1
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Deng LQ, Shi CJ, Zhou ST, Zeng WQ, Xian YF, Wang YY, Fu WM, Lin HL, Liu W, Zhang JF. EIF4A3-negatively driven circular RNA β-catenin (circβ-catenin) promotes colorectal cancer progression via miR-197-3p/CTNND1 regulatory axis. Br J Cancer 2024; 130:1517-1528. [PMID: 38459187 PMCID: PMC11058807 DOI: 10.1038/s41416-024-02612-y] [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: 08/21/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Circβ-catenin, our first reported circRNA, has been reported to mediate tumorigenesis in various cancers. However, its biological functions and underlying mechanisms in colorectal cancer (CRC) remain unknown. METHODS The qRT-PCR examination was used to detect the expression of circβ-catenin, miR-197-3p, and CTNND1 in cells and human tissues. Western blot was conducted to detect the protein expression levels. The biological function of circβ-catenin was verified by MTT, colony formation, wound healing, and transwell assays. The in vivo effects of circβ-catenin were verified by nude mice xenograft and metastasis models. The regulatory network of circβ-catenin/miR-197-3p/CTNND1 was confirmed via dual-luciferase reporter and RIP assays. RESULTS In the present study, circβ-catenin was found to promote CRC cell proliferation and metastasis in vitro and in vivo. Mechanistically, circβ-catenin served as miRNA decoy to directly bind to miR-197-3p, then antagonized the repression of the target gene CTNND1, and eventually promoted the malignant phenotype of CRC. More interestingly, the inverted repeated Alu pairs termed AluJb1/2 and AluY facilitated the biogenesis of circβ-catenin, which could be partially reversed by EIF4A3 binding to Alu element AluJb2. CONCLUSIONS Our findings illustrated a novel mechanism of circβ-catenin in modulating CRC tumorigenesis and metastasis, which provides a potential therapeutic target for CRC patients.
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Affiliation(s)
- Li-Qiang Deng
- Cancer center, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, 518000, China
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
- Research Institute, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, 518000, China
| | - Chuan-Jian Shi
- Cancer center, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, 518000, China
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
- Research Institute, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, 518000, China
| | - Shu-Ting Zhou
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Wei-Qiang Zeng
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Yan-Fang Xian
- School of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Yu-Yan Wang
- Cancer center, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, 518000, China
| | - Wei-Ming Fu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Han-Li Lin
- Research Institute, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, 518000, China.
| | - Wei Liu
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China.
| | - Jin-Fang Zhang
- Cancer center, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, 518000, China.
- Research Institute, Shenzhen Hospital (Futian) of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, 518000, China.
- Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China.
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2
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Ntasis VF, Guigó R. Studying relative RNA localization From nucleus to the cytosol. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583744. [PMID: 38559161 PMCID: PMC10979850 DOI: 10.1101/2024.03.06.583744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The precise coordination of important biological processes, such as differentiation and development, is highly dependent on the regulation of expression of the genetic information. The flow of the genetic information is tightly regulated on multiple levels. Among them, RNA export to cytosol is an essential step for the production of proteins in eukaryotic cells. Hence, estimating the relative concentration of RNA molecules of a given transcript species in the nucleus and in the cytosol is of major significance as it contributes to the understanding of the dynamics of RNA trafficking between the nucleus and the cytosol. The most efficient way to estimate the levels of RNA species genome-wide is through RNA sequencing (RNAseq). While RNAseq can be performed separately in the nucleus and in the cytosol, because measured transcript levels are relative to the total volume of RNA in these compartments, and because this volume is usually unknown, the transcript levels in the nucleus and in the cytosol cannot be directly compared. Here we show theoretically that if, in addition to nuclear and cytosolic RNA-seq, whole cell RNA-seq is also performed, then accurate estimations of the localization of transcripts can be obtained. Based on this, we designed a method that estimates, first the fraction of the total RNA volume in the cytosol (nucleus), and then, this fraction for every transcript. We evaluate our methodology on simulated data and nuclear and cytosolic single cell data available. Finally, we use our method to investigate the cellular localization of transcripts using bulk RNAseq data from the ENCODE project.
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Affiliation(s)
- Vasilis F. Ntasis
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
- Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
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3
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Xue W, Yang L, Chen C, Ashrafizadeh M, Tian Y, Sun R. Wnt/β-catenin-driven EMT regulation in human cancers. Cell Mol Life Sci 2024; 81:79. [PMID: 38334836 PMCID: PMC10857981 DOI: 10.1007/s00018-023-05099-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/09/2023] [Accepted: 12/20/2023] [Indexed: 02/10/2024]
Abstract
Metastasis accounts for 90% of cancer-related deaths among the patients. The transformation of epithelial cells into mesenchymal cells with molecular alterations can occur during epithelial-mesenchymal transition (EMT). The EMT mechanism accelerates the cancer metastasis and drug resistance ability in human cancers. Among the different regulators of EMT, Wnt/β-catenin axis has been emerged as a versatile modulator. Wnt is in active form in physiological condition due to the function of GSK-3β that destructs β-catenin, while ligand-receptor interaction impairs GSK-3β function to increase β-catenin stability and promote its nuclear transfer. Regarding the oncogenic function of Wnt/β-catenin, its upregulation occurs in human cancers and it can accelerate EMT-mediated metastasis and drug resistance. The stimulation of Wnt by binding Wnt ligands into Frizzled receptors can enhance β-catenin accumulation in cytoplasm that stimulates EMT and related genes upon nuclear translocation. Wnt/β-catenin/EMT axis has been implicated in augmenting metastasis of both solid and hematological tumors. The Wnt/EMT-mediated cancer metastasis promotes the malignant behavior of tumor cells, causing therapy resistance. The Wnt/β-catenin/EMT axis can be modulated by upstream mediators in which non-coding RNAs are main regulators. Moreover, pharmacological intervention, mainly using phytochemicals, suppresses Wnt/EMT axis in metastasis suppression.
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Affiliation(s)
- Wenhua Xue
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Lin Yang
- Department of Hepatobiliary Surgery, Xianyang Central Hospital, Xianyang, 712000, Shaanxi, China
| | - Chengxin Chen
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Milad Ashrafizadeh
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Yu Tian
- School of Public Health, Benedictine University, Lisle, USA.
| | - Ranran Sun
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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4
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Isa AI. Exploring signaling pathway crosstalk in glioma by mapping miRNA and WNT pathways: A review. Int J Biol Macromol 2024; 257:128722. [PMID: 38092099 DOI: 10.1016/j.ijbiomac.2023.128722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/26/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Glioma is a significant healthcare burden; nevertheless, the particular genetic regulatory mechanism underpinning its onset and progression is still unknown. Recent research has focused in large part on trying to determine the underlying molecular pathways that contribute to the malignancy of this disease because of the difficulties in treating it. Many tumors have been linked to changes in the expression of microRNAs (miRNAs). miRNAs play a critical role in cancer development by controlling a wide variety of targets and signaling cascades. A rising body of evidence emphasizes WNT pathway dysregulation in glioma, despite the fact that it is dysregulated in many malignancies. Here, we give a detailed analysis of the roles played by miRNAs in the WNT pathway by glioma. We also demonstrate how the WNT pathway cooperates with miRNAs to control a variety of functions, including cell proliferation, invasion, migration, and epithelial-mesenchymal transition.
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Affiliation(s)
- Adamu Imam Isa
- Department of Physiology, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia.
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5
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Feng X, Yang L, Liu X, Liu M, Liu L, Liu J, Luo J. Long non-coding RNA small nucleolar RNA host gene 29 drives chronic myeloid leukemia progression via microRNA-483-3p/Casitas B-lineage Lymphoma axis-mediated activation of the phosphoinositide 3-kinase/Akt pathway. Med Oncol 2024; 41:60. [PMID: 38252204 DOI: 10.1007/s12032-023-02287-0] [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: 04/17/2023] [Accepted: 12/13/2023] [Indexed: 01/23/2024]
Abstract
The aberrant expression of the long non-coding RNA (lncRNA) Small Nucleolar RNA Host Gene 29 (SNHG29) has been associated with various human cancers. However, the role of SNHG29 in chronic myeloid leukemia (CML) remains elusive. Therefore, this study aimed to investigate the function of SNHG29 in CML and unveil its potential underlying mechanisms. Herein, peripheral blood samples from 44 CML patients and 17 healthy subjects were collected. The expressions of SNHG29, microRNA-483-3p (miR-483-3p), and Casitas B-lineage Lymphoma (CBL) were measured using quantitative polymerase chain reaction (qPCR) or Western Blot. Cell viability, apoptosis, and cell cycle progression were evaluated using the Cell Counting Kit-8 assay, 5-ethynyl-2'-deoxyuridine incorporation, and flow cytometry, respectively. Western Blot analysis was employed to assess protein expressions related to cellular proliferation, apoptosis, and oncogenesis. RNA immunoprecipitation and dual-luciferase reporter assays were utilized to verify the interactions among SNHG29, miR-483-3p, and CBL. SNHG29 was significantly overexpressed in both blood samples of CML patients and CML cell lines. In CML, increased expression of SNHG29 was positively correlated with clinical staging, and patients with high SNHG29 expression had poorer survival outcomes. Functionally, knocking down SNHG29 effectively inhibited CML cell proliferation and promoted apoptosis. Mechanistically, SNHG29 acted as a competing endogenous RNA for miR-483-3p to modulate CBL expression, thereby activating the Phosphoinositide 3-Kinase/Akt signaling pathway and mediating CML progression. In summary, these findings reveal that SNHG29 promotes tumorigenesis in CML, offering a potential therapeutic strategy for CML treatment.
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Affiliation(s)
- XueFeng Feng
- Department of Second Ward of Hematology, The Second Hospital of Hebei Medical University, No. 215, Heping West Road, Shijiazhuang City, 050000, Hebei, China
| | - Lin Yang
- Department of Second Ward of Hematology, The Second Hospital of Hebei Medical University, No. 215, Heping West Road, Shijiazhuang City, 050000, Hebei, China
| | - Xiaojun Liu
- Department of Second Ward of Hematology, The Second Hospital of Hebei Medical University, No. 215, Heping West Road, Shijiazhuang City, 050000, Hebei, China
| | - Menghan Liu
- Department of Second Ward of Hematology, The Second Hospital of Hebei Medical University, No. 215, Heping West Road, Shijiazhuang City, 050000, Hebei, China
| | - Lu Liu
- Department of Second Ward of Hematology, The Second Hospital of Hebei Medical University, No. 215, Heping West Road, Shijiazhuang City, 050000, Hebei, China
| | - Jing Liu
- Department of Second Ward of Hematology, The Second Hospital of Hebei Medical University, No. 215, Heping West Road, Shijiazhuang City, 050000, Hebei, China
| | - JianMin Luo
- Department of Second Ward of Hematology, The Second Hospital of Hebei Medical University, No. 215, Heping West Road, Shijiazhuang City, 050000, Hebei, China.
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Yu D, Mei Y, Wang L, Zhao Y, Fan X, Liang D, Li L, Zhu J, Bi S, Wang X, Qi Z, Zhu L, Wang Y. Nano-seq analysis reveals different functional tendency between exosomes and microvesicles derived from hUMSC. Stem Cell Res Ther 2023; 14:272. [PMID: 37749641 PMCID: PMC10521478 DOI: 10.1186/s13287-023-03491-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/07/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Extracellular vesicles (EVs) from human umbilical cord mesenchymal stem cells (hUMSCs) are widely considered to be the best mediators for cell-free therapy. An understanding of their composition, especially RNA, is particularly important for the safe and precise application of EVs. Up to date, the knowledge of their RNA components is limited to NGS sequencing and cannot provide a comprehensive transcriptomic landscape, especially the long and full-length transcripts. Our study first focused on the transcriptomic profile of hUMSC-EVs based on nanopore sequencing. METHODS In this study, different EV subtypes (exosomes and microvesicles) derived from hUMSCs were isolated and identified by density gradient centrifugation. Subsequently, the realistic long transcriptomic profile in different subtypes of hUMSC-EVs was systematically compared by nanopore sequencing and bioinformatic analysis. RESULTS Abundant transcript variants were identified in EVs by nanopore sequencing, 69.34% of which transcripts were fragmented. A series of full-length and long transcripts was also observed and showed a significantly higher proportion of intact or near-complete transcripts in exosomes than that in microvesicles derived from hUMSCs. Although the composition of RNA biotypes transported by different EV subtypes was similar, the distribution of transcripts and genes revealed the inter-heterogeneity and intra-stability between exosomes and microvesicles. Further, 85 different expressed transcripts (56 genes) and 7 fusion genes were identified. Pathway enrichment analysis showed that upregulated-expressed genes in microvesicles were mainly enriched in multiple neurodegenerative diseases, while upregulated-expressed genes in exosomes were mainly enriched in neutrophil extracellular trap formation, suggesting different functional tendencies of EV subtypes. CONCLUSIONS This study provides a novel understanding of different types of hUMSC-EVs, which not only suggests different transcriptome sorting mechanisms between exosomes and microvesicles, but also shows that different EV subtypes from the same source have different physiological functions, suggesting distinct clinical application prospects.
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Affiliation(s)
- Dong Yu
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Shanghai, People's Republic of China
- Department of Stem Cell and Regeneration Medicine, Translational Medicine Research Center, Naval Medical University, Xiangyin Road 800, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Cell Engineering, Shanghai, People's Republic of China
| | - Yue Mei
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Shanghai, People's Republic of China
- Department of Stem Cell and Regeneration Medicine, Translational Medicine Research Center, Naval Medical University, Xiangyin Road 800, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Cell Engineering, Shanghai, People's Republic of China
| | - Ling Wang
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Shanghai, People's Republic of China
- Department of Stem Cell and Regeneration Medicine, Translational Medicine Research Center, Naval Medical University, Xiangyin Road 800, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Cell Engineering, Shanghai, People's Republic of China
| | - Yunpeng Zhao
- Department of Stem Cell and Regeneration Medicine, Translational Medicine Research Center, Naval Medical University, Xiangyin Road 800, Shanghai, People's Republic of China
- Department of Histology and Embryology, Basic Medicine Collage, Naval Medical University, Shanghai, People's Republic of China
| | - Xingfei Fan
- Department of Stem Cell and Regeneration Medicine, Translational Medicine Research Center, Naval Medical University, Xiangyin Road 800, Shanghai, People's Republic of China
- Department of Histology and Embryology, Basic Medicine Collage, Naval Medical University, Shanghai, People's Republic of China
| | - Dong Liang
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Shanghai, People's Republic of China
- Department of Stem Cell and Regeneration Medicine, Translational Medicine Research Center, Naval Medical University, Xiangyin Road 800, Shanghai, People's Republic of China
- Shanghai Key Laboratory of Cell Engineering, Shanghai, People's Republic of China
| | - Li Li
- Department of Histology and Embryology, Basic Medicine Collage, Naval Medical University, Shanghai, People's Republic of China
| | - Jie Zhu
- Department of Plastic and Reconstructive Surgery, Secondary Affiliated Hospital of Naval Medical University, Shanghai, People's Republic of China
| | - Sisi Bi
- Medical College of Guangxi University, Nanning, People's Republic of China
| | - Xue Wang
- Medical College of Guangxi University, Nanning, People's Republic of China
| | - Zhongquan Qi
- Medical College of Guangxi University, Nanning, People's Republic of China
| | - Lie Zhu
- Department of Plastic and Reconstructive Surgery, Secondary Affiliated Hospital of Naval Medical University, Shanghai, People's Republic of China
| | - Yue Wang
- Department of Stem Cell and Regeneration Medicine, Translational Medicine Research Center, Naval Medical University, Xiangyin Road 800, Shanghai, People's Republic of China.
- Department of Histology and Embryology, Basic Medicine Collage, Naval Medical University, Shanghai, People's Republic of China.
- Shanghai Key Laboratory of Cell Engineering, Shanghai, People's Republic of China.
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, People's Republic of China.
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de Almeida MC, Felix JDS, Lopes MFDS, de Athayde FRF, Troiano JA, Scaramele NF, Furlan ADO, Lopes FL. Co-expression analysis of lncRNA and mRNA suggests a role for ncRNA-mediated regulation of host-parasite interactions in primary skin lesions of patients with American tegumentary leishmaniasis. Acta Trop 2023:106966. [PMID: 37302689 DOI: 10.1016/j.actatropica.2023.106966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/25/2023] [Accepted: 06/08/2023] [Indexed: 06/13/2023]
Abstract
Leishmaniasis, caused by different Leishmania species, manifests as cutaneous or visceral forms. In the American continent, the cutaneous form is called American tegumentary leishmaniasis (ATL) and is primarily caused by Leishmania (Viannia) braziliensis. Mucosal leishmaniasis (ML), the most severe form of ATL, arises in approximately 20% of patients from a primary cutaneous lesion. Evidence indicates changes in overall expression patterns of mRNAs and lncRNAs of the host in response to Leishmania infection, with the parasite capable of modulating host immune response, which may contribute to disease progression. We evaluated whether the co-expression of lncRNAs and their putative target mRNAs in primary cutaneous lesions of patients with ATL could be associated with the development of ML. Previously available public RNA-Seq data from primary skin lesions of patients infected with L. braziliensis was employed. We identified 579 mRNAs and 46 lncRNAs differentially expressed in the primary lesion that subsequently progressed to mucosal disease. Co-expression analysis revealed 1,324 significantly correlated lncRNA-mRNA pairs. Among these, we highlight the positive correlation and trans-action between lncRNA SNHG29 and mRNA S100A8, both upregulated in the ML group. S100A8 and its heterodimeric partner S100A9 form a pro-inflammatory complex expressed by immune cells and seems to participate in host innate immune response processes of infection. These findings expand the knowledge of the Leishmania-host interaction and indicate that the expression of lncRNAs in the primary cutaneous lesion could regulate mRNAs and play roles in disease progression.
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Affiliation(s)
- Mariana Cordeiro de Almeida
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | - Juliana de Souza Felix
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | - Maria Fernanda da Silva Lopes
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | - Flávia Regina Florencio de Athayde
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | - Jéssica Antonini Troiano
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | - Natália Francisco Scaramele
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | - Amanda de Oliveira Furlan
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | - Flavia Lombardi Lopes
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil.
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Ravindran F, Jain A, Desai S, Menon N, Srivastava K, Bawa PS, Sateesh K, Srivatsa N, Raghunath SK, Srinivasan S, Choudhary B. Whole-exome sequencing of Indian prostate cancer reveals a novel therapeutic target: POLQ. J Cancer Res Clin Oncol 2023; 149:2451-2462. [PMID: 35737091 DOI: 10.1007/s00432-022-04111-0] [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: 04/21/2022] [Accepted: 06/03/2022] [Indexed: 11/25/2022]
Abstract
PURPOSE Prostate cancer is the second most common cancer diagnosed worldwide and the third most common cancer among men in India. This study's objective was to characterise the mutational landscape of Indian prostate cancer using whole-exome sequencing to identify population-specific polymorphisms. METHODS Whole-exome sequencing was performed of 58 treatment-naive primary prostate tumors of Indian origin. Multiple computational and statistical analyses were used to profile the known common mutations, other deleterious mutations, driver genes, prognostic biomarkers, and gene signatures unique to each clinical parameter. Cox analysis was performed to validate survival-associated genes. McNemar test identified genes significant to recurrence and receiver-operating characteristic (ROC) analysis was conducted to determine its accuracy. OncodriveCLUSTL algorithm was used to deduce driver genes. The druggable target identified was modeled with its known inhibitor using Autodock. RESULTS TP53 was the most commonly mutated gene in our cohort. Three novel deleterious variants unique to the Indian prostate cancer subtype were identified: POLQ, FTHL17, and OR8G1. COX regression analysis identified ACSM5, a mitochondrial gene responsible for survival. CYLC1 gene, which encodes for sperm head cytoskeletal protein, was identified as an unfavorable prognostic biomarker indicative of recurrence. The novel POLQ mutant, also identified as a driver gene, was evaluated as the druggable target in this study. POLQ, a DNA repair enzyme implicated in various cancer types, is overexpressed and is associated with a poor prognosis. The mutant POLQ was subjected to structural analysis and modeled with its known inhibitor novobiocin resulting in decreased binding efficiency necessitating the development of a better drug. CONCLUSION In this pilot study, the molecular profiling using multiple computational and statistical analyses revealed distinct polymorphisms in the Indian prostate cancer cohort. The mutational signatures identified provide a valuable resource for prognostic stratification and targeted treatment strategies for Indian prostate cancer patients. The DNA repair enzyme, POLQ, was identified as the druggable target in this study.
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Affiliation(s)
- Febina Ravindran
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore, Karnataka, India
| | - Anika Jain
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore, Karnataka, India
| | - Sagar Desai
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore, Karnataka, India
- Manipal Academy of Higher Education, Manipal, India
| | - Navjoth Menon
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore, Karnataka, India
| | - Kriti Srivastava
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore, Karnataka, India
| | - Pushpinder Singh Bawa
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore, Karnataka, India
| | - K Sateesh
- Healthcare Global Enterprises Ltd, Cancer Centre, Bangalore, India
| | - N Srivatsa
- Healthcare Global Enterprises Ltd, Cancer Centre, Bangalore, India
| | - S K Raghunath
- Healthcare Global Enterprises Ltd, Cancer Centre, Bangalore, India
| | - Subhashini Srinivasan
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore, Karnataka, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore, Karnataka, India.
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9
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Cheng X, Li Z, Shan R, Li Z, Wang S, Zhao W, Zhang H, Chao L, Peng J, Fei T, Li W. Modeling CRISPR-Cas13d on-target and off-target effects using machine learning approaches. Nat Commun 2023; 14:752. [PMID: 36765063 PMCID: PMC9912244 DOI: 10.1038/s41467-023-36316-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/26/2023] [Indexed: 02/12/2023] Open
Abstract
A major challenge in the application of the CRISPR-Cas13d system is to accurately predict its guide-dependent on-target and off-target effect. Here, we perform CRISPR-Cas13d proliferation screens and design a deep learning model, named DeepCas13, to predict the on-target activity from guide sequences and secondary structures. DeepCas13 outperforms existing methods to predict the efficiency of guides targeting both protein-coding and non-coding RNAs. Guides targeting non-essential genes display off-target viability effects, which are closely related to their on-target efficiencies. Choosing proper negative control guides during normalization mitigates the associated false positives in proliferation screens. We apply DeepCas13 to the guides targeting lncRNAs, and identify lncRNAs that affect cell viability and proliferation in multiple cell lines. The higher prediction accuracy of DeepCas13 over existing methods is extensively confirmed via a secondary CRISPR-Cas13d screen and quantitative RT-PCR experiments. DeepCas13 is freely accessible via http://deepcas13.weililab.org .
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Affiliation(s)
- Xiaolong Cheng
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, 20010, USA
- Department of Genomics and Precision Medicine, George Washington University, Washington, DC, 20010, USA
| | - Zexu Li
- National Frontiers Science Center for Industrial Intelligence and Systems Optimization, Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang, 110819, China
| | - Ruocheng Shan
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, 20010, USA
- Department of Computer Science, George Washington University, Washington, DC, 20052, USA
| | - Zihan Li
- National Frontiers Science Center for Industrial Intelligence and Systems Optimization, Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang, 110819, China
| | - Shengnan Wang
- National Frontiers Science Center for Industrial Intelligence and Systems Optimization, Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang, 110819, China
| | - Wenchang Zhao
- National Frontiers Science Center for Industrial Intelligence and Systems Optimization, Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang, 110819, China
| | - Han Zhang
- National Frontiers Science Center for Industrial Intelligence and Systems Optimization, Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang, 110819, China
| | - Lumen Chao
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, 20010, USA
- Department of Genomics and Precision Medicine, George Washington University, Washington, DC, 20010, USA
| | - Jian Peng
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Teng Fei
- National Frontiers Science Center for Industrial Intelligence and Systems Optimization, Key Laboratory of Bioresource Research and Development of Liaoning Province, College of Life and Health Sciences, Northeastern University, Shenyang, 110819, China.
| | - Wei Li
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, 20010, USA.
- Department of Genomics and Precision Medicine, George Washington University, Washington, DC, 20010, USA.
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10
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Nian Y, Li X, Ma J, Gao T, Liu D. Circ_0075960 targets the miR-202-5p/CTNND1 axis to promote the growth and migration of endometrial carcinoma cells via regulating Wnt/β-catenin signaling activity. J Gynecol Oncol 2023; 34:e11. [PMID: 36424704 PMCID: PMC9807357 DOI: 10.3802/jgo.2023.34.e11] [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: 04/08/2022] [Revised: 07/24/2022] [Accepted: 08/29/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Endometrial carcinoma (EC) is one of the most common malignant tumors of the female reproductive tract, involving multiple molecular alterations. Circular RNA (circRNA) dysregulation is frequently observed in EC tissues, suggesting the involvement of circRNA in EC development. We aimed to investigate the role of circ_0075960 in EC. METHODS Real-time quantitative polymerase chain reaction (RT-qPCR) and western blot assays were applied for expression analysis. CCK-8, EdU, colony formation, flow cytometry and wound healing assays were employed for functional analysis. The predicted binding relationship between miR-202-5p and circ_0075960 or CTNND1 was validated by dual-luciferase reporter experiment. In vivo animal models were constructed in nude mice to verify the role of circ_0075960 in tumor growth. RESULTS Circ_0075960 and CTNND1 were upregulated, while miR-202-5p was downregulated in EC. Knockdown of circ_0075960 induced EC cell apoptosis, suppressed cell proliferation and migration, and repressed tumor growth in animal models. MiR-202-5p was targeted by circ_0075960 and it directly bound to CTNND1 3'UTR. The inhibition of circ_0075960 knockdown or miR-202-5p enrichment on EC cell proliferation and migration was reversed by miR-202-5p depletion or CTNND1 overexpression, respectively. Circ_0075960 targeted miR-202-5p to positively regulate CTNND1 expression. Moreover, circ_0075960 knockdown weakened the activity of Wnt/β-catenin signaling via targeting the miR-202-5p/CTNND1 axis. CONCLUSION Circ_0075960 targets the miR-202-5p/CTNND1 axis to modulate Wnt/β-catenin signaling activity, thus contributing to the malignant development of EC.
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Affiliation(s)
- Yan Nian
- Department of Gynecology, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Xiaorong Li
- Center for Reproductive Medicine, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Jingwen Ma
- Department of Gynecology, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Ting Gao
- Medical College, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Dan Liu
- Department of Gynecology, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China.
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11
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Wei XY, Zhang TQ, Suo R, Qu YY, Chen Y, Zhu YL. Long non-coding RNA RPL34-AS1 ameliorates oxygen-glucose deprivation-induced neuronal injury via modulating miR-223-3p/IGF1R axis. Hum Cell 2022; 35:1785-1796. [PMID: 36006565 DOI: 10.1007/s13577-022-00773-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022]
Abstract
Ribosomal protein L34-antisense RNA 1 (RPL34-AS1), one of the long non-coding RNAs (lncRNAs), plays an important function in regulating diverse human malignant tumors. Nevertheless, the functions of RPL34-AS1 in ischemic stroke remain unclear. The present work focused on determining the candidate targets of RPL34-AS1 and its related mechanism in ischemic injury. The oxygen-glucose deprivation (OGD/R) in vitro cell model and middle cerebral artery occlusion (MCAO) in vivo rat model were utilized to simulate the pathological process of ischemic stroke. Additionally, the CCK8, WB (detecting Bcl-2 and Bax protein levels), and caspase-3 activity assays were done to investigate the anti-apoptotic functions of RPL34-AS1. The relationship among RPL34-AS1, insulin-like growth factor 1 receptor (IGF1R), and microRNA-223-3p (miR-223-3p) was determined through luciferase reporter assay. In this study, RPL34-AS1 expression was reduced in patients suffering from ischemic stroke. The overexpression of RPL34-AS1 reduced ischemic brain damage. However, the cell viability and glucose uptake were increased, and the apoptosis rate was decreased in the OGD/R-induced neurons. Further, miR-223-3p resulted in the decreased cell viability and glucose uptake and the increased cell apoptosis to cause ischemic brain damage. Besides, the neuroprotective effects of RPL34-AS1 on OGD/R injury were partly reversed by miR-223-3p. Mechanistically, lncRNA RPL34-AS1 could function as the competing endogenous RNA (ceRNA) of miR-223-3p to regulate IGF1R. Collectively, our study demonstrated that lncRNA RPL34-AS1 attenuated OGD/R-induced neuronal injury by mediating miR-223-3p/IGF1R axis. This discovery might serve as the candidate therapeutic target for ischemic stroke.
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Affiliation(s)
- Xin-Ya Wei
- Department of Neurology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, People's Republic of China.,Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150001, Heilongjiang, People's Republic of China
| | - Tian-Qi Zhang
- Department of Neurology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, People's Republic of China
| | - Rui Suo
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150001, Heilongjiang, People's Republic of China
| | - You-Yang Qu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150001, Heilongjiang, People's Republic of China
| | - Yan Chen
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150001, Heilongjiang, People's Republic of China
| | - Yu-Lan Zhu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, No. 246, Xuefu Road, Nangang District, Harbin, 150001, Heilongjiang, People's Republic of China.
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12
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Zhang Y, Shi J, Luo J, Liu C, Zhu L. Regulatory mechanisms and potential medical applications of HNF1A-AS1 in cancers. Am J Transl Res 2022; 14:4154-4168. [PMID: 35836869 PMCID: PMC9274608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Long noncoding RNAs (lncRNAs) are defined as a class of non-protein-coding RNAs that are longer than 200 nucleotides. Previous studies have shown that lncRNAs play a vital role in the progression of multiple diseases, which highlights their potential for medical applications. The lncRNA hepatocyte nuclear factor 1 homeobox A (HNF1A) antisense RNA 1 (HNF1A-AS1) is known to be abnormally expressed in multiple cancers. HNF1A-AS1 exerts its oncogenic roles through a variety of molecular mechanisms. Moreover, aberrant HNF1A-AS1 expression is associated with diverse clinical features in cancer patients. Therefore, HNF1A-AS1 is a promising biomarker for tumor diagnosis and prognosis and thus a potential candidate for tumor therapy. This review summarizes current studies on the role and the underlying mechanisms of HNF1A-AS1 various cancer types, including gastric cancer, liver cancer, glioma, lung cancer, colorectal cancer, breast cancer, bladder cancer, osteosarcoma, esophageal adenocarcinoma, hemangioma, oral squamous cell carcinoma, laryngeal squamous cell carcinoma, cervical cancer, as well as gastroenteropancreatic neuroendocrine neoplasms. We also describe the diagnostic, prognostic, and therapeutic value of HNF1A-AS1 for multiple cancer patients.
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Affiliation(s)
- Yang Zhang
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
| | - Jiang Shi
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
| | - Junfang Luo
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
| | - Cong Liu
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
| | - Lixu Zhu
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
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13
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Transcriptome analysis of long noncoding RNAs reveals their potential roles in anthracycline-induced cardiotoxicity. Noncoding RNA Res 2022; 7:106-113. [PMID: 35415316 PMCID: PMC8967700 DOI: 10.1016/j.ncrna.2022.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/07/2022] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
Aims Anthracyclines (ANTs) are essential chemotherapeutic agents; however, their adverse effects can lead to heart failure in cancer survivors. While long non-coding RNAs (lncRNAs) have become new players in cellular processes, there is limited knowledge on lncRNA expression related to anthracyclines-induced cardiotoxicity. This study investigates the lncRNA profiles in human cardiac microtissues exposed to 3 popular ANTs, namely doxorubicin, epirubicin, and idarubicin, as well as in heart biopsies from ANT-treated patients. Methods and results The in vitro microtissues were exposed to each ANT at 2 doses over 2 weeks; the transcriptome data was collected at 7 time points. The human biopsies were collected from heart failure patients who underwent ANT treatment and control subjects. Over 100 lncRNAs were differentially expressed in each in vitro ANT treatment condition compared to control samples; 16 of them were differentially expressed across all ANT-treated conditions. The lncRNA databases and literature revealed insight on how these lncRNAs relate to heart failure and cellular functions. For instance, H19 and RMRP are involved in heart failure progression, while BDNF-AS is a cardiomyocyte damage-associated gene; SNHG7 is a cardiac hypertrophy regulator. PCAT19 can promote the miR‐182/PDK4 axis and modulate p53 expression, whereas SNHG29 can regulate the Wnt/β-catenin signaling pathway via the miR-223–3p/CTNND1 axis. Other lncRNAs, which were only differentially expressed in particular ANT-treated conditions, are also involved in cardiomyocyte damage and heart failure disease. The alterations of these lncRNA expressions in the in vitro cardiac tissue were also affirmed by similar changes in the human biopsies. Conclusion This study revealed several lncRNAs that can be potential biomarkers or targets for further ANT-induced cardiotoxicity investigation, according to the transcriptome in both human cardiac microtissues expose to ANTs as well as in heart biopies form ANT-treated patients. Especially, H19 lncRNA showed its contribution to on-target toxicity, in which it is involved in both chemoresistance and cardiotoxic mechanism.
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14
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Regulatory interplay between microRNAs and WNT pathway in glioma. Biomed Pharmacother 2021; 143:112187. [PMID: 34560532 DOI: 10.1016/j.biopha.2021.112187] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/01/2021] [Accepted: 09/10/2021] [Indexed: 12/17/2022] Open
Abstract
Glioma is one of the most common neoplasms of the central nervous system with a poor survival. Due to the obstacles in treating this disease, a part of recent studies mainly focuses on identifying the underlying molecular mechanisms that contribute to its malignancy. Altering microRNAs (miRNAs) expression pattern has been identified obviously in many cancers. Through regulating various targets and signaling pathways, miRNAs play a pivotal role in cancer progression. As one of the essential signaling pathways, WNT pathway is dysregulated in many cancers, and a growing body of evidence emphasis its dysregulation in glioma. Herein, we provide a comprehensive review of miRNAs involved in WNT pathway in glioma. Moreover, we show the interplay between miRNAs and WNT pathway in regulating different processes such as proliferation, invasion, migration, radio/chemotherapy resistance, and epithelial-mesenchymal-transition. Then, we introduce several drugs and treatments against glioma, which their effects are mediated through the interplay of WNT pathway and miRNAs.
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15
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Liu Y, Zhang H, Wang H, Du J, Dong P, Liu M, Lin Y. Long non-coding RNA DUXAP8 promotes the cell proliferation, migration, and invasion of papillary thyroid carcinoma via miR-223-3p mediated regulation of CXCR4. Bioengineered 2021; 12:496-506. [PMID: 33522355 PMCID: PMC8291844 DOI: 10.1080/21655979.2021.1882134] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Papillary thyroid carcinoma (PTC) is a differentiated type of thyroid malignancy with a high incidence. Long non-coding RNA (lncRNA) DUXAP8 has been reported to participate in the proliferation, migration, and invasion of several cancer types. However, its association with PTC has not yet been reported. The current study aimed to investigate the role of DUXAP8 in PTC and revealed the underlying mechanisms. The expression of DUXAP8 was knocked down in two PTC cell lines and the effects of DUXAP8 on the PTC biological behavior were examined by cell counting kit-8 (CCK-8), wound healing, and transwell invasion assays. Luciferase reporter assay was used to detect the binding activity between miR-223-3p and DUXAP8. We found that knockdown of DUXAP8 inhibited the proliferation, migration, and invasion of PTC cells. DUXAP8 could sponge miR-223-3p through the specific binding site. CXCR4 was a target of miR-223-3p. The malignant phenotypes of the PTC cells were suppressed by the over-expression of miR-223-3p. Moreover, miR-223-3p inhibition or CXCR4 over-expression partly restored the proliferation, migration, and invasion activities of DUXAP8-downregulated PTC cells. The results evidenced that DUXAP8 acted as an oncogene in PTC, these effects seemed to partly dependent on the miR-223-3p/CXCR4 axis.
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Affiliation(s)
- Yan Liu
- Department of Ultrasound, China-Japan Union Hospital of Jilin University , Changchun, People's Republic of China
| | - Hejia Zhang
- Department of Ultrasound, China-Japan Union Hospital of Jilin University , Changchun, People's Republic of China
| | - Hui Wang
- Department of Ultrasound, China-Japan Union Hospital of Jilin University , Changchun, People's Republic of China
| | - Jiarui Du
- Department of Ultrasound, China-Japan Union Hospital of Jilin University , Changchun, People's Republic of China
| | - Peng Dong
- Department of Ultrasound, China-Japan Union Hospital of Jilin University , Changchun, People's Republic of China
| | - Meihan Liu
- Department of Ultrasound, China-Japan Union Hospital of Jilin University , Changchun, People's Republic of China
| | - Yuanqiang Lin
- Department of Ultrasound, China-Japan Union Hospital of Jilin University , Changchun, People's Republic of China
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16
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He F, Yu J, Yang J, Wang S, Zhuang A, Shi H, Gu X, Xu X, Chai P, Jia R. m 6A RNA hypermethylation-induced BACE2 boosts intracellular calcium release and accelerates tumorigenesis of ocular melanoma. Mol Ther 2021; 29:2121-2133. [PMID: 33601055 DOI: 10.1016/j.ymthe.2021.02.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/22/2021] [Accepted: 02/10/2021] [Indexed: 12/11/2022] Open
Abstract
Ocular melanoma, including uveal melanoma (UM) and conjunctival melanoma (CM), is the most common and deadly eye cancer in adults. Both UM and CM originate from melanocytes and exhibit an aggressive growth pattern with high rates of metastasis and mortality. The integral membrane glycoprotein beta-secretase 2 (BACE2), an enzyme that cleaves amyloid precursor protein into amyloid beta peptide, has been reported to play a vital role in vertebrate pigmentation and metastatic melanoma. However, the role of BACE2 in ocular melanoma remains unclear. In this study, we showed that BACE2 was significantly upregulated in ocular melanoma, and inhibition of BACE2 significantly impaired tumor progression both in vitro and in vivo. Notably, we identified that transmembrane protein 38B (TMEM38B), whose expression was highly dependent on BACE2, modulated calcium release from endoplasmic reticulum (ER). Inhibition of the BACE2/TMEM38B axis could trigger exhaustion of intracellular calcium release and inhibit tumor progression. We further demonstrated that BACE2 presented an increased level of N6-methyladenosine (m6A) RNA methylation, which led to the upregulation of BACE2 mRNA. To our knowledge, this study provides a novel pattern of BACE2-mediated intracellular calcium release in ocular melanoma progression, and our findings suggest that m6A/BACE2/TMEM38b could be a potential therapeutic axis for ocular melanoma.
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Affiliation(s)
- Fanglin He
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200001, China
| | - Jie Yu
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200001, China
| | - Jie Yang
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200001, China
| | - Shaoyun Wang
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200001, China
| | - Ai Zhuang
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200001, China
| | - Hanhan Shi
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200001, China
| | - Xiang Gu
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200001, China
| | - Xiaofang Xu
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200001, China
| | - Peiwei Chai
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200001, China
| | - Renbing Jia
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200001, China.
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Zhao J, Song X, Xu T, Yang Q, Liu J, Jiang B, Wu J. Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer. Front Genet 2021; 11:607722. [PMID: 33519912 PMCID: PMC7839966 DOI: 10.3389/fgene.2020.607722] [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: 09/18/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022] Open
Abstract
Increasing lncRNA-associated competing triplets were found to play important roles in cancers. With the accumulation of high-throughput sequencing data in public databases, the size of available tumor samples is becoming larger and larger, which introduces new challenges to identify competing triplets. Here, we developed a novel method, called LncMiM, to detect the lncRNA–miRNA–mRNA competing triplets in ovarian cancer with tumor samples from the TCGA database. In LncMiM, non-linear correlation analysis is used to cover the problem of weak correlations between miRNA–target pairs, which is mainly due to the difference in the magnitude of the expression level. In addition, besides the miRNA, the impact of lncRNA and mRNA on the interactions in triplets is also considered to improve the identification sensitivity of LncMiM without reducing its accuracy. By using LncMiM, a total of 847 lncRNA-associated competing triplets were found. All the competing triplets form a miRNA–lncRNA pair centered regulatory network, in which ZFAS1, SNHG29, GAS5, AC112491.1, and AC099850.4 are the top five lncRNAs with most connections. The results of biological process and KEGG pathway enrichment analysis indicates that the competing triplets are mainly associated with cell division, cell proliferation, cell cycle, oocyte meiosis, oxidative phosphorylation, ribosome, and p53 signaling pathway. Through survival analysis, 107 potential prognostic biomarkers are found in the competing triplets, including FGD5-AS1, HCP5, HMGN4, TACC3, and so on. LncMiM is available at https://github.com/xiaofengsong/LncMiM.
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Affiliation(s)
- Jian Zhao
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Tianyi Xu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Qichang Yang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Jingjing Liu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Bin Jiang
- College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Jing Wu
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
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Caponnetto F, Dalla E, Mangoni D, Piazza S, Radovic S, Ius T, Skrap M, Di Loreto C, Beltrami AP, Manini I, Cesselli D. The miRNA Content of Exosomes Released from the Glioma Microenvironment Can Affect Malignant Progression. Biomedicines 2020; 8:biomedicines8120564. [PMID: 33287106 PMCID: PMC7761654 DOI: 10.3390/biomedicines8120564] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 12/13/2022] Open
Abstract
Low-grade gliomas (LGG) are infiltrative primary brain tumors that in 70% of the cases undergo anaplastic transformation, deeply affecting prognosis. However, the timing of progression is heterogeneous. Recently, the tumor microenvironment (TME) has gained much attention either as prognostic factor or therapeutic target. Through the release of extracellular vesicles, the TME contributes to tumor progression by transferring bioactive molecules such as microRNA. The aim of the study was to take advantage of glioma-associated stem cells (GASC), an in vitro model of the glioma microenvironment endowed with a prognostic significance, and their released exosomes, to investigate the possible role of exosome miRNAs in favoring the anaplastic transformation of LGG. Therefore, by deep sequencing, we analyzed and compared the miRNA profile of GASC and exosomes obtained from LGG patients characterized by different prognosis. Results showed that exosomes presented a different signature, when compared to their cellular counterpart and that, although sharing several miRNAs, exosomes of patients with a bad prognosis, selectively expressed some miRNAs possibly responsible for the more aggressive phenotype. These findings get insights into the value of TME and exosomes as potential biomarkers for precision medicine approaches aimed at improving LGG prognostic stratification and therapeutic strategies.
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Affiliation(s)
- Federica Caponnetto
- Department of Medicine, University of Udine, 33100 Udine, Italy; (E.D.); (C.D.L.); (A.P.B.); (D.C.)
- Correspondence: (F.C.); (I.M.); Tel.: +39-0432-559-412 (F.C. & I.M.)
| | - Emiliano Dalla
- Department of Medicine, University of Udine, 33100 Udine, Italy; (E.D.); (C.D.L.); (A.P.B.); (D.C.)
| | - Damiano Mangoni
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16163 Genova, Italy;
| | - Silvano Piazza
- International Center for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy;
| | | | - Tamara Ius
- Neurosurgery Unit, Department of Neurosciences, University Hospital of Udine, 33100 Udine, Italy; (T.I.); (M.S.)
| | - Miran Skrap
- Neurosurgery Unit, Department of Neurosciences, University Hospital of Udine, 33100 Udine, Italy; (T.I.); (M.S.)
| | - Carla Di Loreto
- Department of Medicine, University of Udine, 33100 Udine, Italy; (E.D.); (C.D.L.); (A.P.B.); (D.C.)
- Institute of Pathology, University Hospital of Udine, 33100 Udine, Italy
| | - Antonio Paolo Beltrami
- Department of Medicine, University of Udine, 33100 Udine, Italy; (E.D.); (C.D.L.); (A.P.B.); (D.C.)
| | - Ivana Manini
- Institute of Pathology, University Hospital of Udine, 33100 Udine, Italy
- Correspondence: (F.C.); (I.M.); Tel.: +39-0432-559-412 (F.C. & I.M.)
| | - Daniela Cesselli
- Department of Medicine, University of Udine, 33100 Udine, Italy; (E.D.); (C.D.L.); (A.P.B.); (D.C.)
- Institute of Pathology, University Hospital of Udine, 33100 Udine, Italy
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Jiang J, Hu H, Chen Q, Zhang Y, Chen W, Huang Q, Chen X, Li J, Zhong M. Long non-coding RNA SNHG29 regulates cell senescence via p53/p21 signaling in spontaneous preterm birth. Placenta 2020; 103:64-71. [PMID: 33080448 DOI: 10.1016/j.placenta.2020.10.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Spontaneous preterm birth affects>5-18% of pregnancies and causes infant morbidity and mortality. Long non-coding RNAs can regulate gene expression and have been associated with preterm birth. In this study, we investigated whether the long non-coding RNA SNHG29 was associated with spontaneous preterm birth. METHODS We collected the placentas from women who underwent preterm/full-term birth with/without labor. We determined the levels of expression of SNHG29 in the placental tissues using quantitative real-time polymerase chain reaction. We generated a senescence model by treating HTR8/SVneo cells with 200 μM H2O2 for 2 h. The degree of senescence induced in cells depleted of or overexpressing SNHG29 was determined by measuring senescence-associated gene expression and β-galactosidase activity. RESULTS SNHG29 was overexpressed in the placentas of women who delivered preterm with labor and in HTR8/SVneo cells treated with H2O2 (p < 0.05). The levels of mRNA of p53 and p21, protein levels of p53, phospho-p53, p21and phospho-p21, and β-galactosidase activity was decreased in HTR8/SVneo cells depleted of SNHG29, while the opposite trend was observed in HTR8/SVneo cells overexpressing SNHG29 (p < 0.05). We observed an increase in the expression of IL-8 and TNF-α in senescent HTR8/SVneo cells (p < 0.05). DISCUSSION SNHG29 was overexpressed in placentas from women who delivered preterm with labor compared to those in women who underwent preterm birth without labor and full-term birth with/without labor. High levels of SNHG29 enhanced senescence in vivo. The increase in pro-inflammatory cytokine expression and release by senescent cells may be pivotal to the pathophysiology of spontaneous preterm birth.
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Affiliation(s)
- Jiayi Jiang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangdong, China
| | - Haoyue Hu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangdong, China
| | - Qian Chen
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangdong, China
| | - Yi Zhang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangdong, China
| | - Wenqian Chen
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangdong, China
| | - Qiuyu Huang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangdong, China
| | - Xiaoli Chen
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangdong, China
| | - Jing Li
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangdong, China.
| | - Mei Zhong
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangdong, China.
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Long non-coding RNA LRRC75A-AS1 facilitates triple negative breast cancer cell proliferation and invasion via functioning as a ceRNA to modulate BAALC. Cell Death Dis 2020; 11:643. [PMID: 32811810 PMCID: PMC7434919 DOI: 10.1038/s41419-020-02821-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/22/2020] [Indexed: 12/14/2022]
Abstract
As a common female malignancy, triple-negative breast cancer (TNBC) is the most serious subtype in breast cancer (BC). BAALC binder of MAP3K1 and KLF4 (BAALC) is a common oncogene in acute myelocytic leukemia (AML). We sought to explore the role of BAALC in TNBC. In this study, BAALC was significantly upregulated in TNBC tissues and cells. Then, the results of functional assays disclosed that BAALC facilitated cell proliferation, invasion, and epithelial–mesenchymal transition (EMT) processes, but repressed cell apoptosis in TNBC. Next, miR-380–3p was identified as the upstream of BAALC in TNBC cells. Moreover, LRRC75A-AS1 (also named small nucleolar RNA host gene 29: SNHG29) was verified to act as the sponge of miR-380–3p to elevate BAALC expression in TNBC. Besides, LRRC75A-AS1 could negatively regulate miR-380–3p but positively regulate BAALC expression. Finally, rescue assays elucidated that LRRC75A-AS1 facilitated cell proliferation, invasion, and EMT processes in TNBC by targeting miR-380–3p/BAALC pathway. Taken together, our study revealed a novel ceRNA network of LRRC75A-AS1/miR-380–3p/BAALC in accelerating TNBC development, indicating new promising targets for TNBC treatment.
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21
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Huang C, Zhan JF, Chen YX, Xu CY, Chen Y. LncRNA-SNHG29 inhibits vascular smooth muscle cell calcification by downregulating miR-200b-3p to activate the α-Klotho/FGFR1/FGF23 axis. Cytokine 2020; 136:155243. [PMID: 32818704 DOI: 10.1016/j.cyto.2020.155243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Vascular calcification (VC) is characterized by mineral accumulation on the walls of arteries and veins, which is a pathological process commonly found in elderly individuals and patients with atherosclerosis, hypertension, and diabetes. Emerging evidence suggests that long non-coding RNAs (lncRNAs) play an important role in VC. However, the role of SNHG29 is less clear. METHODS The expression of SNHG29, miR-200b-3p, α-Klotho, FGFR1 and FGF23 in vascular smooth muscle cells (VSMCs) was quantified by qRT-PCR and western blot assays. β-GP was used to construct an in vitro calcification model, followed by MTT assay to detect cell viability. Calcification was determined by alizarin red S staining and quantified by calcification assay. ALP activity was investigated by ALP staining. The interactions among SNHG29, miR-200b-3p and α-Klotho were verified by luciferase assay. RESULTS In the in vitro calcification model, SNHG29 was downregulated, while miR-200b-3p was upregulated. SNHG29 overexpression and miR-200b-3p knockdown significantly suppressed osteoblast-related factors (RUNX2 and BMP2), accompanied by activation of the α-Klotho/FGFR1/FGF23 axis, further inhibiting the formation of calcified nodules. Moreover, miR-200b-3p overexpression and α-Klotho knockdown reversed the SNHG29 overexpression-induced inhibitory effects on calcified VSMCs. CONCLUSION Our study is the first to demonstrate that SNHG29 could inhibit VSMC calcification by downregulating miR-200b-3p to activate the α-Klotho/FGFR1/FGF23 axis, suggesting SNHG29 as a novel therapeutic target for VC-associated diseases.
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Affiliation(s)
- Chong Huang
- Department of Nephrology, the Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, PR China
| | - Jin-Feng Zhan
- Physical Examination Center of the Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, PR China
| | - Yan-Xia Chen
- Department of Nephrology, the Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, PR China
| | - Cheng-Yun Xu
- Department of Nephrology, the Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, PR China
| | - Yan Chen
- Department of Nephrology, the Second Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, PR China.
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Ren N, Jiang T, Wang C, Xie S, Xing Y, Piao D, Zhang T, Zhu Y. LncRNA ADAMTS9-AS2 inhibits gastric cancer (GC) development and sensitizes chemoresistant GC cells to cisplatin by regulating miR-223-3p/NLRP3 axis. Aging (Albany NY) 2020; 12:11025-11041. [PMID: 32516127 PMCID: PMC7346038 DOI: 10.18632/aging.103314] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 04/28/2020] [Indexed: 12/19/2022]
Abstract
The role of LncRNA ADAMTS9-AS2 in the regulation of chemoresistance of gastric cancer (GC) is largely unknown. Here we found that LncRNA ADAMTS9-AS2 was low-expressed in GC tissues and cells compared to their normal counterparts. In addition, LncRNA ADAMTS9-AS2 inhibited miR-223-3p expressions in GC cells by acting as competing endogenous RNA, and the levels of LncRNA ADAMTS9-AS2 and miR-223-3p showed negative correlations in GC tissues. Of note, overexpression of LncRNA ADAMTS9-AS2 inhibited GC cell viability and motility by sponging miR-223-3p. In addition, the levels of LncRNA ADAMTS9-AS2 were lower, and miR-223-3p was higher in cisplatin-resistant GC (CR-GC) cells than their parental cisplatin-sensitive GC (CS-GC) cells. LncRNA ADAMTS9-AS2 overexpression enhanced the cytotoxic effects of cisplatin on CR-GC cells, which were reversed by overexpressing miR-223-3p. Furthermore, LncRNA ADAMTS9-AS2 increased NLRP3 expressions by targeting miR-223-3p, and upregulation of LncRNA ADAMTS9-AS2 triggered pyroptotic cell death in cisplatin treated CR-GC cells by activating NLRP3 inflammasome through downregulating miR-223-3p. Finally, the promoting effects of LncRNA ADAMTS9-AS2 overexpression on CR-GC cell death were abrogated by pyroptosis inhibitor Necrosulfonamide (NSA). Collectively, LncRNA ADAMTS9-AS2 acted as a tumor suppressor and enhanced cisplatin sensitivity in GC cells by activating NLRP3 mediated pyroptotic cell death through sponging miR-223-3p.
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Affiliation(s)
- Niansheng Ren
- Department of Colorectal Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang, China
| | - Tao Jiang
- Department of Colorectal Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang, China
| | - Chengbo Wang
- Department of Colorectal Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang, China
| | - Shilin Xie
- Department of Colorectal Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang, China
| | - Yanwei Xing
- Department of Colorectal Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang, China
| | - Daxun Piao
- Department of Colorectal Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang, China
| | - Tiemin Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang, China
| | - Yuekun Zhu
- Department of Colorectal Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang, China
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