a prognostic value were identified using Cox regression and survival analyses. Furthermore, the combination of the selected lncRNAs was able to predict the prognosis of patients with ESCA more accurately than any of the four lncRNAs individually. Finally, we constructed a coexpression network of autophagy-related mRNAs and lncRNAs. This study showed that autophagy-related lncRNAs play an important role in the occurrence and development of ESCA and could become a new target for the diagnosis and treatment of this disease.
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Facilitating Mitophagy via Pink1/Parkin2 Signaling Is Essential for the Neuroprotective Effect of β-Caryophyllene against CIR-Induced Neuronal Injury. Brain Sci 2022; 12:brainsci12070868. [PMID: 35884674 PMCID: PMC9313355 DOI: 10.3390/brainsci12070868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 12/01/2022] Open
Abstract
Mitophagy is an important mechanism for maintaining mitochondrial homeostasis through elimination of damaged or dysfunctional mitochondria following cerebral ischemia-reperfusion (CIR) injury. β-Caryophyllene (BCP) is a natural sesquiterpene compound found in the essential oil of plants and has been shown to ameliorate CIR injury. However, whether BCP protects neurons from CIR injury by activating mitophagy is still unclear, and the underlying mechanism remains unknown. In the present study, a mouse neuron HT-22 cell of oxygen-glucose deprivation/reoxygenation (OGD/R) and C57BL/6 male mouse of transient middle artery occlusion followed by 24 h reperfusion (MCAO/R) were established the model of CIR injury. Our results show that BCP remarkably protected against cell death and apoptosis induced by OGD/R, and decreased neurologic injury, infarct volume, and the injury of neurons in CA1 region on MCAO/R mice. In addition, BCP accelerated mitophagy by regulating expression of mitochondrial autophagy marker molecules and the mt-Atp6/Rpl13 ratio (reflecting the relative number of mitochondria), and promoting autophagosome formation compared with OGD/R and MCAO/R groups both in vitro and in vivo. Furthermore, this study revealed that BCP pre-treatment could activate the Pink1/Parkin2 signaling pathway, also with mitophagy activation. To explore the mechanisms, mitochondrial division inhibitor-1 (Mdivi-1) was used to investigate the role of BCP in CIR injury. We found that Mdivi-1 not only decreased BCP-induced facilitation of mitophagy, but also significantly weakened BCP-induced protection against OGD/R and MCAO/R models, which was consistent with levels of Pink1/Parkin2 signaling pathway. Taken together, these results suggest that facilitating mitophagy via Pink1/Parkin2 signaling is essential for the neuroprotective effect of BCP against CIR injury.
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Li C, Wang M, Wang W, Li Y, Zhang D. Autophagy regulates the effects of ADSC-derived small extracellular vesicles on acute lung injury. Respir Res 2022; 23:151. [PMID: 35681240 PMCID: PMC9185906 DOI: 10.1186/s12931-022-02073-y] [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: 12/09/2021] [Accepted: 05/31/2022] [Indexed: 11/16/2022] Open
Abstract
Small extracellular vesicles (sEVs) have been recognized to be more effective than direct stem cell differentiation into functional target cells in preventing tissue injury and promoting tissue repair. Our previous study demonstrated the protective effect of adipose-derived stem cells (ADSCs) on lipopolysaccharide (LPS)-induced acute lung injury and the effect of autophagy on ADSC functions, but the role of ADSC-derived sEVs (ADSC-sEVs) and autophagy-mediated regulation of ADSC-sEVs in LPS-induced pulmonary microvascular barrier damage remains unclear. After treatment with sEVs from ADSCs with or without autophagy inhibition, LPS-induced human pulmonary microvascular endothelial cell (HPMVECs) barrier damage was detected. LPS-induced acute lung injury in mice was assessed in vivo after intravenous administration of sEVs from ADSCs with or without autophagy inhibition. The effects of autophagy on the bioactive miRNA components of ADSC-sEVs were assessed after prior inhibition of cell autophagy. We found that ADSC-sEV effectively alleviated LPS-induced apoptosis, tight junction damage and high permeability of PMVECs. Moreover, in vivo administration of ADSC-sEV markedly inhibited LPS-triggered lung injury. However, autophagy inhibition, markedly weakened the therapeutic effect of ADSC-sEVs on LPS-induced PMVECs barrier damage and acute lung injury. In addition, autophagy inhibition, prohibited the expression of five specific miRNAs in ADSC-sEVs -under LPS-induced inflammatory conditions. Our results indicate that ADSC-sEVs protect against LPS-induced pulmonary microvascular barrier damage and acute lung injury. Autophagy is a positive mediator of sEVs function, at least in part through controlling the expression of bioactive miRNAs in sEVs.
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Affiliation(s)
- Chichi Li
- Plastic Surgery Department, The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang, Wenzhou City, Zhejiang Province, 325000, People's Republic of China
| | - Min Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang, Wenzhou City, Zhejiang Province, 325000, People's Republic of China
| | - Wangjia Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang, Wenzhou City, Zhejiang Province, 325000, People's Republic of China
| | - Yuping Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang, Wenzhou City, Zhejiang Province, 325000, People's Republic of China.
| | - Dan Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang, Wenzhou City, Zhejiang Province, 325000, People's Republic of China.
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Arruri V, Vemuganti R. Role of autophagy and transcriptome regulation in acute brain injury. Exp Neurol 2022; 352:114032. [PMID: 35259350 PMCID: PMC9187300 DOI: 10.1016/j.expneurol.2022.114032] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/17/2022] [Accepted: 02/28/2022] [Indexed: 01/18/2023]
Abstract
Autophagy is an evolutionarily conserved intracellular system that routes distinct cytoplasmic cargo to lysosomes for degradation and recycling. Accumulating evidence highlight the mechanisms of autophagy, such as clearance of proteins, carbohydrates, lipids and damaged organelles. The critical role of autophagy in selective degradation of the transcriptome is still emerging and could shape the total proteome of the cell, and thus can regulate the homeostasis under stressful conditions. Unregulated autophagy that potentiates secondary brain damage is a key pathological features of acute CNS injuries such as stroke and traumatic brain injury. This review discussed the mutual modulation of autophagy and RNA and its significance in mediating the functional consequences of acute CNS injuries.
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Affiliation(s)
- Vijay Arruri
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA; William S. Middleton Memorial Veteran Administration Hospital, Madison, WI, USA.
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22
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Xia C, Sun Y, Li Y, Ma J, Shi J. LncRNA CCAT1 enhances chemoresistance in hepatocellular carcinoma by targeting QKI-5. Sci Rep 2022; 12:7826. [PMID: 35552451 PMCID: PMC9098857 DOI: 10.1038/s41598-022-11644-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/20/2022] [Indexed: 12/24/2022] Open
Abstract
A major reason for treatment failure of cancer is acquisition of drug resistance. The specific mechanisms underlying hepatocellular carcinoma (HCC) chemoresistance need to be fully elucidated. lncRNAs involve in drug resistance in some cancers, however, the exact functions of lncRNA colon cancer-associated transcript 1 (CCAT1) in oxaliplatin resistance in HCC are still unknown. Our study indicated that CCAT1 promoted HCC proliferation and reduced the apoptosis induced by oxaliplatin. Knockout of CCAT1 could increased chemosensitivity in vitro and in vivo. Further study found that QKI-5 was an important mediator and blocking of QKI-5/p38 MAPK signaling pathway could enhance oxaliplatin sensitivity. In conclusions, CCAT1 promoted proliferation and oxaliplatin resistance via QKI-5/p38 MAPK signaling pathway in HCC. Targeting CCAT1 in combination with chemotherapeutics may be a promising alternative to reverse drug resistance in HCC treatment.
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Affiliation(s)
- Chongsheng Xia
- Affiliated Hospital of Jining Medical University, Jining, 272029, Shandong, China
| | - Yurui Sun
- Affiliated Hospital of Jining Medical University, Jining, 272029, Shandong, China
| | - Yang Li
- Affiliated Hospital of Jining Medical University, Jining, 272029, Shandong, China
| | - Junli Ma
- Affiliated Hospital of Jining Medical University, Jining, 272029, Shandong, China
| | - Jing Shi
- Affiliated Hospital of Jining Medical University, Jining, 272029, Shandong, China.
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Yan RL, Luan CL, Liao CC, Liu LH, Chen FY, Chen HY, Chen RH. Long noncoding RNA BCRP3 stimulates VPS34 and autophagy activities to promote protein homeostasis and cell survival. J Biomed Sci 2022; 29:30. [PMID: 35538574 PMCID: PMC9087997 DOI: 10.1186/s12929-022-00815-0] [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: 01/22/2022] [Accepted: 05/04/2022] [Indexed: 01/03/2023] Open
Abstract
Background Autophagy plays important roles in cell homeostasis and protein quality control. Long non-coding RNAs (lncRNAs) have been revealed as an emerging class of autophagy regulators, but the majority of them function in regulating the expression of autophagy-related genes. LncRNAs that directly act on the core autophagic proteins remain to be explored. Methods Immunofluorescence staining and Western blotting were used to evaluate the function of BCRP3 in autophagy and aggrephagy. RNA immunoprecipitation and in vitro RNA–protein binding assay were used to evaluate the interaction of BCRP3 with its target proteins. Phosphatidylinositol 3-phosphate ELISA assay was used to quantify the enzymatic activity of VPS34 complex. qRT-PCR analysis was used to determine BCRP3 expression under stresses, whereas mass spectrometry and Gene Ontology analyses were employed to evaluate the effect of BCRP3 deficiency on proteome changes. Results We identified lncRNA BCRP3 as a positive regulator of autophagy. BCRP3 was mainly localized in the cytoplasm and bound VPS34 complex to increase its enzymatic activity. In response to proteotoxicity induced by proteasome inhibition or oxidative stress, BCRP3 was upregulated to promote aggrephagy, thereby facilitating the clearance of ubiquitinated protein aggregates. Proteomics analysis revealed that BCRP3 deficiency under proteotoxicity resulted in a preferential accumulation of proteins acting in growth inhibition, cell death, apoptosis, and Smad signaling. Accordingly, BCRP3 deficiency in proteotoxic cells compromised cell proliferation and survival, which was mediated in part through the upregulation of TGF-β/Smad2 pathway. Conclusions Our study identifies BCRP3 as an RNA activator of the VPS34 complex and a key role of BCRP3-mediated aggrephagy in protein quality control and selective degradation of growth and survival inhibitors to maintain cell fitness. Supplementary Information The online version contains supplementary material available at 10.1186/s12929-022-00815-0.
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Affiliation(s)
- Ruei-Liang Yan
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.,Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Chiu-Lin Luan
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.,Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei, 106, Taiwan
| | - Chun-Chieh Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.,Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Li-Heng Liu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.,Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Fei-Yun Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Hsin-Yi Chen
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan.,Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan
| | - Ruey-Hwa Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan. .,Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, 100, Taiwan. .,Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei, 106, Taiwan.
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LC3B is an RNA-binding protein to trigger rapid mRNA degradation during autophagy. Nat Commun 2022; 13:1436. [PMID: 35302060 PMCID: PMC8931120 DOI: 10.1038/s41467-022-29139-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 02/23/2022] [Indexed: 12/13/2022] Open
Abstract
LC3/ATG8 has long been appreciated to play a central role in autophagy, by which a variety of cytoplasmic materials are delivered to lysosomes and eventually degraded. However, information on the molecular functions of LC3 in RNA biology is very limited. Here, we show that LC3B is an RNA-binding protein that directly binds to mRNAs with a preference for a consensus AAUAAA motif corresponding to a polyadenylation sequence. Autophagic activation promotes an association between LC3B and target mRNAs and triggers rapid degradation of target mRNAs in a CCR4-NOT–dependent manner before autolysosome formation. Furthermore, our transcriptome-wide analysis reveals that PRMT1 mRNA, which encodes a negative regulator of autophagy, is one of the major substrates. Rapid degradation of PRMT1 mRNA by LC3B facilitates autophagy. Collectively, we demonstrate that LC3B acts as an RNA-binding protein and an mRNA decay factor necessary for efficient autophagy. LC3/ATG8 plays an essential role in autophagy. Here the authors show that LC3B exhibits RNA-binding ability and induces rapid degradation of target mRNAs via autophagic activation, highlighting the interplay between autophagy and RNA biology.
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Wilkinson E, Cui YH, He YY. Roles of RNA Modifications in Diverse Cellular Functions. Front Cell Dev Biol 2022; 10:828683. [PMID: 35350378 PMCID: PMC8957929 DOI: 10.3389/fcell.2022.828683] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/14/2022] [Indexed: 12/19/2022] Open
Abstract
Chemical modifications of RNA molecules regulate both RNA metabolism and fate. The deposition and function of these modifications are mediated by the actions of writer, reader, and eraser proteins. At the cellular level, RNA modifications regulate several cellular processes including cell death, proliferation, senescence, differentiation, migration, metabolism, autophagy, the DNA damage response, and liquid-liquid phase separation. Emerging evidence demonstrates that RNA modifications play active roles in the physiology and etiology of multiple diseases due to their pervasive roles in cellular functions. Here, we will summarize recent advances in the regulatory and functional role of RNA modifications in these cellular functions, emphasizing the context-specific roles of RNA modifications in mammalian systems. As m6A is the best studied RNA modification in biological processes, this review will summarize the emerging advances on the diverse roles of m6A in cellular functions. In addition, we will also provide an overview for the cellular functions of other RNA modifications, including m5C and m1A. Furthermore, we will also discuss the roles of RNA modifications within the context of disease etiologies and highlight recent advances in the development of therapeutics that target RNA modifications. Elucidating these context-specific functions will increase our understanding of how these modifications become dysregulated during disease pathogenesis and may provide new opportunities for improving disease prevention and therapy by targeting these pathways.
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Affiliation(s)
- Emma Wilkinson
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, United States
- Committee on Cancer Biology, University of Chicago, Chicago, IL, United States
| | - Yan-Hong Cui
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, United States
| | - Yu-Ying He
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, United States
- Committee on Cancer Biology, University of Chicago, Chicago, IL, United States
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Li J, Guo S, Sun Z, Fu Y. Noncoding RNAs in Drug Resistance of Gastrointestinal Stromal Tumor. Front Cell Dev Biol 2022; 10:808591. [PMID: 35174150 PMCID: PMC8841737 DOI: 10.3389/fcell.2022.808591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/10/2022] [Indexed: 12/11/2022] Open
Abstract
Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor in the gastrointestinal tracts and a model for the targeted therapy of solid tumors because of the oncogenic driver mutations in KIT and PDGDRA genes, which could be effectively inhibited by the very first targeted agent, imatinib mesylate. Most of the GIST patients could benefit a lot from the targeted treatment of this receptor tyrosine kinase inhibitor. However, more than 50% of the patients developed resistance within 2 years after imatinib administration, limiting the long-term effect of imatinib. Noncoding RNAs (ncRNAs), the non-protein coding transcripts of human, were demonstrated to play pivotal roles in the resistance of various chemotherapy drugs. In this review, we summarized the mechanisms of how ncRNAs functioning on the drug resistance in GIST. During the drug resistance of GIST, there were five regulating mechanisms where the functions of ncRNAs concentrated: oxidative phosphorylation, autophagy, apoptosis, drug target changes, and some signaling pathways. Also, these effects of ncRNAs in drug resistance were divided into two aspects. How ncRNAs regulate drug resistance in GIST was further summarized according to ncRNA types, different drugs and categories of resistance. Moreover, clinical applications of these ncRNAs in GIST chemotherapies concentrated on the prognostic biomarkers and novel therapeutic targets.
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Affiliation(s)
- Jiehan Li
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuning Guo
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Yang Fu, ; Zhenqiang Sun,
| | - Yang Fu
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, China
- *Correspondence: Yang Fu, ; Zhenqiang Sun,
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Tang F, Chen L, Gao H, Xiao D, Li X. m6A: An Emerging Role in Programmed Cell Death. Front Cell Dev Biol 2022; 10:817112. [PMID: 35141221 PMCID: PMC8819724 DOI: 10.3389/fcell.2022.817112] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/10/2022] [Indexed: 12/20/2022] Open
Abstract
Programmed cell death is an active extinction process, including autophagy, ferroptosis, pyroptosis, apoptosis, and necroptosis. m6A is a reversible RNA modification which undergoes methylation under the action of methylases (writers), and is demethylated under the action of demethylases (erasers). The RNA base site at which m6A is modified is recognized by specialized enzymes (readers) which regulate downstream RNA translation, decay, and stability. m6A affects many aspects of mRNA metabolism, and also plays an important role in promoting the maturation of miRNA, the translation and degradation of circRNA, and the stability of lncRNA. The regulatory factors including writers, erasers and readers promote or inhibit programmed cell death via up-regulating or down-regulating downstream targets in a m6A-dependent manner to participate in the process of disease. In this review, we summarize the functions of m6A with particular reference to its role in programmed cell death.
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Affiliation(s)
- Fajuan Tang
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Lin Chen
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Hu Gao
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Dongqiong Xiao
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
- *Correspondence: Dongqiong Xiao, ; Xihong Li,
| | - Xihong Li
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
- *Correspondence: Dongqiong Xiao, ; Xihong Li,
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Lin Q, Shi Y, Liu Z, Mehrpour M, Hamaï A, Gong C. Non-coding RNAs as new autophagy regulators in cancer progression. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166293. [PMID: 34688868 DOI: 10.1016/j.bbadis.2021.166293] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/17/2021] [Accepted: 10/10/2021] [Indexed: 12/09/2022]
Abstract
Recent advances highlight that non-coding RNAs (ncRNAs) are emerging as fundamental regulators in various physiological as well as pathological processes by regulating macro-autophagy. Studies have disclosed that macro-autophagy, which is a highly conserved process involving cellular nutrients, components, and recycling of organelles, can be either selective or non-selective and ncRNAs show their regulation on selective autophagy as well as non-selective autophagy. The abnormal expression of ncRNAs will result in the impairment of autophagy and contribute to carcinogenesis and cancer progression by regulating both selective autophagy as well as non-selective autophagy. This review focuses on the regulatory roles of ncRNAs in autophagy and their involvement in cancer which may provide valuable therapeutic targets for cancer management.
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Affiliation(s)
- Qun Lin
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Bioland Laboratory, 510005 Guangzhou, China
| | - Yu Shi
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Bioland Laboratory, 510005 Guangzhou, China
| | - Zihao Liu
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Bioland Laboratory, 510005 Guangzhou, China
| | - Maryam Mehrpour
- Institut Necker-Enfants Malades (INEM), Inserm U1151-CNRS UMR 8253, 75993, Paris, France; Université Paris Descartes-Sorbonne Paris Cité, 75993 Paris, France
| | - Ahmed Hamaï
- Institut Necker-Enfants Malades (INEM), Inserm U1151-CNRS UMR 8253, 75993, Paris, France; Université Paris Descartes-Sorbonne Paris Cité, 75993 Paris, France
| | - Chang Gong
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Bioland Laboratory, 510005 Guangzhou, China.
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Fairman CM, Lønbro S, Cardaci TD, VanderVeen BN, Nilsen TS, Murphy AE. Muscle wasting in cancer: opportunities and challenges for exercise in clinical cancer trials. JCSM RAPID COMMUNICATIONS 2022; 5:52-67. [PMID: 36118249 PMCID: PMC9481195 DOI: 10.1002/rco2.56] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
BACKGROUND Low muscle in cancer is associated with an increase in treatment-related toxicities and is a predictor of cancer-related and all-cause mortality. The mechanisms of cancer-related muscle loss are multifactorial, including anorexia, hypogonadism, anaemia, inflammation, malnutrition, and aberrations in skeletal muscle protein turnover and metabolism. METHODS In this narrative review, we summarise relevant literature to (i) review the factors influencing skeletal muscle mass regulation, (ii) provide an overview of how cancer/treatments negatively impact these, (iii) review factors beyond muscle signalling that can impact the ability to participate in and respond to an exercise intervention to counteract muscle loss in cancer, and (iv) provide perspectives on critical areas of future research. RESULTS Despite the well-known benefits of exercise, there remains a paucity of clinical evidence supporting the impact of exercise in cancer-related muscle loss. There are numerous challenges to reversing muscle loss with exercise in clinical cancer settings, ranging from the impact of cancer/treatments on the molecular regulation of muscle mass, to clinical challenges in responsiveness to an exercise intervention. For example, tumour-related/treatment-related factors (e.g. nausea, pain, anaemia, and neutropenia), presence of comorbidities (e.g. diabetes, arthritis, and chronic obstructive pulmonary disease), injuries, disease progression and bone metastases, concomitant medications (e.g., metformin), can negatively affect an individual's ability to exercise safely and limit subsequent adaptation. CONCLUSIONS This review identifies numerous gaps and oppportunities in the area of low muscle and muscle loss in cancer. Collaborative efforts between preclinical and clinical researchers are imperative to both understanding the mechanisms of atrophy, and develop appropriate therapeutic interventions.
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Affiliation(s)
- Ciaran M. Fairman
- Department of Exercise Science, University of South Carolina, Columbia, South Carolina 29033, USA
- Correspondence to: Ciaran Fairman, Department of Exercise Science, University of South Carolina, Columbia, SC 29033, USA.
| | - Simon Lønbro
- Department of Public Health, Section for Sports Science, Aarhus University, Aarhus, Denmark
| | - Thomas D. Cardaci
- Department of Exercise Science, University of South Carolina, Columbia, South Carolina 29033, USA
| | - Brandon N. VanderVeen
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, South Carolina, USA
| | - Tormod S. Nilsen
- Department of Physical Performance, Norwegian School of Sports Sciences, Oslo, Norway
| | - Angela E. Murphy
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, South Carolina, USA
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30
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Parker KA, Robinson NJ, Schiemann WP. The role of RNA processing and regulation in metastatic dormancy. Semin Cancer Biol 2022; 78:23-34. [PMID: 33775829 PMCID: PMC8464634 DOI: 10.1016/j.semcancer.2021.03.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 02/07/2023]
Abstract
Tumor dormancy is a major contributor to the lethality of metastatic disease, especially for cancer patients who develop metastases years-to-decades after initial diagnosis. Indeed, tumor cells can disseminate during early disease stages and persist in new microenvironments at distal sites for months, years, or even decades before initiating metastatic outgrowth. This delay between primary tumor remission and metastatic relapse is known as "dormancy," during which disseminated tumor cells (DTCs) acquire quiescent states in response to intrinsic (i.e., cellular) and extrinsic (i.e., microenvironmental) signals. Maintaining dormancy-associated phenotypes requires DTCs to activate transcriptional, translational, and post-translational mechanisms that engender cellular plasticity. RNA processing is emerging as an essential facet of cellular plasticity, particularly with respect to the initiation, maintenance, and reversal of dormancy-associated phenotypes. Moreover, dysregulated RNA processing, particularly that associated with alternative RNA splicing and expression of noncoding RNAs (ncRNAs), can occur in DTCs to mediate intrinsic and extrinsic metastatic dormancy. Here we review the pathophysiological impact of alternative RNA splicing and ncRNAs in promoting metastatic dormancy and disease recurrence in human cancers.
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Affiliation(s)
- Kimberly A. Parker
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Nathaniel J. Robinson
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - William P. Schiemann
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA,Corresponding Author: William P. Schiemann, Case Comprehensive Cancer Center, Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road, Cleveland, OH 44106 Phone: 216-368-5763.
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31
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Xu C, Li T, Lei J, Zhang Y, Zhou J, Hu B. The Autophagy Cargo Receptor SQSTM1 Inhibits Infectious Bursal Disease Virus Infection through Selective Autophagic Degradation of Double-Stranded Viral RNA. Viruses 2021; 13:v13122494. [PMID: 34960763 PMCID: PMC8704251 DOI: 10.3390/v13122494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 11/16/2022] Open
Abstract
Selective autophagy mediates the degradation of cytoplasmic cargos, such as damaged organelles, invading pathogens, and protein aggregates. However, whether it targets double-stranded RNA (dsRNA) of intracellular pathogens is still largely unknown. Here, we show that selective autophagy regulates the degradation of the infectious bursal disease virus (IBDV) dsRNA genome. The amount of dsRNA decreased greatly in cells that overexpressed the autophagy-required protein VPS34 or autophagy cargo receptor SQSTM1, while it increased significantly in SQSTM1 or VPS34 knockout cells or by treating wild-type cells with the autophagy inhibitor chloroquine or wortmannin. Confocal microscopy and structured illumination microscopy showed SQSTM1 colocalized with dsRNA during IBDV infection. A pull-down assay further confirmed the direct binding of SQSTM1 to dsRNA through amino acid sites R139 and K141. Overexpression of SQSTM1 inhibited the replication of IBDV, while knockout of SQSTM1 promoted IBDV replication. Therefore, our findings reveal the role of SQSTM1 in clearing viral dsRNA through selective autophagy, highlighting the antiviral role of autophagy in the removal of the viral genome.
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Affiliation(s)
- Chenyang Xu
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (C.X.); (T.L.); (J.L.)
| | - Tongtong Li
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (C.X.); (T.L.); (J.L.)
| | - Jing Lei
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (C.X.); (T.L.); (J.L.)
| | - Yina Zhang
- MOA Key Laboratory of Animal Virology, Center for Veterinary Sciences, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (J.Z.)
| | - Jiyong Zhou
- MOA Key Laboratory of Animal Virology, Center for Veterinary Sciences, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (J.Z.)
| | - Boli Hu
- MOE International Joint Collaborative Research Laboratory for Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (C.X.); (T.L.); (J.L.)
- MOA Key Laboratory of Animal Virology, Center for Veterinary Sciences, Zhejiang University, Hangzhou 310058, China; (Y.Z.); (J.Z.)
- Correspondence:
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Application of Metabolomics in the Study of Starvation-Induced Autophagy in Saccharomyces cerevisiae: A Scoping Review. J Fungi (Basel) 2021; 7:jof7110987. [PMID: 34829274 PMCID: PMC8619235 DOI: 10.3390/jof7110987] [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: 11/03/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 11/18/2022] Open
Abstract
This scoping review is aimed at the application of the metabolomics platform to dissect key metabolites and their intermediates to observe the regulatory mechanisms of starvation-induced autophagy in Saccharomyces cerevisiae. Four research papers were shortlisted in this review following the inclusion and exclusion criteria. We observed a commonly shared pathway undertaken by S. cerevisiae under nutritional stress. Targeted and untargeted metabolomics was applied in either of these studies using varying platforms resulting in the annotation of several different observable metabolites. We saw a commonly shared pathway undertaken by S. cerevisiae under nutritional stress. Following nitrogen starvation, the concentration of cellular nucleosides was altered as a result of autophagic RNA degradation. Additionally, it is also found that autophagy replenishes amino acid pools to sustain macromolecule synthesis. Furthermore, in glucose starvation, nucleosides were broken down into carbonaceous metabolites that are being funneled into the non-oxidative pentose phosphate pathway. The ribose salvage allows for the survival of starved yeast. Moreover, acute glucose starvation showed autophagy to be involved in maintaining ATP/energy levels. We highlighted the practicality of metabolomics as a tool to better understand the underlying mechanisms involved to maintain homeostasis by recycling degradative products to ensure the survival of S. cerevisiae under starvation. The application of metabolomics has extended the scope of autophagy and provided newer intervention targets against cancer as well as neurodegenerative diseases in which autophagy is implicated.
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Tang T, Zeng F. NFIB-Mediated lncRNA PVT1 Aggravates Laryngeal Squamous Cell Carcinoma Progression via the miR-1301-3p/MBNL1 Axis. J Immunol Res 2021; 2021:8675123. [PMID: 34805417 PMCID: PMC8604577 DOI: 10.1155/2021/8675123] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/07/2021] [Accepted: 10/20/2021] [Indexed: 11/18/2022] Open
Abstract
Laryngeal squamous cell carcinoma (LSCC) is one of the most common malignant tumors of head and neck cancers. In the past decades, although the therapy strategies of LSCC have made considerable improvement, the terrible outcomes of LSCC still bring an enormous burden to the world health care system. Novel therapeutic targets for LSCC are urgently needed. lncRNAs exert important roles in various biological progressions, including LSCC. Here, we aimed to investigate the function of lncRNA PVT1 in LSCC progression and its underlying molecular mechanisms. By conducting multiple experiments, our results showed that lncRNA PVT1 was upregulated in LSCC cell lines and regulated LSCC cell proliferation, apoptosis, and its cell susceptibility to natural killer (NK) cells. Moreover, it was found that lncRNA PVT1 promotes MBNL1 expression to regulate LSCC cellular progression through sponging miR-1301-3p. Our study might provide novel targets for LSCC basic research or clinical management.
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Affiliation(s)
- Tian Tang
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Feng Zeng
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
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34
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Kumaran G, Michaeli S. Eating the messenger (RNA): autophagy shapes the cellular RNA landscape. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6803-6807. [PMID: 34468738 PMCID: PMC8547149 DOI: 10.1093/jxb/erab385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
This article comments on: Hickl D, Drews F, Girke C, Zimmer D, Mühlhaus T, Hauth J, Nordström K, Trentmann O, Neuhaus EH, Scheuring D, Fehlmann T, Keller A, Simon M, Möhlmann T. 2021. Differential degradation of RNA species by autophagy-related pathways in Arabidopsis. Journal of Experimental Botany 72, 6867–6881.
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Affiliation(s)
- Girishkumar Kumaran
- Institute of Postharvest and Food Sciences, Agricultural Research Organization (ARO)-Volcani Institute, Rishon LeZion, Israel
| | - Simon Michaeli
- Institute of Postharvest and Food Sciences, Agricultural Research Organization (ARO)-Volcani Institute, Rishon LeZion, Israel
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35
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Field S, Conner WC, Roberts DM. Arabidopsis CALMODULIN-LIKE 38 Regulates Hypoxia-Induced Autophagy of SUPPRESSOR OF GENE SILENCING 3 Bodies. FRONTIERS IN PLANT SCIENCE 2021; 12:722940. [PMID: 34567037 PMCID: PMC8456008 DOI: 10.3389/fpls.2021.722940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/09/2021] [Indexed: 05/23/2023]
Abstract
During the energy crisis associated with submergence stress, plants restrict mRNA translation and rapidly accumulate stress granules that act as storage hubs for arrested mRNA complexes. One of the proteins associated with hypoxia-induced stress granules in Arabidopsis thaliana is the calcium-sensor protein CALMODULIN-LIKE 38 (CML38). Here, we show that SUPPRESSOR OF GENE SILENCING 3 (SGS3) is a CML38-binding protein, and that SGS3 and CML38 co-localize within hypoxia-induced RNA stress granule-like structures. Hypoxia-induced SGS3 granules are subject to turnover by autophagy, and this requires both CML38 as well as the AAA+-ATPase CELL DIVISION CYCLE 48A (CDC48A). CML38 also interacts directly with CDC48A, and CML38 recruits CDC48A to CML38 granules in planta. Together, this work demonstrates that SGS3 associates with stress granule-like structures during hypoxia stress that are subject to degradation by CML38 and CDC48-dependent autophagy. Further, the work identifies direct regulatory targets for the hypoxia calcium-sensor CML38, and suggest that CML38 association with stress granules and associated regulation of autophagy may be part of the RNA regulatory program during hypoxia stress.
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36
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Identification of Six Autophagy-Related-lncRNA Prognostic Biomarkers in Uveal Melanoma. DISEASE MARKERS 2021; 2021:2401617. [PMID: 34426753 PMCID: PMC8379639 DOI: 10.1155/2021/2401617] [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: 06/07/2021] [Revised: 07/16/2021] [Accepted: 07/23/2021] [Indexed: 12/29/2022]
Abstract
Currently, no autophagy-related long noncoding RNA (lncRNA) has been reported to predict the prognosis of uveal melanoma patients. Our study screened for autophagy-related lncRNAs in 80 samples downloaded from The Cancer Genome Atlas (TCGA) database through lncRNA-mRNA coexpression. We used univariate Cox to further filter the lncRNAs. Multivariate Cox regression and LASSO regression were applied to construct an autophagy-associated lncRNA predictive model and calculate the risk score. Clinical risk factors were validated using Cox regression to determine whether they were independent prognostic indicators. Functional enrichment was performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. The model was built with six predictive autophagy-associated lncRNAs and clustered uveal melanoma patients into high- and low-risk groups. The risk score of our model was a significant independent prognostic factor (hazard ratio = 1.0; p < 0.001). Moreover, these six lncRNAs were significantly concentrated in the biological pathways of cytoplasmic component recycling, energy metabolism, and apoptosis. Thus, the six autophagy-associated lncRNAs are potential molecular biomarkers and treatment targets for uveal melanoma patients.
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37
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Shi J, Guo C, Ma J. CCAT2 enhances autophagy-related invasion and metastasis via regulating miR-4496 and ELAVL1 in hepatocellular carcinoma. J Cell Mol Med 2021; 25:8985-8996. [PMID: 34409736 PMCID: PMC8435435 DOI: 10.1111/jcmm.16859] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 07/07/2021] [Accepted: 07/31/2021] [Indexed: 12/14/2022] Open
Abstract
Autophagy is thought to contribute to the pathogenesis of many diseases, including cancer. Long non‐coding RNA (lncRNA) CCAT2 functions as an oncogene in a variety of tumours. However, it is still unknown whether CCAT2 is involved in autophagy and metastasis of hepatocellular carcinoma (HCC). In our study, we found that lncRNA CCAT2 expression was significantly increased in HCC tissue and was correlated with advanced stage and venous invasion. Further experiments revealed that CCAT2 induced autophagy and promoted migration and invasion in vitro and in vivo. Mechanistic investigations found that CCAT2 involved in HCC by regulating miR‐4496/Atg5 in cytoplasm. In nucleus, CCAT2 bound with ELAVL1/HuR to facilitate HCC progression. Our findings suggest that CCAT2 is an oncogenic factor in the progression of HCC with different regulatory mechanisms and may serve as a target for HCC therapy.
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Affiliation(s)
- Jing Shi
- Affiliated Hospital of Jining Medical University, Jining, China
| | - Cao Guo
- Institute of Medical Sciences, Xiangya Hospital, Central South University, Changsha, China
| | - Junli Ma
- Affiliated Hospital of Jining Medical University, Jining, China
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38
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Chen R, Chen Y, Huang W, Zhao Y, Luo W, Lin J, Wang Z, Yang J. Comprehensive analysis of an immune-related ceRNA network in identifying a novel lncRNA signature as a prognostic biomarker for hepatocellular carcinoma. Aging (Albany NY) 2021; 13:17607-17628. [PMID: 34237706 PMCID: PMC8312417 DOI: 10.18632/aging.203250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/19/2021] [Indexed: 12/13/2022]
Abstract
The function of competitive endogenous RNA (ceRNA) network in the immune regulation of hepatocellular carcinoma (HCC) is unclear. Our study aimed to construct an immune-related ceRNA network and develop an immune-related long noncoding RNA (lncRNA) signature to assess the prognosis of HCC patients and to optimize the treatment methods. We firstly constructed a ceRNA regulatory network for HCC using differentially expressed lncRNAs, mRNAs and microRNAs (miRNAs) from the Cancer Genome Atlas. A signature was constructed by 11 immune-related prognostic lncRNAs from the ceRNA network. The survival analysis and receiver operating characteristic analysis validated the reliability of the signature. Multivariate Cox regression analysis revealed that the signature could act an independent prognostic indicator. This signature also showed high association with immune cell infiltration and immune check blockades. LINC00491 was identified as the hub lncRNA in the signature. In vitro and in vivo evidence demonstrated that silencing of LINC00491 significantly inhibited HCC growth. Finally, 59 lncRNAs, 21 miRNAs, and 26 mRNAs were obtained to build the immune-related ceRNA network for HCC. In conclusion, our novel immune-related lncRNA prognostic signature and the immune-related ceRNA network might provide in-depth insights into tumor-immune interaction of HCC and promote better individual treatment strategies in HCC patients.
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Affiliation(s)
- Rui Chen
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Yunlong Chen
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Wenjie Huang
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, China
| | - Yingnan Zhao
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Wang Luo
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Jinyu Lin
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Zhuangxiong Wang
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Jian Yang
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
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Liu K, Sato R, Shibata T, Hiranuma R, Reuter T, Fukui R, Zhang Y, Ichinohe T, Ozawa M, Yoshida N, Latz E, Miyake K. Skewed endosomal RNA responses from TLR7 to TLR3 in RNase T2-deficient macrophages. Int Immunol 2021; 33:479-490. [PMID: 34161582 DOI: 10.1093/intimm/dxab033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/18/2021] [Indexed: 11/12/2022] Open
Abstract
RNase T2, a ubiquitously expressed RNase, degrades RNAs in the endosomal compartments. RNA sensors, double-stranded RNA (dsRNA)-sensing TLR3 and single-stranded RNA (ssRNA)-sensing TLR7, are localized in the endosomal compartment in mouse macrophages. We here studied the role of RNase T2 in TLR3 and TLR7 responses in macrophages. Macrophages expressed RNase T2 and a member of the RNase A family RNase 4. RNase T2 was also expressed in plasmacytoid and conventional dendritic cells. Treatment with dsRNAs or type I interferon (IFN) upregulated expression of RNase T2 but not RNase 4. RNase T2-deficiency in macrophages upregulated TLR3 responses but impaired TLR7 responses. Mechanistically, RNase T2 degraded both ds- and ssRNAs in vitro, and its mutants showed a positive correlation between RNA degradation and the rescue of altered TLR3 and TLR7 responses. H122A and C188R RNase T2 mutations, not H69A and E118V mutations, impaired both RNA degradation and the rescue of altered TLR3 and TLR7 responses. RNase T2 in bone marrow-derived macrophages was broadly distributed from early endosomes to lysosomes, and colocalized with the internalized TLR3 ligand poly(I:C). These results suggest that RNase T2-dependent RNA degradation in endosomes/lysosomes negatively and positively regulates TLR3 and TLR7 responses, respectively, in macrophages.
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Affiliation(s)
- Kaiwen Liu
- Division of Innate Immunity, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Ryota Sato
- Division of Innate Immunity, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Takuma Shibata
- Division of Innate Immunity, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Ryosuke Hiranuma
- Division of Innate Immunity, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Tatjana Reuter
- Division of Innate Immunity, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan.,Institute of Innate Immunity, Biomedical Center, Venusberg-Campus, University of Bonn, 53127 Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Ryutaro Fukui
- Division of Innate Immunity, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Yun Zhang
- Division of Innate Immunity, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Takeshi Ichinohe
- Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Manabu Ozawa
- Laboratory of Development Genetics, Laboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Nobuaki Yoshida
- Laboratory of Development Genetics, Laboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Eicke Latz
- Institute of Innate Immunity, Biomedical Center, Venusberg-Campus, University of Bonn, 53127 Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany.,Department of Infectious Diseases and Immunology, UMass Medical School, Worcester, MA 01655, USA
| | - Kensuke Miyake
- Division of Innate Immunity, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan.,Laboratory of Innate Immunity, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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A Novel Autophagy-Related lncRNA Gene Signature to Improve the Prognosis of Patients with Melanoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8848227. [PMID: 34250091 PMCID: PMC8238568 DOI: 10.1155/2021/8848227] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 05/20/2021] [Indexed: 01/04/2023]
Abstract
Objective Autophagy and long noncoding RNAs (lncRNAs) have been the focus of research on the pathogenesis of melanoma. However, the autophagy network of lncRNAs in melanoma has not been reported. The purpose of this study was to investigate the lncRNA prognostic markers related to melanoma autophagy and predict the prognosis of patients with melanoma. Methods We downloaded RNA sequencing data and clinical information of melanoma from the Cancer Genome Atlas. The coexpression of autophagy-related genes (ARGs) and lncRNAs was analyzed. The risk model of autophagy-related lncRNAs was established by univariate and multivariate Cox regression analyses, and the best prognostic index was evaluated combined with clinical data. Finally, gene set enrichment analysis was performed on patients in the high- and low-risk groups. Results According to the results of the univariate Cox analysis, only the overexpression of LINC00520 was associated with poor overall survival, unlike HLA-DQB1-AS1, USP30-AS1, AL645929, AL365361, LINC00324, and AC055822. The results of the multivariate Cox analysis showed that the overall survival of patients in the high-risk group was shorter than that recorded in the low-risk group (p < 0.001). Moreover, in the receiver operating characteristic curve of the risk model we constructed, the area under the curve (AUC) was 0.734, while the AUC of T and N was 0.707 and 0.658, respectively. The Gene Ontology was mainly enriched with the positive regulation of autophagy and the activation of the immune system. The results of the Kyoto Encyclopedia of Genes and Genomes enrichment were mostly related to autophagy, immunity, and melanin metabolism. Conclusion The positive regulation of autophagy may slow the transition from low-risk patients to high-risk patients in melanoma. Furthermore, compared with clinical information, the autophagy-related lncRNA risk model may better predict the prognosis of patients with melanoma and provide new treatment ideas.
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Liang J, Zhi Y, Deng W, Zhou W, Li X, Cai Z, Zhu Z, Zeng J, Wu W, Dong Y, Huang J, Zhang Y, Xu S, Feng Y, Ding F, Zhang J. Development and validation of ferroptosis-related lncRNAs signature for hepatocellular carcinoma. PeerJ 2021; 9:e11627. [PMID: 34178478 PMCID: PMC8202323 DOI: 10.7717/peerj.11627] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/26/2021] [Indexed: 12/24/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) with high heterogeneity is one of the most frequent malignant tumors throughout the world. However, there is no research to establish a ferroptosis-related lncRNAs (FRlncRNAs) signature for the patients with HCC. Therefore, this study was designed to establish a novel FRlncRNAs signature to predict the survival of patients with HCC. Method The expression profiles of lncRNAs were acquired from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. FRlncRNAs co-expressed with ferroptosis-related genes were utilized to establish a signature. Cox regression was used to construct a novel three FRlncRNAs signature in the TCGA cohort, which was verified in the GEO validation cohort. Results Three differently expressed FRlncRNAs significantly associated with prognosis of HCC were identified, which composed a novel FRlncRNAs signature. According to the FRlncRNAs signature, the patients with HCC could be divided into low- and high-risk groups. Patients with HCC in the high-risk group displayed shorter overall survival (OS) contrasted with those in the low-risk group (P < 0.001 in TCGA cohort and P = 0.045 in GEO cohort). This signature could serve as a significantly independent predictor in Cox regression (multivariate HR > 1, P < 0.001), which was verified to a certain extent in the GEO cohort (univariate HR > 1, P < 0.05). Meanwhile, it was also a useful tool in predicting survival among each stratum of gender, age, grade, stage, and etiology,etc. This signature was connected with immune cell infiltration (i.e., Macrophage, Myeloid dendritic cell, and Neutrophil cell, etc.) and immune checkpoint blockade targets (PD-1, CTLA-4, and TIM-3). Conclusion The three FRlncRNAs might be potential therapeutic targets for patients, and their signature could be utilized for prognostic prediction in HCC.
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Affiliation(s)
- Jiaying Liang
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China.,Guangzhou University of Chinese Medicine, Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Yaofeng Zhi
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China.,Guangzhou University of Chinese Medicine, Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Wenhui Deng
- Guangzhou University of Chinese Medicine, The fourth Affiliated Hospital of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Weige Zhou
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Xuejun Li
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Zheyou Cai
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Zhijian Zhu
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Jinxiang Zeng
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Wanlan Wu
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Ying Dong
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Jin Huang
- Guangzhou University of Chinese Medicine, Clinic of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuzhuo Zhang
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China.,Guangzhou University of Chinese Medicine, Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Shichao Xu
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China.,Guangzhou University of Chinese Medicine, Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Yixin Feng
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China.,Guangzhou University of Chinese Medicine, Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou, China
| | - Fuping Ding
- Guangzhou University of Chinese Medicine, School of Nursing, Guangzhou, China
| | - Jin Zhang
- Guangzhou University of Chinese Medicine, School of Basic Medical Sciences, Guangzhou, China.,Guangzhou University of Chinese Medicine, Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou, China
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Zheng Q, Jia J, Zhou Z, Chu Q, Lian W, Chen Z. The Emerging Role of Thymopoietin-Antisense RNA 1 as Long Noncoding RNA in the Pathogenesis of Human Cancers. DNA Cell Biol 2021; 40:848-857. [PMID: 34096793 DOI: 10.1089/dna.2021.0024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play essential roles in the occurrence and development of multiple human cancers. An accumulating body of researches have investigated thymopoietin antisense RNA 1 (TMPO-AS1) as a newly discovered lncRNA, which functions as an oncogenic lncRNA that is upregulated in various human malignancies and associated with poor prognosis. Many studies have detected abnormally high expression levels of TMPO-AS1 in multiple cancers, such as lung cancer, breast cancer, colorectal cancer (CRC), hepatocellular carcinoma, CRC, gastric cancer, ovarian cancer, thyroid cancer, esophageal cancer, Wilms tumor, cervical cancer, retinoblastoma, bladder cancer, osteosarcoma, and prostate cancer. TMPO-AS1 has been subsequently demonstrated to play a pivotal role in tumorigenesis and progression. The aberrantly expressed TMPO-AS1 acts as a competing endogenous RNA (ceRNA) that inhibits miRNA expression, thus activating the expression of downstream oncogenes. This study comprehensively summarizes the aberrant expressions of TMPO-AS1 as reported in the current literature and explains the relevant biological regulation mechanisms in carcinogenesis and tumor progression. Corresponding studies have indicated that TMPO-AS1 has a potential value as a promising biomarker or a target for cancer therapy.
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Affiliation(s)
- Qiuxian Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Junjun Jia
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ziyuan Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qingfei Chu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Wenwen Lian
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhi Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Bakowski MA, Beutler N, Wolff KC, Kirkpatrick MG, Chen E, Nguyen TTH, Riva L, Shaabani N, Parren M, Ricketts J, Gupta AK, Pan K, Kuo P, Fuller M, Garcia E, Teijaro JR, Yang L, Sahoo D, Chi V, Huang E, Vargas N, Roberts AJ, Das S, Ghosh P, Woods AK, Joseph SB, Hull MV, Schultz PG, Burton DR, Chatterjee AK, McNamara CW, Rogers TF. Drug repurposing screens identify chemical entities for the development of COVID-19 interventions. Nat Commun 2021; 12:3309. [PMID: 34083527 PMCID: PMC8175350 DOI: 10.1038/s41467-021-23328-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/19/2021] [Indexed: 12/15/2022] Open
Abstract
The ongoing pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), necessitates strategies to identify prophylactic and therapeutic drug candidates for rapid clinical deployment. Here, we describe a screening pipeline for the discovery of efficacious SARS-CoV-2 inhibitors. We screen a best-in-class drug repurposing library, ReFRAME, against two high-throughput, high-content imaging infection assays: one using HeLa cells expressing SARS-CoV-2 receptor ACE2 and the other using lung epithelial Calu-3 cells. From nearly 12,000 compounds, we identify 49 (in HeLa-ACE2) and 41 (in Calu-3) compounds capable of selectively inhibiting SARS-CoV-2 replication. Notably, most screen hits are cell-line specific, likely due to different virus entry mechanisms or host cell-specific sensitivities to modulators. Among these promising hits, the antivirals nelfinavir and the parent of prodrug MK-4482 possess desirable in vitro activity, pharmacokinetic and human safety profiles, and both reduce SARS-CoV-2 replication in an orthogonal human differentiated primary cell model. Furthermore, MK-4482 effectively blocks SARS-CoV-2 infection in a hamster model. Overall, we identify direct-acting antivirals as the most promising compounds for drug repurposing, additional compounds that may have value in combination therapies, and tool compounds for identification of viral host cell targets.
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Affiliation(s)
- Malina A Bakowski
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA.
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karen C Wolff
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | | | - Emily Chen
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Tu-Trinh H Nguyen
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Riva
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Namir Shaabani
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Mara Parren
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - James Ricketts
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Anil K Gupta
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Kastin Pan
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Peiting Kuo
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - MacKenzie Fuller
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- HUMANOID CoRE, UC San Diego, La Jolla, CA, USA
| | - Elijah Garcia
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - John R Teijaro
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Linlin Yang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Debashis Sahoo
- Department of Computer Science and Engineering, Jacobs School of Engineering, UC San Diego, La Jolla, CA, USA
- Department of Pediatrics, UC San Diego, La Jolla, CA, USA
| | - Victor Chi
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Edward Huang
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Natalia Vargas
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Amanda J Roberts
- Animal Models Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Soumita Das
- HUMANOID CoRE, UC San Diego, La Jolla, CA, USA
- Department of Pathology, UC San Diego, La Jolla, CA, USA
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- HUMANOID CoRE, UC San Diego, La Jolla, CA, USA
- Department of Medicine, UC San Diego, La Jolla, CA, USA
| | - Ashley K Woods
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Sean B Joseph
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Mitchell V Hull
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Peter G Schultz
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Case W McNamara
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Thomas F Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- UC San Diego Division of Infectious Diseases and Global Public Health, UC San Diego School of Medicine, La Jolla, CA, USA.
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Xiao B, Liu L, Li A, Wang P, Xiang C, Li H, Xiao T. Identification and validation of immune-related lncRNA prognostic signatures for melanoma. IMMUNITY INFLAMMATION AND DISEASE 2021; 9:1044-1054. [PMID: 34077998 PMCID: PMC8342236 DOI: 10.1002/iid3.468] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/14/2021] [Indexed: 12/15/2022]
Abstract
Introduction Melanoma is a highly aggressive malignant skin tumor as well as the primary reason for skin cancer‐specific deaths. We first identified immune‐related long noncoding RNA (lncRNA) prognostic signature and found potential immunotherapeutic targets for melanoma cancer. Methods RNA‐seq data and clinical features of melanoma samples were obtained from The Cancer Genome Atlas. Samples of melanoma were randomly assigned to the training and testing cohort. The immune‐related lncRNA signature was then obtained via using univariate, LASSO, and multivariate Cox analysis of patients in the training cohort. Eight significant immune‐related lncRNA signature was then subsequently obtained through correlation analysis between immune‐related genes and lncRNAs. The association between risk score and immune cell infiltration was finally assessed using TIMER and CIBERSORT. Results Three hundred and fifty‐six immune‐related lncRNAs were obtained. Among them, eight immune‐related lncRNAs were identified to build a prognostic risk signature model. The model's performance was then confirmed using the Kaplan–Meier curves, risk plots, and time‐dependent receiver‐operating characteristic curves in the training cohort. The risk score was identified and confirmed as an independent prognostic factor through univariate and multivariate Cox regression analyses. These results were further verified in the testing and whole cohorts. CIBERSORT algorithm showed that the infiltration levels of T cells CD8, M1 macrophages, plasma cells, T cells CD4 memory activated, T cells gamma delta, and mast cells activated were significantly lower in the high‐risk group while the infiltration level of macrophages M0 was significantly lower in the low‐risk group. Conclusion The immune‐related lncRNA signature offers prognostic markers and potential immunotherapeutic targets for melanoma.
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Affiliation(s)
- Bo Xiao
- Department of OrthopedicsThe Second Xiangya Hospital of Central South UniversityChangshaHunanChina
| | - Liyan Liu
- Department of OrthopedicsThe Second Xiangya Hospital of Central South UniversityChangshaHunanChina
| | - Aoyu Li
- Department of OrthopedicsThe Second Xiangya Hospital of Central South UniversityChangshaHunanChina
| | - Pingxiao Wang
- Department of OrthopedicsThe Second Xiangya Hospital of Central South UniversityChangshaHunanChina
| | - Cheng Xiang
- Department of OrthopedicsThe Second Xiangya Hospital of Central South UniversityChangshaHunanChina
| | - Hui Li
- Department of OrthopedicsThe Second Xiangya Hospital of Central South UniversityChangshaHunanChina
| | - Tao Xiao
- Department of OrthopedicsThe Second Xiangya Hospital of Central South UniversityChangshaHunanChina
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Xuan Y, Chen W, Liu K, Gao Y, Zuo S, Wang B, Ma X, Zhang X. A Risk Signature with Autophagy-Related Long Noncoding RNAs for Predicting the Prognosis of Clear Cell Renal Cell Carcinoma: Based on the TCGA Database and Bioinformatics. DISEASE MARKERS 2021; 2021:8849977. [PMID: 34040677 PMCID: PMC8121606 DOI: 10.1155/2021/8849977] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 04/02/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Disorders of autophagic processes have been reported to affect the survival outcome of clear cell renal cell carcinoma (ccRCC) patients. The purpose of our study was to identify and validate the candidate prognostic long noncoding RNA signature of autophagy. METHODS Transcriptome profiles were obtained from The Cancer Genome Atlas. The autophagy gene list was obtained from the Human Autophagy Database. Based on coexpression analysis, we obtained a list of autophagy-related lncRNAs (ARlncRNAs). GO enrichment analysis and KEGG pathway analysis were conducted to explore the functional annotation of these ARlncRNAs. Univariate and multivariate Cox regression analyses were conducted to elucidate the correlation between overall survival and the expression level of each ARlncRNAs. We then established a prognostic signature that was a linear combination of the regression coefficients from the multivariate Cox regression model (β) multiplied by the expression levels of the respective ARlncRNAs in the training cohort. The predictive performance was tested in the validation cohort. Additionally, the independence of the risk signature was assessed, and the relationship between the risk signature and conventional clinicopathological features was explored. RESULTS Seven autophagy-related lncRNAs with prognostic value (SNHG3, SNHG17, MELTF-AS1, HOTAIRM1, EPB41L4A-DT, AP003352.1, and AC145423.2) were identified and integrated into a risk signature, dividing patients into low-risk and high-risk groups. The risk signature was independent of conventional clinical characteristics as a prognostic indicator of ccRCC (HR, 1.074, 95% confidence interval: 1.036-1.113, p < 0.001) and was valuable in the prediction of ccRCC progression. CONCLUSION Our risk signature has potential prognostic value in ccRCC, and these ARlncRNAs may play a significant role in ccRCC tumor biology.
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Affiliation(s)
- Yundong Xuan
- Medical School of Chinese PLA, Beijing 100853, China
- Department of Urology, The Third Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing 100853, China
| | - Weihao Chen
- Department of Urology, The Third Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing 100853, China
| | - Kan Liu
- Department of Urology, The Third Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing 100853, China
| | - Yu Gao
- Department of Urology, The Third Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing 100853, China
| | - Shidong Zuo
- Medical School of Chinese PLA, Beijing 100853, China
- Department of Urology, The Third Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing 100853, China
| | - Baojun Wang
- Department of Urology, The Third Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing 100853, China
| | - Xin Ma
- Department of Urology, The Third Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing 100853, China
| | - Xu Zhang
- Department of Urology, The Third Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing 100853, China
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RNA transport and local translation in neurodevelopmental and neurodegenerative disease. Nat Neurosci 2021; 24:622-632. [PMID: 33510479 PMCID: PMC8860725 DOI: 10.1038/s41593-020-00785-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/17/2020] [Indexed: 02/08/2023]
Abstract
Neurons decentralize protein synthesis from the cell body to support the active metabolism of remote dendritic and axonal compartments. The neuronal RNA transport apparatus, composed of cis-acting RNA regulatory elements, neuronal transport granule proteins, and motor adaptor complexes, drives the long-distance RNA trafficking required for local protein synthesis. Over the past decade, advances in human genetics, subcellular biochemistry, and high-resolution imaging have implicated each member of the apparatus in several neurodegenerative diseases, establishing failed RNA transport and associated processes as a unifying pathomechanism. In this review, we deconstruct the RNA transport apparatus, exploring each constituent's role in RNA localization and illuminating their unique contributions to neurodegeneration.
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Almasi S, Crawford Parks TE, Ravel-Chapuis A, MacKenzie A, Côté J, Cowan KN, Jasmin BJ. Differential regulation of autophagy by STAU1 in alveolar rhabdomyosarcoma and non-transformed skeletal muscle cells. Cell Oncol (Dordr) 2021; 44:851-870. [PMID: 33899158 DOI: 10.1007/s13402-021-00607-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2021] [Indexed: 11/30/2022] Open
Abstract
PURPOSE Recent work has highlighted the therapeutic potential of targeting autophagy to modulate cell survival in a variety of diseases including cancer. Recently, we found that the RNA-binding protein Staufen1 (STAU1) is highly expressed in alveolar rhabdomyosarcoma (ARMS) and that this abnormal expression promotes tumorigenesis. Here, we asked whether STAU1 is involved in the regulation of autophagy in ARMS cells. METHODS We assessed the impact of STAU1 expression modulation in ARMS cell lines (RH30 and RH41), non-transformed skeletal muscle cells (C2C12) and STAU1-transgenic mice using complementary techniques. RESULTS We found that STAU1 silencing reduces autophagy in the ARMS cell lines RH30 and RH41, while increasing their apoptosis. Mechanistically, this inhibitory effect was found to be caused by a direct negative impact of STAU1 depletion on the stability of Beclin-1 (BECN1) and ATG16L1 mRNAs, as well as by an indirect inhibition of JNK signaling via increased expression of Dual specificity phosphatase 8 (DUSP8). Pharmacological activation of JNK or expression silencing of DUSP8 was sufficient to restore autophagy in STAU1-depleted cells. By contrast, we found that STAU1 downregulation in non-transformed skeletal muscle cells activates autophagy in a mTOR-dependent manner, without promoting apoptosis. A similar effect was observed in skeletal muscles obtained from STAU1-overexpressing transgenic mice. CONCLUSIONS Together, our data indicate an effect of STAU1 on autophagy regulation in ARMS cells and its differential role in non-transformed skeletal muscle cells. Our findings suggest a cancer-specific potential of targeting STAU1 for the treatment of ARMS.
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Affiliation(s)
- Shekoufeh Almasi
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada.,The Eric J. Poulin Centre for Neuromuscular Diseases, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Tara E Crawford Parks
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada.,The Eric J. Poulin Centre for Neuromuscular Diseases, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Aymeric Ravel-Chapuis
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada.,The Eric J. Poulin Centre for Neuromuscular Diseases, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Alex MacKenzie
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada.,The Eric J. Poulin Centre for Neuromuscular Diseases, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Division of Endocrinology, Department of Paediatric, CHEO, University of Ottawa, Ottawa, ON, Canada
| | - Jocelyn Côté
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada.,The Eric J. Poulin Centre for Neuromuscular Diseases, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Kyle N Cowan
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada.,Division of Paediatric Surgery, Department of Surgery, CHEO, University of Ottawa, Ottawa, ON, Canada.,Molecular Biomedicine Program, CHEO, Ottawa, ON, Canada
| | - Bernard J Jasmin
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada. .,The Eric J. Poulin Centre for Neuromuscular Diseases, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
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Zhou Z, Zhang Y, Gao J, Hao X, Shan C, Li J, Liu C, Wang Y, Li P. Circular RNAs act as regulators of autophagy in cancer. MOLECULAR THERAPY-ONCOLYTICS 2021; 21:242-254. [PMID: 34095462 PMCID: PMC8142048 DOI: 10.1016/j.omto.2021.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Circular RNAs (circRNAs) are a large class of noncoding RNAs that are emerging as critical regulators of various cellular processes that are involved in the physiopathological mechanism of many human diseases, such as cardiovascular disease, atherosclerosis, diabetes mellitus, and carcinogenesis. Autophagy is a conserved and catabolic cellular process that degrades unfolded, misfolded, or damaged protein aggregates or organelles to maintain cellular homeostasis under physiological and pathological conditions. Increasing evidence has shown a link between circRNAs and autophagy that is closely related to the occurrence and development of human diseases, including cancer. In this review, we highlight recent advances in understanding the functions and mechanisms of circRNAs in the regulation of autophagy in cancer. These autophagy-related circRNAs contribute to cancer development and progression in various types of human cancer by activating or inhibiting autophagy. Cumulative research on the relationship between circRNAs and autophagy regulation provides critical insight into the essential role that circRNAs play in carcinogenesis and suggests new targets for tumor therapy.
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Affiliation(s)
- Zhixia Zhou
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, People's Republic of China
| | - Yinfeng Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, People's Republic of China
| | - Jinning Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, People's Republic of China
| | - Xiaodan Hao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, People's Republic of China
| | - Chan Shan
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, People's Republic of China
| | - Jing Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, People's Republic of China
| | - Cuiyun Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, People's Republic of China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, People's Republic of China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, People's Republic of China
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An angiogenesis-related long noncoding RNA signature correlates with prognosis in patients with hepatocellular carcinoma. Biosci Rep 2021; 41:228144. [PMID: 33764367 PMCID: PMC8026853 DOI: 10.1042/bsr20204442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent and lethal cancers worldwide. Neovascularization is closely related to the malignancy of tumors. We constructed a signature of angiogenesis-related long noncoding RNA (lncRNA) to predict the prognosis of patients with HCC. The lncRNA expression matrix of 424 HCC patients was downloaded from The Cancer Genome Atlas (TCGA). First, gene set enrichment analysis (GSEA) was used to distinguish the differentially expressed genes of the angiogenesis genes in liver cancer and adjacent tissues. Next, a signature of angiogenesis-related lncRNAs was constructed using univariate and multivariate analyses, and receiver operating characteristic (ROC) curves were used to assess the accuracy. The signature and relevant clinical information were used to construct the nomogram. A 5-lncRNA signature was highly correlated with overall survival (OS) in HCC patients and performed well in evaluations using the C-index, areas under the curve, and calibration curves. In summary, the 5-lncRNA model can serve as an accurate signature to predict the prognosis of patients with liver cancer, but its mechanism of action must be further elucidated by experiments.
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Xiang Y, Zhou S, Hao J, Zhong C, Ma Q, Sun Z, Wei C. Development and validation of a prognostic model for kidney renal clear cell carcinoma based on RNA binding protein expression. Aging (Albany NY) 2020; 12:25356-25372. [PMID: 33229623 PMCID: PMC7803486 DOI: 10.18632/aging.104137] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/20/2020] [Indexed: 12/18/2022]
Abstract
Dysregulated expression of RNA-binding proteins (RBPs) is strongly associated with the development and progression of multiple tumors. However, little is known about the role of RBPs in kidney renal clear cell carcinoma (KIRC). In this study, we examined RBP expression profiles using The Cancer Genome Atlas database and identified 133 RBPs that were differentially expressed in KIRC and non-tumor tissues. We then systematically analyzed the potential biological functions of these RBPs and established PPIs. Based on Lasso regression and Cox survival analyses, we constructed a risk model that could independently and accurately predict prognosis based on seven RBPs (NOL12, PABPC1L, RNASE2, RPL22L1, RBM47, OASL, and YBX3). Survival times were shorter in patients with high risk scores for cohorts stratified by different characteristics. Gene set enrichment analysis was also performed to further understand functional differences between high- and low-risk groups. Finally, we developed a clinical nomogram with a concordance index of 0.792 for estimating 3- and 5-year survival probabilities. Our results demonstrate that this risk model could potentially improve individualized diagnostic and therapeutic strategies.
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Affiliation(s)
- Yuzhu Xiang
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China
| | - Shengcai Zhou
- Department of Urology, Yiyuan County People's Hospital, Zibo 256100, Shandong, China
| | - Jian Hao
- Department of Urology, Xintai People's Hospital, Xintai 271200, Shandong, China
| | - Chunhong Zhong
- Department of Central Sterile Supply, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China
| | - Qimei Ma
- Department of Rehabilitation Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China
| | - Zhuolun Sun
- Department of Urology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Chunxiao Wei
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China
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