1
|
Huanjie Z, Bukhari I, Fazhan L, Wen H, Wang J, Wanqing W, Yuming F, Youcai T, AlJowaie RM, Aziz IM, Xiufeng C, Yang M, Pengyuan Z. P53-associated lncRNAs regulate immune functions and RNA-modifiers in gastric cancer. Heliyon 2024; 10:e35228. [PMID: 39166030 PMCID: PMC11334848 DOI: 10.1016/j.heliyon.2024.e35228] [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: 02/01/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/22/2024] Open
Abstract
TP53, a guardian of the genome, suppresses or enhances tumors through various regulatory pathways. However, the role of p53-related long non-coding RNAs (lncRNAs) in immune regulation of tumor microenvironment and prognosis of gastric cancer (GC) is so far unelucidated. We analyzed the role of TP53-associated lncRNAs (obtained from the TP53LNC-DB database) in immune regulation, immune cell infiltration and RNA modification in gastric cancer. Firstly, using multivariate COX regression analysis, we identified eight lncRNAs related to the prognosis of GC. Furthermore, based on the expression of the lncRNA signature and risk score, the GC patients were divided into high-risk and low-risk groups. We found that M2-macrophages have significantly higher infiltration in the high-risk group. Similarly, significant differences in immune function (APC_co_stimulation, CCR, and checkpoint) and m6A modification (FTO, ZC3H13, YTHDC1, and RBM15), and m5C modification (NOP2 and TET1) between both groups were also observed. These signature lncRNAs were also positively associated with oxidative stress-related genes (MPO, MAPK14, HMOX1, and APP). Additionally, we found that high expression of GAS5 and low expression of MALAT1 in Helicobacter pylori (H-pylori) positive GC patients. Finally, GC patients in the low-risk group showed higher resistance to immunotherapy while patients in the high-risk group were more sensitive to various chemotherapy drugs. Based on these findings, we conclude that p53-associated lncRNAs signature could potentially predict the immune status and overall survival, and may also be used for risk management and planning immunotherapy for gastric cancer patients.
Collapse
Affiliation(s)
- Zhao Huanjie
- Henan Key Laboratory of Helicobacter Pylori, Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, ErQi 450052, Zhengzhou, Henan, China
| | - Ihtisham Bukhari
- Henan Key Laboratory of Helicobacter Pylori, Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, ErQi 450052, Zhengzhou, Henan, China
- Department of Gastroenterology, Fifth Affiliated Hospital of Zhengzhou University, ErQi, 450052, Zhengzhou, Henan, China
| | - Li Fazhan
- Henan Key Laboratory of Helicobacter Pylori, Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, ErQi 450052, Zhengzhou, Henan, China
| | - Huijuan Wen
- Henan Key Laboratory of Helicobacter Pylori, Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, ErQi 450052, Zhengzhou, Henan, China
| | - Jingyun Wang
- Henan Key Laboratory of Helicobacter Pylori, Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, ErQi 450052, Zhengzhou, Henan, China
- Department of Gastroenterology, Fifth Affiliated Hospital of Zhengzhou University, ErQi, 450052, Zhengzhou, Henan, China
| | - Wu Wanqing
- Department of Gastrointestinal Surgery, the Fifth Affiliated Hospital of Zhengzhou University, ErQi, 450052, Zhengzhou, Henan, China
| | - Fu Yuming
- Department of Gastrointestinal Surgery, the Fifth Affiliated Hospital of Zhengzhou University, ErQi, 450052, Zhengzhou, Henan, China
| | - Tang Youcai
- Department of Pediatrics, the Fifth Affiliated Hospital of Zhengzhou University, ErQi, 450052, Zhengzhou, Henan, China
| | - Reem M. AlJowaie
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ibrahim M. Aziz
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Chu Xiufeng
- Department of Oncology, the Fifth Affiliated Hospital of Zhengzhou University, ErQi, 450052, Zhengzhou, Henan, China
| | - Mi Yang
- Henan Key Laboratory of Helicobacter Pylori, Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, ErQi 450052, Zhengzhou, Henan, China
- Department of Gastroenterology, Fifth Affiliated Hospital of Zhengzhou University, ErQi, 450052, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhongyuan, 450001, Zhengzhou, Henan China, China
- Institute of Rehabilitation Medicine, Henan Academy of Innovations in Medical Sciences, Zhengzhou, Henan, China
| | - Zheng Pengyuan
- Henan Key Laboratory of Helicobacter Pylori, Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, ErQi 450052, Zhengzhou, Henan, China
- Department of Gastroenterology, Fifth Affiliated Hospital of Zhengzhou University, ErQi, 450052, Zhengzhou, Henan, China
- Academy of Medical Science, Zhengzhou University, Zhongyuan, 450001, Zhengzhou, Henan China, China
- Institute of Rehabilitation Medicine, Henan Academy of Innovations in Medical Sciences, Zhengzhou, Henan, China
| |
Collapse
|
2
|
Wan Q, Deng Y, Wei R, Ma K, Tang J, Deng YP. Tumor-infiltrating macrophage associated lncRNA signature in cutaneous melanoma: implications for diagnosis, prognosis, and immunotherapy. Aging (Albany NY) 2024; 16:4518-4540. [PMID: 38475660 PMCID: PMC10968696 DOI: 10.18632/aging.205606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/08/2024] [Indexed: 03/14/2024]
Abstract
Along with the increasing knowledge of long noncoding RNA, the interaction between the long noncoding RNA (lncRNA) and tumor immune infiltration is increasingly valued. However, there is a lack of understanding of correlation between regulation of specific lncRNAs and tumor-infiltrating macrophages within melanoma. In this research, a macrophage associated lncRNA signature was identified by multiple machine learning algorithms and the robust and effectiveness of signature also validated in other independent datasets. The signature contained six specific lncRNAs (PART1, LINC00968, LINC00954, LINC00944, LINC00518 and C20orf197) was constructed, which could diagnose melanoma and predict the prognosis of patients. Moreover, our signature achieves higher accuracy than the previous well-established markers and regarded as an independent prognostic indicator. The pathway enrichment revealed that these lncRNAs were closely correlated with many immune processes. In addition, the signature was associated with different immune microenvironment and applied to predict response of immune checkpoint inhibitor therapy (low risk of patients well respond to anti-PD-1 therapy and high risk is insensitive to anti-CTLA-4 therapy). Therefore, our finding supplies a more accuracy and effective lncRNA signature for tumor-infiltrating macrophages targeting treatment approaches and affords a new clinical application for predicting the response of immunotherapies in melanomas.
Collapse
Affiliation(s)
- Qi Wan
- Department of Ophthalmology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Yuhua Deng
- Department of Infection Control, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Ran Wei
- Department of Ophthalmology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Ke Ma
- Department of Ophthalmology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Jing Tang
- Department of Ophthalmology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Ying-Ping Deng
- Department of Ophthalmology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| |
Collapse
|
3
|
Lin Z, Ji X, Tian N, Gan Y, Ke L. APOB is a potential prognostic biomarker in hepatocellular carcinoma. Discov Oncol 2024; 15:28. [PMID: 38310202 PMCID: PMC10838261 DOI: 10.1007/s12672-024-00877-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/30/2024] [Indexed: 02/05/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is significantly associated with adverse prognostic outcomes. The development and progression of different types of human tumors are significantly influenced by APOB. Nevertheless, the significance and pathomechanisms of APOB in HCC have not been conclusively determined. We assessed APOB expression levels in HCC using three publicly available databases of TIMER2.0, UALCAN and Human Protein Atlas. To identify the biological function of APOB, we conducted enrichment analysis via LinkedOmics. Moreover, UALCAN was employed to assess the relationship between APOB expression and clinicopathological features among HCC patients. Additionally, the Kaplan-Meier plotter was utilized to investigate the prognostic relevance of APOB in HCC. To explore potential regulatory ncRNAs that could bind to APOB, we utilized StarBase and GEPIA. Furthermore, the correlation between APOB expression and immune cell infiltration, as well as immune checkpoint genes, was investigated using Spearman's correlation analysis in TISIDB, GEPIA, and TIMER2.0. The findings of our investigation showed a notable decrease in the expression levels of APOB among individuals diagnosed with HCC. Moreover, a noteworthy correlation was observed between the expression of APOB and immune checkpoint genes, alongside the occurrence of immune cell infiltration. The levels of APOB expression in HCC tissues also showed correlations with various clinicopathological features. According to Cox regression analysis, decreased APOB expression emerged as a potential autonomous predictor for OS, RFS, DSS, and PFS among HCC patients. Furthermore, we identified six potential pathways associated with non-coding RNA (ncRNA) as the most promising pathway for APOB in HCC. Our results illuminate the possible involvement of APOB in HCC and offer understanding into its governing mechanisms and medical importance.
Collapse
Affiliation(s)
- Zhifeng Lin
- Department of Medical Record; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Xiaohui Ji
- Department of Obstetrics and Gynaecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Nana Tian
- Department of Medical Record, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yu Gan
- Department of Medical Record, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Ke
- Department of Medical Record; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| |
Collapse
|
4
|
Fan X, Huang Y, Zhong Y, Yan Y, Li J, Fan Y, Xie F, Luo Q, Zhang Z. A new marker constructed from immune-related lncRNA pairs can be used to predict clinical treatment effects and prognosis: in-depth exploration of underlying mechanisms in HNSCC. World J Surg Oncol 2023; 21:250. [PMID: 37592311 PMCID: PMC10433616 DOI: 10.1186/s12957-023-03066-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/04/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Long non-coding RNA (lncRNA) plays a vital role in tumor proliferation, migration, and treatment. Since it is challenging to standardize the gene expression levels detected by different platforms, the signatures composed of many immune-related single lncRNAs are still inaccurate. Utilizing a gene pair formed of two immune-related lncRNAs and strategically assigning values can effectively meet the demand for a higher-accuracy dual biomarker combination. METHODS Co-expression and differential expression analyses were performed on immune genes and lncRNAs data from The Cancer Genome Atlas and the ImmPort database to obtain differentially expressed immune-related lncRNAs for pairwise pairing. The prognostic-related differentially expressed immune-related lncRNAs (PR-DE-irlncRNAs) pairs were then identified by univariate Cox regression and used for lasso regression to construct a prognostic model. Various methods were used to validate the predictive prognostic performance of the model. Additionally, we explored the potential guiding value of the model in immunotherapy and chemotherapy and constructed a nomogram suitable for efficient prognosis prediction. Mechanistic exploration of anti-tumor immunity and mutational perspectives are also included. We also analyzed the correlation between the model and immune checkpoint inhibitors (ICIs)-related, N6-methyadenosine (m6A)-related, and multidrug resistance genes. RESULTS We used a total of 20 pairs of PR-DE-irlncRNAs to create a prognosis model. Quantitative real-time polymerase chain reaction experiments further verified the abnormal expression of 11 lncRNAs in HNSCC cells. Various methods have confirmed the excellent performance of the model in predicting patient prognosis. We reasoned that lncRNAs/TP53 mutation might play a positive/negative anti-tumor role through the immune system by multi-perspective analyses. Finally, it was found that the prognostic model was closely related to immunotherapy and chemotherapy as well as the expression of ICIs/m6A/multidrug resistance-related genes. CONCLUSION The prognostic model performs excellently in predicting the prognosis of patients and provides the potential value of practical guidance for treatment.
Collapse
Affiliation(s)
- Xin Fan
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Yuhan Huang
- Yunnan University of Chinese Medicine, Kunming, Yunnan Province, China
| | - Yun Zhong
- The First Clinical Medical College of Nanchang University, Nanchang, Jiangxi Province, China
| | - Yujie Yan
- School of Stomatology, Nanchang University, Nanchang, Jiangxi Province, China
| | - Jiaqi Li
- School of Stomatology, Nanchang University, Nanchang, Jiangxi Province, China
| | - Yanting Fan
- The First Clinical Medical College of Nanchang University, Nanchang, Jiangxi Province, China
| | - Fei Xie
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Qing Luo
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Zhiyuan Zhang
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.
| |
Collapse
|
5
|
Chini A, Guha P, Malladi VS, Guo Z, Mandal SS. Novel long non-coding RNAs associated with inflammation and macrophage activation in human. Sci Rep 2023; 13:4036. [PMID: 36899011 PMCID: PMC10006430 DOI: 10.1038/s41598-023-30568-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
Inflammation plays a central role in immune response and macrophage activation. Emerging studies demonstrate that along with proteins and genomic factors, noncoding RNA are potentially involved in regulation of immune response and inflammation. Our recent study demonstrated that lncRNA HOTAIR plays key roles in cytokine expression and inflammation in macrophages. The primary goal of this study is to discover novel lncRNAs that are crucial players in inflammation, macrophage activation, and immune response in humans. Towards this, we have stimulated THP1-derived macrophages (THP1-MΦ) with lipopolysaccharides (LPS) and performed the whole transcriptome RNA-seq analysis. Based on this analysis, we discovered that along with well-known marker for inflammation (such as cytokines), a series of long noncoding RNAs (lncRNAs) expression were highly induced upon LPS-stimulation of macrophages, suggesting their potential roles in inflammation and macrophage activation. We termed these family of lncRNAs as Long-noncoding Inflammation Associated RNA (LinfRNA). Dose and time dependent analysis demonstrated that many human LinfRNA (hLinfRNAs) expressions follow similar patterns as cytokine expressions. Inhibition of NF-κB suppressed the expression of most hLinfRNAs suggesting their potential regulation via NF-κB activation during inflammation and macrophage activation. Antisense-mediated knockdown of hLinfRNA1 suppressed the LPS-induced expression of cytokines and pro-inflammatory genes such as IL6, IL1β, and TNFα expression, suggesting potential functionality of the hLinfRNAs in cytokine regulation and inflammation. Overall, we discovered a series of novel hLinfRNAs that are potential regulators of inflammation and macrophage activation and may be linked to inflammatory and metabolic diseases.
Collapse
Affiliation(s)
- Avisankar Chini
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Prarthana Guha
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Venkat S Malladi
- Lyda Hill Department of Bioinformatics, Bioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Zibiao Guo
- North Texas Genome Center, The University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Subhrangsu S Mandal
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, USA.
| |
Collapse
|
6
|
Yao Y, Yang F, Chen A, Hua Q, Gao W. Costimulatory molecule-related lncRNA model as a potential prognostic biomarker in non-small cell lung cancer. Cancer Med 2023; 12:6419-6436. [PMID: 36305249 PMCID: PMC10028169 DOI: 10.1002/cam4.5391] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 09/14/2022] [Accepted: 10/16/2022] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVE Costimulatory molecules have been demonstrated to exert essential roles in multiple cancers. However, their role in lung cancer remains elusive. Here, we sought to identify costimulatory molecule-related lncRNAs in non-small cell lung cancer (NSCLC) and establish a prognostic signature to predict the prognosis of patients with NSCLC. METHODS A total of 535 lung adenocarcinoma (LUAD) and 502 lung squamous cell carcinoma (LUSC) patients from the cancer genome atlas (TCGA) database were recruited. A novel costimulatory molecule-based lncRNA prognostic model was constructed using the least absolute shrinkage and selection operator (LASSO) algorithm to predict the overall survival. The Homo_sapiens.GRCh38 data set was set as a reference file for probe annotation. RESULTS A total of 593 costimulatory molecule-related lncRNAs were extracted. After analysis, six costimulatory molecule-related lncRNAs (AC084859.1, AC079949.2, HSPC324, LINC01150, LINC01150, and AC090617.5) were screened. A prognostic model based on the six lncRNAs was established using systematic bioinformatics analyses. The prognostic model had a prognostic value in NSCLC patients. Furthermore, a prognostic nomogram was established based on clinical parameters and a risk-score model. Patients with different risk scores had considerably different tumor-infiltrating immune cells, somatic mutational loading, clinical outcomes, signaling pathways, and immunotherapy efficacy. In addition, LINC01137 was associated with unfavorable disease outcomes and fueled tumor progression in NSCLC. CONCLUSION Taken together, our study demonstrated that a costimulatory molecule-related lncRNA model could be a potential prognostic biomarker in NSCLC. Moreover, LINC01137 could facilitate the proliferation and invasion of lung cancer.
Collapse
Affiliation(s)
- Yuanshan Yao
- Department of Thoracic Surgery, Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Department of Thoracic Oncology, Ningbo No. 2 Hospital, Ningbo, China
| | - Fuzhi Yang
- Department of Thoracic Surgery, Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Anna Chen
- Ningbo CRRC Times Transducer Technology Co., Ltd., Ningbo, China
| | - Qingwang Hua
- Department of Thoracic Oncology, Ningbo No. 2 Hospital, Ningbo, China
| | - Wen Gao
- Department of Thoracic Surgery, Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| |
Collapse
|
7
|
Prognostic 7-SLC-Gene Signature Identified via Weighted Gene Co-Expression Network Analysis for Patients with Hepatocellular Carcinoma. JOURNAL OF ONCOLOGY 2023; 2023:4364654. [PMID: 36844876 PMCID: PMC9957622 DOI: 10.1155/2023/4364654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/13/2022] [Accepted: 11/24/2022] [Indexed: 02/19/2023]
Abstract
Background Solute carrier (SLC) proteins play an important role in tumor metabolism. But SLC-associated genes' prognostic significance in hepatocellular carcinoma (HCC) remained elusive. We identified SLC-related factors and developed an SLC-related classifier to predict and improve HCC prognosis and treatment. Methods From the TCGA database, corresponding clinical data and mRNA expression profiles of 371 HCC patients were acquired, and those of 231 tumor samples were derived from the ICGC database. Genes associated with clinical features were filtered using weighted gene correlation network analysis (WGCNA). Next, univariate LASSO Cox regression studies developed SLC risk profiles, with the ICGC cohort data being used in validation. Result Univariate Cox regression analysis revealed that 31 SLC genes (P < 0.05) were related to HCC prognosis. 7 (SLC22A25, SLC2A2, SLC41A3, SLC44A1, SLC48A1, SLC4A2, and SLC9A3R1) of these genes were applied in developing a SLC gene prognosis model. Samples were classified into the low-andhigh-risk groups by the prognostic signature, with those in the high-risk group showing a significantly worse prognosis (P < 0.001 in the TCGA cohort and P=0.0068 in the ICGC cohort). ROC analysis validated the signature's prediction power. In addition, functional analyses showed enrichment of immune-related pathways and different immune status between the two risk groups. Conclusion The 7-SLC-gene prognostic signature established in this study helped predict the prognosis, and was also correlated with the tumor immune status and infiltration of different immune cells in the tumor microenvironment. The current findings may provide important clinical indications for proposing a novel combination therapy consists of targeted anti-SLC therapy and immunotherapy for HCC patients.
Collapse
|
8
|
Jin Y, Ma J, Wang L. Comprehensive analysis of immune-related lncRNAs and their clinical relevance in gastric adenocarcinoma. Funct Integr Genomics 2023; 23:28. [PMID: 36598654 DOI: 10.1007/s10142-022-00938-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 10/24/2022] [Accepted: 11/03/2022] [Indexed: 01/05/2023]
Abstract
Increasing evidence has demonstrated that lncRNA plays a significant role in the immunity regulation of gastric adenocarcinoma. However, the immune-related lncRNAs and the prognostic value in immunotherapies remain largely unexplored. We collected immune-related lncRNA and the associated pathways of gastric cancer from the ImmLnc database. The cox regression model is used to analyze the prognostic value of these lncRNAs. Gastric cancer is further divided into different subtypes based on these lncRNAs. Tumor microenvironment analysis, functional enrichment analysis, and genomic alteration analysis are performed for different subtypes. Furthermore, chemotherapeutic and immunotherapeutic sensitivity are also analyzed among different subtypes. Nine lncRNAs are identified as significant regulators of the immune pathway of gastric cancer. Gastric cancer can be classified into 5 subtypes based on these lncRNAs. Tumor microenvironment analysis shows that cluster C3 has the highest immune score and C5 has the lowest score. Functional analysis shows that these subtypes are enriched with distinct biological processes. Genomic analysis shows that LAMA2 mutation is a protective factor in C3 but a risk factor in C5. Furthermore, these subtypes are found to respond distinctly to the same chemotherapeutic and immunotherapeutic drugs. In this study, we analyzed the immune-related lncRNA and identified the crucial role in the regulation of immune properties, biological processes, and immunotherapeutic sensitivity. These findings can improve our understanding of the epigenetic immunoregulation of lncRNA and advance the research of immunotherapy.
Collapse
Affiliation(s)
- Yan Jin
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, Henan, China.,Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, Henan, China
| | - Jianfei Ma
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Luoyu Road 1037, Wuhan, 430074, China.
| | - Lidong Wang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, Henan, China.
| |
Collapse
|
9
|
Liu Y, Jiang J. A novel cuproptosis-related lncRNA signature predicts the prognosis and immunotherapy for hepatocellular carcinoma. Cancer Biomark 2023; 37:13-26. [PMID: 37005878 DOI: 10.3233/cbm-220259] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most serious malignant tumors with a poor prognosis worldwide. Cuproptosis is a novel copper-dependent cell death form, involving mitochondrial respiration and lipoylated components of the tricarboxylic acid (TCA) cycle. Long non-coding RNAs (lncRNAs) have been demonstrated to affect the tumorigenesis, growth, and metastasis of HCC. OBJECTIVE We explored the potential roles of cuproptosis-related lncRNAs in predicting the prognosis for HCC. METHODS The RNA-seq transcriptome data, mutation data, and clinical information data of HCC patients were downloaded from The Cancer Genome Atlas (TCGA) database. The least absolute shrinkage and selection operator (LASSO) algorithm and Cox regression analyses were performed to identify a prognostic cuproptosis-related lncRNA signature. The receiver operating characteristic (ROC) analysis was used to evaluate the predictive value of the lncRNA signature for HCC. The enrichment pathways, immune functions, immune cell infiltration, tumor mutation burden, and drug sensitivity were also analyzed. RESULTS We constructed a prognostic model consisting of 8 cuproptosis-related lncRNAs for HCC. The patients were divided into high-risk group and low-risk group according to the riskscore calculated using the model. Kaplan-Meier analysis revealed that the high-risk lncRNA signature was correlated with poor overall survival [hazard ratio (HR) =1.009, 95% confidence interval (CI) = 1.002-1.015; p= 0.010)] of HCC. A prognostic nomogram incorporated the lncRNA signature and clinicopathological features were constructed and showed favorable performance for predicting prognosis of HCC patients. In addition, the most immune-related functions were significantly different between the high-risk and low-risk groups. Tumor mutation burden (TMB) and immune checkpoints were also expressed differently between the two risk groups. Finally, HCC patients with low-risk score were more sensitive to several chemotherapy drugs. CONCLUSIONS The novel cuproptosis-related lncRNA signature could be used to predict prognosis and evaluate the effect of chemotherapy for HCC.
Collapse
Affiliation(s)
- Yanqing Liu
- Department of Laboratory Medicine, Ningbo First Hospital, Ningbo, Zhejiang, China
| | - Jianshuai Jiang
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo First Hospital, Ningbo, Zhejiang, China
| |
Collapse
|
10
|
Zhang C, Zhang W, Shui Y, Li P, Tian Z, Duan S, Wei Q. Implications of m6A-associated snRNAs in the prognosis and immunotherapeutic responses of hepatocellular carcinoma. Front Immunol 2022; 13:1001506. [PMID: 36405741 PMCID: PMC9667552 DOI: 10.3389/fimmu.2022.1001506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the most prevalent pathological type of liver cancer worldwide with high mortality and poor prognosis. N6-methyladenosine (m6A) can modify RNAs such as mRNA, lncRNA, miRNA, and tRNA, thereby playing a critical role in the pathogenesis of HCC. However, the role of m6A-associated small nuclear RNA (snRNA) in the prognostic value and immunotherapeutic response in HCC remains unclear. Materials and methods In this study, snRNA expression data, gene mutation data, and clinical data of HCC patients were acquired from The Cancer Genome Atlas (TCGA) database. We used the least absolute shrinkage and selection operator (LASSO) Cox regression analysis to identify significant prognostic m6A-associated snRNAs, and then developed a multivariate Cox model based on the selected snRNAs. HCC patients were split into low- and high-risk groups based on the median risk score. We subsequently performed Kaplan-Meier curve analysis to estimate overall survival (OS) by clinicopathological characteristics and tumor mutational burden (TMB) status in low- and high-risk HCC patients. Finally, we compared the immunotherapeutic response as represented by tumor immune dysfunction and exclusion (TIDE) scores between the two risk groups. Results Eight m6A-associated snRNAs were selected as independent predictors to develop the risk model. Our results revealed that the OS of HCC patients in the high-risk group was significantly worse than that in the low-risk group on clinicopathologic characteristics, including age (≤65 years and >65 years), gender (male), grade (G I-II and G III-IV) and TNM staging (Stage I-II and Stage III-IV). In addition, the OS of low-TMB and low-risk group was longer than that of high-TMB and high-risk group. The TIDE score indicated that HCC patients in the high-risk group were more susceptible to immunotherapy. Conclusion Our study suggests that m6A-associated snRNAs may be useful biomarkers for the prognosis of HCC and that m6A-associated snRNA models can predict the effect of immunotherapy in HCC patients.
Collapse
Affiliation(s)
- Cheng Zhang
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang, China
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wangjian Zhang
- School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yongjie Shui
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ping Li
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhifeng Tian
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shiwei Duan
- School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang, China
- *Correspondence: Qichun Wei, ; Shiwei Duan,
| | - Qichun Wei
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- *Correspondence: Qichun Wei, ; Shiwei Duan,
| |
Collapse
|
11
|
Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting. J Transl Med 2022; 20:442. [PMID: 36180904 PMCID: PMC9523969 DOI: 10.1186/s12967-022-03654-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/19/2022] [Indexed: 11/27/2022] Open
Abstract
Background Advances in our understanding of the tumor microenvironment have radically changed the cancer field, highlighting the emerging need for biomarkers of an active, favorable tumor immune phenotype to aid treatment stratification and clinical prognostication. Numerous immune-related gene signatures have been defined; however, their prognostic value is often limited to one or few cancer types. Moreover, the area of non-coding RNA as biomarkers remains largely unexplored although their number and biological roles are rapidly expanding. Methods We developed a multi-step process to identify immune-related long non-coding RNA signatures with prognostic connotation in multiple TCGA solid cancer datasets. Results Using the breast cancer dataset as a discovery cohort we found 2988 differentially expressed lncRNAs between immune favorable and unfavorable tumors, as defined by the immunologic constant of rejection (ICR) gene signature. Mapping of the lncRNAs to a coding-non-coding network identified 127 proxy protein-coding genes that are enriched in immune-related diseases and functions. Next, we defined two distinct 20-lncRNA prognostic signatures that show a stronger effect on overall survival than the ICR signature in multiple solid cancers. Furthermore, we found a 3 lncRNA signature that demonstrated prognostic significance across 5 solid cancer types with a stronger association with clinical outcome than ICR. Moreover, this 3 lncRNA signature showed additional prognostic significance in uterine corpus endometrial carcinoma and cervical squamous cell carcinoma and endocervical adenocarcinoma as compared to ICR. Conclusion We identified an immune-related 3-lncRNA signature with prognostic connotation in multiple solid cancer types which performed equally well and in some cases better than the 20-gene ICR signature, indicating that it could be used as a minimal informative signature for clinical implementation. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03654-7.
Collapse
|
12
|
Pallozzi M, Di Tommaso N, Maccauro V, Santopaolo F, Gasbarrini A, Ponziani FR, Pompili M. Non-Invasive Biomarkers for Immunotherapy in Patients with Hepatocellular Carcinoma: Current Knowledge and Future Perspectives. Cancers (Basel) 2022; 14:cancers14194631. [PMID: 36230554 PMCID: PMC9559710 DOI: 10.3390/cancers14194631] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/18/2022] [Accepted: 09/20/2022] [Indexed: 12/16/2022] Open
Abstract
Simple Summary The search for non-invasive biomarkers is a hot topic in modern oncology, since a tissue biopsy has significant limitations in terms of cost and invasiveness. The treatment perspectives have been significantly improved after the approval of immunotherapy for patients with hepatocellular carcinoma; therefore, the quick identification of responders is crucial to define the best therapeutic strategy. In this review, the current knowledge on the available non-invasive biomarkers of the response to immunotherapy is described. Abstract The treatment perspectives of advanced hepatocellular carcinoma (HCC) have deeply changed after the introduction of immunotherapy. The results in responders show improved survival compared with Sorafenib, but only one-third of patients achieve a significant benefit from treatment. As the tumor microenvironment exerts a central role in shaping the response to immunotherapy, the future goal of HCC treatment should be to identify a proxy of the hepatic tissue condition that is easy to use in clinical practice. Therefore, the search for biomarkers that are accurate in predicting prognosis will be the hot topic in the therapeutic management of HCC in the near future. Understanding the mechanisms of resistance to immunotherapy may expand the patient population that will benefit from it, and help researchers to find new combination regimens to improve patients’ outcomes. In this review, we describe the current knowledge on the prognostic non-invasive biomarkers related to treatment with immune checkpoint inhibitors, focusing on serological markers and gut microbiota.
Collapse
Affiliation(s)
- Maria Pallozzi
- Internal Medicine and Gastroenterology-Hepatology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Natalia Di Tommaso
- Internal Medicine and Gastroenterology-Hepatology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Valeria Maccauro
- Internal Medicine and Gastroenterology-Hepatology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Francesco Santopaolo
- Internal Medicine and Gastroenterology-Hepatology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Antonio Gasbarrini
- Internal Medicine and Gastroenterology-Hepatology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Translational Medicine and Surgery Department, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Francesca Romana Ponziani
- Internal Medicine and Gastroenterology-Hepatology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Translational Medicine and Surgery Department, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Correspondence: (F.R.P.); (M.P.)
| | - Maurizio Pompili
- Internal Medicine and Gastroenterology-Hepatology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Translational Medicine and Surgery Department, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Correspondence: (F.R.P.); (M.P.)
| |
Collapse
|
13
|
An Immune-Related lncRNA Pairing Model for Predicting the Prognosis and Immune-Infiltrating Cell Condition in Human Ovarian Cancer. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3168408. [PMID: 36033566 PMCID: PMC9400430 DOI: 10.1155/2022/3168408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022]
Abstract
Ovarian cancer is the second common cancer among the gynecological tumors. It is difficult to be found and diagnosed in the early stage and easy to relapse due to chemoresistance and deficiency in choices of treatment. Therefore, future exploring the biomarkers for diagnosis, treatment, and prognosis prediction of ovarian cancer is significant to women in the world. We downloaded data from TCGA and GTEx and used R “limma” package for analyzing the differentially expressed immune-related lncRNA in ovarian cancer and finally got 7 downregulated and 171 upregulated lncRNA. Then, we paired the differentially expressed immune-related lncRNA and constructed a novel lncRNA pairing model containing 7 lncRNA pairs. Based on the cut-off point with the highest AUC value, 102 patients were selected in high-risk group and 272 in low-risk group. The KM analysis suggested that the patients in the low-risk group had a longer overall survival. Future analysis showed the correlations between risk scores and clinicopathological parameters and infiltrating immune cells. In conclusion, we identified an immune-related lncRNA pairing model for predicting the prognosis and immune-infiltrating cell condition in human ovarian cancer, which thus further can instruct immunotherapy.
Collapse
|
14
|
Bao J, Wu Y, Zhang K, Qi H. AC099850.3/NCAPG Axis Predicts Poor Prognosis and is Associated with Resistance to EGFR Tyrosine-Kinase Inhibitors in Lung Adenocarcinoma. Int J Gen Med 2022; 15:6917-6930. [PMID: 36061963 PMCID: PMC9439153 DOI: 10.2147/ijgm.s365695] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/22/2022] [Indexed: 11/23/2022] Open
Abstract
Background TKI-acquired resistance markedly interferes with treatment of lung cancer patients with EGFR mutant features. Long non-coding RNAs (lncRNAs) modify EGFR-TKI resistance during tumor progression. Non-structural maintenance of chromosomes condensin I complex subunit G (NCAPG) is a mitosis-related protein that is involved in tumorigenesis. We investigated the potential regulatory lncRNAs of NCAPG in lung adenocarcinoma (LUAD) and assessed their roles in EGFR-TKI resistance. Methods Data for 1678 lung cancer patients were retrieved from TCGA and GEO databases and used to evaluate NCAPG and lncRNAs expressions, as well as their prognostic significance in LUAD. Protein levels of NCAPG in LUAD were validated by immuno-histochemistry. To assess the relationship between NCAPG levels and EGFR-TKIs sensitivity, a cohort of 57 LUAD patients administered with EGFR-TKIs was used. Results Both NCAPG and lncRNA AC099850.3 were over-expressed in LUAD tissues, and correlated with tumor progression and poor prognosis in LUAD. LncRNA AC099850.3 was identified as a potential regulator of NCAPG expressions. The AC099850.3/NCAGP axis was markedly correlated with EGFR mutations and IC50 of EGFR-TKIs. Besides, elevated NCAPG levels were associated with EGFR-TKIs resistance in 57 LUAD patients undergoing TKIs treatment. Gene set enrichment analysis revealed that both AC099850.3 and NCAGP were abundant in the cell cycle and the p53 signaling pathway. Conclusion The AC099850.3/NCAPG axis is a potential prognostic predictor and therapeutic biomarker for EGFR-TKIs in LUAD.
Collapse
Affiliation(s)
- Jiaqi Bao
- Department of Thoracic Surgery, Affiliated Hospital of Chifeng University, Chifeng, People’s Republic of China
| | - Yanlong Wu
- Department of Urology, Affiliated Hospital of Chifeng University, Chifeng, People’s Republic of China
| | - Kun Zhang
- Department of Radiology, Huhhot First Hospital, Huhhot, People’s Republic of China
| | - Huijuan Qi
- Department of Gynecology, Affiliated Hospital of Chifeng University, Chifeng, People’s Republic of China
- Correspondence: Huijuan Qi, Department of Gynecology, Affiliated Hospital of Chifeng University, Chifeng, People’s Republic of China, Email
| |
Collapse
|
15
|
Novel Prognosis and Therapeutic Response Model of Immune-Related lncRNA Pairs in Clear Cell Renal Cell Carcinoma. Vaccines (Basel) 2022; 10:vaccines10071161. [PMID: 35891325 PMCID: PMC9325030 DOI: 10.3390/vaccines10071161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/11/2022] [Accepted: 07/15/2022] [Indexed: 01/13/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common type of renal carcinoma. It is particularly important to accurately judge the prognosis of patients. Since most tumor prediction models depend on the specific expression level of related genes, a better model therefore needs to be constructed. To provide an immune-related lncRNA (irlncRNAs) tumor prognosis model that is independent of the specific gene expression levels, we first downloaded and sorted out the data on ccRCC in the TCGA database and screened irlncRNAs using co-expression analysis and then obtained the differently expressed irlncRNA (DEirlncRNA) pairs by means of univariate analysis. In addition, we modified LASSO penalized regression. Subsequently, the ROC curve was drawn, and we compared the area under the curve, calculated the Akaike information standard value of the 5-year receiver operating characteristic curve, and determined the cut-off point to establish the best model to distinguish the high- or low-disease-risk group of ccRCC. Subsequently, we reassessed the model from the perspectives of survival, clinic-pathological characteristics, tumor-infiltrating immune cells, chemotherapeutics efficacy, and immunosuppressed biomarkers. A total of 17 DEirlncRNAs pairs (AL031710.1|AC104984.5, AC020907.4|AC127-24.4,AC091185.1|AC005104.1, AL513218.1|AC079015.1, AC104564.3|HOXB-AS3, AC003070.1|LINC01355, SEMA6A-AS1|CR936218.1, AL513327.1|AS005785.1, AC084876.1|AC009704.2, IGFL2-AS1|PRDM16-DT, AC011462.4|MMP25-AS1, AL662844.3I|TGB2-AS1, ARHGAP27P1|AC116914.2, AC093788.1|AC007098.1, MCF2L-AS1|AC093001.1, SMIM25|AC008870.2, and AC027796.4|LINC00893) were identified, all of which were included in the Cox regression model. Using the cut-off point, we can better distinguish patients according to different factors, such as survival status, invasive clinic-pathological features, tumor immune infiltration, whether they are sensitive to chemotherapy or not, and expression of immunosuppressive biomarkers. We constructed the irlncRNA model by means of pairing, which can better eliminate the dependence on the expression level of the target genes. In other words, the signature established by pairing irlncRNA regardless of expression levels showed promising clinical prediction value.
Collapse
|
16
|
Liu J, Lu J, Li W, Mao W, Lu Y. Machine Learning Screens Potential Drugs Targeting a Prognostic Gene Signature Associated With Proliferation in Hepatocellular Carcinoma. Front Genet 2022; 13:900380. [PMID: 35836576 PMCID: PMC9273781 DOI: 10.3389/fgene.2022.900380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/13/2022] [Indexed: 02/05/2023] Open
Abstract
Background: This study aimed to screen potential drugs targeting a new prognostic gene signature associated with proliferation in hepatocellular carcinoma (HCC). Methods: CRISPR Library and TCGA datasets were used to explore differentially expressed genes (DEGs) related to the proliferation of HCC cells. Differential gene expression analysis, univariate COX regression analysis, random forest algorithm and multiple combinatorial screening were used to construct a prognostic gene signature. Then the predictive power of the gene signature was validated in the TCGA and ICGC datasets. Furthermore, potential drugs targeting this gene signature were screened. Results: A total of 640 DEGs related to HCC proliferation were identified. Using univariate Cox analysis and random forest algorithm, 10 hub genes were screened. Subsequently, using multiplex combinatorial screening, five hub genes (FARSB, NOP58, CCT4, DHX37 and YARS) were identified. Taking the median risk score as a cutoff value, HCC patients were divided into high- and low-risk groups. Kaplan-Meier analysis performed in the training set showed that the overall survival of the high-risk group was worse than that of the low-risk group (p < 0.001). The ROC curve showed a good predictive efficiency of the risk score (AUC > 0.699). The risk score was related to gene mutation, cancer cell stemness and immune function changes. Prediction of immunotherapy suggetsted the IC50s of immune checkpoint inhibitors including A-443654, ABT-888, AG-014699, ATRA, AUY-922, and AZ-628 in the high-risk group were lower than those in the low-risk group, while the IC50s of AMG-706, A-770041, AICAR, AKT inhibitor VIII, Axitinib, and AZD-0530 in the high-risk group were higher than those in the low-risk group. Drug sensitivity analysis indicated that FARSB was positively correlated with Hydroxyurea, Vorinostat, Nelarabine, and Lomustine, while negatively correlated with JNJ-42756493. DHX37 was positively correlated with Raltitrexed, Cytarabine, Cisplatin, Tiotepa, and Triethylene Melamine. YARS was positively correlated with Axitinib, Fluphenazine and Megestrol acetate. NOP58 was positively correlated with Vorinostat and 6-thioguanine. CCT4 was positively correlated with Nerabine. Conclusion: The five-gene signature associated with proliferation can be used for survival prediction and risk stratification for HCC patients. Potential drugs targeting this gene signature deserve further attention in the treatment of HCC.
Collapse
Affiliation(s)
- Jun Liu
- Department of Clinical Laboratory, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
- Medical Research Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Jianjun Lu
- Department of Medical Affairs, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wenli Li
- Reproductive Medicine Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Wenjie Mao
- Emergency Department, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Yamin Lu
- Department of Clinical Laboratory, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| |
Collapse
|
17
|
Yang J, Liu F, Wang Y, Qu L, Lin A. LncRNAs in tumor metabolic reprogramming and immune microenvironment remodeling. Cancer Lett 2022; 543:215798. [PMID: 35738332 DOI: 10.1016/j.canlet.2022.215798] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/06/2022] [Accepted: 06/15/2022] [Indexed: 11/02/2022]
Abstract
Evidence accumulated over the past decade has verified that long non-coding RNAs (lncRNAs) exert important functions in multiple cell programs. As a novel class of cellular regulatory molecules, lncRNAs interact with different molecules, such as DNA, RNA or proteins, depending on their subcellular distribution, to modulate gene transcription and kinase cascades. It has been widely clarified that lncRNAs play important roles in modulating metabolic reprogramming and reshaping the immune landscape and serve as hinges bridging tumor metabolism and anti-tumor immunity. Given these facts, lncRNAs, as putative regulators of tumor initiation and progression, have attracted extensive attention in recent years. In this review, we summarized the current research progress on the role of lncRNAs in tumor metabolic reprogramming and tumor-immune microenvironment remodeling, and conclude with our laboratory's contributions in advancing the clinical applications of lncRNAs.
Collapse
Affiliation(s)
- Jiecheng Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang, 310058, China
| | - Fangzhou Liu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang, 310058, China
| | - Ying Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang, 310058, China
| | - Lei Qu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang, 310058, China
| | - Aifu Lin
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang, 310058, China; Breast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China; International School of Medicine, International Institutes of Medicine, The 4th Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, 322000, China; ZJU-QILU Joint Research Institute, Hangzhou, Zhejiang, 310058, China.
| |
Collapse
|
18
|
Zhou D, Wang J, Liu X. Development of six immune-related lncRNA signature prognostic model for smoking-positive lung adenocarcinoma. J Clin Lab Anal 2022; 36:e24467. [PMID: 35561270 PMCID: PMC9169227 DOI: 10.1002/jcla.24467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/10/2022] [Accepted: 04/22/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Smoking is one of the most hazardous risk factors for the development of lung adenocarcinoma (LUAD). Many survival and prognosis-related biomarkers were discovered using database mining. However, the precision of immune-related long noncoding RNAs (lncRNAs) predictions is insufficient. We identified a novel signature to improve the estimate of smoking-related LUAD prognosis. METHODS The Cancer Genome Atlas database (TCGA) was used to obtain the LUAD lncRNA expression profiles. The smoking-related LUAD cohort was randomly split into discovery and validation cohorts. To determine the risk score, use the LASSO Cox regression technique on the prognostic immune-related lncRNA. The risk signature has been developed. RESULTS A total of 643 immune-related lncRNAs were identified as potential candidates for a risk signature. Finally, six immune-related lncRNAs (AL359915.2, AP000695.1, HSPC324, TGFB2-AS1, AC026355.1, and AC002128.2) were identified and used to carry out risk signature, which showed a close association with overall survival in the discovery cohort. We classified patients as high risk or low risk based on a median risk score of 1.0783. In the discovery cohort, overall survival was marginally longer in the low-risk group than in the high-risk category (p = 2.28e08). The area under the curves (AUC) for 1-, 3-, and 5-year survival was 0.67, 0.7, and 0.82, respectively. Furthermore, we successfully validated and combined cohorts using this risk profile. We discovered a strong positive connection between HSPC324 and VIPR1 as a possible novel biomarker for smoking-related LUAD development in our study. CONCLUSIONS Our research has established a six immune-lncRNA signature that may be used to predict the prognosis of smoking-related LUAD with great accuracy.
Collapse
Affiliation(s)
- Dajie Zhou
- Department of Clinical Laboratory CenterYantai Yuhuangding HospitalYantaiChina
| | - Jing Wang
- Department of Clinical Laboratory CenterYantai Yuhuangding HospitalYantaiChina
| | - Xiangdong Liu
- Department of Clinical LaboratoryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
| |
Collapse
|
19
|
Analysis of multiple databases identifies crucial genes correlated with prognosis of hepatocellular carcinoma. Sci Rep 2022; 12:9002. [PMID: 35637248 PMCID: PMC9151754 DOI: 10.1038/s41598-022-13159-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/20/2022] [Indexed: 11/27/2022] Open
Abstract
Despite advancements made in the therapeutic strategies on hepatocellular carcinoma (HCC), the survival rate of HCC patient is not satisfactory enough. Therefore, there is an urgent need for the valuable prognostic biomarkers in HCC therapy. In this study, we aimed to screen hub genes correlated with prognosis of HCC via multiple databases. 117 HCC-related genes were obtained from the intersection of the four databases. We subsequently identify 10 hub genes (JUN, IL10, CD34, MTOR, PTGS2, PTPRC, SELE, CSF1, APOB, MUC1) from PPI network by Cytoscape software analysis. Significant differential expression of hub genes between HCC tissues and adjacent tissues were observed in UALCAN, HCCDB and HPA databases. These hub genes were significantly associated with immune cell infiltrations and immune checkpoints. The hub genes were correlated with clinical parameters and survival probability of HCC patients. 147 potential targeted therapeutic drugs for HCC were identified through the DGIdb database. These hub genes could be used as novel prognostic biomarkers for HCC therapy.
Collapse
|
20
|
Identification and Validation of a GPX4-Related Immune Prognostic Signature for Lung Adenocarcinoma. JOURNAL OF ONCOLOGY 2022; 2022:9054983. [PMID: 35620733 PMCID: PMC9130018 DOI: 10.1155/2022/9054983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 12/24/2022]
Abstract
Lung adenocarcinoma (LUAD) is a commonly occurring histological subtype of lung cancer. Glutathione peroxidase 4 (GPX4) is an important regulatory factor of ferroptosis and is involved in the development of many cancers, but its prognostic significance has not been systematically described in LUAD. In this study, we focused on developing a robust GPX4-related prognostic signature (GPS) for LUAD. Data for the training cohort was extracted from The Cancer Genome Atlas, and that for the validation cohort was sourced from the GSE72094 dataset including 863 LUAD patients. GPX4-related genes were screened out by weighted gene coexpression network analysis and Spearman’s correlation analysis. Then, Cox regression and least absolute shrinkage and selection operator regression analyses were employed to construct a GPS. The ESTIMATE algorithm, single-sample gene set enrichment analysis (ssGSEA), and GSEA were utilized to evaluate the relationship between GPS and the tumor microenvironment (TME). We constructed and validated a GPS premised on four GPX4-related genes (KIF14, LATS2, PRKCE, and TM6SF1), which could classify LUAD patients into low- and high-score cohorts. The high-risk cohort presented noticeably poorer overall survival (OS) as opposed to the low-risk cohort, meaning that the GPS may be utilized as an independent predictor of the OS of LUAD. The GPS was also adversely correlated with multiple tumor-infiltrating immune cells and immune-related processes and pathways in TME. Furthermore, greater sensitivity to erlotinib and lapatinib were identified in the low-risk cohort based on the GDSC database. Our findings suggest that the GPS can effectively forecast the prognosis of LUAD patients and may possibly regulate the TME of LUAD.
Collapse
|
21
|
Rizzo A, Ricci AD. Predictors of response for hepatocellular carcinoma immunotherapy: is there anything on the horizon? EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2022. [DOI: 10.1080/23808993.2022.2075724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Alessandro Rizzo
- Struttura Semplice Dipartimentale di Oncologia Medica per la Presa in Carico Globale del Paziente Oncologico “Don Tonino Bello,” I.R.C.C.S. Istituto Tumori “Giovanni Paolo II”, Bari, Italy
| | - Angela Dalia Ricci
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| |
Collapse
|
22
|
Li X, Zhang Z, Liu M, Fu X, A J, Chen G, Wu S, Dong JT. Establishment of a lncRNA-Based Prognostic Gene Signature Associated With Altered Immune Responses in HCC. Front Immunol 2022; 13:880288. [PMID: 35572559 PMCID: PMC9097819 DOI: 10.3389/fimmu.2022.880288] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/05/2022] [Indexed: 01/01/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a common malignancy with higher mortality, and means are urgently needed to improve the prognosis. T cell exclusion (TCE) plays a pivotal role in immune evasion, and lncRNAs represent a large group of tumor development and progression modulators. Using the TCGA HCC dataset (n=374), we identified 2752 differentially expressed and 702 TCE-associated lncRNAs, of which 336 were in both groups. As identified using the univariate Cox regression analysis, those associated with overall survival (OS) were subjected to the LASSO-COX regression analysis to develop a prognosis signature. The model, which consisted of 11 lncRNAs and was named 11LNCPS for 11-lncRNA prognosis signature, was validated and performed better than two previous models. In addition to OS and TCE, higher 11LNCPS scores had a significant correlation with reduced infiltrations of CD8+ T cells and dendritic cells (DCs) and decreased infiltrations of Th1, Th2, and pro B cells. As expected, these infiltration alterations were significantly associated with worse OS in HCC. Analysis of published data indicates that HCCs with higher 11LNCPS scores were transcriptomically similar to those that responded better to PDL1 inhibitor. Of the 11LNCPS lncRNAs, LINC01134 and AC116025.2 seem more crucial, as their upregulations affected more immune cell types' infiltrations and were significantly associated with TCE, worse OS, and compromised immune responses in HCC. LncRNAs in the 11LNCPS impacted many cancer-associated biological processes and signaling pathways, particularly those involved in immune function and metabolism. The 11LNCPS should be useful for predicting prognosis and immune responses in HCC.
Collapse
Affiliation(s)
- Xiawei Li
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
- Laboratory Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Zhiqian Zhang
- Laboratory Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Mingcheng Liu
- Laboratory Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Xing Fu
- Laboratory Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jun A
- Laboratory Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Guoan Chen
- Laboratory Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Shian Wu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jin-Tang Dong
- Laboratory Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| |
Collapse
|
23
|
Rizzo A, Cusmai A, Gadaleta-Caldarola G, Palmiotti G. Which role for predictors of response to immune checkpoint inhibitors in hepatocellular carcinoma? Expert Rev Gastroenterol Hepatol 2022; 16:333-339. [PMID: 35403533 DOI: 10.1080/17474124.2022.2064273] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Hepatocellular carcinoma (HCC) remains a frequently diagnosed malignancy worldwide, still representing an important cause of cancer-related death. Recent years have seen the emergence of novel systemic treatments for HCC patients, including immune checkpoint inhibitors (ICIs). Nonetheless, several questions regarding HCC immunotherapy remain unanswered, especially in terms of biochemical predictors of response. AREAS COVERED In the current paper, we will discuss available evidence regarding predictive biomarkers of response to HCC immunotherapy. A literature search was conducted in January 2022 of Pubmed/Medline, Cochrane library, and Scopus databases. EXPERT OPINION The identification of predictive biomarkers represents an unmet need in HCC patients receiving ICIs. The HCC medical community is called to further efforts aimed to elucidate the effective role of PD-L1 expression, TMB, MSI, gut microbiota, and other emerging biomarkers.
Collapse
Affiliation(s)
- Alessandro Rizzo
- Struttura Semplice Dipartimentale di Oncologia Medica per la Presa in Carico Globale del Paziente Oncologico "Don Tonino Bello," I.R.C.C.S. Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124 Bari, Italy
| | - Antonio Cusmai
- Struttura Semplice Dipartimentale di Oncologia Medica per la Presa in Carico Globale del Paziente Oncologico "Don Tonino Bello," I.R.C.C.S. Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124 Bari, Italy
| | - Gennaro Gadaleta-Caldarola
- Medical Oncology Unit, 'Mons. R. Dimiccoli' Hospital, Barletta (BT), Azienda Sanitaria Locale Barletta, 76121, Italy
| | - Gennaro Palmiotti
- Struttura Semplice Dipartimentale di Oncologia Medica per la Presa in Carico Globale del Paziente Oncologico "Don Tonino Bello," I.R.C.C.S. Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124 Bari, Italy
| |
Collapse
|
24
|
Zhang Y, Yang X, Zhou L, Gao X, Wu X, Chen X, Hou J, Wang L. Immune-related lincRNA pairs predict prognosis and therapeutic response in hepatocellular carcinoma. Sci Rep 2022; 12:4259. [PMID: 35277569 PMCID: PMC8917134 DOI: 10.1038/s41598-022-08225-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/03/2022] [Indexed: 12/03/2022] Open
Abstract
Growing evidence has demonstrated the functional relevance of long intergenic noncoding RNAs (lincRNAs) to tumorigenesis and immune response. However, immune-related lincRNAs and their value in predicting the clinical outcomes of patients with liver cancer remain largely unexplored. Herein, we utilized the strategy of iterative gene pairing to construct a tumor-specific immune-related lincRNA pairs signature (IRLPS), which did not require specific expression levels, as an indicator of patient outcomes. The 18-IRLPS we developed was associated with overall survival, tumor progression, and recurrence in liver cancer patients. Multivariate analysis revealed that the risk model was an independent predictive factor. A high IRLPS risk was correlated suppressive immune microenvironment, and IRLPS-high patients might benefit more from CD276 blockade or TMIGD2 agonist. Patients in the high-risk group were associated with elevated tumor mutation, increased sensitivity to dopamine receptor antagonists, cisplatin, doxorubicin, and mitomycin but more resistance to vinblastine. Mechanistically, IRLPS high scores might lead to poor prognosis by promoting cell proliferation and metabolic reprogramming. The prognostic significance of the 18-IRLPS was confirmed in independent cancer datasets. These findings highlighted the robust predictive performances of the 18-IRLPS for prognosis and personalized treatment.
Collapse
Affiliation(s)
- Yingna Zhang
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China.,Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, China.,Department of Anatomy, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Xiaofeng Yang
- Department of Immunology, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Lisha Zhou
- Department of Immunology, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Xiangting Gao
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China.,Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, China.,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Xiangwei Wu
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China.,Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Xueling Chen
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China.,Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, China.,Department of Immunology, Shihezi University School of Medicine, Shihezi, Xinjiang, China
| | - Jun Hou
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China. .,Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, China. .,Department of Immunology, Shihezi University School of Medicine, Shihezi, Xinjiang, China.
| | - Lianghai Wang
- NHC Key Laboratory of Prevention and Treatment of Central Asia High Incidence Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China. .,Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, China. .,Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, China.
| |
Collapse
|
25
|
Melixetian M, Pelicci PG, Lanfrancone L. Regulation of LncRNAs in Melanoma and Their Functional Roles in the Metastatic Process. Cells 2022; 11:cells11030577. [PMID: 35159386 PMCID: PMC8834033 DOI: 10.3390/cells11030577] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/02/2022] [Accepted: 02/05/2022] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are key regulators of numerous intracellular processes leading to tumorigenesis. They are frequently deregulated in cancer, functioning as oncogenes or tumor suppressors. As they act through multiple mechanisms, it is not surprising that they may exert dual functions in the same tumor. In melanoma, a highly invasive and metastatic tumor with the propensity to rapidly develop drug resistance, lncRNAs play different roles in: (i) guiding the phenotype switch and leading to metastasis formation; (ii) predicting the response of melanoma patients to immunotherapy; (iii) triggering adaptive responses to therapy and acquisition of drug resistance phenotypes. In this review we summarize the most recent findings on the lncRNAs involved in melanoma growth and spreading to distant sites, focusing on their role as biomarkers for disease diagnosis and patient prognosis, or targets for novel therapeutic approaches.
Collapse
Affiliation(s)
- Marine Melixetian
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (M.M.); (P.G.P.)
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (M.M.); (P.G.P.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Luisa Lanfrancone
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (M.M.); (P.G.P.)
- Correspondence: ; Tel.: +39-02-94375011
| |
Collapse
|
26
|
Zhang WY, Zhan HL, Li MK, Wu GD, Liu Z, Wu LF. Long noncoding RNA Gas5 induces cell apoptosis and inhibits tumor growth via activating the CHOP-dependent endoplasmic reticulum stress pathway in human hepatoblastoma HepG2 cells. J Cell Biochem 2022; 123:231-247. [PMID: 34636091 DOI: 10.1002/jcb.30159] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 02/05/2023]
Abstract
In recent years, long noncoding RNAs (lncRNAs) have been demonstrated to be important tumor-associated regulatory factors. LncRNA growth arrest-specific transcript 5 (Gas5) acts as an anti-oncogene in most cancers. Whether Gas5 acts as an oncogene or anti-oncogene in hepatocellular carcinoma (HCC) remains unclear. In the present study, the expression and role of Gas5 in HCC were investigated in vitro and in vivo. Lower expression levels of Gas5 were determined in HCC tissues and cells by quantitative reverse transcription-polymerase chain reaction. Overexpressed Gas 5 lentiviral vectors were constructed to analyze their influence on cell viability, migration, invasion, and apoptosis. Fluorescence in situ hybridization was used to identify the subcellular localization of Gas5. Protein complexes that bound to Gas5 were isolated from HepG2 cells through pull-down experiments and analyzed by mass spectrometry. A series of novel Gas5-interacting proteins were identified and bioinformatics analysis was carried out. These included ribosomal proteins, proteins involved in protein folding, sorting, and transportation in the ER, some nucleases and protein enzymes involved in gene transcription, translation, and other proteins with various functions.78 kDa glucose-regulated protein (GRP78) was identified as a direct target of Gas5 by Rip-qPCR and Western blot analysis assay. Gas5 inhibited HepG2 cell growth and induced cell apoptosis via upregulating CHOP to activate the ER stress signaling pathway. Further studies indicated that the knockdown of CHOP by shRNA partially reversed Gas5-mediated apoptosis in HepG2 cells. Magnetic resonance imaging showed that the ectopic expression of Gas5 inhibited the growth of HCC in nude mice. These findings suggest that Gas5 functions as a tumor suppressor and induces apoptosis through activation of ER stress by targeting the CHOP signal pathway in HCC.
Collapse
Affiliation(s)
- Wei-Yi Zhang
- Department of Gastroenterology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Hao-Lian Zhan
- Department of Gastroenterology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Ming-Kai Li
- Department of Gastroenterology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Guan-Di Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong Province, China
| | - Zhe Liu
- Department of Gastroenterology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Ling-Fei Wu
- Department of Gastroenterology, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong Province, China
| |
Collapse
|
27
|
Chen Y, Xi L, Wei L, Sun D, Zeng T. Immune-related lncRNA signature delineates an immune-excluded subtype of liver cancer with unfavorable clinical outcomes. J Clin Lab Anal 2022; 36:e24244. [PMID: 35040184 PMCID: PMC8906039 DOI: 10.1002/jcla.24244] [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: 11/25/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play crucial roles in immune regulation and, therefore, may be closely related to the tumor microenvironment (TME). However, there are few studies regarding the relationship between the lncRNAs and the TME in liver cancer. METHODS Firstly, we constructed a lncRNA signature based on the top 10 immune-inversely related lncRNAs obtained from the ImmLnc database and performed disease-free survival (DFS) and overall survival (OS) analyses for the patients included in the Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) stratified by the lncRNA signature. Then, we explored the relationship between the lncRNA signature with distinct mutation profiles and the tumor microenvironment (TME). RESULTS The lncRNA signature was successfully constructed and verified by survival analysis. The high lncRNA signature was correlated with a decreased DFS and OS in liver cancer and other two gastrointestinal cancers. The mutation profiles showed that the Lnc_high group had a higher number of mutations on many genes, mostly enriched in p53 and WNT pathways. The TME results showed that the Lnc_high group had the highest proportion (51%) of lymphocyte depletion-characterized immune subtype, and a higher expression of immune checkpoint molecules such as LAG3, PD-L1, CTLA4. On the contrary, in the Lnc_low group, infiltrating immune-cell proportions were significantly higher, and a significant enhancement of four axes of the cancer immunity cycle immunogram was observed in this group. CONCLUSIONS The lncRNA signature we constructed identified an immune-excluded subtype of liver cancer with unfavorable clinic outcomes, which could be tested as a biomarker for immunotherapy in the future.
Collapse
Affiliation(s)
- Yawei Chen
- Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Leying Xi
- Department of Pediatrics, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Lihui Wei
- Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Debin Sun
- Genecast Biotechnology Co., Ltd, Wuxi, China
| | - Tianmei Zeng
- Department of Oncology, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| |
Collapse
|
28
|
Huang S, Zhang J, Lai X, Zhuang L, Wu J. Identification of Novel Tumor Microenvironment-Related Long Noncoding RNAs to Determine the Prognosis and Response to Immunotherapy of Hepatocellular Carcinoma Patients. Front Mol Biosci 2022; 8:781307. [PMID: 35004851 PMCID: PMC8739902 DOI: 10.3389/fmolb.2021.781307] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/25/2021] [Indexed: 12/12/2022] Open
Abstract
Introduction: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors with poor prognosis. The tumor microenvironment (TME) plays a vital role in HCC progression. Thus, this research was designed to analyze the correlation between the TME and the prognosis of HCC patients and to construct a TME-related long noncoding RNA (lncRNA) signature to determine HCC patients’ prognosis and response to immunotherapy. Methods: We assessed the stromal–immune–estimate scores within the HCC microenvironment using the ESTIMATE (Estimation of Stromal and Immune Cells in Malignant Tumor Tissues Using Expression Data) algorithm based on The Cancer Genome Atlas database, and their associations with survival and clinicopathological parameters were also analyzed. Thereafter, differentially expressed lncRNAs were filtered out according to the immune and stromal scores. Cox regression analysis was performed to build a TME-related lncRNA risk signature. Kaplan–Meier analysis was used to explore the prognostic value of the risk signature. Furthermore, we explored the biological functions and immune microenvironment features in the high- and low-risk groups. Lastly, we probed the association of the risk model with treatment responses to immune checkpoint inhibitors (ICIs) in HCC. Results: The stromal, immune, and estimate scores were obtained utilizing the ESTIMATE algorithm for patients with HCC. Kaplan–Meier analysis showed that high scores were significantly correlated with better prognosis in HCC patients. Six TME-related lncRNAs were screened to construct the prognostic model. The Kaplan–Meier curves suggested that HCC patients with low risk had better prognosis than those with high risk. Receiver operating characteristic (ROC) curve and Cox regression analyses indicated that the risk model could predict HCC survival exactly and independently. Functional enrichment analysis revealed that some tumor- and immune-related pathways were activated in the high-risk group. We also revealed that some immune cells, which were important in enhancing immune responses toward cancer, were significantly increased in the low-risk group. In addition, there was a close correlation between ICIs and the risk signature, which can be used to predict the treatment responses of HCC patients. Conclusion: We analyzed the influence of the stromal, immune, and estimate scores on the prognosis of HCC patients. A novel TME-related lncRNA risk model was established, which could be effectively applied as an independent prognostic biomarker and predictor of ICIs for HCC patients.
Collapse
Affiliation(s)
- Shenglan Huang
- The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Key Laboratory of Clinical and Translational Cancer Research, Nanchang, China
| | - Jian Zhang
- The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Key Laboratory of Clinical and Translational Cancer Research, Nanchang, China
| | - Xiaolan Lai
- Ningde Municipal Hospital Affiliated to Ningde Normal University, Ningde, China
| | - Lingling Zhuang
- The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Key Laboratory of Clinical and Translational Cancer Research, Nanchang, China
| | - Jianbing Wu
- The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Key Laboratory of Clinical and Translational Cancer Research, Nanchang, China
| |
Collapse
|
29
|
Gao M, Liu S, Qi Y, Guo X, Shang X. ImReLnc: Identifying Immune-Related LncRNA Characteristics in Human Cancers Based on Heuristic Correlation Optimization. Front Genet 2022; 12:792541. [PMID: 35082835 PMCID: PMC8784420 DOI: 10.3389/fgene.2021.792541] [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: 10/10/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play critical roles in cancer through gene expression and immune regulation. Identifying immune-related lncRNA (irlncRNA) characteristics would contribute to dissecting the mechanism of cancer pathogenesis. Some computational methods have been proposed to identify irlncRNA characteristics in human cancers, but most of them are aimed at identifying irlncRNA characteristics in specific cancer. Here, we proposed a new method, ImReLnc, to recognize irlncRNA characteristics for 33 human cancers and predict the pathogenicity levels of these irlncRNAs across cancer types. We first calculated the heuristic correlation coefficient between lncRNAs and mRNAs for immune-related enrichment analysis. Especially, we analyzed the relationship between lncRNAs and 17 immune-related pathways in 33 cancers to recognize the irlncRNA characteristics of each cancer. Then, we calculated the Pscore of the irlncRNA characteristics to evaluate their pathogenicity levels. The results showed that highly pathogenic irlncRNAs appeared in a higher proportion of known disease databases and had a significant prognostic effect on cancer. In addition, it was found that the expression of irlncRNAs in immune cells was higher than that of non-irlncRNAs, and the proportion of irlncRNAs related to the levels of immune infiltration was much higher than that of non-irlncRNAs. Overall, ImReLnc accurately identified the irlncRNA characteristics in multiple cancers based on the heuristic correlation coefficient. More importantly, ImReLnc effectively evaluated the pathogenicity levels of irlncRNAs across cancer types. ImReLnc is freely available at https://github.com/meihonggao/ImReLnc.
Collapse
Affiliation(s)
- Meihong Gao
- School of Computer Science and Engineering, Northwestern Polytechnical University, Xi'an, China
| | - Shuhui Liu
- School of Computer Science and Engineering, Northwestern Polytechnical University, Xi'an, China
| | - Yang Qi
- School of Computer Science and Engineering, Northwestern Polytechnical University, Xi'an, China
| | - Xinpeng Guo
- School of Computer Science and Engineering, Northwestern Polytechnical University, Xi'an, China
| | - Xuequn Shang
- School of Computer Science and Engineering, Northwestern Polytechnical University, Xi'an, China
| |
Collapse
|
30
|
Rizzo A, Ricci AD, Di Federico A, Frega G, Palloni A, Tavolari S, Brandi G. Predictive Biomarkers for Checkpoint Inhibitor-Based Immunotherapy in Hepatocellular Carcinoma: Where Do We Stand? Front Oncol 2022; 11:803133. [PMID: 34976841 PMCID: PMC8718608 DOI: 10.3389/fonc.2021.803133] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/01/2021] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) remains the sixth most commonly diagnosed malignancy worldwide, still representing an important cause of cancer-related death. Over the next few years, novel systemic treatment options have emerged. Among these, immune checkpoint inhibitors (ICIs) have been widely evaluated and are under assessment, as monotherapy or in combination with other anticancer agents in treatment-naïve and previously treated patients. In particular, the approval of the PD-L1 inhibitor atezolizumab plus the antiangiogenic agent bevacizumab as front-line treatment for advanced HCC has led to the adoption of this combination in this setting, and the IMbrave 150 phase III trial has established a novel standard of care. However, several questions remain unanswered, including the identification of reliable predictors of response to ICIs in HCC patients. In the current paper, we will provide an updated overview of potentially useful predictive biomarkers of response to immunotherapy in advanced HCC. A literature search was conducted in September 2021 of Pubmed/Medline, Cochrane library and Scopus databases.
Collapse
Affiliation(s)
- Alessandro Rizzo
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Angela Dalia Ricci
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | - Giorgio Frega
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Andrea Palloni
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Simona Tavolari
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giovanni Brandi
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| |
Collapse
|
31
|
Deng W, Wang G, Deng H, Yan Y, Zhu K, Chen R, Liu X, Chen L, Zeng T, Fu B. The Role of Critical N6-Methyladenosine-Related Long Non-Coding RNAs and Their Correlations with Immune Checkpoints in Renal Clear Cell Carcinoma. Int J Gen Med 2021; 14:9773-9787. [PMID: 34934351 PMCID: PMC8684405 DOI: 10.2147/ijgm.s344771] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/01/2021] [Indexed: 12/12/2022] Open
Abstract
Purpose This study aimed to evaluate the functions of critical N6-methyladenosine (m6A)-related long non-coding RNAs (lncRNAs) and their correlations with immunotherapeutic targets in clear cell renal cell carcinoma (ccRCC). Methods m6A-related lncRNAs were analyzed using the dataset from The Cancer Genome Atlas database via Pearson correlation analysis. Then, their prognostic functions in patients with ccRCC were determined via univariate Cox analysis. A prognostic m6A-related lncRNA signature (MRLS) in ccRCC was established using the least absolute shrinkage and selection operator (LASSO) Cox regression model. In addition, the correlations between these prognostic m6A-related lncRNAs with immune checkpoints were further evaluated in clinical samples. Results MRLS was established by the LASSO Cox regression model on the basis of seven prognostic m6A-related lncRNAs. The risk score for each patient was calculated using the MRLS model, and the patients were further stratified into high- and low-risk subgroups. The MRLS model was validated with a robust prognostic ability by the stratification analysis. On the basis of age, grade, stage, and risk score, a nomogram was developed with a strong reliability in forecasting the overall survival percentages of the patients with ccRCC. Moreover, seven prognostic m6A-related lncRNAs enrolled in the MRLS model were found to be correlated with various immunotherapeutic targets, namely, PD-1, PD-L1, CTLA4, and LAG3, and the expression levels of which in the high-risk subgroup were significantly higher than those in the low-risk subgroup. The significant correlations between LINC00342 and the aforementioned immunotherapeutic targets were also confirmed in clinical samples. Conclusion In this study, seven m6A-related lncRNAs were identified as potential biomarkers for forecasting the prognosis of patients with ccRCC and evaluating the efficacy of immunotherapy for these patients. Furthermore, a prognostic and predictive MRLS model with a high reliability was constructed to predict the overall survival probability of patients with ccRCC.
Collapse
Affiliation(s)
- Wen Deng
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province, People's Republic of China
| | - Gongxian Wang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province, People's Republic of China
| | - Huanhuan Deng
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province, People's Republic of China
| | - Yan Yan
- Department of Nephrology, The First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province, People's Republic of China
| | - Ke Zhu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province, People's Republic of China
| | - Ru Chen
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province, People's Republic of China.,Department of Urology, The First Hospital of Putian City, Putian City, Fujian Province, People's Republic of China
| | - Xiaoqiang Liu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province, People's Republic of China
| | - Luyao Chen
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province, People's Republic of China
| | - Tao Zeng
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province, People's Republic of China
| | - Bin Fu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang City, Jiangxi Province, People's Republic of China
| |
Collapse
|
32
|
Deng M, Lin JB, Zhao RC, Li SH, Lin WP, Zou JW, Wei W, Guo RP. Construction of a novel immune-related lncRNA signature and its potential to predict the immune status of patients with hepatocellular carcinoma. BMC Cancer 2021; 21:1347. [PMID: 34923955 PMCID: PMC8684648 DOI: 10.1186/s12885-021-09059-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 11/28/2021] [Indexed: 12/24/2022] Open
Abstract
Background The accuracy of existing biomarkers for predicting the prognosis of hepatocellular carcinoma (HCC) is not satisfactory. It is necessary to explore biomarkers that can accurately predict the prognosis of HCC. Methods In this study, original transcriptome data were downloaded from The Cancer Genome Atlas (TCGA) database. Immune-related long noncoding ribonucleic acids (irlncRNAs) were identified by coexpression analysis, and differentially expressed irlncRNA (DEirlncRNA) pairs were distinguished by univariate analysis. In addition, the least absolute shrinkage and selection operator (LASSO) penalized regression was modified. Next, the cutoff point was determined based on the area under the curve (AUC) and Akaike information criterion (AIC) values of the 5-year receiver operating characteristic (ROC) curve to establish an optimal model for identifying high-risk and low-risk groups of HCC patients. The model was then reassessed in terms of clinicopathological features, survival rate, tumor-infiltrating immune cells, immunosuppressive markers, and chemotherapy efficacy. Results A total of 1009 pairs of DEirlncRNAs were recognized in this study, 30 of these pairs were included in the Cox regression model for subsequent analysis. After regrouping according to the cutoff point, we could more effectively identify factors such as aggressive clinicopathological features, poor survival outcomes, specific immune cell infiltration status of tumors, high expression level of immunosuppressive biomarkers, and low sensitivity to chemotherapy drugs in HCC patients. Conclusions The nonspecific expression level signature involved with irlncRNAs shows promising clinical value in predicting the prognosis of HCC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-09059-x.
Collapse
Affiliation(s)
- Min Deng
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Guangzhou, China.,Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng East Road, Guangzhou, China
| | - Jia-Bao Lin
- Department of Health Management Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Rong-Ce Zhao
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Guangzhou, China.,Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng East Road, Guangzhou, China
| | - Shao-Hua Li
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Guangzhou, China.,Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng East Road, Guangzhou, China
| | - Wen-Ping Lin
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Guangzhou, China.,Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng East Road, Guangzhou, China
| | - Jing-Wen Zou
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Guangzhou, China.,Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng East Road, Guangzhou, China
| | - Wei Wei
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Guangzhou, China.,Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng East Road, Guangzhou, China
| | - Rong-Ping Guo
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China. .,State Key Laboratory of Oncology in South China, Guangzhou, China. .,Collaborative Innovation Center for Cancer Medicine, 651 Dongfeng East Road, Guangzhou, China.
| |
Collapse
|
33
|
Wang X, Wang X, Xu M, Sheng W. Emerging Roles of Long Noncoding RNAs in Immuno-Oncology. Front Cell Dev Biol 2021; 9:722904. [PMID: 34900986 PMCID: PMC8655840 DOI: 10.3389/fcell.2021.722904] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 11/01/2021] [Indexed: 12/21/2022] Open
Abstract
Long noncoding RNAs (lncRNAs), defined as ncRNAs no longer than 200 nucleotides, play an important role in cancer development. Accumulating research on lncRNAs offers a compelling new aspect of genome modulation, in which they are involved in chromatin remodeling, transcriptional and post-transcriptional regulation, and cross-talk with other nucleic acids. Increasing evidence suggests that lncRNAs reshape the tumor microenvironment (TME), which accounts for tumor development and progression. At the same time, the insightful findings on lncRNAs in immune recognition and evasion in tumor-infiltrating immune cells raise concerns with regard to immuno-oncology. In this review, we describe the essential characteristics of lncRNAs, elucidate functions of immune components engaged in tumor surveillance, and present some instructive examples in this new area.
Collapse
Affiliation(s)
- Xin Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Medical Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xu Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Medical Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Midie Xu
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Medical Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Weiqi Sheng
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Medical Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| |
Collapse
|
34
|
Qin Z, Liu X, Li Z, Wang G, Feng Z, Liu Y, Yang H, Tan C, Zhang Z, Li K. LncRNA LINC00667 aggravates the progression of hepatocellular carcinoma by regulating androgen receptor expression as a miRNA-130a-3p sponge. Cell Death Discov 2021; 7:387. [PMID: 34907204 PMCID: PMC8671440 DOI: 10.1038/s41420-021-00787-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/12/2021] [Accepted: 11/30/2021] [Indexed: 12/16/2022] Open
Abstract
Emerging studies have found long noncoding RNAs, widely expressed in eukaryotes, crucial regulators in the progression of human cancers, including hepatocellular carcinoma (HCC). Although the long intergenic noncoding RNA 667 (LINC00667) can promote the progression of a variety of cancer types, the expression pattern, the role in cancer progression, and the molecular mechanism involved in HCC remain unclear. This study aims to investigate the function and mechanism of LINC00667 in HCC progression. The effects of LINC00667 silencing in cell proliferation, cell migration, and cell invasion, and androgen receptor (AR) expression were determined with loss-of-function phenotypic analysis in Huh-7 and HCCLM3 cells, and subsequently testified in vivo in tumor growth. We found that the expression of LINC00667 was upregulated in HCC tissues and cell lines. Upregulation of LINC00667 was significantly associated with the unfavorable prognosis of HCC in our study patients. On the other hand, low expression of LINC00667 significantly inhibited the cell proliferation, cell migration and cell invasion of HCC in vitro and tumor growth in vivo. This inhibitory effect could be counteracted by miR-130a-3p inhibitor. LINC00667 reduced the inhibition of AR expression by miR-130a-3p, which correlated with the progression of HCC. Our finding suggests LINC00667 is a molecular sponge in the miR-130s-3p/AR signal pathway in the progression of HCC, in which it relieves the repressive function of miR-130a-3p on the AR expression. This indicates LINC00667 functions as a tumor promotor in promoting HCC progression through targeting miR-130a-3p/AR axis, making a novel biomarker and potential therapeutic target for HCC.
Collapse
Affiliation(s)
- Zhixiang Qin
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Xiaohong Liu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Zijing Li
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Ganggang Wang
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Zhe Feng
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Ye Liu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Hai Yang
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Chengpeng Tan
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Zidong Zhang
- Department of Health Management and Policy, College for Public Health and Social Justice, St. Louis, MO, USA
- Department of Health and Clinical Outcomes Research, Advanced Health Data Institute, School of Medicine, Saint Louis University, Saint Louis, MO, USA
| | - Kun Li
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| |
Collapse
|
35
|
Han D, Yu Z, Zhang H, Liu H, Wang B, Qian D. Microenvironment-associated gene HSD11B1 may serve as a prognostic biomarker in clear cell renal cell carcinoma: a study based on TCGA, RT‑qPCR, Western blotting, and immunohistochemistry. Bioengineered 2021; 12:10891-10904. [PMID: 34845968 PMCID: PMC8810109 DOI: 10.1080/21655979.2021.1994908] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is one of the most common malignant tumors worldwide. The clinical treatment of ccRCC is strongly associated with the tumor microenvironment (TME). Identifying potential markers of ccRCC is important to improve prognosis. Therefore, in the present study, the levels of immune/stromal components and the proportion of tumor-infiltrating immune cells (TIICs) were determined in 611 ccRCC samples using the ESTIMATE and CIBERSORT analytical tools. Subsequently, hydroxysteroid 11-beta dehydrogenase-1 (HSD11B1) was identified by univariate Cox regression analysis, protein-protein interaction (PPI) networks and clinical survival analysis to be associated with ccRCC prognosis. At the same time, the abundance of HSD11B1 increased significantly in ccRCC was verified by western blotting, RT‑qPCR and immunostaining analysis. Furthermore, Gene Set Enrichment Analysis (GSEA) and TME suggested that HSD11B1 was involved in TME immune-related status. Taken together, the results of the present study demonstrated that HSD11B1 is a potential prognostic biomarker associated with immune cell infiltration in ccRCC.
Collapse
Affiliation(s)
- Di Han
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, P. R. China
| | - Zhongjie Yu
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong, P. R. China
| | - Hong Zhang
- School of Public Health, Qingdao University, Qingdao, Shandong, P. R. China
| | - Haipeng Liu
- Oral Research Center, Qingdao Municipal Hospital, Qingdao, Shandong, P. R. China
| | - Bin Wang
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong, P. R. China
| | - Donmeng Qian
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, P. R. China
| |
Collapse
|
36
|
Ma E, Hou S, Wang Y, Xu X, Wang Z, Zhao J. Identification and Validation of an Immune-Related lncRNA Signature to Facilitate Survival Prediction in Gastric Cancer. Front Oncol 2021; 11:666064. [PMID: 34760687 PMCID: PMC8573392 DOI: 10.3389/fonc.2021.666064] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 10/06/2021] [Indexed: 12/27/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) are versatile in functions and can regulate cancer development, including the modulation of cancer immunity. Immune-related lncRNA signatures predicting prognosis have been reported in multiple cancers, but relevant studies in gastric cancer (GC) are still lacking. Methods We performed a comprehensive analysis using TCGA and Immport databases and identified an immune-related lncRNA signature by univariate and multivariate Cox regression analysis. qRT-PCR and immunohistochemistry assays were used for further validation. KEGG and GO analysis and ceRNA network establishment were carried out to explore the regulatory functions. Results We first identified an immune-related lncRNA signature, which can stratify gastric cancer patients into high- and low-risk subgroups and the high-risk cases frequently suffered from shorter overall survival time. Next, we validated the reliability of the lncRNA signature in an independent 75 gastric cancer samples and demonstrated that the three-year survival rate in high-risk patients was only 30.8% versus 66.5% in low-risk counterparts. Functional exploration indicated that the lncRNA signature might participate in multiple cancer-associated processes including cell adhesion and migration, cytokine-receptor interaction and immune evasion. Additionally, we observed that high-risk samples tended to form an immunosuppressive microenvironment, which had more M2-polarized macrophages and Tregs, but fewer CD8 effector T cells within tumors. Moreover, we found that PD-1 and PD-L1 were dramatically upregulated in a subset of high-risk patients with abundant M2 and Treg infiltration, implying these patients may benefit from anti-PD-1 and PD-L1 immunotherapy. Conclusions These results showed that the immune-related lncRNA signature had a prominent capacity to predict overall survival and the immune status of microenvironment in gastric cancer. Our findings may be useful for the risk-stratification management and provide a valuable clue to identify proper patients potentially benefit from immune checkpoint therapy in gastric cancer.
Collapse
Affiliation(s)
- Ensi Ma
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Organ Transplantation, Fudan University, Shanghai, China
| | - Sen Hou
- Department of Digestive Surgery, Xuchang Central Hospital, Henan, China
| | - Yan Wang
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiao Xu
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhengxin Wang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Organ Transplantation, Fudan University, Shanghai, China
| | - Jing Zhao
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China.,Cancer Metastasis Institute, Fudan University, Shanghai, China
| |
Collapse
|
37
|
Kang W, Hu J, Zhao Q, Song F. Identification of an Autophagy-Related Risk Signature Correlates With Immunophenotype and Predicts Immune Checkpoint Blockade Efficacy of Neuroblastoma. Front Cell Dev Biol 2021; 9:731380. [PMID: 34746127 PMCID: PMC8567030 DOI: 10.3389/fcell.2021.731380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/31/2021] [Indexed: 11/30/2022] Open
Abstract
Neuroblastoma is one of the malignant solid tumors with the highest mortality in childhood. Targeted immunotherapy still cannot achieve satisfactory results due to heterogeneity and tolerance. Exploring markers related to prognosis and evaluating the immune microenvironment remain the major obstacles. Herein, we constructed an autophagy-related gene (ATG) risk model by multivariate Cox regression and least absolute shrinkage and selection operator regression, and identified four prognostic ATGs (BIRC5, GRID2, HK2, and RNASEL) in the training cohort, then verified the signature in the internal and external validation cohorts. BIRC5 and HK2 showed higher expression in MYCN amplified cell lines and tumor tissues consistently, whereas GRID2 and RNASEL showed the opposite trends. The correlation between the signature and clinicopathological parameters was further analyzed and showing consistency. A prognostic nomogram using risk score, International Neuroblastoma Staging System stage, age, and MYCN status was built subsequently, and the area under curves, net reclassification improvement, and integrated discrimination improvement showed more satisfactory prognostic predicting performance. The ATG prognostic signature itself can significantly divide patients with neuroblastoma into high- and low-risk groups; differentially expressed genes between the two groups were enriched in autophagy-related behaviors and immune cell reactions in gene set enrichment analysis (false discovery rate q -value < 0.05). Furthermore, we evaluated the relationship of the signature risk score with immune cell infiltration and the cancer-immunity cycle. The low-risk group was characterized by more abundant expression of chemokines and higher immune checkpoints (PDL1, PD1, CTLA-4, and IDO1). The risk score was significantly correlated with the proportions of CD8+ T cells, CD4+ memory resting T cells, follicular helper T cells, memory B cells, plasma cells, and M2 macrophages in tumor tissues. In conclusion, we developed and validated an autophagy-related signature that can accurately predict the prognosis, which might be meaningful to understand the immune microenvironment and guide immune checkpoint blockade.
Collapse
Affiliation(s)
- Wenjuan Kang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Jiajian Hu
- Tianjin Key Laboratory of Cancer Prevention and Therapy, Department of Pediatric Oncology, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Qiang Zhao
- Tianjin Key Laboratory of Cancer Prevention and Therapy, Department of Pediatric Oncology, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Fengju Song
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| |
Collapse
|
38
|
Fu Y, Wei X, Han Q, Le J, Ma Y, Lin X, Xu Y, Liu N, Wang X, Kong X, Gu J, Tong Y, Wu H. Identification and characterization of a 25-lncRNA prognostic signature for early recurrence in hepatocellular carcinoma. BMC Cancer 2021; 21:1165. [PMID: 34717566 PMCID: PMC8556945 DOI: 10.1186/s12885-021-08827-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/30/2021] [Indexed: 02/06/2023] Open
Abstract
Background Early recurrence is the major cause of poor prognosis in hepatocellular carcinoma (HCC). Long non-coding RNAs (lncRNAs) are deeply involved in HCC prognosis. In this study, we aimed to establish a prognostic lncRNA signature for HCC early recurrence. Methods The lncRNA expression profile and corresponding clinical data were retrieved from total 299 HCC patients in TCGA database. LncRNA candidates correlated to early recurrence were selected by differentially expressed gene (DEG), univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses. A 25-lncRNA prognostic signature was constructed according to receiver operating characteristic curve (ROC). Kaplan-Meier and multivariate Cox regression analyses were used to evaluate the performance of this signature. ROC and nomogram were used to evaluate the integrated models based on this signature with other independent clinical risk factors. Gene set enrichment analysis (GSEA) was used to reveal enriched gene sets in the high-risk group. Tumor infiltrating lymphocytes (TILs) levels were analyzed with single sample Gene Set Enrichment Analysis (ssGSEA). Immune therapy response prediction was performed with TIDE and SubMap. Chemotherapeutic response prediction was conducted by using Genomics of Drug Sensitivity in Cancer (GDSC) pharmacogenomics database. Results Compared to low-risk group, patients in high-risk group showed reduced disease-free survival (DFS) in the training (p < 0.0001) and validation cohort (p = 0.0132). The 25-lncRNA signature, AFP, TNM and vascular invasion could serve as independent risk factors for HCC early recurrence. Among them, the 25-lncRNA signature had the best predictive performance, and combination of those four risk factors further improves the prognostic potential. Moreover, GSEA showed significant enrichment of “E2F TARGETS”, “G2M CHECKPOINT”, “MYC TARGETS V1” and “DNA REPAIR” pathways in the high-risk group. In addition, increased TILs were observed in the low-risk group compared to the high-risk group. The 25-lncRNA signature negatively associates with the levels of some types of antitumor immune cells. Immunotherapies and chemotherapies prediction revealed differential responses to PD-1 inhibitor and several chemotherapeutic drugs in the low- and high-risk group. Conclusions Our study proposed a 25-lncRNA prognostic signature for predicting HCC early recurrence, which may guide postoperative treatment and recurrence surveillance in HCC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08827-z.
Collapse
Affiliation(s)
- Yi Fu
- Affiliated Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.,Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.,School of Medical Instruments, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Xindong Wei
- Nanjing University of Traditional Chinese Medicine, Nanjing, 210000, China
| | - Qiuqin Han
- Affiliated Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.,Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Jiamei Le
- Affiliated Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.,Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Yujie Ma
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Xinjie Lin
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Yuhui Xu
- Graduate School of Art and Sciences, Columbia University, New York, NY, 10027, USA
| | - Ning Liu
- Department of Clinical Oncology, Taian City Central Hospital, Taian, 271000, Shandong, China
| | - Xuan Wang
- Department of General Surgery, Nanjing General Hospital of Nanjing Military Command, Nanjing, 210000, China
| | - Xiaoni Kong
- Institute of Clinical Immunology, Department of Liver Diseases, Central Laboratory, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 200021, China
| | - Jinyang Gu
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
| | - Ying Tong
- Department of Liver Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
| | - Hailong Wu
- Affiliated Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China. .,Shanghai Key Laboratory of Molecular Imaging, Collaborative Innovation Center for Biomedicines, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.
| |
Collapse
|
39
|
Wu L, Liao W, Wang X, Zhao Y, Pang J, Chen Y, Yang H, He Y. Expression, prognosis value, and immune infiltration of lncRNA ASB16-AS1 identified by pan-cancer analysis. Bioengineered 2021; 12:10302-10318. [PMID: 34709970 PMCID: PMC8810074 DOI: 10.1080/21655979.2021.1996054] [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] [Indexed: 02/01/2023] Open
Abstract
Long non-coding RNA known as ASB16 antisense RNA1 (ASB16-AS1) has been proven to be an oncogene, and the relationship between ASB16-AS1 and immunity is still under studied. This study aims to explore the expression and prognostic potential of ASB16-AS1, and to visualize the relationship between ASB16-AS1 expression and immune infiltration in pan-cancer analysis. We clarified ASB16-AS1 expression patterns and its relationship with prognosis through multi-platform and multi-database sources. We also verified the function of ASB16-AS1 in liver hepatocellular carcinoma (LIHC). A variety of immune cell content evaluation methods were used to mutually verify the correlation between ASB16-AS1 and immune infiltration. Finally, the relationships between ASB16-AS1 and molecular characteristics were further explored. In terms of comprehensive analysis, compared with non-tumor tissues, ASB16-AS1 was highly expressed in tumor tissues, and indicated the value of poor prognosis in multiple cancer types. Functional assays, such as counting kit-8 assay, transwell assay and scratch-wound assay verified that high ASB16-AS1 expression promoted tumor progression in LIHC. ASB16-AS1 was positively correlated with B cells, T cells CD4+ and T cells CD8+ in most cancer types, and negatively correlated with macrophages, dendritic cells and neutrophils in some cancer types. In addition, there were different interaction modes between ASB16-AS1 and molecular features, such as the relationship with oncogenic signaling pathways, showing that the high ASB16-AS1 expression was related to alterations in oncogenic signaling pathways. Our study emphasizes that ASB16-AS1 is a potential pan-cancer prognostic marker, whichs is associated with the immune infiltration in multiple cancer types.
Collapse
Affiliation(s)
- Linyong Wu
- Department of Medical Ultrasound, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Wei Liao
- Department of Medical Ultrasound, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Xiaodong Wang
- Department of Medical Ultrasound, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Yujia Zhao
- Department of Medical Ultrasound, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Jinshu Pang
- Department of Medical Ultrasound, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Yuji Chen
- Department of Medical Ultrasound, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Hong Yang
- Department of Medical Ultrasound, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Yun He
- Department of Medical Ultrasound, The First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| |
Collapse
|
40
|
Xue L, Wu P, Zhao X, Jin X, Wang J, Shi Y, Yang X, She Y, Li Y, Li C. Using Immune-Related lncRNA Signature for Prognosis and Response to Immunotherapy in Cutaneous Melanoma. Int J Gen Med 2021; 14:6463-6475. [PMID: 34675614 PMCID: PMC8518697 DOI: 10.2147/ijgm.s335266] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/27/2021] [Indexed: 12/16/2022] Open
Abstract
Background Cutaneous melanoma is a highly malignant skin tumor, and most patients have a poor prognosis. In recent years, immunotherapy has assumed an important role in the treatment of advanced cutaneous melanoma, but only a small percentage of patients benefit from immunotherapy. A growing number of studies have demonstrated that the prognosis of patients with cutaneous melanoma is closely related to long non-coding RNA and the tumor immune microenvironment. Methods We downloaded RNA expression data and immune-related gene lists of cutaneous melanoma patients separately from The Cancer Genome Atlas database and ImmPort website and identified immune-related lncRNAs by co-expression analysis. The prognostic model was constructed by applying least absolute shrinkage and selection operator regression, and all patients were classified into high- and low-risk groups according to the risk score of the model. We evaluated the differences between the two groups in terms of survival outcomes, immune infiltration, pathway enrichment, chemotherapeutic drug sensitivity and immune checkpoint gene expression to verify the impact of lncRNA signature on clinical prognosis and immunotherapy efficacy. Results By correlation analysis and LASSO regression analysis, we constructed an immune-related lncRNA prognostic model based on five lncRNA: HLA-DQB1-AS1, MIR205HG, RP11-643G5.6, USP30-AS1 and RP11-415F23.4. Based on this model, we plotted Kaplan-Meier survival curves and time-dependent ROC curves and analyzed its ability as an independent prognostic factor for cutaneous melanoma in combination with clinicopathological features. The results showed that these lncRNA signature was an independent prognostic factor of cutaneous melanoma with favorable prognostic ability. Our results also show a higher degree of immune infiltration, higher expression of immune checkpoint-associated genes, and better outcome of immunotherapy in the low-risk group of the lncRNA signature. Conclusion The 5 immune-related lncRNA signatures constructed in our study can predict the prognosis of cutaneous melanoma and contribute to the selection of immunotherapy.
Collapse
Affiliation(s)
- Ling Xue
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, People's Republic of China.,Department of Pathology, The 940th Hospital of the Joint Logistic Support of the People's Liberation Army, Lanzhou, 730050, People's Republic of China
| | - Pingfan Wu
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, People's Republic of China.,Department of Pathology, The 940th Hospital of the Joint Logistic Support of the People's Liberation Army, Lanzhou, 730050, People's Republic of China
| | - Xiaowen Zhao
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, People's Republic of China.,Department of Pathology, The 940th Hospital of the Joint Logistic Support of the People's Liberation Army, Lanzhou, 730050, People's Republic of China
| | - Xiaojie Jin
- Provincial-Level Key Laboratory of Molecular Medicine of Major Diseases and Study on Prevention and Treatment of Traditional Chinese Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu, People's Republic of China
| | - Jingjing Wang
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, People's Republic of China
| | - Yuxiang Shi
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, People's Republic of China
| | - Xiaojing Yang
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, People's Republic of China
| | - Yali She
- Provincial-Level Key Laboratory of Molecular Medicine of Major Diseases and Study on Prevention and Treatment of Traditional Chinese Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu, People's Republic of China
| | - Yaling Li
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, People's Republic of China.,Provincial-Level Key Laboratory of Molecular Medicine of Major Diseases and Study on Prevention and Treatment of Traditional Chinese Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu, People's Republic of China
| | - Changtian Li
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, 730000, People's Republic of China
| |
Collapse
|
41
|
Xu D, Wang Y, Wu J, Zhang Y, Liu Z, Chen Y, Zheng J. Systematic Characterization of Novel Immune Gene Signatures Predicts Prognostic Factors in Hepatocellular Carcinoma. Front Cell Dev Biol 2021; 9:686664. [PMID: 34631695 PMCID: PMC8494981 DOI: 10.3389/fcell.2021.686664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 08/20/2021] [Indexed: 01/08/2023] Open
Abstract
Background: The prognosis of patients with hepatocellular carcinoma (HCC) is negatively affected by the lack of effective prognostic indicators. The change of tumor immune microenvironment promotes the development of HCC. This study explored new markers and predicted the prognosis of HCC patients by systematically analyzing immune characteristic genes. Methods: Immune-related genes were obtained, and the differentially expressed immune genes (DEIGs) between tumor and para-cancer samples were identified and analyzed using gene expression profiles from TCGA, HCCDB, and GEO databases. An immune prognosis model was also constructed to evaluate the predictive performance in different cohorts. The high and low groups were divided based on the risk score of the model, and different algorithms were used to evaluate the tumor immune infiltration cell (TIIC). The expression and prognosis of core genes in pan-cancer cohorts were analyzed, and gene enrichment analysis was performed using clusterProfiler. Finally, the expression of the hub genes of the model was validated by clinical samples. Results: Based on the analysis of 730 immune-related genes, we identified 64 common DEIGs. These genes were enriched in the tumor immunologic related signaling pathways. The first 15 genes were selected using RankAggreg analysis, and all the genes showed a consistent expression trend across multi-cohorts. Based on lasso cox regression analysis, a 5-gene signature risk model (ATG10, IL18RAP, PRKCD, SLC11A1, and SPP1) was constructed. The signature has strong robustness and can stabilize different cohorts (TCGA-LIHC, HCCDB18, and GSE14520). Compared with other existing models, our model has better performance. CIBERSORT was used to assess the landscape maps of 22 types of immune cells in TCGA, GSE14520, and HCCDB18 cohorts, and found a consistent trend in the distribution of TIIC. In the high-risk score group, scores of Macrophages M1, Mast cell resting, and T cells CD8 were significantly lower than those of the low-risk score group. Different immune expression characteristics, lead to the different prognosis. Western blot demonstrated that ATG10, PRKCD, and SPP1 were highly expressed in cancer tissues, while IL18RAP and SLC11A1 expression in cancer tissues was lower. In addition, IL18RAP has a highly positive correlation with B cell, macrophage, Neutrophil, Dendritic cell, CD8 cell, and CD4 cell. The SPP1, PRKCD, and SLC11A1 genes have the strongest correlation with macrophages. The expression of ATG10, IL18RAP, PRKCD, SLC11A1, and SPP1 genes varies among different immune subtypes and between different T stages. Conclusion: The 5-immu-gene signature constructed in this study could be utilized as a new prognostic marker for patients with HCC.
Collapse
Affiliation(s)
- Dafeng Xu
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Yu Wang
- Geriatric Medicine Center, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Jincai Wu
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Yuliang Zhang
- Department of Otolaryngology-Head and Neck Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Zhehao Liu
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Yonghai Chen
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Jinfang Zheng
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| |
Collapse
|
42
|
Xu Z, Peng B, Liang Q, Chen X, Cai Y, Zeng S, Gao K, Wang X, Yi Q, Gong Z, Yan Y. Construction of a Ferroptosis-Related Nine-lncRNA Signature for Predicting Prognosis and Immune Response in Hepatocellular Carcinoma. Front Immunol 2021; 12:719175. [PMID: 34603293 PMCID: PMC8484522 DOI: 10.3389/fimmu.2021.719175] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/26/2021] [Indexed: 02/05/2023] Open
Abstract
Ferroptosis is an iron-dependent cell death process that plays important regulatory roles in the occurrence and development of cancers, including hepatocellular carcinoma (HCC). Moreover, the molecular events surrounding aberrantly expressed long non-coding RNAs (lncRNAs) that drive HCC initiation and progression have attracted increasing attention. However, research on ferroptosis-related lncRNA prognostic signature in patients with HCC is still lacking. In this study, the association between differentially expressed lncRNAs and ferroptosis-related genes, in 374 HCC and 50 normal hepatic samples obtained from The Cancer Genome Atlas (TCGA), was evaluated using Pearson's test, thereby identifying 24 ferroptosis-related differentially expressed lncRNAs. The least absolute shrinkage and selection operator (LASSO) algorithm and Cox regression model were used to construct and validate a prognostic risk score model from both TCGA training dataset and GEO testing dataset (GSE40144). A nine-lncRNA-based signature (CTD-2033A16.3, CTD-2116N20.1, CTD-2510F5.4, DDX11-AS1, LINC00942, LINC01224, LINC01231, LINC01508, and ZFPM2-AS1) was identified as the ferroptosis-related prognostic model for HCC, independent of multiple clinicopathological parameters. In addition, the HCC patients were divided into high-risk and low-risk groups according to the nine-lncRNA prognostic signature. The gene set enrichment analysis enrichment analysis revealed that the lncRNA-based signature might regulate the HCC immune microenvironment by interfering with tumor necrosis factor α/nuclear factor kappa-B, interleukin 2/signal transducers and activators of transcription 5, and cytokine/cytokine receptor signaling pathways. The infiltrating immune cell subtypes, such as resting memory CD4(+) T cells, follicular helper T cells, regulatory T cells, and M0 macrophages, were all significantly different between the high-risk group and the low-risk group as indicated in Spearman's correlation analysis. Moreover, a substantial increase in the expression of B7H3 immune checkpoint molecule was found in the high-risk group. Our findings provided a promising insight into ferroptosis-related lncRNAs in HCC and a personalized prediction tool for prognosis and immune responses in patients.
Collapse
Affiliation(s)
- Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Qiuju Liang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Xi Chen
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Shuangshuang Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Kewa Gao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiang Wang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Qiaoli Yi
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| |
Collapse
|
43
|
He Y, Lu M, Che J, Chu Q, Zhang P, Chen Y. Biomarkers and Future Perspectives for Hepatocellular Carcinoma Immunotherapy. Front Oncol 2021; 11:716844. [PMID: 34552872 PMCID: PMC8450565 DOI: 10.3389/fonc.2021.716844] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 08/18/2021] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular cancer is the sixth most frequently diagnosed malignant disease worldwide, and was responsible for tens of millions of deaths in 2020; however, treatment options for patients with advanced hepatocellular carcinoma remain limited. Immunotherapy has undergone rapid development over recent years, especially in the field of immune checkpoint inhibitors (ICIs). These drugs aim to activate and enhance antitumor immunity and represent a new prospect for the treatment of patients with advanced cancer. Nevertheless, only a small proportion of liver cancer patients currently benefit from ICI-based treatment, highlighting the need to better understand how ICIs and tumors interact, as well as identify predictive biomarkers for immunotherapeutic responses. In this review, we highlight clinical trials and basic research in hepatocellular carcinoma, with a particular focus on predictive biomarkers for the therapeutic efficacy of ICIs. Predictive biomarkers for immune-related adverse events are also discussed.
Collapse
Affiliation(s)
- Yuqing He
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mengyao Lu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Che
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Qian Chu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
44
|
Huang YJ, Huang CJ. Construction of a 5 immune-related lncRNA-based prognostic model of NSCLC via bioinformatics. Medicine (Baltimore) 2021; 100:e27222. [PMID: 34664861 PMCID: PMC8448051 DOI: 10.1097/md.0000000000027222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 08/28/2021] [Indexed: 11/25/2022] Open
Abstract
Participate in tumorigenic, oncogenic, and tumor suppressive pathways through gene expression regulation. We aimed to build an immune-related long noncoding RNA (lncRNA) prognostic model to enhance nonsmall cell lung cancer (NSCLC) prognostic prediction.The original data were collected from the cancer genome atlas database. Perl and R software were used for statistical analysis. The effects of lncRNAs expression on prognosis were analyzed by Gene Expression Profiling Interactive Analysis. Silico functional analysis were performed by DAVID Bioinformatics Resources.The median risk score as a dividing value separated patients into high- and low-risk groups. These 2 groups had different 5-year survival rates, median survival times, and immune statuses. The 5-lncRNA signature was validated as an independent prognostic factor with high accuracy (area under the receiver operating characteristic = 0.722). Silico functional analysis connected the lncRNAs with immune-related biological processes and pathways in carcinogenesis.The novel immune-related lncRNA prognostic model had significant clinical implication for enhancing lung adenocarcinoma outcome prediction and guiding the choice of treatment.
Collapse
Affiliation(s)
- Ya-jie Huang
- Department of Medical Oncology, The Fourth hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Chang-jie Huang
- Undergraduate of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| |
Collapse
|
45
|
Rinoldi C, Zargarian SS, Nakielski P, Li X, Liguori A, Petronella F, Presutti D, Wang Q, Costantini M, De Sio L, Gualandi C, Ding B, Pierini F. Nanotechnology-Assisted RNA Delivery: From Nucleic Acid Therapeutics to COVID-19 Vaccines. SMALL METHODS 2021; 5:e2100402. [PMID: 34514087 PMCID: PMC8420172 DOI: 10.1002/smtd.202100402] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/04/2021] [Indexed: 05/07/2023]
Abstract
In recent years, the main quest of science has been the pioneering of the groundbreaking biomedical strategies needed for achieving a personalized medicine. Ribonucleic acids (RNAs) are outstanding bioactive macromolecules identified as pivotal actors in regulating a wide range of biochemical pathways. The ability to intimately control the cell fate and tissue activities makes RNA-based drugs the most fascinating family of bioactive agents. However, achieving a widespread application of RNA therapeutics in humans is still a challenging feat, due to both the instability of naked RNA and the presence of biological barriers aimed at hindering the entrance of RNA into cells. Recently, material scientists' enormous efforts have led to the development of various classes of nanostructured carriers customized to overcome these limitations. This work systematically reviews the current advances in developing the next generation of drugs based on nanotechnology-assisted RNA delivery. The features of the most used RNA molecules are presented, together with the development strategies and properties of nanostructured vehicles. Also provided is an in-depth overview of various therapeutic applications of the presented systems, including coronavirus disease vaccines and the newest trends in the field. Lastly, emerging challenges and future perspectives for nanotechnology-mediated RNA therapies are discussed.
Collapse
Affiliation(s)
- Chiara Rinoldi
- Department of Biosystems and Soft MatterInstitute of Fundamental Technological ResearchPolish Academy of Sciencesul. Pawińskiego 5BWarsaw02‐106Poland
| | - Seyed Shahrooz Zargarian
- Department of Biosystems and Soft MatterInstitute of Fundamental Technological ResearchPolish Academy of Sciencesul. Pawińskiego 5BWarsaw02‐106Poland
| | - Pawel Nakielski
- Department of Biosystems and Soft MatterInstitute of Fundamental Technological ResearchPolish Academy of Sciencesul. Pawińskiego 5BWarsaw02‐106Poland
| | - Xiaoran Li
- Innovation Center for Textile Science and TechnologyDonghua UniversityWest Yan'an Road 1882Shanghai200051China
| | - Anna Liguori
- Department of Chemistry “Giacomo Ciamician” and INSTM UdR of BolognaUniversity of BolognaVia Selmi 2Bologna40126Italy
| | - Francesca Petronella
- Institute of Crystallography CNR‐ICNational Research Council of ItalyVia Salaria Km 29.300Monterotondo – Rome00015Italy
| | - Dario Presutti
- Institute of Physical ChemistryPolish Academy of Sciencesul. M. Kasprzaka 44/52Warsaw01‐224Poland
| | - Qiusheng Wang
- Innovation Center for Textile Science and TechnologyDonghua UniversityWest Yan'an Road 1882Shanghai200051China
| | - Marco Costantini
- Institute of Physical ChemistryPolish Academy of Sciencesul. M. Kasprzaka 44/52Warsaw01‐224Poland
| | - Luciano De Sio
- Department of Medico‐Surgical Sciences and BiotechnologiesResearch Center for BiophotonicsSapienza University of RomeCorso della Repubblica 79Latina04100Italy
- CNR‐Lab. LicrylInstitute NANOTECArcavacata di Rende87036Italy
| | - Chiara Gualandi
- Department of Chemistry “Giacomo Ciamician” and INSTM UdR of BolognaUniversity of BolognaVia Selmi 2Bologna40126Italy
- Interdepartmental Center for Industrial Research on Advanced Applications in Mechanical Engineering and Materials TechnologyCIRI‐MAMUniversity of BolognaViale Risorgimento 2Bologna40136Italy
| | - Bin Ding
- Innovation Center for Textile Science and TechnologyDonghua UniversityWest Yan'an Road 1882Shanghai200051China
| | - Filippo Pierini
- Department of Biosystems and Soft MatterInstitute of Fundamental Technological ResearchPolish Academy of Sciencesul. Pawińskiego 5BWarsaw02‐106Poland
| |
Collapse
|
46
|
Jiang W, Pan S, Chen X, Wang ZW, Zhu X. The role of lncRNAs and circRNAs in the PD-1/PD-L1 pathway in cancer immunotherapy. Mol Cancer 2021; 20:116. [PMID: 34496886 PMCID: PMC8424797 DOI: 10.1186/s12943-021-01406-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/08/2021] [Indexed: 12/15/2022] Open
Abstract
Cancer immunotherapy has recently shown promising antitumor effects in various types of tumors. Among all immune checkpoints, the PD-1/PD-L1 pathway plays an important role in the immune evasion of tumor cells, making it a potent target in antitumor immunity. Accordingly, antibodies targeting the PD-1/PD-L1 pathway have been developed to attack tumor cells; however, resistance to immune therapy remains to be solved. Hence, identification of the underlying modulators of the PD-1/PD-L1 pathway is of significant importance to understand the mechanisms of antitumor immunotherapy. Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) have been identified to regulate the PD-1/PD-L1 pathway, leading to participation in the immune response and immunotherapy. Therefore, this review focuses on the functions of lncRNAs and circRNAs in regulation of the PD-1/PD-L1 axis in tumorigenesis and tumor progression. We hope this review will stimulate research to supply more precise and effective cancer immune checkpoint therapies for a large number of tumors.
Collapse
Affiliation(s)
- Wenxiao Jiang
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, 325027 Zhejiang China
| | - Shuya Pan
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, 325027 Zhejiang China
| | - Xin Chen
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, 325027 Zhejiang China
| | - Zhi-wei Wang
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, 325027 Zhejiang China
| | - Xueqiong Zhu
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, 325027 Zhejiang China
| |
Collapse
|
47
|
Farha M, Jairath NK, Lawrence TS, El Naqa I. Characterization of the Tumor Immune Microenvironment Identifies M0 Macrophage-Enriched Cluster as a Poor Prognostic Factor in Hepatocellular Carcinoma. JCO Clin Cancer Inform 2021; 4:1002-1013. [PMID: 33136432 DOI: 10.1200/cci.20.00077] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Hepatocellular carcinoma (HCC) is characterized by a poor prognosis and a high recurrence rate. The tumor immune microenvironment in HCC has been characterized as shifted toward immunosuppression. We conducted a genomic data-driven classification of immune microenvironment HCC subtypes. In addition, we demonstrated their prognostic value and suggested a potential therapeutic targeting strategy. METHODS RNA sequencing data from The Cancer Genome Atlas-Liver Hepatocellular Carcinoma was used (n = 366). Abundance of immune cells was imputed using CIBERSORT and visualized using unsupervised hierarchic clustering. Overall survival (OS) was analyzed using Kaplan-Meier estimates and Cox regression. Differential expression and gene set enrichment analyses were conducted on immune clusters with poor OS and high programmed death-1 (PD-1)/programmed death-ligand 1 (PD-L1) coexpression. A scoring metric combining differentially expressed genes and immune cell content was created, and its prognostic value and immune checkpoint blockade response prediction was evaluated. RESULTS Two clusters were characterized by macrophage enrichment, with distinct M0Hi and M2Hi subtypes. M2Hi (P = .038) and M0Hi (P = .018) were independently prognostic for OS on multivariable analysis. Kaplan-Meier estimates demonstrated that patients in M0Hi and M2Hi treated with sorafenib had decreased OS (P = .041), and angiogenesis hallmark genes were enriched in the M0Hi group. CXCL6 and POSTN were overexpressed in both the M0Hi and the PD-1Hi/PD-L1Hi groups. A score consisting of CXCL6 and POSTN expression and absolute M0 macrophage content was discriminatory for OS (intermediate: hazard ratio [HR], 1.59; P ≤ .001; unfavorable: HR, 2.08; P = .04). CONCLUSION Distinct immune cell clusters with macrophage predominance characterize an aggressive HCC phenotype, defined molecularly by angiogenic gene enrichment and clinically by poor prognosis and sorafenib response. This novel immunogenomic signature may aid in stratification of unresectable patients to receive checkpoint inhibitor and antiangiogenic therapy combinations.
Collapse
Affiliation(s)
- Mark Farha
- Department of Medical Education, University of Michigan Medical School, Ann Arbor, MI
| | - Neil K Jairath
- Department of Medical Education, University of Michigan Medical School, Ann Arbor, MI
| | | | - Issam El Naqa
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI
| |
Collapse
|
48
|
Rizzo A, Ricci AD. PD-L1, TMB, and other potential predictors of response to immunotherapy for hepatocellular carcinoma: how can they assist drug clinical trials? Expert Opin Investig Drugs 2021; 31:415-423. [PMID: 34429006 DOI: 10.1080/13543784.2021.1972969] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Hepatocellular carcinoma (HCC) represents the sixth most commonly diagnosed malignancy worldwide, accounting for millions of deaths annually. Despite immune checkpoint inhibitors (ICIs) reported important results, only a minority of HCC patients benefit from these treatments, and the identification of predictive biomarkers of response still remains a highly unmet need. AREAS COVERED Herein, we provide a timely overview of available evidence on biochemical predictors of response to immunotherapy in advanced HCC patients; we speculate on how PD-L1, TMB, and other emerging biomarkers could assist drug clinical trials in the near future. A literature search was conducted in June 2021 using Pubmed/Medline, Cochrane library, and Scopus databases. EXPERT OPINION Reliable predictors of response to ICIs are of pivotal importance to allow a proper stratification and selection of HCC patients that could derive more benefit from immunotherapy. Well-designed, multicenter clinical trials specifically focused on predictive biomarkers are warranted in this setting, where most of evidence currently derives from retrospective, single-center studies with small sample size.
Collapse
Affiliation(s)
- Alessandro Rizzo
- Medical Oncology, Irccs Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italia
| | - Angela Dalia Ricci
- Medical Oncology, Irccs Azienda Ospedaliero-Universitaria Di Bologna, Bologna, Italia
| |
Collapse
|
49
|
Wang Y, Li N, Tian D, Zhou CW, Wang YH, Yang C, Zeng MS. Analysis of m6A-Related lncRNAs for Prognosis Value and Response to Immune Checkpoint Inhibitors Therapy in Hepatocellular Carcinoma. Cancer Manag Res 2021; 13:6451-6471. [PMID: 34429653 PMCID: PMC8379396 DOI: 10.2147/cmar.s322179] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/29/2021] [Indexed: 01/03/2023] Open
Abstract
Introduction N6-methyladenosine (m6A) modification and long non-coding RNAs (lncRNAs) play pivotal roles in the progression of hepatocellular carcinoma (HCC). However, how their interaction is involved in the prognostic value of HCC and immune checkpoint inhibitors (ICIs) therapy remains unclear. Methods The RNA sequencing and clinical data of HCC patients were collected from TCGA database. The prognostic m6A-related lncRNAs were screened out with Pearson correlation test, univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) Cox regression. Patients with HCC were classified into 2 subtypes by consensus clustering. Survival analyses were performed to assess the prognostic value of different clusters and risk models. Potential tumor correlated biological pathways correlated with different clusters were explored through gene set enrichment analysis. We also identified the relationship of the risk model and clusters with response to immune checkpoint inhibitors (ICIs) therapy and tumor microenvironment (TME). Furthermore, the prognostic value of the 9 m6A-related lncRNAs was validated in the external cohort. Finally, the role of SNHG4 was explored by silencing and overexpression of SNHG4 through conducting proliferation, migration and invasion experiments. Results Patients from 2 clusters and different risk groups based on m6A-related lncRNAs had significantly different clinicopathological characteristics and overall survival outcomes. Tumor-correlated biological pathways were found to be correlated with Cluster 2 through GSEA. Moreover, we found that patients from different clusters and risk groups expressed higher levels of immune checkpoint genes and had distinct TME and different responses for ICIs therapy. Prognostic value of this risk model was further confirmed in the external cohort. Finally, consistent with the discovery, SNHG4 played an oncogenic role in vitro. Conclusion Our study demonstrated that the 9 m6A-related lncRNA signature may serve as a novel predictor in the prognosis of HCC and optimize (ICIs) therapy. SNHG4 plays an oncogenic role in HCC.
Collapse
Affiliation(s)
- Yi Wang
- Department of Radiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Medical Imaging, Shanghai, 200032, People's Republic of China
| | - Na Li
- Department of Radiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Medical Imaging, Shanghai, 200032, People's Republic of China
| | - Di Tian
- Department of Radiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Medical Imaging, Shanghai, 200032, People's Republic of China
| | - Chang-Wu Zhou
- Department of Radiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Medical Imaging, Shanghai, 200032, People's Republic of China
| | - You-Hua Wang
- Department of Orthopaedics, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, People's Republic of China
| | - Chun Yang
- Department of Radiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Medical Imaging, Shanghai, 200032, People's Republic of China
| | - Meng-Su Zeng
- Department of Radiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Medical Imaging, Shanghai, 200032, People's Republic of China
| |
Collapse
|
50
|
Qiu Y, Wang X, Fan Z, Zhan S, Jiang X, Huang J. Integrated analysis on the N6-methyladenosine-related long noncoding RNAs prognostic signature, immune checkpoints, and immune cell infiltration in clear cell renal cell carcinoma. IMMUNITY INFLAMMATION AND DISEASE 2021; 9:1596-1612. [PMID: 34432955 PMCID: PMC8589390 DOI: 10.1002/iid3.513] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/27/2021] [Accepted: 08/13/2021] [Indexed: 12/17/2022]
Abstract
Background Patients with advanced clear cell renal cell carcinoma (ccRCC) have a poor prognosis and lack effective prognostic biomarkers. N6‐methyladenosine‐related lncRNAs (m6A‐related long noncoding RNAs [lncRNAs]) have been confirmed to be associated with the development of multiple tumors, but its role in ccRCC is not clear. Methods Gene expression data and clinical information of ccRCC patients were extracted from The Cancer Genome Atlas Database. The prognostic m6A‐related lncRNAs were obtained by Pearson's correlation analysis and univariate Cox regression analysis. Afterward, the cluster classification and its correlation with prognosis, clinical characteristics, and immunity were analyzed. LASSO regression was used to establish the prognostic risk model. The predictive performance of the prognostic model was evaluated and validated by survival analysis and receiver operating characteristic curve analysis, et al. The expression of immune checkpoints and immune cell infiltration in patients with different risks were systematically analyzed. Results A total of 27 prognostic m6A‐related lncRNAs were identified. These m6A‐related lncRNAs were differentially expressed between tumor and normal tissues. Among them, 24 high‐risk m6A‐related lncRNAs were overexpressed in Cluster 2 and correlated with poor prognosis, low stromal score, high expression of immune checkpoints, and immunosuppressive cells infiltration. Based upon, a prognostic risk model composed of seven m6A‐related lncRNAs was constructed. After a series of analyses, it was proved that this model had good sensitivity and specificity, and could predict the prognosis of patients with different clinical stratification. The expression of PD‐1, PD‐L1, CTLA‐4, LAG‐3, TIM‐3, and TIGIT were significantly increased in the high‐risk patients, and there was a correlation between the risk score and immune cell infiltration. Conclusions The seven m6A‐related lncRNAs prognostic risk signature showed reliable prognostic predictive power for ccRCC and was associated with the expression of immune checkpoints and immune cell infiltration. This seven m6A‐related lncRNAs signature will be helpful in managing ccRCC and guiding individualized immunotherapy.
Collapse
Affiliation(s)
- Yuqin Qiu
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaogang Wang
- Department of Emergency Medicine, Beijing Haidian Hospital, Haidian Section of Peking University Third Hospital, Beijing, China
| | - Zhenjia Fan
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Shanhui Zhan
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Xin Jiang
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jinchang Huang
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, China.,Institute of Acupuncture and Moxibustion in Cancer Care, Beijing University of Chinese Medicine, Beijing, China
| |
Collapse
|