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Riquelme I, Pérez-Moreno P, Mora-Lagos B, Ili C, Brebi P, Roa JC. Long Non-Coding RNAs (lncRNAs) as Regulators of the PI3K/AKT/mTOR Pathway in Gastric Carcinoma. Int J Mol Sci 2023; 24:ijms24076294. [PMID: 37047267 PMCID: PMC10094576 DOI: 10.3390/ijms24076294] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Gastric cancer (GC) represents ~10% of the global cancer-related deaths, increasingly affecting the younger population in active stages of life. The high mortality of GC is due to late diagnosis, the presence of metastasis and drug resistance development. Additionally, current clinical markers do not guide the patient management adequately, thereby new and more reliable biomarkers and therapeutic targets are still needed for this disease. RNA-seq technology has allowed the discovery of new types of RNA transcripts including long non-coding RNAs (lncRNAs), which are able to regulate the gene/protein expression of many signaling pathways (e.g., the PI3K/AKT/mTOR pathway) in cancer cells by diverse molecular mechanisms. In addition, these lncRNAs might also be proposed as promising diagnostic or prognostic biomarkers or as potential therapeutic targets in GC. This review describes important topics about some lncRNAs that have been described as regulators of the PI3K/AKT/mTOR signaling pathway, and hence, their potential oncogenic role in the development of this malignancy.
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Affiliation(s)
- Ismael Riquelme
- Institute of Biomedical Sciences, Faculty of Health Sciences, Universidad Autónoma de Chile, Temuco 4810101, Chile
- Correspondence: (I.R.); (J.C.R.); Tel.: +56-95923-6933 (I.R.); +56-22354-1061 (J.C.R.)
| | - Pablo Pérez-Moreno
- Millennium Institute on Immunology and Immunotherapy (MIII), Center for Cancer Prevention and Control (CECAN), Department of Pathology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8380000, Chile
| | - Bárbara Mora-Lagos
- Institute of Biomedical Sciences, Faculty of Health Sciences, Universidad Autónoma de Chile, Temuco 4810101, Chile
| | - Carmen Ili
- Millennium Institute on Immunology and Immunotherapy (MIII), Laboratory of Integrative Biology (LIBi), Center for Excellence in Translational Medicine—Scientific and Technological Bioresource Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4810296, Chile
| | - Priscilla Brebi
- Millennium Institute on Immunology and Immunotherapy (MIII), Laboratory of Integrative Biology (LIBi), Center for Excellence in Translational Medicine—Scientific and Technological Bioresource Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4810296, Chile
| | - Juan Carlos Roa
- Millennium Institute on Immunology and Immunotherapy (MIII), Center for Cancer Prevention and Control (CECAN), Department of Pathology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8380000, Chile
- Correspondence: (I.R.); (J.C.R.); Tel.: +56-95923-6933 (I.R.); +56-22354-1061 (J.C.R.)
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Zeng J, Wu Z, Luo M, Xu X, Bai W, Xie G, Chen Q, Liang D, Xu Z, Chen M, Xie J. Development and validation of an endoplasmic reticulum stress long non-coding RNA signature for the prognosis and immune landscape prediction of patients with lung adenocarcinoma. Front Genet 2023; 14:1024444. [PMID: 36891153 PMCID: PMC9986451 DOI: 10.3389/fgene.2023.1024444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 02/07/2023] [Indexed: 02/22/2023] Open
Abstract
Background: Lung adenocarcinoma (LUAD), the most common histotype of lung cancer, may have variable prognosis due to molecular variations. This work investigated long non-coding RNA (lncRNA) related to endoplasmic reticulum stress (ERS) to predict the prognosis and immune landscape for LUAD patients. Methods: RNA data and clinical data from 497 LUAD patients were collected in the Cancer Genome Atlas database. Pearson correlation analysis, univariate Cox regression, least absolute shrinkage and selection operator regression analyses, as well as the Kaplan-Meier method, were used to screen for ERS-related lncRNAs associated with prognosis. The risk score model was developed using multivariate Cox analysis to separate patients into high- and low-risk groups and a nomogram was constructed and evaluated. Finally, we explore the potential functions and compared the immune landscapes of two groups. Quantitative real-time PCR was used to verify the expression of these lncRNAs. Results: Five ERS-related lncRNAs were shown to be strongly linked to patients' prognosis. A risk score model was built by using these lncRNAs to categorize patients based on their median risk scores. For LUAD patients, the model was found to be an independent prognostic predictor (p < 0.001). The signature and clinical variables were then used to construct a nomogram. With 3-year and 5-year OS' AUC of 0.725 and 0.740, respectively, the nomogram's prediction performance is excellent. The 5-lncRNA signature was associated with DNA replication, epithelial-mesenchymal transition, and the pathway of cell cycle, P53 signaling. Between the two risk groups, immune responses, immune cells, and immunological checkpoints were found to be considerably different. Conclusion: Overall, our findings indicate that the 5 ERS-related lncRNA signature was an excellent prognostic indicator and helped to predict the immunotherapy response for patients with LUAD.
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Affiliation(s)
- Jie Zeng
- Department of Thoracic Surgery, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, China
| | - Zhenyu Wu
- Department of Urology, The First People's Hospital of Foshan, Foshan, China
| | - Meijuan Luo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Radiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xie Xu
- Department of Thoracic Surgery, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, China
| | - Wenjie Bai
- Department of Thoracic Surgery, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, China
| | - Guijing Xie
- Department of Thoracic Surgery, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, China
| | - Quhai Chen
- Department of Thoracic Surgery, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, China
| | - Dengfeng Liang
- Department of Thoracic Surgery, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, China
| | - Zixun Xu
- Department of Thoracic Surgery, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, China
| | - Mindong Chen
- Department of Thoracic Surgery, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, China
| | - Jianjiang Xie
- Department of Thoracic Surgery, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, China
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Yao Y, Gu L, Zuo Z, Wang D, Zhou T, Xu X, Yang L, Huang X, Wang L. Necroptosis-related lncRNAs: Combination of bulk and single-cell sequencing reveals immune landscape alteration and a novel prognosis stratification approach in lung adenocarcinoma. Front Oncol 2022; 12:1010976. [PMID: 36605426 PMCID: PMC9808398 DOI: 10.3389/fonc.2022.1010976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/26/2022] [Indexed: 01/07/2023] Open
Abstract
Necroptosis, which is recently recognized as a form of programmed cell death, plays a critical role in cancer biology, including tumorigenesis and cancer immunology. It was recognized not only to defend against tumor progression by suppressing adaptive immune responses but also to promote tumorigenesis and cancer metastasis after recruiting inflammatory responses. Thus the crucial role of necrosis in tumorigenesis has attracted increasing attention. Due to the heterogeneity of the tumor immune microenvironment (TIME) in lung adenocarcinoma (LUAD), the prognosis and the response to immunotherapy vary distinctly across patients, underscoring the need for a stratification algorithm for clinical practice. Although previous studies have formulated the crucial role of lncRNAs in tumorigenicity, the relationship between necroptosis-related lncRNAs, TIME, and the prognosis of patients with LUAD was still elusive. In the current study, a robust and novel prognostic stratification model based on Necroptosis-related LncRNA Risk Scoring (NecroLRS) and clinicopathological parameters was constructed and systemically validated in both internal and external validation cohorts. The expression profile of four key lncRNAs was further validated by qRT-PCR in 4 human LUAD cell lines. And a novel immune landscape alteration was observed between NecroLRS-High and -Low patients. To further elucidate the mechanism of necroptosis in the prognosis of LUAD from a single-cell perspective, a novel stratification algorithm based on K-means clustering was introduced to extract both malignant and NecroLRS-High subsets from epithelial cells. And the necroptosis-related immune infiltration landscape and developmental trajectory were investigated respectively. Critically, NecroLRS was found to be positively correlated with neutrophil enrichment, inflammatory immune response, and malignant phenotypes of LUAD. In addition, novel ligand-receptor pairs between NecroLRS-High cells and other immunocytes were investigated and optimal therapeutic compounds were screened to provide potential targets for future studies. Taken together, our findings reveal emerging mechanisms of necroptosis-induced immune microenvironment alteration on the deteriorative prognosis and may contribute to improved prognosis and individualized precision therapy for patients with LUAD.
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Affiliation(s)
| | | | | | | | | | | | - Lehe Yang
- *Correspondence: Lehe Yang, ; Xiaoying Huang, ; Liangxing Wang,
| | - Xiaoying Huang
- *Correspondence: Lehe Yang, ; Xiaoying Huang, ; Liangxing Wang,
| | - Liangxing Wang
- *Correspondence: Lehe Yang, ; Xiaoying Huang, ; Liangxing Wang,
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Sun X, Huang X, Sun X, Chen S, Zhang Z, Yu Y, Zhang P. Oxidative Stress-Related lncRNAs Are Potential Biomarkers for Predicting Prognosis and Immune Responses in Patients With LUAD. Front Genet 2022; 13:909797. [PMID: 35754800 PMCID: PMC9214656 DOI: 10.3389/fgene.2022.909797] [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: 03/31/2022] [Accepted: 05/04/2022] [Indexed: 12/24/2022] Open
Abstract
Lung adenocarcinoma is increasingly harmful to society and individuals as cancer with an inferior prognosis and insensitive to chemotherapy. Previous studies have demonstrated that oxidative stress and lncRNAs play a vital role in many biological processes. Therefore, we explored the role of lncRNAs associated with oxidative stress in the prognosis and survival of LUAD patients. We examined the expression profiles of lncRNAs and oxidative stress genes in this study. A prognosis prediction model and a nomogram were built based on oxidative stress-related lncRNAs. Functional and drug sensitivity analyses were also performed depending on oxidative stress-related lncRNA signature. Moreover, we investigated the relationship between immune response and immunotherapy. The results showed that a risk scoring model based on 16 critical oxidative stress lncRNAs was able to distinguish the clinical status of LUAD and better predict the prognosis and survival. Additionally, the model demonstrated a close correlation with the tumor immune system, and these key lncRNAs also revealed the relationship between LUAD and chemotherapeutic drug sensitivity. Our work aims to provide new perspectives and new ideas for the treatment and management of LUAD.
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Affiliation(s)
- Xinti Sun
- Department of Thoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Xingqi Huang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaojuan Sun
- Department of Oncology, Qingdao University Affiliated Hospital, Qingdao, China
| | - Si Chen
- Department of Thoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Zeyang Zhang
- Department of Thoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Yao Yu
- Department of Thoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Peng Zhang
- Department of Thoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
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Identification of Differentially Expressed and Prognostic lncRNAs for the Construction of ceRNA Networks in Lung Adenocarcinoma. JOURNAL OF ONCOLOGY 2022; 2021:2659550. [PMID: 34987577 PMCID: PMC8723861 DOI: 10.1155/2021/2659550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/07/2021] [Indexed: 11/18/2022]
Abstract
Background Long noncoding RNAs (lncRNAs) could function as competitive endogenous RNAs (ceRNAs) to competitively adsorb microRNAs (miRNAs), thereby regulating the expression of their target protein-coding mRNAs. In this study, we aim to identify more effective diagnostic and prognostic markers for lung adenocarcinoma (LUAD). Methods We obtained differentially expressed lncRNAs (DElncRNAs), miRNAs (DEmiRNAs), and mRNAs (DEmRNAs) for LUAD by using The Cancer Genomes Atlas (TCGA) portal. Weighted gene coexpression network analysis (WGCNA) was performed to unveil core gene modules associated with LUAD. The Cox proportional hazards model was performed to determine the prognostic significance of DElncRNAs. The diagnostic and prognostic significance of DElncRNAs was further verified based on the receiver operating characteristic curve (ROC). Cytoscape was used to construct the ceRNA networks comprising the lncRNAs-miRNAs-mRNAs axis based on the correlation obtained from the miRcode, miRDB, and TargetScan. Results Compared with normal lung tissues, 2355 DElncRNAs, 820 DEmiRNAs, and 17289 DEmRNAs were identified in LUAD tissues. We generated 8 WGCNA core modules in the lncRNAs coexpression network, 5 modules in the miRNAs, and 12 modules in the mRNAs coexpression network, respectively. One lncRNA module (blue) consisting of 441 lncRNAs, two miRNA modules (blue and turquoise) containing 563 miRNAs, and one mRNA module (turquoise), which consisted of 15162 mRNAs, were mostly significantly related to LUAD status. Furthermore, 67 DEmRNAs were found to be tumor-associated as well as the target genes of the DElncRNAs-DEmiRNAs axis. Survival analyses showed that 6 lncRNAs (LINC01447, WWC2-AS2, OGFRP1, LINC00942, LINC01168, and AC005863.1) were significantly correlated with the prognosis of LUAD patients. Ultimately, the potential ceRNA networks including 6 DElncRNAs, 4 DEmiRNAs, and 22 DEmRNAs were constructed. Conclusion Our study indicated that 6 DElncRNAs had the possibilities as diagnostic and prognostic biomarkers for LUAD. The lncRNA-mediated ceRNA networks might provide novel insights into the molecular mechanisms of LUAD progression.
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Dong H, Liu Q, Chen C, Lu T, Xu K. LncRNA OGFRP1 promotes angiogenesis and epithelial-mesenchymal transition in colorectal cancer cells through miR-423-5p/CTCF axis. Immunobiology 2022; 227:152176. [DOI: 10.1016/j.imbio.2022.152176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/09/2021] [Accepted: 01/02/2022] [Indexed: 01/29/2023]
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Liu Y, Ding W, Yu W, Zhang Y, Ao X, Wang J. Long non-coding RNAs: Biogenesis, functions, and clinical significance in gastric cancer. Mol Ther Oncolytics 2021; 23:458-476. [PMID: 34901389 PMCID: PMC8637188 DOI: 10.1016/j.omto.2021.11.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Gastric cancer (GC) is one of the most prevalent malignant tumor types and the third leading cause of cancer-related death worldwide. Its morbidity and mortality are very high due to a lack of understanding about its pathogenesis and the slow development of novel therapeutic strategies. Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs with a length of more than 200 nt. They play crucial roles in a wide spectrum of physiological and pathological processes by regulating the expression of genes involved in proliferation, differentiation, apoptosis, cell cycle, invasion, metastasis, DNA damage, and carcinogenesis. The aberrant expression of lncRNAs has been found in various cancer types. A growing amount of evidence demonstrates that lncRNAs are involved in many aspects of GC pathogenesis, including its occurrence, metastasis, and recurrence, indicating their potential role as novel biomarkers in the diagnosis, prognosis, and therapeutic targets of GC. This review systematically summarizes the biogenesis, biological properties, and functions of lncRNAs and highlights their critical role and clinical significance in GC. This information may contribute to the development of better diagnostics and treatments for GC.
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Affiliation(s)
- Ying Liu
- Department of Cardiovascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266000, China
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao 266071, China
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao 266021, China
| | - Wei Ding
- Department of Comprehensive Internal Medicine, Affiliated Hospital, Qingdao University, Qingdao 266003, China
| | - Wanpeng Yu
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao 266071, China
| | - Yuan Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao 266021, China
| | - Xiang Ao
- Department of Cardiovascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266000, China
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao 266071, China
| | - Jianxun Wang
- Department of Cardiovascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266000, China
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao 266071, China
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Wang C, Ding T, Yang D, Zhang P, Hu X, Qin W, Zheng J. The lncRNA OGFRP1/miR-149-5p/IL-6 axis regulates prostate cancer chemoresistance. Pathol Res Pract 2021; 224:153535. [PMID: 34293716 DOI: 10.1016/j.prp.2021.153535] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/19/2021] [Accepted: 06/20/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND The long non-coding RNA (lncRNA) OGFRP1 has been found to promote malignancy in prostate cancer (PC) and other cancer types. How this lncRNA functions in the regulation of PC chemoresistance, however, is poorly defined. METHODS qRT-PCR was employed to measure OGFRP1, miR-149-5p, and IL-6 expression in PC tissues and cells. IC50 values for paclitaxel and docetaxel in PC cells were assessed via a CCK-8 assay approach. Putative miR-149-5p binding targets were identified and validated through bioinformatics assays and luciferase reporter assays, respectively. The impact of OGFRP1 on PC chemoresistance in vivo was validated using a xenograft model system. RESULTS Docetaxel-resistant PC (PC/DR) cells and tissues exhibited reduced OGFRP1 expression and increased miR-149-5p expression. Knocking down OGFRP1 augmented the sensitivity of these PC cells to docetaxel and paclitaxel in vitro and in vivo. Mechanistically, OGFRP1 was found to bind and sequester miR-149-5p within PC/DR cells, thereby indirectly regulating IL-6 expression. Consistent with this model, the overexpression of IL-6 reversed the OGFRP1 knockdown-mediated reductions in docetaxel and paclitaxel IC50 values for these PC cells. CONCLUSIONS OGFRP1 can sequester miR-149-5p, thereby indirectly promoting IL-6 upregulation and thereby promoting chemoresistance in PC cells. This OGFRP1/miR-149-5p/IL-6 axis may thus be a promising target for therapeutic efforts aimed at PC chemosensitization and treatment.
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Affiliation(s)
- Chen Wang
- MRI Department, Huadong Hospital Affiliated to Fudan University, Shanghai 200040, China
| | - Tao Ding
- Department of Urology, Shanghai Sixth People's Hospital South Campus Affiliated to Shanghai Jiao Tong University, Shanghai 201499, China
| | - Deping Yang
- Department of Laboratory Medicine, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, China
| | - Ping Zhang
- Department of Laboratory Medicine, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, China
| | - Xiongmin Hu
- Shanghai Runda Rongjia Biotechnology Co., Ltd, Shanghai 200439, China
| | - Wei Qin
- Shanghai Runda Rongjia Biotechnology Co., Ltd, Shanghai 200439, China; Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Jianghua Zheng
- Department of Laboratory Medicine, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, China.
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