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Munroe JA, Doe CQ. Imp is expressed in INPs and newborn neurons where it regulates neuropil targeting in the central complex. Neural Dev 2023; 18:9. [PMID: 38031099 PMCID: PMC10685609 DOI: 10.1186/s13064-023-00177-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
The generation of neuronal diversity remains incompletely understood. In Drosophila, the central brain is populated by neural stem cells derived from progenitors called neuroblasts (NBs). There are two types of NBs, type 1 and 2. T1NBs have a relatively simple lineage, whereas T2NBs expand and diversify the neural population with the generation of intermediate neural progenitors (INPs), contributing many neurons to the adult central complex, a brain region essential for navigation. However, it is not fully understood how neural diversity is created in T2NB and INP lineages. Imp, an RNA-binding protein, is expressed in T2NBs in a high-to-low temporal gradient, while the RNA-binding protein Syncrip forms an opposing gradient. It remains unknown if Imp expression is carried into INPs; whether it forms a gradient similar to NBs; and whether INP expression of Imp is required for generating neuronal identity or morphology. Here, we show that Imp/Syp are both present in INPs, but not always in opposing gradients. We find that newborn INPs adopt their Imp/Syp levels from their parental T2NBs; that Imp and Syp are expressed in stage-specific high-to-low gradients in INPs. In addition, there is a late INP pulse of Imp. We find that neurons born from old INPs (E-PG and PF-R neurons) have altered morphology following both Imp knock-down and Imp overexpression. We conclude that Imp functions in INPs and newborn neurons to determine proper neuronal morphology and central complex neuropil organization.
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Affiliation(s)
- Jordan A Munroe
- Institute of Neuroscience, Howard Hughes Medical Institute, Univ. of Oregon, Eugene, OR, 97403, USA
| | - Chris Q Doe
- Institute of Neuroscience, Howard Hughes Medical Institute, Univ. of Oregon, Eugene, OR, 97403, USA.
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2
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Bin Wang, Yuan C, Qie Y, Dang S. Long non-coding RNAs and pancreatic cancer: A multifaceted view. Biomed Pharmacother 2023; 167:115601. [PMID: 37774671 DOI: 10.1016/j.biopha.2023.115601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/17/2023] [Accepted: 09/25/2023] [Indexed: 10/01/2023] Open
Abstract
Pancreatic cancer (PC) is a highly malignant disease with a 5-year survival rate of only 10%. Families with PC are at greater risk, as are type 2 diabetes, pancreatitis, and other factors. Insufficient early detection methods make this cancer have a poor prognosis. Additionally, the molecular mechanisms underlying PC development remain unclear. Increasing evidence suggests that long non-coding RNAs (lncRNAs) contribute to PC pathology,which may control gene expression by recruiting histone modification complexes to chromatin and interacting with proteins and RNAs. In recent studies, abnormal regulation of lncRNAs has been implicated in PC proliferation, metastasis, invasion, angiogenesis, apoptosis, and chemotherapy resistance suggesting potential clinical implications. The paper reviews the progress of lncRNA research in PC about diabetes mellitus, pancreatitis, cancer metastasis, tumor microenvironment regulation, and chemoresistance. Furthermore, lncRNAs may serve as potential therapeutic targets and biomarkers for PC diagnosis and prognosis. This will help improve PC patients' survival rate from a lncRNA perspective.
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Affiliation(s)
- Bin Wang
- General Surgery Department, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu 212000, China
| | - Chang Yuan
- General Surgery Department, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu 212000, China
| | - Yinyin Qie
- General Surgery Department, Yixing People's Hospital, Wuxi, Jiangsu 214200, China
| | - Shengchun Dang
- General Surgery Department, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu 212000, China; Siyang Hospital, Suqian, Jiangsu 223700, China.
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3
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Li X, Wang Y, Deng S, Zhu G, Wang C, Johnson NA, Zhang Z, Tirado CR, Xu Y, Metang LA, Gonzalez J, Mukherji A, Ye J, Yang Y, Peng W, Tang Y, Hofstad M, Xie Z, Yoon H, Chen L, Liu X, Chen S, Zhu H, Strand D, Liang H, Raj G, He HH, Mendell JT, Li B, Wang T, Mu P. Loss of SYNCRIP unleashes APOBEC-driven mutagenesis, tumor heterogeneity, and AR-targeted therapy resistance in prostate cancer. Cancer Cell 2023; 41:1427-1449.e12. [PMID: 37478850 PMCID: PMC10530398 DOI: 10.1016/j.ccell.2023.06.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 05/24/2023] [Accepted: 06/29/2023] [Indexed: 07/23/2023]
Abstract
Tumor mutational burden and heterogeneity has been suggested to fuel resistance to many targeted therapies. The cytosine deaminase APOBEC proteins have been implicated in the mutational signatures of more than 70% of human cancers. However, the mechanism underlying how cancer cells hijack the APOBEC mediated mutagenesis machinery to promote tumor heterogeneity, and thereby foster therapy resistance remains unclear. We identify SYNCRIP as an endogenous molecular brake which suppresses APOBEC-driven mutagenesis in prostate cancer (PCa). Overactivated APOBEC3B, in SYNCRIP-deficient PCa cells, is a key mutator, representing the molecular source of driver mutations in some frequently mutated genes in PCa, including FOXA1, EP300. Functional screening identifies eight crucial drivers for androgen receptor (AR)-targeted therapy resistance in PCa that are mutated by APOBEC3B: BRD7, CBX8, EP300, FOXA1, HDAC5, HSF4, STAT3, and AR. These results uncover a cell-intrinsic mechanism that unleashes APOBEC-driven mutagenesis, which plays a significant role in conferring AR-targeted therapy resistance in PCa.
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Affiliation(s)
- Xiaoling Li
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yunguan Wang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Su Deng
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Guanghui Zhu
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Choushi Wang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Nickolas A Johnson
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Zeda Zhang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yaru Xu
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Lauren A Metang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Julisa Gonzalez
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Atreyi Mukherji
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jianfeng Ye
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yuqiu Yang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Wei Peng
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yitao Tang
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX, USA
| | - Mia Hofstad
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Zhiqun Xie
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Heewon Yoon
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Liping Chen
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Xihui Liu
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Sujun Chen
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Hong Zhu
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Douglas Strand
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX, USA; Department of Systems Biology, MD Anderson Cancer Center, Houston, TX, USA
| | - Ganesh Raj
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Housheng Hansen He
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Joshua T Mendell
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Bo Li
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ping Mu
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA; Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas, TX, USA.
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4
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Qi X, Yan Q, Shang Y, Zhao R, Ding X, Gao SJ, Li W, Lu C. A viral interferon regulatory factor degrades RNA-binding protein hnRNP Q1 to enhance aerobic glycolysis via recruiting E3 ubiquitin ligase KLHL3 and decaying GDPD1 mRNA. Cell Death Differ 2022; 29:2233-2246. [PMID: 35538151 PMCID: PMC9613757 DOI: 10.1038/s41418-022-01011-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/09/2022] Open
Abstract
Reprogramming of host metabolism is a common strategy of viral evasion of host cells, and is essential for successful viral infection and induction of cancer in the context cancer viruses. Kaposi's sarcoma (KS) is the most common AIDS-associated cancer caused by KS-associated herpesvirus (KSHV) infection. KSHV-encoded viral interferon regulatory factor 1 (vIRF1) regulates multiple signaling pathways and plays an important role in KSHV infection and oncogenesis. However, the role of vIRF1 in KSHV-induced metabolic reprogramming remains elusive. Here we show that vIRF1 increases glucose uptake, ATP production and lactate secretion by downregulating heterogeneous nuclear ribonuclear protein Q1 (hnRNP Q1). Mechanistically, vIRF1 upregulates and recruits E3 ubiquitin ligase Kelch-like 3 (KLHL3) to degrade hnRNP Q1 through a ubiquitin-proteasome pathway. Furthermore, hnRNP Q1 binds to and stabilizes the mRNA of glycerophosphodiester phosphodiesterase domain containing 1 (GDPD1). However, vIRF1 targets hnRNP Q1 for degradation, which destabilizes GDPD1 mRNA, resulting in induction of aerobic glycolysis. These results reveal a novel role of vIRF1 in KSHV metabolic reprogramming, and identifying a potential therapeutic target for KSHV infection and KSHV-induced cancers.
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Affiliation(s)
- Xiaoyu Qi
- State Key Laboratory of Reproductive Medicine, Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, 210004, P. R. China
- Department of Microbiology, Nanjing Medical University, Nanjing, 211166, P. R. China
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, 211166, P. R. China
| | - Qin Yan
- State Key Laboratory of Reproductive Medicine, Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, 210004, P. R. China
- Department of Microbiology, Nanjing Medical University, Nanjing, 211166, P. R. China
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, 211166, P. R. China
| | - Yuancui Shang
- Department of Microbiology, Nanjing Medical University, Nanjing, 211166, P. R. China
| | - Runran Zhao
- Department of Microbiology, Nanjing Medical University, Nanjing, 211166, P. R. China
| | - Xiangya Ding
- State Key Laboratory of Reproductive Medicine, Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, 210004, P. R. China
| | - Shou-Jiang Gao
- Tumor Virology Program, UPMC Hillman Cancer Center, and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15232, USA
| | - Wan Li
- State Key Laboratory of Reproductive Medicine, Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, 210004, P. R. China.
- Department of Microbiology, Nanjing Medical University, Nanjing, 211166, P. R. China.
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, 211166, P. R. China.
| | - Chun Lu
- State Key Laboratory of Reproductive Medicine, Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, 210004, P. R. China.
- Department of Microbiology, Nanjing Medical University, Nanjing, 211166, P. R. China.
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, 211166, P. R. China.
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Ashrafizadeh M, Rabiee N, Kumar AP, Sethi G, Zarrabi A, Wang Y. Long noncoding RNAs (lncRNAs) in pancreatic cancer progression. Drug Discov Today 2022; 27:2181-2198. [PMID: 35589014 DOI: 10.1016/j.drudis.2022.05.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/18/2022] [Accepted: 05/12/2022] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules involved in gene regulation at transcriptional, post-transcriptional, and epigenetic levels. LncRNAs participate in regulating apoptosis and autophagy in pancreatic cancer (PCa) and can promote and/or decrease the proliferation rate of tumor cells. The metastasis of PCa cells is tightly regulated by lncRNAs and they can affect the mechanism of epithelial-mesenchymal transition (EMT) to modulate metastasis. The drug resistance of PCa cells, especially to gemcitabine, can be affected by lncRNAs. In addition, lncRNAs enriched in exosomes can be transferred among tumor cells to regulate their proliferation and metastasis. Antitumor compounds, such as curcumin and ginsenosides, can regulate lncRNA expression in PCa therapy. As we discuss here, the expression level of lncRNAs can be considered as both a diagnostic and prognostic tool in patients with PCa.
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Affiliation(s)
- Milad Ashrafizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Üniversite Caddesi No. 27, Orhanlı, Tuzla, 34956 Istanbul, Turkey.
| | - Navid Rabiee
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea; School of Engineering, Macquarie University, Sydney, NSW 2109, Australia
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117599, Singapore; NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117599, Singapore; NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ali Zarrabi
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Istinye University, Sariyer 34396, Istanbul, Turkey.
| | - Yuzhuo Wang
- Department of Urological Sciences, Vancouver, BC V6H3Z6, Canada; Vancouver Prostate Centre, University of British Columbia, Vancouver, BC V6H3Z6, Canada.
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6
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Yang X, Qin C, Zhao B, Li T, Wang Y, Li Z, Li T, Wang W. Long Noncoding RNA and Circular RNA: Two Rising Stars in Regulating Epithelial-Mesenchymal Transition of Pancreatic Cancer. Front Oncol 2022; 12:910678. [PMID: 35719940 PMCID: PMC9204003 DOI: 10.3389/fonc.2022.910678] [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: 04/01/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly malignant tumor with especially poor prognosis. However, the molecular mechanisms of pancreatic oncogenesis and malignant progression are not fully elucidated. Epithelial-mesenchymal transition (EMT) process is important to drive pancreatic carcinogenesis. Recently, long noncoding RNAs (lncRNAs) and circular RNAs(circRNAs) have been characterized to participate in EMT in PDAC, which can affect the migration and invasion of tumor cells by playing important roles in epigenetic processes, transcription, and post-transcriptional regulation. LncRNAs can act as competing endogenous RNAs (ceRNA) to sequester target microRNAs(miRNAs), bind to the genes which localize physically nearby, and directly interact with EMT-related proteins. Currently known circRNAs mostly regulate the EMT process in PDAC also by acting as a miRNA sponge, directly affecting the protein degradation process. Therefore, exploring the functions of lncRNAs and circRNAs in EMT during pancreatic cancer might help pancreatic cancer treatments.
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Affiliation(s)
- Xiaoying Yang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Cheng Qin
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bangbo Zhao
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tianhao Li
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuanyang Wang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zeru Li
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tianyu Li
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weibin Wang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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7
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Zhu J, Huang Q, Peng X, Luo C, Liu S, Liu Z, Wu X, Luo H. Identification of LncRNA Prognostic Signature Associated With Genomic Instability in Pancreatic Adenocarcinoma. Front Oncol 2022; 12:799475. [PMID: 35433487 PMCID: PMC9012103 DOI: 10.3389/fonc.2022.799475] [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: 10/26/2021] [Accepted: 02/28/2022] [Indexed: 12/21/2022] Open
Abstract
Background Genomic instability (GI) is a critical feature of cancer which plays a key role in the occurrence and development of pancreatic adenocarcinoma (PAAD). Long non-coding RNA (LncRNA) is an emerging prognostic biomarker because it is involved in regulating GI. Recently, researchers used such GI-related LncRNAs (GILncRNAs) to establish a prognostic signature for patients with cancer and helped in predicting the overall prognosis of the patients. However, it is evident that patients with PAAD still lack such prognostic signature constructed with GILncRNA. Methods The present study screened GILncRNAs from 83 patients with PAAD. Prognosis-related GILncRNAs were identified by univariate Cox regression analysis. The correlation coefficients of these GILncRNAs were obtained by multivariate Cox regression analysis and used to construct a signature. The signature in the present study was then assessed through survival analysis, mutation correlation analysis, independent prognostic analysis, and clinical stratification analysis in the training set and validated in the testing as well as all TCGA set. The current study performed external clinical relevance validation of the signature and validated the effect of AC108134.2 in GILncSig on PAAD using in vitro experiments. Finally, the function of GILncRNA signature (GILncSig) dependent on Gene Ontology enrichment analysis was explored and chemotherapeutic drug sensitivity analysis was also performed. Results Results of the present study found that a total of 409 GILncRNAs were identified, 5 of which constituted the prognostic risk signature in this study, namely, AC095057.3, AC108134.2, AC124798.1, AL606834.1, and AC104695.4. It was found that the signature of the present study was better than others in predicting the overall survival and applied to patients with PAAD of all ages, genders, and tumor grades. Further, it was noted that the signature of the current study in the GSE102238, was correlated with tumor length, and tumor stage of patients with PAAD. In vitro, functional experiments were used in the present study to validate that AC108134.2 is associated with PAAD genomic instability and progression. Notably, results of the pRRophetic analysis in the current study showed that the high-risk group possessed reverse characteristics and was sensitive to chemotherapy. Conclusions In conclusion, it was evident that the GILncSig used in the present study has good prognostic performance. Therefore, the signature may become a potential sensitive biological indicator of PAAD chemotherapy, which may help in clinical decision-making and management of patients with cancer.
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Affiliation(s)
- Jinfeng Zhu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Province Key Laboratory of Molecular Medicine, Nanchang, China
| | - Qian Huang
- Department of General Practice, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xingyu Peng
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Province Key Laboratory of Molecular Medicine, Nanchang, China
| | - Chen Luo
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Sicheng Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zitao Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xun Wu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hongliang Luo
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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8
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Eini M, Parsi S, Barati M, Bahramali G, Alizadeh Zarei M, Kiani J, Azarnezhad A, Hosseini A. Bioinformatic Investigation of Micro RNA-802 Target Genes, Protein Networks, and Its Potential Prognostic Value in Breast Cancer. Avicenna J Med Biotechnol 2022; 14:154-164. [PMID: 35633990 PMCID: PMC9077654 DOI: 10.18502/ajmb.v14i2.8882] [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: 06/23/2021] [Accepted: 01/22/2022] [Indexed: 11/24/2022] Open
Abstract
Background An increasing number of studies have suggested that unveiling the molecular network of miRNAs may provide novel therapeutic targets or biomarkers. In this study, we investigated the probable molecular functions that are related to microRNA-802 (miR-802) and evaluated its prognostic value in breast cancer utilizing bioinformatics tools. Methods PPI network, pathway enrichment and transcription factor analysis were applied to obtain hub genes among overlapping genes of four miRNA target prediction databases. Prognosis value assessments and expression analysis of hub genes using bioinformatics tools, as well as their literature validation were performed. Results Our results showed a significant correlation of the miR-802 overexpression with poor patient survival rate (BC, p=2.7e-5). We determined 247 target genes significant for GO and KEGG terms. Analysis of TFs by TRUST showed that RUNX3, FOXO3, and E2F1 are possible TFs that regulate the miR-802 expression and target genes network. According to our analysis; 21 genes might have an important function in miR-802 molecular processes and regulatory networks. The result shows that among these 21 genes, 8 genes (CASC3, ITGA4, AGO3, TARDBP, MED13L, SF1, SNRPE and CRNKL1) are positively correlated with patient survival. Therefore these genes could be considered and experimentally evaluated as a prognostic biomarker for breast cancer. Conclusion The comprehensive bioinformatics study on miR-802 target genes provided insight into miR-802 mediated pathways and processes. Furthermore, representing candidate target genes by prognostic values indicates the potential clinical application of miR-802 in breast cancer.
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Affiliation(s)
- Maryam Eini
- Department of Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sepideh Parsi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, MA, USA
| | - Mahmood Barati
- Department of Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | | | - Jafar Kiani
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Assad Azarnezhad
- Liver and Digestive Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Arshad Hosseini
- Department of Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
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9
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Riccioni V, Trionfetti F, Montaldo C, Garbo S, Marocco F, Battistelli C, Marchetti A, Strippoli R, Amicone L, Cicchini C, Tripodi M. SYNCRIP Modulates the Epithelial-Mesenchymal Transition in Hepatocytes and HCC Cells. Int J Mol Sci 2022; 23:ijms23020913. [PMID: 35055098 PMCID: PMC8780347 DOI: 10.3390/ijms23020913] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) control gene expression by acting at multiple levels and are often deregulated in epithelial tumors; however, their roles in the fine regulation of cellular reprogramming, specifically in epithelial–mesenchymal transition (EMT), remain largely unknown. Here, we focused on the hnRNP-Q (also known as SYNCRIP), showing by molecular analysis that in hepatocytes it acts as a “mesenchymal” gene, being induced by TGFβ and modulating the EMT. SYNCRIP silencing limits the induction of the mesenchymal program and maintains the epithelial phenotype. Notably, in HCC invasive cells, SYNCRIP knockdown induces a mesenchymal–epithelial transition (MET), negatively regulating their mesenchymal phenotype and significantly impairing their migratory capacity. In exploring possible molecular mechanisms underlying these observations, we identified a set of miRNAs (i.e., miR-181-a1-3p, miR-181-b1-3p, miR-122-5p, miR-200a-5p, and miR-let7g-5p), previously shown to exert pro- or anti-EMT activities, significantly impacted by SYNCRIP interference during EMT/MET dynamics and gathered insights, suggesting the possible involvement of this RNA binding protein in their transcriptional regulation.
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Affiliation(s)
- Veronica Riccioni
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Flavia Trionfetti
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, 00149 Rome, Italy;
| | - Claudia Montaldo
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, 00149 Rome, Italy;
| | - Sabrina Garbo
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Francesco Marocco
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Cecilia Battistelli
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Alessandra Marchetti
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Raffaele Strippoli
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, 00149 Rome, Italy;
| | - Laura Amicone
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
| | - Carla Cicchini
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
- Correspondence: (C.C.); (M.T.)
| | - Marco Tripodi
- Department of Molecular Medicine, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (V.R.); (F.T.); (S.G.); (F.M.); (C.B.); (A.M.); (R.S.); (L.A.)
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, 00149 Rome, Italy;
- Correspondence: (C.C.); (M.T.)
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10
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Gao Y, Liu J, Cai B, Chen Q, Wang G, Lu Z, Jiang K, Miao Y. Development of epithelial-mesenchymal transition-related lncRNA signature for predicting survival and immune microenvironment in pancreatic cancerwithexperiment validation. Bioengineered 2021; 12:10553-10567. [PMID: 34854360 PMCID: PMC8809919 DOI: 10.1080/21655979.2021.2000197] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Long non-coding RNAs (LncRNAs) have crucial function in epithelial–mesenchymal transition (EMT) in pancreatic cancer. It is necessary to comprehensively analyze the potential role of EMT-related lncRNA in pancreatic cancer. In the present study, genomic data of pancreatic cancer from the TCGA database were downloaded and we found 368 EMT-related lncRNAs. According to the expression characteristics of prognostic-related lncRNAs, all samples could be divided into two clusters with different clinical outcomes and different tumor microenvironments. Moreover, an eleven EMT-related lncRNAs signature was established and verified. Patients with pancreatic cancer in the high-risk group had a shorter overall survival than those in the low-risk group and the signature could act as an independent prognostic factor. Further analysis suggested that the EMT-related lncRNAs might affect the prognosis of patients through immune mechanisms. All findings indicated that the signature and eleven lncRNAs might serve as potential prognostic biomarkers and therapeutic targets in the treatment of pancreatic cancer.
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Affiliation(s)
- Yong Gao
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Baobao Cai
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Qun Chen
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Guangfu Wang
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Zipeng Lu
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Kuirong Jiang
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Yi Miao
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China.,Pancreas Center, the Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, People's Republic of China
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11
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Peng XF, Huang SF, Chen LJ, Xu L, Ye WC. Targeting epigenetics and lncRNAs in liver disease: From mechanisms to therapeutics. Pharmacol Res 2021; 172:105846. [PMID: 34438063 DOI: 10.1016/j.phrs.2021.105846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/19/2022]
Abstract
Early onset and progression of liver diseases can be driven by aberrant transcriptional regulation. Different transcriptional regulation processes, such as RNA/DNA methylation, histone modification, and ncRNA-mediated targeting, can regulate biological processes in healthy cells, as well also under various pathological conditions, especially liver disease. Numerous studies over the past decades have demonstrated that liver disease has a strong epigenetic component. Therefore, the epigenetic basis of liver disease has challenged our knowledge of epigenetics, and epigenetics field has undergone an important transformation: from a biological phenomenon to an emerging focus of disease research. Furthermore, inhibitors of different epigenetic regulators, such as m6A-related factors, are being explored as potential candidates for preventing and treating liver diseases. In the present review, we summarize and discuss the current knowledge of five distinct but interconnected and interdependent epigenetic processes in the context of hepatic diseases: RNA methylation, DNA methylation, histone methylation, miRNAs, and lncRNAs. Finally, we discuss the potential therapeutic implications and future challenges and ongoing research in the field. Our review also provides a perspective for identifying therapeutic targets and new hepatic biomarkers of liver disease, bringing precision research and disease therapy to the modern era of epigenetics.
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Affiliation(s)
- Xiao-Fei Peng
- Department of General Surgery, Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan 511518, Guangdong Province, China
| | - Shi-Feng Huang
- Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan 511518, Guangdong Province, China
| | - Ling-Juan Chen
- Department of Clinical Laboratory, Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan 511518, Guangdong Province, China
| | - Lingqing Xu
- Department of Clinical Laboratory, Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan 511518, Guangdong Province, China
| | - Wen-Chu Ye
- Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan 511518, Guangdong Province, China.
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12
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Zhang P, Cao M, Zhang Y, Xu L, Meng F, Wu X, Xia T, Chen Q, Shi G, Wu P, Chen L, Lu Z, Yin J, Cai B, Cao S, Miao Y, Jiang K. A novel antisense lncRNA NT5E promotes progression by modulating the expression of SYNCRIP and predicts a poor prognosis in pancreatic cancer. J Cell Mol Med 2020; 24:10898-10912. [PMID: 32770626 PMCID: PMC7521323 DOI: 10.1111/jcmm.15718] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/09/2020] [Accepted: 07/13/2020] [Indexed: 12/13/2022] Open
Abstract
A novel antisense lncRNA NT5E was identified in a previous microarray that was clearly up‐regulated in pancreatic cancer (PC) tissues. However, its biological function remains unclear. Thus, we aimed to explore its function and clinical significance in PC. The lncNT5E expression was determined in PC specimens and cell lines. In vitro and in vivo studies detected the impact of lncNT5E depletion on PC cell proliferation, migration and invasion. Western blotting investigated the epithelial‐mesenchymal transition (EMT) markers. The interaction between lncNT5E and the promoter region of SYNCRIP was detected by dual‐luciferase reporter assay. The role of lncNT5E in modulating SYNCRIP was investigated in vitro. Our results showed that lncNT5E was significantly up‐regulated in PC tissues and cell lines and associated with poor prognosis. LncNT5E depletion inhibited PC cell proliferation, migration, invasion and EMT in vitro and caused tumorigenesis arrest in vivo. Furthermore, SYNCRIP knockdown had effects similar to those of lncNT5E depletion. A significant positive relationship was observed between lncNT5E and SYNCRIP. Moreover, the dual‐luciferase reporter assays indicated that lncNT5E depletion significantly inhibited SYNCRIP promoter activity. Importantly, the malignant phenotypes of lncNT5E depletion were rescued by overexpressing SYNCRIP. In conclusion, lncNT5E predicts poor prognosis and promotes PC progression by modulating SYNCRIP expression.
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Affiliation(s)
- Pengbo Zhang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Meng Cao
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Yi Zhang
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Lei Xu
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Fanchao Meng
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Xinquan Wu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Department of Hepatopancreatobiliary Surgery, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Tianfang Xia
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Department of General Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Qun Chen
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Guodong Shi
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Pengfei Wu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Lei Chen
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Zipeng Lu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Jie Yin
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Baobao Cai
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Shouji Cao
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Yi Miao
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Kuirong Jiang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
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