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Zhang YJ, Huang C, Zu XG, Liu JM, Li YJ. Use of Machine Learning for the Identification and Validation of Immunogenic Cell Death Biomarkers and Immunophenotypes in Coronary Artery Disease. J Inflamm Res 2024; 17:223-249. [PMID: 38229693 PMCID: PMC10790656 DOI: 10.2147/jir.s439315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/28/2023] [Indexed: 01/18/2024] Open
Abstract
Objective Immunogenic cell death (ICD) is part of the immune system's response to coronary artery disease (CAD). In this study, we bioinformatically evaluated the diagnostic and therapeutic utility of immunogenic cell death-related genes (IRGs) and their relationship with immune infiltration features in CAD. Methods We acquired the CAD-related datasets GSE12288, GSE71226, and GSE120521 from the Gene Expression Omnibus (GEO) database and the IRGs from the GeneCards database. After identifying the immune cell death-related differentially expressed genes (IRDEGs), we developed a risk model and detected immune subtypes in CAD. IRDEGs were identified using least absolute shrinkage and selection operator (LASSO) analysis. Using a nomogram, we confirmed that both the LASSO model and ICD signature genes had good diagnostic performance. Results There was a high degree of coincidence and immune representativeness between two CAD groups based on characteristic genes and hub genes. Hub genes were associated with the interaction of neuroactive ligands with receptors and cell adhesion receptors. The two groups differed in terms of adipogenesis, allograft rejection, and apoptosis, as well as the ICD signature and hub gene expression levels. The two CAD-ICD subtypes differed in terms of immune infiltration. Conclusion Quantitative real-time PCR (qRT-PCR) correlated CAD with the expression of OAS3, ITGAV, and PIBF1. The ICD signature genes are candidate biomarkers and reference standards for immune grouping in CAD and can be beneficial in precise immune-targeted therapy.
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Affiliation(s)
- Yan-jiao Zhang
- Department of Cardiology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
| | - Chao Huang
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, People’s Republic of China
| | - Xiu-guang Zu
- Department of Cardiology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
| | - Jin-ming Liu
- Department of Cardiology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
| | - Yong-jun Li
- Department of Cardiology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
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Lu L, Wang H, Fang J, Zheng J, Liu B, Xia L, Li D. Overexpression of OAS1 Is Correlated With Poor Prognosis in Pancreatic Cancer. Front Oncol 2022; 12:944194. [PMID: 35898870 PMCID: PMC9309611 DOI: 10.3389/fonc.2022.944194] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
Background OAS1 expression in pancreatic cancer has been confirmed by many studies. However, the prognostic value and mechanism of OAS1 in pancreatic cancer have not been analyzed. Methods The RNA-seq in pancreatic cancer were obtained by UCSC XENA and GEO database. In addition, immunohistochemical validation and analysis were performed using samples from the 900th hospital. The prognosis of OAS1 was evaluated by timeROC package, Cox regression analysis, and Kaplan-Meier survival curves. Then, the main functional and biological signaling pathways enrichment and its relationship with the abundance of immune cells were analyzed by bioinformatics. Results OAS1 was highly expressed in pancreatic cancer compared with normal pancreatic tissue. High OAS1 expression was associated with poor overall survival (p<0.05). The OAS1 was significantly correlated to TNM staging (p=0.014). The timeROC analysis showed that the AUC of OAS1 was 0.734 for 3-year OS. In addition, the expression of OAS1 was significantly correlated with the abundance of a variety of immune markers. GSEA showed that enhanced signaling pathways associated with OAS1 include Apoptosis, Notch signaling pathway, and P53 signaling pathway. Conclusions OAS1 is a valuable prognostic factor in pancreatic cancer. Moreover, it may be a potential immunotherapeutic target.
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Affiliation(s)
- Lingling Lu
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Huaxiang Wang
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Affiliated Hospital of Hubei University of Medicine, Shiyan, China
| | - Jian Fang
- Department of Hepatobiliary Medicine, The Third Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Jiaolong Zheng
- Department of Hepatobiliary Disease, The 900th Hospital of the People’s Liberation Army Joint Logistics Support Force, Fuzhou, China
| | - Bang Liu
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Lei Xia
- Department of Hepatobiliary Medicine, The Third Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Dongliang Li
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
- Department of Hepatobiliary Disease, The 900th Hospital of the People’s Liberation Army Joint Logistics Support Force, Fuzhou, China
- *Correspondence: Dongliang Li,
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Zhou H, Jia X, Yang F, Shi P. Long noncoding RNA SATB1-AS1 contributes to the chemotherapy resistance through the microRNA-580/ 2'-5'-oligoadenylate synthetase 2 axis in acute myeloid leukemia. Bioengineered 2021; 12:6403-6417. [PMID: 34516354 PMCID: PMC8806783 DOI: 10.1080/21655979.2021.1971508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Acute myeloid leukemia (AML) represents a hematopoietic cancer with an invasive property. Chemoresistance blunts the therapeutic effect of chemotherapeutics in AML. Long noncoding RNAs (lncRNAs) have been implicated in chemotherapy resistance in AML. Transcriptome sequencing in the current study was applied to clarify the differentially expressed lncRNAs between peripheral blood mononuclear cells of AML and normal samples. The expression of special AT-rich sequence binding protein 1 antisense RNA 1 (SATB1-AS1) and 2ʹ-5ʹ-oligoadenylate synthetase 2 (OAS2) in AML patients was evaluated by qRT-PCR. The relationships among SATB1-AS1, microRNA-580 (miR-580) and OAS2 were investigated by dual-luciferase reporter assay. We observed that SATB1-AS1 and OAS2 were upregulated, while miR-580 was downregulated in AML patients. SATB1-AS1 depletion suppressed proliferation, and enhanced apoptosis and sensitivity of AML cells. Additionally, SATB1-AS1 promoted the expression of OAS2 by acting as a molecular sponge of miR-580 in AML. miR-580 downregulation, OAS2 overexpression and a selective glycogen synthase kinase (GSK)-3β inhibitor AR-A014418 abolished the effects of SATB1-AS1 deletion on the chemosensitivity of AML cells. In conclusion, SATB1-AS1 knockdown promotes the sensitivity of AML cells by upregulating miR-580 and downregulating OAS2 through the GSK3β/β-catenin pathway, providing new insights into the function of SATB1-AS1 as a miRNA sponge in AML.
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Affiliation(s)
- Hong Zhou
- Department of Hematology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Xiaofeng Jia
- College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, P.R. China
| | - Fan Yang
- Department of Hematology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Pengfei Shi
- Department of Hematology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
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Padariya M, Sznarkowska A, Kote S, Gómez-Herranz M, Mikac S, Pilch M, Alfaro J, Fahraeus R, Hupp T, Kalathiya U. Functional Interfaces, Biological Pathways, and Regulations of Interferon-Related DNA Damage Resistance Signature (IRDS) Genes. Biomolecules 2021; 11:622. [PMID: 33922087 PMCID: PMC8143464 DOI: 10.3390/biom11050622] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
Interferon (IFN)-related DNA damage resistant signature (IRDS) genes are a subgroup of interferon-stimulated genes (ISGs) found upregulated in different cancer types, which promotes resistance to DNA damaging chemotherapy and radiotherapy. Along with briefly discussing IFNs and signalling in this review, we highlighted how different IRDS genes are affected by viruses. On the contrary, different strategies adopted to suppress a set of IRDS genes (STAT1, IRF7, OAS family, and BST2) to induce (chemo- and radiotherapy) sensitivity were deliberated. Significant biological pathways that comprise these genes were classified, along with their frequently associated genes (IFIT1/3, IFITM1, IRF7, ISG15, MX1/2 and OAS1/3/L). Major upstream regulators from the IRDS genes were identified, and different IFN types regulating these genes were outlined. Functional interfaces of IRDS proteins with DNA/RNA/ATP/GTP/NADP biomolecules featured a well-defined pharmacophore model for STAT1/IRF7-dsDNA and OAS1/OAS3/IFIH1-dsRNA complexes, as well as for the genes binding to GDP or NADP+. The Lys amino acid was found commonly interacting with the ATP phosphate group from OAS1/EIF2AK2/IFIH1 genes. Considering the premise that targeting IRDS genes mediated resistance offers an efficient strategy to resensitize tumour cells and enhances the outcome of anti-cancer treatment, this review can add some novel insights to the field.
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Affiliation(s)
- Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Alicja Sznarkowska
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Maria Gómez-Herranz
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Sara Mikac
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Magdalena Pilch
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Javier Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, F-75010 Paris, France
- Department of Medical Biosciences, Building 6M, Umeå University, 901 85 Umeå, Sweden
- RECAMO, Masaryk Memorial Cancer Institute, Zlutykopec 7, 65653 Brno, Czech Republic
| | - Ted Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
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Zhao J, Zhang X, Cheng M, Guan J, Gai J, Fu L, Zhang R, Du T, Li Q. Expression of IFN-induced 2'-5'-oligoadenylate synthetases correlates with immune infiltration, revealing potential targets and new biomarkers for basal-like breast cancer prognosis. Int Immunopharmacol 2020; 88:106916. [PMID: 32882665 DOI: 10.1016/j.intimp.2020.106916] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 08/15/2020] [Accepted: 08/16/2020] [Indexed: 10/23/2022]
Abstract
Triple-negative breast cancer has been classified as basal-like immune activated (BLIA), basal-like immune-suppressed (BLIS), and two other subtypes, suggesting potential immune therapeutic targets for basal-like breast cancer (BLBC). 2'-5'-Oligoadenylate synthetases (OASs), identified from differentially expressed genes (DEGs) between BLIA and BLIS breast cancers (GSE76124), are involved in antiviral activity induced by interferons. However, the association between the four OASs and prognosis or tumor-infiltrating immune cells (TIICs) remains unclear. Expression, survival data, and immune correlations for OASs in BLBC were assessed using bioinformatics tools. We found that OASs were highly expressed in BLIA breast cancer. Survival analysis suggested that high transcriptional levels of OASs were associated with better overall survival, relapse-free survival, and distant metastasis-free survival in patients with BLBC. Moreover, the prognostic value of OASs with respect to different clinicopathological factors, and especially according to lymph node metastasis, in patients with BLBC was further assessed. Our findings elucidated the expression, prognostic role, and effect of OASs in TIICs on BLBC, which might promote the development of OAS-targeted immunotherapy for BLBC.
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Affiliation(s)
- Jinming Zhao
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China
| | - Xiupeng Zhang
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China
| | - Ming Cheng
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China
| | - Jingqian Guan
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China
| | - Junda Gai
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China
| | - Lin Fu
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China; Department of Pathology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Ruochen Zhang
- Department of Chronic Disease Epidemiology, Yale School of Public Health, Yale University, New Haven, CT, United States
| | - Tengjiao Du
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China
| | - Qingchang Li
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, China; Department of Pathology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China.
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Zhang Y, Yu C. Prognostic characterization of OAS1/OAS2/OAS3/OASL in breast cancer. BMC Cancer 2020; 20:575. [PMID: 32560641 PMCID: PMC7304174 DOI: 10.1186/s12885-020-07034-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/03/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Prognostic biomarkers remain a focus in breast cancer during last decades. More reliable predictors to adequately characterize the prognosis of breast cancer are essential. The 2'-5'-oligoadenylate synthetases (OAS), composing of OAS1, OAS2, OAS3, and OAS-like (OASL), are interferon (IFN)-induced antiviral enzymes, with their prognostic roles remain to be characterized. METHODS Prognostic values of OAS family members were assessed by multiple public available resources. RESULTS High mRNA expression of OAS1 and OAS3 were correlated with worse prognosis for all breast cancer patients, whereas OAS2 was associated with favorable prognosis. The prognostic values of OAS family in different clinicopathologic subtypes were also characterized. In DNA methylation level, cg12560128 in OAS2, cg06800840 and cg26328872 in OASL showed significant prognostic values. The mRNA expression of OAS members signature in high/low risk overall survival groups was opposite to the high/low risk recurrence free survival groups. Neutrophil cell exhibited highest correlation with all OAS members in tumor immune infiltrating estimation. CONCLUSIONS This study provided new insight into the prognostic roles of OAS in breast cancer with potential mechanistic values.
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Affiliation(s)
- Yujie Zhang
- Department of Gastrointestinal Surgery Center and Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
| | - Chaoran Yu
- Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200025, P.R. China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200025, P.R. China.
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Glaß M, Michl P, Hüttelmaier S. RNA Binding Proteins as Drivers and Therapeutic Target Candidates in Pancreatic Ductal Adenocarcinoma. Int J Mol Sci 2020; 21:ijms21114190. [PMID: 32545414 PMCID: PMC7312628 DOI: 10.3390/ijms21114190] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/03/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinomas (PDAC) belong to the most frequent and most deadly malignancies in the western world. Mutations in KRAS and TP53 along with some other frequent polymorphisms occur almost universally and are likely to be responsible for tumor initiation. However, these mutations cannot explain the heterogeneity in therapeutic responses observed in PDAC patients, which limits efficiency of current therapeutic strategies. Instead, recent classifications of PDAC tumor samples are based on transcriptomics data and thus include information about epigenetic, transcriptomic, and post-transcriptomic deregulations. RNA binding proteins (RBPs) are important post-transcriptional regulators involved in every aspect of the RNA life cycle and thus considerably influence the transcriptome. In this study, we systematically investigated deregulated expression, prognostic value, and essentiality reported for RBPs in PDAC or PDAC cancer models using publicly available data. We identified 44 RBPs with suggested oncogenic potential. These include various proteins, e.g., IGF2 mRNA binding proteins (IGF2BPs), with reported tumor-promoting roles. We further characterized these RBPs and found common patterns regarding their expression, interaction, and regulation by microRNAs. These analyses suggest four prime candidate oncogenic RBPs with partially validated target potential: APOBEC1, IGF2BP1 and 3, and OASL.
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Affiliation(s)
- Markus Glaß
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Str. 3a, 06120 Halle, Germany;
- Correspondence:
| | - Patrick Michl
- Universitätsklinik und Poliklinik für Innere Medizin I, Universitätsklinikum Halle (Saale), Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany;
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Str. 3a, 06120 Halle, Germany;
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