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Mo Y, Adu-Amankwaah J, Qin W, Gao T, Hou X, Fan M, Liao X, Jia L, Zhao J, Yuan J, Tan R. Unlocking the predictive potential of long non-coding RNAs: a machine learning approach for precise cancer patient prognosis. Ann Med 2023; 55:2279748. [PMID: 37983519 DOI: 10.1080/07853890.2023.2279748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
The intricate web of cancer biology is governed by the active participation of long non-coding RNAs (lncRNAs), playing crucial roles in cancer cells' proliferation, migration, and drug resistance. Pioneering research driven by machine learning algorithms has unveiled the profound ability of specific combinations of lncRNAs to predict the prognosis of cancer patients. These findings highlight the transformative potential of lncRNAs as powerful therapeutic targets and prognostic markers. In this comprehensive review, we meticulously examined the landscape of lncRNAs in predicting the prognosis of the top five cancers and other malignancies, aiming to provide a compelling reference for future research endeavours. Leveraging the power of machine learning techniques, we explored the predictive capabilities of diverse lncRNA combinations, revealing their unprecedented potential to accurately determine patient outcomes.
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Affiliation(s)
- Yixuan Mo
- Department of Physiology, Basic medical school, Xuzhou Medical University, Xuzhou, China
| | - Joseph Adu-Amankwaah
- Department of Physiology, Basic medical school, Xuzhou Medical University, Xuzhou, China
| | - Wenjie Qin
- Department of Physiology, Basic medical school, Xuzhou Medical University, Xuzhou, China
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Tan Gao
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Xiaoqing Hou
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Mengying Fan
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Xuemei Liao
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Liwei Jia
- Department of Pathology, UT Southwestern Medical Center, Dallas, UT, USA
| | - Jinming Zhao
- Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang, China
- Department of Pathology, The First Hospital of China Medical University, Shenyang, China
| | - Jinxiang Yuan
- The Collaborative Innovation Center, Jining Medical University, Jining, Shandong, China
| | - Rubin Tan
- Department of Physiology, Basic medical school, Xuzhou Medical University, Xuzhou, China
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2
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Gupta M, Kannappan S, Jain M, Douglass D, Shah R, Bose P, Narendran A. Development and validation of a 21-gene prognostic signature in neuroblastoma. Sci Rep 2023; 13:12526. [PMID: 37532697 PMCID: PMC10397261 DOI: 10.1038/s41598-023-37714-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 06/26/2023] [Indexed: 08/04/2023] Open
Abstract
Survival outcomes for patients with neuroblastoma vary markedly and reliable prognostic markers and risk stratification tools are lacking. We sought to identify and validate a transcriptomic signature capable of predicting risk of mortality in patients with neuroblastoma. The TARGET NBL dataset (n = 243) was used to develop the model and two independent cohorts, E-MTAB-179 (n = 478) and GSE85047 (n = 240) were used as validation sets. EFS was the primary outcome and OS was the secondary outcome of interest for all analysis. We identified a 21-gene signature capable of stratifying neuroblastoma patients into high and low risk groups in the E-MTAB-179 (HR 5.87 [3.83-9.01], p < 0.0001, 5 year AUC 0.827) and GSE85047 (HR 3.74 [2.36-5.92], p < 0.0001, 5 year AUC 0.815) validation cohorts. Moreover, the signature remained independent of known clinicopathological variables, and remained prognostic within clinically important subgroups. Further, the signature was effectively incorporated into a risk model with clinicopathological variables to improve prognostic performance across validation cohorts (Pooled Validation HR 6.93 [4.89-9.83], p < 0.0001, 5 year AUC 0.839). Similar prognostic utility was also demonstrated with OS. The identified signature is a robust independent predictor of EFS and OS outcomes in neuroblastoma patients and can be combined with clinically utilized clinicopathological variables to improve prognostic performance.
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Affiliation(s)
- Mehul Gupta
- Department of Pediatrics and Oncology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Sunand Kannappan
- Department of Pediatrics and Oncology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Mohit Jain
- Department of Pediatrics and Oncology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - David Douglass
- Department of Pediatrics, Hematology/Oncology Section, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA
| | - Ravi Shah
- Department of Pediatrics and Oncology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Pinaki Bose
- Departments of Oncology and Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
- Cumming School of Medicine, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada.
| | - Aru Narendran
- Department of Pediatrics and Oncology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
- Departments of Oncology and Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
- Cumming School of Medicine, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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Sarfaraz N, Somarowthu S, Bouchard MJ. The interplay of long noncoding RNAs and hepatitis B virus. J Med Virol 2023; 95:e28058. [PMID: 35946066 DOI: 10.1002/jmv.28058] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 01/11/2023]
Abstract
Hepatitis B Virus (HBV) infections remain a major global health burden with an estimated 296 million people living with a chronic infection and 884,000 HBV-related deaths annually. Notably, patients with a chronic hepatitis B (CHB) infection are at a 30-fold greater risk of developing hepatocellular carcinoma (HCC), the most common type of primary liver cancer, which is the 3rd deadliest cancer worldwide. Several groups have assessed HBV-related aberrant expression of host-cell long noncoding RNAs (lncRNAs) and how altered expression of specific lncRNAs affects HBV replication and progression to associated disease states. Given the challenges in establishing effective HBV models and analyzing transcriptomic data, this review focuses on lncRNA expression data primarily collected from clinical patient samples and primary human hepatocytes, with the subsequent mechanism of action analysis in cell lines or other model systems. Ultimately, understanding HBV-induced lncRNA-expression dysregulation could lead to new treatments and biomarkers for HBV infection and its associated diseases.
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Affiliation(s)
- Nima Sarfaraz
- Graduate Program in Molecular and Cell Biology and Genetics, Graduate School of Biomedical Sciences and Professional Studies, College of Medicine, Drexel University, Philadelphia, Pennsylvania, USA
| | - Srinivas Somarowthu
- Department of Biochemistry and Molecular Biology, College of Medicine, Drexel University, Philadelphia, Pennsylvania, USA
| | - Michael J Bouchard
- Department of Biochemistry and Molecular Biology, College of Medicine, Drexel University, Philadelphia, Pennsylvania, USA
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Chen Y, Li Z, Cao Q, Guan H, Mao L, Zhao M. Ferroptosis-related gene signatures in neuroblastoma associated with prognosis. Front Cell Dev Biol 2022; 10:871512. [PMID: 36147739 PMCID: PMC9486025 DOI: 10.3389/fcell.2022.871512] [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: 02/08/2022] [Accepted: 08/12/2022] [Indexed: 11/28/2022] Open
Abstract
Background: Ferroptosis, a form of regulatory cell death, has been linked to the development of various tumors. Peripheral neuroblastoma (NB) is one of the most common extracranial solid tumors in children, and it has been proposed that regulating tumor cell ferroptosis may be a future treatment for NB. However, it is unclear how ferroptosis contributes to NB development. Methods: Expression data were collected from two independent cohorts (GEO and Arrayexpress databases). Univariate Cox analysis, multivariate Cox analysis, and the least absolute shrinkage and selection operator (Lasso) algorithm were applied to create a prognostic signature, whose performance was quantified using the area under the receiver operating characteristic curve (AUC) and Kaplan–Meier curves. A prognostic meta-analysis was used to test the suitability and stability of the FRG signature. Drug sensitivity analyses were performed using the data collected from Cell Miner™. Results:PROM2, AURKA, STEAP3, CD44, ULK2, MAP1LC3A, ATP6V1G2, and STAT3 are among the eight genes in the FRG prognostic signature, all of which were highly expressed in stage 1 NB, except AURKA. Furthermore, the high-risk group, which was stratified by signature, had a lower overall survival rate than the low-risk group. GSEA revealed that high-risk groups have more biological processes related to ferroptosis. Conclusion: Ferroptosis-related genes are expressed differently between stages 1 and 4 NB. The FRG signature successfully stratified NB patients into two risk groups and can accurately predict the overall survival in NB. In addition, we found that the gene AURKA might have the potential to be a prognostic marker in NB.
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Affiliation(s)
- Yiru Chen
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Zihao Li
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
- Department of Pharmacy, College of Biology, Hunan University, Changsha, China
| | - Qingtai Cao
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Haoyu Guan
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Longfei Mao
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
- Department of Pharmacy, College of Biology, Hunan University, Changsha, China
- *Correspondence: Longfei Mao, ; Mingyi Zhao,
| | - Mingyi Zhao
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Longfei Mao, ; Mingyi Zhao,
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5
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Zhao N, Guo M, Zhang C, Wang C, Wang K. Pan-Cancer Methylated Dysregulation of Long Non-coding RNAs Reveals Epigenetic Biomarkers. Front Cell Dev Biol 2022; 10:882698. [PMID: 35721492 PMCID: PMC9200062 DOI: 10.3389/fcell.2022.882698] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/28/2022] [Indexed: 11/18/2022] Open
Abstract
Different cancer types not only have common characteristics but also have their own characteristics respectively. The mechanism of these specific and common characteristics is still unclear. Pan-cancer analysis can help understand the similarities and differences among cancer types by systematically describing different patterns in cancers and identifying cancer-specific and cancer-common molecular biomarkers. While long non-coding RNAs (lncRNAs) are key cancer modulators, there is still a lack of pan-cancer analysis for lncRNA methylation dysregulation. In this study, we integrated lncRNA methylation, lncRNA expression and mRNA expression data to illuminate specific and common lncRNA methylation patterns in 23 cancer types. Then, we screened aberrantly methylated lncRNAs that negatively regulated lncRNA expression and mapped them to the ceRNA relationship for further validation. 29 lncRNAs were identified as diagnostic biomarkers for their corresponding cancer types, with lncRNA AC027601 was identified as a new KIRC-associated biomarker, and lncRNA ACTA2-AS1 was regarded as a carcinogenic factor of KIRP. Two lncRNAs HOXA-AS2 and AC007228 were identified as pan-cancer biomarkers. In general, the cancer-specific and cancer-common lncRNA biomarkers identified in this study may aid in cancer diagnosis and treatment.
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Affiliation(s)
- Ning Zhao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Maozu Guo
- School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing, China
| | - Chunlong Zhang
- College of Information and Computer Engineering, Northeast Forest University, Harbin, China
| | - Chunyu Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Kuanquan Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.,School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
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6
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Yin X, Lin H, Lin L, Miao L, He J, Zhuo Z. LncRNAs and CircRNAs in cancer. MedComm (Beijing) 2022; 3:e141. [PMID: 35592755 PMCID: PMC9099016 DOI: 10.1002/mco2.141] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 12/24/2022] Open
Affiliation(s)
- Xin Yin
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou Guangdong China
- College of Pharmacy Jinan University Guangzhou Guangdong China
| | - Huiran Lin
- Faculty of Medicine Macau University of Science and Technology Macau China
| | - Lei Lin
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou Guangdong China
| | - Lei Miao
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou Guangdong China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou Guangdong China
| | - Zhenjian Zhuo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou Guangdong China
- Laboratory Animal Center, School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School Shenzhen China
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7
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Zhang Y, Hu R, Xi B, Nie D, Xu H, Liu A. Mechanisms of Senescence-Related NKG2D Ligands Release and Immune Escape Induced by Chemotherapy in Neuroblastoma Cells. Front Cell Dev Biol 2022; 10:829404. [PMID: 35309907 PMCID: PMC8924122 DOI: 10.3389/fcell.2022.829404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 02/10/2022] [Indexed: 11/24/2022] Open
Abstract
Chemotherapy-induced senescence promotes immunocyte aggregation in the tumor microenvironment by upregulating the surface expression of activating ligands in cancer cells. However, these senescent tumor cells cannot be completely cleared and can induce tumor recurrence. Previous studiesshowed that soluble natural killer (NK) group 2D (NKG2D) ligands impair the recognition of multiple immune cells. In this study, we established an in vitro senescence model using neuroblastoma cells subjected to low-dose Chemotherapeutic drug doxorubicin or the Aurora A inhibitor MLN8237. The results showed that different neuroblastoma cell lines showed increased secretion of the NKG2D ligand MHC class I polypeptide-related sequence A/B (MICA/B) following proteolysis after treatment, with MICA/B subsequently recruited to exosomes to downregulate NKG2D expression in NK cells. Interestingly, disintegrin and metalloproteinase domain-containing 10 (ADAM10) was upregulated in senescent tumor cells, and combined treatment with the ADAM10 inhibitor GI254023X and chemotherapeutic drugs inhibited MICA/B secretion and enhanced recognition and killing by NK cells. Additionally, we found that expression of the long noncoding RNA MALAT1 was significantly increased in senescent neuroblastoma cells, and that MALAT1 served as a sponge for microRNA (miR)-92a-3p to counteract miR-92a-3p-mediated repression of ADAM10 levels. Furthermore, administration of a MALAT1 inhibitor or an miR-92a-3p mimic reduced the MICA/B shedding and enhanced recognition and killing by NK cells. These results confirmed that low-dose chemotherapy induces senescence in neuroblastoma cells, and that senescent tumor cells promote the shedding of the NKG2D ligand MICA/B through the MALAT1/miR-92a/ADAM10 axis, thereby contributing to the formation of a suppressive immune microenvironment and promoting immune escape.
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Affiliation(s)
- Yan Zhang
- Department of Pediatrics, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Ruimin Hu
- Department of Pediatrics, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Bixin Xi
- Department of Pediatrics, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Dimin Nie
- Department of Pediatrics, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Hanxiao Xu
- Department of Pediatrics, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Aiguo Liu
- Department of Pediatrics, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
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8
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Gan L, Shangguan Q, Zhang F, Tong X, Qi D, Zhao Y, Ye X. HBV HBx-Downregulated lncRNA LINC01010 Attenuates Cell Proliferation by Interacting with Vimentin. Int J Mol Sci 2021; 22:ijms222212497. [PMID: 34830378 PMCID: PMC8620790 DOI: 10.3390/ijms222212497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 12/31/2022] Open
Abstract
Hepatitis B virus (HBV) infection is closely related to hepatocellular carcinoma (HCC) development. To investigate the mechanism of HBV causing HCC, we previously analyzed the transcription of the HBV-transgenic cell line HepG2-4D14 and parental HepG2 cells and identified a subset of long noncoding RNAs (lncRNAs) differentially expressed between them. In this study, we focus on lncRNA LINC01010, as it is significantly downregulated in HepG2-4D14 cells and in liver tissues of HCC patients, and positively correlated with survival. We found that HBV-encoded HBx can reduce the transcription of LINC01010. Functional analysis showed that the overexpression of LINC01010 inhibits proliferation, migration and invasion of HepG2 cells while the knockdown of LINC01010 promotes these processes. By taking the approach of RNA immunoprecipitation (RIP) and mass spectrometry, we identified that LINC01010 can interact with vimentin. Further studies demonstrated that LINC01010 negatively affects the vimentin network extension and causes more rapid subunit exchange and lower stability of vimentin filaments. In addition, LINC01010 can reduce the amount of insoluble vimentin within cells, which suggests that LINC01010 interfers with vimentin polymerization. These data indicate that LINC01010 can inhibit the assembly of vimentin filament. Thus, we revealed that HBV HBx-downregulated LINC01010, which suppresses cell proliferation and migration by negatively regulating the formation of vimentin filament. Taken together, LINC01010 is a potential tumor suppressor that may restrain HBV-related HCC development.
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Affiliation(s)
- Lipeng Gan
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (L.G.); (Q.S.); (F.Z.); (X.T.); (D.Q.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qilin Shangguan
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (L.G.); (Q.S.); (F.Z.); (X.T.); (D.Q.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Zhang
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (L.G.); (Q.S.); (F.Z.); (X.T.); (D.Q.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomei Tong
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (L.G.); (Q.S.); (F.Z.); (X.T.); (D.Q.)
| | - Dandan Qi
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (L.G.); (Q.S.); (F.Z.); (X.T.); (D.Q.)
| | - Yan Zhao
- Department of General Surgery, Strategic Support Force Medical Center, No.9 Anxiang Beili, Chaoyang District, Beijing 100101, China;
| | - Xin Ye
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China; (L.G.); (Q.S.); (F.Z.); (X.T.); (D.Q.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel.: +86-010-64807508
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Fan L, Ru J, Liu T, Ma C. Identification of a Novel Prognostic Gene Signature From the Immune Cell Infiltration Landscape of Osteosarcoma. Front Cell Dev Biol 2021; 9:718624. [PMID: 34552929 PMCID: PMC8450587 DOI: 10.3389/fcell.2021.718624] [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: 06/01/2021] [Accepted: 08/09/2021] [Indexed: 01/11/2023] Open
Abstract
Background: The tumor microenvironment (TME) mainly comprises tumor cells and tumor-infiltrating immune cells mixed with stromal components. Latestresearch hasdisplayed that tumor immune cell infiltration (ICI) is associated with the clinical outcome of patients with osteosarcoma (OS). This work aimed to build a gene signature according to ICI in OS for predicting patient outcomes. Methods: The TARGET-OS dataset was used for model training, while the GSE21257 dataset was taken forvalidation. Unsupervised clustering was performed on the training cohort based on the ICI profiles. The Kaplan–Meier estimator and univariate Cox proportional hazards models were used to identify the differentially expressed genes between clusters to preliminarily screen for potential prognostic genes. We incorporated these potential prognostic genes into a LASSO regression analysis and produced a gene signature, which was next assessed with the Kaplan–Meier estimator, Cox proportional hazards models, ROC curves, IAUC, and IBS in the training and validation cohorts. In addition, we compared our signature to previous models. GSEAswere deployed to further study the functional mechanism of the signature. We conducted an analysis of 22 TICsfor identifying the role of TICs in the gene signature’s prognosis ability. Results: Data from the training cohort were used to generate a nine-gene signature. The Kaplan–Meier estimator, Cox proportional hazards models, ROC curves, IAUC, and IBS validated the signature’s capacity and independence in predicting the outcomes of OS patients in the validation cohort. A comparison with previous studies confirmed the superiority of our signature regarding its prognostic ability. Annotation analysis revealed the mechanism related to the gene signature specifically. The immune-infiltration analysis uncoveredkey roles for activated mast cells in the prognosis of OS. Conclusion: We identified a robust nine-gene signature (ZFP90, UHRF2, SELPLG, PLD3, PLCB4, IFNGR1, DLEU2, ATP6V1E1, and ANXA5) that can predict OS outcome precisely and is strongly linked to activated mast cells.
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Affiliation(s)
- Lei Fan
- Department of Orthopedics, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Jingtao Ru
- Department of Orthopedics, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Tao Liu
- Department of Orthopedics, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Chao Ma
- Charité - Universitätsmedizin Berlin, Berlin, Germany
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10
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Zhao F, Wang M, Zhu J. Hypoxia-related lncRNAs to build prognostic classifier and reveal the immune characteristics of EGFR wild type and low expression of PD-L1 squamous and adenocarcinoma NSCLC. Cancer Med 2021; 10:6099-6113. [PMID: 34250747 PMCID: PMC8419766 DOI: 10.1002/cam4.4126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/16/2021] [Accepted: 06/25/2021] [Indexed: 02/05/2023] Open
Abstract
Background Recently, the development and application of targeted therapies like tyrosine kinase inhibitors (TKIs) and immune checkpoint inhibitors (ICIs) have achieved remarkable survival benefits in non‐small cell lung cancer (NSCLC) treatment. However, epidermal growth factor receptor (EGFR) wild type and low expression of programmed death‐ligand 1 (PD‐L1) NSCLC remain unmanageable. Few treatments for these patients exist, and more side effects with combination therapies have been observed. We intended to generate a hypoxia‐related lncRNAs (hypolncRNAs) classifier that could successfully identify the high‐risk patients and reveal its underlying molecular immunology characteristics. Methods By identifying the bottom 25% PD‐L1 expression level as low expression of PD‐L1 and removing EGFR mutant samples, a total of 222 lung adenocarcinoma (LUAD) and lung squamous carcinoma (LUSC) samples and 93 adjacent non‐tumor samples were finally extracted from The Cancer Genome Atlas (TCGA). A 0 or 1 matrix was constructed by cyclically pairing hypoxia‐related long non‐coding RNAs (hypolncRNAs) and divided into the train set and test set. The univariate Cox regression analysis determined the prognostic hypolncRNAs pairs. Then, the prognostic classifier contained nine hypolncRNAs pairs which were generated by Lasso regression and multivariate Cox analysis. It successfully stratified EGFR wild type and low expression of PD‐L1 squamous and adenocarcinoma NSCLC (double‐negative LUAD and LUSC) patients into the high‐ and low‐risk groups, whose accuracy was proved by the time‐dependent receiver operating characteristic (ROC) curve. Furthermore, diverse acknowledged immunology methods include XCELL, TIMER, QUANTISEQ, MCPcounter, EPIC, CIBERSORT‐ABS, CIBERSORT, and the single‐sample gene set enrichment analysis (ssGSEA) revealed its underlying antitumor immunosuppressive status in the high‐risk patients. Conclusions It is noteworthy that hypolncRNAs are associated with the survival of double‐negative LUAD and LUSC patients, for which the possible mechanism is inhibiting the antitumor immune process.
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Affiliation(s)
- Fang Zhao
- Department of Intensive Care Unit, The Peoples Hospital of Tongliang District, Chongqing, China
| | - Min Wang
- Department of Respiratory and Geriatrics, Chongqing Public Health Medical Center, Chongqing, China
| | - Jie Zhu
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
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11
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Zhang GZ, Wu ZL, Li CY, Ren EH, Yuan WH, Deng YJ, Xie QQ. Development of a Machine Learning-Based Autophagy-Related lncRNA Signature to Improve Prognosis Prediction in Osteosarcoma Patients. Front Mol Biosci 2021; 8:615084. [PMID: 34095215 PMCID: PMC8176230 DOI: 10.3389/fmolb.2021.615084] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/29/2021] [Indexed: 12/15/2022] Open
Abstract
Background Osteosarcoma is a frequent bone malignancy in children and young adults. Despite the availability of some prognostic biomarkers, most of them fail to accurately predict prognosis in osteosarcoma patients. In this study, we used bioinformatics tools and machine learning algorithms to establish an autophagy-related long non-coding RNA (lncRNA) signature to predict the prognosis of osteosarcoma patients. Methods We obtained expression and clinical data from osteosarcoma patients in the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and Gene Expression Omnibus (GEO) databases. We acquired an autophagy gene list from the Human Autophagy Database (HADb) and identified autophagy-related lncRNAs by co-expression analyses. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the autophagy-related lncRNAs were conducted. Univariate and multivariate Cox regression analyses were performed to assess the prognostic value of the autophagy-related lncRNA signature and validate the relationship between the signature and osteosarcoma patient survival in an independent cohort. We also investigated the relationship between the signature and immune cell infiltration. Results We initially identified 69 autophagy-related lncRNAs, 13 of which were significant predictors of overall survival in osteosarcoma patients. Kaplan-Meier analyses revealed that the 13 autophagy-related lncRNAs could stratify patients based on their outcomes. Receiver operating characteristic curve analyses confirmed the superior prognostic value of the lncRNA signature compared to clinically used prognostic biomarkers. Importantly, the autophagy-related lncRNA signature predicted patient prognosis independently of clinicopathological characteristics. Furthermore, we found that the expression levels of the autophagy-related lncRNA signature were significantly associated with the infiltration levels of different immune cell subsets, including T cells, NK cells, and dendritic cells. Conclusion The autophagy-related lncRNA signature established here is an independent and robust predictor of osteosarcoma patient survival. Our findings also suggest that the expression of these 13 autophagy-related lncRNAs may promote osteosarcoma progression by regulating immune cell infiltration in the tumor microenvironment.
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Affiliation(s)
- Guang-Zhi Zhang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China.,Lintao County Traditional Chinese Medicine Hospital of Gansu Province, Lintao, China
| | - Zuo-Long Wu
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China
| | - Chun-Ying Li
- The Fourth People's Hospital of Qinghai Province, Xining, China
| | - En-Hui Ren
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China.,Department of Orthopaedics, Xining First People's Hospital, Xining, China
| | - Wen-Hua Yuan
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China
| | - Ya-Jun Deng
- The Second Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of Orthopedics, Lanzhou University Second Hospital, Lanzhou, China
| | - Qi-Qi Xie
- Affiliated Hospital of Qinghai University, Xining, China.,Affiliated Cancer Hospital of Qinghai University, Xining, China.,Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, China
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Zhong X, Tao Y, Chang J, Zhang Y, Zhang H, Wang L, Liu Y. Prognostic Signature of Immune Genes and Immune-Related LncRNAs in Neuroblastoma: A Study Based on GEO and TARGET Datasets. Front Oncol 2021; 11:631546. [PMID: 33767996 PMCID: PMC7985261 DOI: 10.3389/fonc.2021.631546] [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: 11/20/2020] [Accepted: 02/02/2021] [Indexed: 12/13/2022] Open
Abstract
Background The prognostic value of immune-related genes and lncRNAs in neuroblastoma has not been elucidated, especially in subgroups with different outcomes. This study aimed to explore immune-related prognostic signatures. Materials and Methods Immune-related prognostic genes and lncRNAs were identified by univariate Cox regression analysis in the training set. The top 20 C-index genes and 17 immune-related lncRNAs were included in prognostic model construction, and random forest and the Least Absolute Shrinkage and Selection Operator (LASSO) regression algorithms were employed to select features. The risk score model was constructed and assessed using the Kaplan-Meier plot and the receiver operating characteristic curve. Functional enrichment analysis of the immune-related lncRNAs was conducted using the STRING database. Results In GSE49710, five immune genes (CDK4, PIK3R1, THRA, MAP2K2, and ULBP2) were included in the risk score five genes (RS5_G) signature, and eleven immune-related lncRNAs (LINC00260, FAM13A1OS, AGPAT4-IT1, DUBR, MIAT, TSC22D1-AS1, DANCR, MIR137HG, ERC2-IT1, LINC01184, LINC00667) were brought into risk score LncRNAs (RS_Lnc) signature. Patients were divided into high/low-risk score groups by the median. Overall survival and event/progression-free survival time were shortened in patients with high scores, both in training and validation cohorts. The same results were found in subgroups. In grouping ability assessment, the area under the curves (AUCs) in distinguishing different groups ranged from 0.737 to 0.94, better in discriminating MYCN status and high risk in training cohort (higher than 0.9). Multivariate Cox analysis demonstrated that RS5_G and RS_Lnc were the independent risk factors for overall and event/progression-free survival (all p-values <0.001). Correlation analysis showed that RS5_G and RS_Lnc were negatively associated with aDC, CD8+ T cells, but positively correlated with Th2 cells. Functional enrichment analyzes demonstrated that immune-related lncRNAs are mainly enriched in cancer-related pathways and immune-related pathways. Conclusion We identified the immune-related prognostic signature RS5_G and RS_Lnc. The predicting and grouping ability is close to being even better than those reported in other studies, especially in subgroups. This study provided prognostic signatures that may help clinicians to choose optimal treatment strategies and showed a new insight for NB treatment. These results need further biological experiments and clinical validation.
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Affiliation(s)
- Xiaodan Zhong
- College of Computer Science and Technology, Jilin University, Changchun, China.,Department of Pediatric Oncology, The First Hospital of Jilin University, Changchun, China.,Key Laboratory of Symbolic Computation and Knowledge Engineering, Ministry of Education, Jilin University, Changchun, China
| | - Ying Tao
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Jian Chang
- Department of Pediatric Oncology, The First Hospital of Jilin University, Changchun, China
| | - Yutong Zhang
- Department of Pediatric Oncology, The First Hospital of Jilin University, Changchun, China
| | - Hao Zhang
- College of Computer Science and Technology, Jilin University, Changchun, China.,Key Laboratory of Symbolic Computation and Knowledge Engineering, Ministry of Education, Jilin University, Changchun, China
| | - Linyu Wang
- College of Computer Science and Technology, Jilin University, Changchun, China.,Key Laboratory of Symbolic Computation and Knowledge Engineering, Ministry of Education, Jilin University, Changchun, China
| | - Yuanning Liu
- College of Computer Science and Technology, Jilin University, Changchun, China.,Key Laboratory of Symbolic Computation and Knowledge Engineering, Ministry of Education, Jilin University, Changchun, China
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Jin W, Zhang Y, Liu Z, Che Z, Gao M, Peng H. Exploration of the molecular characteristics of the tumor-immune interaction and the development of an individualized immune prognostic signature for neuroblastoma. J Cell Physiol 2020; 236:294-308. [PMID: 32510620 DOI: 10.1002/jcp.29842] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/16/2020] [Accepted: 05/19/2020] [Indexed: 12/17/2022]
Abstract
Neuroblastoma (NBL) exists in a complex tumor-immune microenvironment. Immune cell infiltration and tumor-immune molecules play a critical role in tumor development and significantly impact the prognosis of patients. However, the molecular characteristics describing the NBL-immune interaction and their prognostic potential have yet to be investigated systematically. We first employed multiple machine learning algorithms, such as Gene Sets Enrichment Analysis and cell type identification by estimating relative subsets of RNA transcripts, to identify immunophenotypes and immunological characteristics in NBL patient data from public databases and then investigated the prognostic potential and regulatory networks of identified immune-related genes involved in the NBL-immune interaction. The immunity signature combining nine immunity genes was confirmed as more effective for individual risk stratification and survival outcome prediction in NBL patients than common clinical characteristics (area under the curve [AUC] = 0.819, C-index = 0.718, p < .001). A mechanistic exploration revealed the regulatory network of molecules involved in the NBL-immune interaction. These immune molecules were also discovered to possess a significant correlation with plasma cell infiltration, MYCN status, and the level of chemokines and macrophage-related molecules (p < .001). A nomogram was constructed based on the immune signature and clinical characteristics, which showed high potential for prognosis prediction (AUC = 0.856, C-index = 0.755, p < .001). We systematically elucidated the complex regulatory mechanisms and characteristics of the molecules involved in the NBL-immune interaction and their prognostic potential, which may have important implications for further understanding the molecular mechanism of the NBL-immune interaction and identifying high-risk NBL patients to guide clinical treatment.
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Affiliation(s)
- Wenyi Jin
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuchang, Wuhan, China
| | - Yubiao Zhang
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuchang, Wuhan, China
| | - Zilin Liu
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuchang, Wuhan, China
| | - Zhifei Che
- Department of Urology, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Mingyong Gao
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuchang, Wuhan, China
| | - Hao Peng
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuchang, Wuhan, China
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Four genes predict the survival of osteosarcoma patients based on TARGET database. J Bioenerg Biomembr 2020; 52:291-299. [PMID: 32514876 DOI: 10.1007/s10863-020-09836-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/14/2020] [Indexed: 12/31/2022]
Abstract
Osteosarcoma represents one of the most aggressive tumors of bone among adolescents and young adults. Despite improvements in treatment, osteosarcoma has a grave prognosis. The identification of prognostic factors is still in its infancy. Weighted gene correlation network analysis (WGCNA) was conducted on mRNA-sequencing and clinical information (gender, survival and metastasis) of osteosarcoma patients from the TARGET database to obtain genes in modules associated with metastasis of osteosarcoma. The Cox regression analysis was then performed on the gene expression profile from TARGET to screen genes associated with patients' survival. Known genes related to osteosarcoma were obtained by intersecting osteosarcoma-related genes from DisGeNET and DiGSeE, followed by the construction of PPI network of osteosarcoma-related genes and survival-related genes in modules. The screened key genes were subject to multi-factor Cox proportional hazards model, and osteosarcoma patients were classified into high- and low- risk groups according to the risk score to evaluate the potential of key genes to predict the survival of osteosarcoma patients. The WGCNA showed that 4 genes in tan and 19 genes in pink modules were related to the survival of osteosarcoma patients. Osteosarcoma-related known genes (9) were obtained in intersection of DisGeNET and DiGSeE. PPI network identified 4 key genes (KRT5, HIPK2, MAP3K5 and CD5) closely associated with survival of osteosarcoma patients. HIPK2, MAP3K5 and CD5 expression was inversely correlated with survival risk, while KRT5 expression was positively correlated with survival risk. These results show KRT5, HIPK2, MAP3K5 and CD5 serve as prognostic factors of osteosarcoma patients.
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15
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Shen Y, Peng X, Shen C. Identification and validation of immune-related lncRNA prognostic signature for breast cancer. Genomics 2020; 112:2640-2646. [PMID: 32087243 DOI: 10.1016/j.ygeno.2020.02.015] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/10/2020] [Accepted: 02/18/2020] [Indexed: 12/31/2022]
Abstract
The prognosis of patients with breast cancer is closely related to both the infiltration of immune cells and the expression of lncRNAs. In this study, we evaluated the infiltration of immune cells in 1109 breast cancer samples obtained from TCGA by applying the ssGSEA to the transcriptome of these samples, thereby generating high immune cell infiltration group and low immune cell infiltration group. On the basis of these groupings, we found 696 differentially expressed lncRNAs which were sequentially subjected to univariate Cox regression and stepwise multiple Cox regression analysis. 11 lncRNAs were identified as prognostic signature for breast cancer. Kaplan-Meier analysis, univariate Cox regression, multivariate Cox regression, and ROC analyses further revealed that this 11-lncRNA signature was a novel and important prognostic factor independent of multiple clinicopathological parameters. The TIMER database showed that this 11-lncRNA prognostic signature for breast cancer was associated with the infiltration of immune cell subtypes.
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Affiliation(s)
- Yong Shen
- Department of Pathology and Pathophysiology, School of Medicine, Southeast University, 210009 Nanjing, China
| | - Xiaowei Peng
- Department of Pathology and Pathophysiology, School of Medicine, Southeast University, 210009 Nanjing, China
| | - Chuanlu Shen
- Department of Pathology and Pathophysiology, School of Medicine, Southeast University, 210009 Nanjing, China.
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