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Wang D, Zhang Y, Li Q, Li Y, Li W, Zhang A, Xu J, Meng J, Tang L, Lyu S. Epigenetics: Mechanisms, potential roles, and therapeutic strategies in cancer progression. Genes Dis 2024; 11:101020. [PMID: 38988323 PMCID: PMC11233905 DOI: 10.1016/j.gendis.2023.04.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/20/2023] [Accepted: 04/14/2023] [Indexed: 07/12/2024] Open
Abstract
Mutations or abnormal expression of oncogenes and tumor suppressor genes are known to cause cancer. Recent studies have shown that epigenetic modifications are key drivers of cancer development and progression. Nevertheless, the mechanistic role of epigenetic dysregulation in the tumor microenvironment is not fully understood. Here, we reviewed the role of epigenetic modifications of cancer cells and non-cancer cells in the tumor microenvironment and recent research advances in cancer epigenetic drugs. In addition, we discussed the great potential of epigenetic combination therapies in the clinical treatment of cancer. However, there are still some challenges in the field of cancer epigenetics, such as epigenetic tumor heterogeneity, epigenetic drug heterogeneity, and crosstalk between epigenetics, proteomics, metabolomics, and other omics, which may be the focus and difficulty of cancer treatment in the future. In conclusion, epigenetic modifications in the tumor microenvironment are essential for future epigenetic drug development and the comprehensive treatment of cancer. Epigenetic combination therapy may be a novel strategy for the future clinical treatment of cancer.
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Affiliation(s)
- Dong Wang
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yan Zhang
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Qingbo Li
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yu Li
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Wen Li
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Ao Zhang
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jingxuan Xu
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jingyan Meng
- College of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Lin Tang
- College of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Shuhua Lyu
- Department of Pathology, Tianjin Union Medical Center, Tianjin 300121, China
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2
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Zhao Y, Wang L, Li X, Jiang J, Ma Y, Guo S, Zhou J, Li Y. Programmed Cell Death-Related Gene Signature Associated with Prognosis and Immune Infiltration and the Roles of HMOX1 in the Proliferation and Apoptosis were Investigated in Uveal Melanoma. Genes Genomics 2024; 46:785-801. [PMID: 38767825 PMCID: PMC11208274 DOI: 10.1007/s13258-024-01521-x] [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: 12/12/2023] [Accepted: 04/24/2024] [Indexed: 05/22/2024]
Abstract
BACKGROUND Uveal melanoma (UVM) is the most common primary ocular malignancy, with a wide range of symptoms and outcomes. The programmed cell death (PCD) plays an important role in tumor development, diagnosis, and prognosis. There is still no research on the relationship between PCD-related genes and UVM. A novel PCD-associated prognostic model is urgently needed to improve treatment strategies. OBJECTIVE We aim to screen PCD-related prognostic signature and investigate its proliferation ability and apoptosis in UVM cells. METHODS The clinical information and RNA-seq data of the UVM patients were collected from the TCGA cohort. All the patients were classified using consensus clustering by the selected PCD-related genes. After univariate Cox regression and PPI network analysis, the prognostic PCD-related genes were then submitted to the LASSO regression analysis to build a prognostic model. The level of immune infiltration of 8-PCD signature in high- and low-risk patients was analyzed using xCell. The prediction on chemotherapy and immunotherapy response in UVM patients was assessed by GDSC and TIDE algorithm. CCK-8, western blot and Annexin V-FITC/PI staining were used to explore the roles of HMOX1 in UVM cells. RESULTS A total of 8-PCD signature was constructed and the risk score of the PCD signature was negatively correlated with the overall survival, indicating strong predictive ability and independent prognostic value. The risk score was positively correlated with CD8 Tcm, CD8 Tem and Th2 cells. Immune cells in high-risk group had poorer overall survival. The drug sensitivity demonstrated that cisplatin might impact the progression of UVM and better immunotherapy responsiveness in the high-risk group. Finally, Overespression HMOX1 (OE-HMOX1) decreased the cell viability and induced apoptosis in UVM cells. Recuse experiment results showed that ferrostatin-1 (fer-1) protected MP65 cells from apoptosis and necrosis caused by OE-HMOX1. CONCLUSION The PCD signature may have a significant role in the tumor microenvironment, clinicopathological characteristics, prognosis and drug sensitivity. More importantly, HMOX1 depletion greatly induced tumor cell growth and inhibited cell apoptosis and fer-1 protected UVM cells from apoptosis and necrosis induced by OE-HMOX1. This work provides a foundation for effective therapeutic strategy in tumour treatment.
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Affiliation(s)
- Yubao Zhao
- Department of Ophthalmology, Fuyang Cancer Hospital of Fuyang Normal University, Fuyang, 236000, Anhui, China
| | - Liang Wang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510000, Guangdong, China
| | - Xiaoyan Li
- Department of Science and Education, Fuyang Cancer Hospital of Fuyang Normal University, Fuyang, 236000, Anhui, China
| | - Junzhi Jiang
- Department of Ophthalmology, Fuyang Cancer Hospital of Fuyang Normal University, Fuyang, 236000, Anhui, China
| | - Yan Ma
- Department of Ophthalmology, Fuyang Cancer Hospital of Fuyang Normal University, Fuyang, 236000, Anhui, China
| | - Shuxia Guo
- Department of Ophthalmology, Fuyang Cancer Hospital of Fuyang Normal University, Fuyang, 236000, Anhui, China
| | - Jinming Zhou
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510000, Guangdong, China
| | - Yingjun Li
- Department of Ophthalmology, Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China.
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Liang X, Long L, Guan F, Xu Z, Huang H. Research status and potential applications of circRNAs affecting colorectal cancer by regulating ferroptosis. Life Sci 2024; 352:122870. [PMID: 38942360 DOI: 10.1016/j.lfs.2024.122870] [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: 03/11/2024] [Revised: 06/20/2024] [Accepted: 06/23/2024] [Indexed: 06/30/2024]
Abstract
Ferroptosis is an emerging form of non-apoptotic programmed cell death (PCD), characterized by iron-mediated oxidative imbalance. This process plays a significant role in the development and progression of various tumors, including colorectal cancer, gastric cancer, and others. Circular RNA (circRNA) is a stable, non-coding RNA type with a single-stranded, covalently closed loop structure, which is intricately linked to the proliferation, invasion, and metastasis of tumor cells. Recent studies have shown that many circRNAs regulate various pathways leading to cellular ferroptosis. Colorectal cancer, known for its high incidence and mortality among cancers, is marked by a poor prognosis and pronounced chemoresistance. To enhance our understanding of how circRNA-mediated regulation of ferroptosis influences colorectal cancer development, this review systematically examines the mechanisms by which specific circRNAs regulate ferroptosis and their critical role in the progression of colorectal cancer. Furthermore, it explores the potential of circRNAs as biomarkers and therapeutic targets in colorectal cancer treatment, offering a novel approach to clinical management.
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Affiliation(s)
- Xiyuan Liang
- School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Linna Long
- Department of Histology & Embryology, Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Fan Guan
- School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Zilu Xu
- School of Basic Medical Science, Central South University, Changsha 410013, China
| | - He Huang
- Department of Histology & Embryology, Xiangya School of Medicine, Central South University, Changsha 410013, China.
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Wu Z, Huang C. Unveiling the Impact of MRC1 on Immune Infiltration and Patient's Prognosis: A Pan-Cancer Analysis Based on Single-Cell and Bulk Sequencing. Int J Gen Med 2024; 17:2575-2592. [PMID: 38855425 PMCID: PMC11162242 DOI: 10.2147/ijgm.s461144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/20/2024] [Indexed: 06/11/2024] Open
Abstract
Purpose Mannose receptor C-type 1 (MRC1) is an endocytic lectin receptor primarily expressed in macrophages, dendritic cells, and some endothelial cells. However, the role of MRC1 in cancers remains unclear. Methods We analyzed MRC1 expression using The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Cancer Cell Line Encyclopedia (CCLE), and single-cell datasets. We systematically explored the prognostic implications and diagnostic value of MRC1. Immune-related indicators, including immune cells, immune scores, and immune checkpoint molecules, were used to estimate their correlation with MRC1 expression. Finally, we explored its potential ties to immunotherapy success markers such as tumor mutation burden and DNA repair genes. Results MRC1 showed both pro- and anti-tumor leanings depending on the cancer types. High levels correlated with poorer outcomes in six cancers but improved prognosis in some cancers like glioblastoma multiforme. This trend extended to the immune arena, where MRC1 intertwined with diverse immune parameters, suggesting its influence on affecting the tumor's immunological landscape. Intriguingly, its expression positively associated with factors favoring immunotherapy efficacy while negatively correlating with some potential barriers. Single-cell analysis pinpointed a specific link between MRC1 and DNA damage/repair pathways in breast cancer. Conclusion Our study provides a comprehensive landscape of MRC1 levels and diverse regulatory patterns in different cancers, deepening the understanding of MRC1's roles in tumorigenesis and immunity.
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Affiliation(s)
- Zhiwei Wu
- Department of Organ Transplantation, XiangYa Hospital of Central South University, Changsha, People’s Republic of China
| | - Changhao Huang
- Department of Organ Transplantation, XiangYa Hospital of Central South University, Changsha, People’s Republic of China
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Hang X, Du Z, Song J. Exploring the prognostic significance of iron death‑related lncRNAs in colorectal cancer: A systematic review and meta‑analysis. Oncol Lett 2024; 27:284. [PMID: 38736739 PMCID: PMC11083912 DOI: 10.3892/ol.2024.14417] [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: 11/23/2023] [Accepted: 04/05/2024] [Indexed: 05/14/2024] Open
Abstract
Colorectal cancer is a significant health challenge globally, with its prognosis associated with the profile of molecular biomarkers. Recently, the role of iron death-associated long non-coding (lnc)RNAs in cancer development has garnered attention; however, their expression patterns and prognostic value in colorectal cancer remain poorly elucidated. The present study aimed to assess the expression levels of iron death-related lncRNAs in colorectal cancer tissues and evaluate their relationship with patient outcomes through a comprehensive meta-analysis. Systematic searches were performed across multiple databases, including PubMed, Embase, Web of Science, Cochrane Library, CNKI, Wanfang and VIP databases, to identify studies relevant to the objective of the present study. Selected studies met predetermined inclusion criteria, from which data were extracted. R software version 4.3.1 was used for the meta-analysis, evaluating the association between iron death-related lncRNAs expression and colorectal cancer prognosis. Publication bias was assessed using funnel plot analysis, and Begg's and Egger's test. A total of 11 studies, including 3,984 patients with colorectal cancer, were included in the present meta-analysis. The results demonstrated a significant association between iron death-related lncRNAs and tumor stage classification [odds ratio (OR)=2.00; 95% confidence interval (CI), 1.77-2.24]. Notably, a significant association was also revealed between iron death-related lncRNAs and T stage classification in colorectal cancer (OR=1.82; 95% CI, 1.50-2.20). Furthermore, a statistically significant association was demonstrated between iron death-related lncRNAs and lymph node metastasis in colorectal cancer (OR=1.31; 95% CI, 1.03-1.66). The findings also highlighted a significant association between iron death-associated lncRNA and distant metastasis in colon cancer (OR=2.04; 95% CI, 1.62-2.56). Moreover, a significant association between iron death-related lncRNAs and risk score in colorectal cancer was revealed (OR=1.75; 95% CI, 1.25-2.46). In conclusion, the findings of the present meta-analysis underscore the potential of high ferroptosis-associated lncRNA expression as an indicator of adverse outcomes in colorectal cancer, suggesting their viability as biomarkers for cancer progression and prognosis. This insight opens potential new avenues for clinical application and further research into colorectal cancer management.
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Affiliation(s)
- Xiaoli Hang
- Clinical Laboratory, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang 212300, P.R. China
| | - Zhongxiang Du
- Clinical Laboratory, The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang 212300, P.R. China
| | - Jie Song
- Clinical Laboratory, Nantong Fourth People's Hospital, Nantong, Jiangsu 226001, P.R. China
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Sun X, Li L, Yang X, Ke D, Zhong Q, Zhu Y, Yang L, Zhang Z, Lin J. Identification of a novel prognostic cuproptosis-associated LncRNA signature for predicting prognosis and immunotherapy response in patients with esophageal cancer. Heliyon 2024; 10:e30277. [PMID: 38707466 PMCID: PMC11068819 DOI: 10.1016/j.heliyon.2024.e30277] [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: 09/20/2023] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/07/2024] Open
Abstract
Nowadays, effective prognostic models for esophageal cancer (ESCA) are still lacking. Long noncoding RNAs (lncRNAs) are commonly utilized as indicators for diagnosing cancer and forecasting patient outcomes. Cuproptosis is regulated by multiple genes and is crucial to the progression of ESCA. However, it is not yet clear what role the cuproptosis-associated lncRNAs (CuALs) play in ESCA. To tackle this problem, a prognostic signature incorporating three CuALs was created. This signature was constructed by the use of the least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression. Subsequently, the signature effectively stratified ESCA samples into a high-risk group and a low-risk group. Those in the low-risk group demonstrated extended overall survival (OS), as well as increased infiltration of T cells, macrophages, and NK cells, suggesting a potentially enhanced response to immunotherapy. The ROC curve analysis demonstrated that this prognostic signature outperformed conventional clinical factors in predicting patient prognosis (AUC = 0.708). K-M survival analysis and correlation analysis identified UGDH-AS1 (a CuAL) as a protective factor positively associated with patient prognosis. The results of RT-qPCR and wound healing assays indicated that UGDH-AS1 is overexpressed in ESCA and could inhibit cancer cell migration. In general, the prognostic signature of CuALs demonstrated a robust capability in forecasting the immune environment and patient prognosis, highlighting its potential as a tool for enhancing personalized treatment strategies in ESCA.
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Affiliation(s)
- Xinhai Sun
- Department of Thoracic Surgery, Fujian Institute of Thoracic and Cardiac Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Liming Li
- Department of Thoracic Surgery, Fujian Institute of Thoracic and Cardiac Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Xiaojie Yang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dan Ke
- Heilongjiang Key Laboratory of tissue damage and repair, College of life sciences, Mudanjiang Medical University, Mudanjiang, China
| | - Qihong Zhong
- Department of Thoracic Surgery, Fujian Institute of Thoracic and Cardiac Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yuanchang Zhu
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Litao Yang
- Department of Thoracic Surgery, Baoji Traditional Chinese Medicine Hospital, Shaanxi, China
| | - Zhenyang Zhang
- Department of Thoracic Surgery, Fujian Institute of Thoracic and Cardiac Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Jiangbo Lin
- Department of Thoracic Surgery, Fujian Institute of Thoracic and Cardiac Surgery, Fujian Medical University Union Hospital, Fuzhou, China
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Wang HY, Diao Y, Tan PZ, Liang H. Four centrosome-related genes to predict the prognosis and drug sensitivity of patients with colon cancer. World J Gastrointest Oncol 2024; 16:1908-1924. [PMID: 38764831 PMCID: PMC11099447 DOI: 10.4251/wjgo.v16.i5.1908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/08/2024] [Accepted: 02/22/2024] [Indexed: 05/09/2024] Open
Abstract
BACKGROUND As the primary microtubule organizing center in animal cells, centrosome abnormalities are involved in human colon cancer. AIM To explore the role of centrosome-related genes (CRGs) in colon cancer. METHODS CRGs were collected from public databases. Consensus clustering analysis was performed to separate the Cancer Genome Atlas cohort. Univariate Cox and least absolute shrinkage selection operator regression analyses were performed to identify candidate prognostic CRGs and construct a centrosome-related signature (CRS) to score colon cancer patients. A nomogram was developed to evaluate the CRS risk in colon cancer patients. An integrated bioinformatics analysis was conducted to explore the correlation between the CRS and tumor immune microenvironment and response to immunotherapy, chemotherapy, and targeted therapy. Single-cell transcriptome analysis was conducted to examine the immune cell landscape of core prognostic genes. RESULTS A total of 726 CRGs were collected from public databases. A CRS was constructed, which consisted of the following four genes: TSC1, AXIN2, COPS7A, and MTUS1. Colon cancer patients with a high-risk signature had poor survival. Patients with a high-risk signature exhibited decreased levels of plasma cells and activated memory CD4+ T cells. Regarding treatment response, patients with a high-risk signature were resistant to immunotherapy, chemotherapy, and targeted therapy. COPS7A expression was relatively high in endothelial cells and fibroblasts. MTUS1 expression was high in endothelial cells, fibroblasts, and malignant cells. CONCLUSION We constructed a centrosome-related prognostic signature that can accurately predict the prognosis of colon cancer patients, contributing to the development of individualized treatment for colon cancer.
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Affiliation(s)
- Hui-Yan Wang
- Department of Clinical Laboratory, Harbin Medical University Cancer Hospital, Harbin 150086, Heilongjiang Province, China
| | - Yan Diao
- Department of Clinical Laboratory, Heilongjiang Province Hospital, Harbin 150000, Heilongjiang Province, China
| | - Pei-Zhu Tan
- Translational Medicine Center of Northern China, Harbin Medical University, Harbin 150081, Heilongjiang Province, China
| | - Huan Liang
- Department of Clinical Laboratory, Harbin Medical University Cancer Hospital, Harbin 150086, Heilongjiang Province, China
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Wu H, Yang Z, Chang C, Wang Z, Zhang D, Guo Q, Zhao B. A novel disulfide death-related genes prognostic signature identifies the role of IPO4 in glioma progression. Cancer Cell Int 2024; 24:168. [PMID: 38734657 PMCID: PMC11088110 DOI: 10.1186/s12935-024-03358-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/06/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND "Disulfide death," a form of cellular demise, is triggered by the abnormal accumulation of intracellular disulfides under conditions of glucose deprivation. However, its role in the prognosis of glioma remains undetermined. Therefore, the main objective of this study is to establish prognostic signature based on disulfide death-related genes (DDRGs) and to provide new solutions in choosing the effective treatment of glioma. METHODS The RNA transcriptome, clinical information, and mutation data of glioma samples were sourced from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA), while normal samples were obtained from the Genotype-Tissue Expression (GTEx). DDRGs were compiled from previous studies and selected through differential analysis and univariate Cox regression analysis. The molecular subtypes were determined through consensus clustering analysis. Further, LASSO analysis was employed to select characteristic genes, and subsequently, a risk model comprising seven DDRGs was constructed based on multivariable Cox analysis. Kaplan-Meier survival curves were employed to assess survival differences between high and low-risk groups. Additionally, functional analyses (GO, KEGG, GSEA) were conducted to explore the potential biological functions and signaling pathways of genes associated with the model. The study also explored immune checkpoint (ICP) genes, immune cell infiltration levels, and immune stromal scores. Finally, the effect of Importin-4(IPO4) on glioma has been further confirmed through RT-qPCR, Western blot, and cell functional experiments. RESULTS 7 genes associated with disulfide death were obtained and two subgroups of patients with different prognosis and clinical characteristics were identified. Risk signature was subsequently developed and proved to serve as an prognostic predictor. Notably, the high-risk group exhibited an immunosuppressive microenvironment characterized by a high concentration of M2 macrophages and regulatory T cells (Tregs). In contrast, the low-risk group showed lower half-maximal inhibitory concentration (IC50) values. Therefore, patients in the high-risk group may benefit more from immunotherapy, while patients in the low-risk group may benefit more from chemotherapy. In addition, in vitro experiments have shown that inhibition of the expression of IPO4 leads to a significant reduction in the proliferation, migration, and invasion of glioma cells. CONCLUSION This study identified two glioma subtypes and constructed a prognostic signature based on DDRGs. The signature has the potential to optimize the selection of patients for immune- and chemotherapy and provided a potential therapeutic target for glioma.
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Affiliation(s)
- HaoYuan Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - ZhiHao Yang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - ChenXi Chang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - ZhiWei Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - DeRan Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - QingGuo Guo
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China.
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Peng L, Ren M, Huang L, Chen M. GEnDDn: An lncRNA-Disease Association Identification Framework Based on Dual-Net Neural Architecture and Deep Neural Network. Interdiscip Sci 2024:10.1007/s12539-024-00619-w. [PMID: 38733474 DOI: 10.1007/s12539-024-00619-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/02/2024] [Accepted: 02/03/2024] [Indexed: 05/13/2024]
Abstract
Accumulating studies have demonstrated close relationships between long non-coding RNAs (lncRNAs) and diseases. Identification of new lncRNA-disease associations (LDAs) enables us to better understand disease mechanisms and further provides promising insights into cancer targeted therapy and anti-cancer drug design. Here, we present an LDA prediction framework called GEnDDn based on deep learning. GEnDDn mainly comprises two steps: First, features of both lncRNAs and diseases are extracted by combining similarity computation, non-negative matrix factorization, and graph attention auto-encoder, respectively. And each lncRNA-disease pair (LDP) is depicted as a vector based on concatenation operation on the extracted features. Subsequently, unknown LDPs are classified by aggregating dual-net neural architecture and deep neural network. Using six different evaluation metrics, we found that GEnDDn surpassed four competing LDA identification methods (SDLDA, LDNFSGB, IPCARF, LDASR) on the lncRNADisease and MNDR databases under fivefold cross-validation experiments on lncRNAs, diseases, LDPs, and independent lncRNAs and independent diseases, respectively. Ablation experiments further validated the powerful LDA prediction performance of GEnDDn. Furthermore, we utilized GEnDDn to find underlying lncRNAs for lung cancer and breast cancer. The results elucidated that there may be dense linkages between IFNG-AS1 and lung cancer as well as between HIF1A-AS1 and breast cancer. The results require further biomedical experimental verification. GEnDDn is publicly available at https://github.com/plhhnu/GEnDDn.
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Affiliation(s)
- Lihong Peng
- College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou, 412007, China
| | - Mengnan Ren
- College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou, 412007, China
| | - Liangliang Huang
- College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou, 412007, China
| | - Min Chen
- School of Computer Science, Hunan Institute of Technology, Hengyang, 421002, China.
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Hao L, Lu W, Wu J, Chen Y, Xu D, Wang P. Construction and verification of a histone deacetylases-related prognostic signature model for colon cancer. Sci Rep 2024; 14:8983. [PMID: 38637684 PMCID: PMC11026370 DOI: 10.1038/s41598-024-59724-x] [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: 12/16/2023] [Accepted: 04/15/2024] [Indexed: 04/20/2024] Open
Abstract
Histone deacetylases (HDACs) contribute significantly to the initiation, progression, and prognosis of colorectal adenocarcinoma (COAD). Additionally, HDACs regulate the tumor microenvironment, immune escape, and tumor stem cells, and are closely linked to COAD prognosis. We developed a prognostic model for COAD that incorporates HDACs to evaluate their specific roles. The COAD dataset containing clinical and mutation data was collected using the TCGA and GEO databases to obtain genes associated with HDAC. LASSO analysis and univariate and multivariate Cox regression analysis were used to determine the presence of prognostic genes. Multivariate Cox analysis was also used to determine risk scores for HDAC-related features. Furthermore, genomic alterations, immune infiltration, and drug response were compared between high- and low-risk groups. Cellular experiments validated the potential regulatory role of BRD3 on COAD proliferation, migration, and apoptosis. The median risk scores, calculated based on the characteristics, demonstrated a more significant prognostic improvement in patients in the low-risk group. Furthermore, HDAC-related features were identified as important independent prognostic factors for patients with COAD. Additionally, genomic mutation status, immune infiltration, and function, as well as response to immunotherapy and chemotherapy, were found to be associated with risk scores. Subgroup analyses indicate that anti-PD-1 therapy may be beneficial for patients in the low-risk group. Additionally, a decrease in risk score was associated with a decrease in immune infiltration. Finally, HCT116 and HT29 cells exhibited inhibition of BRD3 gene proliferation and migration, as well as promotion of apoptosis. In patients with COAD, HDAC-related characteristics may be useful in predicting survival and selecting treatment.
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Affiliation(s)
- Lei Hao
- Thyroid Hernia Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510405, People's Republic of China
| | - Weiqi Lu
- Thyroid Hernia Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510405, People's Republic of China
| | - Jianyu Wu
- Thyroid Hernia Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510405, People's Republic of China
| | - Yuzhong Chen
- Thyroid Hernia Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510405, People's Republic of China
| | - Dongni Xu
- Department of Anesthesiology, Sun Yat-Sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, People's Republic of China.
| | - Peizong Wang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China.
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11
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Deng W, Yan Y, Shi C, Sui D. Single-cell and bulk RNAseq unveils the immune infiltration landscape and targeted therapeutic biomarkers of psoriasis. Front Genet 2024; 15:1365273. [PMID: 38699235 PMCID: PMC11063342 DOI: 10.3389/fgene.2024.1365273] [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: 01/04/2024] [Accepted: 04/01/2024] [Indexed: 05/05/2024] Open
Abstract
Background Psoriasis represents a multifaceted and debilitating immune-mediated systemic ailment afflicting millions globally. Despite the continuous discovery of biomarkers associated with psoriasis, identifying lysosomal biomarkers, pivotal as cellular metabolic hubs, remains elusive. Methods We employed a combination of differential expression analysis and weighted gene co-expression network analysis (WGCNA) to initially identify lysosomal genes. Subsequently, to mitigate overfitting and eliminate collinear genes, we applied 12 machine learning algorithms to screen robust lysosomal genes. These genes underwent further refinement through random forest (RF) and Lasso algorithms to ascertain the final hub lysosomal genes. To assess their predictive efficacy, we conducted receiver operating characteristic (ROC) analysis and verified the expression of diagnostic biomarkers at both bulk and single-cell levels. Furthermore, we utilized single-sample gene set enrichment analysis (ssGSEA), CIBERSORT, and Pearson's correlation analysis to elucidate the association between immune phenotypes and hub lysosomal genes in psoriatic samples. Finally, employing the Cellchat algorithm, we explored potential mechanisms underlying the participation of these hub lysosomal genes in cell-cell communication. Results Functional enrichment analyses revealed a close association between psoriasis and lysosomal functions. Subsequent intersection analysis identified 19 key lysosomal genes, derived from DEGs, phenotypic genes of WGCNA, and lysosomal gene sets. Following the exclusion of collinear genes, we identified 11 robust genes, further refined through RF and Lasso, yielding 3 hub lysosomal genes (S100A7, SERPINB13, and PLBD1) closely linked to disease occurrence, with high predictive capability for disease diagnosis. Concurrently, we validated their relative expression in separate bulk datasets and single-cell datasets. A nomogram based on these hub genes may offer clinical advantages for patients. Notably, these three hub genes facilitated patient classification into two subtypes, namely metabolic-immune subtype 1 and signaling subtype 2. CMap analysis suggested butein and arachidonic fasudil as preferred treatment agents for subtype 1 and subtype 2, respectively. Finally, through Cellchat and correlation analysis, we identified PRSS3-F2R as potentially promoting the expression of hub genes in the psoriasis group, thereby enhancing keratinocyte-fibroblast interaction, ultimately driving psoriasis occurrence and progression. Conclusion Our study identifies S100A7, SERPINB13, and PLBD1 as potential diagnostic biomarkers, offering promising prospects for more precisely tailored psoriatic immunotherapy designs.
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Affiliation(s)
- Wenhui Deng
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- The First Affiliated Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Yijiao Yan
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- The First Affiliated Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Chengzhi Shi
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- The First Affiliated Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Daoshun Sui
- The First Affiliated Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
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12
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Ding L, Wang Y, Tang Z, Ni C, Zhang Q, Zhai Q, Liang C, Li J. Exploration of vitamin D metabolic activity-related biological effects and corresponding therapeutic targets in prostate cancer. Nutr Metab (Lond) 2024; 21:17. [PMID: 38566155 PMCID: PMC10988890 DOI: 10.1186/s12986-024-00791-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Previous studies have unequivocally demonstrated that the vitamin D (VD) metabolism pathway significantly influences prognosis and sensitivity to hormone therapy in prostate cancer (PCa). However, the precise underlying mechanism remains unclear. METHODS We performed molecular profiling of 1045 PCa patients, leveraging genes linked to VD synthesis and VD receptors. We then identified highly variable gene modules with substantial associations with patient stratification. Subsequently, we intersected these modules with differentially expressed genes between PCa and adjacent paracancerous tissues. Following a meticulous process involving single-factor regression and LASSO regression to eliminate extraneous variables and construct a prognostic model. Within the high-risk subgroup defined by the calculated risk score, we analyzed their differences in cell infiltration, immune status, mutation landscape, and drug sensitivity. Finally, we selected Apolipoprotein E (APOE), which featured prominently in this model for further experimental exploration to evaluate its potential as a therapeutic target. RESULTS The prognostic model established in this study had commendable predictive efficacy. We observed diminished infiltration of various T-cell subtypes and reduced expression of co-stimulatory signals from antigen-presenting cells. Mutation analysis revealed that the high-risk cohort harbored a higher frequency of mutations in the TP53 and FOXA genes. Notably, drug sensitivity analysis suggested the heightened responsiveness of high-risk patients to molecular inhibitors targeting the Bcl-2 and MAPK pathways. Finally, our investigation also confirmed that APOE upregulates the proliferative and invasive capacity of PCa cells and concurrently enhances resistance to androgen receptor antagonist therapy. CONCLUSION This comprehensive study elucidated the potential mechanisms through which this metabolic pathway orchestrates the biological behavior of PCa and findings hold promise in advancing the development of combination therapies in PCa.
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Affiliation(s)
- Lei Ding
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, 210009, Nanjing,, China
| | - Yong Wang
- Department of Urology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, 299 Qingyang Road, 214023, Suqian, China
| | - Zhentao Tang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, 210009, Nanjing,, China
| | - Chenbo Ni
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, 210009, Nanjing,, China
| | - Qian Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, 210009, Nanjing,, China
| | - Qidi Zhai
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, 210009, Nanjing,, China
| | - Chao Liang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, 210009, Nanjing,, China.
| | - Jie Li
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, 210009, Nanjing,, China.
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13
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Saha P, Hegde M, Chakraborty K, Singha A, Mukerjee N, Ghosh D, Kunnumakkara AB, Khan MS, Ahmad MI, Ghosh A, Kumer A, Sil SK. Targeted inhibition of colorectal cancer proliferation: The dual-modulatory role of 2,4-DTBP on anti-apoptotic Bcl-2 and Survivin proteins. J Cell Mol Med 2024; 28:e18150. [PMID: 38494866 PMCID: PMC10945088 DOI: 10.1111/jcmm.18150] [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: 09/20/2023] [Revised: 12/29/2023] [Accepted: 01/16/2024] [Indexed: 03/19/2024] Open
Abstract
The anti-apoptotic proteins, Bcl-2 and Survivin, are consistently overexpressed in numerous human malignancies, notably in colorectal cancer. 2,4-Di-tert-butylphenol (2,4-DTBP) is a naturally occurring phenolic compound known for its diverse biological activities, including anti-cancer properties. The mechanism behind 2,4-DTBP-induced inhibition of cell proliferation and apoptosis in human colorectal cancer cells, specifically regarding Bcl-2 and Survivin, remains to be elucidated. In this study, we employed both in silico and in vitro methodologies to underpin this interaction at the molecular level. Molecular docking demonstrated a substantial binding affinity of 2,4-DTBP towards Bcl-2 (ΔG = -9.8 kcal/mol) and Survivin (ΔG = -5.6 kcal/mol), suggesting a potential inhibitory effect. Further, molecular dynamic simulations complemented by MM-GBSA calculations confirmed the significant binding of 2,4-DTBP with Bcl-2 (dGbind = -54.85 ± 6.79 kcal/mol) and Survivin (dGbind = -32.36 ± 1.29 kcal/mol). In vitro assays using HCT116 colorectal cancer cells revealed that 2,4-DTBP inhibited proliferation and promoted apoptosis in both a dose- and time-dependent manner. Fluorescence imaging and scanning electron microscopy illustrated the classical features associated with apoptosis upon 2,4-DTBP exposure. Cell cycle analysis through flow cytometry highlighted a G1 phase arrest and apoptosis assay demonstrated increased apoptotic cell population. Notably, western blotting results indicated a decreased expression of Bcl-2 and Survivin post-treatment. Considering the cytoprotective roles of Bcl-2 and Survivin through the inhibition of mitochondrial dysfunction, our findings of disrupted mitochondrial bioenergetics, characterized by reduced ATP production and oxygen consumption, further accentuate the functional impairment of these proteins. Overall, the integration of in silico and in vitro data suggests that 2,4-DTBP holds promise as a therapeutic agent targeting Bcl-2 and Survivin in colorectal cancer.
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Affiliation(s)
- Partha Saha
- Molecular Genetics and Cell Physiology Laboratory, Department of Human PhysiologyTripura UniversitySuryamaninagarTripuraIndia
| | - Mangala Hegde
- Cancer Biology Laboratory and DBT‐AIST International Center for Translational and Environmental Research (DAICENTER), Department of Biosciences and BioengineeringIndian Institute of Technology (IIT) GuwahatiGuwahatiAssamIndia
| | - Kanak Chakraborty
- Molecular Genetics and Cell Physiology Laboratory, Department of Human PhysiologyTripura UniversitySuryamaninagarTripuraIndia
| | - Achinta Singha
- Molecular Genetics and Cell Physiology Laboratory, Department of Human PhysiologyTripura UniversitySuryamaninagarTripuraIndia
| | - Nobendu Mukerjee
- Center for Global Health ResearchSaveetha Medical College and Hospital, Saveetha Institute of Medical and Technical SciencesChennaiTamil NaduIndia
- Department of Health SciencesNovel Global Community Educational FoundationHebershamNew South WalesAustralia
| | - Deepshikha Ghosh
- Cell Biology and Physiology DivisionCSIR‐Indian Institute of Chemical BiologyKolkataWest BengalIndia
| | - Ajaikumar B. Kunnumakkara
- Cancer Biology Laboratory and DBT‐AIST International Center for Translational and Environmental Research (DAICENTER), Department of Biosciences and BioengineeringIndian Institute of Technology (IIT) GuwahatiGuwahatiAssamIndia
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of ScienceKing Saud UniversityRiyadhSaudi Arabia
| | - Md Irshad Ahmad
- Department of Structural Biology, School of MedicineUTHEALTH Science CenterSan AntonioTexasUSA
| | - Arabinda Ghosh
- Department of Computational Biology and BiotechnologyMahapurusha Srimanta Sankaradeva ViswavidalayaGuwahatiAssamIndia
| | - Ajoy Kumer
- Department of Chemistry, College of Arts and SciencesIUBAT‐International University of Business Agriculture and TechnologyDhakaBangladesh
| | - Samir Kumar Sil
- Molecular Genetics and Cell Physiology Laboratory, Department of Human PhysiologyTripura UniversitySuryamaninagarTripuraIndia
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14
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Li F, Wang W, Lai G, Lan S, Lv L, Wang S, Liu X, Zheng J. Development and validation of a novel lysosome-related LncRNA signature for predicting prognosis and the immune landscape features in colon cancer. Sci Rep 2024; 14:622. [PMID: 38182713 PMCID: PMC10770065 DOI: 10.1038/s41598-023-51126-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/31/2023] [Indexed: 01/07/2024] Open
Abstract
Lysosomes are essential components for managing tumor microenvironment and regulating tumor growth. Moreover, recent studies have also demonstrated that long non-coding RNAs could be used as a clinical biomarker for diagnosis and treatment of colorectal cancer. However, the influence of lysosome-related lncRNA (LRLs) on the progression of colon cancer is still unclear. This study aimed to identify a prognostic LRL signature in colon cancer and elucidated potential biological function. Herein, 10 differential expressed lysosome-related genes were obtained by the TCGA database and ultimately 4 prognostic LRLs for conducting a risk model were identified by the co-expression, univariate cox, least absolute shrinkage and selection operator analyses. Kaplan-Meier analysis, principal-component analysis, functional enrichment annotation, and nomogram were used to verify the risk model. Besides, the association between the prognostic model and immune infiltration, chemotherapeutic drugs sensitivity were also discussed in this study. This risk model based on the LRLs may be promising for potential clinical prognosis and immunotherapeutic responses related indicator in colon cancer patients.
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Affiliation(s)
- Fengming Li
- Center of Digestive Endoscopy, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, China
| | - Wenyi Wang
- Department of Medical Oncology, Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen, China
| | - Guanbiao Lai
- Center of Digestive Endoscopy, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, China
| | - Shiqian Lan
- Center of Digestive Endoscopy, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, China
| | - Liyan Lv
- Center of Digestive Endoscopy, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, China
| | - Shengjie Wang
- Department of Thyroid and Breast Surgery, Xiamen Humanity Hospital Fujian Medical University, Xiamen, Fujian, China.
| | - Xinli Liu
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China.
| | - Juqin Zheng
- Center of Digestive Endoscopy, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, China.
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15
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He L, Zhang C, He W, Xu M. The emerging role of ectodermal neural cortex 1 in cancer. Sci Rep 2024; 14:513. [PMID: 38177640 PMCID: PMC10766627 DOI: 10.1038/s41598-023-50914-7] [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: 07/23/2023] [Accepted: 12/27/2023] [Indexed: 01/06/2024] Open
Abstract
Ectodermal neural cortex 1 (ENC1) is a protein that plays a crucial role in the regulation of various cellular processes such as cell proliferation, differentiation, and apoptosis. Numerous studies have shown that ENC1 is overexpressed in various types of cancers, including breast, lung, pancreatic, and colorectal cancer, and its upregulation is correlated with a poorer prognosis. In addition to its role in cancer growth and spreading, ENC1 has also been linked to neuronal process development and neural crest cell differentiation. In this review, we provide an overview of the current knowledge on the relationship between ENC1 and cancer. We discuss the molecular mechanisms by which ENC1 contributes to tumorigenesis, including its involvement in multiple oncogenic signaling pathways. We also summarize the potential of targeting ENC1 for cancer therapy, as its inhibition has been shown to significantly reduce cancer cell invasion, growth, and metastasis. Finally, we highlight the remaining gaps in our understanding of ENC1's role in cancer and propose potential directions for future research.
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Affiliation(s)
- Lingling He
- Department of Obstetrics, Jiangxi Provincial Maternal and Child Health Hospital, No. 318, Bayi Avenue, Nanchang, 330006, Jiangxi Province, China.
| | - Chiyu Zhang
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Wenjing He
- Department of Endocrinology, Baoji Gaoxin Hospital, Baoji, 721006, Shanxi Province, China
| | - Minjuan Xu
- Department of Obstetrics and Gynecology, Ganzhou People's Hospital, Ganzhou, 341000, Jiangxi Province, China
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16
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Xu C, Bian Z, Wang X, Niu N, Liu L, Xiao Y, Zhu J, Huang N, Zhang Y, Chen Y, Wu Q, Sun F, Zhu X, Pan Q. SNORA56-mediated pseudouridylation of 28 S rRNA inhibits ferroptosis and promotes colorectal cancer proliferation by enhancing GCLC translation. J Exp Clin Cancer Res 2023; 42:331. [PMID: 38049865 PMCID: PMC10696674 DOI: 10.1186/s13046-023-02906-8] [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: 09/09/2023] [Accepted: 11/16/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common malignancies and is characterized by reprogrammed metabolism. Ferroptosis, a programmed cell death dependent on iron, has emerged as a promising strategy for CRC treatment. Although small nucleolar RNAs are extensively involved in carcinogenesis, it is unclear if they regulate ferroptosis during CRC pathogenesis. METHODS The dysregulated snoRNAs were identified using published sequencing data of CRC tissues. The expression of the candidate snoRNAs, host gene and target gene were assessed by real-time quantitative PCR (RT-qPCR), fluorescence in situ hybridization (FISH), immunohistochemistry (IHC) and western blots. The biological function of critical molecules was investigated using in vitro and in vivo strategies including Cell Counting Kit-8 (CCK8), colony formation assay, flow cytometry, Fe2+/Fe3+, GSH/GSSG and the xenograft mice models. The ribosomal activities were determined by polysome profiling and O-propargyl-puromycin (OP-Puro) assay. The proteomics was conducted to clarify the downstream targets and the underlying mechanisms were validated by IHC, Pearson correlation analysis, protein stability and rescue assays. The clinical significance of the snoRNA was explored using the Cox proportional hazard model, receiver operating characteristic (ROC) and survival analysis. RESULTS Here, we investigated the SNORA56, which was elevated in CRC tissues and plasma, and correlated with CRC prognosis. SNORA56 deficiency in CRC impaired proliferation and triggered ferroptosis, resulting in reduced tumorigenesis. Mechanistically, SNORA56 mediated the pseudouridylation of 28 S rRNA at the U1664 site and promoted the translation of the catalytic subunit of glutamate cysteine ligase (GCLC), an indispensable rate-limiting enzyme in the biosynthesis of glutathione, which can inhibit ferroptosis by suppressing lipid peroxidation. CONCLUSIONS Therefore, the SNORA56/28S rRNA/GCLC axis stimulates CRC progression by inhibiting the accumulation of cellular peroxides, and it may provide biomarker and therapeutic applications in CRC.
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Affiliation(s)
- Chang Xu
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Zhixuan Bian
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Paediatrics, Shanghai, 200127, China
- Sanya Women and Children's Hospital Managed by Shanghai Children's Medical Center, Sanya, 572000, China
| | - Xinyue Wang
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Na Niu
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Li Liu
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Paediatrics, Shanghai, 200127, China
| | - Yixuan Xiao
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Paediatrics, Shanghai, 200127, China
| | - Jiabei Zhu
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Paediatrics, Shanghai, 200127, China
| | - Nan Huang
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Yue Zhang
- Department of Central Laboratory, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Yan Chen
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Qi Wu
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Fenyong Sun
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Xiaoli Zhu
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China.
| | - Qiuhui Pan
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
- College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Paediatrics, Shanghai, 200127, China.
- Sanya Women and Children's Hospital Managed by Shanghai Children's Medical Center, Sanya, 572000, China.
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17
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Cheng TC, Wu JH, Zhu B, Gao HY, Zheng L, Chen WX. Identification of a novel five ferroptosis-related gene signature as a promising prognostic model for breast cancer. J Cancer Res Clin Oncol 2023; 149:16779-16795. [PMID: 37728703 PMCID: PMC10645672 DOI: 10.1007/s00432-023-05423-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/12/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND Breast cancer (BCa) is a major challenge for women's health worldwide. Ferroptosis is closely related to tumorigenesis and cancer progression. However, the prognostic value of ferroptosis-related genes in BCa remains unclear, and more accurate prognostic models are urgently needed. METHODS Gene expression profiles and clinical information of BCa patients were collected from public databases. LASSO and multivariate Cox regression analysis were utilized to construct the prognostic gene signature. Kaplan-Meier plotter, receiver operating characteristic (ROC) curves, and nomogram were used to validate the prognostic value of the gene signature. Gene set enrichment analysis was performed to explore the molecular functions and signaling pathways. RESULTS Differentially expressed ferroptosis-related genes between BCa samples and normal tissues were obtained. A novel five-gene signature including BCL2, SLC40A1, TFF1, APOOL, and PRAME was established for prognosis prediction. Patients stratified into high-risk or low-risk group displayed significantly different survival. Kaplan-Meier and ROC curves showed a good performance for survival prediction in different cohorts. Biological function analysis revealed that the five-gene signature was associated with cancer progression, immune infiltration, immune response, and drug resistance. Nomogram including the five-gene signature was established. CONCLUSION A novel five ferroptosis-related gene signature and nomogram could be used for prognostic prediction in BCa.
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Affiliation(s)
- Tian- Cheng Cheng
- Department of Breast Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, 29 Xinglongxiang, Changzhou, 213000, Jiangsu Province, China
- Graduate School, Bengbu Medical College, Bengbu, 233000, Anhui Province, China
| | - Jia-Hao Wu
- Department of Breast Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, 29 Xinglongxiang, Changzhou, 213000, Jiangsu Province, China
- Graduate School, Dalian Medical University, Dalian, 116000, Liaoning Province, China
| | - Bei Zhu
- Department of Breast Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, 29 Xinglongxiang, Changzhou, 213000, Jiangsu Province, China
| | - Hai-Yan Gao
- Department of Breast Surgery, The Affiliated Changzhou Tumor Hospital of Soochow University, Changzhou, 213000, Jiangsu Province, China
| | - Lin Zheng
- Department of Breast Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, 29 Xinglongxiang, Changzhou, 213000, Jiangsu Province, China.
| | - Wei-Xian Chen
- Department of Breast Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, 29 Xinglongxiang, Changzhou, 213000, Jiangsu Province, China.
- Post-Doctoral Working Station, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, ChangzhouJiangsu Province, 213000, China.
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18
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Li Y, Ma Z, Li W, Xu X, Shen P, Zhang SE, Cheng B, Xia J. PDPN + CAFs facilitate the motility of OSCC cells by inhibiting ferroptosis via transferring exosomal lncRNA FTX. Cell Death Dis 2023; 14:759. [PMID: 37993428 PMCID: PMC10665425 DOI: 10.1038/s41419-023-06280-3] [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: 07/14/2023] [Revised: 10/28/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023]
Abstract
Cancer-associated fibroblasts (CAFs) are abundant and heterogeneous in tumor microenvironment (TME). Cross-talk between cancer cells and CAFs results in cancer progression. Here, we demonstrated that a distinct cancer-associated fibroblasts subset with podoplanin (PDPN) positive expression (PDPN+ CAFs) was correlated with poor survival in oral squamous cell carcinoma (OSCC). PDPN+ CAFs promoted the progression of OSCC by transferring exosomal lncRNA FTX to OSCC cells. Mechanically, FTX bound to flap endonuclease-1 (FEN1), forming an RNA‒protein complex. FTX enhanced promoter demethylation of FEN1 by recruiting ten-eleven translocation-2 (TET2). In addition, FTX/FEN1 axis promoted OSCC cells motility by inhibiting ferroptosis. In xenograft experiments, RSL-3, a ferroptosis-inducing agent, suppressed the tumorigenesis potential of FEN1-overexpressed OSCC cells. Furthermore, Acyl-CoA synthetase long-chain family member 4 (ACSL4) was confirmed to participate in the motility promotion induced by FEN1 overexpression. FEN1 could bind to promoter region of ACSL4 and then inhibit ferroptosis in OSCC cells. Our study reveals that PDPN+ CAFs promote the invasiveness of OSCC cells by inhibiting ferroptosis through FTX/FEN1/ACSL4 signaling cascade. PDPN+ CAFs may serve as a novel potential therapeutic target for OSCC.
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Affiliation(s)
- Yaoyin Li
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, PR China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, PR China
| | - Zeyi Ma
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, PR China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, PR China
| | - Weiyu Li
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, PR China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, PR China
| | - Xiaoqing Xu
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, PR China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, PR China
| | - Peiqi Shen
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, PR China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, PR China
| | - Si-En Zhang
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, PR China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, PR China
| | - Bin Cheng
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, PR China.
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, PR China.
| | - Juan Xia
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, PR China.
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, PR China.
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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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20
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Xiao L, Yin W, Chen X, Zhang X, Zhang C, Yu Z, Lü M. A disulfidptosis-related lncRNA index predicting prognosis and the tumor microenvironment in colorectal cancer. Sci Rep 2023; 13:20135. [PMID: 37978247 PMCID: PMC10656577 DOI: 10.1038/s41598-023-47472-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
Colorectal cancer (CRC) is a common and deadly cancer worldwide with a high lethality rate. Disulfidptosis has been found to be an emerging mode of death in cancer, and the purpose of this study was to explore the relationship between disulfidptosis-related lncRNAs (DRLs) and CRC and to develop a prognostic model for CRC and DRLs. The gene expression data and clinicopathologic information of colorectal cancer patients were obtained from The Cancer Genome Atlas (TCGA) and screened for DRLs based on correlation analysis. The least absolute shrinkage and selection operator (LASSO) and Cox regression were used to construct the prognostic model, and its validation was carried out by PCA and receiver operating characteristic (ROC) curves. We constructed nomograms combined with the model. Finally, the possible mechanisms by which lncRNAs affect CRC were explored by functional enrichment analysis, immune infiltration and immune escape analysis. In summary, we developed a prognostic marker consisting of lncRNAs associated with disulfidptosis to help clinicians predict the survival of different CRC patients and use different targeted therapies and immunotherapies depending on the condition.
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Affiliation(s)
- Lijun Xiao
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou City, China
| | - Wen Yin
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou City, China
| | - Xuanqin Chen
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou City, China
| | - Xu Zhang
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou City, China
| | - Chao Zhang
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou City, China
| | - Zehui Yu
- Laboratory Animal Center, Southwest Medical University, Luzhou City, China.
| | - Muhan Lü
- The Affiliated Hospital of Southwest Medical University, Luzhou City, China.
- Human Microecology and Precision Diagnosis and Treatment of Luzhou Key Laboratory, Luzhou City, China.
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21
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Chen P, Yu J, Luo Q, Li J, Wang W. Construction of disulfidptosis-related lncRNA signature for predicting the prognosis and immune escape in colon adenocarcinoma. BMC Gastroenterol 2023; 23:382. [PMID: 37946148 PMCID: PMC10636996 DOI: 10.1186/s12876-023-03020-x] [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: 08/15/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Colon adenocarcinoma (COAD) is one of the most frequent types of cancer worldwide. Disulfidptosis has been identified as a new mode of cell death recently. The goal of this study was to explore the possibility of a connection between disulfidptosis and COAD. RNA sequencing data from COAD patients were retrieved from the The Cancer Genome Atlas (TCGA) database for this investigation. R software and various methods were used to identify disulfidptosis-related lncRNAs (DRLs) in COAD, and a prognostic model was created based on 6 DRLs (AP003555.1, AL683813.1, SNHG7, ZEB1-AS1, AC074212.1, RPL37A-DT). The prognostic model demonstrated a good accuracy in predicting the prognosis of COAD patients, according to receiver operating characteristic (ROC) curve and Concordance index (C-index) analyses. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed significant differences in biological functions and signaling pathways involved in differential genes in risk subgroups, including protein - DNA complex subunit organization, Hippo signaling pathway, Wnt signaling pathway. TIDE analysis was done on risk groupings in this study, and it found that patients in the high-risk group had more immune escape potential and were less probable to react to immunotherapy. Real-time quantitative pcr (qRT-PCR) was used to identify the relatively high expression of 6 DRLs in colon cancer cell lines. In summary, 6 DRLs were identified as possible novel molecular therapy targets for COAD in this investigation. This prognostic model has the potential to be a novel tool for forecasting COAD prognosis in clinical practice, as well as providing new insights on the potential function and mechanism of disulfidptosis in the COAD process.
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Affiliation(s)
- Pan Chen
- Department of General Surgery, Nanjing Tongren Hospital, School of Medicine, Southeast University, Nanjing, 211102, China
| | - Jun Yu
- Department of Pediatrics, Affiliated Hospital of Nanjing University of Chinese Medicine, Taicang Hospital of Traditional Chinese Medicine, Taicang, 215400, China
| | - Qian Luo
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, 210011, China
| | - Jie Li
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, 210011, China.
| | - Wei Wang
- Department of Clinical Laboratory, Lianshui County People's Hospital, Huai'an, 223400, China.
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22
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Wang X, Zhou L, Wang H, Chen W, Jiang L, Ming G, Wang J. Metabolic reprogramming, autophagy, and ferroptosis: Novel arsenals to overcome immunotherapy resistance in gastrointestinal cancer. Cancer Med 2023; 12:20573-20589. [PMID: 37860928 PMCID: PMC10660574 DOI: 10.1002/cam4.6623] [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: 04/19/2023] [Revised: 09/05/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Gastrointestinal cancer poses a serious health threat owing to its high morbidity and mortality. Although immune checkpoint blockade (ICB) therapies have achieved meaningful success in most solid tumors, the improvement in survival in gastrointestinal cancers is modest, owing to sparse immune response and widespread resistance. Metabolic reprogramming, autophagy, and ferroptosis are key regulators of tumor progression. METHODS A literature review was conducted to investigate the role of the metabolic reprogramming, autophagy, and ferroptosis in immunotherapy resistance of gastrointestinal cancer. RESULTS Metabolic reprogramming, autophagy, and ferroptosis play pivotal roles in regulating the survival, differentiation, and function of immune cells within the tumor microenvironment. These processes redefine the nutrient allocation blueprint between cancer cells and immune cells, facilitating tumor immune evasion, which critically impacts the therapeutic efficacy of immunotherapy for gastrointestinal cancers. Additionally, there exists profound crosstalk among metabolic reprogramming, autophagy, and ferroptosis. These interactions are paramount in anti-tumor immunity, further promoting the formation of an immunosuppressive microenvironment and resistance to immunotherapy. CONCLUSIONS Consequently, it is imperative to conduct comprehensive research on the roles of metabolic reprogramming, autophagy, and ferroptosis in the resistance of gastrointestinal tumor immunotherapy. This understanding will illuminate the clinical potential of targeting these pathways and their regulatory mechanisms to overcome immunotherapy resistance in gastrointestinal cancers.
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Affiliation(s)
- Xiangwen Wang
- Department of General SurgeryThe First Hospital of Lanzhou UniversityLanzhouChina
| | - Liwen Zhou
- Department of StomatologyThe First Hospital of Lanzhou UniversityLanzhouChina
| | - Hongpeng Wang
- Department of General SurgeryThe First Hospital of Lanzhou UniversityLanzhouChina
| | - Wei Chen
- Department of General SurgeryThe First Hospital of Lanzhou UniversityLanzhouChina
| | - Lei Jiang
- Department of General SurgeryThe First Hospital of Lanzhou UniversityLanzhouChina
| | - Guangtao Ming
- Department of General SurgeryThe First Hospital of Lanzhou UniversityLanzhouChina
| | - Jun Wang
- Department of General SurgeryThe First Hospital of Lanzhou UniversityLanzhouChina
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23
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Zhou M, Deng Y, Fu Y, Liang R, Liu Y, Liao Q. A new prognostic model for glioblastoma multiforme based on coagulation-related genes. Transl Cancer Res 2023; 12:2898-2910. [PMID: 37969372 PMCID: PMC10643966 DOI: 10.21037/tcr-23-322] [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: 03/01/2023] [Accepted: 08/10/2023] [Indexed: 11/17/2023]
Abstract
Background Glioblastoma multiforme (GBM) is the most aggressive, common, and lethal type of primary brain tumor. Multiple cancers have been associated with abnormalities in the coagulation system that facilitate tumor invasion and metastasis. In GBM, the prognostic value and underlying mechanism of coagulation-related genes (CRGs) have not been explored. Methods RNA sequencing (RNA-seq) and clinical information on GBM were obtained from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA), respectively. Following the identification of differentially expressed CRGs (DECRGs) between GBM and control samples, the survival-related DECRGs were selected via univariate and multivariate Cox regression analyses to establish a prognostic signature. The prognostic performance and clinical utility of the prognostic signature were assessed by the Kaplan-Meier (KM) analysis and receiver operating characteristic (ROC) curve analysis, and a nomogram was constructed. The signature genes-related underlying mechanisms were analyzed according to gene set enrichment analysis (GSEA), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and single-cell analysis. Finally, the difference in immune cell infiltration, stromal score, immune score, and Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data (ESTIMATE) score were compared between different risk groups. Results A 5-gene prognostic signature (PLAUR, GP6, C5AR1, SERPINA5, F2RL2) was established for overall survival (OS) prediction of GBM patients. The predicted efficiency of the prognostic signature was confirmed in TGGA-GBM dataset and validated in the CGGA-GBM dataset, revealing that it could differentiate GBM patients from controls well, and high risk score was accompanied with poor prognosis. Moreover, biological process (BP) and signaling pathway analyses showed that signature genes were mainly enriched in the functions of blood coagulation and tumor invasion and metastasis. Moreover, high-risk patients exhibited higher levels of immune cell infiltration, stromal score, immune score, and ESTIMATE score than that of low-risk patients. Conclusions An analysis of coagulation-related prognostic signatures was conducted in this study, as well as how signature genes may affect GBM progress, providing information that might provide new ideas for the development of GBM-related molecular targeted therapies.
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Affiliation(s)
- Min Zhou
- Department of Neurosurgery, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Yunbo Deng
- Department of Operating Room, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Ya Fu
- Department of Neurosurgery, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Richu Liang
- Department of Neurosurgery, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Yang Liu
- Department of Neurosurgery, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Quan Liao
- Department of Neurosurgery, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
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Bu T, Li L, Tian J. Unlocking the role of non-coding RNAs in prostate cancer progression: exploring the interplay with the Wnt signaling pathway. Front Pharmacol 2023; 14:1269233. [PMID: 37829301 PMCID: PMC10565042 DOI: 10.3389/fphar.2023.1269233] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023] Open
Abstract
Prostate cancer (PCa) is one of the most common cancers in males, exhibiting a wide spectrum of clinical manifestations that pose challenges in its diagnosis and treatment. The Wnt signaling pathway, a conserved and complex pathway, is crucial for embryonic development, tissue homeostasis, and various physiological processes. Apart from the classical Wnt/β-catenin signaling pathway, there exist multiple non-classical Wnt signaling pathways, including the Wnt/PCP and Wnt/Ca2+ pathways. Non-coding RNAs (ncRNAs) are involved in the occurrence and development of PCa and the response to PCa treatment. ncRNAs are known to execute diverse regulatory roles in cellular processes, despite their inability to encode proteins. Among them, microRNAs, long non-coding RNAs, and circular RNAs play key roles in the regulation of the Wnt signaling pathway in PCa. Aberrant expression of these ncRNAs and dysregulation of the Wnt signaling pathway are one of the causes of cell proliferation, apoptosis, invasion, migration, and angiogenesis in PCa. Moreover, these ncRNAs affect the characteristics of PCa cells and hold promise as diagnostic and prognostic biomarkers. Herein, we summarize the role of ncRNAs in the regulation of the Wnt signaling pathway during the development of PCa. Additionally, we present an overview of the current progress in research on the correlation between these molecules and clinical features of the disease to provide novel insights and strategies for the treatment of PCa.
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Affiliation(s)
| | | | - Jiyu Tian
- Department of Gastroenterology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
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25
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Wang Z, Ma C, Teng Q, Man J, Zhang X, Liu X, Zhang T, Chong W, Chen H, Lu M. Identification of a ferroptosis-related gene signature predicting recurrence in stage II/III colorectal cancer based on machine learning algorithms. Front Pharmacol 2023; 14:1260697. [PMID: 37711170 PMCID: PMC10498388 DOI: 10.3389/fphar.2023.1260697] [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: 07/18/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023] Open
Abstract
Background: Colorectal cancer (CRC) is one of the most prevalent cancer types globally. A survival paradox exists due to the inherent heterogeneity in stage II/III CRC tumor biology. Ferroptosis is closely related to the progression of tumors, and ferroptosis-related genes can be used as a novel biomarker in predicting cancer prognosis. Methods: Ferroptosis-related genes were retrieved from the FerrDb and KEGG databases. A total of 1,397 samples were enrolled in our study from nine independent datasets, four of which were integrated as the training dataset to train and construct the model, and validated in the remaining datasets. We developed a machine learning framework with 83 combinations of 10 algorithms based on 10-fold cross-validation (CV) or bootstrap resampling algorithm to identify the most robust and stable model. C-indice and ROC analysis were performed to gauge its predictive accuracy and discrimination capabilities. Survival analysis was conducted followed by univariate and multivariate Cox regression analyses to evaluate the performance of identified signature. Results: The ferroptosis-related gene (FRG) signature was identified by the combination of Lasso and plsRcox and composed of 23 genes. The FRG signature presented better performance than common clinicopathological features (e.g., age and stage), molecular characteristics (e.g., BRAF mutation and microsatellite instability) and several published signatures in predicting the prognosis of the CRC. The signature was further stratified into a high-risk group and low-risk subgroup, where a high FRG signature indicated poor prognosis among all collected datasets. Sensitivity analysis showed the FRG signature remained a significant prognostic factor. Finally, we have developed a nomogram and a decision tree to enhance prognosis evaluation. Conclusion: The FRG signature enabled the accurate selection of high-risk stage II/III CRC population and helped optimize precision treatment to improve their clinical outcomes.
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Affiliation(s)
- Ze Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Chenghao Ma
- Department of Gastroenterological Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Qiong Teng
- Department of Gastroenterological Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Jinyu Man
- Department of Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Xuening Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Xinjie Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Tongchao Zhang
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
- Clinical Research Center of Shandong University, Jinan, China
| | - Wei Chong
- Department of Gastrointestinal Surgery, Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Hao Chen
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
- Clinical Research Center of Shandong University, Jinan, China
| | - Ming Lu
- Department of Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
- Clinical Research Center of Shandong University, Jinan, China
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26
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Zhou C, Shen S, Zhang M, Luo H, Zhang Y, Wu C, Zeng L, Ruan H. Mechanisms of action and synergetic formulas of plant-based natural compounds from traditional Chinese medicine for managing osteoporosis: a literature review. Front Med (Lausanne) 2023; 10:1235081. [PMID: 37700771 PMCID: PMC10493415 DOI: 10.3389/fmed.2023.1235081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/15/2023] [Indexed: 09/14/2023] Open
Abstract
Osteoporosis (OP) is a systemic skeletal disease prevalent in older adults, characterized by substantial bone loss and deterioration of microstructure, resulting in heightened bone fragility and risk of fracture. Traditional Chinese Medicine (TCM) herbs have been widely employed in OP treatment owing to their advantages, such as good tolerance, low toxicity, high efficiency, and minimal adverse reactions. Increasing evidence also reveals that many plant-based compounds (or secondary metabolites) from these TCM formulas, such as resveratrol, naringin, and ginsenoside, have demonstrated beneficial effects in reducing the risk of OP. Nonetheless, the comprehensive roles of these natural products in OP have not been thoroughly clarified, impeding the development of synergistic formulas for optimal OP treatment. In this review, we sum up the pathological mechanisms of OP based on evidence from basic and clinical research; emphasis is placed on the in vitro and preclinical in vivo evidence-based anti-OP mechanisms of TCM formulas and their chemically active plant constituents, especially their effects on imbalanced bone homeostasis regulated by osteoblasts (responsible for bone formation), osteoclasts (responsible for bone resorption), bone marrow mesenchymal stem cells as well as bone microstructure, angiogenesis, and immune system. Furthermore, we prospectively discuss the combinatory ingredients from natural products from these TCM formulas. Our goal is to improve comprehension of the pharmacological mechanisms of TCM formulas and their chemically active constituents, which could inform the development of new strategies for managing OP.
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Affiliation(s)
- Chengcong Zhou
- Institute of Orthopaedics and Traumatology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, China
| | - Shuchao Shen
- Institute of Orthopaedics and Traumatology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, China
| | - Muxin Zhang
- Institute of Orthopaedics and Traumatology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, China
| | - Huan Luo
- Department of Pharmacy, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuliang Zhang
- Hangzhou Fuyang Hospital of TCM Orthopedics and Traumatology, Hangzhou, China
| | - Chengliang Wu
- Institute of Orthopaedics and Traumatology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, China
| | - Lingfeng Zeng
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hongfeng Ruan
- Institute of Orthopaedics and Traumatology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, China
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Dong X, Liao P, Liu X, Yang Z, Wang Y, Zhong W, Wang B. Construction and Validation of a Reliable Disulfidptosis-Related LncRNAs Signature of the Subtype, Prognostic, and Immune Landscape in Colon Cancer. Int J Mol Sci 2023; 24:12915. [PMID: 37629096 PMCID: PMC10454603 DOI: 10.3390/ijms241612915] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Disulfidptosis, a novel form of regulated cell death (RCD) associated with metabolism, represents a promising intervention target in cancer therapy. While abnormal lncRNA expression is associated with colon cancer development, the prognostic potential and biological characteristics of disulfidptosis-related lncRNAs (DRLs) remain unclear. Consequently, the research aimed to discover a novel indication of DRLs with significant prognostic implications, and to investigate their possible molecular role in the advancement of colon cancer. Here, we acquired RNA-seq data, pertinent clinical data, and genomic mutations of colon adenocarcinoma (COAD) from the TCGA database, and then DRLs were determined through Pearson correlation analysis. A total of 434 COAD patients were divided in to three subgroups through clustering analysis based on DRLs. By utilizing univariate Cox regression, the least absolute shrinkage and selection operator (LASSO) algorithm, and multivariate Cox regression analysis, we ultimately created a prognostic model consisting of four DRLs (AC007728.3, AP003555.1, ATP2B1.AS1, and NSMCE1.DT), and an external database was used to validate the prognostic features of the risk model. According to the Kaplan-Meier curve analysis, patients in the low-risk group exhibited a considerably superior survival time in comparison to those in the high-risk group. Enrichment analysis revealed a significant association between metabolic processes and the genes that were differentially expressed in the high- and low-risk groups. Additionally, significant differences in the tumor immune microenvironment landscape were observed, specifically pertaining to immune cells, function, and checkpoints. High-risk patients exhibited a low likelihood of immune evasion, as indicated by the Tumor Immune Dysfunction and Exclusion (TIDE) analysis. Patients who exhibit both a high risk and high Tumor Mutational Burden (TMB) experience the least amount of time for survival, whereas those belonging to the low-risk and low-TMB category demonstrate the most favorable prognosis. In addition, the risk groups determined by the 4-DRLs signature displayed distinct drug sensitivities. Finally, we confirmed the levels of expression for four DRLs through rt-qPCR in both tissue samples from colon cancer patients and cell lines. Taken together, the first 4-DRLs-based signature we proposed may serve for a hopeful instrument for forecasting the prognosis, immune landscape, and therapeutic responses in colon cancer patients, thereby facilitating optimal clinical decision-making.
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Affiliation(s)
- Xiaoqian Dong
- School of Medicine, Nankai University, Tianjin 300071, China; (X.D.)
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin 300052, China
| | - Pan Liao
- School of Medicine, Nankai University, Tianjin 300071, China; (X.D.)
| | - Xiaotong Liu
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin 300052, China
| | - Zhenni Yang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin 300052, China
| | - Yali Wang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin 300052, China
| | - Weilong Zhong
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin 300052, China
| | - Bangmao Wang
- School of Medicine, Nankai University, Tianjin 300071, China; (X.D.)
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin 300052, China
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Chu Y, Yao Y, Hu Q, Song Q. Riskscore Model Based on Oxidative Stress-Related Genes May Facilitate the Prognosis Evaluation for Patients With Colon Cancer. Clin Transl Gastroenterol 2023; 14:e00582. [PMID: 36927989 PMCID: PMC10299772 DOI: 10.14309/ctg.0000000000000582] [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: 09/29/2022] [Accepted: 02/15/2023] [Indexed: 03/18/2023] Open
Abstract
INTRODUCTION This study aims to identify the oxidative stress-related genes (OSRGs) with prognostic value and develop a riskscore model for prognosis evaluation in colon cancer. METHODS The transcriptome data and corresponding clinical information about colon cancer were extracted from The Cancer Genome Atlas database. Differentially expressed OSRGs and transcription factors (TFs) were identified between the normal and tumor samples. A riskscore model was established with OSRGs filtered from Cox regression analysis. This riskscore model was appraised by Kaplan-Meier plot, receiver operating characteristic curve, and Cox regression analysis. The clinical relevance of riskscore and its association with immune cell infiltration were also evaluated. RESULTS A total of 307 differentially expressed OSRGs and 64 differential TFs were identified. A TF-OSRG regulatory network was constructed in Cytoscape software. A riskscore model was established based on 17 OSRGs with independent prognostic value. This riskscore model could separate the patients into low-risk and high-risk groups. It also had good predictive ability, with an area under the curve = 0.8. In multivariate Cox regression analysis, age, T stage, and riskscore were identified as independent risk factors in colon cancer. Riskscore was significantly correlated with T stage, N stage, and immune cell infiltration. DISCUSSION We established a useful riskscore model with 17 OSRGs for prognosticating the overall survival in patients with colon cancer. This study provides a new insight into the clinical utility of OSRG-based riskscore model, which will hopefully facilitate the prognosis evaluation of patients with colon cancer.
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Affiliation(s)
- Yuxin Chu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yi Yao
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qinyong Hu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
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29
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Liu H, Che H, Zhang M, Lv J, Pu C, Wu J, Zhang Y, Gu Y. Developing CuS for Predicting Aggressiveness and Prognosis in Lung Adenocarcinoma. Genes (Basel) 2023; 14:genes14051055. [PMID: 37239416 DOI: 10.3390/genes14051055] [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: 03/29/2023] [Revised: 05/03/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
Cuproptosis is a newfound cell death form that depends on copper (Cu) ionophores to transport Cu into cancer cells. Studies on the relationship have covered most common cancer types and analyzed the links between cuproptosis-related genes (CRGs) and various aspects of tumor characteristics. In this study, we evaluated the role of cuproptosis in lung adenocarcinoma (LUAD) and constructed the cuproptosis-related score (CuS) to predict aggressiveness and prognosis in LUAD, so as to achieve precise treatment for patients. CuS had a better predictive performance than cuproptosis genes, possibly due to the synergy of SLC family genes, and patients with a high CuS had a poor prognosis. Functional enrichment analysis revealed the correlation between CuS and immune and mitochondrial pathways in multiple datasets. Furthermore, we predicted six potential drugs targeting high-CuS patients, including AZD3759, which is a targeted drug for LUAD. In conclusion, cuproptosis is involved in LUAD aggressiveness, and CuS can accurately predict the prognosis of patients. These findings provide a basis for precise treatment of patients with high CuS in LUAD.
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Affiliation(s)
- Honghao Liu
- Computational Biology Research Center, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Haijun Che
- College of Pharmacy, Chengdu Airport Campus, Southwest Minzu University, Chengdu 610041, China
| | - Mengyan Zhang
- Computational Biology Research Center, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Jinyue Lv
- Computational Biology Research Center, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Chengjie Pu
- Computational Biology Research Center, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Jiawei Wu
- State Key Laboratory of Agrobiotechnology, School of Life Science, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Yan Zhang
- Computational Biology Research Center, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
- College of Pathology, Qiqihar Medical University, Qiqihar 161042, China
| | - Yue Gu
- Computational Biology Research Center, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
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30
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Li D, Qu G, Ling S, Sun Y, Cui Y, Yang Y, Cao X. A cuproptosis-related lncRNA signature to predict prognosis and immune microenvironment of colon adenocarcinoma. Sci Rep 2023; 13:6284. [PMID: 37072493 PMCID: PMC10113217 DOI: 10.1038/s41598-023-33557-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/14/2023] [Indexed: 05/03/2023] Open
Abstract
Cuproptosis is a novel cell death modality but its regulatory role in the colon cancer remains obscure. This study is committed to establishing a cuproptosis-related lncRNA (CRL) signature to forecast the prognosis for colon adenocarcinoma (COAD). The Cancer Genome Atlas (TCGA) samples were randomly divided into training and validation cohorts. LASSO-COX analysis was performed to construct a prognostic signature consisting of five CRLs (AC015712.2, ZEB1-AS1, SNHG26, AP001619.1, and ZKSCAN2-DT). We found the patients with high-risk scores suffered from poor prognosis in training cohort (p < 0.001) and validation cohort (p = 0.004). Nomogram was created based on the 5-CRL signature. Calibration curves, receiver operating characteristic (ROC) curves, and decision curve analysis (DCA) demonstrated the nomogram performed well in 1‑, 3‑, and 5‑year overall survival (OS). Subsequently, we observed increased infiltration of multiple immune cells and upregulated expression of immune checkpoints and RNA methylation modification genes in high-risk patients. Additionally, gene set enrichment analysis (GSEA) revealed two tumor-related pathways, including MAPK and Wnt signaling pathways. Finally, we found AKT inhibitors, all-trans retinoic acid (ATRA), camptothecin, and thapsigargin had more sensitivity to antitumor therapy in high-risk patients. Collectively, this CRL signature is promising for the prognostic prediction and precise therapy of COAD.
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Affiliation(s)
- Dongming Li
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, 130021, Jilin, China
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing, 100050, China
| | - Guangzhen Qu
- Department of Interventional Radiology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, China
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing, 100050, China
| | - Shen Ling
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing, 100050, China
| | - Yuanlin Sun
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, 130021, Jilin, China
| | - Yingnan Cui
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, 130021, Jilin, China
| | - Yingchi Yang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Diseases, Beijing, 100050, China.
| | - Xueyuan Cao
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, 130021, Jilin, China.
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Wu Z, Lin C, Zhang F, Lu Z, Wang Y, Liu Y, Zhou Z, Li L, Song L. TIGD1 Function as a Potential Cuproptosis Regulator Following a Novel Cuproptosis-Related Gene Risk Signature in Colorectal Cancer. Cancers (Basel) 2023; 15:cancers15082286. [PMID: 37190215 DOI: 10.3390/cancers15082286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 05/17/2023] Open
Abstract
Cuproptosis is a new form of copper-dependent programmed cell death commonly occurring within the body. There is emerging evidence indicating that cuproptosis has a significant regulatory function in the onset and progression of cancer. However, it is still unclear how cuproptosis regulates cancer and whether other genes are involved in the regulation. Using the TCGA-COAD dataset of 512 samples, we found that seven of ten cuproptosis markers showed prognostic value in colorectal cancer (CRC) using Kaplan-Meier survival analysis. Furthermore, 31 prognostic cuproptosis-related genes were identified using weighted gene co-expression network analysis and univariate Cox analysis. Subsequently, we constructed a 7-PCRG signature using least absolute shrinkage and selection operator (LASSO)-Cox regression analysis. The risk score predicting survival in patients with CRC was evaluated. Two risk groups were classified based on their risk scores. The two groups revealed a significant difference in immune cells, such as B and T cells. Furthermore, we identified differences in many immune functions and checkpoints, including CD276 and CD28. In vitro experiments showed that a hub cuproptosis-related gene, TIGD1, could significantly regulate cuproptosis in CRC after exposure to elesclomol. This study validated that cuproptosis was closely related to the progression of CRC. Seven new cuproptosis-related genes were identified, and the function of TIGD1 in cuproptosis was preliminarily understood. Since a certain concentration of copper in CRC cells is important, cuproptosis may provide a new target for cancer therapy. This study may provide novel insights into the treatment of CRC.
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Affiliation(s)
- Zhiwei Wu
- Department of Health Management, The Third Xiangya Hospital, Central South University, Changsha 410013, China
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Changwei Lin
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Fan Zhang
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Zhixing Lu
- Department of Gastrointestinal, Hernia and Enterofistula Surgery, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning 530016, China
| | - Yaohui Wang
- Department of Health Management, The Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Yang Liu
- Department of Pathology, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Zhijiao Zhou
- Department of Pathology, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Liang Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Liying Song
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Tongzipo Road, Changsha 410013, China
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Wang S, Zhu S. Comprehensive analysis of novel cancer prediction genes and tumor microenvironment infiltration in colon cancer. Clin Transl Oncol 2023:10.1007/s12094-023-03145-1. [PMID: 37016097 DOI: 10.1007/s12094-023-03145-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/01/2023] [Indexed: 04/06/2023]
Abstract
BACKGROUND Colon cancer with high incidence and mortality is a severe public health problem. As an emerging therapy, immunotherapy has played an active clinical role in tumor treatment, but only a small number of patients respond. METHODS By univariate Cox regression analysis of 165 novel cancer prediction genes (NCPGs), 29 NCPGs related to prognosis were screened. Based on these 29 NCPGs and 336 differentially expressed genes, we constructed two colon cancer subgroups and three gene clusters and analyzed prognosis, activation pathways, and immune infiltration characteristics under various modification patterns. Then each patient was scored and divided into high or low NCPG_score groups. A comprehensive evaluation between NCPG_score and clinical characteristics, tumor microenvironment (TME), tumor somatic mutations, and the potential for immunotherapy was conducted. RESULTS Patients with high NCPG_score were characterized by high tumor mutation burden and high microsatellite instability and were more suitable for immunotherapy. CONCLUSIONS This study screened 29 NCPGs as independent prognostic markers in colon cancer patients, demonstrating their TME, clinicopathological features, and potential roles in immunotherapy, helping to assess prognosis and guiding more personalized immunotherapy.
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Affiliation(s)
- Shixin Wang
- Department of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Sujie Zhu
- Department of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
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Hu C, Zeng X, Zhu Y, Huang Z, Liu J, Ji D, Zheng Z, Wang Q, Tan W. Regulation of ncRNAs involved with ferroptosis in various cancers. Front Genet 2023; 14:1136240. [PMID: 37065473 PMCID: PMC10090411 DOI: 10.3389/fgene.2023.1136240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/08/2023] [Indexed: 03/31/2023] Open
Abstract
As a special pattern of programmed cell death, ferroptosis is reported to participate in several processes of tumor progression, including regulating proliferation, suppressing apoptotic pathways, increasing metastasis, and acquiring drug resistance. The marked features of ferroptosis are an abnormal intracellular iron metabolism and lipid peroxidation that are pluralistically modulated by ferroptosis-related molecules and signals, such as iron metabolism, lipid peroxidation, system Xc−, GPX4, ROS production, and Nrf2 signals. Non-coding RNAs (ncRNAs) are a type of functional RNA molecules that are not translated into a protein. Increasing studies demonstrate that ncRNAs have a diversity of regulatory roles in ferroptosis, thus influencing the progression of cancers. In this study, we review the fundamental mechanisms and regulation network of ncRNAs on ferroptosis in various tumors, aiming to provide a systematic understanding of recently emerging non-coding RNAs and ferroptosis.
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Affiliation(s)
- Chenxi Hu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiangbo Zeng
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yuanchao Zhu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zehai Huang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jiacheng Liu
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People’s Hospital, Beijing, China
| | - Ding Ji
- Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zaosong Zheng
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- *Correspondence: Zaosong Zheng, ; Qiong Wang, ; Wanlong Tan,
| | - Qiong Wang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- *Correspondence: Zaosong Zheng, ; Qiong Wang, ; Wanlong Tan,
| | - Wanlong Tan
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- *Correspondence: Zaosong Zheng, ; Qiong Wang, ; Wanlong Tan,
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Chen R, Wei JM. Integrated analysis identifies oxidative stress-related lncRNAs associated with progression and prognosis in colorectal cancer. BMC Bioinformatics 2023; 24:76. [PMID: 36869292 PMCID: PMC9985255 DOI: 10.1186/s12859-023-05203-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/23/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common cancers in the world. Oxidative stress reactions have been reportedly associated with oncogenesis and tumor progression. By analyzing mRNA expression data and clinical information from The Cancer Genome Atlas (TCGA), we aimed to construct an oxidative stress-related long noncoding RNA (lncRNA) risk model and identify oxidative stress-related biomarkers to improve the prognosis and treatment of CRC. RESULTS Differentially expressed oxidative stress-related genes (DEOSGs) and oxidative stress-related lncRNAs were identified by using bioinformatics tools. An oxidative stress-related lncRNA risk model was constructed based on 9 lncRNAs (AC034213.1, AC008124.1, LINC01836, USP30-AS1, AP003555.1, AC083906.3, AC008494.3, AC009549.1, and AP006621.3) by least absolute shrinkage and selection operator (LASSO) analysis. The patients were then divided into high- and low-risk groups based on the median risk score. The high-risk group had a significantly worse overall survival (OS) (p < 0.001). Receiver operating characteristic (ROC) and calibration curves displayed the favorable predictive performance of the risk model. The nomogram successfully quantified the contribution of each metric to survival, and the concordance index and calibration plots demonstrated its excellent predictive capacity. Notably, different risk subgroups showed significant differences in terms of their metabolic activity, mutation landscape, immune microenvironment and drug sensitivity. Specifically, differences in the immune microenvironment implied that CRC patients in certain subgroups might be more responsive to immune checkpoint inhibitors. CONCLUSIONS Oxidative stress-related lncRNAs can predict the prognosis of CRC patients, which provides new insight for future immunotherapies based on potential oxidative stress targets.
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Affiliation(s)
- Rui Chen
- Department of Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jun-Min Wei
- Department of Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.
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Construction and Validation of a Novel Prognosis Model in Colon Cancer Based on Cuproptosis-Related Long Non-Coding RNAs. J Clin Med 2023; 12:jcm12041528. [PMID: 36836069 PMCID: PMC9960235 DOI: 10.3390/jcm12041528] [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: 11/24/2022] [Revised: 02/01/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Colon cancer (CC) is one of the most common (6%) malignancies and leading cause of cancer-associated death (more than 0.5 million) worldwide, which demands reliable prognostic biomarkers. Cuproptosis is a novel modality of regulated cell death triggered by the accumulation of intracellular copper. LncRNAs have been reported as prognostic signatures in different types of tumors. However, the correlation between cuproptosis-related lncRNAs (CRLs) and CC remains unclear. Data of CC patients were downloaded from public databases. The prognosis-associated CRLs were identified by co-expression analysis and univariate Cox. Least absolute shrinkage and selection operator were utilized to construct the CRLs-based prognostic signature in silico for CC patients. CRLs level was validated in human CC cell lines and patient tissues. ROC curve and Kaplan-Meier curve results revealed that high CRLs-risk score was associated with poor prognosis in CC patients. Moreover, the nomogram revealed that this model possessed a steady prognostic prediction capability with C-index as 0.68. More importantly, CC patients with high CRLs-risk score were more sensitive to eight targeted therapy drugs. The prognostic prediction power of the CRLs-risk score was further confirmed by cell lines, tissues and two independent CC cohorts. This study constructed a novel ten-CRLs-based prognosis model for CC patients. The CRLs-risk score is expected to serve as a promising prognostic biomarker and predict targeted therapy response in CC patients.
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36
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Song YQ, Yan XD, Wang Y, Wang ZZ, Mao XL, Ye LP, Li SW. Role of ferroptosis in colorectal cancer. World J Gastrointest Oncol 2023; 15:225-239. [PMID: 36908317 PMCID: PMC9994046 DOI: 10.4251/wjgo.v15.i2.225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/15/2022] [Accepted: 01/10/2023] [Indexed: 02/14/2023] Open
Abstract
Colorectal cancer (CRC) is the second deadliest cancer and the third-most common malignancy in the world. Surgery, chemotherapy, and targeted therapy have been widely used to treat CRC, but some patients still develop resistance to these treatments. Ferroptosis is a novel non-apoptotic form of cell death. It is an iron-dependent non-apoptotic cell death characterized by the accumulation of lipid reactive oxygen species and has been suggested to play a role in reversing resistance to anticancer drugs. This review summarizes recent advances in the prognostic role of ferroptosis in CRC and the mechanism of action in CRC.
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Affiliation(s)
- Ya-Qi Song
- Taizhou Hospital of Zhejiang Province, Zhejiang University, Linhai 317000, Zhejiang Province, China
| | - Xiao-Dan Yan
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Yi Wang
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Zhen-Zhen Wang
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Xin-Li Mao
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Li-Ping Ye
- Taizhou Hospital of Zhejiang Province, Zhejiang University, Linhai 317000, Zhejiang Province, China
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
- Institute of Digestive Disease, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
| | - Shao-Wei Li
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
- Institute of Digestive Disease, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
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37
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Deng Z, Xu Y, Cai Y, Lin W, Zhang L, Jiang A, Zhou Y, Zhao R, Zhao H, Liu Z, Yan T. Inhibition of Ribosomal RNA Processing 15 Homolog (RRP15) Suppressed Tumor Growth, Invasion and Epithelial to Mesenchymal Transition (EMT) of Colon Cancer. Int J Mol Sci 2023; 24:3528. [PMID: 36834940 PMCID: PMC9965612 DOI: 10.3390/ijms24043528] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Although ribosomal RNA processing 15 Homolog (RRP15) has been implicated in the occurrence of various cancers and is considered a potential target for cancer treatment, its significance in colon cancer (CC) is unclear. Thus, this present study aims to determine RRP15 expression and biological function in CC. The results demonstrated a strong expression of RRP15 in CC compared to normal colon specimens, which was correlated with poorer overall survival (OS) and disease-free survival (DFS) of the patients. Among the nine investigated CC cell lines, RRP15 demonstrated the highest and lowest expression in HCT15 and HCT116 cells, respectively. In vitro assays demonstrated that the knockdown of RRP15 inhibited the growth, colony-forming ability and invasive ability of the CC cells whereas its overexpression enhanced the above oncogenic function. Moreover, subcutaneous tumors in nude mice showed that RRP15 knockdown inhibited the CC growth while its overexpression enhanced their growth. Additionally, the knockdown of RRP15 inhibited the epithelial-mesenchymal transition (EMT), whereas overexpression of RRP15 promoted the EMT process in CC. Collectively, inhibition of RRP15 suppressed tumor growth, invasion and EMT of CC, and might be considered a promising therapeutic target for treating CC.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Zhaoguo Liu
- Department of Pharmacology, School of Pharmacy, Nantong University, Nantong 226001, China
| | - Tingdong Yan
- Department of Pharmacology, School of Pharmacy, Nantong University, Nantong 226001, China
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38
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Wu Z, Fang ZX, Hou YY, Wu BX, Deng Y, Wu HT, Liu J. Review of ferroptosis in colorectal cancer: Friends or foes? World J Gastroenterol 2023; 29:469-486. [PMID: 36688016 PMCID: PMC9850932 DOI: 10.3748/wjg.v29.i3.469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/30/2022] [Accepted: 12/21/2022] [Indexed: 01/12/2023] Open
Abstract
Ferroptosis is a newly discovered type of cell-regulated death. It is characterized by the accumulation of iron-dependent lipid peroxidation and can be distinguished from other forms of cell-regulated death by different morphology, biochemistry, and genetics. Recently, studies have shown that ferroptosis is associated with a variety of diseases, including liver, kidney and neurological diseases, as well as cancer. Ferroptosis has been shown to be associated with colorectal epithelial disorders, which can lead to cancerous changes in the gut. However, the potential role of ferroptosis in the occurrence and development of colorectal cancer (CRC) is still controversial. To elucidate the underlying mechanisms of ferroptosis in CRC, this article systematically reviews ferroptosis, and its cellular functions in CRC, for furthering the understanding of the pathogenesis of CRC to aid clinical treatment.
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Affiliation(s)
- Zheng Wu
- Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Ze-Xuan Fang
- Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Yan-Yu Hou
- Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Bing-Xuan Wu
- Department of General Surgery, First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Yu Deng
- Department of General Surgery, First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Hua-Tao Wu
- Department of General Surgery, First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Jing Liu
- Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
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Revealing Prognostic and Immunotherapy-Sensitive Characteristics of a Novel Cuproptosis-Related LncRNA Model in Hepatocellular Carcinoma Patients by Genomic Analysis. Cancers (Basel) 2023; 15:cancers15020544. [PMID: 36672493 PMCID: PMC9857215 DOI: 10.3390/cancers15020544] [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: 11/29/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Immunotherapy has shown strong anti-tumor activity in a subset of patients. However, many patients do not benefit from the treatment, and there is no effective method to identify sensitive immunotherapy patients. Cuproptosis as a non-apoptotic programmed cell death caused by excess copper, whether it is related to tumor immunity has attracted our attention. In the study, we constructed the prognostic model of 9 cuproptosis-related LncRNAs (crLncRNAs) and assessed its predictive capability, preliminarily explored the potential mechanism causing treatment sensitivity difference between the high-/low-risk group. Our results revealed that the risk score was more effective than traditional clinical features in predicting the survival of HCC patients (AUC = 0.828). The low-risk group had more infiltration of immune cells (B cells, CD8+ T cells, CD4+ T cells), mainly with anti-tumor immune function (p < 0.05). It showed higher sensitivity to immune checkpoint inhibitors (ICIs) treatment (p < 0.001) which may exert the effect through the AL365361.1/hsa-miR-17-5p/NLRP3 axis. In addition, NLRP3 mutation-sensitive drugs (VNLG/124, sunitinib, linifanib) may have better clinical benefits in the high-risk group. All in all, the crLncRNAs model has excellent specificity and sensitivity, which can be used for classifying the therapy-sensitive population and predicting the prognosis of HCC patients.
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40
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A Hypoxia Molecular Signature-Based Prognostic Model for Endometrial Cancer Patients. Int J Mol Sci 2023; 24:ijms24021675. [PMID: 36675190 PMCID: PMC9866886 DOI: 10.3390/ijms24021675] [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: 11/21/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023] Open
Abstract
Endometrial cancer has the highest incidence of uterine corpus cancer, the sixth most typical cancer in women until 2020. High recurrence rate and frequent adverse events were reported in either standard chemotherapy or combined therapy. Hence, developing precise diagnostic and prognostic approaches for endometrial cancer was on demand. Four hypoxia-related genes were screened for the EC prognostic model by the univariate, LASSO, and multivariate Cox regression analysis from the TCGA dataset. QT-PCR and functional annotation analysis were performed. Associations between predicted risk and immunotherapy and chemotherapy responses were investigated by evaluating expressions of immune checkpoint inhibitors, infiltrated immune cells, m6a regulators, and drug sensitivity. The ROC curve and calibration plot indicated a fair predictability of our prognostic nomogram model. NR3C1 amplification, along with IL-6 and SRPX suppressions, were detected in tumor. High stromal score and enriched infiltrated aDCs and B cells in the high-risk group supported the hypothesis of immune-deserted tumor. Hypoxia-related molecular subtypes of EC were then identified via the gene signature. Cluster 2 patients showed a significant sensitivity to Vinblastine. In summary, our hypoxia signature model accurately predicted the survival outcome of EC patients and assessed translational and transcriptional dysregulations to explore targets for precise medical treatment.
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Chen H, Peng L, Zhou D, Tan N, Qu G. A risk stratification and prognostic prediction model for lung adenocarcinoma based on aging-related lncRNA. Sci Rep 2023; 13:460. [PMID: 36627319 PMCID: PMC9832126 DOI: 10.1038/s41598-022-26897-2] [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: 06/27/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Abstract
To create a risk model of aging-related long non-coding RNAs (arlncRNAs) and determine whether they might be useful as markers for risk stratification, prognosis prediction, and targeted therapy guidance for patients with lung adenocarcinoma (LUAD). Data on aging genes and lncRNAs from LUAD patients were obtained from Human Aging Genomic Resources 3 and The Cancer Genome Atlas, and differential co-expression analysis of established differentially expressed arlncRNAs (DEarlncRNAs) was performed. They were then paired with a matrix of 0 or 1 by cyclic single pairing. The risk coefficient for each sample of LUAD individuals was obtained, and a risk model was constructed by performing univariate regression, least absolute shrinkage and selection operator regression analysis, and univariate and multivariate Cox regression analysis. Areas under the curve were calculated for the 1-, 3-, and 5-year receiver operating characteristic curves to determine Akaike information criterion-based cutoffs to identify high- and low-risk groups. The survival rate, correlation of clinical characteristics, malignant-infiltrating immune-cell expression, ICI-related gene expression, and chemotherapeutic drug sensitivity were contrasted with the high- and low-risk groups. We found that 99 DEarlncRNAs were upregulated and 12 were downregulated. Twenty pairs of DEarlncRNA pairs were used to create a prognostic model. The 1-, 3-, and 5-year survival curve areas of LUAD individuals were 0.805, 0.793, and 0.855, respectively. The cutoff value to classify patients into two groups was 0.992. The mortality rate was higher in the high-risk group. We affirmed that the LUAD outcome-related independent predictor was the risk score (p < 0.001). Validation of tumor-infiltrating immune cells and ICI-related gene expression differed substantially between the groups. The high-risk group was highly sensitive to docetaxel, erlotinib, gefitinib, and paclitaxel. Risk models constructed from arlncRNAs can be used for risk stratification in patients with LUAD and serve as prognostic markers to identify patients who might benefit from targeted and chemotherapeutic agents.
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Affiliation(s)
- HuiWei Chen
- grid.501248.aDepartment of Emergency, Zhuzhou Central Hospital, Zhuzhou, 412007 Hunan China
| | - Lihua Peng
- grid.501248.aDepartment of Otolaryngology Head and Neck Surgery, Zhuzhou Central Hospital, Zhuzhou, 412007 Hunan China
| | - Dujuan Zhou
- grid.501248.aDepartment of Teaching, Zhuzhou Central Hospital, Zhuzhou, 412007 Hunan China
| | - NianXi Tan
- Department of Cardiothoracic Vascular Surgery, Zhuzhou Central Hospital, Zhuzhou, 412007, Hunan, China.
| | - GenYi Qu
- Department of Urology, Zhuzhou Central Hospital, Zhuzhou, 412007, China.
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Polyphenols: a route from bioavailability to bioactivity addressing potential health benefits to tackle human chronic diseases. Arch Toxicol 2023; 97:3-38. [PMID: 36260104 DOI: 10.1007/s00204-022-03391-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/26/2022] [Indexed: 02/07/2023]
Abstract
Chronic pathologies or non-communicable diseases (NCDs) include cardiovascular diseases, metabolic syndrome, neurological diseases, respiratory disorders and cancer. They are the leading global cause of human mortality and morbidity. Given their chronic nature, NCDs represent a growing social and economic burden, hence urging the need for ameliorating the existing preventive strategies, and for finding novel tackling therapies. NCDs are highly correlated with unhealthy lifestyle habits (such as high-fat and high-glucose diet, or sedentary life). In general, lifestyle approaches that might improve these habits, including dietary consumption of fresh vegetables, fruits and fibers, may contrast NCD symptoms and prolong life expectancy of affected people. Polyphenols (PPLs) are plant-derived molecules with demonstrated biological activities in humans, which include: radical scavenging and anti-oxidant activities, capability to modulate inflammation, as well as human enzymes, and even to bind nuclear receptors. For these reasons, PPLs are currently tested, both preclinically and clinically, as dietary adjuvants for the prevention and treatment of NCDs. In this review, we describe the human metabolism and bioactivity of PPLs. Also, we report what is currently known about PPLs interaction with gastro-intestinal enzymes and gut microbiota, which allows their biotransformation in many different metabolites with several biological functions. The systemic bioactivity of PPLs and the newly available PPL-delivery nanosystems are also described in detail. Finally, the up-to-date clinical studies assessing both safety and efficacy of dietary PPLs in individuals with different NCDs are hereby reported. Overall, the clinical results support the notion that PPLs from fruits, vegetables, but also from leaves or seeds extracts, are safe and show significant positive results in ameliorating symptoms and improving the whole quality of life of people with NCDs.
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Insights on Ferroptosis and Colorectal Cancer: Progress and Updates. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010243. [PMID: 36615434 PMCID: PMC9821926 DOI: 10.3390/molecules28010243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/25/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022]
Abstract
Patients with advanced-stage or treatment-resistant colorectal cancer (CRC) benefit less from traditional therapies; hence, new therapeutic strategies may help improve the treatment response and prognosis of these patients. Ferroptosis is an iron-dependent type of regulated cell death characterized by the accumulation of lipid reactive oxygen species (ROS), distinct from other types of regulated cell death. CRC cells, especially those with drug-resistant properties, are characterized by high iron levels and ROS. This indicates that the induction of ferroptosis in these cells may become a new therapeutic approach for CRC, particularly for eradicating CRC resistant to traditional therapies. Recent studies have demonstrated the mechanisms and pathways that trigger or inhibit ferroptosis in CRC, and many regulatory molecules and pathways have been identified. Here, we review the current research progress on the mechanism of ferroptosis, new molecules that mediate ferroptosis, including coding and non-coding RNA; novel inducers and inhibitors of ferroptosis, which are mainly small-molecule compounds; and newly designed nanoparticles that increase the sensitivity of cells to ferroptosis. Finally, the gene signatures and clusters that have predictive value on CRC are summarized.
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Liu B, Pang K, Feng C, Liu Z, Li C, Zhang H, Liu P, Li Z, He S, Tu C. Comprehensive analysis of a novel cuproptosis-related lncRNA signature associated with prognosis and tumor matrix features to predict immunotherapy in soft tissue carcinoma. Front Genet 2022; 13:1063057. [PMID: 36568384 PMCID: PMC9768346 DOI: 10.3389/fgene.2022.1063057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
Background: A crucial part of the malignant processes of soft tissue sarcoma (STS) is played by cuproptosis and lncRNAs. However, the connection between cuproptosis-related lncRNAs (CRLs) and STS is nevertheless unclear. As a result, our objective was to look into the immunological activity, clinical significance, and predictive accuracy of CRLs in STS. Methods: The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases, respectively, provided information on the expression patterns of STS patients and the general population. Cuproptosis-related lncRNA signature (CRLncSig) construction involved the univariate, multivariate, and least absolute shrinkage and selection operator Cox regression analysis. The predictive performance of the CRLncSig was evaluated using a serial analysis. Further research was done on the connections between the CRLncSig and the tumor immune milieu, somatic mutation, immunotherapy response, and chemotherapeutic drug susceptibility. Notably, an in vitro investigation served to finally validate the expression of the hallmark CRLs. Results: A novel efficient CRLncSig composed of seven CRLs was successfully constructed. Additionally, the low-CRLncSig group's prognosis was better than that of the high-CRLncSig group's based on the new CRLncSig. The innovative CRLncSig then demonstrated outstanding, consistent, and independent prognostic and predictive usefulness for patients with STS, according to the evaluation and validation data. The low-CRLncSig group's patients also displayed improved immunoreactivity phenotype, increased immune infiltration abundance and checkpoint expression, and superior immunotherapy response, whereas those in the high-CRLncSig group with worse immune status, increased tumor stemness, and higher collagen levels in the extracellular matrix. Additionally, there is a noticeable disparity in the sensitivity of widely used anti-cancer drugs amongst various populations. What's more, the nomogram constructed based on CRLncSig and clinical characteristics of patients also showed good predictive ability. Importantly, Real-Time Quantitative Polymerase Chain Reaction (RT-qPCR) demonstrated that the signature CRLs exhibited a significantly differential expression level in STS cell lines. Conclusion: In summary, this study revealed the novel CRLncSig could be used as a promising predictor for prognosis prediction, immune activity, tumor immune microenvironment, immune response, and chemotherapeutic drug susceptibility in patients with STS. This may provide an important direction for the clinical decision-making and personalized therapy of STS.
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Affiliation(s)
- Binfeng Liu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ke Pang
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Chengyao Feng
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhongyue Liu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Chenbei Li
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Haixia Zhang
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ping Liu
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhihong Li
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Shasha He
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,*Correspondence: Shasha He, ; Chao Tu,
| | - Chao Tu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,*Correspondence: Shasha He, ; Chao Tu,
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Sun M, Ji X, Xie M, Chen X, Zhang B, Luo X, Feng Y, Liu D, Wang Y, Li Y, Liu B, Xia L, Huang W. Identification of necroptosis-related subtypes, development of a novel signature, and characterization of immune infiltration in colorectal cancer. Front Immunol 2022; 13:999084. [PMID: 36544770 PMCID: PMC9762424 DOI: 10.3389/fimmu.2022.999084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction Necroptosis, a type of programmed cell death, has recently been extensively studied as an important pathway regulating tumor development, metastasis, and immunity. However, the expression patterns of necroptosis-related genes (NRGs) in colorectal cancer (CRC) and their potential roles in the tumor microenvironment (TME) have not been elucidated. Methods We explored the expression patterns of NRGs in 1247 colorectal cancer samples from genetics and transcriptional perspective. Based on a consensus clustering algorithm, we identified NRG molecular subtypes and gene subtypes, respectively. Furthermore, we constructed a necroptosis-related signature for predicting overall survival time and verified the predictive ability of the model. Using the ESTIMATE, CIBERSORT, and ssGSEA algorithms, we assessed the association between the above subtypes, scores and immune infiltration. Results Most NRGs were differentially expressed between CRC tissues and normal tissues. We found that distinct subtypes exhibited different NRGs expression, patients' prognosis, immune checkpoint gene expression, and immune infiltration characteristics. The scores calculated from the necroptosis-related signature can be used to classify patients into high-risk and low-risk groups, with the high-risk group corresponding to reduced immune cell infiltration and immune function, and a greater risk of immune dysfunction and immune escape. Discussion Our comprehensive analysis of NRGs in CRC demonstrated their potential role in clinicopathological features, prognosis, and immune infiltration in the TME. These findings help us deepen our understanding of NRGs and the tumor microenvironment landscape, and lay a foundation for effectively assessing patient outcomes and promoting more effective immunotherapy.
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Affiliation(s)
- Mengyu Sun
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoyu Ji
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Meng Xie
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoping Chen
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, China
- Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, China
| | - Bixiang Zhang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, China
- Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, China
| | - Xiangyuan Luo
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yangyang Feng
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Danfei Liu
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yijun Wang
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yiwei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Bifeng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Limin Xia
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wenjie Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, China
- Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, China
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Cui J, Guo F, Yu Y, Ma Z, Hong Y, Su J, Ge Y. Development and validation of a prognostic 9-gene signature for colorectal cancer. Front Oncol 2022; 12:1009698. [DOI: 10.3389/fonc.2022.1009698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/01/2022] [Indexed: 11/19/2022] Open
Abstract
IntroductionColorectal cancer (CRC) is one of the most prevalent cancers globally with a high mortality rate. Predicting prognosis using disease progression and cancer pathologic stage is insufficient, and a prognostic factor that can accurately evaluate patient prognosis needs to be developed. In this study, we aimed to infer a prognostic gene signature to identify a functional signature associated with the prognosis of CRC patients.MethodsFirst, we used univariate Cox regression, least absolute shrinkage and selection operator (lasso) regression, and multivariate Cox regression analyses to screen genes significantly associated with CRC patient prognosis, from colorectal cancer RNA sequencing data in The Cancer Genome Atlas (TCGA) database. We then calculated the risk score (RS) for each patient based on the expression of the nine candidate genes and developed a prognostic signature.ResultsBased on the optimal cut-off on the receiver operating characteristic (ROC) curve, patients were separated into high- and low-risk groups, and the difference in overall survival between the two groups was examined. Patients in the low-risk group had a better overall survival rate than those in the high-risk group. The results were validated using the GSE72970, GSE39582, and GSE17536 Gene Expression Omnibus (GEO) datasets, and the same conclusions were reached. ROC curve test of the RS signature also indicated that it had excellent accuracy. The RS signature was then compared with traditional clinical factors as a prognostic indicator, and we discovered that the RS signature had superior predictive ability.ConclusionThe RS signature developed in this study has excellent predictive power for the prognosis of patients with CRC and broad applicability as a prognostic indicator for patients.
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Xu R, Wu X, Du A, Zhao Q, Huang H. Identification of cuproptosis-related long non-coding ribonucleic acid signature as a novel prognosis model for colon cancer. Am J Cancer Res 2022; 12:5241-5254. [PMID: 36504883 PMCID: PMC9729908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/12/2022] [Indexed: 12/15/2022] Open
Abstract
Cuproptosis is a novel type of cell death that may play a vital role in preventing various types of cancer. Studies examining cuproptosis are limited, and the cuproptosis-related lncRNAs (long non-Coding ribonucleic acids) involved in the regulation of colon cancer remain unclear. This study aimed to identify the prognostic signature of cupronosis-related lncRNAs and explore their potential molecular functions in colon cancer. Data on the clinical correlation were obtained from The Cancer Genome Atlas (TCGA) database. The differentially expressed cuproptosis-related long non-coding ribonucleic acids (lncRNAs) were analyzed using the "limma" package. Then, the prognostic cuproptosis-related lncRNA signature (CupRLSig) was identified through univariate Cox and co-expression analyses, and a prognostic model was constructed based on CupRLSig using the least absolute shrinkage selection operator (LASSO) algorithm and Cox regression analysis. The Kaplan-Meier survival curve and receiver operating characteristic (ROC) curve were used for evaluating the model's capacity for prognosis prediction. In addition, the immune landscape, and drug sensitivity of CupRLSig were analyzed. Finally, the functions of AL512306.3 and ZEB1-AS1 were verified through in vitro experiments. The high- or low-risk groups were classified according to the risk score. The signature-based risk score showed a stronger ability to predict patient's survival compared with the traditional clinicopathological features. In addition, immune responses, such as inflammation-promoting response and T-cell co-inhibition, were significantly different between the two groups. Moreover, chemotherapy drugs or inhibitors, such as axitinib, cisplatin, doxorubicin, and elesclomol, may be considered as potential therapeutic drugs for patients in high-risk groups. Finally, inhibition of AL512306.3 and ZEB1-AS1 significantly suppressed the cell proliferation in colon cancer cells. These results provide novel insights into the pathogenesis of colon cancer and offer promising biomarkers with the potential to guide research on carcinogenesis and cancer treatment.
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Affiliation(s)
- Rong Xu
- NHC Key Laboratory of Carcinogenesis, Cancer Research Institute and School of Basic Medicine, Central South UniversityChangsha 410078, Hunan, China,Department of Histology and Embryology, Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
| | - Xin Wu
- Department of Orthopedics, The Third Xiangya Hospital, Central South UniversityChangsha 410013, Hunan, China
| | - Ashuai Du
- Department of Cell Biology, School of Life Sciences, Central South UniversityChangsha 410013, Hunan, China
| | - Qiangqiang Zhao
- Department of Hematology, The Qinghai Provincial People’s HospitalXining 810007, Qinghai, China
| | - He Huang
- NHC Key Laboratory of Carcinogenesis, Cancer Research Institute and School of Basic Medicine, Central South UniversityChangsha 410078, Hunan, China,Department of Histology and Embryology, Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
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Li Z, Yu J, Lv C, Luo Z. Cancer-associated fibroblasts-derived lncRNA signature as a putative biomarker in breast cancer. Front Oncol 2022; 12:1028664. [PMID: 36408190 PMCID: PMC9667072 DOI: 10.3389/fonc.2022.1028664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/18/2022] [Indexed: 01/25/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have been reported to play a key role in regulating tumor microenvironment and immunity. Cancer-associated fibroblasts (CAFs) are abundant in many tumors. However, the functional and clinical significance of lncRNAs specifically expressed in CAFs has not been fully elucidated. In this study, we identified a list of 95 CAF-specific lncRNAs (FibLnc), including HHLA3, TP53TG1, ST7-AS1, LINC00536, ZNF503-AS1, MIR22HG, and MAPT-AS1, based on immune cell transcriptome expression profiling data. Based on the Cancer Genome Atlas and Gene Expression Omnibus datasets, we found that the FibLnc score predicted differences in overall patient survival and performed well in multiple datasets. FibLnc score was associated with the clinical stage of patients with breast cancer but did not significantly correlate with the PAM50 classification. Functional analysis showed that FibLnc was positively correlated with signaling pathways associated with malignant tumor progression. In addition, FibLnc was positively correlated with tumor mutational load and could predict immunotherapy response in patients with breast cancer receiving anti-PD-1 or anti-CTLA4 therapy. Our proposed FibLnc score was able to reflect the status of the immune environment and immunotherapeutic response in breast cancer, which could help explore potential therapeutic decisions and regulatory mechanisms of CAF-specific lncRNAs.
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The Role of Ferroptosis-Related Molecules and Significance of Ferroptosis Score in Cervical Cancer. JOURNAL OF ONCOLOGY 2022; 2022:7835698. [PMID: 36349201 PMCID: PMC9637471 DOI: 10.1155/2022/7835698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/15/2022] [Indexed: 11/23/2022]
Abstract
Background Ferroptosis, a form of cell death driven by iron-dependent lipid peroxidation, may be a potential treatment for many cancers, including cervical cancer (CC). However, the regulation of long noncoding RNAs (lncRNAs) in the process of ferroptosis and whether ferroptosis inducers could increase the cytotoxicity of conventional chemotherapy drugs remain to be further elucidated. Methods We analyzed the variation of 55 differentially ferroptosis-related genes (FRGs) and the influence of mutations in CC patients. The patients with CC were classified into two ferroptosis clusters by the non-negative matrix factorization (NMF) algorithm. The principal components analysis (PCA) was used to measure the ferroptosis score (FerroScore) in patients with CC. Besides, FerroScore was used to predict the sensitivity of chemotherapy and responses to immunotherapy in patients with CC. Finally, experiments were performed to verify the regulatory effect of AC026790.1 on erastin-induced ferroptosis, as well as the effect of erastin in combination with cisplatin on the toxicity of CC cells (SiHa, HeLa). Result There were significant differences in the overall survival and immune cell infiltration between the two ferroptosis clusters. Patients with low FerroScore were more sensitive to chemotherapy drugs such as cisplatin and docetaxel. The low-FerroScore group had higher CD8+ T cell infiltration and immune checkpoint expression, demonstrating that patients with lower FerroScores were more sensitive to immunotherapy, which was consistent with the result of the submap method. In vitro, overexpression of AC026790.1 could promote erastin-induced ferroptosis, and the combination of erastin and cisplatin could increase the toxicity of CC cells. Conclusion FerroScore has a potential prognostic value for CC that may provide a reference for chemotherapy and immunotherapy. LncRNA AC026790.1 can influence ferroptosis, and the combination of ferroptosis inducers and chemotherapy drugs can provide a new perspective on cancer treatment.
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Zhou N, Yuan X, Du Q, Zhang Z, Shi X, Bao J, Ning Y, Peng L. FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations. Nucleic Acids Res 2022; 51:D571-D582. [PMID: 36305834 PMCID: PMC9825716 DOI: 10.1093/nar/gkac935] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/16/2022] [Accepted: 10/27/2022] [Indexed: 01/29/2023] Open
Abstract
Ferroptosis is a mode of regulated cell death characterized by iron-dependent accumulation of lipid peroxidation. It is closely linked to the pathophysiological processes in many diseases. Since our publication of the first ferroptosis database in 2020 (FerrDb V1), many new findings have been published. To keep up with the rapid progress in ferroptosis research and to provide timely and high-quality data, here we present the successor, FerrDb V2. It contains 1001 ferroptosis regulators and 143 ferroptosis-disease associations manually curated from 3288 articles. Specifically, there are 621 gene regulators, of which 264 are drivers, 238 are suppressors, 9 are markers, and 110 are unclassified genes; and there are 380 substance regulators, with 201 inducers and 179 inhibitors. Compared to FerrDb V1, curated articles increase by >300%, ferroptosis regulators increase by 175%, and ferroptosis-disease associations increase by 50.5%. Circular RNA and pseudogene are novel regulators in FerrDb V2, and the percentage of non-coding RNA increases from 7.3% to 13.6%. External gene-related data were integrated, enabling thought-provoking and gene-oriented analysis in FerrDb V2. In conclusion, FerrDb V2 will help to acquire deeper insights into ferroptosis. FerrDb V2 is freely accessible at http://www.zhounan.org/ferrdb/.
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Affiliation(s)
| | | | | | - Zhiyu Zhang
- College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Xiaolei Shi
- Research Institute, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou 510370, China
| | - Jinku Bao
- Correspondence may also be addressed to Jinku Bao.
| | - Yuping Ning
- Correspondence may also be addressed to Yuping Ning.
| | - Li Peng
- To whom correspondence should be addressed. Tel: +86 20 81332402; Fax: +86 20 81332601;
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