1
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Saleem A, Saleem Bhat S, A. Omonijo F, A Ganai N, M. Ibeagha-Awemu E, Mudasir Ahmad S. Immunotherapy in mastitis: state of knowledge, research gaps and way forward. Vet Q 2024; 44:1-23. [PMID: 38973225 PMCID: PMC11232650 DOI: 10.1080/01652176.2024.2363626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 05/27/2024] [Indexed: 07/09/2024] Open
Abstract
Mastitis is an inflammatory condition that affects dairy cow's mammary glands. Traditional treatment approaches with antibiotics are increasingly leading to challenging scenarios such as antimicrobial resistance. In order to mitigate the unwanted side effects of antibiotics, alternative strategies such as those that harness the host immune system response, also known as immunotherapy, have been implemented. Immunotherapy approaches to treat bovine mastitis aims to enhance the cow's immune response against pathogens by promoting pathogen clearance, and facilitating tissue repair. Various studies have demonstrated the potential of immunotherapy for reducing the incidence, duration and severity of mastitis. Nevertheless, majority of reported therapies are lacking in specificity hampering their broad application to treat mastitis. Meanwhile, advancements in mastitis immunotherapy hold great promise for the dairy industry, with potential to provide effective and sustainable alternatives to traditional antibiotic-based approaches. This review synthesizes immunotherapy strategies, their current understanding and potential future perspectives. The future perspectives should focus on the development of precision immunotherapies tailored to address individual pathogens/group of pathogens, development of combination therapies to address antimicrobial resistance, and the integration of nano- and omics technologies. By addressing research gaps, the field of mastitis immunotherapy can make significant strides in the control, treatment and prevention of mastitis, ultimately benefiting both animal and human health/welfare, and environment health.
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Affiliation(s)
- Afnan Saleem
- Division of Animal Biotechnology, SKUAST-K, Srinagar, India
| | | | - Faith A. Omonijo
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Canada
| | | | - Eveline M. Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Canada
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2
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Li W, Zhang H, You Z, Guo B. LncRNAs in Immune and Stromal Cells Remodel Phenotype of Cancer Cell and Tumor Microenvironment. J Inflamm Res 2024; 17:3173-3185. [PMID: 38774447 PMCID: PMC11108079 DOI: 10.2147/jir.s460730] [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: 01/22/2024] [Accepted: 05/07/2024] [Indexed: 05/24/2024] Open
Abstract
Emerging studies suggest that long non-coding RNAs (lncRNAs) participate in the mutual regulation of cells in tumor microenvironment, thereby affecting the anti-tumor immune activity of immune cells. Additionally, the intracellular pathways mediated by lncRNAs can affect the expression of immune checkpoints or change the cell functions, including cytokines secretion, of immune and stromal cells in tumor microenvironment, which further influences cancer patients' prognosis and treatment response. With the in-depth research, lncRNAs have shown great potency as a new immunotherapy target and predict immunotherapy response. The research on lncRNAs provides us with a new insight into developing new immunotherapy drugs and predicting the outcome of immunotherapy. With development of RNA sequencing technology, amounts of lncRNAs were found to be dysregulated in immune and stromal cells rather than tumor cells. These lncRNAs function through ceRNA network or regulating transcript factor activity, thus leading abnormal differentiation and activation of immune and stromal cells. Here, we review the function of lncRNAs in the immune microenvironment and focus on the alteration of lncRNAs in immune and stromal cells, and discuss how these alterations affect tumor growth, metastasis and treatment response.
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Affiliation(s)
- Wenbin Li
- Department of Clinical Oncology, Qianjiang Hospital Affiliated to Renmin Hospital of Wuhan University, Qianjiang, Hubei, People’s Republic of China
- Department of Clinical Oncology, Qianjiang Central Hospital of Hubei Province, Qianjiang, Hubei, People’s Republic of China
| | - Haohan Zhang
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Zuo You
- Department of Traditional Chinese Medicine, Xianfeng County People’s Hospital, Enshi, Hubei, People’s Republic of China
| | - Baozhu Guo
- Department of Pain, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
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3
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Kong R, Wang N, Zhou CL, Lu J. Prognostic Value of an Immune Long Non-Coding RNA Signature in Liver Hepatocellular Carcinoma. J Microbiol Biotechnol 2024; 34:958-968. [PMID: 38494878 DOI: 10.4014/jmb.2308.08022] [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: 08/14/2023] [Revised: 11/28/2023] [Accepted: 01/18/2024] [Indexed: 03/19/2024]
Abstract
In recent years, there has been a growing recognition of the important role that long non-coding RNAs (lncRNAs) play in the immunological process of hepatocellular carcinoma (LIHC). An increasing number of studies have shown that certain lncRNAs hold great potential as viable options for diagnosis and treatment in clinical practice. The primary objective of our investigation was to devise an immune lncRNA profile to explore the significance of immune-associated lncRNAs in the accurate diagnosis and prognosis of LIHC. Gene expression profiles of LIHC samples obtained from TCGA database were screened for immune-related genes. The optimal immune-related lncRNA signature was built via correlational analysis, univariate and multivariate Cox analysis. Then, the Kaplan-Meier plot, ROC curve, clinical analysis, gene set enrichment analysis, and principal component analysis were performed to evaluate the capability of the immune lncRNA signature as a prognostic indicator. Six long non-coding RNAs were identified via correlation analysis and Cox regression analysis considering their interactions with immune genes. Subsequently, tumor samples were categorized into two distinct risk groups based on different clinical outcomes. Stratification analysis indicated that the prognostic ability of this signature acted as an independent factor. The Kaplan-Meier method was employed to conduct survival analysis, results showed a significant difference between the two risk groups. The predictive performance of this signature was validated by principal component analysis (PCA). Additionally, data obtained from gene set enrichment analysis (GSEA) revealed several potential biological processes in which these biomarkers may be involved. To summarize, this study demonstrated that this six-lncRNA signature could be identified as a potential factor that can independently predict the prognosis of LIHC patients.
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Affiliation(s)
- Rui Kong
- Department of Gastroenterology, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, P.R. China
| | - Nan Wang
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Chun Li Zhou
- Department of Gastroenterology, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, P.R. China
| | - Jie Lu
- Department of Gastroenterology, Pu Dong Area Gongli Hospital, School of Medicine, Shanghai University, Shanghai 200135, P.R. China
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
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4
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Qu C, Cui H, Xiao S, Dong L, Lu Q, Zhang L, Wang P, Xin M, Zhi H, Liu C, Ning S, Gao Y. The landscape of immune checkpoint-related long non-coding RNAs core regulatory circuitry reveals implications for immunoregulation and immunotherapy responses. Commun Biol 2024; 7:327. [PMID: 38485995 PMCID: PMC10940638 DOI: 10.1038/s42003-024-06004-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 03/01/2024] [Indexed: 03/18/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) could modulate expression of immune checkpoints (ICPs) by cooperating with immunity genes in tumor immunization. However, precise functions in immunity and potential for predicting ICP inhibitors (ICI) response have been described for only a few lncRNAs. Here we present an integrated framework that leverages network-based analyses and Bayesian network inference to identify the regulated relationships including lncRNA, ICP and immunity genes as ICP-related LncRNAs mediated Core Regulatory Circuitry Triplets (ICP-LncCRCTs) that can make robust predictions. Hub ICP-related lncRNAs such as MIR155HG and ADAMTS9-AS2 were highlighted to play central roles in immune regulation. Specific ICP-related lncRNAs could distinguish cancer subtypes. Moreover, the ICP-related lncRNAs are likely to significantly correlated with immune cell infiltration, MHC, CYT. Some ICP-LncCRCTs such as CXCL10-MIR155HG-ICOS could better predict one-, three- and five-year prognosis compared to single molecule in melanoma. We also validated that some ICP-LncCRCTs could effectively predict ICI-response using three kinds of machine learning algorithms follow five independent datasets. Specially, combining ICP-LncCRCTs with the tumor mutation burden (TMB) improves the prediction of ICI-treated melanoma patients. Altogether, this study will improve our grasp of lncRNA functions and accelerating discovery of lncRNA-based biomarkers in ICI treatment.
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Affiliation(s)
- Changfan Qu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Hao Cui
- The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Song Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Longlong Dong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Qianyi Lu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Lei Zhang
- The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Mengyu Xin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Chenyu Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
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5
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Meng L, Wu H, Wu J, Ding P, He J, Sang M, Liu L. Mechanisms of immune checkpoint inhibitors: insights into the regulation of circular RNAS involved in cancer hallmarks. Cell Death Dis 2024; 15:3. [PMID: 38177102 PMCID: PMC10766988 DOI: 10.1038/s41419-023-06389-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 01/06/2024]
Abstract
Current treatment strategies for cancer, especially advanced cancer, are limited and unsatisfactory. One of the most substantial advances in cancer therapy, in the last decades, was the discovery of a new layer of immunotherapy approach, immune checkpoint inhibitors (ICIs), which can specifically activate immune cells by targeting immune checkpoints. Immune checkpoints are a type of immunosuppressive molecules expressed on immune cells, which can regulate the degree of immune activation and avoid autoimmune responses. ICIs, such as anti-PD-1/PD-L1 drugs, has shown inspiring efficacy and broad applicability across various cancers. Unfortunately, not all cancer patients benefit remarkably from ICIs, and the overall response rates to ICIs remain relatively low for most cancer types. Moreover, the primary and acquired resistance to ICIs pose serious challenges to the clinical application of cancer immunotherapy. Thus, a deeper understanding of the molecular biological properties and regulatory mechanisms of immune checkpoints is urgently needed to improve clinical options for current therapies. Recently, circular RNAs (circRNAs) have attracted increasing attention, not only due to their involvement in various aspects of cancer hallmarks, but also for their impact on immune checkpoints in shaping the tumor immune microenvironment. In this review, we systematically summarize the current status of immune checkpoints in cancer and the existing regulatory roles of circRNAs on immune checkpoints. Meanwhile, we also aim to settle the issue in an evidence-oriented manner that circRNAs involved in cancer hallmarks regulate the effects and resistance of ICIs by targeting immune checkpoints.
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Affiliation(s)
- Lingjiao Meng
- Department of Tumor Immunotherapy, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050035, China
- Research Center and Tumor Research Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Haotian Wu
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050011, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, 050011, China
| | - Jiaxiang Wu
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050011, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, 050011, China
| | - Ping'an Ding
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050011, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, 050011, China
| | - Jinchen He
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050011, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, Shijiazhuang, 050011, China
| | - Meixiang Sang
- Research Center and Tumor Research Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, China.
- Science and Education Department, Shanghai Electric Power Hospital, Shanghai, 20050, China.
| | - Lihua Liu
- Department of Tumor Immunotherapy, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050035, China.
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Wang P, Zhang T, Jiang N, Wang K, Feng L, Liu T, Yang X. PDIA6, which is regulated by TRPM2-AS/miR-424-5p axis, promotes endometrial cancer progression via TGF-beta pathway. Cell Death Dis 2023; 14:829. [PMID: 38097564 PMCID: PMC10721792 DOI: 10.1038/s41419-023-06297-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 10/26/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023]
Abstract
PDIA6 have been reported to be involved in a variety of cancers, however, the underlying role in endometrial cancer is still unclear. In this study, we aimed to study the function of PDIA6 in endometrial cancer. Firstly, we verified that PDIA6 was significantly upregulated in endometrial cancer, which was correlated with the progression of endometrial cancer patients. Furthermore, we identified PDIA6 significantly altered the ability of endometrial cancer cells to proliferate and metastasize. In addition, our result illustrated the oncogene effects of PDIA6 in promoting malignant biological behavior of endometrial cancer cells by regulating TGF-β pathway and being modulated by TRPM2-AS/miR-424-5p axis for the first time. Taken together, this study suggested that PDIA6 may be a new candidate target for endometrial cancer therapy.
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Affiliation(s)
- Pengling Wang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Tianli Zhang
- Department of Gynecology, The Second Hospital of Shandong University, Jinan, Shandong, 250033, People's Republic of China
| | - Nan Jiang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Kun Wang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Liping Feng
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, People's Republic of China
| | - Ting Liu
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, People's Republic of China.
| | - Xingsheng Yang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, People's Republic of China.
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7
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Liu K, Yuan S, Wang C, Zhu H. Resistance to immune checkpoint inhibitors in gastric cancer. Front Pharmacol 2023; 14:1285343. [PMID: 38026944 PMCID: PMC10679741 DOI: 10.3389/fphar.2023.1285343] [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: 08/29/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Gastric cancer (GC) is one of the most common gastrointestinal malignancies worldwide. In the past decade, with the development of early diagnostic techniques, a clear decline in GC incidence has been observed, but its mortality remains high. The emergence of new immunotherapies such as immune checkpoint inhibitors (ICIs) has changed the treatment of GC patients to some extent. However, only a small number of patients with advanced GC have a durable response to ICI treatment, and the efficacy of ICIs is very limited. Existing studies have shown that the failure of immunotherapy is mainly related to the development of ICI resistance in patients, but the understanding of the resistance mechanism is still insufficient. Therefore, clarifying the mechanism of GC immune resistance is critical to improve its treatment and clinical benefit. In this review, we focus on summarizing the mechanisms of primary or acquired resistance to ICI immunotherapy in GC from both internal and external aspects of the tumor. At the same time, we also briefly discuss some other possible resistance mechanisms in light of current studies.
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Affiliation(s)
- Kai Liu
- The Clinical Medical College, Guizhou Medical University, Guiyang, China
| | - Shiman Yuan
- The Clinical Medical College, Guizhou Medical University, Guiyang, China
| | - Chenyu Wang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Hong Zhu
- Cancer Center, Department of Medical Oncology, West China Hospital, Sichuan University, Chengdu, China
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8
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Zhang M, Zuo Y, Guo J, Yang L, Wang Y, Tan M, Guo X. A novel signature for predicting prognosis and immune landscape in cutaneous melanoma based on anoikis-related long non-coding RNAs. Sci Rep 2023; 13:16332. [PMID: 37770477 PMCID: PMC10539372 DOI: 10.1038/s41598-023-39837-5] [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: 01/23/2023] [Accepted: 07/31/2023] [Indexed: 09/30/2023] Open
Abstract
Anoikis is a unique form of apoptosis associated with vascularization and distant metastasis in cancer. Eliminating anoikis resistance in tumor cells could be a promising target for improving the prognosis of terminal cancer patients. However, current studies have not elaborated on the prognosis effect of anoikis-related long non-coding RNAs (lncRNAs) in cutaneous melanoma. Pre-processed data, including RNA sequences and clinical information, were retrieved from TCGA and GTEx databases. After a series of statistical analyses, anoikis-related lncRNAs with prognostic significance were identified, and a unique risk signature was constructed. Risk scores were further analyzed in relation to the tumor microenvironment, tumor immune dysfunction and exclusion, immune checkpoint genes, and RNA methylation genes. The indicators were also used to predict the potentially sensitive anti-cancer drugs. An anoikis-related lncRNAs risk signature consisting of LINC01711, POLH-AS1, MIR205HG, and LINC02416 was successfully established in cutaneous melanoma. Overall survival and progression-free survival of patients were strongly linked with the risk score, independently of other clinical factors. The low-risk group exhibited a more beneficial immunological profile, was less affected by RNA methylation, and was more sensitive to the majority of anti-cancer drugs, all of which indicated a better prognostic outcome. The 4 hub lncRNAs may be fundamental to studying the mechanism of anoikis in cutaneous melanoma and provide personalized therapy for salvaging drug resistance.
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Affiliation(s)
- Miao Zhang
- Department of Plastic and Burns Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yuzhi Zuo
- Department of Plastic and Burns Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jian Guo
- Vascular Surgery Department, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Lushan Yang
- Department of Plastic and Burns Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yizhi Wang
- Department of Plastic and Burns Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Meiyun Tan
- Department of Orthopaedics, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.
| | - Xing Guo
- Department of Plastic and Burns Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.
- Center of Ambulatory Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.
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9
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Wang M, Yu F, Li P. Noncoding RNAs as an emerging resistance mechanism to immunotherapies in cancer: basic evidence and therapeutic implications. Front Immunol 2023; 14:1268745. [PMID: 37767098 PMCID: PMC10520974 DOI: 10.3389/fimmu.2023.1268745] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The increasing knowledge in the field of oncoimmunology has led to extensive research into tumor immune landscape and a plethora of clinical immunotherapy trials in cancer patients. Immunotherapy has become a clinically beneficial alternative to traditional treatments by enhancing the power of the host immune system against cancer. However, it only works for a minority of cancers. Drug resistance continues to be a major obstacle to the success of immunotherapy in cancer. A fundamental understanding of the detailed mechanisms underlying immunotherapy resistance in cancer patients will provide new potential directions for further investigations of cancer treatment. Noncoding RNAs (ncRNAs) are tightly linked with cancer initiation and development due to their critical roles in gene expression and epigenetic modulation. The clear appreciation of the role of ncRNAs in tumor immunity has opened new frontiers in cancer research and therapy. Furthermore, ncRNAs are increasingly acknowledged as a key factor influencing immunotherapeutic treatment outcomes. Here, we review the available evidence on the roles of ncRNAs in immunotherapy resistance, with an emphasis on the associated mechanisms behind ncRNA-mediated immune resistance. The clinical implications of immune-related ncRNAs are also discussed, shedding light on the potential ncRNA-based therapies to overcome the resistance to immunotherapy.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | | | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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10
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Vishnubalaji R, Alajez NM. Long non-coding RNA AC099850.4 correlates with advanced disease state and predicts worse prognosis in triple-negative breast cancer. Front Med (Lausanne) 2023; 10:1149860. [PMID: 37727755 PMCID: PMC10505935 DOI: 10.3389/fmed.2023.1149860] [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: 01/23/2023] [Accepted: 07/25/2023] [Indexed: 09/21/2023] Open
Abstract
Our understanding of the function of long non-coding RNAs (lncRNAs) in health and disease states has evolved over the past decades due to the many advances in genome research. In the current study, we characterized the lncRNA transcriptome enriched in triple-negative breast cancer (TNBC, n = 42) and estrogen receptor (ER+, n = 42) breast cancer compared to normal breast tissue (n = 56). Given the aggressive nature of TNBC, our data revealed selective enrichment of 57 lncRNAs in TNBC. Among those, AC099850.4 lncRNA was chosen for further investigation where it exhibited elevated expression, which was further confirmed in a second TNBC cohort (n = 360) where its expression correlated with a worse prognosis. Network analysis of AC099850.4high TNBC highlighted enrichment in functional categories indicative of cell cycle activation and mitosis. Ingenuity pathway analysis on the differentially expressed genes in AC099850.4high TNBC revealed the activation of the canonical kinetochore metaphase signaling pathway, pyridoxal 5'-phosphate salvage pathway, and salvage pathways of pyrimidine ribonucleotides. Additionally, upstream regulator analysis predicted the activation of several upstream regulator networks including CKAP2L, FOXM1, RABL6, PCLAF, and MITF, while upstream regulator networks of TP53, NUPR1, TRPS1, and CDKN1A were suppressed. Interestingly, elevated expression of AC099850.4 correlated with worse short-term relapse-free survival (log-rank p = 0.01). Taken together, our data are the first to reveal AC099850.4 as an unfavorable prognostic marker in TNBC, associated with more aggressive clinicopathological features, and suggest its potential utilization as a prognostic biomarker and therapeutic target in TNBC.
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Affiliation(s)
- Radhakrishnan Vishnubalaji
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Nehad M. Alajez
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
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11
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Guo R, Li J, Hu J, Fu Q, Yan Y, Xu S, Wang X, Jiao F. Combination of epidrugs with immune checkpoint inhibitors in cancer immunotherapy: From theory to therapy. Int Immunopharmacol 2023; 120:110417. [PMID: 37276826 DOI: 10.1016/j.intimp.2023.110417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/28/2023] [Accepted: 05/30/2023] [Indexed: 06/07/2023]
Abstract
Immunotherapy based on immune checkpoint inhibitors (ICIs) has revolutionized treatment strategies in multiple types of cancer. However, the resistance and relapse as associated with the extreme complexity of cancer-immunity interactions remain a major challenge to be resolved. Owing to the epigenome plasticity of cancer and immune cells, a growing body of evidence has been presented indicating that epigenetic treatments have the potential to overcome current limitations of immunotherapy, thus providing a rationalefor the combination of ICIs with epigenetic agents (epidrugs). In this review, we first make an overview about the epigenetic regulations in tumor biology and immunodevelopment. Subsequently, a diverse array of inhibitory agents under investigations targeted epigenetic modulators (Azacitidine, Decitabine, Vorinostat, Romidepsin, Belinostat, Panobinostat, Tazemetostat, Enasidenib and Ivosidenib, etc.) and immune checkpoints (Atezolizmab, Avelumab, Cemiplimab, Durvalumb, Ipilimumab, Nivolumab and Pembrolizmab, etc.) to increase anticancer responses were described and the potential mechanisms were further discussed. Finally, we summarize the findings of clinical trials and provide a perspective for future clinical studies directed at investigating the combination of epidrugs with ICIs as a treatment for cancer.
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Affiliation(s)
- Ruoyu Guo
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, PR China
| | - Jixia Li
- Department of Clinical Laboratory Medicine, Yantaishan Hospital, Yantai 264003, PR China
| | - Jinxia Hu
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, PR China
| | - Qiang Fu
- School of Pharmacology, Institute of Aging Medicine, Binzhou Medical University, Yantai 264003, PR China
| | - Yunfei Yan
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, PR China
| | - Sen Xu
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, PR China
| | - Xin Wang
- Department of Clinical Laboratory & Health Service Training, 970 Hospital of the PLA Joint Logistic Support Force, Yantai 264002, PR China.
| | - Fei Jiao
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, PR China.
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12
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Liu L, Wang Q, Zhou JY, Zhang B. Developing four cuproptosis-related lncRNAs signature to predict prognosis and immune activity in ovarian cancer. J Ovarian Res 2023; 16:88. [PMID: 37122030 PMCID: PMC10150549 DOI: 10.1186/s13048-023-01165-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 04/25/2023] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND There has been a recent discovery of a new type of cell death produced by copper-iron ions, called Cuproptosis (copper death). The purpose of this study was to identify LncRNA signatures associated with Cuproptosis in ovarian cancer that could be used as prognostic indicators. METHODS RNA sequencing (RNA-seq) profiles with clinicopathological data from TCGA database were used to select prognostic CRLs and then constructed prognostic risk model using multivariate regression analysis and LASSO algorithms. An independent dataset from GEO database was used to validate the prognostic performance. Combined with clinical factors, we further constructed a prognostic nomogram. In addition, tumor immune microenvironment, somatic mutation and drug sensitivity were analyzed using ssGSEA, GSVA, ESTIMATE and CIBERSORT algorithms. RESULT A total of 129 CRLs were selected whose expression levels were significantly related to expression levels of 10 cuproptosis-related genes. The univariate Cox regression analysis showed that 12 CRLs were associated with overall survival (OS). Using LASSO algorithms and multivariate regression analysis, we constructed a four-CRLs prognostic signature in the training dataset. Patients in the training dataset could be classified into high- or low-risk subgroups with significantly different OS (log-rank p < 0.001). The prognostic performance was confirmed in TCGA-OC cohort (log-rank p < 0.001) and an independent GEO cohort (log-rank p = 0.023). Multivariate cox regression analysis proved the four-CRLs signature was an independent prognostic factor for OC. Additionally, different risk subtypes showed significantly different levels of immune cells, signal pathways, and drug response. CONCLUSION We established a prognostic signature based on cuproptosis-related lncRNAs for OC patients, which will be of great value in predicting the prognosis patients and may provide a new perspective for research and individualized treatment.
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Affiliation(s)
- Li Liu
- Department of Obstetrics and Gynecology, Graduate School of Bengbu Medical College, Bengbu, China
- Department of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou, China
| | - Qing Wang
- Department of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou, China
| | - Jia-Yun Zhou
- Department of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou, China
- Department of Obstetrics and Gynecology, Graduate School of Xuzhou Medical University, Xuzhou, China
| | - Bei Zhang
- Department of Obstetrics and Gynecology, Graduate School of Bengbu Medical College, Bengbu, China.
- Department of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou, China.
- Department of Obstetrics and Gynecology, Graduate School of Xuzhou Medical University, Xuzhou, China.
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Avila JP, Carvalho BM, Coimbra EC. A Comprehensive View of the Cancer-Immunity Cycle (CIC) in HPV-Mediated Cervical Cancer and Prospects for Emerging Therapeutic Opportunities. Cancers (Basel) 2023; 15:cancers15041333. [PMID: 36831674 PMCID: PMC9954575 DOI: 10.3390/cancers15041333] [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] [Received: 12/31/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Cervical cancer (CC) is the fourth most common cancer in women worldwide, with more than 500,000 new cases each year and a mortality rate of around 55%. Over 80% of these deaths occur in developing countries. The most important risk factor for CC is persistent infection by a sexually transmitted virus, the human papillomavirus (HPV). Conventional treatments to eradicate this type of cancer are accompanied by high rates of resistance and a large number of side effects. Hence, it is crucial to devise novel effective therapeutic strategies. In recent years, an increasing number of studies have aimed to develop immunotherapeutic methods for treating cancer. However, these strategies have not proven to be effective enough to combat CC. This means there is a need to investigate immune molecular targets. An adaptive immune response against cancer has been described in seven key stages or steps defined as the cancer-immunity cycle (CIC). The CIC begins with the release of antigens by tumor cells and ends with their destruction by cytotoxic T-cells. In this paper, we discuss several molecular alterations found in each stage of the CIC of CC. In addition, we analyze the evidence discovered, the molecular mechanisms and their relationship with variables such as histological subtype and HPV infection, as well as their potential impact for adopting novel immunotherapeutic approaches.
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Liu J, Zhang H, Xia P, Zhu Y, Xu K, Liu Z, Yuan Y. Genome stability‑related lncRNA ZFPM2‑AS1 promotes tumor progression via miR‑3065‑5p/XRCC4 in hepatocellular carcinoma. Int J Oncol 2023; 62:19. [PMID: 36524359 PMCID: PMC9812252 DOI: 10.3892/ijo.2022.5467] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/11/2022] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have a certain link to genomic stability (GS). However, the regulatory relationship of lncRNAs and GS has not been thoroughly investigated in hepatocellular carcinoma (HCC). In the present study, samples were retrieved from The Cancer Genome Atlas with somatic mutations and lncRNA expression data. Cox regression analysis was used to identify independent prognostic factors. The RNA levels were determined by reverse transcription‑quantitative PCR and protein levels were detected by western blot analysis. Cell Counting Kit‑8 and colony‑formation assays were used to assess cell viability. Cell migration was measured by wound‑healing and Transwell assays. Cell apoptosis and cell‑cycle progression were evaluated by flow cytometry. GS was detected by alkaline comet and chromosomal aberration assays. A xenograft model and lung metastasis model were used to assess the role of zinc finger protein, FOG family member 2 antisense 1 (ZFPM2‑AS1) in tumor growth in vivo. The molecular mechanisms underlying the biological functions of ZFPM2‑AS1 were investigated through bioinformatics prediction, RNA pull‑down and luciferase reporter assays. A total of 85 genomic instability‑related lncRNAs were identified and a prognostic model was developed. The prognostic model exhibited good predictive power (area under the receiver operating characteristic curve, 0.786). ZFPM2‑AS1 was significantly upregulated in tumor tissues (P<0.001) and it promoted DNA damage repair (P<0.01) and tumor progression in vitro and in vivo. Luciferase reporter assays demonstrated that miR‑3065‑5p was able to bind directly with ZFPM2‑AS1 and X‑ray repair cross complementing 4 (XRCC4). ZFPM2‑AS1 upregulated XRCC4 expression by acting as a sponge (P<0.001). In the present study, a prognostic model for HCC was developed and validated, and one lncRNA of its components was experimentally investigated. ZFPM2‑AS1 regulates XRCC4 by sponging miR‑3065‑5p to promote GS and HCC progression.
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Affiliation(s)
- Jie Liu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, Hubei 430071, P.R. China
| | - Hao Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, Hubei 430071, P.R. China
| | - Peng Xia
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, Hubei 430071, P.R. China
| | - Yimin Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, Hubei 430071, P.R. China
| | - Kequan Xu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, Hubei 430071, P.R. China
| | - Zhisu Liu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, Hubei 430071, P.R. China
| | - Yufeng Yuan
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary and Pancreatic Diseases of Hubei Province, Wuhan, Hubei 430071, P.R. China
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Long noncoding RNA DIO3OS induces glycolytic-dominant metabolic reprogramming to promote aromatase inhibitor resistance in breast cancer. Nat Commun 2022; 13:7160. [PMID: 36418319 PMCID: PMC9684133 DOI: 10.1038/s41467-022-34702-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 11/03/2022] [Indexed: 11/24/2022] Open
Abstract
Aromatase inhibition is an efficient endocrine therapy to block ectopic estrogen production for postmenopausal estrogen receptor (ER)-positive breast cancer patients, but many develop resistance. Here, we show that aromatase inhibitor (AI)-resistant breast tumors display features of enhanced aerobic glycolysis with upregulation of long noncoding RNA (lncRNA) DIO3OS, which correlates with poor prognosis of breast cancer patients on AI therapies. Long-term estrogen deprivation induces DIO3OS expression in ER-positive breast tumor cells, which further enhances aerobic glycolysis and promotes estrogen-independent cell proliferation in vitro and in vivo. Mechanistically, DIO3OS interacts with polypyrimidine tract binding protein 1 (PTBP1) and stabilizes the mRNA of lactate dehydrogenase A (LDHA) by protecting the integrity of its 3'UTR, and subsequently upregulates LDHA expression and activates glycolytic metabolism in AI-resistant breast cancer cells. Our findings highlight the role of lncRNA in regulating the key enzyme of glycolytic metabolism in response to endocrine therapies and the potential of targeting DIO3OS to reverse AI resistance in ER-positive breast cancer.
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Cui M, Liu Y, Cheng L, Li T, Deng Y, Liu D. Research progress on anti-ovarian cancer mechanism of miRNA regulating tumor microenvironment. Front Immunol 2022; 13:1050917. [DOI: 10.3389/fimmu.2022.1050917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
Abstract
Ovarian cancer is the most deadly malignancy among women, but its complex pathogenesis is unknown. Most patients with ovarian cancer have a poor prognosis due to high recurrence rates and chemotherapy resistance as well as the lack of effective early diagnostic methods. The tumor microenvironment mainly includes extracellular matrix, CAFs, tumor angiogenesis and immune-associated cells. The interaction between tumor cells and TME plays a key role in tumorigenesis, progression, metastasis and treatment, affecting tumor progression. Therefore, it is significant to find new tumor biomarkers and therapeutic targets. MicroRNAs are non-coding RNAs that post-transcriptionally regulate the expression of target genes and affect a variety of biological processes. Studies have shown that miRNAs regulate tumor development by affecting TME. In this review, we summarize the mechanisms by which miRNAs affect ovarian cancer by regulating TME and highlight the key role of miRNAs in TME, which provides new targets and theoretical basis for ovarian cancer treatment.
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Shaath H, Vishnubalaji R, Elango R, Kardousha A, Islam Z, Qureshi R, Alam T, Kolatkar PR, Alajez NM. Long non-coding RNA and RNA-binding protein interactions in cancer: Experimental and machine learning approaches. Semin Cancer Biol 2022; 86:325-345. [PMID: 35643221 DOI: 10.1016/j.semcancer.2022.05.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 01/27/2023]
Abstract
Understanding the complex and specific roles played by non-coding RNAs (ncRNAs), which comprise the bulk of the genome, is important for understanding virtually every hallmark of cancer. This large group of molecules plays pivotal roles in key regulatory mechanisms in various cellular processes. Regulatory mechanisms, mediated by long non-coding RNA (lncRNA) and RNA-binding protein (RBP) interactions, are well documented in several types of cancer. Their effects are enabled through networks affecting lncRNA and RBP stability, RNA metabolism including N6-methyladenosine (m6A) and alternative splicing, subcellular localization, and numerous other mechanisms involved in cancer. In this review, we discuss the reciprocal interplay between lncRNAs and RBPs and their involvement in epigenetic regulation via histone modifications, as well as their key role in resistance to cancer therapy. Other aspects of RBPs including their structural domains, provide a deeper knowledge on how lncRNAs and RBPs interact and exert their biological functions. In addition, current state-of-the-art knowledge, facilitated by machine and deep learning approaches, unravels such interactions in better details to further enhance our understanding of the field, and the potential to harness RNA-based therapeutics as an alternative treatment modality for cancer are discussed.
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Affiliation(s)
- Hibah Shaath
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Radhakrishnan Vishnubalaji
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Ramesh Elango
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Ahmed Kardousha
- College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Zeyaul Islam
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110, Doha, Qatar
| | - Rizwan Qureshi
- College of Science and Engineering, Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110, Doha, Qatar
| | - Tanvir Alam
- College of Science and Engineering, Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110, Doha, Qatar
| | - Prasanna R Kolatkar
- College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar; Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110, Doha, Qatar
| | - Nehad M Alajez
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar; College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar.
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Zhai F, Wang J, Yang W, Ye M, Jin X. The E3 Ligases in Cervical Cancer and Endometrial Cancer. Cancers (Basel) 2022; 14:5354. [PMID: 36358773 PMCID: PMC9658772 DOI: 10.3390/cancers14215354] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 07/28/2023] Open
Abstract
Endometrial (EC) and cervical (CC) cancers are the most prevalent malignancies of the female reproductive system. There is a global trend towards increasing incidence and mortality, with a decreasing age trend. E3 ligases label substrates with ubiquitin to regulate their activity and stability and are involved in various cellular functions. Studies have confirmed abnormal expression or mutations of E3 ligases in EC and CC, indicating their vital roles in the occurrence and progression of EC and CC. This paper provides an overview of the E3 ligases implicated in EC and CC and discusses their underlying mechanism. In addition, this review provides research advances in the target of ubiquitination processes in EC and CC.
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Affiliation(s)
- Fengguang Zhai
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Jie Wang
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Weili Yang
- Department of Gynecology, The Affiliated People’s Hospital of Ningbo University, Ningbo 315040, China
| | - Meng Ye
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Xiaofeng Jin
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
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Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting. J Transl Med 2022; 20:442. [PMID: 36180904 PMCID: PMC9523969 DOI: 10.1186/s12967-022-03654-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/19/2022] [Indexed: 11/27/2022] Open
Abstract
Background Advances in our understanding of the tumor microenvironment have radically changed the cancer field, highlighting the emerging need for biomarkers of an active, favorable tumor immune phenotype to aid treatment stratification and clinical prognostication. Numerous immune-related gene signatures have been defined; however, their prognostic value is often limited to one or few cancer types. Moreover, the area of non-coding RNA as biomarkers remains largely unexplored although their number and biological roles are rapidly expanding. Methods We developed a multi-step process to identify immune-related long non-coding RNA signatures with prognostic connotation in multiple TCGA solid cancer datasets. Results Using the breast cancer dataset as a discovery cohort we found 2988 differentially expressed lncRNAs between immune favorable and unfavorable tumors, as defined by the immunologic constant of rejection (ICR) gene signature. Mapping of the lncRNAs to a coding-non-coding network identified 127 proxy protein-coding genes that are enriched in immune-related diseases and functions. Next, we defined two distinct 20-lncRNA prognostic signatures that show a stronger effect on overall survival than the ICR signature in multiple solid cancers. Furthermore, we found a 3 lncRNA signature that demonstrated prognostic significance across 5 solid cancer types with a stronger association with clinical outcome than ICR. Moreover, this 3 lncRNA signature showed additional prognostic significance in uterine corpus endometrial carcinoma and cervical squamous cell carcinoma and endocervical adenocarcinoma as compared to ICR. Conclusion We identified an immune-related 3-lncRNA signature with prognostic connotation in multiple solid cancer types which performed equally well and in some cases better than the 20-gene ICR signature, indicating that it could be used as a minimal informative signature for clinical implementation. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03654-7.
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Li M, Huang F, Xie Z, Hong H, Xu Q, Peng Z. Identification of three small nucleolar RNAs (snoRNAs) as potential prognostic markers in diffuse large B-cell lymphoma. Cancer Med 2022; 12:3812-3829. [PMID: 36812125 PMCID: PMC9939161 DOI: 10.1002/cam4.5115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 07/13/2022] [Accepted: 07/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Diffuse large B-cell lymphoma (DLBCL) is a non-Hodgkin lymphoma with high mortality rates. Small nucleolar RNAs (snoRNAs) are tumor-specific biological markers, but there are few studies on the role of snoRNAs in DLBCL. MATERIALS AND METHODS Survival-related snoRNAs were selected to construct a specific snoRNA-based signature via computational analyses (Cox regression and independent prognostic analyses) to predict the prognosis of DLBCL patients. To assist in clinical applications, a nomogram was built by combining the risk model and other independent prognostic factors. Pathway analysis, gene ontology analysis, transcription factor enrichment, protein-protein interactions, and single nucleotide variant analysis were used to explore the potential biological mechanisms of co-expressed genes. RESULTS Twelve prognosis-correlated snoRNAs were selected from the DLBCL patient cohort of microarray profiles, and a three-snoRNA signature consisting of SNORD1A, SNORA60, and SNORA66 was constructed. DLBCL patients could be divided into high-risk and low-risk cohorts using the risk model, and the high-risk group and activated B cell-like (ABC) type DLBCL were linked with disappointing survival. In addition, SNORD1A co-expressed genes were inseparably linked to the biological functions of the ribosome and mitochondria. Potential transcriptional regulatory networks have also been identified. MYC and RPL10A were the most mutated SNORD1A co-expressed genes in DLBCL. CONCLUSION Put together, our findings explored the potential biological effects of snoRNAs in DLBCL, and provided a new predictor for DLBCL prediction.
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Affiliation(s)
- Mei‐wei Li
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
| | - Feng‐xiang Huang
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
| | - Zu‐cheng Xie
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
| | - Hao‐yuan Hong
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
| | - Qing‐yuan Xu
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
| | - Zhi‐gang Peng
- Department of Medical OncologyFirst Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP. R. China
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LncRNA-Based Classification of Triple Negative Breast Cancer Revealed Inherent Tumor Heterogeneity and Vulnerabilities. Noncoding RNA 2022; 8:ncrna8040044. [PMID: 35893227 PMCID: PMC9326727 DOI: 10.3390/ncrna8040044] [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: 04/21/2022] [Revised: 05/25/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022] Open
Abstract
Triple negative breast cancer (TNBC) represents a diverse group of cancers based on their gene expression profiles. While the current mRNA-based classification of TNBC has contributed to our understanding of the heterogeneity of this disease, whether such heterogeneity can be resolved employing a long noncoding RNA (lncRNA) transcriptome has not been established thus far. Herein, we used iterative clustering and guide-gene selection (ICGS) and uniform manifold approximation and projection (UMAP) dimensionality reduction analysis on a large cohort of TNBC transcriptomic data (TNBC = 360, normal = 88) and classified TNBC into four main clusters: LINC00511-enriched, LINC00393-enriched, FIRRE-enriched, and normal tissue-like. Delving into associated gene expression profiles revealed remarkable differences in canonical, casual, upstream, and functional categories among different lncRNA-derived TNBC clusters, suggesting functional consequences for altered lncRNA expression. Correlation and survival analysis comparing mRNA- and lncRNA-based clustering revealed similarities and differences between the two classification approaches. To provide insight into the potential role of the identified lncRNAs in TNBC biology, CRISPR-Cas9 mediated LINC00511 promoter deletion reduced colony formation and enhanced the sensitivity of TNBC cells to paclitaxel, suggesting a role for LINC00511 in conferring tumorigenicity and resistance to therapy. Our data revealed a novel lncRNA-based classification of TNBC and suggested their potential utilization as disease biomarkers and therapeutic targets.
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22
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Xie J, Tian W, Tang Y, Zou Y, Zheng S, Wu L, Zeng Y, Wu S, Xie X, Xie X. Establishment of a Cell Necroptosis Index to Predict Prognosis and Drug Sensitivity for Patients With Triple-Negative Breast Cancer. Front Mol Biosci 2022; 9:834593. [PMID: 35601830 PMCID: PMC9117653 DOI: 10.3389/fmolb.2022.834593] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/04/2022] [Indexed: 12/25/2022] Open
Abstract
Background: Necroptosis has been an alternatively identified mechanism of programmed cancer cell death, which plays a significant role in cancer. However, research about necroptosis-related long noncoding RNAs (lncRNAs) in cancer are still few. Moreover, the potentially prognostic value of necroptosis-related lncRNAs and their correlation with the immune microenvironment remains unclear. The present study aimed to explore the potential prognostic value of necroptosis-related lncRNAs and their relationship to immune microenvironment in triple-negative breast cancer (TNBC). Methods: The RNA expression matrix of patients with TNBC was obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Finally, 107 patients of GSE58812, 159 patients of TCGA, and 143 patients of GSE96058 were included. Necroptosis-related lncRNAs were screened by Cox regression and Pearson correlation analysis with necroptosis-related genes. By LASSO regression analysis, nine necroptosis-related lncRNAs were employed, and a cell necroptosis index (CNI) was established; then, we evaluated its prognostic value, clinical significance, pathways, immune infiltration, and chemotherapeutics efficacy. Results: Based on the CNI value, the TNBC patients were divided into high- and low-CNI groups, and the patients with high CNI had worse prognosis, more lymph node metastasis, and larger tumor (p < 0.05). The receiver operating characteristic (ROC) analysis showed that the signature performed well. The result of the infiltration proportion of different immune cell infiltration further explained that TNBC patients with high CNI had low immunogenicity, leading to poor therapeutic outcomes. Moreover, we found significant differences of the IC50 values of various chemotherapeutic drugs in the two CNI groups, which might provide a reference to make a personalized chemotherapy for them. Conclusion: The novel prognostic marker CNI could not only precisely predict the survival probability of patients with TNBC but also demonstrate a potential role in antitumor immunity and drug sensitivity.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xinhua Xie
- *Correspondence: Xinhua Xie, ; Xiaoming Xie,
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Abstract
With the development of precision medicine, the efficiency of tumor treatment has been significantly improved. More attention has been paid to targeted therapy and immunotherapy as the key to precision treatment of cancer. Targeting epidermal growth factor receptor (EGFR) has become one of the most important targeted treatments for various cancers. Comparing with traditional chemotherapy drugs, targeting EGFR is highly selective in killing tumor cells with better safety, tolerability and less side effect. In addition, tumor immunotherapy has become the fourth largest tumor therapy after surgery, radiotherapy and chemotherapy, especially immune checkpoint inhibitors. However, these treatments still produce a certain degree of drug resistance. Non-coding RNAs (ncRNAs) were found to play a key role in carcinogenesis, treatment and regulation of the efficacy of anticancer drugs in the past few years. Therefore, in this review, we aim to summarize the targeted treatment of cancers and the functions of ncRNAs in cancer treatment.
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Zhang Z, Xu Z, Yan Y. Role of a Pyroptosis-Related lncRNA Signature in Risk Stratification and Immunotherapy of Ovarian Cancer. Front Med (Lausanne) 2022; 8:793515. [PMID: 35096881 PMCID: PMC8791230 DOI: 10.3389/fmed.2021.793515] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/13/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Pyroptosis is a newly recognized form of cell death. Emerging evidence has suggested the crucial role of long non-coding RNAs (lncRNAs) in the tumorigenesis and progression of ovarian cancer (OC). However, there is still poor understanding of pyroptosis-related lncRNAs in OC. Methods: The TCGA database was accessed for gene expression and clinical data of 377 patients with OC. Two cohorts for training and validation were established by random allocation. Correlation analysis and Cox regression analysis were performed to identify pyroptosis-related lncRNAs and construct a risk model. Results: Six pyroptosis-related lncRNAs were included in the final signature with unfavorable survival data. Subsequent ROC curves showed promising predictive value of patient prognosis. Further multivariate regression analyses confirmed the signature as an independent risk factor in the training (HR: 2.242, 95% CI: 1.598-3.145) and validation (HR: 1.884, 95% CI: 1.204-2.95) cohorts. A signature-based nomogram was also established with a C-index of.684 (95% CI: 0.662-0.705). Involvement of the identified signature in multiple immune-related pathways was revealed by functional analysis. Moreover, the signature was also associated with higher expression of three immune checkpoints (PD-1, B7-H3, and VSIR), suggesting the potential of the signature as an indicator for OC immunotherapies. Conclusion: This study suggests that the identified pyroptosis-related lncRNA signature and signature-based nomogram may serve as methods for risk stratification of OC. The signature is also associated with the tumor immune microenvironment, potentially providing an indicator for patient selection of immunotherapy in OC.
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Affiliation(s)
- Zeyu Zhang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
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Lin Y, Pan X, Chen Z, Lin S, Shen Z, Chen S. Prognostic value and immune infiltration of novel signatures in colon cancer microenvironment. Cancer Cell Int 2021; 21:679. [PMID: 34922547 PMCID: PMC8684099 DOI: 10.1186/s12935-021-02342-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 11/15/2021] [Indexed: 12/16/2022] Open
Abstract
Background Growing evidence has shown that the prognosis for colon cancer depends on changes in microenvironment. The purpose of this study was to elucidate the prognostic value of long noncoding RNAs (lncRNAs) related to immune microenvironment (IM) in colon cancer. Methods Single sample gene set enrichment analysis (ssGSEA) was used to identify the subtypes of colon cancer based on the immune genomes of 29 immune signatures. Cox regression analysis identified a lncRNA signatures associated with immune infiltration. The Tumor Immune Estimation Resource database was used to analyze immune cell content. Results Colon cancer samples were divided into three subtypes by unsupervised cluster analysis. Cox regression analysis identified an immune infiltration-related 5-lncRNA signature. This signature combined with clinical factors can effectively improve the predictive ability for the overall survival (OS) of colon cancer. At the same time, we found that the expression of H19 affects the content of B cells and macrophages in the microenvironment of colon cancer and affects the prognosis of colon cancer. Finally, we constructed the H19 regulatory network and further analyzed the possible mechanisms. We found that knocking down the expression of H19 can significantly inhibit the expression of CCND1 and VEGFA. At the same time, the immunohistochemical assay found that the expression of CCND1 and VEGFA protein was significantly positively correlated with the infiltration of M2 type macrophages. Conclusion The findings may help to formulate clinical strategies and understand the underlying mechanisms of H19 regulation. H19 may be a biomarker for targeted treatment of colon cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02342-8.
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Affiliation(s)
- Yilin Lin
- Department of Gastroenterological Surgery, Peking University People's Hospital, 11 Xizhimen South Street, Xicheng, Beijing, China
| | - Xiaoxian Pan
- Department of Radiotherapy, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Zhihua Chen
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Fujian Medical University, No. 20, Chazhong Road, Taijiang, Fuzhou, Fujian, China
| | - Suyong Lin
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Fujian Medical University, No. 20, Chazhong Road, Taijiang, Fuzhou, Fujian, China
| | - Zhanlong Shen
- Department of Gastroenterological Surgery, Peking University People's Hospital, 11 Xizhimen South Street, Xicheng, Beijing, China.
| | - Shaoqin Chen
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Fujian Medical University, No. 20, Chazhong Road, Taijiang, Fuzhou, Fujian, China.
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26
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Xiong J, Wu L, Huang L, Wu C, Liu Z, Deng W, Ma S, Zhou Z, Yu H, Cao K. LncRNA FOXP4-AS1 Promotes Progression of Ewing Sarcoma and Is Associated With Immune Infiltrates. Front Oncol 2021; 11:718876. [PMID: 34765540 PMCID: PMC8577041 DOI: 10.3389/fonc.2021.718876] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/05/2021] [Indexed: 12/25/2022] Open
Abstract
Ewing sarcoma (ES) is a highly malignant primary bone tumor with poor prognosis. Studies have shown that abnormal expression of lncRNA influences the prognosis of tumor patients. Herein, we established that FOXP4-AS1 was up-regulated in ES and this correlated with poor prognosis. Further analysis illustrated that FOXP4-AS1 down-regulation repression growth, migration, along with invasion of ES. On the contrary, up-regulation of FOXP4-AS1 promoted the growth, migration, as well as invasion of ES. To explore the mechanism of FOXP4-AS1, Spearman correlation analysis was carried out to determine genes that were remarkably linked to FOXP4-AS1 expression. The potential functions and pathways involving FOXP4-AS1 were identified by GO analysis, Hallmark gene set enrichment analysis, GSEA, and GSVA. The subcellular fractionation results illustrated that FOXP4-AS1 was primarily located in the cytoplasm of ES cells. Then a ceRNA network of FOXP4-AS1 was constructed. Analysis of the ceRNA network and GSEA yielded two candidate mRNAs for FOXP4-AS1. Results of the combined survival analysis led us to speculate that FOXP4-AS1 may affect the expression of TMPO by sponging miR-298, thereby regulating the malignant phenotype of ES. Finally, we found that FOXP4-AS1 may modulates the tumor immune microenvironment in an extracellular vesicle-mediated manner. In summary, FOXP4-AS1 correlates with poor prognosis of ES. It promotes the growth, migration, as well as invasion of ES cells and may modulate the tumor immune microenvironment.
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Affiliation(s)
- Jiachao Xiong
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Department of Orthopedics, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Liang Wu
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Lu Huang
- Child Health Department of the Maternal and Children Health Hospital of Jiangxi Province, Nanchang, China
| | - Chunyang Wu
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhiming Liu
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wenqiang Deng
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shengbiao Ma
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhenhai Zhou
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Honggui Yu
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Kai Cao
- The Orthopedics Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, China
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Ma B, Jiang H, Luo Y, Liao T, Xu W, Wang X, Dong C, Ji Q, Wang Y. Tumor-Infiltrating Immune-Related Long Non-Coding RNAs Indicate Prognoses and Response to PD-1 Blockade in Head and Neck Squamous Cell Carcinoma. Front Immunol 2021; 12:692079. [PMID: 34737735 PMCID: PMC8562720 DOI: 10.3389/fimmu.2021.692079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 09/20/2021] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) in immune cells play critical roles in tumor cell–immune cell interactions. This study aimed to characterize the landscape of tumor-infiltrating immune-related lncRNAs (Ti-lncRNAs) and reveal their correlations with prognoses and immunotherapy response in head and neck squamous cell carcinoma (HNSCC). We developed a computational model to identify Ti-lncRNAs in HNSCC and analyzed their associations with clinicopathological features, molecular alterations, and immunotherapy response. A signature of nine Ti-lncRNAs demonstrated an independent prognostic factor for both overall survival and disease-free survival among the cohorts from Fudan University Shanghai Cancer Center, The Cancer Genome Atlas, GSE41613, and GSE42743. The Ti-lncRNA signature scores in immune cells showed significant associations with TP53 mutation, CDKN2A mutation, and hypoxia. Inferior signature scores were enriched in patients with high levels of PDCD1 and CTLA4 and high expanded immune gene signature (IGS) scores, who displayed good response to PD-1 blockade in HNSCC. Consistently, superior clinical response emerged in melanoma patients with low signature scores undergoing anti-PD-1 therapy. Moreover, the Ti-lncRNA signature was a prognostic factor independent of PDCD1, CTLA4, and the expanded IGS score. In conclusion, tumor-infiltrating immune profiling identified a prognostic Ti-lncRNA signature indicative of clinical response to PD-1 blockade in HNSCC.
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Affiliation(s)
- Ben Ma
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hongyi Jiang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Luo
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Tian Liao
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Weibo Xu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chuanpeng Dong
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Biohealth Informatics, School of Informatics and Computing, Indiana University, Indianapolis, IN, United States
| | - Qinghai Ji
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Wang C, Wang Z, Zhang L, Lin X. MiR-29c inhibits the metastasis of oral squamous cell carcinoma and promotes its cell cycle arrest by targeting SERPINH1. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1423. [PMID: 34733975 PMCID: PMC8506711 DOI: 10.21037/atm-21-3720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/02/2021] [Indexed: 02/04/2023]
Abstract
Background A large number of studies have shown that the imbalance of micro RNA (miRNA) and its target genes can promote the development of tumors. The purpose of this study was to investigate the biological role and molecular mechanism of serpin peptidase inhibitor clade H member 1 (SERPINH1) and its upstream regulator miR-29c in oral squamous cell carcinoma (OSCC). Methods The expression levels of SERPINH1 and miR-29c were detected by quantitative reverse transcription polymerase chain reaction (RT-qPCR) and western blotting. The proliferation, apoptosis, metastasis, and cell cycle were detected by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay, would healing assay, transwell assay, flow cytometry, and dual luciferase reporter assay. Results High expression of SERPINH1 was detected in patients with OSCC and it can be used as a prognostic biomarker for OSCC. Cell function experiments showed that silencing the expression of SERPINH1 inhibited the proliferation and migration of OSCC cells and caused cell cycle arrest at S phase. Bioinformatics analysis showed that there was a binding site between miR-29c and SERPINH1, indicating that miR-29c may regulate the expression of SERPINH1. In addition, miR-29c overexpression inhibited the proliferation and metastasis of OSCC cells, and the subsequent rescue experiment showed that SERPINH1 overexpression can reverse the inhibitory effect of miR-29c in OSCC cell proliferation, migration, apoptosis, and cell cycle arrest. Conclusions The miRNA, miR-29c can regulate the proliferation, migration, invasion, and cell cycle of OSCC cells by targeting SERPINH1.
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Affiliation(s)
- Chuanning Wang
- Department of Stomatology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhiming Wang
- Department of Stomatology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Liping Zhang
- Department of Stomatology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaoping Lin
- Department of Stomatology, Shengjing Hospital of China Medical University, Shenyang, China
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29
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ceRNAs in Cancer: Mechanism and Functions in a Comprehensive Regulatory Network. JOURNAL OF ONCOLOGY 2021; 2021:4279039. [PMID: 34659409 PMCID: PMC8516523 DOI: 10.1155/2021/4279039] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 12/15/2022]
Abstract
Noncoding RNAs have been shown with powerful ability in post-transcriptional regulation, enabling intertwined RNA crosstalk and global molecular interaction in a large amount of dysfunctional conditions including cancer. Competing endogenous RNAs (ceRNAs) are those competitively binding with shared microRNAs (miRNAs), freeing their counterparts from miRNA-induced degradation, thus actively influencing and connecting with each other. Constantly updated analytical approaches boost outstanding advancement achieved in this burgeoning hotspot in multilayered intracellular communication, providing new insights into pathogenesis and clinical treatment. Here, we summarize the mechanisms and correlated factors under this RNA interplay and deregulated transcription profile in neoplasm and tumor progression, underscoring the great significance of ceRNAs for diagnostic values, monitoring biomarkers, and prognosis evaluation in cancer.
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30
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Beylerli O, Khasanov D, Gareev I, Valitov E, Sokhatskii A, Wang C, Pavlov V, Khasanova G, Ahmad A. Differential non-coding RNAs expression profiles of invasive and non-invasive pituitary adenomas. Noncoding RNA Res 2021; 6:115-122. [PMID: 34322647 PMCID: PMC8283030 DOI: 10.1016/j.ncrna.2021.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pituitary adenoma (PA) accounts for 10-15% of all intracranial neoplasms. Despite their benign nature, PA often shows invasive growth. MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are a class of non-coding RNAs that play important roles in PA initiation and progression. AIM The aim of this study was to find specific profiles of miR-200a and long non-coding RNA (lncRNA) antisense non-coding RNA in the INK4 locus (ANRIL) in PA based on a comparative study using Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) analyses of tumor tissue and plasma. METHODS Plasma and PA tissue samples were obtained from two groups of included patients (15 invasive and 15 non-invasive PA). In addition, plasma samples from patients with invasive PA have collected pre- and post-operation. Plasma and tissue samples subjected to qRT-PCR analyses for the expression levels of miR-200a and lncRNA ANRIL. RESULTS The expression levels of miR-200a and lncRNA ANRIL were increased in tissue samples patients with invasive PA than in the patients with non-invasive PA. In addition, the expression levels of circulating miR-200a and lncRNA ANRIL were increased in patients with invasive PA than in patients with non-invasive PA in the pre-operation period. However, the expression level of plasma circulating miR-200a and lncRNA ANRIL was decreased in patients with invasive PA in the post-operation period. Our results depicted a miR-200a and lncRNA ANRIL expression in tissue and plasma samples in the patients with invasive PA. In addition, Receiver Operating Characteristic (ROC) curve was used to evaluate the diagnostic value of these circulating miR-200a and lncRNA ANRIL. CONCLUSION The expression of these tumor-associated ncRNAs has been elevated in the PAs. Therefore, miR-200a and lncRNA ANRIL represents as biomarkers for diagnosis and potential targets for novel invasive PA treatment strategies.
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Affiliation(s)
- Ozal Beylerli
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Dinar Khasanov
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Ilgiz Gareev
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Elvir Valitov
- Nyagan District Hospital, Nyagan, Khanty-Mansiysk Autonomous District, Tyumen Region, 628181, Russia
| | - Andrei Sokhatskii
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Chunlei Wang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
- Institute of Brain Science, Harbin Medical University, Harbin, 150001, China
| | - Valentin Pavlov
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Guzel Khasanova
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Aamir Ahmad
- University of Alabama at Birmingham, AL, 35294, USA
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31
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Zhao H, Li Y, Dong N, Zhang L, Chen X, Mao H, Al-Ameri SAAE, Wang X, Wang Q, Du L, Wang C, Mao H. LncRNA LINC01088 inhibits the function of trophoblast cells, activates the MAPK-signaling pathway and associates with recurrent pregnancy loss. Mol Hum Reprod 2021; 27:gaab047. [PMID: 34264302 DOI: 10.1093/molehr/gaab047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/16/2021] [Indexed: 11/14/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been reported to be involved in various cellular processes and to participate in a variety of human diseases. Recently, increasing studies have reported that lncRNAs are related to many reproductive diseases, such as pathogenesis of recurrent pregnancy loss (RPL), preeclampsia (PE) and gestational diabetes mellitus (GDM). In this study, we aimed to investigate the effect of LINC01088 in trophoblast cells and its potential role in pathogenesis of RPL. LINC01088 was found to be upregulated in first-trimester chorionic villi tissues from RPL patients. Increased LINC01088 repressed proliferation, migration and invasion of trophoblast cells, and promoted apoptosis of trophoblast cells. Further exploration indicated that LINC01088 decreased the production of nitric oxide (NO) by binding and increasing Arginase-1 and decreasing eNOS protein levels. Importantly, JNK and p38 MAPK-signaling pathways were active after overexpression of LINC01088. In conclusion, our studies demonstrated that LINC01088 plays an important role in the pathogenesis of RPL, and is a potential therapeutic target for the treatment of RPL.
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Affiliation(s)
- Hui Zhao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Yali Li
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Nana Dong
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Lei Zhang
- Department of Obstetrics, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Xi Chen
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Huihui Mao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Samed Ahmed Al-Ezzi Al-Ameri
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Xiaoling Wang
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Qun Wang
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
| | - Haiting Mao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, People's Republic of China
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Sun Q, Luo M, Gao Z, Han X, Wu W, Zhao H. Long non-coding RNA OIP5-AS1 aggravates acute lung injury by promoting inflammation and cell apoptosis via regulating the miR-26a-5p/TLR4 axis. BMC Pulm Med 2021; 21:236. [PMID: 34261477 PMCID: PMC8281572 DOI: 10.1186/s12890-021-01589-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/13/2021] [Indexed: 12/03/2022] Open
Abstract
Background Acute lung injury (ALI) is a pulmonary disorder that leads to acute respiration failure and thereby results in a high mortality worldwide. Increasing studies have indicated that toll-like receptor 4 (TLR4) is a promoter in ALI, and we aimed to explore the underlying upstream mechanism of TLR4 in ALI. Methods We used lipopolysaccharide (LPS) to induce an acute inflammatory response in vitro model and a murine mouse model. A wide range of experiments including reverse transcription quantitative polymerase chain reaction, western blot, enzyme linked immunosorbent assay, flow cytometry, hematoxylin–eosin staining, RNA immunoprecipitation, luciferase activity and caspase-3 activity detection assays were conducted to figure out the expression status, specific role and potential upstream mechanism of TLR4 in ALI. Result TLR4 expression was upregulated in ALI mice and LPS-treated primary bronchial/tracheal epithelial cells. Moreover, miR-26a-5p was confirmed to target TLR4 according to results of luciferase reporter assay. In addition, miR-26a-5p overexpression decreased the contents of proinflammatory factors and inhibited cell apoptosis, while upregulation of TLR4 reversed these effects of miR-26a-5p mimics, implying that miR-26a-5p alleviated ALI by regulating TLR4. Afterwards, OPA interacting protein 5 antisense RNA 1 (OIP5-AS1) was identified to bind with miR-26a-5p. Functionally, OIP5-AS1 upregulation promoted the inflammation and miR-26a-5p overexpression counteracted the influence of OIP5-AS1 upregulation on cell inflammatory response and apoptosis. Conclusion OIP5-AS1 promotes ALI by regulating the miR-26a-5p/TLR4 axis in ALI mice and LPS-treated cells, which indicates a promising insight into diagnostics and therapeutics in ALI. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-021-01589-1.
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Affiliation(s)
- Qingsong Sun
- Department of Emergency, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1, Huanghe West Road, Huaiyin District, Huaian, 223300, Jiangsu, China
| | - Man Luo
- Department of Emergency, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1, Huanghe West Road, Huaiyin District, Huaian, 223300, Jiangsu, China
| | - Zhiwei Gao
- Department of Emergency, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1, Huanghe West Road, Huaiyin District, Huaian, 223300, Jiangsu, China
| | - Xiang Han
- Department of Emergency, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1, Huanghe West Road, Huaiyin District, Huaian, 223300, Jiangsu, China
| | - Weiqin Wu
- Department of Emergency, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1, Huanghe West Road, Huaiyin District, Huaian, 223300, Jiangsu, China
| | - Hongmei Zhao
- Department of Emergency, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1, Huanghe West Road, Huaiyin District, Huaian, 223300, Jiangsu, China.
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Chen R, Chen Y, Huang W, Zhao Y, Luo W, Lin J, Wang Z, Yang J. Comprehensive analysis of an immune-related ceRNA network in identifying a novel lncRNA signature as a prognostic biomarker for hepatocellular carcinoma. Aging (Albany NY) 2021; 13:17607-17628. [PMID: 34237706 PMCID: PMC8312417 DOI: 10.18632/aging.203250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/19/2021] [Indexed: 12/13/2022]
Abstract
The function of competitive endogenous RNA (ceRNA) network in the immune regulation of hepatocellular carcinoma (HCC) is unclear. Our study aimed to construct an immune-related ceRNA network and develop an immune-related long noncoding RNA (lncRNA) signature to assess the prognosis of HCC patients and to optimize the treatment methods. We firstly constructed a ceRNA regulatory network for HCC using differentially expressed lncRNAs, mRNAs and microRNAs (miRNAs) from the Cancer Genome Atlas. A signature was constructed by 11 immune-related prognostic lncRNAs from the ceRNA network. The survival analysis and receiver operating characteristic analysis validated the reliability of the signature. Multivariate Cox regression analysis revealed that the signature could act an independent prognostic indicator. This signature also showed high association with immune cell infiltration and immune check blockades. LINC00491 was identified as the hub lncRNA in the signature. In vitro and in vivo evidence demonstrated that silencing of LINC00491 significantly inhibited HCC growth. Finally, 59 lncRNAs, 21 miRNAs, and 26 mRNAs were obtained to build the immune-related ceRNA network for HCC. In conclusion, our novel immune-related lncRNA prognostic signature and the immune-related ceRNA network might provide in-depth insights into tumor-immune interaction of HCC and promote better individual treatment strategies in HCC patients.
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Affiliation(s)
- Rui Chen
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Yunlong Chen
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Wenjie Huang
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, China
| | - Yingnan Zhao
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Wang Luo
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Jinyu Lin
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Zhuangxiong Wang
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Jian Yang
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
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Chen W, Liu S, Wang F. Potential impact and mechanism of Long Non-coding RNAs on cancer and associated T cells. J Cancer 2021; 12:4873-4882. [PMID: 34234857 PMCID: PMC8247393 DOI: 10.7150/jca.58859] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/30/2021] [Indexed: 01/01/2023] Open
Abstract
The discovery of many aberrant expressions of long non-coding RNAs (lncRNAs) in various cancers has focused attention on the effects of lncRNA on cancer cells themselves, including cell proliferation, growth inhibition, cell migration, cell immortality, vascular regeneration and cell viability. But with the increasing role of immunotherapy in cancer therapy, a large number of studies have revealed that the regulatory role of lncRNAs in immunity such as differentiation of immune cells can also influence the development and progression of cancer. In particular, recent publications have suggested that lncRNAs play critical roles in T-lymphocyte activation, proliferation, differentiation, function, apoptosis and metabolism. To elucidate the actual functions of lncRNAs at the molecular level of cancer pathogenesis, we summarize some of the current lncRNA regulatory mechanisms associated with T cell to discuss their effects in cancer in the hope of providing potential cancer therapeutic targets or cancer biomarkers. However, we all know that the differentiation and function of T cells is an extremely complex process that involves the expression and regulation of multiple lncRNAs. As a result, more regulatory mechanisms of lncRNAs need to be further studied.
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Affiliation(s)
- Wenxiu Chen
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China, 210029.,National Key Clinical Department of Laboratory Medicine, Nanjing, China, 210029
| | - Shuna Liu
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China, 210029.,National Key Clinical Department of Laboratory Medicine, Nanjing, China, 210029
| | - Fang Wang
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China, 210029.,National Key Clinical Department of Laboratory Medicine, Nanjing, China, 210029
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Ding C, Shan Z, Li M, Xia Y, Jin Z. Exploration of the Associations of lncRNA Expression Patterns with Tumor Mutation Burden and Prognosis in Colon Cancer. Onco Targets Ther 2021; 14:2893-2909. [PMID: 33958876 PMCID: PMC8096447 DOI: 10.2147/ott.s300095] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/22/2021] [Indexed: 12/24/2022] Open
Abstract
Background Tumor mutation burden (TMB) is emerging as a new biomarker to monitor the response of cancer patients to immunotherapy. Long non-coding RNAs (lncRNAs) are critical in regulating gene expression and play a significant role in cancer-associated immune responses. However, the association between lncRNA expression patterns and TMB levels and survival outcomes remains unknown in colon cancer. Methods In colon cancer patients from The Cancer Genome Atlas Program (TCGA), a multi-lncRNAs based classifier for predicting TMB levels was established using the least absolute shrinkage and selection operator (LASSO) method. The association between classifier index and immune-related characteristics of patients was also investigated. Quantitative polymerase chain reaction (qPCR) was used to verify the expression levels of these lncRNAs in normal and CRC cell lines. Results The multi-lncRNAs based classifier had ability to predict TMB level of patients with accuracy (AUC= 0.70), and the general applicability of this classifier was proved in the validation set (AUC= 0.71) and the pooled set (AUC= 0.70). The classifier index was related to three immune checkpoints (PD1, PD-L1, and CTLA-4), the infiltration level of immune cells, and immune response-related score (IFN-γ score, gene expression profiles (GEP) score, cytolytic activity (CYT) score and MHC score). A nomogram, which integrates classifier and some common clinical information, was able to predict the overall survival of colon cancer patients accurately. Conclusion LncRNA expression patterns are associated with TMB, which may serve as a classifier to predict the TMB in colon cancer patients. The nomogram could potentially evaluate survival outcomes and provide a reference to better manage colon cancer patients.
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Affiliation(s)
- Chengsheng Ding
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, People's Republic of China
| | - Zezhi Shan
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Mengcheng Li
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, People's Republic of China
| | - Yang Xia
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, People's Republic of China
| | - Zhiming Jin
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, People's Republic of China
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Zhu T, Ma Z, Wang H, Wei D, Wang B, Zhang C, Fu L, Li Z, Yu G. Immune-Related Long Non-coding RNA Signature and Clinical Nomogram to Evaluate Survival of Patients Suffering Esophageal Squamous Cell Carcinoma. Front Cell Dev Biol 2021; 9:641960. [PMID: 33748133 PMCID: PMC7969885 DOI: 10.3389/fcell.2021.641960] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/26/2021] [Indexed: 12/13/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) turns out to be one of the most prevalent cancer types, leading to a relatively high mortality among worldwide sufferers. In this study, gene microarray data of ESCC patients were obtained from the GEO database, with the samples involved divided into a training set and a validation set. Based on the immune-related differential long non-coding RNAs (lncRNAs) we identified, a prognostic eight-lncRNA-based risk signature was constructed following regression analyses. Then, the predictive capacity of the model was evaluated in the training set and validation set using survival curves and receiver operation characteristic curves. In addition, univariate and multivariate regression analyses based on clinical information and the model-based risk score also demonstrated the ability of the risk score in independently determining the prognosis of patients. Besides, based on the CIBERSORT tool, the abundance of immune infiltrates in tumor samples was scored, and a significant difference was presented between the high- and low- risk groups. Correlation analysis with immune checkpoints (PD1, PDL1, and CTLA4) indicated that the eight-lncRNA signature–based risk score was negatively correlated with PD1 expression, suggesting that the eight-lncRNA signature may have an effect in immunotherapy for ESCC. Finally, GO annotation was performed for the differential mRNAs that were co-expressed with the eight lncRNAs, and it was uncovered that they were remarkably enriched in immune-related biological functions. These results suggested that the eight-lncRNA signature–based risk model could be employed as an independent biomarker for ESCC prognosis and might play a part in evaluating the response of ESCC to immunotherapy with immune checkpoint blockade.
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Affiliation(s)
- Ting Zhu
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, China
| | - Zhifeng Ma
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, China
| | - Haiyong Wang
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, China
| | - Desheng Wei
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, China
| | - Bin Wang
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, China
| | - Chu Zhang
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, China
| | - Linhai Fu
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, China
| | - Zhupeng Li
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, China
| | - Guangmao Yu
- Department of Thoracic Surgery, Shaoxing People's Hospital, Shaoxing, China
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Xiang X, Fu Y, Zhao K, Miao R, Zhang X, Ma X, Liu C, Zhang N, Qu K. Cellular senescence in hepatocellular carcinoma induced by a long non-coding RNA-encoded peptide PINT87aa by blocking FOXM1-mediated PHB2. Theranostics 2021; 11:4929-4944. [PMID: 33754036 PMCID: PMC7978318 DOI: 10.7150/thno.55672] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/11/2021] [Indexed: 12/18/2022] Open
Abstract
Rationale: Recently, long non-coding RNAs (lncRNAs), known to be involved in human cancer progression, have been shown to encode peptides with biological functions, but the role of lncRNA-encoded peptides in cellular senescence is largely unexplored. We previously reported the tumor-suppressive role of PINT87aa, a peptide encoded by the long intergenic non-protein coding RNA, p53 induced transcript (LINC-PINT). Here, we investigated PINT87aa's role in hepatocellular carcinoma (HCC) cellular senescence. Methods: We examined PINT87aa and truncated PINT87aa functions in vitro by monitoring cell proliferation and performed flow cytometry, senescence-associated β-galactosidase staining, JC-1 staining indicative of mitochondrial membrane potential, the ratio of the overlapping area of light chain 3 beta (LC3B) and mitochondrial probes and the ratio of lysosomal associated membrane protein 1 (LAMP1) overlapping with cytochrome c oxidase subunit 4I1 (COXIV) denoting mitophagy. PINT87aa and truncated PINT87aa functions in vivo were verified by subcutaneously transplanted tumors in nude mice. The possible binding between PINT87aa and forkhead box M1 (FOXM1) was predicted through structural analysis and verified by co-immunoprecipitation and immunofluorescence co-localization. Rescue experiments were performed in vivo and in vitro following FOXM1 overexpression. Further, chromatin immunoprecipitation, polymerase chain reaction, and dual-luciferase reporter gene assay were conducted to validate FOXM1 binding to the prohibitin 2 (PHB2) promoter. Results: PINT87aa was significantly increased in the hydrogen peroxide-induced HCC cell senescence model. Overexpression of PINT87aa induced growth inhibition, cellular senescence, and decreased mitophagy in vitro and in vivo. In contrast, FOXM1 gain-of-function could partially reduce the proportion of senescent HCC cells and enhance mitophagy. PINT87aa overexpression did not affect the expression of FOXM1 itself but reduced that of its target genes involved in cell cycle and proliferation, especially PHB2, which was involved in mitophagy and transcribed by FOXM1. Structural analysis indicated that PINT87aa could bind to the DNA-binding domain of FOXM1, which was confirmed by co-immunoprecipitation and immunofluorescence co-localization. Furthermore, we demonstrated that the 2 to 39 amino acid truncated form of the peptide exerted effects similarly to the full form. Conclusion: Our study established the role of PINT87aa as a novel biomarker and a key regulator of cellular senescence in HCC and identified PINT87aa as a potential therapeutic target for HCC.
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Affiliation(s)
- Xiaohong Xiang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Yunong Fu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Kun Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, PR China
| | - Runchen Miao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Xing Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Xiaohua Ma
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Chang Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Nu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, PR China
| | - Kai Qu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
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Circulating long non-coding RNAs HOTAIR, Linc-p21, GAS5 and XIST expression profiles in diffuse large B-cell lymphoma: association with R-CHOP responsiveness. Sci Rep 2021; 11:2095. [PMID: 33483590 PMCID: PMC7822898 DOI: 10.1038/s41598-021-81715-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
The reliable identification of diffuse large B-cell lymphoma (DLBCL)-specific targets owns huge implications for its diagnosis and treatment. Long non-coding RNAs (lncRNAs) are implicated in DLBCL pathogenesis; however, circulating DLBCL-related lncRNAs are barely investigated. We investigated plasma lncRNAs; HOTAIR, Linc-p21, GAS5 and XIST as biomarkers for DLBCL diagnosis and responsiveness to R-CHOP therapy. Eighty-four DLBCL patients and thirty-three healthy controls were included. Only plasma HOTAIR, XIST and GAS5 were differentially expressed in DLBCL patients compared to controls. Pretreatment plasma HOTAIR was higher, whereas GAS5 was lower in non-responders than responders to R-CHOP. Plasma GAS5 demonstrated superior diagnostic accuracy (AUC = 0.97) whereas a panel of HOTAIR + GAS5 superiorly discriminated responders from non-responders by ROC analysis. In multivariate analysis, HOTAIR was an independent predictor of non-response. Among patients, plasma HOTAIR, Linc-p21 and XIST were correlated. Plasma GAS5 negatively correlated with International Prognostic Index, whereas HOTAIR positively correlated with performance status, denoting their prognostic potential. We constructed the lncRNAs-related protein-protein interaction networks linked to drug response via bioinformatics analysis. In conclusion, we introduce plasma HOTAIR, GAS5 and XIST as potential non-invasive diagnostic tools for DLBCL, and pretreatment HOTAIR and GAS5 as candidates for evaluating therapy response, with HOTAIR as a predictor of R-CHOP failure. We provide novel surrogates for future predictive studies in personalized medicine.
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Xu Q, Wang Y, Huang W. Identification of immune-related lncRNA signature for predicting immune checkpoint blockade and prognosis in hepatocellular carcinoma. Int Immunopharmacol 2021; 92:107333. [PMID: 33486322 DOI: 10.1016/j.intimp.2020.107333] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/02/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND An increasing body of evidence has supported that long non-coding RNAs (lncRNAs) can play as essential roles of various physiological process and pathological diseases. We aimed to construct a robust immune-associated lncRNA signature associated with the prognosis for HCC survival prediction. METHODS 7 immune-associated lncRNAs presenting significant correlation with survival were screened through stepwise univariate Cox regression and LASSO algorithm, and multivariate Cox regression. Kaplan-Meier analysis, proportional hazards model, and ROC analyses further conducted. Gene set enrichment analysis (GSEA) was applied for functional annotation. We conducted quantitative real-time polymerase chain reaction to determine NRAV expression and preliminarily explored the latent role of NRAV in prognosis of HCC patients. RESULTS Finally, 7 immune-related lncRNA signature composed of AC007405.3, AC023157.3, NRAV, CASC19, MSC-AS1, GASAL1, and LINC00942 were validated. This lncRNAs signature can serve as an independent predictive biomolecular factor. This signature was further confirmed in the validation group and the entire cohort. We demonstrated that NRAV was significantly upregulated in HCC cell lines and it may serve as a key regulator in HCC. Our signature was associated to apoptosis and immunologic characteristics. This signature mediated immune cell infiltration (i.e., Dendritic, etc.,) and immune checkpoint blockade (ICB) immunotherapy-related molecules (i.e., CD274, etc.,). CONCLUSION This immune-related lncRNA signature possesses promising prognostic value in HCC and may have the potentiality to predict clinical outcome of ICB immunotherapy.
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Affiliation(s)
- Qianhui Xu
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Yuxin Wang
- Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Wen Huang
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China.
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40
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Identification of a Nine Immune-Related lncRNA Signature as a Novel Diagnostic Biomarker for Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9798231. [PMID: 33506049 PMCID: PMC7808810 DOI: 10.1155/2021/9798231] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 10/20/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) ranks fifth among common cancers and is the second most common cause of cancer-related mortality worldwide. This study is aimed at identifying an immune-related long noncoding RNA (lncRNA) signature as a potential biomarker with prognostic value to improve early diagnosis and provide potential therapeutic targets for HCC patients. The subjects of this study were HCC samples with complete transcriptome data and clinical information downloaded from The Cancer Genome Atlas (TCGA) database. We then extracted the immune-related mRNA and lncRNA expression profiles. Based on the expression profiles of immune-related lncRNAs, we identified a nine-lncRNA signature that was related to the progression of HCC. The risk score was calculated based on the expression level of the nine lncRNAs of each sample, which divided patients into high-risk and low-risk groups. We found that the increased risk score was associated with a poor prognosis of HCC patients. To assess the accuracy of the survival model, we calculated a receiver operating characteristic (ROC) for validation. The curve showed that the area under the curve (AUC) for the risk score was 0.792. Besides, both principal component analysis (PCA) and gene set enrichment analysis (GSEA) were further used for functional annotation. We found that the distribution patterns were different between the low-risk and high-risk groups in PCA, and the underlying mechanism by which the nine lncRNAs promoted the progression of HCC involved an abnormal immune status. Finally, we analyzed the infiltration of twenty-nine kinds of immune cells and the activation of immune function in HCC using the ssGSEA algorithm. The results showed that aDCs, iDCs, macrophages, Tfh, Th1, Treg, and NK cells were correlated with the progress of HCC patients. And the immune functions including APC costimulation, CCR, check point, HLA, MHC class I, and Type II IFN responses were also significantly different between the high-risk and low-risk groups. In conclusion, our study identified a nine-lncRNA signature with potential prognostic value for patients with HCC, which could be used as a new biomarker for the diagnosis and immunotherapy of HCC.
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Jiang X, Xing L, Chen Y, Qin R, Song S, Lu Y, Xie S, Wang L, Pu H, Gui X, Li T, Xu J, Li J, Jia S, Lu D. CircMEG3 inhibits telomerase activity by reducing Cbf5 in human liver cancer stem cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 23:310-323. [PMID: 33425489 PMCID: PMC7779543 DOI: 10.1016/j.omtn.2020.11.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022]
Abstract
Circular RNA (CircRNA) is a newly identified special class of non-coding RNA (ncRNA) that plays an important regulatory role in the progression of certain diseases. Herein, our results indicate that CircMEG3 is downregulated expression and negatively correlated with the expression of telomerase-related gene Cbf5 in human liver cancer. Moreover, CircMEG3 inhibits the growth of human liver cancer stem cells in vivo and in vitro. CircMEG3 inhibits the expression of m6A methyltransferase METTL3 dependent on HULC. Moreover, CircMEG3 inhibits the expression of Cbf5, a component of telomere synthetase H/ACA ribonucleoprotein (RNP; catalyst RNA pseudouracil modification) through METTL3 dependent on HULC. Thereby, CircMEG3 inhibits telomerase activity and shortens telomere lifespan dependent on HULC and Cbf5 in human liver cancer stem cell. Strikingly, increased Cbf5 abrogates the ability of CircMEG3 to inhibit malignant differentiation of human liver cancer stem cells. In summary, these observations provide important basic information for finding effective liver cancer therapeutic targets.
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Affiliation(s)
- Xiaoxue Jiang
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Libo Xing
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Yingjie Chen
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Rushi Qin
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Shuting Song
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Yanan Lu
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Sijie Xie
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Liyan Wang
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Hu Pu
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Xin Gui
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Tianming Li
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Jie Xu
- School of Medicine, Tongji University, Shanghai 200092, China
| | - Jiao Li
- School of Medicine, Tongji University, Shanghai 200092, China
| | - Song Jia
- School of Medicine, Tongji University, Shanghai 200092, China
| | - Dongdong Lu
- Shanghai Putuo District People's Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
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Lazăr AD, Dinescu S, Costache M. The Non-Coding Landscape of Cutaneous Malignant Melanoma: A Possible Route to Efficient Targeted Therapy. Cancers (Basel) 2020; 12:cancers12113378. [PMID: 33203119 PMCID: PMC7696690 DOI: 10.3390/cancers12113378] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 02/06/2023] Open
Abstract
Considered to be highly lethal if not diagnosed in early stages, cutaneous malignant melanoma is among the most aggressive and treatment-resistant human cancers, and its incidence continues to rise, largely due to ultraviolet radiation exposure, which is the main carcinogenic factor. Over the years, researchers have started to unveil the molecular mechanisms by which malignant melanoma can be triggered and sustained, in order to establish specific, reliable biomarkers that could aid the prognosis and diagnosis of this fatal disease, and serve as targets for development of novel efficient therapies. The high mutational burden and heterogeneous nature of melanoma shifted the main focus from the genetic landscape to epigenetic and epitranscriptomic modifications, aiming at elucidating the role of non-coding RNA molecules in the fine tuning of melanoma progression. Here we review the contribution of microRNAs and lncRNAs to melanoma invasion, metastasis and acquired drug resistance, highlighting their potential for clinical applications as biomarkers and therapeutic targets.
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Affiliation(s)
- Andreea D. Lazăr
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania; (A.D.L.); (M.C.)
| | - Sorina Dinescu
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania; (A.D.L.); (M.C.)
- Research Institute of the University of Bucharest, 050663 Bucharest, Romania
- Correspondence:
| | - Marieta Costache
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania; (A.D.L.); (M.C.)
- Research Institute of the University of Bucharest, 050663 Bucharest, Romania
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Sun JY, Zhang D, Wu S, Xu M, Zhou X, Lu XJ, Ji J. Resistance to PD-1/PD-L1 blockade cancer immunotherapy: mechanisms, predictive factors, and future perspectives. Biomark Res 2020; 8:35. [PMID: 32864132 PMCID: PMC7450549 DOI: 10.1186/s40364-020-00212-5] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/07/2020] [Indexed: 12/16/2022] Open
Abstract
PD-1/PD-L1 blockade therapy is a promising cancer treatment strategy, which has revolutionized the treatment landscape of malignancies. Over the last decade, PD-1/PD-L1 blockade therapy has been trialed in a broad range of malignancies and achieved clinical success. Despite the potentially cure-like survival benefit, only a minority of patients are estimated to experience a positive response to PD-1/PD-L1 blockade therapy, and the primary or acquired resistance might eventually lead to cancer progression in patients with clinical responses. Accordingly, the resistance to PD-1/PD-L1 blockade remains a significant challenge hindering its further application. To overcome the limitation in therapy resistance, substantial effort has been made to improve or develop novel anti-PD-1/PD-L1 based immunotherapy strategies with better clinical response and reduced immune-mediated toxicity. In this review, we provide an overview on the resistance to PD-1/PD-L1 blockade and briefly introduce the mechanisms underlying therapy resistance. Moreover, we summarize potential predictive factors for the resistance to PD-1/PD-L1 blockade. Furthermore, we give an insight into the possible solutions to improve efficacy and clinical response. In the following research, combined efforts of basic researchers and clinicians are required to address the limitation of therapy resistance.
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Affiliation(s)
- Jin-Yu Sun
- The First College of Clinical Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China
| | - Dengke Zhang
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital of Zhejiang University/ The Fifth Affiliated Hospital of Wenzhou Medical University/ Clinical Medicine of Center Hospital of Lishui College, Lishui, 323000 China
- College of Medicine, Lishui College, Lishui, 323000 China
| | - Songquan Wu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital of Zhejiang University/ The Fifth Affiliated Hospital of Wenzhou Medical University/ Clinical Medicine of Center Hospital of Lishui College, Lishui, 323000 China
- College of Medicine, Lishui College, Lishui, 323000 China
| | - Min Xu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital of Zhejiang University/ The Fifth Affiliated Hospital of Wenzhou Medical University/ Clinical Medicine of Center Hospital of Lishui College, Lishui, 323000 China
- College of Medicine, Lishui College, Lishui, 323000 China
| | - Xiao Zhou
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiao-Jie Lu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jiansong Ji
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital of Zhejiang University/ The Fifth Affiliated Hospital of Wenzhou Medical University/ Clinical Medicine of Center Hospital of Lishui College, Lishui, 323000 China
- College of Medicine, Lishui College, Lishui, 323000 China
- Department of radiology, Affiliated Lishui Hospital of Zhejiang University, Lishui, 323000 China
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Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response. Genes (Basel) 2020; 11:genes11070760. [PMID: 32646047 PMCID: PMC7397219 DOI: 10.3390/genes11070760] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 06/28/2020] [Accepted: 07/03/2020] [Indexed: 12/14/2022] Open
Abstract
The global spread of COVID-19, caused by pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for an imminent response from medical research communities to better understand this rapidly spreading infection. Employing multiple bioinformatics and computational pipelines on transcriptome data from primary normal human bronchial epithelial cells (NHBE) during SARS-CoV-2 infection revealed activation of several mechanistic networks, including those involved in immunoglobulin G (IgG) and interferon lambda (IFNL) in host cells. Induction of acute inflammatory response and activation of tumor necrosis factor (TNF) was prominent in SARS-CoV-2 infected NHBE cells. Additionally, disease and functional analysis employing ingenuity pathway analysis (IPA) revealed activation of functional categories related to cell death, while those associated with viral infection and replication were suppressed. Several interferon (IFN) responsive gene targets (IRF9, IFIT1, IFIT2, IFIT3, IFITM1, MX1, OAS2, OAS3, IFI44 and IFI44L) were highly upregulated in SARS-CoV-2 infected NBHE cell, implying activation of antiviral IFN innate response. Gene ontology and functional annotation of differently expressed genes in patient lung tissues with COVID-19 revealed activation of antiviral response as the hallmark. Mechanistic network analysis in IPA identified 14 common activated, and 9 common suppressed networks in patient tissue, as well as in the NHBE cell model, suggesting a plausible role for these upstream regulator networks in the pathogenesis of COVID-19. Our data revealed expression of several viral proteins in vitro and in patient-derived tissue, while several host-derived long noncoding RNAs (lncRNAs) were identified. Our data highlights activation of IFN response as the main hallmark associated with SARS-CoV-2 infection in vitro and in human, and identified several differentially expressed lncRNAs during the course of infection, which could serve as disease biomarkers, while their precise role in the host response to SARS-CoV-2 remains to be investigated.
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Wang L, Liu Y. Long noncoding RNA RHPN1-AS1 exerts pro-oncogenic actions in osteosarcoma by functioning as a molecular sponge of miR-506 to positively regulate SNAI2 expression. Cell Cycle 2020; 19:1517-1529. [PMID: 32401134 PMCID: PMC7469572 DOI: 10.1080/15384101.2020.1762039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/06/2020] [Accepted: 03/11/2020] [Indexed: 12/28/2022] Open
Abstract
The long noncoding RNA, RHPN1 antisense RNA 1 (RHPN1-AS1), performs important regulatory actions in the progression of many human cancers. In this study, we aimed to analyze RHPN1-AS1 expression in osteosarcoma (OS) and to assess the influence of RHPN1-AS1 knockdown on the malignant behavior of OS cells. The molecular mechanisms by which RHPN1-AS1 affects the oncogenicity of OS were explored too. The expression of RHPN1-AS1 in OS was measured by RT-qPCR. The effects of the RHPN1-AS1 silencing in OS cells were studied both in vitro (in a Cell Counting Kit-8 assay, apoptosis analysis, and Transwell migration and invasion assays) and in vivo (by means of tumor xenografts in nude mice). Herein, RHPN1-AS1 expression was found to be significantly upregulated in OS tissues and cell lines. The elevated expression of RHPN1-AS1 closely correlated with the tumor size, TNM stage, distal metastasis and shorter overall survival in patients with OS. The depletion of RHPN1-AS1 restrained OS cell proliferation, migration, and invasion, and exerted proapoptotic effects in vitro. Furthermore, the knockdown of RHPN1-AS1 effectively reduced the tumor growth of OS cells in vivo. As for the mechanism, RHPN1-AS1 increased snail family zinc finger 2 (SNAI2 also known as SNAIL2) expression by acting as a competing endogenous RNA of miR-506. Notably, increasing the amount of miR-506 partially reversed the effects of the RHPN1-AS1 downregulation on OS cells. In conclusion, RHPN1-AS1 contributes to the malignancy of OS cells in vitro and in vivo, largely via upregulation of the miR-506-SNAI2 axis output.
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Affiliation(s)
- Limin Wang
- Department of Spinal Surgery, Shijiazhuang Third Hospital, Shijiazhuang, Hebei, P.R. China
| | - Yanbing Liu
- Department of Spinal Surgery, Shijiazhuang Third Hospital, Shijiazhuang, Hebei, P.R. China
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Elango R, Alsaleh KA, Vishnubalaji R, Manikandan M, Ali AM, Abd El-Aziz N, Altheyab A, Al-Rikabi A, Alfayez M, Aldahmash A, Alajez NM. MicroRNA Expression Profiling on Paired Primary and Lymph Node Metastatic Breast Cancer Revealed Distinct microRNA Profile Associated With LNM. Front Oncol 2020; 10:756. [PMID: 32509578 PMCID: PMC7248321 DOI: 10.3389/fonc.2020.00756] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/20/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) is the foremost cause of cancer-related deaths in women. BC patients are oftentimes presented with lymph node metastasis (LNM), which increases their risk of recurrence. Compelling data have recently implicated microRNAs in promoting BC metastasis. Therefore, the identification of microRNA (miRNA)-based molecular signature associated with LNM could provide an opportunity for a more personalized treatment for BC patients with high risk of LNM. In current study, we performed comprehensive miRNA profiling in matched primary breast and LNM and identified 40 miRNAs, which were differentially expressed in LNM compared to primary tumors. The expression of 14 miRNAs (Up: hsa-miR-155-5p, hsa-miR-150-5p, hsa-miR-146a-5p, hsa-miR-142-5p and down: hsa-miR-200a-3p, hsa-miR-200b-3p, hsa-miR-200c-3p, hsa-miR-205-5p, hsa-miR-210-3p, hsa-miR-214-3p, hsa-miR-141-3p, hsa-miR-127-3p, hsa-miR-125a-5p, and hsa-let-7c-5p) was subsequently validated in a second cohort of 32 breast and 32 matched LNM tumor tissues. Mechanistically, forced expression of hsa-miR-205-5p, or hsa-miR-214-3p epigenetically inhibited MDA-MB-231 cell proliferation, colony formation, and cell migration. Global gene expression profiling on MDA-MB-231 cells overexpressing hsa-miR-205-5p, or hsa-miR-214-3p in combination with in silico target prediction and ingenuity pathway analyses identified multiple bona fide targets for hsa-miR-205-5p, hsa-miR-214-3p affecting cellular proliferation and migration. Interestingly, interrogation of the expression levels of hsa-miR-205 and hsa-miR-214 in the METABRIC breast cancer dataset revealed significantly poor overall survival in patients with downregulated expression of miR-205 [HR = 0.75 (0.61–0.91)], p = 0.003 and hsa-miR-214 [HR = 0.74 (0.59–0.93) p = 0.008]. Our data unraveled the miRNA-transcriptional landscape associated with LNM and provide novel insight on the role of several miRNAs in promoting BC LNM, and suggest their potential utilization in the clinical management of BC patients.
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Affiliation(s)
- Ramesh Elango
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Khalid A Alsaleh
- Department of Medicine, Oncology Center, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Radhakrishnan Vishnubalaji
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Muthurangan Manikandan
- Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Arwa M Ali
- Medical Oncology Department, Prince of Wales Hospital, Randwick, NSW, Australia.,Department of Medical Oncology, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
| | - Nashwa Abd El-Aziz
- Department of Medical Oncology, South Egypt Cancer Institute, Assiut University, Assiut, Egypt.,Division of Hematology-Oncology, Oncology Center, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrhaman Altheyab
- Department of Medicine, Oncology Center, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ammar Al-Rikabi
- Department of Pathology, King Saud University Medical City, Riyadh, Saudi Arabia
| | - Musaad Alfayez
- Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah Aldahmash
- Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Nehad M Alajez
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
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47
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Zhang Y, Zhang L, Xu Y, Wu X, Zhou Y, Mo J. Immune-related long noncoding RNA signature for predicting survival and immune checkpoint blockade in hepatocellular carcinoma. J Cell Physiol 2020; 235:9304-9316. [PMID: 32330311 DOI: 10.1002/jcp.29730] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 12/24/2022]
Abstract
Long noncoding RNAs (lncRNAs) show multiple functions, including immune response. Recently, the immune-related lncRNAs have been reported in some cancers. We first investigated the immune-related lncRNA signature as a potential target in hepatocellular carcinoma (HCC) survival. The training set (n = 368) and the independent external validation cohort (n = 115) were used. Immune genes and lncRNAs coexpression were constructed to identify immune-related lncRNAs. Cox regression analyses were perfumed to establish the immune-related lncRNA signature. Regulatory roles of this signature on cancer pathways and the immunologic features were investigated. The correlation between immune checkpoint inhibitors and this signature was examined. In this study, the immune-related lncRNA signature was identified in HCC, which could stratify patients into high- and low-risk groups. This immune-related lncRNA signature was correlated with disease progression and worse survival and was an independent prognostic biomarker. Our immune-related lncRNA signature was still a powerful tool in predicting survival in each stratum of age, gender, and tumor stage. This signature mediated cell cycle, glycolysis, DNA repair, mammalian target of rapamycin signaling, and immunologic characteristics (i.e., natural killer cells vs. Th1 cells down, etc). This signature was associated with immune cell infiltration (i.e., macrophages M0, Tregs, CD4 memory T cells, and macrophages M1, etc.,) and immune checkpoint blockade (ICB) immunotherapy-related molecules (i.e., PD-L1, PD-L2, and IDO1). Our findings suggested that the immune-related lncRNA signature had an important value for survival prediction and may have the potential to measure the response to ICB immunotherapy. This signature may guide the selection of the immunotherapy for HCC.
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Affiliation(s)
- Yaqiong Zhang
- Department of Clinical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang Province, China
| | - Liming Zhang
- Department of Clinical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang Province, China
| | - Youwen Xu
- Department of Clinical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang Province, China
| | - Xiaoyu Wu
- Department of Clinical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang Province, China
| | - Yong Zhou
- Department of Clinical Laboratory, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang Province, China
| | - Jinggang Mo
- Department of Hepatobiliary Surgery, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang Province, China
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Elango R, Alsaleh KA, Vishnubalaji R, Manikandan M, Ali AM, Abd El-Aziz N, Altheyab A, Al-Rikabi A, Alfayez M, Aldahmash A, Alajez NM. MicroRNA Expression Profiling on Paired Primary and Lymph Node Metastatic Breast Cancer Revealed Distinct microRNA Profile Associated With LNM. Front Oncol 2020. [PMID: 32509578 DOI: 10.3389/fonc.2020.00756/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
Breast cancer (BC) is the foremost cause of cancer-related deaths in women. BC patients are oftentimes presented with lymph node metastasis (LNM), which increases their risk of recurrence. Compelling data have recently implicated microRNAs in promoting BC metastasis. Therefore, the identification of microRNA (miRNA)-based molecular signature associated with LNM could provide an opportunity for a more personalized treatment for BC patients with high risk of LNM. In current study, we performed comprehensive miRNA profiling in matched primary breast and LNM and identified 40 miRNAs, which were differentially expressed in LNM compared to primary tumors. The expression of 14 miRNAs (Up: hsa-miR-155-5p, hsa-miR-150-5p, hsa-miR-146a-5p, hsa-miR-142-5p and down: hsa-miR-200a-3p, hsa-miR-200b-3p, hsa-miR-200c-3p, hsa-miR-205-5p, hsa-miR-210-3p, hsa-miR-214-3p, hsa-miR-141-3p, hsa-miR-127-3p, hsa-miR-125a-5p, and hsa-let-7c-5p) was subsequently validated in a second cohort of 32 breast and 32 matched LNM tumor tissues. Mechanistically, forced expression of hsa-miR-205-5p, or hsa-miR-214-3p epigenetically inhibited MDA-MB-231 cell proliferation, colony formation, and cell migration. Global gene expression profiling on MDA-MB-231 cells overexpressing hsa-miR-205-5p, or hsa-miR-214-3p in combination with in silico target prediction and ingenuity pathway analyses identified multiple bona fide targets for hsa-miR-205-5p, hsa-miR-214-3p affecting cellular proliferation and migration. Interestingly, interrogation of the expression levels of hsa-miR-205 and hsa-miR-214 in the METABRIC breast cancer dataset revealed significantly poor overall survival in patients with downregulated expression of miR-205 [HR = 0.75 (0.61-0.91)], p = 0.003 and hsa-miR-214 [HR = 0.74 (0.59-0.93) p = 0.008]. Our data unraveled the miRNA-transcriptional landscape associated with LNM and provide novel insight on the role of several miRNAs in promoting BC LNM, and suggest their potential utilization in the clinical management of BC patients.
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Affiliation(s)
- Ramesh Elango
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Khalid A Alsaleh
- Department of Medicine, Oncology Center, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Radhakrishnan Vishnubalaji
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Muthurangan Manikandan
- Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Arwa M Ali
- Medical Oncology Department, Prince of Wales Hospital, Randwick, NSW, Australia
- Department of Medical Oncology, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
| | - Nashwa Abd El-Aziz
- Department of Medical Oncology, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
- Division of Hematology-Oncology, Oncology Center, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrhaman Altheyab
- Department of Medicine, Oncology Center, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ammar Al-Rikabi
- Department of Pathology, King Saud University Medical City, Riyadh, Saudi Arabia
| | - Musaad Alfayez
- Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah Aldahmash
- Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Nehad M Alajez
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
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Heart Failure with Reduced Ejection Fraction (HFrEF) and Preserved Ejection Fraction (HFpEF): The Diagnostic Value of Circulating MicroRNAs. Cells 2019; 8:cells8121651. [PMID: 31888288 PMCID: PMC6952981 DOI: 10.3390/cells8121651] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 12/28/2022] Open
Abstract
Circulating microRNAs offer attractive potential as epigenetic disease biomarkers by virtue of their biological stability and ready accessibility in liquid biopsies. Numerous clinical cohort studies have revealed unique microRNA profiles in different disease settings, suggesting utility as markers with diagnostic and prognostic applications. Given the complex network of microRNA functions in modulating gene expression and post-transcriptional modifications, the circulating microRNA landscape in disease may reflect pathophysiological status, providing valuable information for delineating distinct subtypes and/or stages of complex diseases. Heart failure (HF) is an increasingly significant global health challenge, imposing major economic liability and health care burden due to high hospitalization, morbidity, and mortality rates. Although HF is defined as a syndrome characterized by symptoms and findings on physical examination, it may be further differentiated based on left ventricular ejection fraction (LVEF) and categorized as HF with reduced ejection fraction (HFrEF) and HF with preserved ejection fraction (HFpEF). The presenting clinical syndromes in HFpEF and HFrEF are similar but mortality differs, being somewhat lower in HFpEF than in HFrEF. However, while HFrEF is responsive to an array of therapies, none has been shown to improve survival in HFpEF. Herein, we review recent HF cohort studies focusing on the distinct microRNA profiles associated with HF subtypes to reveal new insights to underlying mechanisms and explore the possibility of exploiting these differences for diagnostic/prognostic applications.
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