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Cheng X, Yang F, Li Y, Cao Y, Zhang M, JI J, Bai Y, Li Q, Yu Q, Gao D. The crosstalk role of CDKN2A between tumor progression and cuproptosis resistance in colorectal cancer. Aging (Albany NY) 2024; 16:10512-10538. [PMID: 38888512 PMCID: PMC11236303 DOI: 10.18632/aging.205945] [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: 12/05/2023] [Accepted: 04/15/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND Cuproptosis is a type of cell death characterized by excessive copper-lipid reactions in the tricarboxylic acid cycle, resulting in protein toxicity stress and cell death. Although known as a cuproptosis inhibitor through CRISPR-Cas9 screening, the role of cyclin-dependent kinase inhibitor 2A (CDKN2A) in cuproptosis resistance and its connection to tumor development remains unclear. METHODS In this study, we combined single-cell sequencing, spatial transcriptomics, pathological image analysis, TCGA multi-omics analysis and in vitro experimental validation to comprehensively investigate CDKN2A distribution, expression, epigenetic modification, regulation and genomic features in colorectal cancer cells. We further explored the associations between CDKN2A and cellular pathway, immune infiltration and spatial signal communication. RESULTS Our findings showed an increasing trend in cuproptosis in the trajectory of tumor progression, accompanied by an upward trend of CDKN2A. CDKN2A underwent transcriptional activation by MEF2D and via the SNHG7/miR-133b axis, upregulating glycolysis, copper metabolism and copper ion efflux. CDKN2A likely drives epithelial-mesenchymal transition (EMT) and progression by activating Wnt signaling. CDKN2A is associated with high genomic instability and sensitivity to radiation and chemotherapy. Tumor regions expressing CDKN2A exhibit distinctive SPP1+ tumor-associated macrophage (TAM) infiltration and MMP7 enrichment, along with unique signaling crosstalk with adjacent areas. CONCLUSIONS CDKN2A mediates cuproptosis resistance through regulating glycolysis and copper homeostasis, accompanied by a malignant phenotype and pro-tumor niche. Radiation and chemotherapy are expected to potentially serve as therapeutic approaches for cuproptosis-resistant colorectal cancer with high CDKN2A expression.
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Affiliation(s)
- Xifu Cheng
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- School of Ophthalmology and Optometry, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Famin Yang
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Yuanheng Li
- Queen Mary School, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
- Department of Gastroenterology and Hepatology, Shenzhen Hospital of Southern Medical University, Shenzhen 518000, China
| | - Yuke Cao
- School of Ophthalmology and Optometry, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Meng Zhang
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Jiameng JI
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Yuxiao Bai
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Qing Li
- Department of Oncology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Qiongfang Yu
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Dian Gao
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
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Yu S, Tang L, Zhang Q, Li W, Yao S, Cai Y, Cheng H. A cuproptosis-related lncRNA signature for predicting prognosis and immunotherapy response of lung adenocarcinoma. Hereditas 2023; 160:31. [PMID: 37482612 PMCID: PMC10364405 DOI: 10.1186/s41065-023-00293-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 07/10/2023] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND Copper-induced cell death (cuproptosis) is a new regulatory cell death mechanism. Long noncoding RNAs (lncRNAs) are related to tumor immunity and metastasis. However, the correlation of cuproptosis-related lncRNAs with the immunotherapy response and prognosis of lung adenocarcinoma (LUAD) patients is not clear. METHODS We obtained the clinical characteristics and transcriptome data from TCGA-LUAD dataset (containing 539 LUAD and 59 paracancerous tissues). By utilizing LASSO-penalized Cox regression analysis, we identified a prognostic signature composed of cuproptosis-related lncRNAs. This signature was then utilized to segregate patients into two different risk categories based on their respective risk scores. The identification of differentially expressed genes (DEGs) between high- and low-risk groups was carried out using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. We evaluated the immunotherapy response by analyzing tumor mutational burden (TMB), immunocyte infiltration and Tumor Immune Dysfunction and Exclusion (TIDE) web application. The "pRRophetic" R package was utilized to conduct further screening of potential therapeutic drugs for their sensitivity. RESULTS We ultimately identified a prognostic risk signature that includes six cuproptosis-related lncRNAs (AP003778.1, AC011611.2, CRNDE, AL162632.3, LY86-AS1, and AC090948.1). Compared with clinical characteristics, the signature was significantly correlated with prognosis following the control of confounding variables (HR = 2.287, 95% CI = 1.648-3.174, p ˂ 0.001), and correctly predicted 1-, 2-, and 3-year overall survival (OS) rates (AUC value = 0.725, 0.715, and 0.662, respectively) in LUAD patients. In terms of prognosis, patients categorized as low risk exhibited more positive results in comparison to those in the high-risk group. The enrichment analysis showed that the two groups had different immune signaling pathways. Immunotherapy may offer a more appropriate treatment option for high-risk patients due to their higher TMB and lower TIDE scores. The higher risk score may demonstrate increased sensitivity to bexarotene, cisplatin, epothilone B, and vinorelbine. CONCLUSIONS Based on cuproptosis-related lncRNAs, we constructed and validated a novel risk signature that may be used to predict immunotherapy efficacy and prognosis in LUAD patients.
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Affiliation(s)
- Sheng Yu
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, 678 Furong Road, Hefei, Anhui, 230601, China
- Shenzhen Clinical Medical School, Southern Medical University, Shenzhen, Guangdong, China
- Department of Oncology, Shenzhen Hospital of Southern Medical University, Shenzhen, China
| | - Lingxue Tang
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, 678 Furong Road, Hefei, Anhui, 230601, China
| | - Qianqian Zhang
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, 678 Furong Road, Hefei, Anhui, 230601, China
| | - Wen Li
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, 678 Furong Road, Hefei, Anhui, 230601, China
| | - Senbang Yao
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, 678 Furong Road, Hefei, Anhui, 230601, China
| | - Yinlian Cai
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, 678 Furong Road, Hefei, Anhui, 230601, China
| | - Huaidong Cheng
- Shenzhen Clinical Medical School, Southern Medical University, Shenzhen, Guangdong, China.
- Department of Oncology, Shenzhen Hospital of Southern Medical University, Shenzhen, China.
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Wu Y, Montrose L, Kochmanski JK, Dolinoy DC, Téllez-Rojo MM, Cantoral A, Mercado-García A, Peterson KE, Goodrich JM. Is adiposity related to repeat measures of blood leukocyte DNA methylation across childhood and adolescence? Clin Obes 2023; 13:e12566. [PMID: 36416295 PMCID: PMC9991944 DOI: 10.1111/cob.12566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 11/24/2022]
Abstract
Epigenetic modifications such as DNA methylation may influence gene expression and phenotypes, including obesity in childhood. The directionality of this relationship is nevertheless unclear, and some evidence suggests that adiposity modifies the epigenome, rather than the other way around. In this pilot study, we utilize data from the Early Life Exposures in Mexico to Environmental Toxicants (ELEMENT) study to examine whether measures of adiposity in childhood and early adolescence are associated with repeated measures of blood leukocyte DNA methylation at LINE-1 repetitive elements and two genes implicated in growth and adiposity: H19 and HSD11B2. Longitudinal epigenetic data were generated from cord blood and blood from follow-up visits in early and late adolescence. We assessed interactions between age and measures of body mass index (BMI) at 5 years of age and weight, BMI and waist circumference in early adolescence to infer whether adiposity deflects age-related DNA methylation changes throughout childhood. Applying linear mixed-effects models, we found an inverse association between measures of childhood BMI (kg/m2 ) and early-teen weight (kg) with repeat measures of H19 DNA methylation. We did not observe any statistically significant associations (p-value <.05) between any anthropometric measures and DNA methylation at LINE-1 or HSD11B2. We did not demonstrate statistically significant evidence in support of deflection of age-related DNA methylation trajectories by adiposity-related measures (age by adiposity interaction term). Given the pilot nature of this study, the relationships between repeat measures of DNA methylation and adiposity-measures across childhood merit further exploration in larger study populations.
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Affiliation(s)
- Yue Wu
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, CN
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Luke Montrose
- Department of Community and Environmental Health, Boise State University, Boise, ID, USA
| | - Joseph K. Kochmanski
- Department of Translational Neuroscience, Michigan State University, Grand Rapids, MI, USA
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Martha M Téllez-Rojo
- Center for Nutrition and Health Research, National Institute of Public Health, Cuernavaca, Morelos, MX
| | | | - Adriana Mercado-García
- Center for Nutrition and Health Research, National Institute of Public Health, Cuernavaca, Morelos, MX
| | - Karen E. Peterson
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
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Ren L, Yang X, Wang W, Lin H, Huang G, Liu Z, Pan J, Mao X. A cuproptosis-related LncRNA signature: Integrated analysis associated with biochemical recurrence and immune landscape in prostate cancer. Front Genet 2023; 14:1096783. [PMID: 36911392 PMCID: PMC9999016 DOI: 10.3389/fgene.2023.1096783] [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: 11/12/2022] [Accepted: 02/10/2023] [Indexed: 03/14/2023] Open
Abstract
Background: As a new form of regulated cell death, cuproptosis differs profoundly from apoptosis, ferroptosis, pyroptosis, and necroptosis. The correlation between cuproptosis and long non-coding RNAs (lncRNAs) has been increasingly studied recently. In this study, a novel cuproptosis-related lncRNA prognostic signature was developed to investigate biochemical recurrence (BCR) and tumor immune landscape in prostate cancer (PCa). Methods and Materials: The transcriptome data and clinicopathologic information of PCa patients were downloaded from The Cancer Genome Atlas (TCGA). Pearson's correlation analysis was applied to identify lncRNAs associated with cuproptosis. Based on Cox regression analysis and the least absolute shrinkage and selection operator (LASSO) regression analysis, we developed a cuproptosis-related lncRNA prognostic model (risk score) to predict the BCR of PCa patients. Additionally, we also constructed a nomogram with the risk score and clinicopathologic features. The biological function, tumor mutation burden (TMB), immune cell infiltration, expression levels of immune checkpoint genes, and anti-cancer drug sensitivity were investigated. Results: We constructed and validated the cuproptosis-related lncRNA signature prognostic model (risk score) by six crlncRNAs. All patients were divided into the low- and high-risk groups based on the median risk score. The Kaplan-Meier (KM) survival analysis revealed that the high-risk group had shorter BCR-free survival (BCRFS). The risk score has been proven to be an independent prognostic factor of BCR in PCa patients. In addition, a nomogram of risk scores and clinicopathologic features was established and demonstrated an excellent predictive capability of BCR. The ROC curves further validated that this nomogram had higher accuracy of predicting the BCR compared to other clinicopathologic features. We also found that the high-risk group had higher TMB levels and more infiltrated immune cells. Furthermore, patients with high TMB in the high-risk group were inclined to have the shortest BCRFS. Finally, patients in the high-risk group were more susceptible to docetaxel, gefitinib, methotrexate, paclitaxel, and vinblastine. Conclusion: The novel crlncRNA signature prognostic model shows a greatly prognostic prediction value of BCR for PCa patients, extends our thought on the association of cuproptosis and PCa, and provides novel insights into individual-based treatment strategies for PCa.
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Affiliation(s)
- Lei Ren
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China
| | - Xu Yang
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China
| | - Weifeng Wang
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China
| | - Hansen Lin
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China
| | - Guankai Huang
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China
| | - Zixiong Liu
- Department of Urology, The Seventh Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jincheng Pan
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China
| | - Xiaopeng Mao
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China
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Zhang G, Sun J, Zhang X. A novel Cuproptosis-related LncRNA signature to predict prognosis in hepatocellular carcinoma. Sci Rep 2022; 12:11325. [PMID: 35790864 PMCID: PMC9256635 DOI: 10.1038/s41598-022-15251-1] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/21/2022] [Indexed: 12/16/2022] Open
Abstract
Increased intracellular toxicity due to an imbalance in copper homeostasis caused by copper ion accumulation could regulate the rate of cancer cell growth and proliferation. The goal of this study was to create a novel Cuproptosis-related lncRNA signature that may be utilized to predict survival and immunotherapy in HCC patients. Cuproptosis-associated lncRNAs and differentially expressed lncRNAs between HCC tumor tissue and normal tissue were discovered first. By LASSO-Cox analysis, the overlapping lncRNAs were then utilized to build a Cuproptosis-associated lncRNA signature, which might be used to predict patient prognosis and responsiveness to immune checkpoint blockade (ICB) therapy. Differences in the infiltration of immune cell subpopulations between high and low-risk score subgroups were also analyzed. Moreover, a nomogram based on the Cuproptosis-associated lncRNA signature and clinical features was developed and demonstrated to have good predictive potential. Finally, qRT-PCR was performed in HerpG2 and MHCC-97H cell lines to explore whether these lncRNAs were indeed involved in the process of Cuproptosis. In summary, we created a prognostic lncRNA profile linked to Cuproptosis to forecast response to immunotherapy, which may provide a new potential non-apoptotic therapeutic perspective for HCC patients.
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Affiliation(s)
- Genhao Zhang
- grid.412633.10000 0004 1799 0733Department of Blood Transfusion, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianping Sun
- Department of Pathology, Zhengzhou YIHE Hospital, Zhengzhou, China
| | - Xianwei Zhang
- Medical School, Huanghe Science and Technology University, Zhengzhou, China.
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