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Zhang M, Wu Y, Mou J, Yao Y, Wen P, Liu X, Shang S, Kang X, Tian J, Liu Y, Lv E, Wang L. The global landscape of immune-derived lncRNA signature in colorectal cancer. Heliyon 2024; 10:e25568. [PMID: 38420407 PMCID: PMC10900961 DOI: 10.1016/j.heliyon.2024.e25568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 01/12/2024] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a highly heterogeneous cancer. This heterogeneity has an impact on the efficacy of immunotherapy. Long noncoding RNAs (lncRNAs) have been found to play regulatory functions in cancer immunity. However, the global landscape of immune-derived lncRNA signatures has not yet been explored in colorectal cancer. METHODS In this study, we applied DESeq2 to identify differentially expressed lncRNAs in colon cancer. Next, we performed an integrative analysis to globally identify immune-driven lncRNA markers in CRC, including immune-associated pathways, tumor immunogenomic features, tumor-infiltrating immune cells, immune checkpoints, microsatellite instability (MSI) and tumor mutation burden (TMB). RESULTS We also identified dysregulated lncRNAs, such as LINC01354 and LINC02257, and their clinical relevance in CRC. Our findings revealed that the differentially expressed lncRNAs were closely associated with immune pathways. In addition, we found that RP11-354P11.3 and RP11-545G3.1 had the highest association with the immunogenomic signature. As a result, these signatures could serve as markers to assess immunogenomic activity in CRC. Among the immune cells, resting mast cells and M0 macrophages had the highest association with lncRNAs in CRC. The AC006129.2 gene was significantly associated with several immune checkpoints, for example, programmed cell death protein 1 (PD-1) and B and T lymphocyte attenuator (BTLA). Therefore, the AC006129.2 gene could be targeted to regulate the condition of immune cells or immune checkpoints to enhance the efficacy of immunotherapy in CRC patients. Finally, we identified 15 immune-related lncRNA-generated open reading frames (ORFs) corresponding to 15 cancer immune epitopes. CONCLUSION In conclusion, we provided a genome-wide immune-driven lncRNA signature for CRC that might provide new insights into clinical applications and immunotherapy.
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Affiliation(s)
- Mengying Zhang
- School of Medical Information and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yifei Wu
- School of Medical Information and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jingyi Mou
- Department of Clinical Medicine, School of 1st Clinical Medicine, Xuzhou Medical University, Xuzhou, China
| | - Yang Yao
- School of Medical Information and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Pengbo Wen
- School of Medical Information and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xin Liu
- School of Medical Information and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Shipeng Shang
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Xingxing Kang
- School of Medical Information and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jiaqi Tian
- School of Medical Information and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yan Liu
- School of Life Sciences, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Enhui Lv
- School of Medical Information and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Liang Wang
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, China
- Division of Microbiology and Immunology, School of Biomedical Sciences, The University of Western Australia, Crawley, Western Australia, Australia
- Centre for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Perth, Western Australia, Australia
- School of Agriculture and Food Sustainability, University of Queensland, Brisbane, Queensland, Australia
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Feng J, Huang Y, Huang M, Li X, Amoah K, Huang Y, Jian J. Apolipoprotein Eb (On-ApoEb) protects Oreochromis niloticus against Streptococcus agalactiae infection. Fish Shellfish Immunol 2023; 141:109069. [PMID: 37696347 DOI: 10.1016/j.fsi.2023.109069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
Apolipoprotein E (ApoE), a critical targeting protein, has been found to play an essential role in the protection against infection and inflammation. However, the immune functions of ApoE against bacterial infection in fish have not been investigated. In this study, a full-length cDNA for ApoE, named On-ApoEb was cloned from Oreochromis niloticus. The predicted cDNA sequence was 831bp in length and coded for a protein of 276 amino acid residues, which shared 63.87%-98.55% identity with ApoEb from other fishes, and about 22% identity with ApoEb from mammals. On-ApoEb from O. niloticus was highly expressed in the liver and could be activated in the tissues (liver, spleen, brain, and intestine) after infection with Streptococcus agalactiae. Moreover, the results revealed that On-ApoEb could decrease the expression levels of pro-inflammatory factors, immune-related pathways, and apoptosis, while increasing the expression levels of anti-inflammatory factors. Furthermore, On-ApoEb was noted to improve the survival rate and reduce the bacterial load in the liver and spleen. These results suggested that On-ApoEb was connected with immune response and had anti-inflammation and anti-apoptosis activities.
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Affiliation(s)
- Jiamin Feng
- Fisheries College of Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture & Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Zhanjiang, 524088, China
| | - Yongxiong Huang
- Fisheries College of Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture & Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Zhanjiang, 524088, China
| | - Meiling Huang
- Fisheries College of Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture & Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Zhanjiang, 524088, China
| | - Xing Li
- Fisheries College of Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture & Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Zhanjiang, 524088, China
| | - Kwaku Amoah
- Fisheries College of Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture & Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Zhanjiang, 524088, China
| | - Yu Huang
- Fisheries College of Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture & Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Zhanjiang, 524088, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China.
| | - Jichang Jian
- Fisheries College of Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture & Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Zhanjiang, 524088, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China.
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Li K, Qin L, Jiang S, Li A, Zhang C, Liu G, Sun J, Sun H, Zhao Y, Li N, Zhang Y. The signature of HBV-related liver disease in peripheral blood mononuclear cell DNA methylation. Clin Epigenetics 2020; 12:81. [PMID: 32513305 PMCID: PMC7278209 DOI: 10.1186/s13148-020-00847-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/08/2020] [Indexed: 12/20/2022] Open
Abstract
Background Hepatitis B virus (HBV)-related liver disease induces liver damage by hepatic immune and inflammatory response. The association between aberrant peripheral blood mononuclear cell (PBMC) DNA methylation and progression of liver disease and fibrosis remains unclear. Results Here we applied Infinium 450 K BeadChip investigating PBMC genome-wide methylation profiling of 48 HBV-related liver disease patients including 24 chronic hepatitis B (CHB), 14 compensated liver cirrhosis (LC), and 10 decompensated liver cirrhosis (DLC). In total, there were 7888 differentially methylated CpG sites (36.06% hypermethylation, 63.94% hypomethylation) correlate with liver disease progression. LC was difficult to be diagnosed, intermediating between CHB and DLC. We used least absolute shrinkage and selection operator (LASSO)-logistic regression method to perform a LC predictive model. The predicted probability (P) of having LC was estimated by the combined model: P = 1/(1 − e−x), where X = 11.52 − 2.82 × (if AST within the normal range − 0.19 × (percent methylation of cg05650055) − 0.21 × (percent methylation of cg17149911 ). Pyrosequencing validation and confusion matrix analysis was used for internal testing, area under receiver operating characteristic curve (AUROC) of model was 0.917 (95% CI, 0.80–0.977). On the fibrosis progress, there were 1705 genes in LC compared with CHB, whose differentially methylated CpG sites loading within the “promoter” regions (including TSS1500, TSS200, 5′UTR, and the 1st exon of genes) subject into the enrichment analysis using Ingenuity Pathway Analysis (IPA). There were 113 enriched immune-related pathways indicated that HBV-related liver fibrosis progression caused epigenetic reprogramming of the immune and inflammatory response. Conclusions These data support idea that development of HBV-related chronic liver disease is linked with robust and broad alteration of methylation in peripheral immune system. CpG methylation sites serve as relevant biomarker candidates to monitor and diagnose LC, providing new insight into the immune mechanisms understanding the progression of HBV-related liver fibrosis and cirrhosis.
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Affiliation(s)
- Kang Li
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Ling Qin
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China.,Schools of Basic Medical Science, Capital Medical University, Beijing, China
| | | | - Ang Li
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Chi Zhang
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Guihai Liu
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China.,University of Oxford, Oxford, UK
| | - Jianping Sun
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Huanqing Sun
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Yan Zhao
- Clinical Laboratory Center, Beijing You'An hospital, Capital Medical University, Beijing, China
| | - Ning Li
- Departments of Hepatobiliary Surgery, Beijing You'An Hospital, Capital Medical University, Beijing, China.
| | - Yonghong Zhang
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China.
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