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Fariha A, Hami I, Tonmoy MIQ, Akter S, Al Reza H, Bahadur NM, Rahaman MM, Hossain MS. Cell cycle associated miRNAs as target and therapeutics in lung cancer treatment. Heliyon 2022; 8:e11081. [PMID: 36303933 PMCID: PMC9593298 DOI: 10.1016/j.heliyon.2022.e11081] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/17/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Lung cancer is the primary cause of cancer related deaths worldwide. Limited therapeutic options and resistance to existing drugs are the major hindrances to the clinical success of this cancer. In the past decade, several studies showed the role of microRNA (miRNA) driven cell cycle regulation in lung cancer progression. Therefore, these small nucleotide molecules could be utilized as promising tools in lung cancer therapy. In this review, we highlighted the recent advancements in lung cancer therapy using cell cycle linked miRNAs. By highlighting the roles of the specific cell cycle core regulators affiliated miRNAs in lung cancer, we further outlined how these miRNAs can be explored in early diagnosis and treatment strategies to prevent lung cancer. With the provided information from our review, more medical efforts can ensure a potential breakthrough in miRNA-based lung cancer therapy.
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Affiliation(s)
- Atqiya Fariha
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Ithmam Hami
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Shahana Akter
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Hasan Al Reza
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md. Mizanur Rahaman
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh,Corresponding author.
| | - Md Shahadat Hossain
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh,Corresponding author.
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52
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He J, Wu W. Comprehensive landscape and future perspectives of long noncoding RNAs (lncRNAs) in colorectal cancer (CRC): Based on a bibliometric analysis. Noncoding RNA Res 2022; 8:33-52. [PMID: 36311994 PMCID: PMC9582894 DOI: 10.1016/j.ncrna.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/03/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
This review aimed to use bibliometric analysis to sort out, analyze and summarize the knowledge foundation and hot topics in the field of long noncoding RNAs (lncRNAs) in colorectal cancer (CRC), and point out future trends to inspire related research and innovation. We used CiteSpace to analyze publication outputs, countries, institutions, authors, journals, references, and keywords. Knowledge foundations, hotspots, and future trends were then depicted. The overall research showed the trend of biomedical-oriented multidisciplinary. Much evidence indicates that lncRNA plays the role of oncogene or tumor suppressor in the occurrence and development of CRC. Besides, many lncRNAs have multiple mechanisms. lncRNAs and metastasis of CRC, lncRNAs and drug resistance of CRC, and the clinical application of lncRNAs in CRC are current research hotspots. Through insight into the development trend of lncRNAs in CRC, this study will help researchers extract hidden valuable information for further research.
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Affiliation(s)
- Jia He
- Faculty Affairs and Human Resources Management Department, Southwest Medical University, Luzhou, China
| | - Wenhan Wu
- Department of General Surgery (Gastrointestinal Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou, China,Corresponding author.
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WalyEldeen AA, El-Shorbagy HM, Hassaneen HM, Abdelhamid IA, Sabet S, Ibrahim SA. [1,2,4] Triazolo [3,4-a]isoquinoline chalcone derivative exhibits anticancer activity via induction of oxidative stress, DNA damage, and apoptosis in Ehrlich solid carcinoma-bearing mice. Naunyn Schmiedebergs Arch Pharmacol 2022; 395:1225-1238. [PMID: 35881165 PMCID: PMC9467967 DOI: 10.1007/s00210-022-02269-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 07/03/2022] [Indexed: 12/30/2022]
Abstract
Despite the advances made in cancer therapeutics, their adverse effects remain a major concern, putting safer therapeutic options in high demand. Since chalcones, a group of flavonoids and isoflavonoids, act as promising anticancer agents, we aimed to evaluate the in vivo anticancer activity of a synthetic isoquinoline chalcone (CHE) in a mice model with Ehrlich solid carcinoma. Our in vivo pilot experiments revealed that the maximum tolerated body weight-adjusted CHE dose was 428 mg/kg. Female BALB/c mice were inoculated with Ehrlich ascites carcinoma cells and randomly assigned to three different CHE doses administered intraperitoneally (IP; 107, 214, and 321 mg/kg) twice a week for two consecutive weeks. A group injected with doxorubicin (DOX; 4 mg/kg IP) was used as a positive control. We found that in CHE-treated groups: (1) tumor weight was significantly decreased; (2) the total antioxidant concentration was substantially depleted in tumor tissues, resulting in elevated oxidative stress and DNA damage evidenced through DNA fragmentation and comet assays; (3) pro-apoptotic genes p53 and Bax, assessed via qPCR, were significantly upregulated. Interestingly, CHE treatment reduced immunohistochemical staining of the proliferative marker ki67, whereas BAX was increased. Notably, histopathological examination indicated that unlike DOX, CHE treatment had minimal toxicity on the liver and kidney. In conclusion, CHE exerts antitumor activity via induction of oxidative stress and DNA damage that lead to apoptosis, making CHE a promising candidate for solid tumor therapy.
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Affiliation(s)
| | - Haidan M El-Shorbagy
- Zoology Department, Faculty of Science, Cairo University, Giza, 12613, Egypt
- Faculty of Biotechnology, October University for Modern Science and Art (MSA), 6th October, Cairo, Egypt
| | - Hamdi M Hassaneen
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Ismail A Abdelhamid
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Salwa Sabet
- Zoology Department, Faculty of Science, Cairo University, Giza, 12613, Egypt
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54
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Bakrim S, Benkhaira N, Bourais I, Benali T, Lee LH, El Omari N, Sheikh RA, Goh KW, Ming LC, Bouyahya A. Health Benefits and Pharmacological Properties of Stigmasterol. Antioxidants (Basel) 2022; 11:1912. [PMID: 36290632 PMCID: PMC9598710 DOI: 10.3390/antiox11101912] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/17/2022] [Accepted: 09/21/2022] [Indexed: 07/30/2023] Open
Abstract
Stigmasterol is an unsaturated phytosterol belonging to the class of tetracyclic triterpenes. It is one of the most common plant sterols, found in a variety of natural sources, including vegetable fats or oils from many plants. Currently, stigmasterol has been examined via in vitro and in vivo assays and molecular docking for its various biological activities on different metabolic disorders. The findings indicate potent pharmacological effects such as anticancer, anti-osteoarthritis, anti-inflammatory, anti-diabetic, immunomodulatory, antiparasitic, antifungal, antibacterial, antioxidant, and neuroprotective properties. Indeed, stigmasterol from plants and algae is a promising molecule in the development of drugs for cancer therapy by triggering intracellular signaling pathways in numerous cancers. It acts on the Akt/mTOR and JAK/STAT pathways in ovarian and gastric cancers. In addition, stigmasterol markedly disrupted angiogenesis in human cholangiocarcinoma by tumor necrosis factor-α (TNF-α) and vascular endothelial growth factor receptor-2 (VEGFR-2) signaling down-regulation. The association of stigmasterol and sorafenib promoted caspase-3 activity and down-regulated levels of the anti-apoptotic protein Bcl-2 in breast cancer. Antioxidant activities ensuring lipid peroxidation and DNA damage lowering conferred to stigmasterol chemoprotective activities in skin cancer. Reactive oxygen species (ROS) regulation also contributes to the neuroprotective effects of stigmasterol, as well as dopamine depletion and acetylcholinesterase inhibition. The anti-inflammatory properties of phytosterols involve the production of anti-inflammatory cytokines, the decrease in inflammatory mediator release, and the inhibition of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2). Stigmasterol exerts anti-diabetic effects by reducing fasting glucose, serum insulin levels, and oral glucose tolerance. Other findings showed the antiparasitic activities of this molecule against certain strains of parasites such as Trypanosoma congolense (in vivo) and on promastigotes and amastigotes of the Leishmania major (in vitro). Some stigmasterol-rich plants were able to inhibit Candida albicans, virusei, and tropicalis at low doses. Accordingly, this review outlines key insights into the pharmacological abilities of stigmasterol and the specific mechanisms of action underlying some of these effects. Additionally, further investigation regarding pharmacodynamics, pharmacokinetics, and toxicology is recommended.
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Affiliation(s)
- Saad Bakrim
- Molecular Engineering, Biotechnologies and Innovation Team, Geo-Bio-Environment Engineering and Innovation Laboratory, Polydisciplinary Faculty of Taroudant, Ibn Zohr University, Agadir 80000, Morocco
| | - Nesrine Benkhaira
- Laboratory of Microbial Biotechnology and Bioactive Molecules, Department of Biology, Faculty of Sciences and Techniques, University Sidi Mohamed Ben Abdellah, Fez 1975, Morocco
| | - Ilhame Bourais
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat 10106, Morocco
| | - Taoufiq Benali
- Environment and Health Team, Polydisciplinary Faculty of Safi, Cadi Ayyad University, Sidi Bouzid B.P. 4162, Morocco
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia
| | - Nasreddine El Omari
- Laboratory of Histology, Embryology, and Cytogenetic, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat 10100, Morocco
| | - Ryan A. Sheikh
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Khang Wen Goh
- Faculty of Data Science and Information Technology, INTI International University, Nilai 71800, Malaysia
| | - Long Chiau Ming
- PAP Rashidah Sa’adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong BE1410, Brunei
| | - Abdelhakim Bouyahya
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat 10106, Morocco
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Guardiola S, Sánchez-Navarro M, Rosell R, Giralt E, Codony-Servat J. Anti-EGF nanobodies enhance the antitumoral effect of osimertinib and overcome resistance in non-small cell lung cancer (NSCLC) cellular models. Med Oncol 2022; 39:195. [PMID: 36071367 DOI: 10.1007/s12032-022-01800-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/15/2022] [Indexed: 10/14/2022]
Abstract
Osimertinib is a third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) that is effective against the EGFR T790M mutation in patients with advanced non-small-cell lung cancer (NSCLC). However, acquired resistance appears invariably due to several mechanisms. The strategy of using EGF-targeted nanobodies (Nbs) to block the initial step of the EGFR pathway constitutes a new research area. Nbs offer several advantages compared to traditional mAbs, such as their reduced size, increased stability, and tissue penetration, which provide key advantages for targeting soluble tumoral growth factors. In this study we investigated the efficacy of anti-EGF Nbs to reduce Osimertinib resistance. Two anti-EGF Nbs, generated in our laboratory, were shown to inhibit cell viability and colony formation in PC9 and PC9-derived osimertinib-resistant cell lines. The combination of these Nbs with osimertinib improved the antitumor efficacy of this EGFR-TKI in cell viability and colony formation experiments. In a mechanistic study of the EGFR pathway, the combination treatment dampened the activation of downstream proteins such as Akt and Erk1/2 MAP kinases. In addition, it increased cellular apoptosis and decreased the expression of Hes1, a cancer stem cell marker involved in metastasis and osimertinib resistance. We conclude that the addition of anti-EGF nanobodies enhances the antitumor properties of osimertinib, thus representing a potentially effective strategy for NSCLC patients.
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56
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Brito S, Heo H, Cha B, Lee SH, Chae S, Lee MG, Kwak BM, Bin BH. A systematic exploration reveals the potential of spermidine for hypopigmentation treatment through the stabilization of melanogenesis-associated proteins. Sci Rep 2022; 12:14478. [PMID: 36008447 DOI: 10.1038/s41598-022-18629-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/16/2022] [Indexed: 11/08/2022] Open
Abstract
Spermidine (SPD), a polyamine naturally present in living organisms, is known to prolong the lifespan of animals. In this study, the role of SPD in melanogenesis was investigated, showing potential as a pigmenting agent. SPD treatment increased melanin production in melanocytes in a dose dependent manner. Computational analysis with RNA-sequencing data revealed the alteration of protein degradation by SPD treatment without changes in the expressions of melanogenesis-related genes. Indeed, SPD treatment significantly increased the stabilities of tyrosinase-related protein (TRP)-1 and -2 while inhibiting ubiquitination, which was confirmed by treatment of proteasome inhibitor MG132. Inhibition of protein synthesis by cycloheximide (CHX) showed that SPD treatment increased the resistance of TRP-1 and TRP-2 to protein degradation. To identify the proteins involved in SPD transportation in melanocytes, the expression of several solute carrier (SLC) membrane transporters was assessed and, among 27 transporter genes, SLC3A2, SLC7A1, SLC18B1, and SLC22A18 were highly expressed, implying they are putative SPD transporters in melanocytes. Furthermore, SLC7A1 and SLC22A18 were downregulated by SPD treatment, indicating their active involvement in polyamine homeostasis. Finally, we applied SPD to a human skin equivalent and observed elevated melanin production. Our results identify SPD as a potential natural product to alleviate hypopigmentation.
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Ozgiray E, Sogutlu F, Biray Avci C. Chk1/2 inhibitor AZD7762 enhances the susceptibility of IDH-mutant brain cancer cells to temozolomide. Med Oncol 2022; 39:166. [PMID: 35972603 DOI: 10.1007/s12032-022-01769-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/13/2022] [Indexed: 11/28/2022]
Abstract
The IDH mutation initially exhibits chemosensitive properties, progression-free survival cannot be achieved in the later grades, and malignant transformation occurs as a result of TMZ-induced hypermutation profile and adaptation to this profile. In this study, we evaluated the potential of the combination of TMZ and AZD7762 at molecular level, to increase the anticancer activity of TMZ in IDH-mutant U87-mg cells. We used the WST-1 test to evaluate cytotoxic effect of TMZ and AZD7762 combination with dose-effect and isobologram curves. The effects of the inhibitory and effective concentrations of the combination on apoptosis, cell cycle and γ-H2AX phosphorylation were analyzed with flow cytometry. The expression of genes responsible for the DNA damage response was analyzed with qRT-PCR. The combination showed a synergistic effect with high dose reduction index. Single and combined administrations of TMZ and AZD7762 increased in G2/M arrest from 24 to 48 h, and cells in the G2/M phase shifted towards octaploidy at 72 h. While no double-strand breaks were detected after TMZ treatment, AZD7762 and combination treatments caused a significant increase in γ-H2AX phosphorylation and increased apoptotic stimulation towards 72 h although TMZ did not cause apoptotic effect in IDH-mutant U87-mg cells. The genes controlling the apoptosis were determined to be upregulated in all three groups, and genes regarding cell cycle checkpoints were downregulated. Targeting Chk1/2 with AZD7762 simultaneously with TMZ may be a potential therapeutic strategy for both increasing the sensitivity of IDH-mutant glioma cells to TMZ and reducing the dose of TMZ. In IDH-mutant glioma cells, AZD7762, the Chk1/2 inhibitor, can increase the efficacy of Temozolomide by (i) increasing mitotic chaos, and (ii) inhibiting double-strand break repair, (iii) thereby inducing cell death.
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Affiliation(s)
- Erkin Ozgiray
- Department of Neurosurgery, Medicine Faculty, Ege University, Izmir, Turkey
| | - Fatma Sogutlu
- Department of Medical Biology, Medicine Faculty, Ege University, Izmir, Turkey
| | - Cigir Biray Avci
- Department of Medical Biology, Medicine Faculty, Ege University, Izmir, Turkey.
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58
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Zhang L, Tian R, Wang K. NEAT1 promotes keratinocyte migration and proliferation during wound healing by regulating miR-26a-5p/LGR4 axis. Mol Cell Toxicol 2022. [DOI: 10.1007/s13273-022-00275-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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59
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Lee S, Osmanbeyoglu HU. Chromatin accessibility landscape and active transcription factors in primary human invasive lobular and ductal breast carcinomas. Breast Cancer Res 2022; 24:54. [PMID: 35906698 PMCID: PMC9338552 DOI: 10.1186/s13058-022-01550-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/25/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Invasive lobular breast carcinoma (ILC), the second most prevalent histological subtype of breast cancer, exhibits unique molecular features compared with the more common invasive ductal carcinoma (IDC). While genomic and transcriptomic features of ILC and IDC have been characterized, genome-wide chromatin accessibility pattern differences between ILC and IDC remain largely unexplored. METHODS Here, we characterized tumor-intrinsic chromatin accessibility differences between ILC and IDC using primary tumors from The Cancer Genome Atlas (TCGA) breast cancer assay for transposase-accessible chromatin with sequencing (ATAC-seq) dataset. RESULTS We identified distinct patterns of genome-wide chromatin accessibility in ILC and IDC. Inferred patient-specific transcription factor (TF) motif activities revealed regulatory differences between and within ILC and IDC tumors. EGR1, RUNX3, TP63, STAT6, SOX family, and TEAD family TFs were higher in ILC, while ATF4, PBX3, SPDEF, PITX family, and FOX family TFs were higher in IDC. CONCLUSIONS This study reveals the distinct epigenomic features of ILC and IDC and the active TFs driving cancer progression that may provide valuable information on patient prognosis.
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Affiliation(s)
- Sanghoon Lee
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, USA.,UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA
| | - Hatice Ulku Osmanbeyoglu
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, USA. .,Department of Bioengineering, School of Engineering, University of Pittsburgh, Pittsburgh, USA. .,UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA. .,Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, USA.
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60
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Sawong S, Pekthong D, Suknoppakit P, Winitchaikul T, Kaewkong W, Somran J, Intapa C, Parhira S, Srisawang P. Calotropis gigantea stem bark extracts inhibit liver cancer induced by diethylnitrosamine. Sci Rep 2022; 12:12151. [PMID: 35840761 DOI: 10.1038/s41598-022-16321-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 07/08/2022] [Indexed: 11/09/2022] Open
Abstract
Several fractions of Calotropis gigantea extracts have been proposed to have potential anticancer activity in many cancer models. The present study evaluated the anticancer activity of C. gigantea stem bark extracts in liver cancer HepG2 cells and diethylnitrosamine (DEN)-induced primary liver cancer in rats. The carcinogenesis model induced by DEN administration has been widely used to study pathophysiological features and responses in rats that are comparable to those seen in cancer patients. The dichloromethane (CGDCM), ethyl acetate, and water fractions obtained from partitioning crude ethanolic extract were quantitatively analyzed for several groups of secondary metabolites and calactin contents. A combination of C. gigantea stem bark extracts with doxorubicin (DOX) was assessed in this study to demonstrate the enhanced cytotoxic effect to cancer compared to the single administration. The combination of DOX and CGDCM, which had the most potential cytotoxic effect in HepG2 cells when compared to the other three fractions, significantly increased cytotoxicity through the apoptotic effect with increased caspase-3 expression. This combination treatment also reduced ATP levels, implying a correlation between ATP and apoptosis induction. In a rat model of DEN-induced liver cancer, treatment with DOX, C. gigantea at low (CGDCM-L) and high (CGDCM-H) doses, and DOX + CGDCM-H for 4 weeks decreased the progression of liver cancer by lowering the liver weight/body weight ratio and the occurrence of liver hyperplastic nodules, fibrosis, and proliferative cells. The therapeutic applications lowered TNF-α, IL-6, TGF-β, and α-SMA inflammatory cytokines in a similar way, implying that CGDCM had a curative effect against the inflammation-induced liver carcinogenesis produced by DEN exposure. Furthermore, CGDCM and DOX therapy decreased ATP and fatty acid synthesis in rat liver cancer, which was correlated with apoptosis inhibition. CGDCM reduced cleaved caspase-3 expression in liver cancer rats when used alone or in combination with DOX, implying that apoptosis-inducing hepatic carcinogenesis was suppressed. Our results also verified the low toxicity of CGDCM injection on the internal organs of rats. Thus, this research clearly demonstrated a promising, novel anticancer approach that could be applied in future clinical studies of CGDCM and combination therapy.
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Vijayan S, Loganathan C, Sakayanathan P, Thayumanavan P. Synthesis and Characterization of Plumbagin S-Allyl Cysteine Ester: Determination of Anticancer Activity In Silico and In Vitro. Appl Biochem Biotechnol 2022; 194:5827-5847. [PMID: 35819687 DOI: 10.1007/s12010-022-04079-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022]
Abstract
In recent years, derivatives of natural compounds are synthesized to increase the bioavailability, pharmacology, and pharmacokinetics properties. The naphthoquinone, plumbagin (PLU), is well known for its anticancer activity. However, the clinical use of PLU is hindered due to its toxicity. Previous reports have shown that modification of PLU at 5'-hydroxyl group has reduced its toxicity towards normal cell line. In accordance, in the present study, 5'-hydroxyl group of PLU was esterified with S-allyl cysteine (SAC) to obtain PLU-SAC ester. The drug-likeness of PLU-SAC was understood by in silico ADME analysis. PLU-SAC was characterized by UV-visible spectroscopy, mass spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy. Molecular docking and dynamics simulation analysis revealed the interaction of PLU-SAC with proteins of interest in cancer therapy such as human estrogen receptor α, tumor protein p53 negative regulator mouse double minute 2, and cyclin-dependent kinase 2. MMGBSA calculation showed the favorable binding energy which in turn demonstrated the stable binding of PLU-SAC with these proteins. PLU-SAC showed apoptosis in breast cancer cell line (MCF-7) by inducing oxidative stress, disturbing mitochondrial function, arresting cells at G1 phase of cell cycle, and initiating DNA fragmentation. However, PLU-SAC did not show toxicity towards normal Vero cell line. PLU-SAC was synthesized and structurally characterized, and its anticancer activity was determined by in silico and in vitro analysis.
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Affiliation(s)
- Sudha Vijayan
- Department of Biochemistry, Periyar University, Salem, Tamil Nadu, 636011, India
| | - Chitra Loganathan
- Department of Biochemistry, Periyar University, Salem, Tamil Nadu, 636011, India.,Research and Development Center, Bioinnov Solutions LLP, Salem, Tamil Nadu, 636002, India
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Beykou M, Arias-Garcia M, Roumeliotis TI, Choudhary JS, Moser N, Georgiou P, Bakal C. Proteomic characterisation of triple negative breast cancer cells following CDK4/6 inhibition. Sci Data 2022; 9:395. [PMID: 35817775 PMCID: PMC9273754 DOI: 10.1038/s41597-022-01512-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/28/2022] [Indexed: 01/10/2023] Open
Abstract
When used in combination with hormone treatment, Palbociclib prolongs progression-free survival of patients with hormone receptor positive breast cancer. Mechanistically, Palbociclib inhibits CDK4/6 activity but the basis for differing sensitivity of cancer to Palbociclib is poorly understood. A common observation in a subset of Triple Negative Breast Cancers (TNBCs) is that prolonged CDK4/6 inhibition can engage a senescence-like state where cells exit the cell cycle, whilst, remaining metabolically active. To better understand the senescence-like cell state which arises after Palbociclib treatment we used mass spectrometry to quantify the proteome, phosphoproteome, and secretome of Palbociclib-treated MDA-MB-231 TNBC cells. We observed altered levels of cell cycle regulators, immune response, and key senescence markers upon Palbociclib treatment. These datasets provide a starting point for the derivation of biomarkers which could inform the future use CDK4/6 inhibitors in TNBC subtypes and guide the development of potential combination therapies.
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Affiliation(s)
- Melina Beykou
- Imperial College London, Department of Electrical and Electronic Engineering, Circuits and Systems Group, South Kensington Campus, London, SW7 2AZ, UK.
- Institute of Cancer Research, Division of Cancer Biology, Dynamical Cell Systems, London, SW3 6JB, UK.
- Cancer Research UK Convergence Science Centre, South Kensington Campus, London, SW7 2AZ, UK.
| | - Mar Arias-Garcia
- Institute of Cancer Research, Division of Cancer Biology, Dynamical Cell Systems, London, SW3 6JB, UK
| | - Theodoros I Roumeliotis
- Institute of Cancer Research, Division of Cancer Biology, Functional Proteomics, London, SW3 6JB, UK
| | - Jyoti S Choudhary
- Institute of Cancer Research, Division of Cancer Biology, Functional Proteomics, London, SW3 6JB, UK
| | - Nicolas Moser
- Imperial College London, Department of Electrical and Electronic Engineering, Circuits and Systems Group, South Kensington Campus, London, SW7 2AZ, UK.
- Cancer Research UK Convergence Science Centre, South Kensington Campus, London, SW7 2AZ, UK.
| | - Pantelis Georgiou
- Imperial College London, Department of Electrical and Electronic Engineering, Circuits and Systems Group, South Kensington Campus, London, SW7 2AZ, UK.
- Cancer Research UK Convergence Science Centre, South Kensington Campus, London, SW7 2AZ, UK.
| | - Chris Bakal
- Institute of Cancer Research, Division of Cancer Biology, Dynamical Cell Systems, London, SW3 6JB, UK.
- Cancer Research UK Convergence Science Centre, South Kensington Campus, London, SW7 2AZ, UK.
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Abstract
The bulk of evidence has revealed that dysregulated expression of long non-coding RNAs (lncRNAs) plays a crucial functional role in cancer biology. However, the mechanistic role of lncRNAs in the initiation, progression and immune landscape of thyroid carcinoma (THCA) still remains largely unknown. This study aimed to explore the significance of H19 in the diagnostic and immune related roles in THCA. The expression level of H19 was analyzed using the TNMplot, GSCA, UALCAN, GEPIA, Wanderer, UCSC Xena and GEO databases. Enrichment analyses were performed to investigate the possible underlying biological pathways by LinkedOmics. Moreover, cBioPortal web tool was used to analyze genetic alterations of H19. Finally, we used TIMER and GEPIA databases to explore the correlations between H19 and tumor-infiltrated immune cells and immune markers. LncRNA H19 was differentially expressed in various cancers and also remarkably downregulated in the THCA tissues compared to the normal ones. Genetic alteration analysis revealed that there was a significant correlation between alterations in H19 and overall survival of THCA patients. Furthermore, enrichment analysis indicated the functional relationship between co-expression network of H19 and extracellular structure organization, and immune microenvironment. In addition, H19 expression was positively correlated with infiltration level of diverse immune cells including CD4+T cells, CD8+T cells, B cells, dendritic cells, neutrophils and macrophages and was closely associated with multiple immune markers in THCA. Conclusively, this comprehensive study indicates the lncRNA H19 might have a significant role in the initiation and progression of THCA. Hence, our findings might provide ideas on the selection of novel diagnostic biomarkers and assist in the designing of the effective pharmaceutical targets for THCA.
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Affiliation(s)
- Yunus Sahin
- Department of Medical Biology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey.
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64
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Sahin Y. LncRNA H19 is a potential biomarker and correlated with immune infiltration in thyroid carcinoma. Clin Exp Med 2022:10.1007/s10238-022-00853-w. [PMID: 35810257 DOI: 10.1007/s10238-022-00853-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 06/15/2022] [Indexed: 11/03/2022]
Abstract
The bulk of evidence has revealed that dysregulated expression of long non-coding RNAs (lncRNAs) plays a crucial functional role in cancer biology. However, the mechanistic role of lncRNAs in the initiation, progression and immune landscape of thyroid carcinoma (THCA) still remains largely unknown. This study aimed to explore the significance of H19 in the diagnostic and immune related roles in THCA. The expression level of H19 was analyzed using the TNMplot, GSCA, UALCAN, GEPIA, Wanderer, UCSC Xena and GEO databases. Enrichment analyses were performed to investigate the possible underlying biological pathways by LinkedOmics. Moreover, cBioPortal web tool was used to analyze genetic alterations of H19. Finally, we used TIMER and GEPIA databases to explore the correlations between H19 and tumor-infiltrated immune cells and immune markers. LncRNA H19 was differentially expressed in various cancers and also remarkably downregulated in the THCA tissues compared to the normal ones. Genetic alteration analysis revealed that there was a significant correlation between alterations in H19 and overall survival of THCA patients. Furthermore, enrichment analysis indicated the functional relationship between co-expression network of H19 and extracellular structure organization, and immune microenvironment. In addition, H19 expression was positively correlated with infiltration level of diverse immune cells including CD4+T cells, CD8+T cells, B cells, dendritic cells, neutrophils and macrophages and was closely associated with multiple immune markers in THCA. Conclusively, this comprehensive study indicates the lncRNA H19 might have a significant role in the initiation and progression of THCA. Hence, our findings might provide ideas on the selection of novel diagnostic biomarkers and assist in the designing of the effective pharmaceutical targets for THCA.
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Affiliation(s)
- Yunus Sahin
- Department of Medical Biology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey.
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65
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Ghafouri-Fard S, Khoshbakht T, Hussen BM, Taheri M, Samadian M. A review on the role of MCM3AP-AS1 in the carcinogenesis and tumor progression. Cancer Cell Int 2022; 22:225. [PMID: 35790972 PMCID: PMC9258118 DOI: 10.1186/s12935-022-02644-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/29/2022] [Indexed: 11/29/2022] Open
Abstract
Minichromosome Maintenance Complex Component 3 Associated Protein Antisense 1 (MCM3AP-AS1) is an RNA gene located on 21q22.3. The sense transcript from this locus has dual roles in the pathogenesis of solid tumors and hematological malignancies. MCM3AP-AS1 has been shown to sequester miR-194-5p, miR-876-5p, miR-543-3p, miR-28-5p, miR-93, miR-545, miR-599, miR‐193a‐5p, miR-363-5p, miR-204-5p, miR-211-5p, miR-15a, miR-708-5p, miR-138, miR-138-5p, miR-34a, miR-211, miR‐340‐5p, miR-148a, miR-195-5p and miR-126. Some cancer-related signaling pathway, namely PTEN/AKT, PI3K/AKT and ERK1/2 are influenced by this lncRNA. Cell line studies, animal studies and clinical studies have consistently reported oncogenic role of MCM3AP-AS1 in different tissues except for cervical cancer in which this lncRNA has tumor suppressor role. In the current manuscript, we collected evidence from these three sources of evidence to review the impact of MCM3AP-AS1 in the carcinogenesis.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq.,Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany. .,Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Samadian
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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66
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Mohamadian M, Ahmadi SS, Bahrami A, Ferns GA. Review on the Therapeutic Potential of Curcumin and its Derivatives on Glioma Biology. Neurochem Res 2022; 47:2936-2953. [PMID: 35790698 DOI: 10.1007/s11064-022-03666-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/15/2022] [Accepted: 06/18/2022] [Indexed: 11/24/2022]
Abstract
Gliomas are common and aggressive brain tumors that carry a poor prognosis. The current multimodal therapeutic option for glioma includes surgery subsequently temozolomide chemotherapy and/or radiation; but gliomas are often associated with multidrug resistance, intensive adverse events, and tumor relapse. Thus, novel interventions that can enhance successful chemo-prevention and overcome therapeutic resistance are urgently needed. Phytochemicals have several biological properties with multi-target sites and relatively limited degrees of toxicity. Curcumin is a natural polyphenolic compound with several anti-tumor effects which potentially inhibit tumor growth, development, proliferation, invasion, dissemination, and angiogenesis in different human malignancies. Experimental model studies have demonstrated that curcumin attenuates glioma cell viability by G2/M cell cycle arrest, apoptosis, induction of autophagy, gene expression alteration, and disruption of multi-molecular pathways. Moreover, curcumin has been reported to re-sensitize cancer to chemotherapeutics as well as augment the effect of radiotherapy on glioma cells. In this review, we have provided an update on the in vitro and in vivo effects of curcumin-based therapy on gliomas. We have also discussed the use of curcumin in combination therapies, its effectiveness on drug-resistant cells, and new formulations of curcumin in the treatment of gliomas.
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Affiliation(s)
- Malihe Mohamadian
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Seyed Sajad Ahmadi
- Department of Ophthalmology, Khatam Ol-Anbia Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Afsane Bahrami
- Clinical Research Development Unit, Faculty of Medicine, Imam Reza Hospital, Mashhad University of Medical Sciences, Mashhad, Iran. .,Clinical Research Development Unit of Akbar Hospital, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Department of Medical Education, Falmer, Brighton, BN1 9PH, Sussex, UK
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67
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Internò V, Triggiano G, De Santis P, Stucci LS, Tucci M, Porta C. Molecular Aberrations Stratify Grade 2 Astrocytomas Into Several Rare Entities: Prognostic and Therapeutic Implications. Front Oncol 2022; 12:866623. [PMID: 35756624 PMCID: PMC9226400 DOI: 10.3389/fonc.2022.866623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
The identification of specific molecular aberrations guides the prognostic stratification and management of grade 2 astrocytomas. Mutations in isocitrate dehydrogenase (IDH) 1 and 2, found in the majority of adult diffuse low-grade glioma (DLGG), seem to relate to a favorable prognosis compared to IDH wild-type (IDH-wt) counterparts. Moreover, the IDH-wt group can develop additional molecular alterations worsening the prognosis, such as epidermal growth factor receptor amplification (EGFR-amp) and mutation of the promoter of telomerase reverse transcriptase (pTERT-mut). This review analyzes the prognostic impact and therapeutic implications of genetic alterations in adult LGG.
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Affiliation(s)
- Valeria Internò
- Department of Interdisciplinary Medicine, University of Bari 'Aldo Moro', Bari, Italy.,Division of Medical Oncology, Policlinico Hospital of Bari, Bari, Italy
| | - Giacomo Triggiano
- Division of Medical Oncology, Policlinico Hospital of Bari, Bari, Italy
| | | | | | - Marco Tucci
- Department of Interdisciplinary Medicine, University of Bari 'Aldo Moro', Bari, Italy.,Division of Medical Oncology, Policlinico Hospital of Bari, Bari, Italy
| | - Camillo Porta
- Department of Interdisciplinary Medicine, University of Bari 'Aldo Moro', Bari, Italy.,Division of Medical Oncology, Policlinico Hospital of Bari, Bari, Italy
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68
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Tonmoy MIQ, Fariha A, Hami I, Kar K, Reza HA, Bahadur NM, Hossain MS. Computational epigenetic landscape analysis reveals association of CACNA1G-AS1, F11-AS1, NNT-AS1, and MSC-AS1 lncRNAs in prostate cancer progression through aberrant methylation. Sci Rep 2022; 12:10260. [PMID: 35715447 PMCID: PMC9205881 DOI: 10.1038/s41598-022-13381-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 05/24/2022] [Indexed: 12/24/2022] Open
Abstract
Aberrant expression of long non-coding RNAs (lncRNAs), caused by alterations in DNA methylation, is a driving factor in several cancers. Interplay between lncRNAs’ aberrant methylation and expression in prostate cancer (PC) progression still remains largely elusive. Therefore, this study characterized the genome-wide epigenetic landscape and expression profiles of lncRNAs and their clinical impact by integrating multi-omics data implementing bioinformatics approaches. We identified 62 differentially methylated CpG-sites (DMCs) and 199 differentially expressed lncRNAs (DElncRNAs), where 32 DElncRNAs contain 32 corresponding DMCs within promoter regions. Significant negative correlation was observed between 8 DElncRNAs-DMCs pairs. 3 (cg23614229, cg23957912, and cg11052780) DMCs and 4 (CACNA1G-AS1, F11-AS1, NNT-AS1, and MSC-AS1) DElncRNAs were identified as high-risk factors for poor prognosis of PC patients. Overexpression of hypo-methylated CACNA1G-AS1, F11-AS1, and NNT-AS1 and down-regulation of hyper-methylated MSC-AS1 significantly lower the survival of PC patients and could be a potential prognostic and therapeutic biomarker. These DElncRNAs were found to be associated with several molecular functions whose deregulation can lead to cancer. Involvement of these epigenetically deregulated DElncRNAs in cancer-related biological processes was also noticed. These findings provide new insights into the understanding of lncRNA regulation by aberrant DNA methylation which will help to clarify the epigenetic mechanisms underlying PC.
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Affiliation(s)
- Mahafujul Islam Quadery Tonmoy
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh.,Computational Biology and Chemistry Lab (CBC), Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Atqiya Fariha
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh.,Computational Biology and Chemistry Lab (CBC), Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Ithmam Hami
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Kumkum Kar
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Hasan Al Reza
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh.,Computational Biology and Chemistry Lab (CBC), Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Shahadat Hossain
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh. .,Computational Biology and Chemistry Lab (CBC), Noakhali Science and Technology University, Noakhali, Bangladesh.
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69
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Ghasemian M, Rajabibazl M, Sahebi U, Sadeghi S, Maleki R, Hashemnia V, Mirfakhraie R. Long non-coding RNA MIR4435-2HG: a key molecule in progression of cancer and non-cancerous disorders. Cancer Cell Int 2022; 22:215. [PMID: 35715800 PMCID: PMC9205143 DOI: 10.1186/s12935-022-02633-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/11/2022] [Indexed: 12/18/2022] Open
Abstract
MIR4435-2HG (LINC00978) is a long non-coding RNA (lncRNA) that acts as an oncogene in almost all cancers. This lncRNA participates in the molecular cascades involved in other disorders such as coronary artery diseases, osteonecrosis, osteoarthritis, osteoporosis, and periodontitis. MIR4435-2HG exerts its functions via the spectrum of different mechanisms, including inhibition of apoptosis, sponging microRNAs (miRNAs), promoting cell proliferation, increasing cell invasion and migration, and enhancing epithelial to mesenchymal transition (EMT). MIR4435-2HG can regulate several signaling pathways, including Wnt, TGF-β/SMAD, Nrf2/HO-1, PI3K/AKT, MAPK/ERK, and FAK/AKT/β‑catenin signaling pathways; therefore, it can lead to tumor progression. In the present review, we aimed to discuss the potential roles of lncRNA MIR4435-2HG in developing cancerous and non-cancerous conditions. Due to its pivotal role in different disorders, this lncRNA can serve as a potential biomarker in future investigations. Moreover, it may serve as a potential therapeutic target for the treatment of various diseases.
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Affiliation(s)
- Majid Ghasemian
- Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Rajabibazl
- Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Unes Sahebi
- Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samira Sadeghi
- Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran
| | - Reza Maleki
- Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Veys Hashemnia
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Hematopoietic Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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70
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Miyamoto S, Tanaka T, Hirosuna K, Nishie R, Ueda S, Hashida S, Terada S, Konishi H, Kogata Y, Taniguchi K, Komura K, Ohmichi M. Validation of a Patient-Derived Xenograft Model for Cervical Cancer Based on Genomic and Phenotypic Characterization. Cancers (Basel) 2022; 14:cancers14122969. [PMID: 35740635 PMCID: PMC9221029 DOI: 10.3390/cancers14122969] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary The rate of total tumor engraftment of patient-derived xenografts is 50% in cervical cancer. These cancers retain their histopathological characteristics. The gene mutations and expression patterns associated with carcinogenesis and infiltration and the expression levels of genes in extracellular vesicles released from the tumors are similar between patient-derived xenograft models and primary tumors. Patient-derived xenograft models of cervical cancer could be potentially useful tools for translational research. Abstract Patient-derived xenograft (PDX) models are useful tools for preclinical drug evaluation, biomarker identification, and personalized medicine strategies, and can be developed by the heterotopic or orthotopic grafting of surgically resected tumors into immunodeficient mice. We report the PDX models of cervical cancer and demonstrate the similarities among original and different generations of PDX tumors. Fresh tumor tissues collected from 22 patients with primary cervical cancer were engrafted subcutaneously into NOD.CB17-PrkdcSCID/J mice. Histological and immunohistochemical analyses were performed to compare primary and different generations of PDX tumors. DNA and RNA sequencing were performed to verify the similarity between the genetic profiles of primary and PDX tumors. Total RNA in extracellular vesicles (EVs) released from primary and PDX tumors was also quantified to evaluate gene expression. The total tumor engraftment rate was 50%. Histologically, no major differences were observed between the original and PDX tumors. Most of the gene mutations and expression patterns related to carcinogenesis and infiltration were similar between the primary tumor and xenograft. Most genes associated with carcinogenesis and infiltration showed similar expression levels in the primary tumor and xenograft EVs. Therefore, compared with primary tumors, PDX models could be potentially more useful for translational research.
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Affiliation(s)
- Shunsuke Miyamoto
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7, Daigaku-machi, Takatsuki 569-8686, Osaka, Japan; (S.M.); (R.N.); (S.U.); (S.H.); (S.T.); (H.K.); (Y.K.); (M.O.)
- Translational Research Program, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7, Daigaku-machi, Takatsuki 569-8686, Osaka, Japan; (K.H.); (K.T.); (K.K.)
| | - Tomohito Tanaka
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7, Daigaku-machi, Takatsuki 569-8686, Osaka, Japan; (S.M.); (R.N.); (S.U.); (S.H.); (S.T.); (H.K.); (Y.K.); (M.O.)
- Translational Research Program, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7, Daigaku-machi, Takatsuki 569-8686, Osaka, Japan; (K.H.); (K.T.); (K.K.)
- Correspondence: ; Tel.: +81-726-83-1221
| | - Kensuke Hirosuna
- Translational Research Program, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7, Daigaku-machi, Takatsuki 569-8686, Osaka, Japan; (K.H.); (K.T.); (K.K.)
| | - Ruri Nishie
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7, Daigaku-machi, Takatsuki 569-8686, Osaka, Japan; (S.M.); (R.N.); (S.U.); (S.H.); (S.T.); (H.K.); (Y.K.); (M.O.)
| | - Shoko Ueda
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7, Daigaku-machi, Takatsuki 569-8686, Osaka, Japan; (S.M.); (R.N.); (S.U.); (S.H.); (S.T.); (H.K.); (Y.K.); (M.O.)
| | - Sousuke Hashida
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7, Daigaku-machi, Takatsuki 569-8686, Osaka, Japan; (S.M.); (R.N.); (S.U.); (S.H.); (S.T.); (H.K.); (Y.K.); (M.O.)
| | - Shinichi Terada
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7, Daigaku-machi, Takatsuki 569-8686, Osaka, Japan; (S.M.); (R.N.); (S.U.); (S.H.); (S.T.); (H.K.); (Y.K.); (M.O.)
| | - Hiromi Konishi
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7, Daigaku-machi, Takatsuki 569-8686, Osaka, Japan; (S.M.); (R.N.); (S.U.); (S.H.); (S.T.); (H.K.); (Y.K.); (M.O.)
| | - Yuhei Kogata
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7, Daigaku-machi, Takatsuki 569-8686, Osaka, Japan; (S.M.); (R.N.); (S.U.); (S.H.); (S.T.); (H.K.); (Y.K.); (M.O.)
| | - Kohei Taniguchi
- Translational Research Program, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7, Daigaku-machi, Takatsuki 569-8686, Osaka, Japan; (K.H.); (K.T.); (K.K.)
| | - Kazumasa Komura
- Translational Research Program, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7, Daigaku-machi, Takatsuki 569-8686, Osaka, Japan; (K.H.); (K.T.); (K.K.)
| | - Masahide Ohmichi
- Department of Obstetrics and Gynecology, Educational Foundation of Osaka Medical and Pharmaceutical University, 2-7, Daigaku-machi, Takatsuki 569-8686, Osaka, Japan; (S.M.); (R.N.); (S.U.); (S.H.); (S.T.); (H.K.); (Y.K.); (M.O.)
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71
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Gore S, Azad RK. CancerNet: a unified deep learning network for pan-cancer diagnostics. BMC Bioinformatics 2022; 23:229. [PMID: 35698059 PMCID: PMC9195411 DOI: 10.1186/s12859-022-04783-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/06/2022] [Indexed: 11/10/2022] Open
Abstract
Background Despite remarkable advances in cancer research, cancer remains one of the leading causes of death worldwide. Early detection of cancer and localization of the tissue of its origin are key to effective treatment. Here, we leverage technological advances in machine learning or artificial intelligence to design a novel framework for cancer diagnostics. Our proposed framework detects cancers and their tissues of origin using a unified model of cancers encompassing 33 cancers represented in The Cancer Genome Atlas (TCGA). Our model exploits the learned features of different cancers reflected in the respective dysregulated epigenomes, which arise early in carcinogenesis and differ remarkably between different cancer types or subtypes, thus holding a great promise in early cancer detection. Results Our comprehensive assessment of the proposed model on the 33 different tissues of origin demonstrates its ability to detect and classify cancers to a high accuracy (> 99% overall F-measure). Furthermore, our model distinguishes cancers from pre-cancerous lesions to metastatic tumors and discriminates between hypomethylation changes due to age related epigenetic drift and true cancer. Conclusions Beyond detection of primary cancers, our proposed computational model also robustly detects tissues of origin of secondary cancers, including metastatic cancers, second primary cancers, and cancers of unknown primaries. Our assessment revealed the ability of this model to characterize pre-cancer samples, a significant step forward in early cancer detection. Deployed broadly this model can deliver accurate diagnosis for a greatly expanded target patient population. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04783-y.
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Affiliation(s)
- Steven Gore
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA
| | - Rajeev K Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA. .,Department of Mathematics, University of North Texas, Denton, TX, 76203, USA.
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72
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Liu X, Liu P. Elevated AST/ALT ratio is associated with all-cause mortality in patients with stable coronary artery disease: a secondary analysis based on a retrospective cohort study. Sci Rep 2022; 12:9231. [PMID: 35654995 DOI: 10.1038/s41598-022-13355-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/24/2022] [Indexed: 11/23/2022] Open
Abstract
The aim of this study is to explore the association between the aspartate amino transferase (AST)/alanine aminotransferase (ALT) ratio and all-cause mortality (ACM) in stable coronary artery disease (CAD) patients treated by percutaneous coronary intervention (PCI). The study is a secondary analysis of a retrospective cohort study involving 203 stable CAD patients. Patients were divided into two groups, based on the optimal AST/ALT ratio threshold calculated by the ROC curve (low group: AST/ALT ratio < 1.40; high group: AST/ALT ratio ≥ 1.40). Results were compared using hazard ratio (HR) and a 95% confidence interval (CI). ACM occurred in 18 patients after an average follow-up time of 749 (435–1122) days. Among them, ACM occurred in 6 patients in the low group and 12 patients in the high group, with significant differences between the groups (4.65% versus 16.22%, P value = 0.005). In the Kaplan–Meier analysis, an elevated AST/ALT ratio was associated with increased ACM in stable ACD patients (HR 3.78, 95% CI 1.44–9.93, P value < 0.001). An elevated AST/ALT ratio was still found to be an independent prognostic factor for ACM (HR 2.93, 95% CI 1.08–7.91, P value = 0.034) after adjusting for potential confounders. Therefore, an elevated AST/ALT ratio is an independent prognostic factor for ACM in stable ACD patients.
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Khan A, Vallini L, Aziz S, Khan H, Zaib K, Nigar K, Ayub Q, Wang LX, Pagani L, Wen SQ. Cross-continental admixture in the Kho population from northwest Pakistan. Eur J Hum Genet 2022; 30:740-6. [PMID: 35217804 DOI: 10.1038/s41431-022-01057-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 11/25/2021] [Accepted: 01/25/2022] [Indexed: 01/01/2023] Open
Abstract
Northern Pakistan is home to many diverse ethnicities and languages. The region acted as a prime corridor for ancient invasions and population migrations between Western Eurasia and South Asia. Kho, one of the major ethnic groups living in this region, resides in the remote and isolated mountainous region in the Chitral Valley of the Hindu Kush Mountain range. They are culturally and linguistically distinct from the rest of the Pakistani population groups and their genetic ancestry is still unknown. In this study, we generated genome-wide genotype data of ~1 M loci (Illumina WeGene array) for 116 unrelated Kho individuals and carried out comprehensive analyses in the context of worldwide extant and ancient anatomically modern human populations across Eurasia. The results inferred that the Kho can trace a large proportion of their ancestry to the population who migrated south from the Southern Siberian steppes during the second millennium BCE ~110 generations ago. An additional wave of gene flow from a population carrying East Asian ancestry was also identified in the Kho that occurred ~60 generations ago and may possibly be linked to the expansion of the Tibetan Empire during 7th to 9th centuries CE (current era) in the northwestern regions of the Indian sub-continent. We identified several candidate regions suggestive of positive selection in the Kho, that included genes mainly involved in pigmentation, immune responses, muscular development, DNA repair, and tumor suppression.
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Zhao R, Yin N, Ma L, Zhang J, Luo Y, Guo Z, Fa M, Yang D, Wang D, Yao X. Surface Plasmon Resonance (SPR) Determination of Adenosine Triphosphate (ATP) Using Silver (I) induced Configuration Changes of a Single Stranded DNA Probe with Cytosine (C). ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2081335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Ruihuan Zhao
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Nan Yin
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lixin Ma
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Jie Zhang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yangkai Luo
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhimin Guo
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Mengmei Fa
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Dingding Yang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Dengchao Wang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xin Yao
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
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da Paixão VF, Sosa OJ, da Silva Pellegrina DV, Dazzani B, Corrêa TB, Risério Bertoldi E, da Cruz E Alves-de-Moraes LB, de Oliveira Pessoa D, de Paiva Oliveira V, Alberto Chiong Zevallos R, Russo LC, Forti FL, Eduardo Ferreira J, Carioca Freitas H, Jukemura J, Machado MCC, Dirlei Begnami M, Setubal JC, Bassères DS, Moraes Reis E. Annotation and functional characterization of long noncoding RNAs deregulated in pancreatic adenocarcinoma. Cell Oncol (Dordr) 2022; 45:479-504. [PMID: 35567709 DOI: 10.1007/s13402-022-00678-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2022] [Indexed: 02/01/2023] Open
Abstract
PURPOSE Transcriptome analysis of pancreatic ductal adenocarcinoma (PDAC) has been useful to identify gene expression changes that sustain malignant phenotypes. Yet, most studies examined only tumor tissues and focused on protein-coding genes, leaving long non-coding RNAs (lncRNAs) largely underexplored. METHODS We generated total RNA-Seq data from patient-matched tumor and nonmalignant pancreatic tissues and implemented a computational pipeline to survey known and novel lncRNAs. siRNA-mediated knockdown in tumor cell lines was performed to assess the contribution of PDAC-associated lncRNAs to malignant phenotypes. Gene co-expression network and functional enrichment analyses were used to assign deregulated lncRNAs to biological processes and molecular pathways. RESULTS We detected 9,032 GENCODE lncRNAs as well as 523 unannotated lncRNAs, including transcripts significantly associated with patient outcome. Aberrant expression of a subset of novel and known lncRNAs was confirmed in patient samples and cell lines. siRNA-mediated knockdown of a subset of these lncRNAs (LINC01559, LINC01133, CCAT1, LINC00920 and UCA1) reduced cell proliferation, migration and invasion. Gene co-expression network analysis associated PDAC-deregulated lncRNAs with diverse biological processes, such as cell adhesion, protein glycosylation and DNA repair. Furthermore, UCA1 knockdown was shown to specifically deregulate co-expressed genes involved in DNA repair and to negatively impact DNA repair following damage induced by ionizing radiation. CONCLUSIONS Our study expands the repertoire of lncRNAs deregulated in PDAC, thereby revealing novel candidate biomarkers for patient risk stratification. It also provides a roadmap for functional assays aimed to characterize novel mechanisms of action of lncRNAs in pancreatic cancer, which could be explored for therapeutic development.
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Affiliation(s)
- Vinicius Ferreira da Paixão
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Omar Julio Sosa
- Programa Interunidades de Pós-Graduação em Bioinformática, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - Bianca Dazzani
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Thalita Bueno Corrêa
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Ester Risério Bertoldi
- Programa Interunidades de Pós-Graduação em Bioinformática, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Luís Bruno da Cruz E Alves-de-Moraes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Diogo de Oliveira Pessoa
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Victoria de Paiva Oliveira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Ricardo Alberto Chiong Zevallos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Lilian Cristina Russo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Fabio Luis Forti
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - João Eduardo Ferreira
- Departamento de Ciência da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - José Jukemura
- Departamento de Gastroenterologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - Maria Dirlei Begnami
- Departamento de Anatomia Patológica - AC Camargo Cancer Center, São Paulo, SP, Brazil
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Daniela Sanchez Bassères
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil
| | - Eduardo Moraes Reis
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, Cidade Universitária, São Paulo, SP, 05508-900, Brazil.
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76
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Yang T, Sun J, Wang W, Li D, Yang X, Jia A, Ma Y, Fan Z. Hsa_circ_0006732 regulates colorectal cancer cell proliferation, invasion and EMT by miR-127-5p/RAB3D axis. Mol Cell Biochem 2022; 477:2751-2760. [PMID: 35616807 DOI: 10.1007/s11010-022-04458-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/27/2022] [Indexed: 11/29/2022]
Abstract
Colorectal cancer (CRC) remains a malignancy tumor with high metastasis and poor prognosis. We aimed to explore the effect of circular RNA (circRNA) hsa_circ_0006732 in the progression of CRC. Hsa_circ_0006732 expression in CRC tissues and cell lines were detected using qRT-PCR. The relationship between hsa_circ_0006732 expression and clinicopathologic characteristics of patients with CRC was analyzed. Loss-of-function assay was conducted to determine the regulatory effect of hsa_circ_0006732 on CRC cell proliferation, migration and invasion by using the CCK-8, wound-healing assay and transwell assays. Protein expression changes on epithelial mesenchymal transition (EMT)-related factors were detected by western blotting. The downstream signaling pathway was investigated by bioinformatics, dual-luciferase reporter assay. Rescue assay was further examined for prediction validation. It was found that hsa_circ_0006732 was highly expressed in CRC tissues and cell lines. Downregulation of hsa_circ_0006732 suppressed the proliferation, migration, invasion and EMT of CRC cells. Further mechanistic investigations proved that hsa_circ_0006732 functioned as a competitive endogenous RNA (ceRNA) by directly sponging of miR-127-3p, which further affected the expression of Ras-related protein Rab-3D (Rab3D). Taken together, these findings indicated that hsa_circ_0006732 might be an oncogene in CRC through the regulation of the miR-127-5p/RAB3D axis. Thus, hsa_circ_0006732 might serve as a potential therapeutic target for the treatment of CRC.
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Affiliation(s)
- Tao Yang
- The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, 510000, China.,Department of General Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121010, China
| | - Jufeng Sun
- Orthopedic Department, First Affiliated Hospital of Jinzhou Medical University, No.2 Renmin Street, Jinzhou, 121000, China
| | - Wei Wang
- Department of General Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121010, China
| | - Dongsheng Li
- Department of General Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121010, China
| | - Xianxu Yang
- Orthopedic Department, First Affiliated Hospital of Jinzhou Medical University, No.2 Renmin Street, Jinzhou, 121000, China
| | - Ang Jia
- Orthopedic Department, First Affiliated Hospital of Jinzhou Medical University, No.2 Renmin Street, Jinzhou, 121000, China
| | - Yinda Ma
- Orthopedic Department, First Affiliated Hospital of Jinzhou Medical University, No.2 Renmin Street, Jinzhou, 121000, China
| | - Zhongkai Fan
- The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, 510000, China. .,Orthopedic Department, First Affiliated Hospital of Jinzhou Medical University, No.2 Renmin Street, Jinzhou, 121000, China.
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77
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Wang Y, Gao X, Ru X, Sun P, Wang J. Identification of gene signatures for COAD using feature selection and Bayesian network approaches. Sci Rep 2022; 12:8761. [PMID: 35610288 DOI: 10.1038/s41598-022-12780-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/03/2022] [Indexed: 12/13/2022] Open
Abstract
The combination of TCGA and GTEx databases will provide more comprehensive information for characterizing the human genome in health and disease, especially for underlying the cancer genetic alterations. Here we analyzed the gene expression profile of COAD in both tumor samples from TCGA and normal colon tissues from GTEx. Using the SNR-PPFS feature selection algorithms, we discovered a 38 gene signatures that performed well in distinguishing COAD tumors from normal samples. Bayesian network of the 38 genes revealed that DEGs with similar expression patterns or functions interacted more closely. We identified 14 up-DEGs that were significantly correlated with tumor stages. Cox regression analysis demonstrated that tumor stage, STMN4 and FAM135B dysregulation were independent prognostic factors for COAD survival outcomes. Overall, this study indicates that using feature selection approaches to select key gene signatures from high-dimensional datasets can be an effective way for studying cancer genomic characteristics.
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78
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Riba A, Oravecz A, Durik M, Jiménez S, Alunni V, Cerciat M, Jung M, Keime C, Keyes WM, Molina N. Cell cycle gene regulation dynamics revealed by RNA velocity and deep-learning. Nat Commun 2022; 13:2865. [PMID: 35606383 PMCID: PMC9126911 DOI: 10.1038/s41467-022-30545-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/06/2022] [Indexed: 11/15/2022] Open
Abstract
Despite the fact that the cell cycle is a fundamental process of life, a detailed quantitative understanding of gene regulation dynamics throughout the cell cycle is far from complete. Single-cell RNA-sequencing (scRNA-seq) technology gives access to these dynamics without externally perturbing the cell. Here, by generating scRNA-seq libraries in different cell systems, we observe cycling patterns in the unspliced-spliced RNA space of cell cycle-related genes. Since existing methods to analyze scRNA-seq are not efficient to measure cycling gene dynamics, we propose a deep learning approach (DeepCycle) to fit these patterns and build a high-resolution map of the entire cell cycle transcriptome. Characterizing the cell cycle in embryonic and somatic cells, we identify major waves of transcription during the G1 phase and systematically study the stages of the cell cycle. Our work will facilitate the study of the cell cycle in multiple cellular models and different biological contexts. Single-cell RNA-sequencing technology gives access to cell cycle dynamics without externally perturbing the cell. Here the authors present DeepCycle,a robust deep learning method to infer the cell cycle state in single cells from scRNA-seq data.
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79
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Ghafouri-Fard S, Khoshbakht T, Hussen BM, Baniahmad A, Taheri M, Samadian M. A review on the role of DANCR in the carcinogenesis. Cancer Cell Int 2022; 22:194. [PMID: 35590326 PMCID: PMC9118872 DOI: 10.1186/s12935-022-02612-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/06/2022] [Indexed: 11/23/2022] Open
Abstract
DANCR is an RNA gene located on chr4. This gene has several splice variants. Up-regulation of DANCR has been reported in many types of cancers. This lncRNA is mainly located in the cytoplasm and regulates genes expression at post-transcriptional level. In fact, it acts as a molecular sponge for a variety of miRNAs, including miR-874-3P, miR-335, miR-149, miR-4319, miR-758-3p, miR-216a-5p, miR-874-3p, miR-33a-5p, miR-335-5p, miR-145-3p, miR-665, miR-345-5p and miR-125b-5p. DANCR also regulates activity of PI3K/AKT/NF-κB, Wnt/β-catenin, ERK/SMAD, MAPK, IL-6/JAK1/STAT3, Smad2/3, p53, FAK/PI3K/AKT/GSK3β/Snail pathways. In the current narrative review article, we summarize the roles of DANCR in the carcinogenesis, with an especial emphasis on its role in the development of osteosarcoma and lung, liver, pancreatic and colorectal cancers.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq.,Center of Research and Strategic Studies, Lebanese French University, Erbil, Kurdistan Region, Iraq
| | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany. .,Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Samadian
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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80
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Zahra K, Shabbir M, Badshah Y, Trembley JH, Badar Z, Khan K, Afsar T, Almajwal A, Alruwaili NW, Razak S. Determining KLF14 tertiary structure and diagnostic significance in brain cancer progression. Sci Rep 2022; 12:8039. [PMID: 35577881 PMCID: PMC9110742 DOI: 10.1038/s41598-022-12072-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/03/2022] [Indexed: 12/14/2022] Open
Abstract
Expression analysis of new protein targets may play a crucial role in the early detection and diagnosis of brain tumor progression. The study aimed to investigate the possible relation of KLF14, TPD52, miR-124, and PKCε in the development and progression of brain cancer and space occupying lesion (SOL) of the brain. One hundred human blood samples comprising varying diagnostic groups (SOL brain, grade I, II, III, IV) were analyzed by real-time quantitative PCR to determine the expression level of KLF14, TPD52, miR-124, and PKCε. TPD52 and PKCε were upregulated in brain cancer by 2.5- and 1.6-fold, respectively, whereas, KLF14 and miR-124 were downregulated in brain cancer. In metastatic and high-grade brain cancer, TPD52 and PKCε expression were up-regulated and KLF14 and miR-124 expression were down-regulated. Further, these genes were found to be differentially expressed in the blood of patients with SOL. Upregulation of TPD52 and PKCε, however, reduced expression of KLF14 and miR-124 in SOL of the brain as compared to healthy controls. Expression analysis of TPD52, KLF14, miR-124, and PKCε provided useful information on the differences existing between the normal brain and SOL, in addition to gliomas; thus, might prove to be useful having diagnostic or prognostic value.
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Affiliation(s)
- Kainat Zahra
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Maria Shabbir
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan.
| | - Yasmin Badshah
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Janeen H Trembley
- Minneapolis VA Health Care System Research Service, Minneapolis, MN, USA.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Zunaira Badar
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Khushbukhat Khan
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Nawaf W Alruwaili
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
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81
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Khodeer S, Klungland A, Dahl JA. ALKBH5 regulates somatic cell reprogramming in a phase specific manner. J Cell Sci 2022; 135:275396. [PMID: 35552718 PMCID: PMC9234673 DOI: 10.1242/jcs.259824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/03/2022] [Indexed: 11/20/2022] Open
Abstract
Establishment of the pluripotency regulatory network in somatic cells by introducing four transcription factors (octamer binding transcription factor 4 (OCT4), sex determining region Y (SRY)-box 2 (SOX2), Kruppel-like factor 4 (KLF4), and cellular myelocytomatosis (c-MYC)) provides a promising tool for cell-based therapies in regenerative medicine. Nevertheless, the mechanisms at play when generating induced pluripotent stem cells from somatic cells are only partly understood. Here, we show that the RNA specific N6-methyladenosine (m6A) demethylase ALKBH5 regulates somatic cell reprogramming in a stage-specific manner through its catalytic activity. Knockdown or knockout of Alkbh5 in the early reprogramming phase impairs reprogramming efficiency by reducing the proliferation rate through arresting the cells at G2/M phase and decreasing the upregulation of epithelial markers. On the other hand, ALKBH5 overexpression at the early reprogramming phase has no significant impact on reprogramming efficiency, while overexpression at the late phase enhances reprogramming by stabilizing Nanog transcripts, resulting in upregulated Nanog expression. Our study provides mechanistic insight into the crucial dynamic role of ALKBH5 through its catalytic activity in regulating somatic cell reprogramming at the posttranscriptional level.
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Affiliation(s)
- Sherif Khodeer
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Forskningsveien 1, 0373. Oslo, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Forskningsveien 1, 0373. Oslo, Norway.,Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316. Oslo, Norway
| | - John Arne Dahl
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Forskningsveien 1, 0373. Oslo, Norway
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82
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Žarković M, Hufsky F, Markert UR, Marz M. The Role of Non-Coding RNAs in the Human Placenta. Cells 2022; 11:cells11091588. [PMID: 35563893 PMCID: PMC9104507 DOI: 10.3390/cells11091588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) play a central and regulatory role in almost all cells, organs, and species, which has been broadly recognized since the human ENCODE project and several other genome projects. Nevertheless, a small fraction of ncRNAs have been identified, and in the placenta they have been investigated very marginally. To date, most examples of ncRNAs which have been identified to be specific for fetal tissues, including placenta, are members of the group of microRNAs (miRNAs). Due to their quantity, it can be expected that the fairly larger group of other ncRNAs exerts far stronger effects than miRNAs. The syncytiotrophoblast of fetal origin forms the interface between fetus and mother, and releases permanently extracellular vesicles (EVs) into the maternal circulation which contain fetal proteins and RNA, including ncRNA, for communication with neighboring and distant maternal cells. Disorders of ncRNA in placental tissue, especially in trophoblast cells, and in EVs seem to be involved in pregnancy disorders, potentially as a cause or consequence. This review summarizes the current knowledge on placental ncRNA, their transport in EVs, and their involvement and pregnancy pathologies, as well as their potential for novel diagnostic tools.
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Affiliation(s)
- Milena Žarković
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; (M.Ž.); (F.H.)
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
- Placenta Lab, Department of Obstetrics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany;
| | - Franziska Hufsky
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; (M.Ž.); (F.H.)
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Udo R. Markert
- Placenta Lab, Department of Obstetrics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany;
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; (M.Ž.); (F.H.)
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
- FLI Leibniz Institute for Age Research, Beutenbergstraße 11, 07745 Jena, Germany
- Aging Research Center (ARC), 07745 Jena, Germany
- Correspondence:
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83
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Roohaninasab M, Yavari SF, Babazadeh M, Hagh RA, Pazoki M, Amrovani M. Evaluating the Role of lncRNAs in the Incidence of Cardiovascular Diseases in Androgenetic Alopecia Patients. Cardiovasc Toxicol 2022; 22:603-619. [PMID: 35507254 DOI: 10.1007/s12012-022-09742-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/11/2022] [Indexed: 11/28/2022]
Abstract
Hair loss occurs in patients with Androgenetic Alopecia (AGA). The pattern of hair loss is different between men and women. The main cause of hair loss is increased cell apoptosis and decreased regeneration, proliferation and differentiation processes in hair follicles. Long Non-Coding RNAs (lncRNAs) are one of the most important molecules that regulate the processes of apoptosis, regeneration, proliferation and differentiation in hair follicles. Since studies have shown that lncRNAs can be effective in the development of cardiotoxicity and induction of cardiovascular disease (CVD); so effective lncRNAs in the regulation of regeneration, proliferation, differentiation and apoptosis of hair follicles can be involved in the development of CVD in AGA patients with. Therefore, this study investigated the lncRNAs involved in increasing apoptosis and reducing the processes of regeneration, proliferation and differentiation of hair follicles. The aim of the current study was to evaluate the role of lncRNAs as a risk factor in the incidence of CVD in AGA patients; it will help to design treatment strategies by targeting signaling pathways without any cardiotoxicity complications.
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Affiliation(s)
- Masoumeh Roohaninasab
- Department of Dermatology, Rasool Akram Medical Complex, Iran University of Medical Sciences, Sattarkhan St, Tehran, 1445613131, Iran
| | - Shadnaz Fakhteh Yavari
- Department of Tissue Engineering and Applied Cell Science, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Science, Tehran, Iran.,Parvaz Research Ideas Supporter Institute, Tehran, Iran
| | - Motahareh Babazadeh
- Department of Dermatology, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Mahboubeh Pazoki
- Department of Cardiology, Rasoul Akram General Hospital, Iran University of Medical Sciences, Tehran, Iran.
| | - Mehran Amrovani
- High Institute for Education and Research in Transfusion Medicine, Tehran, Iran.
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84
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Ghafouri-Fard S, Khoshbakht T, Hussen BM, Taheri M, Samsami M. Emerging role of circular RNAs in the pathogenesis of ovarian cancer. Cancer Cell Int 2022; 22:172. [PMID: 35488239 PMCID: PMC9052556 DOI: 10.1186/s12935-022-02602-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/18/2022] [Indexed: 01/11/2023] Open
Abstract
Ovarian cancer is a female malignancy with high fatality-to-case ratio, which is due to late detection of cancer. Understanding the molecular mechanisms participating in these processes would facilitate design of therapeutic modalities and identification of novel tumor markers. Recent investigations have shown contribution of circular RNAs (circRNAs) in the evolution of ovarian cancer. These transcripts are produced through a back-splicing mechanism. The enclosed configuration of circRNAs protects them from degradation and potentiates them as biomarkers. Several circRNAs such as circMUC16, circRNA_MYLK, circRNA-UBAP2, circWHSC1, hsa_circ_0013958, circFGFR3, hsa_circRNA_102958 and circ_0072995 have been found to be up-regulated in this cancer, acting as oncogenes. On the other hand, circ-ITCH, circPLEKHM3, circ_100395, circ_0078607, circATRNL1, circHIPK3, circRHOBTB3, circEXOC6B, circ9119 and CDR1as are among down-regulated circRNAs in ovarian cancer. Expression levels of circCELSR1, circ_CELSR1, circATL2, circNRIP1, circTNPO3 and hsa_circ_0000714 have been shown to affect resistance of ovarian cancer cells to chemotherapy. Moreover, circ_100395, circFGFR3, circ_0000554, circCELSR1, circ-PTK2, circLNPEP, circ-CSPP1, circ_0000745, circ_100395 and circPLEKHM3 have been shown to regulate epithelial-mesenchymal transition and metastatic ability of ovarian cancer cells. In the current review, we explain the roles of circRNAs in the evolution and progression of ovarian cancer.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Arbīl, Kurdistan Region, Iraq
- Center of Research and Strategic Studies, Lebanese French University, Arbīl, Kurdistan Region, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
| | - Majid Samsami
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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85
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Singh P, Singh A, Gupta N, Raja KD, Singh P, Agarwal S, Sharma A. Non-invasive diagnostic potential of microRNA-203 in liquid biopsy of urothelial carcinoma of bladder. Mol Cell Biochem 2022. [PMID: 35445913 DOI: 10.1007/s11010-022-04431-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/01/2022] [Indexed: 11/07/2022]
Abstract
Increased CD44 antigen activity has been reported in recurrent cases of UBC. To date, no reliable biomarker is available with high significance and specificity for non-invasive detection of UBC. This study aimed to identify a CD44-linked microRNAs (miRNAs) (miR-9, miR-34a, miR-203) for non-invasive diagnosis of bladder cancer from other urinary tract malignancies. The expression of CD44-linked miRNAs was examined in serum, urine, and tissue specimens of Indian UBC patients (N = 25). For this purpose, healthy subjects (N = 25) and benign prostatic hyperplasia (BPH) (N = 10) patients were taken as controls. The relative expression of miRNAs was analyzed in serum, urine, and tissue samples using real-time quantitative reverse transcription PCR (qRT-PCR). The diagnostic potential of these miRNAs was accessed by plotting ROC curve. Increased miR-9 expression was observed in serum of UBC patients than healthy and BPH controls. In UBC patients, miR-34a expression was lower than healthy controls but non-significant as compared to BPH. miR-203 expression was considerably higher in serum of UBC patients but non-significant as compared to BPH controls. miR-203 was found to be considerably higher in urine samples from UBC patients as compared to BPH and healthy controls. The diagnostic potential of these miRNAs was evaluated using the ROC curve. Higher miR-203 levels in the urine of Indian UBC patients demonstrate its non-invasive diagnostic ability out of the three miRNAs studied. Our results characterize the non-invasive diagnostic potential of CD44-linked miR-203 in the urine of Indian UBC patients, which could be utilized in clinical settings in future after validation in larger patient cohort.
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86
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Naimi A, Mohammed RN, Raji A, Chupradit S, Yumashev AV, Suksatan W, Shalaby MN, Thangavelu L, Kamrava S, Shomali N, Sohrabi AD, Adili A, Noroozi-Aghideh A, Razeghian E. Tumor immunotherapies by immune checkpoint inhibitors (ICIs); the pros and cons. Cell Commun Signal 2022; 20:44. [PMID: 35392976 PMCID: PMC8991803 DOI: 10.1186/s12964-022-00854-y] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/02/2022] [Indexed: 02/07/2023] Open
Abstract
The main breakthrough in tumor immunotherapy was the discovery of immune checkpoint (IC) proteins, which act as a potent suppressor of the immune system by a myriad of mechanisms. After that, scientists focused on the immune checkpoint molecules mainly. Thereby, much effort was spent to progress novel strategies for suppressing these inhibitory axes, resulting in the evolution of immune checkpoint inhibitors (ICIs). Then, ICIs have become a promising approach and shaped a paradigm shift in tumor immunotherapies. CTLA-4 plays an influential role in attenuation of the induction of naïve and memory T cells by engagement with its responding ligands like B7-1 (CD80) and B7-2 (CD86). Besides, PD-1 is predominantly implicated in adjusting T cell function in peripheral tissues through its interaction with programmed death-ligand 1 (PD-L1) and PD-L2. Given their suppressive effects on anti-tumor immunity, it has firmly been documented that ICIs based therapies can be practical and rational therapeutic approaches to treat cancer patients. Nonetheless, tumor inherent or acquired resistance to ICI and some treatment-related toxicities restrict their application in the clinic. The current review will deliver a comprehensive overview of the ICI application to treat human tumors alone or in combination with other modalities to support more desired outcomes and lower toxicities in cancer patients. Video Abstract.
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Affiliation(s)
- Adel Naimi
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Rebar N. Mohammed
- Medical Laboratory Analysis Department, Cihan University Sulaimaniya, Sulaymaniyah, 46001 Kurdistan Region Iraq
- College of Veterinary Medicine, University of Sulaimani, Suleimanyah, Iraq
| | - Ahmed Raji
- College of Medicine, University of Babylon, Department of Pathology, Babylon, Iraq
| | - Supat Chupradit
- Department of Occupational Therapy, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200 Thailand
| | | | - Wanich Suksatan
- Faculty of Nursing, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, 10210 Thailand
| | - Mohammed Nader Shalaby
- Associate Professor of Biological Sciences and Sports Health Department, Faculty of Physical Education, Suez Canal University, Ismailia, Egypt
| | - Lakshmi Thangavelu
- Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Science, Saveetha University, Chennai, India
| | - Siavash Kamrava
- Department of Surgery, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Navid Shomali
- Immunology Research Center (IRC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Armin D. Sohrabi
- Immunology Research Center (IRC), Tabriz University of Medical Sciences, Tabriz, Iran
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Adili
- Department of Oncology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Noroozi-Aghideh
- Department of Hematology, Faculty of Paramedicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ehsan Razeghian
- Human Genetics Division, Medical Biotechnology Department, National Institute of Genetics Engineering and Biotechnology (NIGEB), Tehran, Iran
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87
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Booth ME, Smyth EC. Immunotherapy in Gastro-Oesophageal Cancer: Current Practice and the Future of Personalised Therapy. BioDrugs 2022; 36:473-485. [PMID: 35384619 DOI: 10.1007/s40259-022-00527-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2022] [Indexed: 11/02/2022]
Abstract
Initial studies of immune checkpoint inhibitors in biomarker unselected gastro-oesophageal cancer yielded limited improvement in survival. However, emerging data from recent clinical trials suggest immunotherapies may offer a meaningful clinical benefit within selected populations. Gastro-oesophageal cancer is a heterogeneous disease with respect to histopathological and molecular features; hypermutation and the biology of immune checkpoint pathways are key to appropriate selection of populations most likely to benefit from immune checkpoint inhibitors. Programmed death-ligand 1 expression, typically measured using the combined positive score, is an important biomarker in determining which patients may benefit from immunotherapy agents. However, combined positive score thresholds are not standardised across trials and the benefit in programmed death-ligand 1-negative cohorts is uncertain. Data suggest that patients with tumours with microsatellite instability, high tumour mutational burden and Epstein-Barr Virus positivity are more likely to benefit from immunotherapy, which may be of importance within programmed death-ligand 1-negative populations. Here, we describe the current evidence base for the use of checkpoint inhibitors in the treatment of advanced gastro-oesophageal cancer and adjuvant treatment of high-risk oesophageal cancer, as well as the ongoing studies of immunotherapy in the treatment of patients with gastro-oesophageal cancers across an increasing range of clinical settings.
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Affiliation(s)
| | - Elizabeth C Smyth
- Department of Oncology, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK
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88
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Yang M, Li H, Li X, Huang K, Xu W, Zhu L. Catalytic hairpin self-assembly regulated chameleon silver nanoclusters for the ratiometric detection of CircRNA. Biosens Bioelectron 2022; 209:114258. [DOI: 10.1016/j.bios.2022.114258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/23/2022] [Accepted: 04/05/2022] [Indexed: 12/12/2022]
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89
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Wu X, Cao W, Lu C, Zuo L, Liu X, Qi M. circ3323 Motivates Host Gene to Promote the Aggressiveness of Bladder Cancer. Biochem Genet 2022; 60:2327-2345. [PMID: 35362879 DOI: 10.1007/s10528-022-10210-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 02/24/2022] [Indexed: 11/24/2022]
Abstract
Bladder cancer (BCa) is the most common cancer in the urinary system with high recurrence rate and poor prognosis. Circular RNA (circRNA) is a novel subclass of noncoding-RNA which participate in progression of BCa. Here, we identified a novel circRNA-circ3323 and aimed to investigate the role of circ3323 in progression of BCa. Public data of RNA sequencing was used to identify significant circRNA related to BCa. The role of circRNAs in progression of BCa was assessed in cytotoxicity assay, transwell assay and flow cytometry. Biotin-coupled RNA pull-down and fluorescence in situ hybridization were performed to evaluate the interaction between circRNAs and miRNAs. The expression of circ3323 was higher in BCa tissues and cells than in normal samples. Experiments in vitro showed that the knockdown of circ3323 inhibited cell proliferation and impeded the metastasis of BCa cells. Mechanistically, we demonstrated that circ3323 acts as a sponge for miR-186-5p and promotes host gene APP's expression. Clinically, circ3323 predicts worse overall survival of BCa patients, indicating its prognostic value. Our study identified that circ3323 modulates metastasis of BCa through miR-186-5p/APP axis and may serve as a promising prognostic biomarker for BCa, which provides novel insights into treatment of BCa.
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Affiliation(s)
- Xingyu Wu
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Xinglong Road 29, Tianning, Changzhou, 213000, China
| | - Wei Cao
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Xinglong Road 29, Tianning, Changzhou, 213000, China
| | - Chao Lu
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Xinglong Road 29, Tianning, Changzhou, 213000, China
| | - Li Zuo
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Xinglong Road 29, Tianning, Changzhou, 213000, China
| | - Xiaowu Liu
- Department of Urology Surgery, Changzhou Wujin People's Hospital, Wujin Hospital Affiliated Jiangsu University, The Wujin Clinical College of Xuzhou Medical University, Changzhou, China
| | - Minjun Qi
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Xinglong Road 29, Tianning, Changzhou, 213000, China.
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90
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Tian X, Yang H, Fang Q, Quan H, Lu H, Wang X. Circ_ZFR affects FABP7 expression to regulate breast cancer progression by acting as a sponge for miR-223-3p. Thorac Cancer 2022; 13:1369-1380. [PMID: 35355424 PMCID: PMC9058297 DOI: 10.1111/1759-7714.14401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Breast cancer (BC) is a common malignancy in women. Circular RNAs (circRNAs) have been reported to play a key role in the development of BC; however, the effect of circular RNA zinc finger RNA binding protein (circ_ZFR) in BC is unknown. METHODS Abundances of circ_ZFR, fatty acid binding protein 7 (FABP7), and microRNA-223-3p (miR-223-3p) were measured by quantitative real-time polymerase chain reaction (qRT-PCR). The circular structure of circ_ZFR was validated by RNase R treatment. Cell proliferation, migration, invasion, and apoptosis were assessed by colony formation, cell counting kit-8, Transwell, flow cytometry assays, respectively. All protein levels were determined by Western blot. Dual-luciferase reporter assay was used to confirm the relationship between miR-223-3p and circ_ZFR or FABP7. A xenograft model was established to understand the effect of circ_ZFR on BC cell growth in vivo. RESULTS The expression levels of circ_ZFR and FABP7 were higher in BC tissues and cell lines, whereas miR-223-3p expression was lower. Knockdown of circ_ZFR or FABP7 in BC cells reduced proliferation, migration, invasion, and epithelial mesenchymal transition (EMT), and induced apoptosis in vitro, whereas the opposite effects were observed in circ_ZFR-overexpressed cells. Furthermore, circ_ZFR might act as a sponge for miR-223-3p to regulate FABP7 expression, thereby promoting the progression of BC cells in vitro and in vivo. CONCLUSION Circ_ZFR might act as a miRNA sponge for miR-223-3p to regulate FABP7, thereby promoting proliferation, migration, invasion, and EMT of BC cells, and inhibiting cell apoptosis.
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Affiliation(s)
- Xiuling Tian
- Department of Oncology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Hong Yang
- Department of Oncology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Qian Fang
- Department of General Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Hongmei Quan
- Department of Oncology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Hongyu Lu
- Department of Oncology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Xin Wang
- Department of General Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
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91
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Abstract
Colorectal cancer (CRC) is one of the most lethal and prevalent solid malignancies worldwide. There is a great need of accelerating the development and diagnosis of CRC. Long noncoding RNAs (lncRNA) as transcribed RNA molecules play an important role in every level of gene expression. Metastasis‐associated lung adenocarcinoma transcript‐1 (MALAT1) is a highly conserved nucleus-restricted lncRNA that regulates genes at the transcriptional and post-transcriptional levels. High expression of MALAT1 is closely related to numerous human cancers. It is generally believed that MALAT1 expression is associated with CRC cell proliferation, tumorigenicity, and metastasis. MALAT1 by targeting multiple signaling pathways and microRNAs (miRNAs) plays a pivotal role in CRC pathogenesis. Therefore, MALAT1 can be a potent gene for cancer prediction and diagnosis. In this review, we will demonstrate signaling pathways associated with MALAT1 in CRC.
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92
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Nukala SB, Jousma J, Cho Y, Lee WH, Ong SG. Long non-coding RNAs and microRNAs as crucial regulators in cardio-oncology. Cell Biosci 2022; 12:24. [PMID: 35246252 PMCID: PMC8895873 DOI: 10.1186/s13578-022-00757-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/10/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer is one of the leading causes of morbidity and mortality worldwide. Significant improvements in the modern era of anticancer therapeutic strategies have increased the survival rate of cancer patients. Unfortunately, cancer survivors have an increased risk of cardiovascular diseases, which is believed to result from anticancer therapies. The emergence of cardiovascular diseases among cancer survivors has served as the basis for establishing a novel field termed cardio-oncology. Cardio-oncology primarily focuses on investigating the underlying molecular mechanisms by which anticancer treatments lead to cardiovascular dysfunction and the development of novel cardioprotective strategies to counteract cardiotoxic effects of cancer therapies. Advances in genome biology have revealed that most of the genome is transcribed into non-coding RNAs (ncRNAs), which are recognized as being instrumental in cancer, cardiovascular health, and disease. Emerging studies have demonstrated that alterations of these ncRNAs have pathophysiological roles in multiple diseases in humans. As it relates to cardio-oncology, though, there is limited knowledge of the role of ncRNAs. In the present review, we summarize the up-to-date knowledge regarding the roles of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in cancer therapy-induced cardiotoxicities. Moreover, we also discuss prospective therapeutic strategies and the translational relevance of these ncRNAs.
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Affiliation(s)
- Sarath Babu Nukala
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL, 60612, USA
| | - Jordan Jousma
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL, 60612, USA
| | - Yoonje Cho
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL, 60612, USA
| | - Won Hee Lee
- Department of Basic Medical Sciences, University of Arizona College of Medicine, ABC-1 Building, 425 North 5th Street, Phoenix, AZ, 85004, USA.
| | - Sang-Ging Ong
- Department of Pharmacology & Regenerative Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL, 60612, USA.
- Division of Cardiology, Department of Medicine, The University of Illinois College of Medicine, 909 S Wolcott Ave, COMRB 4100, Chicago, IL, 60612, USA.
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93
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Paul U, Banerjee S. The functional significance and cross-talk of non-coding RNAs in triple negative and quadruple negative breast cancer. Mol Biol Rep 2022; 49:6899-6918. [PMID: 35235157 DOI: 10.1007/s11033-022-07288-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/18/2022] [Indexed: 12/13/2022]
Abstract
One of the leading causes of cancer-related deaths worldwide is breast cancer, among which triple-negative breast cancer (TNBC) is the most malignant and lethal subtype. This cancer accounts for 10-20% of all breast cancer deaths. Proliferation, tumorigenesis, and prognosis of TNBC are affected when the androgen receptor (AR) is not expressed, and it is classified as quadruple negative breast cancer (QNBC). Non-coding RNAs, such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), play a significant role in tumorigenesis by virtue of their oncogenic and tumor-suppressive properties. To regulate tumorigenesis, miRNAs interact with their target mRNAs and modulate their expression, whereas lncRNAs can either act alone or interact with miRNAs or other molecules through various signaling pathways. Conversely, circRNAs regulate tumorigenesis by acting as miRNA sponges predominantly. Recently, non-coding RNAs were studied comprehensively for their roles in tumor proliferation, progression, and metastasis. As a result of existing studies and research progress, non-coding RNAs have been implicated in TNBC, necessitating their use as biomarkers for future diagnostic applications. In this review, the non-coding RNAs are explicitly implicated in the regulation of breast cancer, and their cross-talk between TNBC and QNBC is also discussed.
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Affiliation(s)
- Utpalendu Paul
- School of Bio Science and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Satarupa Banerjee
- School of Bio Science and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India.
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94
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Toolabi N, Daliri FS, Mokhlesi A, Talkhabi M. Identification of key regulators associated with colon cancer prognosis and pathogenesis. J Cell Commun Signal 2022; 16:115-127. [PMID: 33770351 PMCID: PMC8688655 DOI: 10.1007/s12079-021-00612-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 12/11/2022] Open
Abstract
Colon cancer (CC) is the fourth deadliest cancer in the world. New insights into prognostication might be helpful to define the optimal adjuvant treatments for patients in routine clinical practice. Here, a microarray dataset with 30 primary tumors and 30 normal samples was analyzed using GEO2R to find differentially expressed genes (DEGs). Then, DAVID, KEGG, ChEA and X2K were used to analyze DEGs-related Gene Ontology, pathways, transcription factors (TFs) and kinases, respectively. Protein-protein interaction (PPI) networks were constructed using the STRING database and Cytoscape. The modules and hub genes of DEGs was determined through MCODE and CytoHubba plugins, and the expression of hub genes was verified using GEPIA. To find microRNAs and metabolites associated with DEGs, miRTarBase and HMDB were used, respectively. It was found that 233 and 373 genes were upregulated and downregulated in CC, respectively. GO analysis showed that the upregulated DEGs were mainly involved in mitotic nuclear division and cell division. Top 10 hub genes were identified, including AURKB, CDK1, DLGAP5, AURKA, CCNB2, CCNB1, BUB1B, CCNA2, KIF20A and BUB1. Whereas, FOMX1, E2F7, E2F1, E2F4 and AR were identified as top 5 TFs in CC. Moreover, CDK1, CDC2, MAPK14, ATM and CK2ALPHA was identified as top 5 kinases in CC. miRNAs analysis showed that Hsa-miR-215-5p hsa-miR-193b-3p, hsa-miR-192-5p and hsa-miR-16-5p could target the largest number of CC genes. Taken together, CC-related genes, especially the hub genes, TFs, and metabolites might be used as novel biomarkers for CC, as well as for diagnosis and guiding therapeutic strategies for CC.
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Affiliation(s)
- Narges Toolabi
- Department of Animal Sciences and Marine Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Fattane Sam Daliri
- Department of Animal Sciences and Marine Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Amir Mokhlesi
- Department of Animal Sciences and Marine Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Mahmood Talkhabi
- Department of Animal Sciences and Marine Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
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95
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Zou Z, He T, Liu Y, Zheng L, Zhong Y, Mo Y, Peng S, Shuai C. Emerging role of m6A modification in osteogenesis of stem cells. J Bone Miner Metab 2022; 40:177-188. [PMID: 35091784 DOI: 10.1007/s00774-021-01297-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/20/2021] [Indexed: 12/19/2022]
Abstract
The differentiation of stem cells into osteoblasts is a key link in the treatment of bone defects and other orthopedic diseases. N6-methyladenosine (m6A) modification, an important post-transcriptional modification, is a methylation that occurs at the N6 site of RNA adenylate. The modification plays a regulatory role in the growth and development of biological individuals, the directional differentiation of stem cells and the occurrence of diseases. It is involved in various processes of the fate decision of stem cells. And it regulates the development and constant renewal of bone and keeps bone homeostasis by controlling and maintaining the balance between osteogenesis and adipogenesis. Meanwhile, it also affects the progress of orthopedic-associated diseases such as degenerative osteoporosis and bone tumor. In this review, we mainly summarize the new findings of three key molecules including Writers, Erasers and Readers which regulate m6A modification, and the emerging role of m6A modification in determining the fate and directed differentiation potential of stem cells, especially highlight the regulatory mechanism of osteogenic differentiation, the balance between osteogenesis and adipogenesis and the occurrence and development of bone-related diseases. It may provide some important ideas about finding new strategies to recover from bone defect and degenerative bone disease.
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Affiliation(s)
- Zi Zou
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism of Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, 410078, Hunan, China
- Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Tiantian He
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism of Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, 410078, Hunan, China
- Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Ying Liu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism of Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, 410078, Hunan, China
- Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Leliang Zheng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism of Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, 410078, Hunan, China
- Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Yancheng Zhong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism of Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, 410078, Hunan, China
- Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Yuqing Mo
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism of Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, 410078, Hunan, China
- Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - Shuping Peng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism of Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, 410078, Hunan, China.
- Hunan Key Laboratory of Non Resolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China.
| | - Cijun Shuai
- Institute of Additive Manufacturing, Jiangxi University of Science and Technology, Nanchang, 330013, China.
- State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha, 410083, China.
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96
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Wang Z, Xiong H, Zuo Y, Hu S, Zhu C, Min A. PSMC2 knockdown inhibits the progression of oral squamous cell carcinoma by promoting apoptosis via PI3K/Akt pathway. Cell Cycle 2022; 21:477-488. [PMID: 34979867 PMCID: PMC8942557 DOI: 10.1080/15384101.2021.2021722] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Proteasome 26S subunit, ATPase 2 (PSMC2) is a recently identified gene which is potentially associated with human carcinogenesis. However, the effects of PSMC2 on oral squamous cell carcinoma (OSCC) is still unclear. Here, we investigated PSMC2 expression in OSCC tissues and explored its effects on the biological behaviors of OSCC cells. PSMC2 expression was evaluated by immunohistochemistry in a tissue microarray containing 60 OSCC tissues and 9 normal tissues. PSMC2 was knocked down through lentivirus infection in OSCC cell lines. MTT, colony formation, flow cytometry, transwell, and scratch assays were performed to detect effects of PSMC2 knockdown on phenotypes of OSCC cells. Human apoptosis antibody array was used to screen potential downstream of PSMC2 in OSCC. Finally, the effects of PSMC2 knockdown on tumor growth were assessed in a tumor xenograft model using BALB/c nude mice. PSMC2 expression was significantly upregulated in OSCC tissues compared with normal tissues and correlated with poor prognosis. PSMC2 knockdown significantly suppressed cell proliferation, migration, but promoted apoptosis of OSCC cells. Additionally, we confirmed that PSMC2 knockdown can increase the expression of pro-apoptotic proteins. Furthermore, we found that PSMC2 knockdown downregulated expression of p100, p-Akt, CDK6, and upregulated of MAPK9. Xenograft experiments revealed that PSMC2 knockdown can suppress OSCC tumor growth and promote apoptosis. This study demonstrated that PSMC2 plays a critical role in OSCC progression through affecting pro-apoptotic protein expression and apoptosis pathways. It indicated that targeting PSMC2 might be a promising strategy for OSCC treatment.
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Affiliation(s)
- Zijia Wang
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital, Central South University, Changsha, China
| | - Haofeng Xiong
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital, Central South University, Changsha, China
| | - Yijie Zuo
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital, Central South University, Changsha, China
| | - Shujun Hu
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital, Central South University, Changsha, China
| | - Chao Zhu
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital, Central South University, Changsha, China
| | - Anjie Min
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital, Central South University, Changsha, China,Institute of Oral Precancerous Lesions, Central South University, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China,CONTACT Anjie Min Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital, Central South University, Changsha410005, China
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97
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Ong SN, Tan BC, Al-Idrus A, Teo CH. Small open reading frames in plant research: from prediction to functional characterization. 3 Biotech 2022; 12:76. [PMID: 35251879 DOI: 10.1007/s13205-022-03147-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 02/11/2022] [Indexed: 11/01/2022] Open
Abstract
Gene prediction is a laborious and time-consuming task. The advancement of sequencing technologies and bioinformatics tools, coupled with accelerated rate of ribosome profiling and mass spectrometry development, have made identification of small open reading frames (sORFs) (< 100 codons) in various plant genomes possible. The past 50 years have seen sORFs being isolated from many organisms. However, to date, a comprehensive sORF annotation pipeline is as yet unavailable, hence, addressed in our review. Here, we also provide current information on classification and functions of plant sORFs and their potential applications in crop improvement programs.
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98
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Ghafouri-Fard S, Khoshbakht T, Hussen BM, Taheri M, Jamali E. The emerging role non-coding RNAs in B cell-related disorders. Cancer Cell Int 2022; 22:91. [PMID: 35193592 PMCID: PMC8862212 DOI: 10.1186/s12935-022-02521-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/10/2022] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs and microRNAs have recently attained much attention regarding their role in the development of B cell lineage as well as participation in the lymphomagenesis. These transcripts have a highly cell type specific signature which endows them the potential to be used as biomarkers for clinical situations. Aberrant expression of several non-coding RNAs has been linked with B cell malignancies and immune related disorders such as rheumatoid arthritis, systemic lupus erythematous, asthma and graft-versus-host disease. Moreover, these transcripts can alter response of immune system to infectious conditions. miR-7, miR-16-1, miR-15a, miR-150, miR-146a, miR-155, miR-212 and miR-132 are among microRNAs whose role in the development of B cell-associated disorders has been investigated. Similarly, SNHG14, MALAT1, CRNDE, AL133346.1, NEAT1, SMAD5-AS1, OR3A4 and some other long non-coding RNAs participate in this process. In the current review, we describe the role of non-coding RNAs in B cell malignancies.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq.,Center of Research and Strategic Studies, Lebanese French University, Erbil, Kurdistan Region, Iraq
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran. .,Institute of Human Genetics, Jena University Hospital, Jena, Germany.
| | - Elena Jamali
- Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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99
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Abstract
Advances in proteomic and metabolomic technologies have accelerated our understanding of multiple aspects of cancer biology across distinct tumour types. Here we review the current state-of-the-art in the use of proteomics and metabolomics in soft tissue sarcomas. We highlight the utility of these Omics-based methodologies to identify new drug targets, synthetic lethal interactions, candidate therapeutics and novel biomarkers to facilitate patient stratification. Due to the unbiased and global nature of these profiling methods to assess the levels of protein expression, post-translational modifications such as phosphorylation and glycosylation as well as key metabolites, many of these findings have broad applications not just in specific histotypes but across multiple STS subtypes. Specific examples of proteomic and metabolomic findings that have led to the development of early phase clinical trials of investigational agents will be discussed. While promising, the use of these technologies in the study of sarcoma is still limited, and there is a need for further research in this area. In particular, it would be important to integrate these approaches with other Omics strategies such as genomics and epigenomics as well as implement these tools alongside clinical trials in order to maximize the impact of these tools on our biological understanding and treatment of this group of rare diseases of unmet need.
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Affiliation(s)
- Madhumeeta Chadha
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, SM2 5NG, UK
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, SM2 5NG, UK.
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100
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Zheng Y, Su L, Tan J, Dong F. Actinidia chinensis Planch Root extract suppresses the growth and metastasis of hypopharyngeal carcinoma by inhibiting E2F Transcription Factor 1-mediated MNX1 antisense RNA 1. Bioengineered 2022; 13:4911-4922. [PMID: 35152841 PMCID: PMC8973797 DOI: 10.1080/21655979.2022.2037226] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Increasing evidence has shown that traditional Chinese medicines and their bioactive components exert an anti-tumor effect, representing a novel treatment strategy. Actinidia chinensis Planch Root extracts (acRoots) have been reported to repress cancer cell proliferation and metastasis. The effect of acRoots on hypopharyngeal carcinoma progression was explored in this study. Firstly, data from MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) and colony formation assays showed that incubation with accRoots reduced cell proliferation of hypopharyngeal carcinoma cells. Moreover, acRoots promoted the cell apoptosis of hypopharyngeal carcinoma. Secondly, cell migration and invasion of hypopharyngeal carcinoma cells were suppressed by acRoots. Thirdly, E2F1 (E2F Transcription Factor 1) and lncRNA MNX1-AS1 (MNX1 antisense RNA 1) were up-regulated in hypopharyngeal carcinoma tissues, and reduced in hypopharyngeal carcinoma cells post acRoots incubation. Overexpression of E2F1 attenuated acRoots-induced decrease in MNX1-AS1 in hypopharyngeal carcinoma cells. Lastly, administration with acRoots retarded in vivo hypopharyngeal carcinoma growth through down-regulation of E2F1-mediated MNX1-AS1. In conclusion, acRoots exerted tumor-suppressive role in hypopharyngeal carcinoma through inhibition of E2F1-mediated MNX1-AS1.
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Affiliation(s)
- Yi Zheng
- Medical College, Soochow University, Suzhou, China
- Head and Neck & Otolaryngology Center, Plastic Surgery Center, Cancer Center, Department of Otolaryngology, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Lizhong Su
- Head and Neck & Otolaryngology Center, Plastic Surgery Center, Cancer Center, Department of Otolaryngology, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Jun Tan
- Head and Neck & Otolaryngology Center, Plastic Surgery Center, Cancer Center, Department of Otolaryngology, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Feilin Dong
- Head and Neck & Otolaryngology Center, Plastic Surgery Center, Cancer Center, Department of Otolaryngology, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
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