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Wu W, Zhu S, Wu Y, Dai L, Zhao J, Jiang Z. Long intergenic non-protein-coding RNA 1547 acts as a competing endogenous RNA and exerts cancer-promoting activity in non-small cell lung cancer by targeting the microRNA-195-5p/ homeobox C8 axis. Heliyon 2023; 9:e18015. [PMID: 37560663 PMCID: PMC10407678 DOI: 10.1016/j.heliyon.2023.e18015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 06/28/2023] [Accepted: 07/05/2023] [Indexed: 08/11/2023] Open
Abstract
Long intergenic non-protein coding RNA 1547 (LINC01547) presents a notable relationship with prognosis in patients with ovarian cancer. Herein, we examined the expression of LINC01547 in non-small cell lung cancer (NSCLC) to ascertain its clinical significance. We also explored the detailed functions of LINC01547 in regulating the aggressive phenotype of NSCLC and the molecular mechanism of action underlying its carcinogenic activities events in NSCLC. Furthermore, we applied the data acquired from the tissue specimens and the Cancer Genome Atlas (TCGA) database to analyze the level of LINC01547 in NSCLC and conducted functional assays to address the regulatory effect of LINC01547. Further, we examined the mechanistic interaction among LINC01547, microRNA-195-5p (miR-195-5p), and homeobox C8 (HOXC8) using bioinformatics prediction and luciferase reporter assay. LINC01547 was noticeably overexpressed, as affirmed by data from TCGA and our own cohort; moreover, poor prognosis was associated with increased LINC01547 levels in patients with NSCLC. LINC01547 regulates cell proliferation, colony-forming, migration, and invasion, and its absence produced tumor-repressing effects in NSCLC. Mechanistically, as a competitive endogenous RNA, LINC01547 decoyed miR-195-5p and consequently resulted in the overexpression of HOXC8 in NSCLC cells. Using rescue experiments, we found that the regulatory activities of LINC01547 deficient in repressing the malignant properties of NSCLC cells could be counteracted by hindering miR-195-5p or overexpressing HOXC8. Conclusively, LINC01547 serves as a crucial component to worsen the oncogenicity of NSCLC cells by controlling the miR-195-5p/HOXC8 axis. Thus, the newly identified competing endogenous RNA pathway may potentially be an attractive therapeutic for NSCLC management.
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Affiliation(s)
- Wenjie Wu
- Department of Chest Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Siyu Zhu
- Department of Chest Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510095, China
- Baiyun Lake Community Health Service Center of Baiyun District, Guangzhou 510450, China
| | - Yonghui Wu
- Department of Chest Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Lu Dai
- Department of Chest Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Jian Zhao
- Department of Chest Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Zeyong Jiang
- Department of Chest Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510095, China
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Zhang Z, Chen L, Zhao C, Gong Q, Tang Z, Li H, Tao J. CASC9 potentiates gemcitabine resistance in pancreatic cancer by reciprocally activating NRF2 and the NF-κB signaling pathway. Cell Biol Toxicol 2023; 39:1549-1560. [PMID: 35913601 DOI: 10.1007/s10565-022-09746-w] [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: 06/04/2022] [Accepted: 07/06/2022] [Indexed: 11/02/2022]
Abstract
Gemcitabine resistance is a frequently occurring and intractable obstacle in pancreatic cancer treatment. However, the underlying mechanisms require further investigation. Adaptive regulation of oxidative stress and aberrant activation of the NF-κB signaling pathway are associated with resistance to chemotherapy. Here, we found that gemcitabine upregulated the expression of CASC9 in a dose-dependent manner, partially via induction of reactive oxygen species, whereas inhibition of CASC9 expression enhanced gemcitabine-induced oxidative stress and apoptosis in pancreatic cancer cells. Furthermore, suppression of CASC9 level inhibited the expression of NRF2 and the downstream genes NQO1 and HO-1, and vice versa, indicating that CASC9 forms a positive feedback loop with NRF2 signaling and modulates the level of oxidative stress. Silencing CASC9 attenuated NF-κB pathway activation in pancreatic cancer cells and synergistically enhanced the cytotoxic effect of gemcitabine chemotherapy in vivo. In conclusion, our findings suggest that CASC9 plays a key role in driving resistance to gemcitabine through a reciprocal loop with the NRF2-antioxidant signaling pathway and by activating NF-κB signaling. Our study reveals potential targets that can effectively reverse resistance to gemcitabine chemotherapy.
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Affiliation(s)
- Zhengle Zhang
- Department of Pancreatic Surgery, Renmin Hospital, Wuhan University, 238 Jiefang Road, Wuhan, 430060, Hubei Province, China
| | - Longjiang Chen
- Department of Pancreatic Surgery, Renmin Hospital, Wuhan University, 238 Jiefang Road, Wuhan, 430060, Hubei Province, China
| | - Chuanbing Zhao
- Department of Pancreatic Surgery, Renmin Hospital, Wuhan University, 238 Jiefang Road, Wuhan, 430060, Hubei Province, China
| | - Qiong Gong
- Department of Pancreatic Surgery, Renmin Hospital, Wuhan University, 238 Jiefang Road, Wuhan, 430060, Hubei Province, China
| | - Zhigang Tang
- Department of Pancreatic Surgery, Renmin Hospital, Wuhan University, 238 Jiefang Road, Wuhan, 430060, Hubei Province, China
| | - Hanjun Li
- Department of Pancreatic Surgery, Renmin Hospital, Wuhan University, 238 Jiefang Road, Wuhan, 430060, Hubei Province, China.
| | - Jing Tao
- Department of Pancreatic Surgery, Renmin Hospital, Wuhan University, 238 Jiefang Road, Wuhan, 430060, Hubei Province, China.
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Liao J, Chen B, Zhu Z, Du C, Gao S, Zhao G, Zhao P, Wang Y, Wang A, Schwartz Z, Song L, Hong J, Wagstaff W, Haydon RC, Luu HH, Fan J, Reid RR, He TC, Shi L, Hu N, Huang W. Long noncoding RNA (lncRNA) H19: An essential developmental regulator with expanding roles in cancer, stem cell differentiation, and metabolic diseases. Genes Dis 2023; 10:1351-1366. [PMID: 37397543 PMCID: PMC10311118 DOI: 10.1016/j.gendis.2023.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/07/2023] [Accepted: 02/08/2023] [Indexed: 07/04/2023] Open
Abstract
Recent advances in deep sequencing technologies have revealed that, while less than 2% of the human genome is transcribed into mRNA for protein synthesis, over 80% of the genome is transcribed, leading to the production of large amounts of noncoding RNAs (ncRNAs). It has been shown that ncRNAs, especially long non-coding RNAs (lncRNAs), may play crucial regulatory roles in gene expression. As one of the first isolated and reported lncRNAs, H19 has gained much attention due to its essential roles in regulating many physiological and/or pathological processes including embryogenesis, development, tumorigenesis, osteogenesis, and metabolism. Mechanistically, H19 mediates diverse regulatory functions by serving as competing endogenous RNAs (CeRNAs), Igf2/H19 imprinted tandem gene, modular scaffold, cooperating with H19 antisense, and acting directly with other mRNAs or lncRNAs. Here, we summarized the current understanding of H19 in embryogenesis and development, cancer development and progression, mesenchymal stem cell lineage-specific differentiation, and metabolic diseases. We discussed the potential regulatory mechanisms underlying H19's functions in those processes although more in-depth studies are warranted to delineate the exact molecular, cellular, epigenetic, and genomic regulatory mechanisms underlying the physiological and pathological roles of H19. Ultimately, these lines of investigation may lead to the development of novel therapeutics for human diseases by exploiting H19 functions.
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Affiliation(s)
- Junyi Liao
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Orthopedic Research Center, Chongqing Medical University, Chongqing 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Bowen Chen
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Orthopedic Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Zhenglin Zhu
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Orthopedic Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Chengcheng Du
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Orthopedic Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Shengqiang Gao
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Orthopedic Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Guozhi Zhao
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Piao Zhao
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Orthopedic Research Center, Chongqing Medical University, Chongqing 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Yonghui Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Clinical Laboratory Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200000, China
| | - Annie Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Zander Schwartz
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- School of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Lily Song
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Jeffrey Hong
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- The Medical Scientist Training Program, The University of Chicago Pritzker School of Medicine, Chicago, IL 60637, USA
| | - Rex C. Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Hue H. Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Jiaming Fan
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Ministry of Education Key Laboratory of Diagnostic Medicine, Department of Clinical Biochemistry, The School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Russell R. Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Laboratory of Craniofacial Suture Biology and Development, Department of Surgery Section of Plastic Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Laboratory of Craniofacial Suture Biology and Development, Department of Surgery Section of Plastic Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Lewis Shi
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Ning Hu
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Orthopedic Research Center, Chongqing Medical University, Chongqing 400016, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Wei Huang
- Departments of Orthopedic Surgery and Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Orthopedic Research Center, Chongqing Medical University, Chongqing 400016, China
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Baba SK, Baba SK, Mir R, Elfaki I, Algehainy N, Ullah MF, Barnawi J, Altemani FH, Alanazi M, Mustafa SK, Masoodi T, Akil ASA, Bhat AA, Macha MA. Long non-coding RNAs modulate tumor microenvironment to promote metastasis: novel avenue for therapeutic intervention. Front Cell Dev Biol 2023; 11:1164301. [PMID: 37384249 PMCID: PMC10299194 DOI: 10.3389/fcell.2023.1164301] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/22/2023] [Indexed: 06/30/2023] Open
Abstract
Cancer is a devastating disease and the primary cause of morbidity and mortality worldwide, with cancer metastasis responsible for 90% of cancer-related deaths. Cancer metastasis is a multistep process characterized by spreading of cancer cells from the primary tumor and acquiring molecular and phenotypic changes that enable them to expand and colonize in distant organs. Despite recent advancements, the underlying molecular mechanism(s) of cancer metastasis is limited and requires further exploration. In addition to genetic alterations, epigenetic changes have been demonstrated to play an important role in the development of cancer metastasis. Long non-coding RNAs (lncRNAs) are considered one of the most critical epigenetic regulators. By regulating signaling pathways and acting as decoys, guides, and scaffolds, they modulate key molecules in every step of cancer metastasis such as dissemination of carcinoma cells, intravascular transit, and metastatic colonization. Gaining a good knowledge of the detailed molecular basis underlying lncRNAs regulating cancer metastasis may provide previously unknown therapeutic and diagnostic lncRNAs for patients with metastatic disease. In this review, we concentrate on the molecular mechanisms underlying lncRNAs in the regulation of cancer metastasis, the cross-talk with metabolic reprogramming, modulating cancer cell anoikis resistance, influencing metastatic microenvironment, and the interaction with pre-metastatic niche formation. In addition, we also discuss the clinical utility and therapeutic potential of lncRNAs for cancer treatment. Finally, we also represent areas for future research in this rapidly developing field.
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Affiliation(s)
- Sana Khurshid Baba
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Kashmir, India
| | - Sadaf Khursheed Baba
- Department of Microbiology, Sher-I-Kashmir Institute of Medical Science (SKIMS), Soura, Kashmir, India
| | - Rashid Mir
- Department of Medical Lab Technology, Prince Fahd Bin Sultan Research Chair Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Imadeldin Elfaki
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Naseh Algehainy
- Department of Medical Lab Technology, Prince Fahd Bin Sultan Research Chair Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Mohammad Fahad Ullah
- Department of Medical Lab Technology, Prince Fahd Bin Sultan Research Chair Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Jameel Barnawi
- Department of Medical Lab Technology, Prince Fahd Bin Sultan Research Chair Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Faisal H. Altemani
- Department of Medical Lab Technology, Prince Fahd Bin Sultan Research Chair Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Mohammad Alanazi
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Syed Khalid Mustafa
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Tariq Masoodi
- Human Immunology Department, Research Branch, Sidra Medicine, Doha, Qatar
| | - Ammira S. Alshabeeb Akil
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity, and Cancer Program, Sidra Medicine, Doha, Qatar
| | - Ajaz A. Bhat
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity, and Cancer Program, Sidra Medicine, Doha, Qatar
| | - Muzafar A. Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Kashmir, India
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Gilyazova I, Enikeeva K, Rafikova G, Kagirova E, Sharifyanova Y, Asadullina D, Pavlov V. Epigenetic and Immunological Features of Bladder Cancer. Int J Mol Sci 2023; 24:9854. [PMID: 37373000 DOI: 10.3390/ijms24129854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/02/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Bladder cancer (BLCA) is one of the most common types of malignant tumors of the urogenital system in adults. Globally, the incidence of BLCA is more than 500,000 new cases worldwide annually, and every year, the number of registered cases of BLCA increases noticeably. Currently, the diagnosis of BLCA is based on cystoscopy and cytological examination of urine and additional laboratory and instrumental studies. However, cystoscopy is an invasive study, and voided urine cytology has a low level of sensitivity, so there is a clear need to develop more reliable markers and test systems for detecting the disease with high sensitivity and specificity. Human body fluids (urine, serum, and plasma) are known to contain significant amounts of tumorigenic nucleic acids, circulating immune cells and proinflammatory mediators that can serve as noninvasive biomarkers, particularly useful for early cancer detection, follow-up of patients, and personalization of their treatment. The review describes the most significant advances in epigenetics of BLCA.
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Affiliation(s)
- Irina Gilyazova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Kadriia Enikeeva
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Guzel Rafikova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Evelina Kagirova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Yuliya Sharifyanova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Dilara Asadullina
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Valentin Pavlov
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
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Liu Y, Liu Y, Ye S, Feng H, Ma L. A new ferroptosis-related signature model including messenger RNAs and long non-coding RNAs predicts the prognosis of gastric cancer patients. J Transl Int Med 2023; 11:145-155. [PMID: 38025952 PMCID: PMC10680379 DOI: 10.2478/jtim-2023-0089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Background and Objectives Gastric cancer (GC) is among the most malignant tumor types, which causes heavy healthy and economic burden to the people and societies all around the world. Establishment of an effective set of prognostic marker will benefit a lot to the treatment of GC patients clinically. Ferroptosis is a newly identified regulated cell death modality, with tight relevance with GC development. However, its application in the prognosis of GC has not been studied in detail. Deregulated messenger RNA (mRNA) and long non-coding RNA (lncRNA) expression profile in tumor can serve as novel prognostic marker for predicting the survival and cancer relapse in patients. Methods We downloaded ferroptosis-related gene expression microarray data, clinicopathologic information and a list of 259 ferroptosis-related genes from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and Ferroptosis database, respectively. Then, correlation analysis, univariate and multivariate Cox regression analysis were used to construct a novel prognostic model for GC. Then, we validated the model in the GEO datasets. Finally, we evaluated the differences in immune microenvironment between high- and low-risk groups. Results We utilized the ferroptosis-related mRNA and lncRNA profile to successfully construct a prognostic model (incorporating 2 mRNAs and 15 lncRNAs) in GC. Our model, integrating diverse clinical traits and critical factors of GC, showed desirable efficacy in the prognosis of GC patients. This model also manifested effectively in validation by using external patients' data. Conclusions Our study developed a novel ferroptosis-related signature to predict the prognosis of gastric cancer patients. The ferroptosis-related signature had a favorable predictive ability. This model may greatly boost the treatment of GC patients in clinical practice.
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Affiliation(s)
- Yang Liu
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun130033, Jilin Province, China
| | - Yanqing Liu
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York10032, NY, USA
| | - Shujun Ye
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun130033, Jilin Province, China
| | - Huijin Feng
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York10032, NY, USA
| | - Lianjun Ma
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun130033, Jilin Province, China
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Liu S, Shi G, Pan Z, Cheng W, Xu L, Lin X, Lin Y, Zhang L, Ji G, Lv X, Wang D. Integrated Bioinformatics Analysis for the Identification of Key lncRNAs, mRNAs, and Potential Drugs in Clear Cell Renal Cell Carcinomas. Int J Gen Med 2023; 16:2063-2080. [PMID: 37275334 PMCID: PMC10238222 DOI: 10.2147/ijgm.s409711] [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: 03/08/2023] [Accepted: 05/18/2023] [Indexed: 06/07/2023] Open
Abstract
Purpose The overall survival of clear cell renal cell carcinoma (ccRCC) is poor. Markers for early detection and progression could improve disease outcomes. This study aims to reveal the potential pathogenesis of ccRCC by integrative bioinformatics analysis and to further develop new therapeutic strategies. Patients and Methods RNA-seq data of 530 ccRCC cases in TCGA were downloaded, and a comprehensive analysis was carried out using bioinformatics tools. Another 14 tissue samples were included to verify the expression of selected lncRNAs by qRT-PCR. DGIdb database was used to screen out potential drugs, and molecular docking was used to explore the interaction and mechanism between candidate drugs and targets. Results A total of 58 differentially expressed lncRNAs (DElncRNAs) and 660 differentially expressed mRNAs (DEmRNAs) were identified in ccRCC. LINC02038, FAM242C, LINC01762, and PVT1 were identified as the optimal diagnostic lncRNAs, of which PVT1 was significantly correlated with the survival rate of ccRCC. GO analysis of cell components showed that DEmRNAs co-expressed with 4 DElncRNAs were mainly distributed in the extracellular area and the plasma membrane, involved in the transport of metal ions, the transport of proteins across membranes, and the binding of immunoglobulins. Immune infiltration analysis showed that MDSC was the most correlated immune cells with PVT1 and key mRNA SIGLEC8. Validation analysis showed that GABRD, SIGLEC8 and CDKN2A were significantly overexpressed, while ESRRB, ELF5 and UMOD were significantly down-regulated, which was consistent with the expression in our analysis. Furthermore, 84 potential drugs were screened by 6 key mRNAs, of which ABEMACICLIB and RIBOCICLIB were selected for molecular docking with CDKN2A, with stable binding affinity. Conclusion In summary, 4 key lncRNAs and key mRNAs of ccRCC were identified by integrative bioinformatics analysis. Potential drugs were screened for the treatment of ccRCC, providing a new perspective for disease diagnosis and treatment.
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Affiliation(s)
- Sheng Liu
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Guanyun Shi
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Zhengbo Pan
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Weisong Cheng
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Linfei Xu
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Xingzhang Lin
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Yongfeng Lin
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Liming Zhang
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Guanghua Ji
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Xin Lv
- Department of Urinary Surgery, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
| | - Dongguo Wang
- Department of Central Laboratory, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang Province, People’s Republic of China
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Anwar A, Sapra L, Gupta N, Ojha RP, Verma B, Srivastava RK. Fine-tuning osteoclastogenesis: An insight into the cellular and molecular regulation of osteoclastogenesis. J Cell Physiol 2023. [PMID: 37183350 DOI: 10.1002/jcp.31036] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/16/2023]
Abstract
Osteoclasts, the bone-resorbing cells, are essential for the bone remodeling process and are involved in the pathophysiology of several bone-related diseases. The extensive corpus of in vitro research and crucial mouse model studies in the 1990s demonstrated the key roles of monocyte/macrophage colony-stimulating factor, receptor activator of nuclear factor kappa B ligand (RANKL) and integrin αvβ3 in osteoclast biology. Our knowledge of the molecular mechanisms by which these variables control osteoclast differentiation and function has significantly advanced in the first decade of this century. Recent developments have revealed a number of novel insights into the fundamental mechanisms governing the differentiation and functional activity of osteoclasts; however, these mechanisms have not yet been adequately documented. Thus, in the present review, we discuss various regulatory factors including local and hormonal factors, innate as well as adaptive immune cells, noncoding RNAs (ncRNAs), etc., in the molecular regulation of the intricate and tightly regulated process of osteoclastogenesis. ncRNAs have a critical role as epigenetic controllers of osteoclast physiologic activities, including differentiation and bone resorption. The primary ncRNAs, which include micro-RNAs, circular RNAs, and long noncoding RNAs, form a complex network that affects gene transcription activities associated with osteoclast biological activity. Greater knowledge of the involvement of ncRNAs in osteoclast biological activities will contribute to the treatment and management of several skeletal diseases such as osteoporosis, osteoarthritis, rheumatoid arthritis, etc. Moreover, we further outline potential therapies targeting these regulatory pathways of osteoclastogenesis in distinct bone pathologies.
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Affiliation(s)
- Aleena Anwar
- Translational Immunology, Osteoimmunology & Immunoporosis Lab (TIOIL), Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Leena Sapra
- Translational Immunology, Osteoimmunology & Immunoporosis Lab (TIOIL), Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Navita Gupta
- Department of Allied Health Sciences, Chitkara School of Health Sciences, Chitkara University, Chandigarh, Punjab, India
| | - Rudra P Ojha
- Department of Zoology, Nehru Gram Bharati University, Prayagraj, Uttar Pradesh, India
| | - Bhupendra Verma
- Translational Immunology, Osteoimmunology & Immunoporosis Lab (TIOIL), Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Rupesh K Srivastava
- Translational Immunology, Osteoimmunology & Immunoporosis Lab (TIOIL), Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
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Dabi Y, Favier A, Razakamanantsoa L, Suisse S, Marie Y, Touboul C, Ferrier C, Bendifallah S, Daraï E. Value of non-coding RNAs to assess lymph node status in cervical cancer. Front Oncol 2023; 13:1144672. [PMID: 37234986 PMCID: PMC10206114 DOI: 10.3389/fonc.2023.1144672] [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: 01/14/2023] [Accepted: 04/18/2023] [Indexed: 05/28/2023] Open
Abstract
Cervical cancer (CC) is the fourth cancer in women and is the leading cause of cancer death in 42 countries. Lymph node metastasis is a determinant prognostic factor, as underlined in the latest FIGO classification. However, assessment of lymph node status remains difficult, despite the progress of imaging such as PET-CT and MRI. In the specific setting of CC, all data underlined the need for new biomarkers easily available to assess lymph node status. Previous studies have underlined the potential value of ncRNA expression in gynecological cancers. In this review, we aimed to evaluate the contribution of ncRNAs in tissue and biofluid samples to determine lymph node status in CC with potential impact on both surgical and adjuvant therapies. In tissue samples, our analysis found that there are arguments to support the role of ncRNAs in physiopathology, differential diagnosis from normal tissue, preinvasive and invasive tumors. In biofluids, despite small studies especially concerning miRNAs expression, promising data opens up new avenue to establish a non-invasive signature for lymph node status as well as a tool to predict response to neo- and adjuvant therapies, thus improving management algorithm of patients with CC.
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Affiliation(s)
- Yohann Dabi
- Sorbonne University, Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Paris, France
- Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), Paris, France
| | - Amelia Favier
- Sorbonne University, Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Paris, France
- Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), Paris, France
| | - Léo Razakamanantsoa
- Sorbonne University, Inserm UMR S 938, Centre de recherche de saint Antoine (CRSA), Hôpital Saint Antoine, Paris, France
- Department of Radiology imaging and Interventional speciality imaging, Tenon Hospital, Paris, France
| | | | - Yannick Marie
- Gentoyping and Sequencing core facility, iGenSeq, Institut du Cerveau et de la Moelle épinière, Institut du Cerveau et de la Moelle (ICM), Hôpital Pitié-Salpêtrière, Paris, France
| | - Cyril Touboul
- Sorbonne University, Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Paris, France
- Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), Paris, France
| | - Clément Ferrier
- Sorbonne University, Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Paris, France
- Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), Paris, France
| | - Sofiane Bendifallah
- Sorbonne University, Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Paris, France
- Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), Paris, France
| | - Emile Daraï
- Sorbonne University, Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, Paris, France
- Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), Paris, France
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Asemi R, Rajabpoor Nikoo N, Asemi Z, Shafabakhsh R, Hajijafari M, Sharifi M, Homayoonfal M, Davoodvandi A, Hakamifard A. Modulation of long non-coding RNAs by resveratrol as a potential therapeutic approach in cancer: A comprehensive review. Pathol Res Pract 2023; 246:154507. [PMID: 37196467 DOI: 10.1016/j.prp.2023.154507] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/05/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023]
Abstract
LncRNAs, or long non-coding RNAs, are a subset of RNAs that play a regulatory role in a wide range of biological functions, including RNA processing, epigenetic regulation, and signal transduction. Recent research indicates that lncRNAs play a key role in the development and spread of cancer by being dysregulated in the disease. In addition, lncRNAs have been linked to the overexpression of certain proteins that are involved in tumor development and progression. Resveratrol has anti-inflammatory and anti-cancer properties that it exerts through regulating different lncRNAs. By the regulation of tumor-supportive and tumor-suppressive lncRNAs, resveratrol acts as an anti-cancer agent. By downregulating the tumor-supportive lncRNAs DANCR, MALAT1, CCAT1, CRNDE, HOTAIR, PCAT1, PVT1, SNHG16, AK001796, DIO3OS, GAS5 and H19, and upregulating MEG3, PTTG3P, BISPR, PCAT29, GAS5, LOC146880, HOTAIR, PCA3, NBR2, this herbal remedy causes apoptosis and cytotoxicity. For the purpose of using polyphenols in cancer therapy, it would be helpful to have more in-depth knowledge about lncRNA modulation via resveratrol. Here, we discuss the current knowledge and future promise of resveratrol as modulators of lncRNAs in different cancers.
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Affiliation(s)
- Reza Asemi
- Department of Internal Medicine, School of Medicine, Cancer Prevention Research Center, Seyyed Al-Shohada Hospital, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran.
| | - Nesa Rajabpoor Nikoo
- Department of Gynecology and Obstetrics, Tehran University of Medical Sciences, Tehran, Islamic Republic of Iran.
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran.
| | - Rana Shafabakhsh
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran.
| | - Mohammad Hajijafari
- Department of Anesthesiology, School of Medicine, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran.
| | - Mehran Sharifi
- Department of Internal Medicine, School of Medicine, Cancer Prevention Research Center, Seyyed Al-Shohada Hospital, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran.
| | - Mina Homayoonfal
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran.
| | - Amirhossein Davoodvandi
- Cancer Immunology Project (CIP), Universal Scientific Education and Research Network (USERN), Tehran, Islamic Republic of Iran.
| | - Atousa Hakamifard
- Department of Infectious Diseases, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran.
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Han Y, Zhu Y, Dutta S, Almuntashiri S, Wang X, Zhang D. A proinflammatory long noncoding RNA Lncenc1 regulates inflammasome activation in macrophage. Am J Physiol Lung Cell Mol Physiol 2023; 324:L584-L595. [PMID: 36880658 PMCID: PMC10085550 DOI: 10.1152/ajplung.00056.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Mammalian genomes encode thousands of long noncoding RNAs (lncRNAs). LncRNAs are extensively expressed in various immune cells. The lncRNAs have been reported to be involved in diverse biological processes, including the regulation of gene expression, dosage compensation, and genomic imprinting. However, very little research has been conducted to explore how they alter innate immune responses during host-pathogen interactions. In this study, we found that a lncRNA, named long noncoding RNA, embryonic stem cells expressed 1 (Lncenc1), was strikingly increased in mouse lungs after gram-negative (G-) bacterial infection or exposure to lipopolysaccharides (LPS). Interestingly, our data indicated that Lncenc1 was upregulated in macrophages but not in primary epithelial cells (PECs) or polymorphonuclear leukocytes (PMN). The upregulation was also observed in human THP-1 and U937 macrophages. Besides, Lncenc1 was highly induced during ATP-induced inflammasome activation. Functionally, Lncenc1 showed proinflammatory effects in macrophages as demonstrated by increased expressions of cytokine and chemokines, as well as enhanced NF-κB promoter activity. Overexpression of Lncenc1 promoted the releases of IL-1β and IL-18, and Caspase-1 activity in macrophages, suggesting a role in inflammasome activation. Consistently, knockdown of Lncenc1 inhibited inflammasome activation in LPS-treated macrophages. Moreover, knockdown of Lncenc1 using antisense oligo (ASO)-loaded exosomes (EXO) attenuated LPS-induced lung inflammation in mice. Similarly, Lncenc1 deficiency protects mice from bacteria-induced lung injury and inflammasome activation. Taken together, our work identified Lncenc1 as a modulator of inflammasome activation in macrophages during bacterial infection. Our study suggested that Lncenc1 could serve as a therapeutic target for lung inflammation and injury.
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Affiliation(s)
- Yohan Han
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
| | - Yin Zhu
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
| | - Saugata Dutta
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
| | - Sultan Almuntashiri
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
- Department of Clinical Pharmacy, College of Pharmacy, University of Hail, Hail, Saudi Arabia
| | - Xiaoyun Wang
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
| | - Duo Zhang
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
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Li ZY, Zhu YX, Chen JR, Chang X, Xie ZZ. The role of KLF transcription factor in the regulation of cancer progression. Biomed Pharmacother 2023; 162:114661. [PMID: 37068333 DOI: 10.1016/j.biopha.2023.114661] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 04/19/2023] Open
Abstract
Kruppel-like factors (KLFs) are a family of zinc finger transcription factors that have been found to play an essential role in the development of various human tissues, including epithelial, teeth, and nerves. In addition to regulating normal physiological processes, KLFs have been implicated in promoting the onset of several cancers, such as gastric cancer, lung cancer, breast cancer, liver cancer, and colon cancer. To inhibit cancer progression, various existing medicines have been used to modulate the expression of KLFs, and anti-microRNA treatments have also emerged as a potential strategy for many cancers. Investigating the possibility of targeting KLFs in cancer therapy is urgently needed, as the roles of KLFs in cancer have not received enough attention in recent years. This review summarizes the factors that regulate KLF expression and function at both the transcriptional and posttranscriptional levels, which could aid in understanding the mechanisms of KLFs in cancer progression. We hope that this review will contribute to the development of more effective anti-cancer medicines targeting KLFs in the future.
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Affiliation(s)
- Zi-Yi Li
- College of Basic Medical, Nanchang University, Nanchang, Jiangxi 330006, PR China; Queen Mary School, Medical Department, Nanchang University, Nanchang, Jiangxi 330006, PR China
| | - Yu-Xin Zhu
- College of Basic Medical, Nanchang University, Nanchang, Jiangxi 330006, PR China; Queen Mary School, Medical Department, Nanchang University, Nanchang, Jiangxi 330006, PR China
| | - Jian-Rui Chen
- College of Basic Medical, Nanchang University, Nanchang, Jiangxi 330006, PR China; Queen Mary School, Medical Department, Nanchang University, Nanchang, Jiangxi 330006, PR China
| | - Xu Chang
- College of Basic Medical, Nanchang University, Nanchang, Jiangxi 330006, PR China; Queen Mary School, Medical Department, Nanchang University, Nanchang, Jiangxi 330006, PR China
| | - Zhen-Zhen Xie
- College of Basic Medical, Nanchang University, Nanchang, Jiangxi 330006, PR China; Experimental teaching center of Basic Medical College, Nanchang University, Nanchang, Jiangxi 330006, PR China.
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Mishra A, Kumar R, Mishra SN, Vijayaraghavalu S, Tiwari NK, Shukla GC, Gurusamy N, Kumar M. Differential Expression of Non-Coding RNAs in Stem Cell Development and Therapeutics of Bone Disorders. Cells 2023; 12:cells12081159. [PMID: 37190068 PMCID: PMC10137108 DOI: 10.3390/cells12081159] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/26/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023] Open
Abstract
Stem cells' self-renewal and multi-lineage differentiation are regulated by a complex network consisting of signaling factors, chromatin regulators, transcription factors, and non-coding RNAs (ncRNAs). Diverse role of ncRNAs in stem cell development and maintenance of bone homeostasis have been discovered recently. The ncRNAs, such as long non-coding RNAs, micro RNAs, circular RNAs, small interfering RNA, Piwi-interacting RNAs, etc., are not translated into proteins but act as essential epigenetic regulators in stem cells' self-renewal and differentiation. Different signaling pathways are monitored efficiently by the differential expression of ncRNAs, which function as regulatory elements in determining the fate of stem cells. In addition, several species of ncRNAs could serve as potential molecular biomarkers in early diagnosis of bone diseases, including osteoporosis, osteoarthritis, and bone cancers, ultimately leading to the development of new therapeutic strategies. This review aims to explore the specific roles of ncRNAs and their effective molecular mechanisms in the growth and development of stem cells, and in the regulation of osteoblast and osteoclast activities. Furthermore, we focus on and explore the association of altered ncRNA expression with stem cells and bone turnover.
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Affiliation(s)
- Anurag Mishra
- Department of Biochemistry, Faculty of Science, University of Allahabad, Prayagraj 211002, India
| | - Rishabh Kumar
- Department of Biochemistry, Faculty of Science, University of Allahabad, Prayagraj 211002, India
| | - Satya Narayan Mishra
- Maa Gayatri College of Pharmacy, Dr. APJ Abdul Kalam Technical University, Prayagraj 211009, India
| | | | - Neeraj Kumar Tiwari
- Department of IT-Satellite Centre, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, India
| | - Girish C Shukla
- Department of Biological, Geological, and Environmental Sciences, 2121 Euclid Ave., Cleveland, OH 44115, USA
- Center for Gene Regulation in Health and Disease, 2121 Euclid Ave., Cleveland, OH 44115, USA
| | - Narasimman Gurusamy
- Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Munish Kumar
- Department of Biochemistry, Faculty of Science, University of Allahabad, Prayagraj 211002, India
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Ye C, Lin Q, Zheng C. Overexpressed RBPMS-AS1 increased cell radiosensitivity by sponging miR-19a-3p in lung cancer cell lines (A549 and SK-MES-1) via regulating PTEN/AKT axis. Int J Radiat Biol 2023; 99:1352-1363. [PMID: 36912590 DOI: 10.1080/09553002.2023.2181997] [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: 07/04/2022] [Revised: 01/14/2023] [Accepted: 02/13/2023] [Indexed: 03/14/2023]
Abstract
PURPOSE This paper intended to study RBPMS-AS1 in lung cancer (LC) radiosensitivity. MATERIALS AND METHODS LC cells were transfected with RBPMS-AS1 overexpression plasmid and miR-19a-3p mimic and treated with radiation. PTEN, AKT, p-AKT, RBPMS-AS1, and miR-19a-3p expressions were detected via Western blot and qRT-PCR. The localization of RBPMS-AS1 in cells was determined through fluorescence in situ hybridization assay. The targeting relationships of RBPMS-AS1 and miR-19a-3p/miR-19a-3p and PTEN were determined through RIP and dual luciferase reporter analysis. Cell survival, viability, and apoptosis were assessed through colony formation, CCK-8, and flow-cytometry assays. RESULTS RBPMS-AS1 was downregulated in LC and mainly distributed in cytoplasm. RBPMS-AS1 targeted miR-19a-3p in LC cells. Radiation suppressed LC cell survival, viability, and induced apoptosis, as overexpressed RBPMS-AS1 performed the similar effects and enhanced those effects induced by radiation. MiR-19a-3p mimic reversed the effect of overexpressed RBPMS-AS1 on enhancing radiation-induced LC cell apoptosis. MiR-19a-3p targeted PTEN and miR-19a-3p mimic reversed the effect of overexpressed RBPMS-AS1 on PTEN and phosphorylation of AKT in LC cells. CONCLUSION Overexpressed RBPMS-AS1 sponged miR-19a-3p to increase cell radiosensitivity in LC via regulating PTEN/AKT axis.
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Affiliation(s)
- Chengyu Ye
- Department of Radiotherapy, Wenzhou Central Hospital/Theorem Hospital Affiliated of Wenzhou Medical University, Wenzhou, China
| | - Quanbing Lin
- Department of Radiotherapy, Wenzhou Central Hospital/Theorem Hospital Affiliated of Wenzhou Medical University, Wenzhou, China
| | - Cuiping Zheng
- Department of Chemotherapy, Wenzhou Central Hospital/Theorem Hospital Affiliated of Wenzhou Medical University, Wenzhou, China
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Insight on Non-Coding RNAs from Biofluids in Ovarian Tumors. Cancers (Basel) 2023; 15:cancers15051539. [PMID: 36900328 PMCID: PMC10001105 DOI: 10.3390/cancers15051539] [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: 01/14/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Ovarian tumors are the most frequent adnexal mass, raising diagnostic and therapeutic issues linked to a large spectrum of tumors, with a continuum from benign to malignant. Thus far, none of the available diagnostic tools have proven efficient in deciding strategy, and no consensus exists on the best strategy between "single test", "dual testing", "sequential testing", "multiple testing options" and "no testing". In addition, there is a need for prognostic tools such as biological markers of recurrence and theragnostic tools to detect women not responding to chemotherapy in order to adapt therapies. Non-coding RNAs are classified as small or long based on their nucleotide count. Non-coding RNAs have multiple biological functions such as a role in tumorigenesis, gene regulation and genome protection. These ncRNAs emerge as new potential tools to differentiate benign from malignant tumors and to evaluate prognostic and theragnostic factors. In the specific setting of ovarian tumors, the goal of the present work is to offer an insight into the contribution of biofluid non-coding RNAs (ncRNA) expression.
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Liu L, Zheng J, Xia H, Wu Q, Cai X, Ji L, Sun Y. Construction and comprehensive analysis of a curoptosis-related lncRNA signature for predicting prognosis and immune response in cervical cancer. Front Genet 2023; 14:1023613. [PMID: 36777734 PMCID: PMC9911828 DOI: 10.3389/fgene.2023.1023613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
Cuproptosis (copper-ion-dependent cell death) is an unprogrammed cell death, and intracellular copper accumulation, causing copper homeostasis imbalance and then leading to increased intracellular toxicity, which can affect the rate of cancer cell growth and proliferation. This study aimed to create a newly cuproptosis-related lncRNA signature that can be used to predict survival and immunotherapy in patients with cervical cancer, but also to predict prognosis in patients treated with radiotherapy and may play a role in predicting radiosensitivity. First of all, we found lncRNAs associated with cuproptosis between cervical cancer tumor tissues and normal tissues. By LASSO-Cox analysis, overlapping lncRNAs were then used to construct lncRNA signatures associated with cuproptosis, which can be used to predict the prognosis of patients, especially the prognosis of radiotherapy patients, ROC curves and PCA analysis based on cuprotosis-related lncRNA signature and clinical signatures were developed and demonstrated to have good predictive potential. In addition, differences in immune cell subset infiltration and differences in immune checkpoint expression between high-risk and low-risk score groups were analyzed, and we investigated the relationship between this signature and tumor mutation burden. In summary, we constructed a lncRNA prediction signature associated with cuproptosis. This has important clinical implications, including improving the predictive value of cervical cancer patients and providing a biomarker for cervical cancer.
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Affiliation(s)
- Li Liu
- Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Jianfeng Zheng
- Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Hongmei Xia
- Department of Gynecology, Fujian Cancer Hospital, Fuzhou, China
| | - Qiaoling Wu
- Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Xintong Cai
- Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Liyan Ji
- Geneplus-Beijing Institute, Beijing, China
| | - Yang Sun
- Department of Gynecology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China,*Correspondence: Yang Sun,
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Barbagallo C, Stella M, Broggi G, Russo A, Caltabiano R, Ragusa M. Genetics and RNA Regulation of Uveal Melanoma. Cancers (Basel) 2023; 15:775. [PMID: 36765733 PMCID: PMC9913768 DOI: 10.3390/cancers15030775] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Uveal melanoma (UM) is the most common intraocular malignant tumor and the most frequent melanoma not affecting the skin. While the rate of UM occurrence is relatively low, about 50% of patients develop metastasis, primarily to the liver, with lethal outcome despite medical treatment. Notwithstanding that UM etiopathogenesis is still under investigation, a set of known mutations and chromosomal aberrations are associated with its pathogenesis and have a relevant prognostic value. The most frequently mutated genes are BAP1, EIF1AX, GNA11, GNAQ, and SF3B1, with mutually exclusive mutations occurring in GNAQ and GNA11, and almost mutually exclusive ones in BAP1 and SF3B1, and BAP1 and EIF1AX. Among chromosomal aberrations, monosomy of chromosome 3 is the most frequent, followed by gain of chromosome 8q, and full or partial loss of chromosomes 1 and 6. In addition, epigenetic mechanisms regulated by non-coding RNAs (ncRNA), namely microRNAs and long non-coding RNAs, have also been investigated. Several papers investigating the role of ncRNAs in UM have reported that their dysregulated expression affects cancer-related processes in both in vitro and in vivo models. This review will summarize current findings about genetic mutations, chromosomal aberrations, and ncRNA dysregulation establishing UM biology.
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Affiliation(s)
- Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy
| | - Michele Stella
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy
| | - Giuseppe Broggi
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia—Section of Anatomic Pathology, University of Catania, 95123 Catania, Italy
| | - Andrea Russo
- Department of Ophthalmology, University of Catania, 95123 Catania, Italy
| | - Rosario Caltabiano
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia—Section of Anatomic Pathology, University of Catania, 95123 Catania, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy
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Chen H, Yu Y, Zhou L, Chen J, Li Z, Tan X. Cuproptosis-related LncRNAs signature as biomarker of prognosis and immune infiltration in pancreatic cancer. Front Genet 2023; 14:1049454. [PMID: 36713077 PMCID: PMC9880288 DOI: 10.3389/fgene.2023.1049454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/02/2023] [Indexed: 01/14/2023] Open
Abstract
Background: Pancreatic cancer (PC) is a malignant gastrointestinal tumor with a terrible prognosis. Cuproptosis is a recently discovered form of cell death. This study is intended to explore the relationship between cuproptosis-related lncRNAs (CRLncs) signature with the prognosis and the tumor microenvironment (TME) of PC. Methods: Transcript sequencing data of PC samples with clinical information were obtained from the Cancer Genome Atlas (TCGA). Univariate Cox regression analysis and LASSO regression analysis were employed to construct the prognostic signature based on CRLncs associated with PC survival. A nomogram was created according to this signature, and the signaling pathway enrichment was analyzed. Subsequently, we explored the link between this prognostic signature with the mutational landscape and TME. Eventually, drug sensitivity was predicted based on this signature. Results: Forty-six of 159 CRLncs were most significantly relevant to the prognosis of PC, and a 6-lncRNA prognostic signature was established. The expression level of signature lncRNAs were detected in PC cell lines. The AUC value of the ROC curve for this risk score predicting 5-year survival in PC was .944, which was an independent prognostic factor for PC. The risk score was tightly related to the mutational pattern of PC, especially the driver genes of PC. Single-sample gene set enrichment analysis (ssGSEA) demonstrated a significant correlation between signature with the TME of PC. Ultimately, compounds were measured for therapy in high-risk and low-risk PC patients, respectively. Conclusion: A prognostic signature of CRLncs for PC was established in the current study, which may serve as a promising marker for the outcomes of PC patients and has important forecasting roles for gene mutations, immune cell infiltration, and drug sensitivity in PC.
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Affiliation(s)
| | | | | | | | | | - Xiaodong Tan
- Department of General Surgery, Pancreatic, and Thyroid Ward, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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Mutharasu G, Murugesan A, Kondamani S, Thiyagarajan R, Yli-Harja O, Kandhavelu M. Signaling landscape of mitochondrial non-coding RNAs. J Biomol Struct Dyn 2023; 41:12016-12025. [PMID: 36617957 DOI: 10.1080/07391102.2022.2164520] [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: 10/07/2022] [Accepted: 12/27/2022] [Indexed: 01/10/2023]
Abstract
Human mitochondria are the vital cell organelle acting as a storehouse of energy generation and diverse regulatory functions. Mitochondrial DNA comprises 93% coding region and 7% non-coding regions, in which the non-coding region hypothesized as responsible for signaling is our specific interest. Here, we explored the unknown functions of mitochondrial non-coding RNAs by studying their respective signaling pathways. We retrieved conserved motifs of interactions from known experimental protein-RNA complexes to model unknown mitochondrial ncRNA sequences. Our results provide the ncRNAs list and show their involvement in four crucial pathways, such as (i) Processing of Capped Intron-Containing Pre-mRNA, (ii) Spliceosome, (iii) Spliceosomal assembly, and (iv) RNA Polymerase II Transcription, respectively. The interactome analysis revealed that the SRSF2 and U2AF2 proteins interact with ncRNAs. Further, we have simulated the selected ncRNA-protein complexes in cell-like environmental conditions and found them stable in terms of energetics. Through our study, we have identified an apparent interaction of mitochondrial ncRNAs with proteins and their role in critical signaling pathways, providing new insights into mitochondrial ncRNA-dependent gene regulation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gnanavel Mutharasu
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Akshaya Murugesan
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Molecular Signaling Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Biotechnology, Lady Doak College, Thallakulam, Madurai, Tamil Nadu, India
| | - Saravnan Kondamani
- Department of Biotechnology, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Ramesh Thiyagarajan
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Kingdom of Saudi Arabia
| | - Olli Yli-Harja
- Computaional Systems Biology Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Institute for Systems Biology, Seattle, WA, USA
| | - Meenakshisundaram Kandhavelu
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Molecular Signaling Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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70
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Ray SK, Mukherjee S. Interaction Among Noncoding RNAs, DNA Damage Reactions, and Genomic Instability in the Hypoxic Tumor: Is it Therapeutically Exploitable Practice? Curr Mol Med 2023; 23:200-215. [PMID: 35048804 DOI: 10.2174/1566524022666220120123557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 02/08/2023]
Abstract
Hypoxia is a classical function of the tumor's microenvironment with a substantial effect on the development and therapeutic response of cancer. When put in hypoxic environments, cells undergo several biological reactions, including activation of signaling pathways that control proliferation, angiogenesis, and death. These pathways have been adapted by cancer cells to allow tumors to survive and even develop in hypoxic conditions, and poor prognosis is associated with tumor hypoxia. The most relevant transcriptional regulator in response to hypoxia, Hypoxia-inducible factor-1 alpha (HIF-1α), has been shown to modulate hypoxic gene expression and signaling transduction networks significantly. The significance of non-coding RNAs in hypoxic tumor regions has been revealed in an increasing number of studies over the past few decades. In regulating hypoxic gene expression, these hypoxia-responsive ncRNAs play pivotal roles. Hypoxia, a general characteristic of the tumor's microenvironment, significantly affects the expression of genes and is closely associated with the development of cancer. Indeed, the number of known hypoxia-associated lncRNAs has increased dramatically, demonstrating the growing role of lncRNAs in cascades and responses to hypoxia signaling. Decades of research have helped us create an image of the shift in hypoxic cancer cells' DNA repair capabilities. Emerging evidence suggests that hypoxia can trigger genetic instability in cancer cells because of microenvironmental tumor stress. Researchers have found that critical genes' expression is coordinately repressed by hypoxia within the DNA damage and repair pathways. In this study, we include an update of current knowledge on the presentation, participation, and potential clinical effect of ncRNAs in tumor hypoxia, DNA damage reactions, and genomic instability, with a specific emphasis on their unusual cascade of molecular regulation and malignant progression induced by hypoxia.
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Affiliation(s)
| | - Sukhes Mukherjee
- Department of Biochemistry All India Institute of Medical Sciences. Bhopal, Madhya Pradesh-462020. India
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71
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Mao K, Tang R, Wu Y, Zhang Z, Gao Y, Huang H. Prognostic markers of ferroptosis-related long non-coding RNA in lung adenocarcinomas. Front Genet 2023; 14:1118273. [PMID: 36923797 PMCID: PMC10009162 DOI: 10.3389/fgene.2023.1118273] [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: 12/07/2022] [Accepted: 02/15/2023] [Indexed: 03/02/2023] Open
Abstract
Ferroptosis is a recently established type of iron-dependent programmed cell death. Growing studies have focused on the function of ferroptosis in cancers, including lung adenocarcinoma (LUAD). However, the factors involved in the regulation of ferroptosis-related genes are not fully understood. In this study, we collected data from lung adenocarcinoma datasets of the Cancer Genome Atlas (TCGA-LUAD). The expression profiles of 60 ferroptosis-related genes were screened, and two differentially expressed ferroptosis subtypes were identified. We found the two ferroptosis subtypes can predict clinical outcomes and therapeutic responses in LUAD patients. Furthermore, key long non-coding RNAs (lncRNAs) were screened by single factor Cox and least absolute shrinkage and selection operator (LASSO) based on which co-expressed with the 60 ferroptosis-related genes. We then established a risk score model which included 13 LUAD ferroptosis-related lncRNAs with a multi-factor Cox regression. The risk score model showed a good performance in evaluating the outcome of LUAD. What's more, we divided TCGA-LUAD tumor samples into two groups with high- and low-risk scores and further explored the differences in clinical characteristics, tumor mutation burden, and tumor immune cell infiltration among different LUAD tumor risk score groups and evaluate the predictive ability of risk score for immunotherapy benefit. Our findings provide good support for immunotherapy in LUAD in the future.
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Affiliation(s)
- Kaimin Mao
- Department of Critical Care Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Ri Tang
- Department of Critical Care Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yali Wu
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiyun Zhang
- Department of Critical Care Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yuan Gao
- Department of Critical Care Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Huijing Huang
- Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
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72
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A 5-Pathway Signature Predicts Prognosis Based on Immune-Derived lncRNAs in Patients with Breast Cancer. JOURNAL OF ONCOLOGY 2022; 2022:2906049. [PMID: 36545126 PMCID: PMC9763012 DOI: 10.1155/2022/2906049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 11/21/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022]
Abstract
Background Currently, predictive models were not developed based on the signaling pathway signatures of immune-related lncRNAs in breast cancer (BRCA) patients. Methods We selected unsupervised hierarchical clustering algorithm to classify patients with BRCA based on the significant immune-derived lncRNAs from the TCGA dataset. And different methods including ESTIMATE, ImmuneCellAI, and CIBERSORT were performed to evaluate the immune infiltration of tumor microenvironment. Using Lasso regression algorithm, we filtered the significant signaling pathways enriched by GSEA, GSVA, or PPI analysis to develop a prognostic model. And a nomogram integrated with clinical factors and significant pathways was constructed to predict the precise probability of overall survival (OS) of BRCA patients in the TCGA dataset (n = 1,098) and another two testing sets (n = 415). Results BRCA patients were stratified into the PC (n = 571) and GC (n = 527) subgroup with significantly different prognosis with 550 immune-related lncRNAs in the TCGA dataset. Integrated analysis revealed different immune response, oncogenic signaling, and metabolic reprograming pathways between these two subgroups. And a 5-pathway signature could predict the prognosis of BRCA patients between these two subgroups independently in the TCGA dataset, which was confirmed in another two cohorts from the GEO dataset. In the TCGA dataset, 5-year OS rate was 78% (95% CI: 73-84) vs. 82% (95% CI: 77-87) for the PC and GC group (HR = 1.63 (95% CI: 1.17-2.28), p = 0.004). The predictive power was similar in another two testing sets (HR > 1.20, p < 0.01). Finally, a nomogram is developed for clinical application, which integrated this signature and age to accurately predict the survival probability in BRCA patients. Conclusion This 5-pathway signature correlated with immune-derived lncRNAs was able to precisely predict the prognosis for patients with BRCA and provided a rich source characterizing immune-related lncRNAs and further informed strategies to target BRCA vulnerabilities.
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73
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Qi Y, Wang M, Jiang Q. PABPC1--mRNA stability, protein translation and tumorigenesis. Front Oncol 2022; 12:1025291. [PMID: 36531055 PMCID: PMC9753129 DOI: 10.3389/fonc.2022.1025291] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/08/2022] [Indexed: 09/29/2023] Open
Abstract
Mammalian poly A-binding proteins (PABPs) are highly conserved multifunctional RNA-binding proteins primarily involved in the regulation of mRNA translation and stability, of which PABPC1 is considered a central regulator of cytoplasmic mRNA homing and is involved in a wide range of physiological and pathological processes by regulating almost every aspect of RNA metabolism. Alterations in its expression and function disrupt intra-tissue homeostasis and contribute to the development of various tumors. There is increasing evidence that PABPC1 is aberrantly expressed in a variety of tumor tissues and cancers such as lung, gastric, breast, liver, and esophageal cancers, and PABPC1 might be used as a potential biomarker for tumor diagnosis, treatment, and clinical application in the future. In this paper, we review the abnormal expression, functional role, and molecular mechanism of PABPC1 in tumorigenesis and provide directions for further understanding the regulatory role of PABPC1 in tumor cells.
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Affiliation(s)
- Ya Qi
- Department of Gynecology and Obstetrics, Shengjing Hospital Affiliated of China Medical University, Shenyang, Liaoning, China
| | - Min Wang
- Department of Gynecology and Obstetrics, Shengjing Hospital Affiliated of China Medical University, Shenyang, Liaoning, China
| | - Qi Jiang
- Second Department of Clinical Medicine, China Medical University, Shenyang, Liaoning, China
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Zhang H, Zhang G, Zhang F, Yang X, Li E, Wang B, Xu P, Zhang D, Guo L, Huang X. LINC00958 may be a new prognostic biomarker in various cancers: A meta-analysis and bioinformatics analysis. Front Genet 2022; 13:998442. [PMID: 36437914 PMCID: PMC9691855 DOI: 10.3389/fgene.2022.998442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022] Open
Abstract
Background: There have been many studies on long non-coding RNAs (lncRNAs) as tumor markers. LINC00958 is a lncRNA that has been studied in a variety of tumor types. This meta-analysis aims to explore the relationship between LINC00958 and clinical prognosis and pathological characteristics in various cancers. Methods: We searched for related studies from PubMed, Web of Science, The Cochrane Library and Embase (up to October 2021). The association of LINC00958 expression with clinicopathological characteristics and prognosis was evaluated using the pooled odds ratios (ORs) or hazard ratios (HRs) with 95% confidence intervals (CIs). Results: 16 studies (1,121 patients) were included in this meta-analysis, we found that overexpression of LINC00958 was associated with poor overall survival (OS) (HR = 1.84; 95% CI: 1.36-2.49; p < 0.001). We also found that LINC00958 overexpression was correlated with positive lymph node metastasis (LNM) (OR = 1.91; 95% CI: 1.39-2.63; p < 0.001), advanced degree of infiltration (OR = 1.64; 95% CI: 1.11-2.41; p = 0.013), advanced tumor-node-metastasis (TNM) stage (OR = 2.80; 95% CI: 1.48-5.33; p = 0.002). Other clinicopathological characteristics have no obvious correlation, such as age, sex, tumor size, distant metastasis, and differentiation grade (p > 0.05). Conclusion: In summary, the overexpression of LINC00958 is significantly correlated with poor OS, positive LNM, advanced degree of infiltration, and advanced TNM stage. LINC00958 might serve as a potential prognostic biomarker and therapeutic target for a variety of cancers. However, rigorous studies with large sample sizes are still needed for further research and demonstration.
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Affiliation(s)
- Helin Zhang
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
- Gansu Provincial Hospital, Lanzhou, China
| | - Guangming Zhang
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
- Gansu Provincial Hospital, Lanzhou, China
| | - Fan Zhang
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
- Gansu Provincial Hospital, Lanzhou, China
| | | | - Erqiang Li
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
- Gansu Provincial Hospital, Lanzhou, China
| | - Bo Wang
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
- Gansu Provincial Hospital, Lanzhou, China
| | - Peng Xu
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
- Gansu Provincial Hospital, Lanzhou, China
| | - Dengxiao Zhang
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
- Gansu Provincial Hospital, Lanzhou, China
| | - Lijun Guo
- Gansu Provincial Hospital, Lanzhou, China
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75
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Sonawala K, Ramalingam S, Sellamuthu I. Influence of Long Non-Coding RNA in the Regulation of Cancer Stem Cell Signaling Pathways. Cells 2022; 11:3492. [PMID: 36359888 PMCID: PMC9656902 DOI: 10.3390/cells11213492] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 08/03/2023] Open
Abstract
Over the past two decades, cancer stem cells (CSCs) have emerged as an immensely studied and experimental topic, however a wide range of questions concerning the topic still remain unanswered; in particular, the mechanisms underlying the regulation of tumor stem cells and their characteristics. Understanding the cancer stem-cell signaling pathways may pave the way towards a better comprehension of these mechanisms. Signaling pathways such as WNT, STAT, Hedgehog, NOTCH, PI3K/AKT/mTOR, TGF-β, and NF-κB are responsible not only for modulating various features of CSCs but also their microenvironments. Recently, the prominent roles of various non-coding RNAs such as small non-coding RNAs (sncRNAs) and long non-coding RNAs (lncRNAs) in developing and enhancing the tumor phenotypes have been unfolded. This review attempts to shed light on understanding the influence of long non- coding RNAs in the modulation of various CSC-signaling pathways and its impact on the CSCs and tumor properties; highlighting the protagonistic and antagonistic roles of lncRNAs.
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Affiliation(s)
| | | | - Iyappan Sellamuthu
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Chennai 603202, India
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Lu Z, Feng Y. Foreboding lncRNA markers of low-grade gliomas dependent on metabolism. Medicine (Baltimore) 2022; 101:e31302. [PMID: 36343057 PMCID: PMC9646492 DOI: 10.1097/md.0000000000031302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
At present, there is no systematic study on the signature of long-chain noncoding RNAs (lncRNAs) involved in metabolism that can fully predict the prognosis in patients with low-grade gliomas (LGGs). Therefore, consistent metabolic-related lncRNA signatures need to be established. The Cancer Genome Atlas (TCGA) was used to identify the expression profile of lncRNAs containing 529 LGGs samples. LncRNAs and genes related to metabolism are used to establish a network in the form of coexpression to screen lncRNAs related to metabolism. LncRNA was more clearly described by univariate Cox regression. Moreover, lncRNA signatures were explored by multivariate Cox regression and lasso regression. The risk score was established according to the signature and it was an unattached prognostic marker according to Cox regression analysis. Functional enrichment of lncRNAs was shown by employing Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Univariate Cox retrospective analysis showed that 543 metabolism-related lncRNAs were independent prognostic factors of LGG, and multivariate Cox regression analysis confirmed that 19 metabolism-related lncRNAs were prognostic genes of LGG. In the risk model, the low-risk group had a higher Overall survival (OS) than the high-risk group (P < .001). Univariate Cox regression analysis of risk score and clinical factors showed that risk score was an independent prognostic factor (P < .001, HR = 1.047, 95% CI: 1.038-1.056). Multivariate Cox results showed that risk score could predict the prognosis of LGG (P < .001, HR = 1.036, 95% CI: 1.026-1.045). ROC curve analysis showed that risk score could predict the prognosis of LGG. The areas of 1-year, 3-years, and 5 years are 0.891, 0.904 and 0.832. GO and KEGG analysis showed that metabolism-related lncRNAs was mainly concentrated in the pathways related to tumor metabolism. In order to find a more stable and reliable target for the treatment of LGG, we established 19 metabolic-related lncRNAs prognostic model, and determined that it can predict the prognosis of LGG patients. This provides a new solution approach to the poor prognosis of patients with LGG and may reverse the trend of LGG's transformation to high-grade gliomas.
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Affiliation(s)
- Zhuangzhuang Lu
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yugong Feng
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao, China
- * Correspondence: Yugong Feng, Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao 266000, China (e-mail: )
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Dabi Y, Bendifallah S, Suisse S, Haury J, Touboul C, Puchar A, Favier A, Daraï E. Overview of non-coding RNAs in breast cancers. Transl Oncol 2022; 25:101512. [PMID: 35961269 PMCID: PMC9382556 DOI: 10.1016/j.tranon.2022.101512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/18/2022] [Accepted: 08/02/2022] [Indexed: 12/24/2022] Open
Abstract
Breast cancer in women is the second most common cancer and the fifth leading cause of cancer death worldwide. Although earlier diagnosis and detection of breast cancer has resulted in lower mortality rates, further advances in prevention, detection, and treatment are needed to improve outcomes and survival for women with breast cancer as well as to offer a personalized therapeutic approach. It is now well-established that non-coding RNAs (ncRNAs) represent 98% of the transcriptome but in-depth knowledge about their involvement in the regulation of gene expression is lacking. A growing body of research indicates that ncRNAs are essential for tumorigenesis by regulating the expression of tumour-related genes. In this review, we focus on their implication in breast cancer genesis but also report the latest knowledge of their theragnostic and therapeutic role. We highlight the need for accurate quantification of circulating ncRNAs which is determinant to develop reliable biomarkers. Further studies are mandatory to finally enter the era of personalized medicine for women with breast cancer.
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Affiliation(s)
- Yohann Dabi
- Sorbonne University - Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020 Paris; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU); INSERM UMR_S_938, Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine (CRSA), Sorbonne University, Paris 75020, France.
| | - Sofiane Bendifallah
- Sorbonne University - Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020 Paris; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU); INSERM UMR_S_938, Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine (CRSA), Sorbonne University, Paris 75020, France
| | | | - Julie Haury
- Sorbonne University - Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020 Paris
| | - Cyril Touboul
- Sorbonne University - Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020 Paris; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU); INSERM UMR_S_938, Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine (CRSA), Sorbonne University, Paris 75020, France
| | - Anne Puchar
- Sorbonne University - Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020 Paris
| | - Amélia Favier
- Sorbonne University - Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020 Paris
| | - Emile Daraï
- Sorbonne University - Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020 Paris; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU); INSERM UMR_S_938, Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine (CRSA), Sorbonne University, Paris 75020, France
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Zhao J, Li G, Zhao G, Wang W, Shen Z, Yang Y, Huang Y, Ye L. Prognostic signature of lipid metabolism associated LncRNAs predict prognosis and treatment of lung adenocarcinoma. Front Oncol 2022; 12:986367. [PMID: 36387240 PMCID: PMC9664164 DOI: 10.3389/fonc.2022.986367] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/17/2022] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the most predominant histological subtype of lung cancer. Abnormal lipid metabolism is closely related to the development of LUAD. LncRNAs are involved in the regulation of various lipid metabolism-related genes in various cancer cells including LUAD. Here, we aimed to identify lipid metabolism-related lncRNAs associated with LUAD prognosis and to propose a new prognostic signature. METHODS First, differentially expressed lncRNAs (DE-lncRNAs) from the TCGA-LUAD and the GSE31210 dataset were identified. Then the correlation analysis between DE-lncRNAs and lipid metabolism genes was performed to screen lipid metabolism-related lncRNAs. Cox regression analyses were performed in the training set to establish a prognostic model and the model was validated in the testing set and the validation set. Moreover, The role of this model in the underlying molecular mechanisms, immunotherapy, and chemotherapeutic drug sensitivity analysis was predicted by methods such as Gene Set Enrichment Analysis, immune infiltration, tumor mutational burden (TMB), neoantigen, Tumor Immune Dysfunction and Exclusion, chemosensitivity analysis between the high- and low-risk groups. The diagnostic ability of prognostic lncRNAs has also been validated. Finally, we validated the expression levels of selected prognostic lncRNAs by quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS The prognostic model was constructed based on four prognostic lncRNAs (LINC00857, EP300-AS1, TBX5-AS1, SNHG3) related to lipid metabolism. The receiver operating characteristic curve (ROC) and Kaplan Meier (KM) curves of the risk model showed their validity. The results of Gene Set Enrichment Analysis suggested that differentially expressed genes in high- and low-risk groups were mainly enriched in immune response and cell cycle. There statistical differences in TMB and neoantigen between high- and low-risk groups. Drug sensitivity analysis suggested that patients with low risk scores may have better chemotherapy outcomes. The results of qRT-PCR were suggesting that compared with the normal group, the expressions of EP300-AS1 and TBX5-AS1 were down-regulated in the tumor group, while the expressions of LINC00857 and SNHG3 were up-regulated. The four prognostic lncRNAs had good diagnostic capabilities, and the overall diagnostic model of the four prognostic lncRNAs was more effective. CONCLUSION A total of 4 prognostic lncRNAs related to lipid metabolism were obtained and an effective risk model was constructed.
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Affiliation(s)
- Jie Zhao
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), Kunming, China
| | - Guangjian Li
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), Kunming, China
| | - Guangqiang Zhao
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), Kunming, China
| | - Wei Wang
- Department of Thoracic Surgery, Taihe Hospital (Hubei University of Medicine), Shiyan, China
| | - Zhenghai Shen
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), Kunming, China
| | - Yantao Yang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), Kunming, China
| | - Yunchao Huang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), Kunming, China
| | - Lianhua Ye
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital), Kunming, China
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79
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Advanced Bladder Cancer: Changing the Treatment Landscape. J Pers Med 2022; 12:jpm12101745. [PMID: 36294884 PMCID: PMC9604712 DOI: 10.3390/jpm12101745] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/08/2022] [Accepted: 10/14/2022] [Indexed: 11/17/2022] Open
Abstract
Bladder cancer is the 10th most common cancer type in the world. There were more than 573,000 new cases of bladder cancer in 2020. It is the 13th most common cause of cancer death with an estimated more than 212,000 deaths worldwide. Low-grade non-muscle-invasive bladder cancer (NMIBC) is usually successfully managed with transurethral resection (TUR) and overall survival for NMIBC reaches 90% according to some reports. However, long-term survival for muscle-invasive bladder cancer (MIBC) and metastatic bladder cancer remains low. Treatment options for bladder cancer have undergone a rapid change in recent years. Immune checkpoint inhibitors (ICI), targeted therapies, and antibody-drug conjugates are available now. As bladder cancer is genetically heterogeneous, the optimization of patient selection to identify those most likely to benefit from a specific therapy is an urgent issue in the treatment of patients with bladder cancer.
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80
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Agostini M, Mancini M, Candi E. Long non-coding RNAs affecting cell metabolism in cancer. Biol Direct 2022; 17:26. [PMID: 36182907 PMCID: PMC9526990 DOI: 10.1186/s13062-022-00341-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 11/27/2021] [Indexed: 11/10/2022] Open
Abstract
Metabolic reprogramming is commonly recognized as one important hallmark of cancers. Cancer cells present significant alteration of glucose metabolism, oxidative phosphorylation, and lipid metabolism. Recent findings demonstrated that long non-coding RNAs control cancer development and progression by modulating cell metabolism. Here, we give an overview of breast cancer metabolic reprogramming and the role of long non-coding RNAs in driving cancer-specific metabolic alteration.
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Affiliation(s)
- Massimiliano Agostini
- Department Experimental Medicine, University of Rome "Tor Vergata", TOR, Via Montpellier,1, 00133, Rome, Italy
| | - Mara Mancini
- IDI-IRCCS, Via Monti di Creta 104, 00166, Rome, Italy
| | - Eleonora Candi
- Department Experimental Medicine, University of Rome "Tor Vergata", TOR, Via Montpellier,1, 00133, Rome, Italy. .,IDI-IRCCS, Via Monti di Creta 104, 00166, Rome, Italy.
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81
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Shen C, Chen Z, Jiang J, Zhang Y, Xu W, Peng R, Zuo W, Jiang Q, Fan Y, Fang X, Zheng B. A new CCCH-type zinc finger-related lncRNA signature predicts the prognosis of clear cell renal cell carcinoma patients. Front Genet 2022; 13:1034567. [PMID: 36246657 PMCID: PMC9562972 DOI: 10.3389/fgene.2022.1034567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/20/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Clear cell renal cell carcinoma (ccRCC) is the main component of renal cell carcinoma (RCC), and advanced ccRCC frequently indicates a poor prognosis. The significance of the CCCH-type zinc finger (CTZF) gene in cancer has been increasingly demonstrated during the past few years. According to studies, targeted radical therapy for cancer treatment may be a revolutionary therapeutic approach. Both lncRNAs and CCCH-type zinc finger genes are essential in ccRCC. However, the predictive role of long non-coding RNA (lncRNA) associated with the CCCH-type zinc finger gene in ccRCC needs further elucidation. This study aims to predict patient prognosis and investigate the immunological profile of ccRCC patients using CCCH-type zinc finger-associated lncRNAs (CTZFLs). Methods: From the Cancer Genome Atlas database, RNA-seq and corresponding clinical and prognostic data of ccRCC patients were downloaded. Univariate and multivariate Cox regression analyses were conducted to acquire CTZFLs for constructing prediction models. The risk model was verified using receiver operating characteristic curve analysis. The Kaplan-Meier method was used to analyze the overall survival (OS) of high-risk and low-risk groups. Multivariate Cox and stratified analyses were used to assess the prognostic value of the predictive feature in the entire cohort and different subgroups. In addition, the relationship between risk scores, immunological status, and treatment response was studied. Results: We constructed a signature consisting of eight CTZFLs (LINC02100, AC002451.1, DBH-AS1, AC105105.3, AL357140.2, LINC00460, DLGAP1-AS2, AL162377.1). The results demonstrated that the prognosis of ccRCC patients was independently predicted by CTZFLs signature and that the prognosis of high-risk groups was poorer than that of the lower group. CTZFLs markers had the highest diagnostic adequacy compared to single clinicopathologic factors, and their AUC (area under the receiver operating characteristic curve) was 0.806. The overall survival of high-risk groups was shorter than that of low-risk groups when patients were divided into groups based on several clinicopathologic factors. There were substantial differences in immunological function, immune cell score, and immune checkpoint expression between high- and low-risk groups. Additionally, Four agents, including ABT737, WIKI4, afuresertib, and GNE 317, were more sensitive in the high-risk group. Conclusion: The Eight-CTZFLs prognostic signature may be a helpful prognostic indicator and may help with medication selection for clear cell renal cell carcinoma.
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Affiliation(s)
- Cheng Shen
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, China
- Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Zhan Chen
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, China
- Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Jie Jiang
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, China
- Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Yong Zhang
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, China
- Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Wei Xu
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, China
- Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Rui Peng
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, China
- Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Wenjing Zuo
- Department of Orthopedics, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Qian Jiang
- Department of Paediatric, Chinese Medicine Hospital of Rudong, Nantong, China
| | - Yihui Fan
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, China
| | - Xingxing Fang
- Nephrology Department, The Second Affiliated Hospital of Nantong University, Nantong, China
- *Correspondence: Bing Zheng, ; Xingxing Fang,
| | - Bing Zheng
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, China
- *Correspondence: Bing Zheng, ; Xingxing Fang,
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Jia Y, Yan Q, Zheng Y, Li L, Zhang B, Chang Z, Wang Z, Tang H, Qin Y, Guan XY. Long non-coding RNA NEAT1 mediated RPRD1B stability facilitates fatty acid metabolism and lymph node metastasis via c-Jun/c-Fos/SREBP1 axis in gastric cancer. J Exp Clin Cancer Res 2022; 41:287. [PMID: 36171622 PMCID: PMC9520879 DOI: 10.1186/s13046-022-02449-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/26/2022] [Indexed: 11/23/2022] Open
Abstract
Background Lymph node metastasis is one of most common determinants of the stage and prognosis of gastric cancer (GC). However, the key molecular events and mechanisms mediating lymph node metastasis remain elusive. Methods RNA sequencing was used to identify driver genes responsible for lymph node metastasis in four cases of gastric primary tumors, metastatic lesions of lymph nodes and matched normal gastric epithelial tissue. qRT–PCR and IHC were applied to examine RPRD1B expression. Metastatic functions were evaluated in vitro and in vivo. RNA-seq was used to identify target genes. ChIP, EMSA and dual luciferase reporter assays were conducted to identify the binding sites of target genes. Co-IP, RIP, MeRIP, RNA-FISH and ubiquitin assays were applied to explore the underlying mechanisms. Results The top 8 target genes (RPRD1B, MAP4K4, MCM2, TOPBP1, FRMD8, KBTBD2, ADAM10 and CXCR4) that were significantly upregulated in metastatic lymph nodes of individuals with GC were screened. The transcriptional cofactor RPRD1B (regulation of nuclear pre-mRNA domain containing 1B) was selected for further characterization. The clinical analysis showed that RPRD1B was significantly overexpressed in metastatic lymph nodes and associated with poor outcomes in patients with GC. The Mettl3-induced m6A modification was involved in the upregulation of RPRD1B. Functionally, RPRD1B promoted lymph node metastasis capabilities in vitro and in vivo. Mechanistic studies indicated that RPRD1B increased fatty acid uptake and synthesis by transcriptionally upregulating c-Jun/c-Fos and activating the c-Jun/c-Fos/SREBP1 axis. In addition, NEAT1 was upregulated significantly by c-Jun/c-Fos in RPRD1B-overexpressing cells. NEAT1, in turn, increased the stability of the RPRD1B mRNA by recruiting the m6A “reader” protein hnRNPA2B1 and reduced the degradation of the RPRD1B protein by inhibiting TRIM25-mediated ubiquitination. Notably, this functional circuitry was disrupted by an inhibitor of c-Jun/c-Fos/AP1 proteins (SR11302) and small interfering RNAs targeting NEAT1, leading to a preferential impairment of lymph node metastasis. Conclusions Based on these findings, RPRD1B facilitated FA metabolism and assisted primary tumor implantation in lymph nodes via the c-Jun/c-Fos/SREBP1 axis, which was enhanced by a NEAT1-mediated positive feedback loop, serving as a potential therapeutic target for GC treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02449-4.
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Shen X, Wang X, Lu X, Zhao Y, Guan W. Molecular biology of pancreatic neuroendocrine tumors: From mechanism to translation. Front Oncol 2022; 12:967071. [PMID: 36248960 PMCID: PMC9554633 DOI: 10.3389/fonc.2022.967071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Pancreatic neuroendocrine tumors (pNETs) are a group of heterogeneous tumors originated from progenitor cells. As these tumors are predominantly non-functional, most of them display asymptomatic characteristics, making it difficult to be realized from early onset. Therefore, patients with pNETs are usually diagnosed with metastatic disease or at a late disease stage. The relatively low incidence also limits our understanding of the biological background of pNETs, which largely impair the development of new effective drugs. The fact that up to 10% of pNETs develop in patients with genetic syndromes have promoted researchers to focus on the gene mutations and driver mutations in MEN1, DAXX/ATRX and mTOR signaling pathway genes have been implicated in disease development and progression. Recent advances in sequencing technologies have further enriched our knowledge of the complex molecular landscape of pNETs, pointing out crucial roles of genes in DNA damage pathways, chromosomal and telomere alterations and epigenetic dysregulation. These novel findings may not only benefit early diagnosis of pNETs, but also help to uncover tumor heterogeneity and shape the future of translational medical treatment. In this review, we focus on the current molecular biology of pNETs and decipher how these findings may translate into future development of targeted therapy.
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Affiliation(s)
- Xiaofei Shen
- Department of General Surgery, Affiliated Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Xingzhou Wang
- Department of General Surgery, Affiliated Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Xiaofeng Lu
- Department of General Surgery, Affiliated Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Yang Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Wenxian Guan, ; Yang Zhao,
| | - Wenxian Guan
- Department of General Surgery, Affiliated Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
- *Correspondence: Wenxian Guan, ; Yang Zhao,
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The Emerging Role of Noncoding RNA Regulation of the Ferroptosis in Cardiovascular Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:3595745. [PMID: 36187333 PMCID: PMC9519351 DOI: 10.1155/2022/3595745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022]
Abstract
Cardiovascular disease (CVD) is a significant public health issue due to its high prevalence and considerable contribution to the global disease burden. Recent studies suggest that genetic factors, including noncoding RNAs, have an important role in the progression of CVD. Noncoding RNA plays a critical role in genetic programming and gene regulation during development. Ferroptosis is a form of iron-dependent regulated cell death (RCD), which is mainly caused by increased lipid hydroperoxide and redox imbalance. Ferroptosis is essentially different from other forms of RCD in morphology and mechanism, such as apoptosis, autophagic cell death, pyroptosis, and necroptosis. Much evidence suggested ferroptosis is involved in the development of various CVDs, especially in cardiac ischemia/reperfusion injury, heart failure, and aortic dissection. Here, we review the latest findings based on noncoding RNA regulation of ferroptosis and its involvement in the pathogenesis of CVD and related treatments, aimed at providing insights into the impact of noncoding RNA regulation of ferroptosis for CVD.
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Long non-coding RNA LINC01018 inhibits human glioma cell proliferation and metastasis by directly targeting miRNA-182-5p. J Neurooncol 2022; 160:67-78. [PMID: 36094613 DOI: 10.1007/s11060-022-04113-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/04/2022] [Indexed: 10/14/2022]
Abstract
AIM Accumulating evidence suggests that lncRNAs are potential biomarkers and key regulators of tumor development and progression. However, the precise function of most lncRNAs in glioma remains unknown. In this study, we explored the role of long intergenic non-protein coding RNA 1018 (LINC01018) in human glioma. METHODS Expression levels of LINC01018 and miR-182-5p in clinical glioma tissues and cell lines were detected by quantitative real-time PCR (qRT-PCR). Cell proliferation, migration, and invasion were determined by Cell Counting Kit-8 (CCK-8) assay and Transwell assay. Epithelial-mesenchymal transition (EMT) related proteins were measured by Western blotting. Direct relationship between LINC01018 and miR-182-5p was tested by dual-luciferase reporter assay, RNA immunoprecipitation assay (RIP), and rescue assays. Lastly, bioinformatics analyses were conducted to predict the downstream factors of LINC01018/miR-182-5p axis in glioma. RESULTS LINC01018 was significantly down-regulated in glioma tissues and cell lines. Overexpression of LINC01018 dramatically inhibited cell proliferation, migration, and invasion and reverse EMT process in glioma. LINC01018 directly target to miR-182-5p. Forced up-regulation of miR-182-5p reversed the inhibitory effects on proliferative and metastatic abilities of glioma cells with LINC01018 overexpression. Lastly, the bioinformatics analyses revealed that LINC01018/miR-182-5p axis mediated a cluster of downstream genes (ADRA2C, RAB6B, RAB27B, RAPGEF5, STEAP2, TAGLN3, and UNC13C), which were potential key factors in the development of glioma. CONCLUSION LINC01018 inhibits cell proliferation and metastasis in human glioma by targeting miR-182-5p, and should be considered as a potential therapeutic target in this cancer.
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Zhu X, Yu R, Peng Y, Miao Y, Jiang K, Li Q. Identification of genomic instability related lncRNA signature with prognostic value and its role in cancer immunotherapy in pancreatic cancer. Front Genet 2022; 13:990661. [PMID: 36118868 PMCID: PMC9481284 DOI: 10.3389/fgene.2022.990661] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/08/2022] [Indexed: 12/02/2022] Open
Abstract
Background: Increasing evidence suggested the critical roles of lncRNAs in the maintenance of genomic stability. However, the identification of genomic instability-related lncRNA signature (GILncSig) and its role in pancreatic cancer (PC) remains largely unexplored. Methods: In the present study, a systematic analysis of lncRNA expression profiles and somatic mutation profiles was performed in PC patients from The Cancer Genome Atlas (TCGA). We then develop a risk score model to describe the characteristics of the model and verify its prediction accuracy. ESTIMATE algorithm, single-sample gene set enrichment analysis (ssGSEA), and CIBERSORT analysis were employed to reveal the correlation between tumor immune microenvironment, immune infiltration, immune checkpoint blockade (ICB) therapy, and GILncSig in PC. Results: We identified 206 GILnc, of which five were screened to develop a prognostic GInLncSig model. Multivariate Cox regression analysis and stratified analysis revealed that the prognostic value of the GILncSig was independent of other clinical variables. Receiver operating characteristic (ROC) analysis suggested that GILncSig is better than the existing lncRNA-related signatures in predicting survival. Additionally, the prognostic performance of the GILncSig was also found to be favorable in patients carrying wild-type KRAS, TP53, and SMAD4. Besides, a nomogram exhibited appreciable reliability for clinical application in predicting the prognosis of patients. Finally, the relationship between the GInLncSig model and the immune landscape in PC reflected its application value in clinical immunotherapy. Conclusion: In summary, the GILncSig identified by us may serve as novel prognostic biomarkers, and could have a crucial role in immunotherapy decisions for PC patients.
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Affiliation(s)
- Xiaole Zhu
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Pancreas Institute, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Rong Yu
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Pancreas Institute, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yunpeng Peng
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Pancreas Institute, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yi Miao
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Pancreas Institute, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Kuirong Jiang
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Pancreas Institute, Nanjing Medical University, Nanjing, Jiangsu, China
- *Correspondence: Kuirong Jiang, ; Qiang Li,
| | - Qiang Li
- Pancreas Center, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Pancreas Institute, Nanjing Medical University, Nanjing, Jiangsu, China
- *Correspondence: Kuirong Jiang, ; Qiang Li,
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Cao S, Wang X, Liu X, Li J, Duan L, Gao Z, Lun S, Zhu Y, Yang H, Zhang H, Zhou F. Integrative Analysis of Angiogenesis-Related Long Non-Coding RNA and Identification of a Six-DEARlncRNA Signature Associated with Prognosis and Therapeutic Response in Esophageal Squamous Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14174195. [PMID: 36077731 PMCID: PMC9454540 DOI: 10.3390/cancers14174195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a lethal gastrointestinal malignancy worldwide. We aimed to identify an angiogenesis-related lncRNAs (ARlncRNAs) signature that could predict the prognosis in ESCC. The GSE53624 and GSE53622 datasets were derived from the GEO database. The differently expressed ARlncRNAs (DEARlncRNAs) were retrieved by the weighted gene co-expression network analysis (WGCNA), differential expression analysis, and correlation analysis. Optimal lncRNA biomarkers were screened from the training set and the six-DEARlncRNA signature comprising AP000696.2, LINC01711, RP11-70C1.3, AP000487.5, AC011997.1, and RP11-225N10.1 could separate patients into high- and low-risk groups with markedly different survival. The validation of the reliability of the risk model was performed by the Kaplan-Meier test, ROC curves, and risk curves in the test set and validation set. Predictive independence analysis indicated that risk score is an independent prognostic biomarker for predicting the prognosis of ESCC patients. Subsequently, a ceRNA regulatory network and functional enrichment analysis were performed. The IC50 test revealed that patients in the high-risk group were resistant to Gefitinib and Lapatinib. Finally, the six DEARlncRNAs were detected by qRT-PCR. In conclusion, we demonstrated a novel ARlncRNA signature as an independent prognostic factor to distinguish the risk of ESCC patients and benefit the personalized clinical applications.
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Affiliation(s)
- Shasha Cao
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Xiaomin Wang
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Xiaohui Liu
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Junkuo Li
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Lijuan Duan
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Zhaowei Gao
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Shumin Lun
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Yanju Zhu
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Haijun Yang
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
| | - Hao Zhang
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China
- Correspondence: (H.Z.); (F.Z.)
| | - Fuyou Zhou
- Henan Medical Key Laboratory, Precise Prevention and Treatment of Esophageal Cancer, Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang 455000, China
- Correspondence: (H.Z.); (F.Z.)
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Ashrafi Dehkordi K, Asadi-Samani M, Shojaeian A, Mahmoudian-Sani MR. Decreased cell proliferation and induced apoptosis in human B-chronic lymphocytic leukemia following miR-221 inhibition through modulation of p27 expression. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00345-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
This study aimed to investigate the effects of the miR-221 inhibition on the human B-chronic lymphocytic leukemia (B-CLL) cell viability and the p27 gene expression, to introduce a new treatment approach for this type of cancer. In this context, the cyclin-dependent kinase (Cdk) inhibitor 1B (p27Kip1) is considered as an enzyme inhibitor that encodes a protein belonging to the Cip/Kip family of the Cdk inhibitor proteins.
Methods
The affected miR-221 inhibition in the B-CLL cell viability was initially assessed. The inhibition of miR-221 in the B-CLL cell line (183-E95) was thus performed using locked nucleic acid (LNA) as an antagomir. After the LNA-anti-miR-221 transfection, the miR-221 quantification, cell viability, and apoptosis assays were evaluated at different intervals by the reverse transcription-quantitative polymerase chain reaction (RT-qPCR), the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay, and flow cytometry (FC), respectively. The qRT-PCR was also completed for the p27 gene. The data were subsequently analyzed by independent-samples t-test and one-way analysis of variance (ANOVA).
Results
A gradual reduction was observed in the B-CLL cell viability, and consequently the transfected LNA-anti-miR cell viability reached below 55% of the untreated cells after 72 h of transfection. A statistically significant difference was found in the cell viability between the LNA-anti-miR-treated and control groups (p-value ≤ 0.043). The downregulation of miR-221 in the B-CLL (183-E95) cells was further conducted by LNA-anti-miR-221.
Conclusion
The miR-221 inhibition significantly decreases cell viability through augmenting the p27 gene expression and inducing apoptosis. Moreover, the findings demonstrated that the inhibition of miR-221 might be a new treatment approach for B-CLL, although more confirmation is needed by investigating appropriate animal models.
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Li X, Yu K, Li F, Lu W, Wang Y, Zhang W, Bai Y. Novel Method of Full-Length RNA-seq That Expands the Identification of Non-Polyadenylated RNAs Using Nanopore Sequencing. Anal Chem 2022; 94:12342-12351. [PMID: 36018770 DOI: 10.1021/acs.analchem.2c01128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The occurrence of diseases displayed transcriptome alteration, including both coding and non-coding transcripts. The third-generation sequencing (TGS) technologies allow for intensive and comprehensive research of the transcriptome. However, the present standard TGS RNA sequencing method is unable to detect many of the non-polyadenylated [non-poly(A)] RNAs. To obtain more complete transcriptome information, we presented a new comprehensive sequencing approach by performing conventional poly(A) RNA-sequencing combined with the sequencing of non-poly(A) RNA fraction which was tailed by poly(U) on HepG2 and HL-7702 cell lines, enabling the detection of multiple categories of non-poly(A) RNAs excluded by the existing standard approach. Moreover, the length distribution of the full-splice match transcripts was longer than that assembled by short-reads, which contributed to characterizing alternative splicing events and provided a comprehensive portrait of transcriptional complexity. Besides the detection of genes with differential expression patterns in the poly(A) library between HepG2 and HL-7702, we also found a cancer-related non-coding gene in the poly(U) data, that is, growth arrest special 5 (GAS5). Collectively, our results suggested that the novel method effectively captured both poly(A) and non-poly(A) transcripts in the tested cell lines and allowed a deeper exploration of the transcriptome.
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Affiliation(s)
- Xiaohan Li
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Kequan Yu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Fuyu Li
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Wenxiang Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Ying Wang
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Weizhong Zhang
- Department of Ophthalmology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yunfei Bai
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
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During HCV DAA Therapy Plasma Mip1B, IP10, and miRNA Profile Are Distinctly Associated with Subsequent Diagnosis of Hepatocellular Carcinoma: A Pilot Study. BIOLOGY 2022; 11:biology11091262. [PMID: 36138741 PMCID: PMC9495750 DOI: 10.3390/biology11091262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/11/2022] [Accepted: 08/13/2022] [Indexed: 01/07/2023]
Abstract
Background: Hepatitis C virus (HCV) therapy lowers risk of hepatocellular carcinoma (HCC). Little is known about factors driving/preceding HCC in treated persons. MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) regulate host response and pathogenesis of disease. We investigated plasma levels of these RNAs and select serum markers before, during, and after HCV therapy, preceding HCC. Methods: Of 187 DAA treated HCV patients where therapy oriented longitudinal sampling was performed at a time without HCC diagnosis, 9 were subsequently diagnosed with HCC within 2 years of therapy. They were matched with 7 patients not diagnosed with HCC over the same time period. RNASeq was performed on plasma, and serum was assessed for biomarkers of inflammation by ELISA. Results: HCC diagnosis was 19 months (6-28) after therapy start in the HCC group. 73 and 63 miRs were differentially expressed at baseline (before DAA therapy) and 12 weeks after DAA therapy comparing HCC and non-HCC groups. Several lncRNA- showed differential expression as well. Several miRNA suppressors of cancer-related pathways, lncRNA- and mRNA-derived stabilized short RNAs were consistently absent in the plasma of patients who developed HCC. Serum IP10, and MCP-1 level was higher in the HCC group 12 weeks after therapy, and distinct miRNAs correlated with IP10 and MCP-1. Finally, in a focused analysis of 8 miRNAs best associated with HCC we observed expression of mi576 and mi-5189 correlation with expression of a select group of PBMC mRNA. Conclusions: These results are consistent with complex interplay between RNA-mediated host immune regulation and cancer suppression, strikingly skewed 12 weeks following therapy, prior to HCC diagnosis.
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Yan X, Wang N, Dong J, Wang F, Zhang J, Hu X, Zhao H, Gao X, Liu Z, Li Y, Hu S. A cuproptosis-related lncRNAs signature for prognosis, chemotherapy, and immune checkpoint blockade therapy of low-grade glioma. Front Mol Biosci 2022; 9:966843. [PMID: 36060266 PMCID: PMC9428515 DOI: 10.3389/fmolb.2022.966843] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 07/25/2022] [Indexed: 12/25/2022] Open
Abstract
Cuproptosis is a new type of cell death that is associated with mitochondrial respiration of the tricarboxylic acid cycle. Previous studies showed that long non-coding RNAs (lncRNAs) regulated low-grade glioma (LGG) progression. However, the potential applications of cuproptosis-related lncRNAs (CRLs) in LGG were not explored. A comprehensive analysis was performed in The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) cohorts. We first screened two distinct cuproptosis subtypes based on prognostic CRLs using consensus clustering. To facilitate individualized survival prediction in LGG, we constructed a prognostic signature (including CRNDE, HAR1A, and FAM181A-AS1) in the TCGA dataset. The prognostic signature exhibited excellent predictive ability and reliability, which was validated in the CGGA_325 and CGGA_693 datasets. Notably, patients in the high-risk group had increased immune cell infiltration and expression of immune checkpoints, which indicated that they may benefit more from immune checkpoint blockade (ICB) therapy. Finally, the prognostic signature screened the population with sensitivity to chemotherapy and ICB therapy. In summary, this study initially explored the mechanism of CRLs in LGG and provides some insights into chemotherapy and ICB therapy of LGG.
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Affiliation(s)
- Xiuwei Yan
- Department of Neurosurgery, Cancer Center, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Nan Wang
- Department of Neurosurgery, Cancer Center, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Jiawei Dong
- Department of Neurosurgery, Cancer Center, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Fang Wang
- Department of Neurosurgery, Cancer Center, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Jiheng Zhang
- Department of Neurosurgery, Cancer Center, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Xueyan Hu
- Department of Neurosurgery, Cancer Center, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Hongtao Zhao
- Department of Neurosurgery, Cancer Center, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Xin Gao
- Department of Neurosurgery, Cancer Center, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Zhihui Liu
- Department of Neurosurgery, Cancer Center, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Zhihui Liu, ; Yongzhe Li, ; Shaoshan Hu,
| | - Yongzhe Li
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Zhihui Liu, ; Yongzhe Li, ; Shaoshan Hu,
| | - Shaoshan Hu
- Department of Neurosurgery, Cancer Center, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Zhihui Liu, ; Yongzhe Li, ; Shaoshan Hu,
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A novel molecular subtypes and risk model based on inflammatory response-related lncrnas for bladder cancer. Hereditas 2022; 159:32. [PMID: 35964079 PMCID: PMC9375404 DOI: 10.1186/s41065-022-00245-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/28/2022] [Indexed: 12/24/2022] Open
Abstract
Background Inflammation and long noncoding RNAs (lncRNAs) are gradually becoming important in the development of bladder cancer (BC). Nevertheless, the potential of inflammatory response-related lncRNAs (IRRlncRNAs) as a prognostic signature remains unexplored in BC. Methods The Cancer Genome Atlas (TCGA) provided RNA expression profiles and clinical information of BC samples, and GSEA Molecular Signatures database provided 1171 inflammation-related genes. IRRlncRNAs were identified using Pearson correlation analysis. After that, consensus clustering was performed to form molecular subtypes. After performing least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analyses, a risk model constructed based on the prognostic IRRlncRNAs was validated in an independent cohort. Kaplan–Meier (KM) analysis, univariate and multivariate Cox regression, clinical stratification analysis, and time-dependent receiver operating characteristic (ROC) curves were utilized to assess clinical effectiveness and accuracy of the risk model. In clusters and risk model, functional enrichment was investigated using GSEA and GSVA, and immune cell infiltration analysis was demonstrated by ESTIMATE and CIBERSORT analysis. Results A total of 174 prognostic IRRlncRNAs were confirmed, and 406 samples were divided into 2 clusters, with cluster 2 having a significantly inferior prognosis. Moreover, cluster 2 exhibited a higher ESTIMATE score, immune infiltration, and PD-L1 expression, with close relationships with the inflammatory response. Further, 12 IRRlncRNAs were identified and applied to construct the risk model and divide BC samples into low-risk and high-risk groups successfully. KM, ROC, and clinical stratification analysis demonstrated that the risk model performed well in predicting prognosis. The risk score was identified as an independently significant indicator, enriched in immune, cell cycle, and apoptosis-related pathways, and correlated with 9 immune cells. Conclusion We developed an inflammatory response-related subtypes and steady prognostic risk model based on 12 IRRlncRNAs, which was valuable for individual prognostic prediction and stratification and outfitted new insight into inflammatory response in BC. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-022-00245-w.
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93
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A comprehensive analysis of avian lymphoid leukosis-like lymphoma transcriptomes including identification of LncRNAs and the expression profiles. PLoS One 2022; 17:e0272557. [PMID: 35939448 PMCID: PMC9359530 DOI: 10.1371/journal.pone.0272557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 07/21/2022] [Indexed: 11/22/2022] Open
Abstract
Avian lymphoid leukosis-like (LL-like) lymphoma has been observed in some experimental and commercial lines of chickens that are free of exogenous avian leukosis virus. Reported cases of avian lymphoid leukosis-like lymphoma incidences in the susceptible chickens are relatively low, but the apathogenic subgroup E avian leukosis virus (ALV-E) and the Marek’s disease vaccine, SB-1, significantly escalate the disease incidence in the susceptible chickens. However, the underlying mechanism of tumorigenesis is poorly understood. In this study, we bioinformatically analyzed the deep RNA sequences of 6 lymphoid leukosis-like lymphoma samples, collected from susceptible chickens post both ALV-E and SB-1 inoculation, and identified a total of 1,692 novel long non-coding RNAs (lncRNAs). Thirty-nine of those novel lncRNAs were detected with altered expression in the LL-like tumors. In addition, 13 lncRNAs whose neighboring genes also showed differentially expression and 2 conserved novel lncRNAs, XLOC_001407 and XLOC_022595, may have previously un-appreciated roles in tumor development in human. Furthermore, 14 lncRNAs, especially XLOC_004542, exhibited strong potential as competing endogenous RNAs via sponging miRNAs. The analysis also showed that ALV subgroup E viral gene Gag/Gag-pol and the MD vaccine SB-1 viral gene R-LORF1 and ORF413 were particularly detectable in the LL-like tumor samples. In addition, we discovered 982 novel lncRNAs that were absent in the current annotation of chicken genome and 39 of them were aberrantly expressed in the tumors. This is the first time that lncRNA signature is identified in avian lymphoid leukosis-like lymphoma and suggests the epigenetic factor, lncRNA, is involved with the avian lymphoid leukosis-like lymphoma formation and development in susceptible chickens. Further studies to elucidate the genetic and epigenetic mechanisms underlying the avian lymphoid leukosis-like lymphoma is indeed warranted.
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94
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Zhang X, Sun B, Bai Y, Canário AVM, Xu X, Li J. Long non-coding RNAs are involved in immune resistance to Aeromonas hydrophila in black carp (Mylopharyngodon piceus). FISH & SHELLFISH IMMUNOLOGY 2022; 127:366-374. [PMID: 35772677 DOI: 10.1016/j.fsi.2022.06.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/24/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
A growing number of studies identified long non-coding RNAs (lncRNAs) to be closely associated with immune function through the regulation of immune cell differentiation and immune cell effector function. Here we tested whether lncRNAs are involved in immune function in black carp (Mylopharyngodon piceus) through the exposure to Aeromonas hydrophila and analysis of the spleen gene expression response using RNA-seq. A total of 9036 lncRNAs were identified with high confidence. Differential expression analysis identified a total of 3558 DElncRNAs (Differential expression lncRNA) involved in A. hydrophila infection and 4526 target genes corresponding to DElncRNAs. After screening 4526 target genes in the InnateDB database, a total of 150 immunity genes were identified. After GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis of the obtained immunity genes, the Toll-like receptor (TLR) signaling pathway, TLR2, TLR3, TLR5, and TLR8 were identified as particularly significant in A. hydrophyla-resistant black carp. At the same time, the Ras signaling pathway was particularly enriched in the spleen of susceptible black carp. Analysis of PPI (protein-protein interaction) networks of the obtained immune genes identified SRC (SRC Proto-Oncogene), MYD88 (Myeloid differentiation primary response 88), MAPK3 (Mitogen-Activated Protein Kinase 3), MYC (MYC Proto-Oncogene) as main hub genes regulated by lncRNA and possibly mediating a mechanism of susceptibility to bacteria. These results establish a functional role of lncRNAs and a mechanistic base for the immune response in black carp resistant to A. hydrophila.
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Affiliation(s)
- Xueshu Zhang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; CCMAR/CIMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Bingyan Sun
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Yulin Bai
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
| | - Adelino V M Canário
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; CCMAR/CIMAR Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.
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95
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Wang Y, Tang Z, Guo W. XIST sponges miR-320d to promote chordoma progression by regulating ARF6. J Bone Oncol 2022; 35:100447. [PMID: 35899235 PMCID: PMC9309415 DOI: 10.1016/j.jbo.2022.100447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/06/2022] [Accepted: 07/13/2022] [Indexed: 11/30/2022] Open
Abstract
XIST was highly expressed in chordoma tissues. XIST knockdown inhibited chordoma progression by downregulating ARF6. MiR-320d inhibited the malignant behaviors of chordoma cells. XIST positively upregulated ARF6 expression via sponging miR-320d in chordoma cells.
Background Long non-coding RNAs (lncRNAs) have been demonstrated to play important roles in various tumors, including chordoma. The purpose of this study was to investigate the role and mechanism of lncRNA X-inactive specific transcript (XIST) in chordoma. Methods RNA levels and protein levels were measured by real-time quantitative polymerase chain reaction (RT‑qPCR) and western blot assay, respectively. Cell proliferation was assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, 5-ethynyl-2′-deoxyuridine (EdU) assay and colony formation assay. Tanswell assay was used to examine cell migration and invasion. Cellular glycolysis was examined via the measurement of extracellular acidification rate (ECAR) and lactate production. The interaction between microRNA-320d (miR-320d) and XIST or ADP-ribosylation factor 6 (ARF6) was predicted by bioinformatics analysis and verified by a dual-luciferase reporter and RNA-pull down assays. The xenograft tumor model was used to explore the biological function of XIST in vivo. Results XIST was overexpressed in chordoma tissues. XIST knockdown suppressed chordoma cell proliferation, migration, invasion, and glycolysis. XIST acted as a sponge of miR-320d. Moreover, miR-320d overexpression inhibited the proliferation, migration, invasion, and glycolysis of chordoma cells. ARF6 was a direct target of miR-320d, and XIST upregulated ARF6 expression via sponging miR-320d. Furthermore, overexpression of ARF6 reversed the inhibitory effects of XIST knockdown on chordoma cell proliferation, migration, invasion, and glycolysis. Importantly, XIST silencing blocked xenograft tumor growth in vivo. Conclusion XIST knockdown inhibited chordoma progression via regulating the miR-320d/ARF6 axis, providing a novel insight into chordoma pathogenesis.
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Affiliation(s)
- Yonggang Wang
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Zhouzhou Tang
- Department of Orthopedics, Jingzhou Central Hospital, Jingzhou 434020, Hubei Province, China
| | - Weichun Guo
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
- Corresponding author at: Department of Orthopedics, Renmin Hospital of Wuhan University, No. 238, Jiefang Road, Wuchang District, Wuhan City, Hubei Province, China.
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96
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Thanh Thi Ngoc Nguyen, Nguyen THN, Phan HN, Nguyen HT. Seven-Single Nucleotide Polymorphism Polygenic Risk Score for Breast Cancer Risk Prediction in a Vietnamese Population. CYTOL GENET+ 2022. [DOI: 10.3103/s0095452722040065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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97
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Athanasopoulou K, Adamopoulos PG, Scorilas A. Structural characterization and expression analysis of novel MAPK1 transcript variants with the development of a multiplexed targeted nanopore sequencing approach. Int J Biochem Cell Biol 2022; 150:106272. [PMID: 35878809 DOI: 10.1016/j.biocel.2022.106272] [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: 02/08/2022] [Revised: 06/17/2022] [Accepted: 07/21/2022] [Indexed: 11/27/2022]
Abstract
Mitogen-activated protein kinases (MAPKs) represent a protein family firmly involved in many signaling cascades, regulating a vast spectrum of stimulated cellular processes. Studies have shown that alternatively spliced isoforms of MAPKs play a crucial role in determining the desired cell fate in response to specific stimulations. Although the implication of most MAPKs transcript variants in the MAPK signaling cascades has been clarified, the transcriptional profile of a pivotal member, MAPK1, has not been investigated for the existence of additional isoforms. In the current study we developed and implemented targeted long-read and short-read sequencing approaches to identify novel MAPK1 splice variants. The combination of nanopore sequencing and NGS enabled the implementation of a long-read polishing pipeline using error-rate correction algorithms, which empowered the high accuracy of the results and increased the sequencing efficiency. The utilized multiplexing option in the nanopore sequencing approach allowed not only the identification of novel MAPK1 mRNAs, but also elucidated their expression profile in multiple human malignancies and non-cancerous cell lines. Our study highlights for the first time the existence of ten previously undescribed MAPK1 mRNAs (MAPK1 v.3 - v.12) and evaluates their relative expression levels in comparison to the main MAPK1 v.1. The optimization and employment of qPCR assays revealed that MAPK1 v.3 - v.12 can be quantified in a wide spectrum of human cell lines with notable specificity. Finally, our findings suggest that the novel protein-coding mRNAs are highly expected to participate in the regulation of MAPK pathways, demonstrating differential localizations and functionalities.
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Affiliation(s)
- Konstantina Athanasopoulou
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece.
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98
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Huang CM, Tsai HL, Chen YC, Huang CW, Li CC, Su WC, Chang TK, Yeh YS, Chen PJ, Huang MY, Wang JY. Role of non-coding RNAs in radiosensitivity of colorectal cancer: A narrative review. Front Oncol 2022; 12:889658. [PMID: 35936676 PMCID: PMC9354854 DOI: 10.3389/fonc.2022.889658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/27/2022] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is a global public health concern because of its high prevalence and mortality. Although radiotherapy is a key method for treating CRC, radioresistance is an obstacle to radiotherapy use. The molecular mechanisms underlying the radioresistance of CRC remain unclear. Increasing evidence has revealed the multiple regulatory functions of non-coding RNAs (ncRNAs) in numerous malignancies, including CRC. Several ncRNAs have been reported to be involved in the determination of radiosensitivity of CRC cells, and some have excellent potential to be prognostic biomarkers or therapeutic targets in CRC treatment. The present review discusses the biological functions and underlying mechanisms of ncRNAs (primarily lncRNA, miRNA, and circRNA) in the regulation of the radiosensitivity of CRC. We also evaluate studies that examined ncRNAs as biomarkers of response to radiation and as therapeutic targets for enhancing radiosensitivity.
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Affiliation(s)
- Chun-Ming Huang
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Radiation Oncology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Radiation Oncology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hsiang-Lin Tsai
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yen-Cheng Chen
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ching-Wen Huang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ching-Chun Li
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wei-Chih Su
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tsung-Kun Chang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yung-Sung Yeh
- Division of Trauma and Surgical Critical Care, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Emergency Medicine, Faculty of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Injury Prevention and Control, College of Public Health, Taipei Medical University, Taipei, Taiwan
| | - Po-Jung Chen
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Yii Huang
- Department of Radiation Oncology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Radiation Oncology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jaw-Yuan Wang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Pingtung Hospital, Ministry of Health and Welfare, Pingtung, Taiwan
- *Correspondence: Jaw-Yuan Wang, ;
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Sargazi S, Zahedi Abghari A, Mirinejad S, Heidari Nia M, Majidpour M, Danesh H, Saravani R, Sheervalilou R, Shakiba M, Zahedi Abghari F. Long noncoding RNA HOTAIR polymorphisms and susceptibility to bipolar disorder: a preliminary case-control study. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:684-701. [PMID: 35469536 DOI: 10.1080/15257770.2022.2065017] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Recent studies have shown that long noncoding RNAs contribute to the pathogenesis of bipolar disorder (BD). In this study, we genotyped four HOX Transcript Antisense Intergenic RNA (HOTAIR) gene polymorphisms to investigate if these variations could affect the risk of BD and its clinical subtypes. A total of 357 subjects, comprised of 194 BD patients and 163 age-matched healthy controls, were enrolled. Genotyping was carried out using PCR-RFLP and ARMS-PCR methods. We detected significant associations between the HOTAIR gene rs1899663 G/T, rs12826786 C/T, rs4759314 A/G, and rs920778 C/T polymorphism and the risk of BD under allelic, recessive, dominant, and codominant contrasted genetic models. The CT genotype of rs920778 C/T, GT genotype of rs1899663 G/T, and CT genotype of rs12826786 C/T polymorphisms enhanced the risk of BD type II (BDII). In contrast, the GG genotype of rs4759314 A/G polymorphism significantly diminished BDII risk by 83%. A positive association was noticed between CTTA and CTCG haplotypes of rs920778/rs1899663/rs12826786/rs4759314 and BD risk. Our findings reveal an interactive effect of HOTAIR polymorphisms on the development of BD and its subtypes. Further functional studies are needed to elucidate the role of these variations on HOTAIR expression and epigenetic status.
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Affiliation(s)
- Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Armin Zahedi Abghari
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Milad Heidari Nia
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mahdi Majidpour
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Hiva Danesh
- Department of Clinical Biochemistry, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ramin Saravani
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | | | - Mansoor Shakiba
- Department of Psychiatry, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Fateme Zahedi Abghari
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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Diao X, Guo C, Li S. Construction of a Novel Prognostic Signature in Lung Adenocarcinoma Based on Necroptosis-Related lncRNAs. Front Genet 2022; 13:833362. [PMID: 35938013 PMCID: PMC9354127 DOI: 10.3389/fgene.2022.833362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Long non-coding RNAs (lncRNAs) are drawing increasing attention as promising predictors of prognosis for lung adenocarcinoma (LUAD) patients. Necroptosis, a novel regulated mechanism of necrotic cell death, plays an important role in the biological process of cancer. The aim of this study was to identify the necroptosis-related lncRNAs (NRLRs) in a LUAD cohort and establish a necroptosis-related lncRNA signature (NRLSig) to stratify LUAD patients.Methods: NRLRs were identified in LUAD patients from The Cancer Genome Atlas (TCGA) database using Pearson correlation analysis between necroptosis-related genes and lncRNAs. Then the NRLSig was identified using univariate Cox regression analysis and LASSO regression analysis. Assessments of the signature were performed based on survival analysis, receiver operating characteristic (ROC) curve analysis and clustering analysis. Next, a nomogram containing the NRLSig and clinical information was developed through univariate and multivariate Cox regression analysis. Further, functional enrichment analysis of the selected lncRNAs in NRLSig and the association between NRLSig and the immune infiltration were also evaluated.Results: A 4-lncRNA signature, incorporating LINC00941, AP001453.2, AC026368.1, and AC236972.3, was identified to predict overall survival (OS) and stratify LUAD patients into different groups. Survival analysis, ROC curve analysis and clustering analysis showed good performance in the prognostic prediction of the lncRNA signature. Then, a nomogram containing the NRLSig was developed and showed satisfactory predictive accuracy, calibration and clinical usefulness. The co-expressed genes of selected NRLRs were enriched in several biological functions and signaling pathways. Finally, differences in the abundance of immune cells were investigated among the high-risk group and low-risk group divided by the NRLSig.Conclusion: The proposed NRLSig may provide promising therapeutic targets or prognostic predictors for LUAD patients.
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