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Wang X, Pan Y, Ou Y, Duan T, Zou Y, Zhou X. Construction and validation of immune-related LncRNAs classifier to predict prognosis and immunotherapy response in laryngeal squamous cell carcinoma. World J Surg Oncol 2022; 20:164. [PMID: 35606755 PMCID: PMC9128282 DOI: 10.1186/s12957-022-02608-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/19/2022] [Indexed: 11/24/2022] Open
Abstract
Background Rapid advances in transcriptomic profiles have resulted in recognizing IRLs (immune-related long noncoding RNAs), as modulators of the expression of genes related to immune cells that mediate immune inhibition as well as immune stimulatory, indicating LncRNAs play fundamental roles in immune modulation. Hence, we establish an IRL classifier to precisely predict prognosis and immunotherapeutic efficiency in laryngeal squamous cell carcinoma (LSCC). Methods LSCC RNA-seq (RNA sequencing) datasets, somatic mutation data, and corresponding clinicopathologic information were acquired from TCGA (the Cancer Genome Atlas) and Gene Expression Omnibus (GEO) databases. Spearman correlation analysis identified LncRNAs associated with immune-related genes (IRG). Based on Lasso penalized regression and random forest (RF), we constructed an IRL classifier associated with prognosis. GEO database was utilized to validate the IRL classifier. The predictive precision and clinical application of the IRL classifier were assessed and compared to clinicopathologic features. The immune cell infiltration of LSCC was calculated via CIBERSORTx tools and ssGSEA (single-sample gene set enrichment analysis). Then, we systematically correlated the IRL classifier with immunological characteristics from multiple perspectives, such as immune-related cells infiltrating, tumor microenvironment (TME) scoring, microsatellite instability (MSI), tumor mutation burden (TMB), and chemokines. Finally, the TIDE (tumor immune dysfunction and exclusion) algorithm was used to predict response to immunotherapy. Results Based on machine learning approach, three prognosis-related IRLs (BARX1-DT, KLHL7-DT, and LINC02154) were selected to build an IRL classifier. The IRL classifier could availably classify patients into the low-risk and high-risk groups based on the different endpoints, including recurrence-free survival (RFS) and overall survival (OS). In terms of predictive ability and clinical utility, the IRL classifier was superior to other clinical characteristics. Encouragingly, similar results were observed in the GEO databases. Immune infiltration analysis displayed immune cells that are significantly richer in low-risk group, CD8 T cells and activated NK cells via CIBERSORTx algorithm as well as activated CD8 T cell via ssGSEA. Additionally, compared with the high-risk group, immune score, CD8 T effector was higher in the low-risk group, yet stromal score, score of p53 signaling pathway and TGFher in the Tx algorithm, was lower in the low-risk group. Corresponding results were confirmed in GEO dataset. Finally, TIDE analysis uncovered that the IRL classifier may be effectually predict the clinical response of immunotherapy in LSCC. Conclusion Based on BARX1-DT, KLHL7-DT, and LINC02154, the IRL classifier was established, which can be used to predict the prognosis, immune infiltration status, and immunotherapy response in LSCC patients and might facilitate personalized counseling for immunotherapy. Supplementary Information The online version contains supplementary material available at 10.1186/s12957-022-02608-z.
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Affiliation(s)
- Xiaofeng Wang
- Department of Otolaryngology-Head and Neck Surgery, the First Affiliated Hospital of Hainan Medical University, Haikou, 570102, Hainan Province, People's Republic of China
| | - Ya Pan
- Department of Otolaryngology-Head and Neck Surgery, the First Affiliated Hospital of Hainan Medical University, Haikou, 570102, Hainan Province, People's Republic of China
| | - Yangpeng Ou
- Department of Oncology, Huizhou Third People's Hospital, Guangzhou Medical University, Huizhou, 516000, Guangdong Province, People's Republic of China
| | - Tingting Duan
- Department of Otolaryngology-Head and Neck Surgery, the First Affiliated Hospital of Hainan Medical University, Haikou, 570102, Hainan Province, People's Republic of China.
| | - Yuxia Zou
- Department of Otolaryngology-Head and Neck Surgery, the First Affiliated Hospital of Hainan Medical University, Haikou, 570102, Hainan Province, People's Republic of China.
| | - Xuejun Zhou
- Department of Otolaryngology-Head and Neck Surgery, the First Affiliated Hospital of Hainan Medical University, Haikou, 570102, Hainan Province, People's Republic of China.
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2
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Construction of immune-related LncRNAs classifier to predict prognosis and immunotherapy response in thymic epithelial tumors. Biosci Rep 2022; 42:231178. [PMID: 35438133 PMCID: PMC9109460 DOI: 10.1042/bsr20220317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/23/2022] [Accepted: 04/06/2022] [Indexed: 11/17/2022] Open
Abstract
The primary objective of this study was to construct an immune-related long non-coding RNAs (IRLs) classifier to precisely predict the prognosis and immunotherapy response of patients with thymic epithelial tumors (TET).Based on univariable Cox regression analysis and Lasso regression, six prognosis-related IRLs (AC004466.3,AC138207.2, AC148477.2, AL450270.1, HOXB-AS1 and SNHG8) were selected to build an IRL classifier. Importantly, results of qRT-PCR validated that higher expression levels of AC138207.2, AC148477.2, AL450270.1 and SNHG8 as well as lower expression levels of AC004466.3, and HOXB-AS1 in TETs samples compared to normal controls. The IRL classifier could effectively classify patients into the low-risk and high-risk groups based on the different survival parameters. In terms of predictive ability and clinical utility, the IRL classifier was superior to Masaoka staging system. Additionally, IRL classifier is significantly associated with immune cells infiltration (dendritic cells, activated CD4 memory T cells and tumor-infiltrating lymphocyte (TIL), T cell subsets in particular), immune microenvironment (immune score and immune checkpoint inhibitors), and immunogenicity (TMB) in TETs, which hints that IRL classifier is tightly correlated with immune characteristics and might guide more effective immunotherapy strategies for TETs patients. Encouragingly, according to TIDE algorithm, there were more immunotherapy responders in the low-risk IRL subgroup and the IRL score was robustly negatively linked to the immunotherapeutic response. To sum up, the IRL classifier was established, which can be used to predict the prognosis, immune infiltration status, immunotherapy response in TETs patients, and may facilitate personalized counseling for immunotherapy.
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Mallick P, Maity S, Chakrabarti O, Chakrabarti S. Role of systems biology and multi-omics analyses in delineating spatial interconnectivity and temporal dynamicity of ER stress mediated cellular responses. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119210. [PMID: 35032474 DOI: 10.1016/j.bbamcr.2022.119210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/01/2021] [Accepted: 12/30/2021] [Indexed: 06/14/2023]
Abstract
The endoplasmic reticulum (ER) is a membranous organelle involved in calcium storage, lipid biosynthesis, protein folding and processing. Many patho-physiological conditions and pharmacological agents are known to perturb normal ER function and can lead to ER stress, which severely compromise protein folding mechanism and hence poses high risk of proteotoxicity. Upon sensing ER stress, the different stress signaling pathways interconnect with each other and work together to preserve cellular homeostasis. ER stress response is a part of the integrative stress response (ISR) and might play an important role in the pathogenesis of chronic neurodegenerative diseases, where misfolded protein accumulation and cell death are common. The initiation, manifestation and progression of ER stress mediated unfolded protein response (UPR) is a complex procedure involving multiple proteins, pathways and cellular organelles. To understand the cause and consequences of such complex processes, implementation of an integrative holistic approach is required to identify novel players and regulators of ER stress. As multi-omics data-based systems analyses have shown potential to unravel the underneath molecular mechanism of complex biological systems, it is important to emphasize the utility of this approach in understanding the ER stress biology. In this review we first discuss the ER stress signaling pathways and regulatory players, along with their inter-connectivity. We next highlight the importance of systems and network biology approaches using multi-omics data in understanding ER stress mediated cellular responses. This report would help advance our current understanding of the multivariate spatial interconnectivity and temporal dynamicity of ER stress.
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Affiliation(s)
- Priyanka Mallick
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, IICB TRUE Campus, CN-6, Sector 5, Salt Lake, Kolkata Pin 700091, WB, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Sebabrata Maity
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhabha National Institute, India
| | - Oishee Chakrabarti
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhabha National Institute, India.
| | - Saikat Chakrabarti
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, IICB TRUE Campus, CN-6, Sector 5, Salt Lake, Kolkata Pin 700091, WB, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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4
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A four immune-related long noncoding RNAs signature as predictors for cervical cancer. Hum Cell 2021; 35:348-359. [PMID: 34846702 DOI: 10.1007/s13577-021-00654-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/22/2021] [Indexed: 10/19/2022]
Abstract
The progression, metastasis, and prognosis of cervical cancer (CC) is influenced by the tumor immune microenvironment. Studies proved that long non-coding RNAs (lncRNAs) to engage in cervical cancer development, especially immune-related lncRNAs, have emerged crucial in the tumor immune process. This study was set out to identify an immune-related lncRNA signature. In total, 13,838 lncRNA expression profiles and 328 immune genes were acquired from the clnical data of 306 CC tissues and 3 non-CC tissues. From the 433 identified immune-related lncRNAs, 4 candidate immune-related lncRNAs (SOX21-AS1, AC005332.4, NCK1-DT, LINC01871) were considered independent indicators of cervical cancer prognosis through the univariate and multivariate Cox regression analysis, and they were used to construct a prognostic and survival lncRNA signature model followed by the bootstrap method for further verification. Kaplan-Meier curves illustrated that cervical cancer patients could be divided into high-risk and low-risk groups with significant differences (P = 2.052e - 05), and the discrepancy of immune profiles between these two risk groups was illustrated by principal components analysis. Taken together, the novel survival predictive model created by the four immune-related lncRNAs showed promising clinical prediction value in cervical cancer.
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Schwerdtfeger M, Desiderio V, Kobold S, Regad T, Zappavigna S, Caraglia M. Long non-coding RNAs in cancer stem cells. Transl Oncol 2021; 14:101134. [PMID: 34051619 PMCID: PMC8176362 DOI: 10.1016/j.tranon.2021.101134] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/29/2021] [Accepted: 05/19/2021] [Indexed: 12/11/2022] Open
Abstract
Long non coding RNAs are involved in the regulation of multiple cellular processes. Cancer stemness and escape from immunological anti-cancer mechanisms are important mechanisms of resistance to anti-cancer agents and are pivotal in controlling cancer development and metastases. Long non coding RNAs have deep effects on the immune-modulation and on the control of cancer stem cells. Several pathways involved in immunological escape and cancer stemness are modulated by long non coding RNAs. Targeting long non coding RNAs is a potential new strategy to control tumor development and metastases.
In recent years, it has been evidenced that the human transcriptome includes several types of non-coding RNAs (ncRNAs) that are mainly involved in the regulation of different cellular processes. Among ncRNAs, long-non-coding RNAs (lncRNAs) are defined as longer than 200 nucleotides and have been shown to be involved in several physiological and pathological events, including immune system regulation and cancer. Cancer stem cells (CSCs) are defined as a population of cancer cells that possess characteristics, such as resistance to standard treatments, cancer initiation, ability to undergo epithelial-to-mesenchymal transition, and the ability to invade, spread, and generate metastases. The cancer microenvironment, together with genetic and epigenetic factors, is fundamental for CSC maintenance and tumor growth and progression. Unsurprisingly, lncRNAs have been involved in both CSC biology and cancer progression, prognosis and recurrence. Here we review the most recent literature on IncRNAs involvement in CSC biology and function.
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Affiliation(s)
- Melanie Schwerdtfeger
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy; Center of Integrated Protein Science Munich (CIPS-M) and Division of Clinical Pharmacology, Department of Medicine IV, Klinikum der Universität München, LMU Munich, Germany, Member of the German Center for Lung Research (DZL)
| | - Vincenzo Desiderio
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Sebastian Kobold
- Center of Integrated Protein Science Munich (CIPS-M) and Division of Clinical Pharmacology, Department of Medicine IV, Klinikum der Universität München, LMU Munich, Germany, Member of the German Center for Lung Research (DZL); German Center for Translational Cancer Research (DKTK), Partner site Munich, Munich, Germany
| | - Tarik Regad
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Silvia Zappavigna
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
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6
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MicroRNAs and Long Noncoding RNAs as Novel Therapeutic Targets in Estrogen Receptor-Positive Breast and Ovarian Cancers. Int J Mol Sci 2021; 22:ijms22084072. [PMID: 33920789 PMCID: PMC8071157 DOI: 10.3390/ijms22084072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 01/27/2023] Open
Abstract
Aromatase inhibitors (AIs) such as anastrozole, letrozole, and exemestane have shown to prevent metastasis and angiogenesis in estrogen receptor (ER)-positive breast and ovarian tumors. They function primarily by reducing estrogen production in ER-positive post-menopausal breast and ovarian cancer patients. Unfortunately, current AI-based therapies often have detrimental side-effects, along with acquired resistance, with increased cancer recurrence. Thus, there is an urgent need to identify novel AIs with fewer side effects and improved therapeutic efficacies. In this regard, we and others have recently suggested noncoding RNAs (ncRNAs), specifically microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), as potential molecular targets for utilization in modulating cancer hallmarks and overcoming drug resistance in several cancers, including ER-positive breast and ovarian cancer. Herein, we describe the disruptive functions of several miRNAs and lncRNAs seen in dysregulated cancer metabolism, with a focus on the gene encoding for aromatase (CYP19A1 gene) and estrogen synthesis as a novel therapeutic approach for treating ER-positive breast and ovarian cancers. Furthermore, we discuss the oncogenic and tumor-suppressive roles of several miRNAs (oncogenic miRNAs: MIR125b, MIR155, MIR221/222, MIR128, MIR2052HG, and MIR224; tumor-suppressive miRNAs: Lethal-7f, MIR27B, MIR378, and MIR98) and an oncogenic lncRNA (MIR2052HG) in aromatase-dependent cancers via transcriptional regulation of the CYP19A1 gene. Additionally, we discuss the potential effects of dysregulated miRNAs and lncRNAs on the regulation of critical oncogenic molecules, such as signal transducer, and activator of transcription 3, β-catenin, and integrins. The overall goal of this review is to stimulate further research in this area and to facilitate the development of ncRNA-based approaches for more efficacious treatments of ER-positive breast and ovarian cancer patients, with a slight emphasis on associated treatment–delivery mechanisms.
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Abstract
The immune system can recognize tumor cells to mount antigen-specific T cell response. Central to the establishment of T cell-mediated adaptive immunity are the inflammatory events that facilitate antigen presentation by stimulating the expression of MHC and costimulatory molecules and the secretion of pro-inflammatory cytokines. Such inflammatory events can be triggered upon cytotoxic treatments that induce immunogenic cancer cell death modalities. However, cancers have acquired a plethora of mechanisms to subvert, or to hide from, host-encoded immunosurveillance. Here, we discuss how tumor intrinsic oncogenic factors subvert desirable intratumoral inflammation by suppressing immunogenic cell death.
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Affiliation(s)
- Samuel T Workenhe
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Jonathan Pol
- Gustave Roussy Comprehensive Cancer Institute, Villejuif, France.,Inserm U1138, Paris, France.,Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre De Recherche Des Cordeliers, Paris, France.,Université De Paris, Paris, France.,Sorbonne Université, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | - Guido Kroemer
- Gustave Roussy Comprehensive Cancer Institute, Villejuif, France.,Inserm U1138, Paris, France.,Equipe 11 Labellisée Par La Ligue Nationale Contre Le Cancer, Centre De Recherche Des Cordeliers, Paris, France.,Université De Paris, Paris, France.,Sorbonne Université, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France.,Institut Universitaire De France, Paris, France.,Pôle De Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.,Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China.,Department of Women's and Children's Health, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
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8
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Wu M, Fu P, Qu L, Liu J, Lin A. Long Noncoding RNAs, New Critical Regulators in Cancer Immunity. Front Oncol 2020; 10:550987. [PMID: 33194608 PMCID: PMC7662117 DOI: 10.3389/fonc.2020.550987] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play crucial roles in various aspects of cellular functions. Recent studies have revealed that lncRNAs are critical players in the immune system by modulating immune cell differentiation and functions, particularly in cancer immunity. Here we systematically summarize how lncRNAs are involved in different processes of the cancer immunity cycle, including immune cell differentiation, proliferation, trafficking, and infiltration. Moreover, the limitations of the current understanding of lncRNA’s functions in cancer immunity are described, such as the complexity of the cancer immunity system, the inclusive functions of lncRNAs in this system, and the associated immune response. In sum, the comprehensive investigation of the roles of lncRNAs in cancer immunity aids in cancer diagnosis and therapies.
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Affiliation(s)
- Minjie Wu
- Breast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Peifen Fu
- Breast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lei Qu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian Liu
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Aifu Lin
- Breast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
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9
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Liu L, Wang Q, Qiu Z, Kang Y, Liu J, Ning S, Yin Y, Pang D, Xu S. Noncoding RNAs: the shot callers in tumor immune escape. Signal Transduct Target Ther 2020; 5:102. [PMID: 32561709 PMCID: PMC7305134 DOI: 10.1038/s41392-020-0194-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 01/17/2023] Open
Abstract
Immunotherapy, designed to exploit the functions of the host immune system against tumors, has shown considerable potential against several malignancies. However, the utility of immunotherapy is heavily limited due to the low response rate and various side effects in the clinical setting. Immune escape of tumor cells may be a critical reason for such low response rates. Noncoding RNAs (ncRNAs) have been identified as key regulatory factors in tumors and the immune system. Consequently, ncRNAs show promise as targets to improve the efficacy of immunotherapy in tumors. However, the relationship between ncRNAs and tumor immune escape (TIE) has not yet been comprehensively summarized. In this review, we provide a detailed account of the current knowledge on ncRNAs associated with TIE and their potential roles in tumor growth and survival mechanisms. This review bridges the gap between ncRNAs and TIE and broadens our understanding of their relationship, providing new insights and strategies to improve immunotherapy response rates by specifically targeting the ncRNAs involved in TIE.
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Affiliation(s)
- Lei Liu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Qin Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Zhilin Qiu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Yujuan Kang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Jiena Liu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Shipeng Ning
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Yanling Yin
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Da Pang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China. .,Heilongjiang Academy of Medical Sciences, Harbin, 150086, China.
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China.
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10
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Zhao Y, Teng H, Yao F, Yap S, Sun Y, Ma L. Challenges and Strategies in Ascribing Functions to Long Noncoding RNAs. Cancers (Basel) 2020; 12:cancers12061458. [PMID: 32503290 PMCID: PMC7352683 DOI: 10.3390/cancers12061458] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/16/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are involved in many physiological and pathological processes, such as development, aging, immunity, and cancer. Mechanistically, lncRNAs exert their functions through interaction with proteins, genomic DNA, and other RNA, leading to transcriptional and post-transcriptional regulation of gene expression, either in cis or in trans; it is often difficult to distinguish between these two regulatory mechanisms. A variety of approaches, including RNA interference, antisense oligonucleotides, CRISPR-based methods, and genetically engineered mouse models, have yielded abundant information about lncRNA functions and underlying mechanisms, albeit with many discrepancies. In this review, we elaborate on the challenges in ascribing functions to lncRNAs based on the features of lncRNAs, including the genomic location, copy number, domain structure, subcellular localization, stability, evolution, and expression pattern. We also describe a framework for the investigation of lncRNA functions and mechanisms of action. Rigorous characterization of cancer-implicated lncRNAs is critical for the identification of bona fide anticancer targets.
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Affiliation(s)
- Yang Zhao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (H.T.); (F.Y.); (S.Y.)
| | - Hongqi Teng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (H.T.); (F.Y.); (S.Y.)
| | - Fan Yao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (H.T.); (F.Y.); (S.Y.)
| | - Shannon Yap
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (H.T.); (F.Y.); (S.Y.)
| | - Yutong Sun
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Li Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (H.T.); (F.Y.); (S.Y.)
- UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence: ; Tel.: +1-713-792-6590
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11
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Galluzzi L, Vitale I, Warren S, Adjemian S, Agostinis P, Martinez AB, Chan TA, Coukos G, Demaria S, Deutsch E, Draganov D, Edelson RL, Formenti SC, Fucikova J, Gabriele L, Gaipl US, Gameiro SR, Garg AD, Golden E, Han J, Harrington KJ, Hemminki A, Hodge JW, Hossain DMS, Illidge T, Karin M, Kaufman HL, Kepp O, Kroemer G, Lasarte JJ, Loi S, Lotze MT, Manic G, Merghoub T, Melcher AA, Mossman KL, Prosper F, Rekdal Ø, Rescigno M, Riganti C, Sistigu A, Smyth MJ, Spisek R, Stagg J, Strauss BE, Tang D, Tatsuno K, van Gool SW, Vandenabeele P, Yamazaki T, Zamarin D, Zitvogel L, Cesano A, Marincola FM. Consensus guidelines for the definition, detection and interpretation of immunogenic cell death. J Immunother Cancer 2020; 8:e000337. [PMID: 32209603 PMCID: PMC7064135 DOI: 10.1136/jitc-2019-000337] [Citation(s) in RCA: 562] [Impact Index Per Article: 140.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2020] [Indexed: 12/20/2022] Open
Abstract
Cells succumbing to stress via regulated cell death (RCD) can initiate an adaptive immune response associated with immunological memory, provided they display sufficient antigenicity and adjuvanticity. Moreover, multiple intracellular and microenvironmental features determine the propensity of RCD to drive adaptive immunity. Here, we provide an updated operational definition of immunogenic cell death (ICD), discuss the key factors that dictate the ability of dying cells to drive an adaptive immune response, summarize experimental assays that are currently available for the assessment of ICD in vitro and in vivo, and formulate guidelines for their interpretation.
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Affiliation(s)
- Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York City, New York, USA
- Sandra and Edward Meyer Cancer Center, New York City, New York, USA
- Caryl and Israel Englander Institute for Precision Medicine, New York City, New York, USA
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut, USA
- Université de Paris, Paris, France
| | - Ilio Vitale
- IIGM - Italian Institute for Genomic Medicine, c/o IRCSS, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Italy
| | - Sarah Warren
- NanoString Technologies, Seattle, Washington, USA
| | - Sandy Adjemian
- VIB Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
| | - Patrizia Agostinis
- Cell Death Research & Therapy (CDRT) Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- VIB-KU Leuven Center for Cancer Biology, KU Leuevn, Leuven, Belgium
| | - Aitziber Buqué Martinez
- Department of Radiation Oncology, Weill Cornell Medical College, New York City, New York, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - George Coukos
- Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | - Sandra Demaria
- Department of Radiation Oncology, Weill Cornell Medical College, New York City, New York, USA
- Sandra and Edward Meyer Cancer Center, New York City, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Eric Deutsch
- Department of Radiation Oncology, Gustave Roussy Cancer Campus, Villejuif, France
- INSERM "Molecular Radiotherapy and therapeutic innovation", U1030 Molecular Radiotherapy, Gustave Roussy Cancer Campus, Villejuif, France
- SIRIC SOCRATES, DHU Torino, Faculté de Medecine, Université Paris-Saclay, Kremlin-Bicêtre, France
| | | | - Richard L Edelson
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut, USA
- Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Silvia C Formenti
- Department of Radiation Oncology, Weill Cornell Medical College, New York City, New York, USA
- Sandra and Edward Meyer Cancer Center, New York City, New York, USA
| | - Jitka Fucikova
- Department of Immunology, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
- Sotio, Prague, Czech Republic
| | - Lucia Gabriele
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Udo S Gaipl
- Universitätsklinikum Erlangen, Erlangen, Germany
| | - Sofia R Gameiro
- Laboratory of Tumor Immunology and Biology, National Cancer Institute/Center for Cancer Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Abhishek D Garg
- Cell Death Research & Therapy (CDRT) Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Encouse Golden
- Department of Radiation Oncology, Weill Cornell Medical College, New York City, New York, USA
- Sandra and Edward Meyer Cancer Center, New York City, New York, USA
| | - Jian Han
- iRepertoire, Inc, Huntsville, Alabama, USA
| | - Kevin J Harrington
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital/Institute of Cancer Research National Institute for Health Biomedical Research Centre, London, UK
| | - Akseli Hemminki
- Cancer Gene Therapy Group, Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - James W Hodge
- Laboratory of Tumor Immunology and Biology, National Cancer Institute/Center for Cancer Research, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Tim Illidge
- University of Manchester, NIHR Manchester Biomedical Research Centre, Christie Hospital, Manchester, UK
| | - Michael Karin
- Department of Pharmacology and Pathology, University of California at San Diego (UCSD) School of Medicine, La Jolla, California, USA
| | - Howard L Kaufman
- Division of Surgical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Replimune, Inc, Woburn, Massachusetts, USA
| | - Oliver Kepp
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
| | - Guido Kroemer
- Université de Paris, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
- Gustave Roussy Comprehensive Cancer Institute, Villejuif, France
- INSERM, U1138, Paris, France
- Sorbonne Université, Paris, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
- Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden
- Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China
| | - Juan Jose Lasarte
- Program of Immunology and Immunotherapy, Centro de Investigación Médica Aplicada (CIMA), University of Navarra, Pamplona, Spain
| | - Sherene Loi
- Division of Research and Clinical Medicine, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Michael T Lotze
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Bioengineering, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Gwenola Manic
- IIGM - Italian Institute for Genomic Medicine, c/o IRCSS, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Italy
| | - Taha Merghoub
- Ludwig Collaborative and Swim Across America Laboratory, MSKCC, New York City, New York, USA
- Weill Cornell Medical College, New York City, New York, USA
- Parker Institute for Cancer Immunotherapy, MSKCC, New York City, New York, USA
| | | | | | - Felipe Prosper
- Hematology and Cell Therapy, Clinica Universidad de Navarra, Pamplona, Spain
| | - Øystein Rekdal
- Lytix Biopharma, Oslo, Norway
- Department of Medical Biology, University of Tromsø, Tromsø, Norway
| | - Maria Rescigno
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
- Humanitas University, Department of Biomedical Sciences, Pieve Emanuele, Milan, Italy
| | - Chiara Riganti
- Department of Oncology, University of Torino, Torino, Italy
- Interdepartmental Research Center of Molecular Biotechnology, University of Torino, Torino, Italy
| | - Antonella Sistigu
- UOSD Immunology and Immunotherapy Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
- Istituto di Patologia Generale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Mark J Smyth
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Radek Spisek
- Department of Immunology, Charles University, 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
- Sotio, Prague, Czech Republic
| | - John Stagg
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Quebec City, Canada
- Institut du Cancer de Montréal, Montréal, Quebec City, Canada
- Faculté de Pharmacie de l'Université de Montréal, Montréal, Quebec City, Canada
| | - Bryan E Strauss
- Centro de Investigação Translacional em Oncologia/LIM24, Instituto do Câncer do Estado de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brasil
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Kazuki Tatsuno
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut, USA
| | | | - Peter Vandenabeele
- VIB Center for Inflammation Research (IRC), Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
- Methusalem program, Ghent University, Ghent, Belgium
| | - Takahiro Yamazaki
- Department of Radiation Oncology, Weill Cornell Medical College, New York City, New York, USA
| | - Dmitriy Zamarin
- Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Laurence Zitvogel
- Gustave Roussy Comprehensive Cancer Institute, Villejuif, France
- Equipe labellisée par la Ligue contre le cancer, Gustave Roussy, Villejuif, France
- Faculty of Medicine, University of Paris Sud/Paris Saclay, Le Kremlin-Bicêtre, France
- INSERM U1015, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
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12
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Abstract
Retinoblastoma (Rb) is the most common ocular pediatric malignancy that arises from the retina and is caused by a mutation of the two alleles of the tumor suppressor gene, RB1. Although early detection provides the opportunity of controlling the primary tumor with effective therapies, metastatic activity is fatal. Non-coding RNAs (ncRNAs) have emerged as important modifiers of a plethora of biological mechanisms including those involved in cancer. They are classified into short and long ncRNAs according to their length. Deregulation of all these molecules has also been shown to play a critical role in Rb pathogenesis and progression. It is believed that ncRNAs can provide new insights into novel regulatory mechanisms associated with clinical pathological characteristics, facilitating the development of therapeutic alternatives for the treatment of Rb. In this review, we describe a variety of ncRNAs, which capable of regulating the most likely candidate genes involved in the tumorigenesis of Rb, could prove useful in analyzing different aspects of this cancer.
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Affiliation(s)
- Meropi Plousiou
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Ivan Vannini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
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13
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Subhash S, Mishra K, Akhade VS, Kanduri M, Mondal T, Kanduri C. H3K4me2 and WDR5 enriched chromatin interacting long non-coding RNAs maintain transcriptionally competent chromatin at divergent transcriptional units. Nucleic Acids Res 2019; 46:9384-9400. [PMID: 30010961 PMCID: PMC6182144 DOI: 10.1093/nar/gky635] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 07/03/2018] [Indexed: 12/21/2022] Open
Abstract
Recently lncRNAs have been implicated in the sub-compartmentalization of eukaryotic genome via genomic targeting of chromatin remodelers. To explore the function of lncRNAs in the maintenance of active chromatin, we characterized lncRNAs from the chromatin enriched with H3K4me2 and WDR5 using chromatin RNA immunoprecipitation (ChRIP). Significant portion of these enriched lncRNAs were arranged in antisense orientation with respect to their protein coding partners. Among these, 209 lncRNAs, commonly enriched in H3K4me2 and WDR5 chromatin fractions, were named as active chromatin associated lncRNAs (active lncCARs). Interestingly, 43% of these active lncCARs map to divergent transcription units. Divergent transcription (XH) units were overrepresented in the active lncCARs as compared to the inactive lncCARs. ChIP-seq analysis revealed that active XH transcription units are enriched with H3K4me2, H3K4me3 and WDR5. WDR5 depletion resulted in the loss of H3K4me3 but not H3K4me2 at the XH promoters. Active XH CARs interact with and recruit WDR5 to XH promoters, and their depletion leads to decrease in the expression of the corresponding protein coding genes and loss of H3K4me2, H3K4me3 and WDR5 at the active XH promoters. This study unravels a new facet of chromatin-based regulation at the divergent XH transcription units by this newly identified class of H3K4me2/WDR5 chromatin enriched lncRNAs.
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Affiliation(s)
- Santhilal Subhash
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg 40530, Sweden
| | - Kankadeb Mishra
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg 40530, Sweden
| | - Vijay Suresh Akhade
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg 40530, Sweden
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Sweden
| | - Tanmoy Mondal
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg 40530, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg 40530, Sweden
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14
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Indovina P, Pentimalli F, Conti D, Giordano A. Translating RB1 predictive value in clinical cancer therapy: Are we there yet? Biochem Pharmacol 2019; 166:323-334. [PMID: 31176618 DOI: 10.1016/j.bcp.2019.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/03/2019] [Indexed: 12/16/2022]
Abstract
The retinoblastoma RB1 gene has been identified in the 80s as the first tumor suppressor. RB1 loss of function, as well alterations in its pathway, occur in most human cancers and often have prognostic value. RB1 has a key role in restraining cell cycle entry and, along with its family members, regulates a myriad of cellular processes and affects cell response to a variety of stimuli, ultimately determining cell fate. Consistently, RB1 status is a crucial determinant of the cell response to antitumoral therapies, impacting on the outcome of both traditional and modern anti-cancer strategies, including precision medicine approaches, such as kinase inhibitors, and immunotherapy. Despite many efforts however, the predictive value of RB1 status in the clinical practice is still underused, mainly owing to the complexity of RB1 function, to differences depending on the cellular context and on the therapeutic strategies, and, not-lastly, to technical issues. Here, we provide an overview of studies analyzing the role of RB1 in response to conventional cytotoxic and cytostatic therapeutic agents in different cancer types, including hormone dependent ones. We also review RB1 predictive value in the response to the last generation CDK4/6 inhibitors, other kinase inhibitors, and immunotherapy and discuss new emerging non-canonical roles of RB1 that could impact on the response to antitumoral treatments.
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Affiliation(s)
- Paola Indovina
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Francesca Pentimalli
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, IRCCS, Fondazione G. Pascale, Napoli 80131, Italy
| | - Daniele Conti
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA; Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA; Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy.
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15
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Zhang X, Wang J, Li J, Chen W, Liu C. CRlncRC: a machine learning-based method for cancer-related long noncoding RNA identification using integrated features. BMC Med Genomics 2018; 11:120. [PMID: 30598114 PMCID: PMC6311943 DOI: 10.1186/s12920-018-0436-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are widely involved in the initiation and development of cancer. Although some computational methods have been proposed to identify cancer-related lncRNAs, there is still a demanding to improve the prediction accuracy and efficiency. In addition, the quick-update data of cancer, as well as the discovery of new mechanism, also underlay the possibility of improvement of cancer-related lncRNA prediction algorithm. In this study, we introduced CRlncRC, a novel Cancer-Related lncRNA Classifier by integrating manifold features with five machine-learning techniques. RESULTS CRlncRC was built on the integration of genomic, expression, epigenetic and network, totally in four categories of features. Five learning techniques were exploited to develop the effective classification model including Random Forest (RF), Naïve bayes (NB), Support Vector Machine (SVM), Logistic Regression (LR) and K-Nearest Neighbors (KNN). Using ten-fold cross-validation, we showed that RF is the best model for classifying cancer-related lncRNAs (AUC = 0.82). The feature importance analysis indicated that epigenetic and network features play key roles in the classification. In addition, compared with other existing classifiers, CRlncRC exhibited a better performance both in sensitivity and specificity. We further applied CRlncRC to lncRNAs from the TANRIC (The Atlas of non-coding RNA in Cancer) dataset, and identified 121 cancer-related lncRNA candidates. These potential cancer-related lncRNAs showed a certain kind of cancer-related indications, and many of them could find convincing literature supports. CONCLUSIONS Our results indicate that CRlncRC is a powerful method for identifying cancer-related lncRNAs. Machine-learning-based integration of multiple features, especially epigenetic and network features, had a great contribution to the cancer-related lncRNA prediction. RF outperforms other learning techniques on measurement of model sensitivity and specificity. In addition, using CRlncRC method, we predicted a set of cancer-related lncRNAs, all of which displayed a strong relevance to cancer as a valuable conception for the further cancer-related lncRNA function studies.
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Affiliation(s)
- Xuan Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, Yunnan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Jun Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, Yunnan, People's Republic of China.,Institute of Medical Sciences, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
| | - Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, Yunnan, People's Republic of China
| | - Wen Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, Yunnan, People's Republic of China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, Yunnan, People's Republic of China.
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16
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Li J, Jiang X, Li Z, Huang L, Zhou Y, Liu Y, Cui Y. Long noncoding RNA GHET1 in human cancer. Clin Chim Acta 2018; 488:111-115. [PMID: 30399371 DOI: 10.1016/j.cca.2018.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 02/06/2023]
Abstract
LncRNAs are a group of noncoding RNAs that are >200 nucleotides in length. These RNAs have no significant protein-coding potential due to the lack of obvious open reading frames. To date, accumulating evidence has demonstrated that dysregulation of lncRNAs exhibits indispensable roles in the pathological processes of human cancers. These RNAs function as either oncogenes or tumor suppressor genes to regulate proliferation, migration and invasion of cancer cells. GHET1, a prominent oncogenic lncRNA, is highly expressed in diverse malignancies. Furthermore, GHET1 performs key functions in carcinogenesis and progression, suggesting that GHET1 is expected to be a prospective biomarker or therapeutic target for cancers. In this review, we provide a summary of the current evidence concerning the biological functions, underlying mechanisms and clinical significance of GHET1 during tumor development.
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Affiliation(s)
- Jinglin Li
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, No.246 Xuefu Avenue, Harbin 150086, China
| | - Xingming Jiang
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, No.246 Xuefu Avenue, Harbin 150086, China
| | - Zhenglong Li
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, No.246 Xuefu Avenue, Harbin 150086, China
| | - Lining Huang
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, No.246 Xuefu Avenue, Harbin 150086, China
| | - Yuanshi Zhou
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, No.246 Xuefu Avenue, Harbin 150086, China
| | - Yueping Liu
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, No.246 Xuefu Avenue, Harbin 150086, China
| | - Yunfu Cui
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, No.246 Xuefu Avenue, Harbin 150086, China.
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17
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Garg AD, Agostinis P. Cell death and immunity in cancer: From danger signals to mimicry of pathogen defense responses. Immunol Rev 2018; 280:126-148. [PMID: 29027218 DOI: 10.1111/imr.12574] [Citation(s) in RCA: 277] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The immunogenicity of cancer cells is an emerging determinant of anti-cancer immunotherapy. Beyond developing immunostimulatory regimens like dendritic cell-based vaccines, immune-checkpoint blockers, and adoptive T-cell transfer, investigators are beginning to focus on the immunobiology of dying cancer cells and its relevance for the success of anticancer immunotherapies. It is currently accepted that cancer cells may die in response to anti-cancer therapies through regulated cell death programs, which may either repress or increase their immunogenic potential. In particular, the induction of immunogenic cancer cell death (ICD), which is hallmarked by the emission of damage-associated molecular patterns (DAMPs); molecules analogous to pathogen-associated molecular patterns (PAMPs) acting as danger signals/alarmins, is of great relevance in cancer therapy. These ICD-associated danger signals favor immunomodulatory responses that lead to tumor-associated antigens (TAAs)-directed T-cell immunity, which paves way for the removal of residual, treatment-resistant cancer cells. It is also emerging that cancer cells succumbing to ICD can orchestrate "altered-self mimicry" i.e. mimicry of pathogen defense responses, on the levels of nucleic acids and/or chemokines (resulting in type I interferon/IFN responses or pathogen response-like neutrophil activity). In this review, we exhaustively describe the main molecular, immunological, preclinical, and clinical aspects of immunosuppressive cell death or ICD (with respect to apoptosis, necrosis and necroptosis). We also provide an extensive historical background of these fields, with special attention to the self/non-self and danger models, which have shaped the field of cell death immunology.
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Affiliation(s)
- Abhishek D Garg
- Cell Death Research & Therapy (CDRT) Laboratory, Department for Cellular and Molecular Medicine, KU Leuven University of Leuven, Leuven, Belgium
| | - Patrizia Agostinis
- Cell Death Research & Therapy (CDRT) Laboratory, Department for Cellular and Molecular Medicine, KU Leuven University of Leuven, Leuven, Belgium
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18
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Wang JX, Yang Y, Li K. Long noncoding RNA DANCR aggravates retinoblastoma through miR-34c and miR-613 by targeting MMP-9. J Cell Physiol 2018; 233:6986-6995. [PMID: 29744877 DOI: 10.1002/jcp.26621] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/28/2018] [Indexed: 12/31/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been identified to play vital roles in cancers, including human retinoblastoma (RB). However, the deepgoing mechanism is still ambiguous. In present study, we investigate the biological role of lncRNA DANCR (differentiation antagonizing non-protein coding RNA) in carcinogenesis of RB. Results revealed that DANCR was up-regulated in RB tissue and cell lines. Moreover, the ectopic overexpression of DANCR indicated poor overall survivals and disease free survival (DFS) for RB patients. In vitro and in vivo experiments, DANCR knockdown suppress the proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) correlated protein (N-cadherin, Vimentin) of RB cells. Bioinformatics analysis predicted that miR-34c and miR-613 targeted with 3'-UTR of DANCR, besides, miR-34c and miR-613 also targeted with 3'-UTR of MMP-9, which was validated by luciferase reporter assay. Functional experiments demonstrated that miR-34c and miR-613 could reverse the oncogenic function of DANCR in RB tumorigenesis. In conclusion, our results reveal that DANCR function as competing endogenous RNA (ceRNA) for miR-34c and miR-613 to modulate progression and metastasis in RB oncogenesis via targeting MMP-9, presenting the in-depth regulation of DANCR in RB and providing a novel insight for ceRNA mechanism for RB.
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Affiliation(s)
- Jing-Xian Wang
- Department of General Surgery Five, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Yuan Yang
- Examination Room of Eye Department, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Kun Li
- Pediatric Department of Ophthalmology, Cangzhou Central Hospital, Cangzhou, Hebei, China
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19
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Cruickshank B, Giacomantonio M, Marcato P, McFarland S, Pol J, Gujar S. Dying to Be Noticed: Epigenetic Regulation of Immunogenic Cell Death for Cancer Immunotherapy. Front Immunol 2018; 9:654. [PMID: 29666625 PMCID: PMC5891575 DOI: 10.3389/fimmu.2018.00654] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/16/2018] [Indexed: 12/13/2022] Open
Abstract
Immunogenic cell death (ICD) activates both innate and adaptive arms of the immune system during apoptotic cancer cell death. With respect to cancer immunotherapy, the process of ICD elicits enhanced adjuvanticity and antigenicity from dying cancer cells and consequently, promotes the development of clinically desired antitumor immunity. Cancer ICD requires the presentation of various "hallmarks" of immunomodulation, which include the cell-surface translocation of calreticulin, production of type I interferons, and release of high-mobility group box-1 and ATP, which through their compatible actions induce an immune response against cancer cells. Interestingly, recent reports investigating the use of epigenetic modifying drugs as anticancer therapeutics have identified several connections to ICD hallmarks. Epigenetic modifiers have a direct effect on cell viability and appear to fundamentally change the immunogenic properties of cancer cells, by actively subverting tumor microenvironment-associated immunoevasion and aiding in the development of an antitumor immune response. In this review, we critically discuss the current evidence that identifies direct links between epigenetic modifications and ICD hallmarks, and put forward an otherwise poorly understood role for epigenetic drugs as ICD inducers. We further discuss potential therapeutic innovations that aim to induce ICD during epigenetic drug therapy, generating highly efficacious cancer immunotherapies.
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Affiliation(s)
| | | | - Paola Marcato
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Sherri McFarland
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, United States
- Department of Chemistry, Acadia University, Wolfville, NS, Canada
| | - Jonathan Pol
- Gustave Roussy Comprehensive Cancer Institute, Villejuif, France
- INSERM, U1138, Paris, France
- Equipe 11 labellisée par la Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
- Université Paris Descartes, Université Sorbonne Paris Cité, Paris, France
- Université Pierre et Marie Curie, Paris, France
| | - Shashi Gujar
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Department of Biology, Dalhousie University, Halifax, NS, Canada
- Centre for Innovative and Collaborative Health Services Research, IWK Health Centre, Halifax, NS, Canada
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20
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Romano E, Rufo N, Korf H, Mathieu C, Garg AD, Agostinis P. BNIP3 modulates the interface between B16-F10 melanoma cells and immune cells. Oncotarget 2018; 9:17631-17644. [PMID: 29707136 PMCID: PMC5915144 DOI: 10.18632/oncotarget.24815] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 02/27/2018] [Indexed: 01/10/2023] Open
Abstract
The hypoxia responsive protein BNIP3, plays an important role in promoting cell death and/or autophagy, ultimately resulting in a cancer type-dependent, tumour-enhancer or tumour-suppressor activity. We previously reported that in melanoma cells, BNIP3 regulates cellular morphology, mitochondrial clearance, cellular viability and maintains protein expression of CD47, a pro-cancerous, immunosuppressive 'don't eat me' signal. Surface exposed CD47 is often up-regulated by cancer cells to avoid clearance by phagocytes and to suppress immunogenic cell death (ICD) elicited by anticancer therapies. However, whether melanoma-associated BNIP3 modulates CD47-associated immunological effects or ICD has not been explored properly. To this end, we evaluated the impact of the genetic ablation of BNIP3 (i.e. BNIP3KD) in melanoma cells, on macrophage-based phagocytosis, polarization and chemotaxis. Additionally, we tested its effects on crucial determinants of chemotherapy-induced ICD (i.e. danger signals), as well as in vivo anticancer vaccination effect. Interestingly, loss of BNIP3 reduced the expression of CD47 both in normoxic and hypoxic conditions while macrophage phagocytosis and chemotaxis were accentuated only when BNIP3KD melanoma cells were exposed to hypoxia. Moreover, when exposed to the ICD inducer mitoxantrone, the loss of melanoma cell-associated BNIP3 did not alter apoptosis induction, but significantly prevented ATP secretion and reduced phagocytic clearance of dying cells. In line with this, prophylactic vaccination experiments showed that the loss of BNIP3 tends to increase the intrinsic resistance of B16-F10 melanoma cells to ICD-associated anticancer vaccination effect in vivo. Thus, normoxic vs. hypoxic and live vs. dying cell contexts influence the ultimate immunomodulatory roles of melanoma cell-associated BNIP3.
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Affiliation(s)
- Erminia Romano
- Laboratory for Cell Death Research and Therapy (CDRT), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Nicole Rufo
- Laboratory for Cell Death Research and Therapy (CDRT), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Hannelie Korf
- Laboratory of Hepatology, Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), KU Leuven, Leuven, Belgium
- Laboratory of Clinical and Experimental Endocrinology (CEE), Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), KU Leuven, Leuven, Belgium
| | - Chantal Mathieu
- Laboratory of Clinical and Experimental Endocrinology (CEE), Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), KU Leuven, Leuven, Belgium
| | - Abhishek D Garg
- Laboratory for Cell Death Research and Therapy (CDRT), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Patrizia Agostinis
- Laboratory for Cell Death Research and Therapy (CDRT), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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21
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Yu WD, Wang H, He QF, Xu Y, Wang XC. Long noncoding RNAs in cancer-immunity cycle. J Cell Physiol 2018; 233:6518-6523. [PMID: 29574911 DOI: 10.1002/jcp.26568] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/27/2018] [Indexed: 12/29/2022]
Abstract
The imbalance of immune status in cancer microenvironment plays an important role in the development and progression of cancer. Immunotherapy based on this has become an important field of cancer research in recent years. Many studies on long noncoding RNA (lncRNA) in cancer have focus on its regulation in cancer development and metastasis. Recent studies have suggested that lncRNAs play crucial roles in different phases of cancer immunity, including antigen releasing, antigen presentation, immune activation, immune cells migration, infiltrating into cancer tissues, and killing cancer cells. The functional studies of lncRNAs in cancer immuntity revealed the complicated molecular mechanisms in cancer immunity from a new point of view, which may provide novel potential targets for cancer immunotherapies. Based on the classical cancer-immunity cycle theory, we review the recent studies on the functions and mechanisms of immune-related lncRNAs in different stages of cancer immunity, to summarize the relationship between lncRNAs, and cancer immunity and to provide a framework for further research.
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Affiliation(s)
- Wei-Di Yu
- Liver Transplantation Center of The First Affiliated Hospital and Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P. R. China
| | - Huanhuan Wang
- Nursing Department, Dongnan University Affiliated Xuzhou Center Hospital, Xuzhou, Jiangsu Province, P. R. China
| | - Qi-Feng He
- Liver Transplantation Center of The First Affiliated Hospital and Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P. R. China
| | - Yong Xu
- Department of Nephrology, Huai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu Province, P. R. China
| | - Xiao-Chen Wang
- Liver Transplantation Center of The First Affiliated Hospital and Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P. R. China
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22
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Quan H, Fan Q, Li C, Wang YY, Wang L. The transcriptional profiles and functional implications of long non-coding RNAs in the unfolded protein response. Sci Rep 2018; 8:4981. [PMID: 29563563 PMCID: PMC5862980 DOI: 10.1038/s41598-018-23289-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 03/08/2018] [Indexed: 01/03/2023] Open
Abstract
The unfolded protein response (UPR) is activated, when the folding capacity is compromised in the endoplasmic reticulum (ER). To date, most studies focused on the coding genes and microRNAs in UPR. Other non-coding RNAs affected by UPR and their roles in UPR have not been systematically studied. Long noncoding RNAs (lncRNAs) are increasingly recognized as powerful epigenetic regulators. In this study, we transcriptomically profiled the lncRNAs and mRNAs from mouse embryonic fibroblasts under ER stress, and identified many differentially expressed lncRNAs and mRNAs. Genomic location and mRNA-lncRNA co-expression analyses predicted a number of lncRNAs, which potentially regulate the expression of UPR genes. In particular, FR229754, an exonic sense lncRNA, is significantly up-regulated in UPR. FR229754 overlaps with Sel1l, and their expressions correlated with each other. Sel1l is involved in the ER-associated protein degradation. Silencing of FR229754 did not much affect the expression of Sel1l, but markedly reduced the levels of BiP/GRP78/Hspa5, a major ER chaperon up-regulated in UPR. Probing with pathway-specific inhibitors showed that up-regulation of FR229754 and Sel1 depended on the activation of PERK. Together, our study identified a number of candidate lncRNAs and paved the way for future characterization of their functions in UPR.
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Affiliation(s)
- Hongyang Quan
- Department of Physiology, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, 5 Dong Dan San Tiao, Beijing, 100005, China.,Patent Examination Corporation, State Intellectual Property Office, 2028 Tianfu Avenue South, Chengdu, 610213, China
| | - Qianqian Fan
- Department of Physiology, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, 5 Dong Dan San Tiao, Beijing, 100005, China.,National Research Institute for Family Planning, 12 Da Hui Si, Beijing, 100080, China
| | - Chuang Li
- Department of Physiology, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, 5 Dong Dan San Tiao, Beijing, 100005, China
| | - Yan-Ying Wang
- Department of Physiology, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, 5 Dong Dan San Tiao, Beijing, 100005, China
| | - Lin Wang
- Department of Physiology, Institute of Basic Medical Sciences, School of Basic Medicine Peking Union Medical College, Chinese Academy of Medical Sciences, 5 Dong Dan San Tiao, Beijing, 100005, China.
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23
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Vučićević D, Gehre M, Dhamija S, Friis-Hansen L, Meierhofer D, Sauer S, Ørom UA. The long non-coding RNA PARROT is an upstream regulator of c-Myc and affects proliferation and translation. Oncotarget 2017; 7:33934-47. [PMID: 27129154 PMCID: PMC5085129 DOI: 10.18632/oncotarget.8985] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 04/16/2016] [Indexed: 12/26/2022] Open
Abstract
Long non-coding RNAs are important regulators of gene expression and signaling pathways. The expression of long ncRNAs is dysregulated in cancer and other diseases. The identification and characterization of long ncRNAs is often challenging due to their low expression level and localization to chromatin. Here, we identify a functional long ncRNA, PARROT (Proliferation Associated RNA and Regulator Of Translation) transcribed by RNA polymerase II and expressed at a relatively high level in a number of cell lines. The PARROT long ncRNA is associated with proliferation in both transformed and normal cell lines. We characterize the long ncRNA PARROT as an upstream regulator of c-Myc affecting cellular proliferation and translation using RNA sequencing and mass spectrometry following depletion of the long ncRNA. PARROT is repressed during senescence of human mammary epithelial cells and overexpressed in some cancers, suggesting an important association with proliferation through regulation of c-Myc. With this study, we add to the knowledge of cytoplasmic functional long ncRNAs and extent the long ncRNA-Myc regulatory network in transformed and normal cells.
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Affiliation(s)
- Dubravka Vučićević
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Maja Gehre
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,EMBL, Heidelberg, Germany
| | - Sonam Dhamija
- Medizinische Hochschule Hannover Institute of Biochemistry, Hannover, Germany.,RNA Biology and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
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24
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Li J, Li Z, Leng K, Xu Y, Ji D, Huang L, Cui Y, Jiang X. ZEB1-AS1: A crucial cancer-related long non-coding RNA. Cell Prolif 2017; 51. [PMID: 29226522 DOI: 10.1111/cpr.12423] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 11/15/2017] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) recently emerge as a novel class of non-coding RNAs (ncRNAs) with larger than 200 nucleotides in length. Due to lack an obvious open reading frame, lncRNAs have no or limited protein-coding potential. To date, accumulating evidence indicates the vital regulatory function of lncRNAs in pathological processes of human diseases, especially in carcinogenesis and development. Deregulation of lncRNAs not only alters cellular biological behavior, such as proliferation, migration and invasion, but also represents the poor clinical outcomes. Zinc finger E-box binding homeobox 1 antisense 1 (ZEB1-AS1), an outstanding cancer-related lncRNA, is identified as an oncogenic regulator in diverse malignancies. Dysregulation of ZEB1-AS1 has been demonstrated to exhibit a pivotal role in tumorigenesis and progression, suggesting its potential clinical value as a promising biomarker or therapeutic target for cancers. In this review, we make a summary on the current findings regarding the biological functions, underlying mechanisms and clinical significance of ZEB1-AS1 in cancer progression.
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Affiliation(s)
- Jinglin Li
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhenglong Li
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Kaiming Leng
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yi Xu
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Daolin Ji
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lining Huang
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yunfu Cui
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xingming Jiang
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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25
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Goyal A, Myacheva K, Groß M, Klingenberg M, Duran Arqué B, Diederichs S. Challenges of CRISPR/Cas9 applications for long non-coding RNA genes. Nucleic Acids Res 2017; 45:e12. [PMID: 28180319 PMCID: PMC5388423 DOI: 10.1093/nar/gkw883] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 09/01/2016] [Accepted: 09/23/2016] [Indexed: 12/14/2022] Open
Abstract
The CRISPR/Cas9 system provides a revolutionary genome editing tool for all areas of molecular biology. In long non-coding RNA (lncRNA) research, the Cas9 nuclease can delete lncRNA genes or introduce RNA-destabilizing elements into their locus. The nuclease-deficient dCas9 mutant retains its RNA-dependent DNA-binding activity and can modulate gene expression when fused to transcriptional repressor or activator domains. Here, we systematically analyze whether CRISPR approaches are suitable to target lncRNAs. Many lncRNAs are derived from bidirectional promoters or overlap with promoters or bodies of sense or antisense genes. In a genome-wide analysis, we find only 38% of 15929 lncRNA loci are safely amenable to CRISPR applications while almost two-thirds of lncRNA loci are at risk to inadvertently deregulate neighboring genes. CRISPR- but not siPOOL or Antisense Oligo (ASO)-mediated targeting of lncRNAs NOP14-AS1, LOC389641, MNX1-AS1 or HOTAIR also affects their respective neighboring genes. Frequently overlooked, the same restrictions may apply to mRNAs. For example, the tumor suppressor TP53 and its head-to-head neighbor WRAP53 are jointly affected by the same sgRNAs but not siPOOLs. Hence, despite the advantages of CRISPR/Cas9 to modulate expression bidirectionally and in cis, approaches based on ASOs or siPOOLs may be the better choice to target specifically the transcript from complex loci.
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Affiliation(s)
- Ashish Goyal
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Ksenia Myacheva
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Cancer Research, Dept. of Thoracic Surgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Matthias Groß
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Marcel Klingenberg
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), University of Heidelberg, Heidelberg, Germany
| | - Berta Duran Arqué
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sven Diederichs
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Division of Cancer Research, Dept. of Thoracic Surgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), University of Heidelberg, Heidelberg, Germany
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26
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Garg AD, More S, Rufo N, Mece O, Sassano ML, Agostinis P, Zitvogel L, Kroemer G, Galluzzi L. Trial watch: Immunogenic cell death induction by anticancer chemotherapeutics. Oncoimmunology 2017; 6:e1386829. [PMID: 29209573 DOI: 10.1080/2162402x.2017.1386829] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 09/26/2017] [Indexed: 12/21/2022] Open
Abstract
The expression "immunogenic cell death" (ICD) refers to a functionally unique form of cell death that facilitates (instead of suppressing) a T cell-dependent immune response specific for dead cell-derived antigens. ICD critically relies on the activation of adaptive responses in dying cells, culminating with the exposure or secretion of immunostimulatory molecules commonly referred to as "damage-associated molecular patterns". Only a few agents can elicit bona fide ICD, including some clinically established chemotherapeutics such as doxorubicin, epirubicin, idarubicin, mitoxantrone, bleomycin, bortezomib, cyclophosphamide and oxaliplatin. In this Trial Watch, we discuss recent progress on the development of ICD-inducing chemotherapeutic regimens, focusing on studies that evaluate clinical efficacy in conjunction with immunological biomarkers.
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Affiliation(s)
- Abhishek D Garg
- Cell Death Research & Therapy (CDRT) Lab, Department of Cellular & Molecular Medicine, KU Leuven University of Leuven, Leuven, Belgium
| | - Sanket More
- Cell Death Research & Therapy (CDRT) Lab, Department of Cellular & Molecular Medicine, KU Leuven University of Leuven, Leuven, Belgium
| | - Nicole Rufo
- Cell Death Research & Therapy (CDRT) Lab, Department of Cellular & Molecular Medicine, KU Leuven University of Leuven, Leuven, Belgium
| | - Odeta Mece
- Cell Death Research & Therapy (CDRT) Lab, Department of Cellular & Molecular Medicine, KU Leuven University of Leuven, Leuven, Belgium
| | - Maria Livia Sassano
- Cell Death Research & Therapy (CDRT) Lab, Department of Cellular & Molecular Medicine, KU Leuven University of Leuven, Leuven, Belgium
| | - Patrizia Agostinis
- Cell Death Research & Therapy (CDRT) Lab, Department of Cellular & Molecular Medicine, KU Leuven University of Leuven, Leuven, Belgium
| | - Laurence Zitvogel
- Gustave Roussy Comprehensive Cancer Institute, Villejuif, France.,INSERM, Villejuif, France.,Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France.,Université Paris Sud/Paris XI, Le Kremlin-Bicêtre, France
| | - Guido Kroemer
- Université Paris Descartes/Paris V, Paris, France.,Université Pierre et Marie Curie/Paris VI, Paris, France.,Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France.,Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden.,Pôle de Biologie, Hopitâl Européen George Pompidou, Paris, France
| | - Lorenzo Galluzzi
- Université Paris Descartes/Paris V, Paris, France.,Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA.,Sandra and Edward Meyer Cancer Center, New York, NY, USA
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27
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Schneider K, Bol V, Grégoire V. Lack of differences in radiation-induced immunogenicity parameters between HPV-positive and HPV-negative human HNSCC cell lines. Radiother Oncol 2017; 124:411-417. [PMID: 28916224 DOI: 10.1016/j.radonc.2017.08.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 08/23/2017] [Accepted: 08/25/2017] [Indexed: 01/11/2023]
Abstract
BACKGROUND AND PURPOSE Clinical studies indicate that patients with HPV/p16-associated head & neck squamous cell carcinoma (HNSCC) represent a subgroup with a better prognosis and improved response to conventional radiotherapy. Involvement of immune-based factors has been hypothesized. In the present study, we investigated radiation-induced differences in release of damage associated molecular patterns (DAMPs), cytokines and activation of dendritic cells (DCs) in HPV-positive and negative HNSCC cancer cell lines. MATERIAL AND METHODS Calreticulin (CRT) exposure was detected on cancer cell surface. ATP, HMGB1 and cytokines were measured in culture supernatants. Maturation marker CD83 surface exposure was determined on DCs after co-incubation with irradiated tumor cells. RESULTS There was no increase in DAMPs and cytokine profiles after radiation treatment and no difference between HPV+ and HPV- cell lines. The HPV/p16-positive SCC90 cells showed a trend for increased total CRT, HMGB1, and number of cytokines compared to all other cell lines. None of the irradiated cancer cell lines could affect DC maturation. CONCLUSIONS Radiation treatment did not increase immunogenicity of HNSCC cell lines assessed by membrane CRT, ATP, HMGB1, cytokines production, and by activation of immature DCs. There was no difference between HPV-positive and HPV-negative cell lines.
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Affiliation(s)
- Karolin Schneider
- Center for Molecular Imaging, Radiotherapy and Oncology, Institute for Experimental and Clinical Research, Université Catholique de Louvain, Brussels, Belgium
| | - Vanesa Bol
- Center for Molecular Imaging, Radiotherapy and Oncology, Institute for Experimental and Clinical Research, Université Catholique de Louvain, Brussels, Belgium
| | - Vincent Grégoire
- Center for Molecular Imaging, Radiotherapy and Oncology, Institute for Experimental and Clinical Research, Université Catholique de Louvain, Brussels, Belgium; Radiation Oncology Department, St-Luc University Hospital, Brussels, Belgium.
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28
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Li J, Li Z, Zheng W, Li X, Wang Z, Cui Y, Jiang X. LncRNA-ATB: An indispensable cancer-related long noncoding RNA. Cell Prolif 2017; 50. [PMID: 28884871 DOI: 10.1111/cpr.12381] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/06/2017] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES Long non-coding RNAs (lncRNAs) are a group of non-protein-coding RNAs that are greater than 200 nucleotides in length. Increasing evidence indicates that lncRNAs, which may serve as either oncogenes or tumour suppressor genes, play a vital role in the pathophysiology of human diseases, especially in tumourigenesis and progression. Deregulation of lncRNAs impacts different cellular processes, such as proliferation, dedifferentiation, migration, invasion and anti-apoptosis. The aim of this review was to explore the molecular mechanism and clinical significance of long non-coding RNA-activated by transforming growth factor β (lncRNA-ATB) in various types of cancers. MATERIALS AND METHODS In this review, we summarize and analyze current studies concerning the biological functions and mechanisms of lncRNA-ATB in tumour development. The related studies were obtained through a systematic search of Pubmed, Web of Science, Embase and Cochrane Library. RESULTS Long non-coding RNAs-ATB is a novel cancer-related lncRNA that was recently found to exhibit aberrant expression in a variety of malignancies, including hepatocellular carcinoma, colorectal cancer, gastric cancer, and lung cancer. Dysregulation of lncRNA-ATB has been shown to contribute to proliferation, migration and invasion of cancer cells. Long non-coding RNAs-ATB promotes tumourigenesis and progression mainly through competitively binding miRNAs to induce epithelial-mesenchymal transition (EMT). CONCLUSIONS Long non-coding RNAs-ATB likely represents a feasible cancer biomarker or therapeutic target.
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Affiliation(s)
- Jinglin Li
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhenglong Li
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wangyang Zheng
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinheng Li
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhidong Wang
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yunfu Cui
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xingming Jiang
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
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29
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McMahon M, Samali A, Chevet E. Regulation of the unfolded protein response by noncoding RNA. Am J Physiol Cell Physiol 2017. [DOI: 10.1152/ajpcell.00293.2016] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells are exposed to various intrinsic and extrinsic stresses in both physiological and pathological conditions. To adapt to those conditions, cells have evolved various mechanisms to cope with the disturbances in protein demand, largely through the unfolded protein response (UPR) in the endoplasmic reticulum (ER), but also through the integrated stress response (ISR). Both responses initiate downstream signaling to transcription factors that, in turn, trigger adaptive programs and/or in the case of prolonged stress, cell death mechanisms. Recently, noncoding RNAs, including microRNA and long noncoding RNA, have emerged as key players in the stress responses. These noncoding RNAs act as both regulators and effectors of the UPR and fine-tune the output of the stress signaling pathways. Although much is known about the UPR and the cross talk that exists between pathways, the contribution of small noncoding RNA has not been fully assessed. Herein we bring together and review the current known functions of noncoding RNA in regulating adaptive pathways in both physiological and pathophysiological conditions, illustrating how they operate within the known UPR functions and contribute to diverse cellular outcomes.
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Affiliation(s)
- Mari McMahon
- INSERM U1242 “Chemistry, Oncogenesis, Stress, Signalling,” Université de Rennes 1, Rennes, France
- Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France; and
- Apoptosis Research Centre, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Afshin Samali
- Apoptosis Research Centre, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Eric Chevet
- INSERM U1242 “Chemistry, Oncogenesis, Stress, Signalling,” Université de Rennes 1, Rennes, France
- Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France; and
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30
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Wiedmeier JE, Ohlrich A, Chu A, Rountree MR, Turker MS. Induction of the long noncoding RNA NBR2 from the bidirectional BRCA1 promoter under hypoxic conditions. Mutat Res 2017; 796:13-19. [PMID: 28249151 DOI: 10.1016/j.mrfmmm.2017.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 01/27/2017] [Accepted: 02/09/2017] [Indexed: 06/06/2023]
Abstract
BRCA1 plays an important role in preventing breast cancer and is often silenced or repressed in sporadic cancer. The BRCA1 promoter is bidirectional: it drives transcription of the long non-coding (lnc) NBR2 transcript in the opposite orientation relative to the BRCA1 transcript. Hypoxic conditions repress BRCA1 transcription, but their effect on expression of the NBR2 transcript has not been reported. We used quantitative RT-PCR to measure BRCA1 and NBR2 transcript levels in 0% and 1% oxygen in MCF-7 breast cancer cells and found that NBR2 transcript levels increased as a function of time under hypoxic conditions, whereas BRCA1 mRNA levels were repressed. Hypoxic conditions were ineffective in reducing BRCA1 mRNA in the UACC-3199 breast cancer cell line, which is reported to have an epigenetically silenced BRCA1 promoter, even though appreciable levels of BRCA1 and NBR2 mRNA were detected. Significant recovery back to baseline RNA levels occurred within 48h after the MCF-7 cells were restored to normoxic conditions. We used a construct with the 218bp minimal BRCA1 promoter linked to marker genes to show that this minimal promoter repressed expression bidirectionally under hypoxic conditions, which suggests that the elements necessary for induction of NBR2 are located elsewhere.
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Affiliation(s)
- J Erin Wiedmeier
- University of Utah School of Medicine, Salt Lake City, UT 84132, United States
| | - Anna Ohlrich
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, 97239, United States
| | - Adrian Chu
- University of Utah School of Medicine, Salt Lake City, UT 84132, United States
| | | | - Mitchell S Turker
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, 97239, United States; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, United States.
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31
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Chen X, Fosco D, Kline DE, Kline J. Calreticulin promotes immunity and type I interferon-dependent survival in mice with acute myeloid leukemia. Oncoimmunology 2017; 6:e1278332. [PMID: 28507789 PMCID: PMC5414882 DOI: 10.1080/2162402x.2016.1278332] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 12/24/2016] [Accepted: 12/28/2016] [Indexed: 12/12/2022] Open
Abstract
Exposure of cancer cells to particular chemotherapeutic agents or γ-irradiation induces a form of cell death that stimulates an immune response in mice. This “immunogenic cell death” requires calreticulin (CRT) translocation to the plasma membrane, which has been shown to promote cancer cell phagocytosis. However, it remains unclear whether the effect of CRT on cancer cell phagocytosis is alone sufficient to affect tumor immunity. Acute myeloid leukemia (AML) cells expressing cell-surface CRT were generated in order to characterize the mechanism(s) through which CRT activates tumor immune responses. Potent immune-mediated control or rejection of AML was observed in mice with CRT-expressing leukemia. The “CRT effect” was ultimately T-cell dependent, but dendritic cells (DCs), and CD8α+ DCs in particular, were also necessary, indicating that CRT might act directly on these DCs. CRT-expressing AML cells were slightly more susceptible to phagocytosis by DCs in vivo, but this effect was unlikely to explain the potent immunity observed. CRT did not affect classical DC maturation markers, but induced expression of type I interferon (IFN), which was critical for its positive effect on survival. In conclusion, CRT functions as a “danger signal” that promotes a host type I IFN response associated with the induction of potent leukemia-specific T-cell immunity.
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Affiliation(s)
- Xiufen Chen
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Dominick Fosco
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Douglas E Kline
- Department of Medicine, University of Chicago, Chicago, IL, USA.,Committee on Immunology, University of Chicago, Chicago, IL, USA
| | - Justin Kline
- Department of Medicine, University of Chicago, Chicago, IL, USA.,Committee on Immunology, University of Chicago, Chicago, IL, USA.,University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
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Garg AD, Elsen S, Krysko DV, Vandenabeele P, de Witte P, Agostinis P. Resistance to anticancer vaccination effect is controlled by a cancer cell-autonomous phenotype that disrupts immunogenic phagocytic removal. Oncotarget 2016; 6:26841-60. [PMID: 26314964 PMCID: PMC4694957 DOI: 10.18632/oncotarget.4754] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/10/2015] [Indexed: 12/22/2022] Open
Abstract
Immunogenic cell death (ICD) is a well-established instigator of ‘anti-cancer vaccination-effect (AVE)’. ICD has shown considerable preclinical promise, yet there remain subset of cancer patients that fail to respond to clinically-applied ICD inducers. Non-responsiveness to ICD inducers could be explained by the existence of cancer cell-autonomous, anti-AVE resistance mechanisms. However such resistance mechanisms remain poorly investigated. In this study, we have characterized for the first time, a naturally-occurring preclinical cancer model (AY27) that exhibits intrinsic anti-AVE resistance despite treatment with ICD inducers like mitoxantrone or hypericin-photodynamic therapy. Further mechanistic analysis revealed that this anti-AVE resistance was associated with a defect in exposing the important ‘eat me’ danger signal, surface-calreticulin (ecto-CRT/CALR). In an ICD setting, this defective ecto-CRT further correlated with severely reduced phagocytic clearance of AY27 cells as well as the failure of these cells to activate AVE. Defective ecto-CRT in response to ICD induction was a result of low endogenous CRT protein levels (i.e. CRTlow-phenotype) in AY27 cells. Exogenous reconstitution of ecto-rCRT (recombinant-CRT) improved the phagocytic removal of ICD inducer-treated AY27 cells, and importantly, significantly increased their AVE-activating ability. Moreover, we found that a subset of cancer patients of various cancer-types indeed possessed CALRlow or CRTlow-tumours. Remarkably, we found that tumoural CALRhigh-phenotype was predictive of positive clinical responses to therapy with ICD inducers (radiotherapy and paclitaxel) in lung and ovarian cancer patients, respectively. Furthermore, only in the ICD clinical setting, tumoural CALR levels positively correlated with the levels of various phagocytosis-associated genes relevant for phagosome maturation or processing. Thus, we reveal the existence of a cancer cell-autonomous, anti-AVE or anti-ICD resistance mechanism that has profound clinical implications for anticancer immunotherapy and cancer predictive biomarker analysis.
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Affiliation(s)
- Abhishek D Garg
- Cell Death Research & Therapy (CDRT) Unit, Department of Cellular and Molecular Medicine, KU Leuven University of Leuven, Leuven, Belgium
| | - Sanne Elsen
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical Sciences, KU Leuven, Leuven, Belgium
| | - Dmitri V Krysko
- Molecular Signaling and Cell Death Unit, Department for Molecular Biomedical Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Peter Vandenabeele
- Molecular Signaling and Cell Death Unit, Department for Molecular Biomedical Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Peter de Witte
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical Sciences, KU Leuven, Leuven, Belgium
| | - Patrizia Agostinis
- Cell Death Research & Therapy (CDRT) Unit, Department of Cellular and Molecular Medicine, KU Leuven University of Leuven, Leuven, Belgium
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Stoll G, Iribarren K, Michels J, Leary A, Zitvogel L, Cremer I, Kroemer G. Calreticulin expression: Interaction with the immune infiltrate and impact on survival in patients with ovarian and non-small cell lung cancer. Oncoimmunology 2016; 5:e1177692. [PMID: 27622029 DOI: 10.1080/2162402x.2016.1177692] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 04/05/2016] [Accepted: 04/06/2016] [Indexed: 10/21/2022] Open
Abstract
Loss of expression of calreticulin (CALR) has been detected by immunohistochemistry in a fraction of non-small cell lung cancers (NSCLC) and has been demonstrated to have a major negative prognostic impact on overall patient survival. Here, we analyzed the impact of CALR expression levels detected by microarray finding a positive correlation between CALR and the expression of a metagene indicating the presence of cytotoxic T lymphocytes (CTL) in NSCLC and ovarian cancer. In addition, we detected a positive correlation with a metagene suggestive of activated dendritic cell (aDC) infiltration in ovarian cancer. Combination of two parameters (CALR + DC (dendritic cell) in NSCL and CALR + aDC in ovarian cancer) or three parameters (CALR + CTL + DC in NSCL and CALR + CTL + aDC in ovarian cancer) had a significant impact on overall patient survival in NSCL (Adenoconsortium) and ovarian cancer (TCGA collection), allowing the stratification of patients in high-risk and low-risk groups. In addition, CALR and aDC alone have a significant impact on overall survival in ovarian cancer. In contrast, in mammary, colorectal and prostate cancer, CALR had no impact on patient survival if analyzed alone or in combination with the immune infiltrate. In addition, CALR correlates with CTL infiltrate in three cancer types (colorectal, breast, ovarian). Altogether, these results support the contention that, at least in some cancers, loss of CALR expression may negatively affect immunosurveillance, thereby reducing patient survival.
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Affiliation(s)
- Gautier Stoll
- Equipe 11 labellisée Ligue contre le Cancer, Center de Recherche des Cordeliers, INSERM U 1138, 15 rue de l'Ecole de Médecine, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 15 rue de l'Ecole de Médecine, Paris, France; Université Pierre et Marie Curie, 15 rue de l'Ecole de Médecine, Paris, France
| | - Kristina Iribarren
- Université Paris Descartes, Sorbonne Paris Cité, 15 rue de l'Ecole de Médecine, Paris, France; Université Pierre et Marie Curie, 15 rue de l'Ecole de Médecine, Paris, France; Laboratory "Cancer, Immune control and escape," Center de Recherche des Cordeliers, INSERM U 1138, 15 rue de l'Ecole de Médecine, Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France
| | - Judith Michels
- Department of Medical Oncology, Gustave Roussy Cancer Campus (GRCC) , 114 rue Edouard Vaillant , Villejuif, France
| | - Alexandra Leary
- Department of Medical Oncology, Gustave Roussy Cancer Campus (GRCC), 114 rue Edouard Vaillant, Villejuif, France; Laboratory 'Predictive Biomarkers and New Therapeutic Strategies in Oncology' INSERM U981, Gustave Roussy Cancer Campus, 114 rue Edouard Vaillant, Villejuif, France
| | - Laurence Zitvogel
- Université Paris Sud, Université Paris Saclay, Kremlin Bicêtre, France; Institut National de la Santé Et de la Recherche Medicale (INSERM), U1015, GRCC, Villejuif, France; Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 507, Villejuif, France
| | - Isabelle Cremer
- Université Paris Descartes, Sorbonne Paris Cité, 15 rue de l'Ecole de Médecine, Paris, France; Université Pierre et Marie Curie, 15 rue de l'Ecole de Médecine, Paris, France; Laboratory "Cancer, Immune control and escape," Center de Recherche des Cordeliers, INSERM U 1138, 15 rue de l'Ecole de Médecine, Paris, France
| | - Guido Kroemer
- Université Paris Descartes, Sorbonne Paris Cité, 15 rue de l'Ecole de Médecine, Paris, France; Université Pierre et Marie Curie, 15 rue de l'Ecole de Médecine, Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France; Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France; Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden
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Füssel S, Kramer MW, Stöhr R, Olbert P, Nawroth R, Schulz WA. [Report on the 5th symposium of the German research network bladder carcinoma]. Urologe A 2016; 55:663-4. [PMID: 27138635 DOI: 10.1007/s00120-016-0100-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- S Füssel
- Klinik für Urologie, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Deutschland
| | - M W Kramer
- Klinik für Urologie, Universitätsklinikum Lübeck, Lübeck, Deutschland
| | - R Stöhr
- Institut für Pathologie, Universitätsklinik Erlangen, Erlangen, Deutschland
| | - P Olbert
- Klinik für Urologie und Kinderurologie, Universitätsklinikum Marburg, Marburg, Deutschland
| | - R Nawroth
- Klinik für Urologie, Klinikum rechts der Isar, Technische Universität München, München, Deutschland
| | - W A Schulz
- Klinik für Urologie, Medizinische Fakultät, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Deutschland.
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Garg AD, Agostinis P. Editorial: Immunogenic Cell Death in Cancer: From Benchside Research to Bedside Reality. Front Immunol 2016; 7:110. [PMID: 27066003 PMCID: PMC4810155 DOI: 10.3389/fimmu.2016.00110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/14/2016] [Indexed: 12/24/2022] Open
Affiliation(s)
- Abhishek D Garg
- Cell Death Research and Therapy (CDRT) Laboratory, Department of Cellular Molecular Medicine, KU Leuven University of Leuven , Leuven , Belgium
| | - Patrizia Agostinis
- Cell Death Research and Therapy (CDRT) Laboratory, Department of Cellular Molecular Medicine, KU Leuven University of Leuven , Leuven , Belgium
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Eggleton P, Bremer E, Dudek E, Michalak M. Calreticulin, a therapeutic target? Expert Opin Ther Targets 2016; 20:1137-47. [DOI: 10.1517/14728222.2016.1164695] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Albrecht AS, Ørom UA. Bidirectional expression of long ncRNA/protein-coding gene pairs in cancer. Brief Funct Genomics 2015; 15:167-73. [DOI: 10.1093/bfgp/elv048] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Xiao T, Liu L, Li H, Sun Y, Luo H, Li T, Wang S, Dalton S, Zhao RC, Chen R. Long Noncoding RNA ADINR Regulates Adipogenesis by Transcriptionally Activating C/EBPα. Stem Cell Reports 2015; 5:856-865. [PMID: 26489893 PMCID: PMC4649137 DOI: 10.1016/j.stemcr.2015.09.007] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 09/09/2015] [Accepted: 09/10/2015] [Indexed: 01/09/2023] Open
Abstract
C/EBPα is a critical transcriptional regulator of adipogenesis. How C/EBPα transcription is itself regulated is poorly understood, however, and remains a key question that needs to be addressed for a complete understanding of adipogenic development. Here, we identify a lncRNA, ADINR (adipogenic differentiation induced noncoding RNA), transcribed from a position ∼450 bp upstream of the C/EBPα gene, that orchestrates C/EBPα transcription in vivo. Depletion of ADINR leads to a severe adipogenic defect that is rescued by overexpression of C/EBPα. Moreover, we reveal that ADINR RNA specifically binds to PA1 and recruits MLL3/4 histone methyl-transferase complexes so as to increase H3K4me3 and decrease H3K27me3 histone modification in the C/EBPα locus during adipogenesis. These results show that ADINR plays important roles in regulating the differentiation of human mesenchymal stem cells into adipocytes by modulating C/EBPα in cis. The lncRNA ADINR is developmentally regulated during adipogenesis ADINR promotes adipogenesis by activating C/EBPα transcription in cis ADINR activates C/EBPα transcription by an MLL3/4-dependent mechanism MLL3/4 recruitment to the C/EBPα promoter requires binding of PA1 to ADINR
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Affiliation(s)
- Tengfei Xiao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02215, USA
| | - Lihui Liu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Graduate School of the Chinese Academy of Sciences, Beijing 100080, China
| | - Hongling Li
- Center of Excellence in Tissue Engineering, Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yu Sun
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Graduate School of the Chinese Academy of Sciences, Beijing 100080, China
| | - Huaxia Luo
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Graduate School of the Chinese Academy of Sciences, Beijing 100080, China
| | - Tangping Li
- Center of Excellence in Tissue Engineering, Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Shihua Wang
- Center of Excellence in Tissue Engineering, Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Stephen Dalton
- Paul D. Coverdell Center for Biomedical and Health Sciences, Department of Biochemistry and Molecular Biology, The University of Georgia, 500 D.W. Brooks Drive, Athens, GA 30602, USA
| | - Robert Chunhua Zhao
- Center of Excellence in Tissue Engineering, Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China.
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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