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Chini A, Guha P, Rishi A, Obaid M, Udden SN, Mandal SS. Discovery and functional characterization of LncRNAs associated with inflammation and macrophage activation. Methods 2024; 227:1-16. [PMID: 38703879 DOI: 10.1016/j.ymeth.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024] Open
Abstract
Long noncoding RNAs (lncRNA) are emerging players in regulation of gene expression and cell signaling and their dysregulation has been implicated in a multitude of human diseases. Recent studies from our laboratory revealed that lncRNAs play critical roles in cytokine regulation, inflammation, and metabolism. We demonstrated that lncRNA HOTAIR, which is a well-known regulator of gene silencing, plays critical roles in modulation of cytokines and proinflammatory genes, and glucose metabolism in macrophages during inflammation. In addition, we recently discovered a series of novel lncRNAs that are closely associated with inflammation and macrophage activation. We termed these as long-noncoding inflammation associated RNAs (LinfRNAs). We are currently engaged in the functional characterization of these hLinfRNAs (human LinfRNAs) with a focus on their roles in inflammation, and we are investigating their potential implications in chronic inflammatory human diseases. Here, we have summarized experimental methods that have been utilized for the discovery and functional characterization of lncRNAs in inflammation and macrophage activation.
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Affiliation(s)
- Avisankar Chini
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Prarthana Guha
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Ashcharya Rishi
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Monira Obaid
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Sm Nashir Udden
- Department of Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Subhrangsu S Mandal
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA.
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2
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Wei H, Wu X, Huang L, Long C, Lu Q, Huang Z, Huang Y, Li W, Pu J. LncRNA MEG3 Reduces the Ratio of M2/M1 Macrophages Through the HuR/CCL5 Axis in Hepatocellular Carcinoma. J Hepatocell Carcinoma 2024; 11:543-562. [PMID: 38496248 PMCID: PMC10943271 DOI: 10.2147/jhc.s449090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/07/2024] [Indexed: 03/19/2024] Open
Abstract
Objective Tumor-associated macrophages play a crucial role in the development of hepatocellular carcinoma (HCC). Our study aimed to investigate the relationship between long coding RNA (lncRNA) maternally expressed gene 3 (MEG3), RNA-binding protein human antigen R (HuR), and messenger RNA C-C motif chemokine 5 (CCL5) in the modulation of M1 and M2 macrophage polarization in HCC. Methods To induce M1 or M2 polarization, LPS/IFNγ- or IL4/IL13 were used to treat bone marrow derived macrophages (BMDMs). The localization of MEG3 in M1 and M2 macrophages was assessed using fluorescence in situ hybridization assay. Expression levels of MEG3, HuR, CCL5, M1, and M2 markers were measured by RT-qPCR or immunofluorescence staining. Flow cytometry was performed to determine the proportion of F4/80+CD206+ and F4/80+CD68+ cells. RNA pulldown assay was performed to detect the binding of lncRNA MEG3 and HuR. The impacts of HuR on CCL5 stability and activity of CCL5 promoter were evaluated using actinomycin D treatment and luciferase reporter assay. Cell migration, invasiveness, and angiogenesis were assessed using transwell migration and invasion assays and a tube formation assay. A mixture of Huh-7 cells and macrophages were injected into nude mice to explore the effect of MEG3 on tumorigenesis. Results MEG3 promoted M1-like polarization while dampening M2-like polarization of BMDMs. MEG3 bound to HuR in M1 and M2 macrophages. HuR downregulated CCL5 by inhibiting CCL5 transcription in macrophages. In addition, overexpression of MEG3 suppressed cell metastasis, invasion, and angiogenesis by obstructing macrophage M2 polarization. MEG3 inhibited tumorigenesis in HCC via promotion of M1-like polarization and inhibition of M2-like polarization. Rescue experiments showed that depletion of CCL5 in M2 macrophages reversed MEG3-induced suppressive effect on cell migration, invasion, and tube formation. Conclusion MEG3 suppresses HCC progression by promoting M1-like while inhibiting M2-like macrophage polarization via binding to HuR and thus upregulating CCL5.
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Affiliation(s)
- Huamei Wei
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, People’s Republic of China
| | - Xianjian Wu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, People’s Republic of China
| | - Lizheng Huang
- Graduate College of Youjiang Medical University for Nationalities, Baise, Guangxi, People’s Republic of China
| | - Chen Long
- Graduate College of Youjiang Medical University for Nationalities, Baise, Guangxi, People’s Republic of China
| | - Qi Lu
- Graduate College of Youjiang Medical University for Nationalities, Baise, Guangxi, People’s Republic of China
| | - Zheng Huang
- Graduate College of Youjiang Medical University for Nationalities, Baise, Guangxi, People’s Republic of China
| | - Yanyan Huang
- Graduate College of Youjiang Medical University for Nationalities, Baise, Guangxi, People’s Republic of China
| | - Wenchuan Li
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, People’s Republic of China
| | - Jian Pu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, People’s Republic of China
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Yao Y, Yang K, Wang Q, Zhu Z, Li S, Li B, Feng B, Tang C. Prediction of CAF-related genes in immunotherapy and drug sensitivity in hepatocellular carcinoma: a multi-database analysis. Genes Immun 2024; 25:55-65. [PMID: 38233508 PMCID: PMC10873201 DOI: 10.1038/s41435-024-00252-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 12/20/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
This study aims to identify the cancer-associated fibroblasts (CAF)-related genes that can affect immunotherapy and drug sensitivity in hepatocellular carcinoma (HCC). Expression data and survival data associated with HCC were obtained in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Weighted correlation network analysis (WGCNA) analysis was performed to obtain CAF-related genes. Least Absolute Shrinkage and Selection Operator (LASSO) regression was used for regression analysis and risk models. Subsequently, Gene Set Enrichment Analysis (GSEA) analysis, Gene Set Enrichment Analysis (ssGSEA) analysis, Tumor Immune Dysfunction and Exclusion (TIDE) analysis and drug sensitivity analysis were performed on the risk models. Survival analysis of CAF scores showed that the survival rate was lower in samples with high CAF scores than those with low scores. However, this difference was not significant, suggesting CAF may not directly influence the prognosis of HCC patients. Further screening of CAF-related genes yielded 33 CAF-related genes. Seven risk models constructed based on CDR2L, SPRED1, PFKP, ENG, KLF2, FSCN1 and VCAN, showed significant differences in immunotherapy and partial drug sensitivity in HCC. Seven CAF-related genes may have important roles in immunotherapy, drug sensitivity and prognostic survival in HCC patients.
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Affiliation(s)
- Yi Yao
- Division 1, Department of Hepatobiliary and Pancreatic Surgery, Zhuzhou Central Hospital, Zhuzhou, Hunan, China
| | - KaiQing Yang
- Division 1, Department of Hepatobiliary and Pancreatic Surgery, Zhuzhou Central Hospital, Zhuzhou, Hunan, China
| | - Qiang Wang
- Division 1, Department of Hepatobiliary and Pancreatic Surgery, Zhuzhou Central Hospital, Zhuzhou, Hunan, China
| | - Zeming Zhu
- Division 2, Department of Hepatobiliary and Pancreatic Surgery, Zhuzhou Central Hospital, Zhuzhou, Hunan, China
| | - Sheng Li
- Division 1, Department of Hepatobiliary and Pancreatic Surgery, Zhuzhou Central Hospital, Zhuzhou, Hunan, China
| | - Bin Li
- Division 1, Department of Hepatobiliary and Pancreatic Surgery, Zhuzhou Central Hospital, Zhuzhou, Hunan, China
| | - Bin Feng
- Department of Hepatobiliary and Pancreatic Surgery, Zhuzhou Central Hospital, Zhuzhou, Hunan, China.
| | - Caixi Tang
- Department of Hepatobiliary and Pancreatic Surgery, Zhuzhou Central Hospital, Zhuzhou, Hunan, China.
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Naaldijk Y, Sherman LS, Turrini N, Kenfack Y, Ratajczak MZ, Souayah N, Rameshwar P, Ulrich H. Mesenchymal Stem Cell-Macrophage Crosstalk Provides Specific Exosomal Cargo to Direct Immune Response Licensing of Macrophages during Inflammatory Responses. Stem Cell Rev Rep 2024; 20:218-236. [PMID: 37851277 DOI: 10.1007/s12015-023-10612-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2023] [Indexed: 10/19/2023]
Abstract
Neurodegenerative diseases (NDDs) continue to be a significant healthcare problem. The economic and social implications of NDDs increase with longevity. NDDs are linked to neuroinflammation and activated microglia and astrocytes play a central role. There is a growing interest for stem cell-based therapy to deliver genes, and for tissue regeneration. The promise of mesenchymal stem cells (MSC) is based on their availability as off-the-shelf source, and ease of expanding from discarded tissues. We tested the hypothesis that MSC have a major role of resetting activated microglial cells. We modeled microglial cell lines by using U937 cell-derived M1 and M2 macrophages. We studied macrophage types, alone, or in a non-contact culture with MSCs. MSCs induced significant release of exosomes from both types of macrophages, but significantly more of the M1 type. RNA sequencing showed enhanced gene expression within the exosomes with the major changes linked to the inflammatory response, including cytokines and the purinergic receptors. Computational analyses of the transcripts supported the expected effect of MSCs in suppressing the inflammatory response of M1 macrophages. The inflammatory cargo of M1 macrophage-derived exosomes revealed involvement of cytokines and purinergic receptors. At the same time, the exosomes from MSC-M2 macrophages were able to reset the classical M2 macrophages to more balanced inflammation. Interestingly, we excluded transfer of purinergic receptor transcripts from the co-cultured MSCs by analyzing these cells for the identified purinergic receptors. Since exosomes are intercellular communicators, these findings provide insights into how MSCs may modulate tissue regeneration and neuroinflammation.
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Affiliation(s)
- Yahaira Naaldijk
- Department of Medicine, Rutgers New Jersey Medical School (NJMS), Newark, NJ, USA
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Lauren S Sherman
- Department of Medicine, Rutgers New Jersey Medical School (NJMS), Newark, NJ, USA
- Rutgers School of Graduate Studies at NHMS, Newark, NJ, USA
| | - Natalia Turrini
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, 05508-000, Brazil
| | | | - Mariusz Z Ratajczak
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
- Laboratory of Regenerative Medicine at Medical University of Warsaw, Warsaw, Poland
| | - Nizar Souayah
- Department of Neurology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Pranela Rameshwar
- Department of Medicine, Rutgers New Jersey Medical School (NJMS), Newark, NJ, USA.
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, 05508-000, Brazil.
- Department of Neuroscience and Physiology, Rutgers New Jersey Medical School, Newark, NJ, USA.
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5
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Hayashi Y, Yamamoto Y, Murakami I. Micromorphological observation of HLE cells under knockdown of Fascin using LV-SEM. Med Mol Morphol 2023; 56:257-265. [PMID: 37526656 DOI: 10.1007/s00795-023-00362-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/19/2023] [Indexed: 08/02/2023]
Abstract
Liver cancer is one of the most prevalent cancers in Japan with hepatocellular carcinoma (HCC) as the major histological subtype. Successful novel treatments for HCC have been reported; however, recurrences or metastasis may occur, which results in poor prognoses and high mortality of HCC patients. Fascin, an actin-bundling protein, regulates cell adhesion, migration, and invasion. Its overexpression positively correlates with poor prognosis of malignant tumors, and Fascin is considered as one of the tumor biomarkers and therapeutic target proteins. In this study, we attempted to reveal the relationship between Fascin and HCC using HLE, one of the human HCC cell lines. We performed the study with classical immunocytochemistry and recently developed techniques, such as wound-healing assay, spheroid cultivation, and low-vacuum scanning electron microscopy (LV-SEM). Non-Fascin-knockdown (FKD) cell spheroid had a regular spherical appearance with tight cell-cell connections, while FKD cell spheroid had an irregular shape with loose cell-cell connections. Cells of non-FKD spheroid presented fibrous protrusions on the cell surface, contrarily, cells of FKD spheroids showed bulbous-shaped protrusions. Morphological observation of FKD and non-FKD HLE spheroids were performed using LV-SEM. Our study may help to reveal the roles of Fascin in the process of HCC formation and its malignancy.
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Affiliation(s)
- Yoshihiro Hayashi
- Department of Pathology, School of Medicine, Kochi University, 185-1, Kohasu, Oko-Cho, Nankoku, 783-8505, Japan
- Equipment of Support Planning Office, Kochi University, 185-1, Kohasu, Oko-Cho, Nankoku, 783-8505, Japan
| | - Yumiko Yamamoto
- Department of Diagnostic Pathology, Kochi University Hospital, Kochi University, 185-1, Kohasu, Oko-Cho, Nankoku, 783-8505, Japan.
| | - Ichiro Murakami
- Department of Pathology, School of Medicine, Kochi University, 185-1, Kohasu, Oko-Cho, Nankoku, 783-8505, Japan
- Department of Diagnostic Pathology, Kochi University Hospital, Kochi University, 185-1, Kohasu, Oko-Cho, Nankoku, 783-8505, Japan
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Wei H, Huang L, Lu Q, Huang Z, Huang Y, Xu Z, Li W, Pu J. N 6-Methyladenosine-Modified LEAWBIH Drives Hepatocellular Carcinoma Progression through Epigenetically Activating Wnt/β-Catenin Signaling. J Hepatocell Carcinoma 2023; 10:1991-2007. [PMID: 37954496 PMCID: PMC10637240 DOI: 10.2147/jhc.s433070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
Purpose N6-methyladenosine (m6A) modification plays an important role in regulating RNA maturation, stability, and translation. Thus, m6A modification is involved in various pathophysiological processes including hepatocellular carcinoma (HCC). However, the direct contribution of m6A modifications to RNA function in HCC remains unclear. Here, we identified LEAWBIH (long non-coding RNA epigenetically activating Wnt/β-catenin signalling in HCC) as an m6A-modified long non-coding RNA (lncRNA) and investigated the effects of m6A on the function of LEAWBIH in HCC. Methods Quantitative polymerase chain reaction was performed to measure the gene expression in tissues and cells. The level of m6A modification was detected using a methylated RNA immunoprecipitation assay and single-base elongation- and ligation-based qPCR amplification method. Cell proliferation was evaluated using the Glo cell viability and CCK-8 assays. Cell migration and invasion were evaluated using Transwell migration and invasion assays. The mechanisms of m6A modified LEAWBIH were investigated using chromatin isolation by RNA purification, chromatin immunoprecipitation, and dual-luciferase reporter assays. Results LEAWBIH was highly expressed and correlated with poor survival in HCC patients. LEAWBIH was identified as a m6A-modified transcript. m6A modification increased LEAWBIH transcript stability. The m6A modification level of LEAWBIH was increased in HCC, and a high m6A modification level of LEAWBIH predicted poor survival. LEAWBIH promotes HCC cell proliferation, migration, and invasion in an m6A modification-dependent manner. Mechanistic investigations revealed that m6A-modified LEAWBIH activated Wnt/β-catenin signaling. m6A-modified LEAWBIH binds to the m6A reader YTHDC1, which further interacts with and recruits H3K9me2 demethylase KDM3B to CTNNB1 promoter, leading to H3K9me2 demethylation and CTNNB1 transcription activation. Functional rescue assays showed that blocking Wnt/β-catenin signaling abolished the role of LEAWBIH in HCC. Conclusion m6A-modified LEAWBIH exerts oncogenic effects in HCC by epigenetically activating Wnt/β-catenin signaling, highlighting m6A-modified LEAWBIH as a promising therapeutic target for HCC.
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Affiliation(s)
- Huamei Wei
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, People’s Republic of China
| | - Lizheng Huang
- Graduate College of Youjiang Medical University for Nationalities, Baise, People’s Republic of China
| | - Qi Lu
- Graduate College of Youjiang Medical University for Nationalities, Baise, People’s Republic of China
| | - Zheng Huang
- Graduate College of Youjiang Medical University for Nationalities, Baise, People’s Republic of China
| | - Yanyan Huang
- Graduate College of Youjiang Medical University for Nationalities, Baise, People’s Republic of China
| | - Zuoming Xu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, People’s Republic of China
| | - Wenchuan Li
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, People’s Republic of China
| | - Jian Pu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, People’s Republic of China
- Guangxi Clinical Medical Research Center of Hepatobiliary Disease, Baise, People’s Republic of China
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7
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Wei H, Yang J, Lu R, Huang Y, Huang Z, Huang L, Zeng M, Wei Y, Xu Z, Li W, Pu J. m 6A modification of AC026356.1 facilitates hepatocellular carcinoma progression by regulating the IGF2BP1-IL11 axis. Sci Rep 2023; 13:19124. [PMID: 37926706 PMCID: PMC10625930 DOI: 10.1038/s41598-023-45449-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023] Open
Abstract
N6-methyladenosine (m6A) is the most common RNA modification in eukaryotic RNAs. Although the important roles of m6A in RNA fate have been revealed, the potential contribution of m6A to RNA function in various diseases, including hepatocellular carcinoma (HCC), is still unclear. In this study, we identified a novel m6A-modified RNA AC026356.1. We found that AC026356.1 was increased in HCC tissues and cell lines. High expression of AC026356.1 was correlated with poor survival of HCC patients. m6A modification level of AC026356.1 was also increased in HCC and more significantly correlated with poor survival of HCC patients. Functional assays showed that m6A-modified AC026356.1 promoted HCC cellular proliferation, migration, and liver metastasis. Gene set enrichment analysis showed that AC026356.1 activated IL11/STAT3 signaling. Mechanistic investigation showed that m6A-modified AC026356.1 bound to IGF2BP1. The interaction between m6A-modified AC026356.1 and IGF2BP1 promoted the binding of IL11 mRNA to IGF2BP1, leading to increased IL11 mRNA stability and IL11 secretion. Functional rescue assays showed that depletion of IL11 reversed the oncogenic roles of AC026356.1. These findings revealed the potential influences of m6A modification on RNA biological functions and suggested that targeting m6A modification may be a novel strategy for HCC treatment.
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Affiliation(s)
- Huamei Wei
- Clinical Pathological Diagnosis and Research Centre, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Jinhun Yang
- Graduate College of Youjiang Medical University for Nationalities, Baise, China
| | - Rongzhou Lu
- Graduate College of Youjiang Medical University for Nationalities, Baise, China
| | - Yanyan Huang
- Graduate College of Youjiang Medical University for Nationalities, Baise, China
| | - Zheng Huang
- Graduate College of Youjiang Medical University for Nationalities, Baise, China
| | - Lizheng Huang
- Graduate College of Youjiang Medical University for Nationalities, Baise, China
| | - Min Zeng
- Graduate College of Youjiang Medical University for Nationalities, Baise, China
| | - Yunyu Wei
- Graduate College of Youjiang Medical University for Nationalities, Baise, China
| | - Zuoming Xu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, No. 18 Zhongshan Two Road, Baise, 533000, China
| | - Wenchuan Li
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, No. 18 Zhongshan Two Road, Baise, 533000, China
| | - Jian Pu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, No. 18 Zhongshan Two Road, Baise, 533000, China.
- Guangxi Clinical Medical Research Center of Hepatobiliary Diseases, Baise, China.
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8
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Yang D, Kuang T, Zhou Y, Su Y, Shen J, Yu B, Zhao K, Ding Y. Tumor-associated endothelial cell prognostic risk model and tumor immune environment modulation in liver cancer based on single-cell and bulk RNA sequencing: Experimental verification. Int Immunopharmacol 2023; 124:110870. [PMID: 37690233 DOI: 10.1016/j.intimp.2023.110870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 08/08/2023] [Accepted: 08/27/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND To build a prognostic and immunotherapeutic response prediction model for liver cancer based on marker genes of tumor-associated endothelial cell (TEC). METHOD Single cell sequencing data from Gene Expression Omnibus (GEO) liver cancer patients were utilized to identify TEC subpopulations. Models were built from transcriptomic and clinical data of TCGA liver cancer patients. The GSE76427 and ICGC databases were used as independent validation sets. Time-dependent receiver operating characteristic (ROC) curves and Kaplan-Meier curves were used to verify the ability of the model to predict survival. XCELL, TIMER, QUANTISEQ, CIBERSORT, CIBERSORT-ABS, and ssGSEA were applied to evaluate tumor immune cell infiltration. The TIDE score was used to predict the effect of immunotherapy. Immune blockade checkpoint gene, tumor mutational load and GSVA enrichment analyses were further explored. The expression levels of candidate genes were measured and validated by real-time PCR between liver cancer tissues and adjacent nontumor liver tissues. RESULTS Eighty-seven genes were identified as marker genes for TECs. IGFBP3, RHOC, S100A16, FSCN1, and CLEC3B were included in the constructed prognostic model. Time-dependent ROC curve values were higher than 0.700 in both the model and validation groups. The low risk group exhibited high immune cell infiltration and function than the higher risk group. The TIDE score indicated that the low-risk group benefited more from immunotherapy than the high-risk group. The risk score and multiple immune blockade checkpoint genes and immune-related pathways were strongly correlated. CONCLUSION Novel signatures of TEC marker genes showed a powerful ability to predict prognosis and immunotherapy response in patients with liver cancer.
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Affiliation(s)
- Dashuai Yang
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, No. 99 Zhangzhidong Road, Wuchang District, Wuhan 430060, China.
| | - Tianrui Kuang
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, No. 99 Zhangzhidong Road, Wuchang District, Wuhan 430060, China.
| | - Yu Zhou
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, No. 99 Zhangzhidong Road, Wuchang District, Wuhan 430060, China.
| | - Yang Su
- Department of Gastrointestinal Surgery, Tongji Hospital, Tongji Medical College in Huazhong University of Science and Technology, Wuhan 430060, Hubei, China.
| | - Jie Shen
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, No. 99 Zhangzhidong Road, Wuchang District, Wuhan 430060, China.
| | - Bin Yu
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, No. 99 Zhangzhidong Road, Wuchang District, Wuhan 430060, China.
| | - Kailiang Zhao
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, No. 99 Zhangzhidong Road, Wuchang District, Wuhan 430060, China.
| | - Youming Ding
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, No. 99 Zhangzhidong Road, Wuchang District, Wuhan 430060, China.
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9
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Pu J, Xu Z, Huang Y, Nian J, Yang M, Fang Q, Wei Q, Huang Z, Liu G, Wang J, Wu X, Wei H. N 6 -methyladenosine-modified FAM111A-DT promotes hepatocellular carcinoma growth via epigenetically activating FAM111A. Cancer Sci 2023; 114:3649-3665. [PMID: 37400994 PMCID: PMC10475779 DOI: 10.1111/cas.15886] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 07/05/2023] Open
Abstract
As an epitranscriptomic modulation manner, N6 -methyladenosine (m6 A) modification plays important roles in various diseases, including hepatocellular carcinoma (HCC). m6 A modification affects the fate of RNAs. The potential contributions of m6 A to the functions of RNA still need further investigation. In this study, we identified long noncoding RNA FAM111A-DT as an m6 A-modified RNA and confirmed three m6 A sites on FAM111A-DT. The m6 A modification level of FAM111A-DT was increased in HCC tissues and cell lines, and increased m6 A level was correlated with poor survival of HCC patients. m6 A modification increased the stability of FAM111A-DT transcript, whose expression level showed similar clinical relevance to that of the m6 A level of FAM111A-DT. Functional assays found that only m6 A-modified FAM111A-DT promoted HCC cellular proliferation, DNA replication, and HCC tumor growth. Mutation of m6 A sites on FAM111A-DT abolished the roles of FAM111A-DT. Mechanistic investigations found that m6 A-modified FAM111A-DT bound to FAM111A promoter and also interacted with m6 A reader YTHDC1, which further bound and recruited histone demethylase KDM3B to FAM111A promoter, leading to the reduction of the repressive histone mark H3K9me2 and transcriptional activation of FAM111A. The expression of FAM111A was positively correlated with the m6 A level of FAM111A-DT, and the expression of methyltransferase complex, YTHDC1, and KDM3B in HCC tissues. Depletion of FAM111A largely attenuated the roles of m6 A-modified FAM111A-DT in HCC. In summary, the m6 A-modified FAM111A-DT/YTHDC1/KDM3B/FAM111A regulatory axis promoted HCC growth and represented a candidate therapeutic target for HCC.
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Affiliation(s)
- Jian Pu
- Department of Hepatobiliary SurgeryAffiliated Hospital of Youjiang Medical University for NationalitiesBaiseChina
| | - Zuoming Xu
- Department of Hepatobiliary SurgeryAffiliated Hospital of Youjiang Medical University for NationalitiesBaiseChina
| | - Youguan Huang
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Jiahui Nian
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Meng Yang
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Quan Fang
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Qing Wei
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Zihua Huang
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Guoman Liu
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Jianchu Wang
- Department of Hepatobiliary SurgeryAffiliated Hospital of Youjiang Medical University for NationalitiesBaiseChina
| | - Xianjian Wu
- Graduate College of Youjiang Medical University for NationalitiesBaiseChina
| | - Huamei Wei
- Department of PathologyAffiliated Hospital of Youjiang Medical University for NationalitiesBaiseChina
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Kimura T, Tartaglia GG. Editorial: Mechanisms of action of natural antisense transcripts on the post-transcriptional regulation of sense protein coding gene expression during development and in cancer. Front Mol Biosci 2023; 10:1268124. [PMID: 37711390 PMCID: PMC10499381 DOI: 10.3389/fmolb.2023.1268124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 09/16/2023] Open
Affiliation(s)
- Tominori Kimura
- Laboratory of Microbiology and Cell Biology, Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
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11
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Cao M, Ren Y, Li Y, Deng J, Su X, Tang Y, Yuan F, Deng H, Yang G, He Z, Liu B, Yao Z, Deng M. Lnc-ZEB2-19 Inhibits the Progression and Lenvatinib Resistance of Hepatocellular Carcinoma by Attenuating the NF-κB Signaling Pathway through the TRA2A/RSPH14 Axis. Int J Biol Sci 2023; 19:3678-3693. [PMID: 37564197 PMCID: PMC10411463 DOI: 10.7150/ijbs.85270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023] Open
Abstract
Long non-coding RNAs have been reported to play a crucial role in tumor progression in hepatocellular carcinoma (HCC). Lnc-ZEB2-19 has been validated to be deficiently expressed in HCC. However, the capabilities and underlying mechanisms of lnc-ZEB2-19 remain uncertain. In this study, we verified that the downregulation of lnc-ZEB2-19 was prevalent in HCC and significantly correlated with the unfavorable prognosis. Further in vitro and in vivo verified that lnc-ZEB2-19 notably inhibited the proliferation, metastasis, stemness, and lenvatinib resistance (LR) of HCC cells. Mechanistically, lnc-ZEB2-19 inhibited HCC progression and LR by specifically binding to transformer 2α (TRA2A) and promoting its degradation, which resulted in the instability of RSPH14 mRNA, leading to the downregulation of Rela(p65) and p-Rela(p-p65). Furthermore, rescue assays showed that silencing RSPH14 partially restrained the effect of knockdown expression of lnc-ZEB2-19 on HCC cell metastatic ability and stemness. The findings describe a novel regulatory axis, lnc-ZEB2-19/TRA2A/RSPH14, downregulating the nuclear factor kappa B to inhibit HCC progression and LR.
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Affiliation(s)
- Mingbo Cao
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Yupeng Ren
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Yuxuan Li
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Junfeng Deng
- Department of Hepatobiliary & Pancreatic Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Xiaorui Su
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Yongchang Tang
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, China
| | - Feng Yuan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Haixia Deng
- Department of Hepatobiliary & Pancreatic Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Gaoyuan Yang
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Zhiwei He
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Bo Liu
- Department of Hepatobiliary & Pancreatic Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Zhicheng Yao
- Department of Hepatobiliary & Pancreatic Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Meihai Deng
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
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12
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Khorkova O, Stahl J, Joji A, Volmar CH, Zeier Z, Wahlestedt C. Long non-coding RNA-targeting therapeutics: discovery and development update. Expert Opin Drug Discov 2023; 18:1011-1029. [PMID: 37466388 DOI: 10.1080/17460441.2023.2236552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023]
Abstract
INTRODUCTION lncRNAs are major players in regulatory networks orchestrating multiple cellular functions, such as 3D chromosomal interactions, epigenetic modifications, gene expression and others. Due to progress in the development of nucleic acid-based therapeutics, lncRNAs potentially represent easily accessible therapeutic targets. AREAS COVERED Currently, significant efforts are directed at studies that can tap the enormous therapeutic potential of lncRNAs. This review describes recent developments in this field, particularly focusing on clinical applications. EXPERT OPINION Extensive druggable target range of lncRNA combined with high specificity and accelerated development process of nucleic acid-based therapeutics open new prospects for treatment in areas of extreme unmet medical need, such as genetic diseases, aggressive cancers, protein deficiencies, and subsets of common diseases caused by known mutations. Although currently wide acceptance of lncRNA-targeting nucleic acid-based therapeutics is impeded by the need for parenteral or direct-to-CNS administration, development of less invasive techniques and orally available/BBB-penetrant nucleic acid-based therapeutics is showing early successes. Recently, mRNA-based COVID-19 vaccines have demonstrated clinical safety of all aspects of nucleic acid-based therapeutic technology, including multiple chemical modifications of nucleic acids and nanoparticle delivery. These trends position lncRNA-targeting drugs as significant players in the future of drug development, especially in the area of personalized medicine.
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Affiliation(s)
- Olga Khorkova
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Jack Stahl
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Aswathy Joji
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Claude-Henry Volmar
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Zane Zeier
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
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13
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Mosca N, Russo A, Potenza N. Making Sense of Antisense lncRNAs in Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:8886. [PMID: 37240232 PMCID: PMC10219390 DOI: 10.3390/ijms24108886] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Transcriptome complexity is emerging as an unprecedented and fascinating domain, especially by high-throughput sequencing technologies that have unveiled a plethora of new non-coding RNA biotypes. This review covers antisense long non-coding RNAs, i.e., lncRNAs transcribed from the opposite strand of other known genes, and their role in hepatocellular carcinoma (HCC). Several sense-antisense transcript pairs have been recently annotated, especially from mammalian genomes, and an understanding of their evolutionary sense and functional role for human health and diseases is only beginning. Antisense lncRNAs dysregulation is significantly involved in hepatocarcinogenesis, where they can act as oncogenes or oncosuppressors, thus playing a key role in tumor onset, progression, and chemoradiotherapy response, as deduced from many studies discussed here. Mechanistically, antisense lncRNAs regulate gene expression by exploiting various molecular mechanisms shared with other ncRNA molecules, and exploit special mechanisms on their corresponding sense gene due to sequence complementarity, thus exerting epigenetic, transcriptional, post-transcriptional, and translational controls. The next challenges will be piecing together the complex RNA regulatory networks driven by antisense lncRNAs and, ultimately, assigning them a function in physiological and pathological contexts, in addition to defining prospective novel therapeutic targets and innovative diagnostic tools.
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Affiliation(s)
| | | | - Nicoletta Potenza
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (N.M.); (A.R.)
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14
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Hashemi M, Nadafzadeh N, Imani MH, Rajabi R, Ziaolhagh S, Bayanzadeh SD, Norouzi R, Rafiei R, Koohpar ZK, Raei B, Zandieh MA, Salimimoghadam S, Entezari M, Taheriazam A, Alexiou A, Papadakis M, Tan SC. Targeting and regulation of autophagy in hepatocellular carcinoma: revisiting the molecular interactions and mechanisms for new therapy approaches. Cell Commun Signal 2023; 21:32. [PMID: 36759819 PMCID: PMC9912665 DOI: 10.1186/s12964-023-01053-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/15/2023] [Indexed: 02/11/2023] Open
Abstract
Autophagy is an evolutionarily conserved process that plays a role in regulating homeostasis under physiological conditions. However, dysregulation of autophagy is observed in the development of human diseases, especially cancer. Autophagy has reciprocal functions in cancer and may be responsible for either survival or death. Hepatocellular carcinoma (HCC) is one of the most lethal and common malignancies of the liver, and smoking, infection, and alcohol consumption can lead to its development. Genetic mutations and alterations in molecular processes can exacerbate the progression of HCC. The function of autophagy in HCC is controversial and may be both tumor suppressive and tumor promoting. Activation of autophagy may affect apoptosis in HCC and is a regulator of proliferation and glucose metabolism. Induction of autophagy may promote tumor metastasis via induction of EMT. In addition, autophagy is a regulator of stem cell formation in HCC, and pro-survival autophagy leads to cancer cell resistance to chemotherapy and radiotherapy. Targeting autophagy impairs growth and metastasis in HCC and improves tumor cell response to therapy. Of note, a large number of signaling pathways such as STAT3, Wnt, miRNAs, lncRNAs, and circRNAs regulate autophagy in HCC. Moreover, regulation of autophagy (induction or inhibition) by antitumor agents could be suggested for effective treatment of HCC. In this paper, we comprehensively review the role and mechanisms of autophagy in HCC and discuss the potential benefit of targeting this process in the treatment of the cancer. Video Abstract.
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Affiliation(s)
- Mehrdad Hashemi
- grid.411463.50000 0001 0706 2472Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran ,grid.411463.50000 0001 0706 2472Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Niloufar Nadafzadeh
- grid.411463.50000 0001 0706 2472Faculty of Veterinary Medicine, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Hassan Imani
- grid.411463.50000 0001 0706 2472Department of Clinical Science, Faculty of Veterinary Medicine, Shahr-E Kord Branch, Islamic Azad University, Tehran, Chaharmahal and Bakhtiari Iran
| | - Romina Rajabi
- grid.411463.50000 0001 0706 2472Faculty of Veterinary Medicine, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Setayesh Ziaolhagh
- grid.411463.50000 0001 0706 2472Faculty of Veterinary Medicine, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Seyedeh Delaram Bayanzadeh
- grid.411463.50000 0001 0706 2472Faculty of Veterinary Medicine, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Raheleh Norouzi
- grid.411463.50000 0001 0706 2472Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Reihaneh Rafiei
- grid.411463.50000 0001 0706 2472Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Zeinab Khazaei Koohpar
- grid.464599.30000 0004 0494 3188Department of Cell and Molecular Biology, Faculty of Biological Sciences, Tonekabon Branch, Islamic Azad University, Tonekabon, Iran
| | - Behnaz Raei
- grid.411463.50000 0001 0706 2472Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohammad Arad Zandieh
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
| | - Shokooh Salimimoghadam
- grid.412504.60000 0004 0612 5699Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Maliheh Entezari
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran. .,Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran. .,Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Athanasios Alexiou
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, Australia ,AFNP Med Austria, Vienna, Austria
| | - Marios Papadakis
- Department of Surgery II, University Hospital Witten-Herdecke, University of Witten-Herdecke, Heusnerstrasse 40, 42283, Wuppertal, Germany.
| | - Shing Cheng Tan
- grid.412113.40000 0004 1937 1557UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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15
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Khorkova O, Stahl J, Joji A, Volmar CH, Zeier Z, Wahlestedt C. Natural antisense transcripts as drug targets. Front Mol Biosci 2022; 9:978375. [PMID: 36250017 PMCID: PMC9563854 DOI: 10.3389/fmolb.2022.978375] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
The recent discovery of vast non-coding RNA-based regulatory networks that can be easily modulated by nucleic acid-based drugs has opened numerous new therapeutic possibilities. Long non-coding RNA, and natural antisense transcripts (NATs) in particular, play a significant role in networks that involve a wide variety of disease-relevant biological mechanisms such as transcription, splicing, translation, mRNA degradation and others. Currently, significant efforts are dedicated to harnessing these newly emerging NAT-mediated biological mechanisms for therapeutic purposes. This review will highlight the recent clinical and pre-clinical developments in this field and survey the advances in nucleic acid-based drug technologies that make these developments possible.
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Affiliation(s)
- Olga Khorkova
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
| | - Jack Stahl
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
| | - Aswathy Joji
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
- Department of Chemistry, University of Miami, Miami, FL, United States
| | - Claude-Henry Volmar
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
| | - Zane Zeier
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
| | - Claes Wahlestedt
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
- Department of Chemistry, University of Miami, Miami, FL, United States
- *Correspondence: Claes Wahlestedt,
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16
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Qu X, Zhao X, Lin K, Wang N, Li X, Li S, Zhang L, Shi Y. M2-like tumor-associated macrophage-related biomarkers to construct a novel prognostic signature, reveal the immune landscape, and screen drugs in hepatocellular carcinoma. Front Immunol 2022; 13:994019. [PMID: 36177006 PMCID: PMC9513313 DOI: 10.3389/fimmu.2022.994019] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/25/2022] [Indexed: 12/23/2022] Open
Abstract
BackgroundM2-like tumor-associated macrophages (M2-like TAMs) have important roles in the progression and therapeutics of cancers. We aimed to detect novel M2-like TAM-related biomarkers in hepatocellular carcinoma (HCC) via integrative analysis of single-cell RNA-seq (scRNA-seq) and bulk RNA-seq data to construct a novel prognostic signature, reveal the “immune landscape”, and screen drugs in HCC.MethodsM2-like TAM-related genes were obtained by overlapping the marker genes of TAM identified from scRNA-seq data and M2 macrophage modular genes identified by weighted gene co-expression network analysis (WGCNA) using bulk RNA-seq data. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses were carried out to screen prognostic genes from M2-like TAM-related genes, followed by a construction of a prognostic signature, delineation of risk groups, and external validation of the prognostic signature. Analyses of immune cells, immune function, immune evasion scores, and immune-checkpoint genes between high- and low-risk groups were done to further reveal the immune landscape of HCC patients. To screen potential HCC therapeutic agents, analyses of gene–drug correlation and sensitivity to anti-cancer drugs were conducted.ResultsA total of 127 M2-like TAM-related genes were identified by integrative analysis of scRNA-seq and bulk-seq data. PDLIM3, PAM, PDLIM7, FSCN1, DPYSL2, ARID5B, LGALS3, and KLF2 were screened as prognostic genes in HCC by univariate Cox regression and LASSO regression analyses. Then, a prognostic signature was constructed and validated based on those genes for predicting the survival of HCC patients. In terms of drug screening, expression of PAM and LGALS3 was correlated positively with sensitivity to simvastatin and ARRY-162, respectively. Based on risk grouping, we predicted 10 anticancer drugs with high sensitivity in the high-risk group, with epothilone B having the lowest half-maximal inhibitory concentration among all drugs tested.ConclusionsOur findings enhance understanding of the M2-like TAM-related molecular mechanisms involved in HCC, reveal the immune landscape of HCC, and provide potential targets for HCC treatment.
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17
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The cell-line-derived subcutaneous tumor model in preclinical cancer research. Nat Protoc 2022; 17:2108-2128. [PMID: 35859135 DOI: 10.1038/s41596-022-00709-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 03/31/2022] [Indexed: 01/09/2023]
Abstract
Tumor-bearing experimental animals are essential for preclinical cancer drug development. A broad range of tumor models is available, with the simplest and most widely used involving a tumor of mouse or human origin growing beneath the skin of a mouse: the subcutaneous tumor model. Here, we outline the different types of in vivo tumor model, including some of their advantages and disadvantages and how they fit into the drug-development process. We then describe in more detail the subcutaneous tumor model and key steps needed to establish it in the laboratory, namely: choosing the mouse strain and tumor cells; cell culture, preparation and injection of tumor cells; determining tumor volume; mouse welfare; and an appropriate experimental end point. The protocol leads to subcutaneous tumor growth usually within 1-3 weeks of cell injection and is suitable for those with experience in tissue culture and mouse experimentation.
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18
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Lu X, Zhao N, Duan G, Deng Z, Lu Y. Testis developmental related gene 1 promotes non-small-cell lung cancer through the microRNA-214-5p/Krüppel-like factor 5 axis. Bioengineered 2022; 13:603-616. [PMID: 34856848 PMCID: PMC8805868 DOI: 10.1080/21655979.2021.2012406] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/25/2021] [Indexed: 10/29/2022] Open
Abstract
Non-small-cell lung cancer (NSCLC) is a frequent malignancy and has a high global incidence. Long noncoding RNAs (lncRNAs) are implicated in carcinogenesis and tumor progression. LncRNA testis developmental related gene 1 (TDRG1) plays a pivotal role in many cancers. This study researched the biological regulatory mechanisms of TDRG1 in NSCLC. Gene expression was assessed by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR). Changes in the NSCLC cell phenotypes were examined using 5-ethynyl-2'-deoxyuridine (EdU), cell counting kit-8 (CCK-8), wound healing, flow cytometry, and Transwell assays. The binding capacity between TDRG1, microRNA-214-5p (miR‑214-5p), and Krüppel-like factor 5 (KLF5) was tested using luciferase reporter and RNA immunoprecipitation (RIP) assays. In this study, we found that TDRG1 was upregulated in NSCLC samples. Functionally, TDRG1 depletion inhibited NSCLC cell growth, migration, and invasion and accelerated apoptosis. In addition, TDRG1 interacted with miR-214-5p, and miR-214-5p directly targeted KLF5. The suppressive effect of TDRG1 knockdown on NSCLC cellular processes was abolished by KLF5 overexpression. Overall, TDRG1 exerts carcinogenic effects in NSCLC by regulating the miR-214-5p/KLF5 axis.
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Affiliation(s)
- Xudong Lu
- Soochow University, Suzhou, Jiangsu, China
- Department of Pulmonary and Critical Care Medicine, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, Jiangsu, China
| | - Nian Zhao
- Department of Pulmonary and Critical Care Medicine, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, Jiangsu, China
| | - Guangjun Duan
- Department of Pulmonary and Critical Care Medicine, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, Jiangsu, China
| | - Zhiyong Deng
- Department of Science and Technology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, Jiangsu, China
| | - Yimin Lu
- Soochow University, Suzhou, Jiangsu, China
- Department of Pulmonary and Critical Care Medicine, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, Jiangsu, China
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