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Modi AD, Zahid H, Southerland AC, Modi DM. Epitranscriptomics and cervical cancer: the emerging role of m 6A, m 5C and m 1A RNA modifications. Expert Rev Mol Med 2024; 26:e20. [PMID: 39377535 DOI: 10.1017/erm.2024.20] [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] [Indexed: 10/09/2024]
Abstract
Cervical cancer (CC), one of the most prevalent and detrimental gynaecologic cancers, evolves through genetic and epigenetic alterations resulting in the promotion of oncogenic activity and dysfunction of tumour-suppressing mechanisms. Despite medical advancement, the prognosis for advanced-stage patients remains extremely low due to high recurrence rates and resistance to existing treatments. Thereby, the search for potential prognostic biomarkers is heightened to unravel new modalities of CC pathogenesis and to develop novel anti-cancer therapies. Epitranscriptomic modifications, reversible epigenetic RNA modifications, regulate various biological processes by deciding RNA fate to mediating RNA interactions. This narrative review provides insight into the cellular and molecular roles of endogenous RNA-editing proteins and their associated epitranscriptomic modifications, especially N6-methyladenosine (m6A), 5-methylcytosine (m5C) and N1-methyladenosine (m1A), in governing the development, progression and metastasis of CC. We discussed the in-depth epitranscriptomic mechanisms underlying the regulation of over 50 RNAs responsible for tumorigenesis, proliferation, migration, invasion, survival, autophagy, stemness, epithelial-mesenchymal transition, metabolism (glucose, lipid, glutamate and glutamine), resistance (drug and radiation), angiogenesis and recurrence of CC. Additionally, we provided a concise overview of the therapeutic potential of targeting the altered expression of endogenous RNA-editing proteins and aberrant deposition of RNA modifications on both coding and non-coding RNAs in CC.
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Affiliation(s)
- Akshat D Modi
- Department of Biological Sciences, University of Toronto, Scarborough, Canada
| | - Hira Zahid
- Department of Biology, University of Toronto, Mississauga, Canada
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Zhang Y, Lin H, Liang L, Jin S, Lv J, Zhou Y, Xu F, Liu F, Feng N. Intratumoral microbiota as a novel prognostic indicator in bladder cancer. Sci Rep 2024; 14:22198. [PMID: 39333148 PMCID: PMC11437234 DOI: 10.1038/s41598-024-72918-7] [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: 06/22/2024] [Accepted: 09/11/2024] [Indexed: 09/29/2024] Open
Abstract
Microbes are important components of the tumor microenvironment and have a close relationship with tumors. However, there is still a lack of research on the intratumoral microbiota in bladder cancer and its impact on the tumor immune microenvironment. In this study, we used fluorescence in situ hybridization (FISH) and observed a substantial presence of microbiota in bladder cancer tissues, with greater abundance compared to that in normal bladder tissues. Based on the BIC database, we found that the microbiome of bladder cancer is highly diverse and its structure is significantly different from that of other tumors. To investigate the relationships among the intratumoral microbiota, tumor immunity, and prognosis in bladder cancer patients, we analyzed bladder cancer-specific differentially expressed immune- and antimicrobial-related genes from the ImmPort, TISIDB, and TCGA databases. We identified 11 hub genes and constructed a prognostic risk model. Further analysis revealed differences at the family and genus levels between distinct groups. Using LEfSe analysis, we identified six hub biomarkers and developed a novel microbial-based scoring system. The scoring system allows subgrouping of bladder cancer patients, with significant differences in prognosis, immune cell infiltration, tumor mutation burden, and immune checkpoints among different groups. Further FISH and immunofluorescence co-staining experiments initially verified that the specific distribution of microorganisms and M2 macrophages in bladder cancer may be closely related to the poor prognosis of patients. In conclusion, this study revealed the characteristics of the intratumoral microbiota in bladder cancer and identified potential prognostic targets for clinical application.
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Affiliation(s)
- Yuwei Zhang
- Medical School of Nantong University, 9 Qiangyuan Road, Nantong, 226019, China
- Department of Urology, Jiangnan University Medical Center, No. 1800, Lihu Avenue, Wuxi, 214122, China
| | - Hao Lin
- Department of Urology, Jiangnan University Medical Center, No. 1800, Lihu Avenue, Wuxi, 214122, China
- Department of Urology, Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, China
| | - Linghui Liang
- Department of Urology, Jiangnan University Medical Center, No. 1800, Lihu Avenue, Wuxi, 214122, China
- Department of Urology, Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, China
| | - Shengkai Jin
- Department of Urology, Jiangnan University Medical Center, No. 1800, Lihu Avenue, Wuxi, 214122, China
| | - Jing Lv
- Department of Urology, Jiangnan University Medical Center, No. 1800, Lihu Avenue, Wuxi, 214122, China
| | - Yuhua Zhou
- Department of Urology, Jiangnan University Medical Center, No. 1800, Lihu Avenue, Wuxi, 214122, China
| | - Feng Xu
- Department of Urology, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, 22 Hankou Road, Nanjing, 210093, China.
| | - Fengping Liu
- Department of Urology, Jiangnan University Medical Center, No. 1800, Lihu Avenue, Wuxi, 214122, China.
| | - Ninghan Feng
- Medical School of Nantong University, 9 Qiangyuan Road, Nantong, 226019, China.
- Department of Urology, Jiangnan University Medical Center, No. 1800, Lihu Avenue, Wuxi, 214122, China.
- Department of Urology, Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, China.
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Xu W, Sang S, Wang J, Guo S, Zhang X, Zhou H, Chen Y. Identification of telomere-related lncRNAs and immunological analysis in ovarian cancer. Front Immunol 2024; 15:1452946. [PMID: 39355254 PMCID: PMC11442270 DOI: 10.3389/fimmu.2024.1452946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 08/26/2024] [Indexed: 10/03/2024] Open
Abstract
Background Ovarian cancer (OC) is a global malignancy characterized by metastatic invasiveness and recurrence. Long non-coding RNAs (lncRNAs) and Telomeres are closely connected with several cancers, but their potential as practical prognostic markers in OC is less well-defined. Methods Relevant mRNA and clinical data for OC were sourced from The Cancer Genome Atlas (TCGA) database. The telomere-related lncRNAs (TRLs) prognostic model was established by univariate/LASSO/multivariate regression analyses. The effectiveness of the TRLs model was evaluated and measured via the nomogram. Additionally, immune infiltration, tumor mutational load (TMB), and drug sensitivity were evaluated. We validated the expression levels of prognostic genes. Subsequently, PTPRD-AS1 knockdown was utilized to perform the CCK8 assay, colony formation assay, transwell assay, and wound healing assay of CAOV3 cells. Results A six-TRLs prognostic model (PTPRD-AS1, SPAG5-AS1, CHRM3-AS2, AC074286.1, FAM27E3, and AC018647.3) was established, which can effectively predict patient survival rates and was successfully validated using external datasets. According to the nomogram, the model could effectively predict prognosis. Furthermore, we detected the levels of regulatory T cells and M2 macrophages were comparatively higher in the high-risk TRLs group, but the levels of activated CD8 T cells and monocytes were the opposite. Finally, the low-risk group was more sensitive to anti-cancer drugs. The mRNA levels of PTPRD-AS1, SPAG5-AS1, FAM27E3, and AC018647.3 were significantly over-expressed in OC cell lines (SKOV3, A2780, CAOV3) in comparison to normal IOSE-80 cells. AC074286.1 were over-expressed in A2780 and CAOV3 cells and CHRM3-AS2 only in A2780 cells. PTPRD-AS1 knockdown decreased the proliferation, cloning, and migration of CAOV3 cells. Conclusion Our study identified potential biomarkers for the six-TRLs model related to the prognosis of OC.
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Affiliation(s)
- Weina Xu
- Department of TCM, Zhoujiadu Community Health Service of Shanghai Pudong New Area, Shanghai, China
| | - Shuliu Sang
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jun Wang
- Department of TCM, Zhoujiadu Community Health Service of Shanghai Pudong New Area, Shanghai, China
| | - Shanshan Guo
- Department of Gynecology, Longhua Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiao Zhang
- Department of Gynecology, Longhua Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hailun Zhou
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yijia Chen
- Department of Gynecology, Longhua Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Zhao F, Hong J, Zhou G, Huang T, Lin Z, Zhang Y, Liang L, Tang H. Elucidating the role of tumor-associated ALOX5+ mast cells with transformative function in cervical cancer progression via single-cell RNA sequencing. Front Immunol 2024; 15:1434450. [PMID: 39224598 PMCID: PMC11366577 DOI: 10.3389/fimmu.2024.1434450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 07/24/2024] [Indexed: 09/04/2024] Open
Abstract
Background Cervical cancer (CC) is the fourth most common malignancy among women globally and serves as the main cause of cancer-related deaths among women in developing countries. The early symptoms of CC are often not apparent, with diagnoses typically made at advanced stages, which lead to poor clinical prognoses. In recent years, numerous studies have shown that there is a close relationship between mast cells (MCs) and tumor development. However, research on the role MCs played in CC is still very limited at that time. Thus, the study conducted a single-cell multi-omics analysis on human CC cells, aiming to explore the mechanisms by which MCs interact with the tumor microenvironment in CC. The goal was to provide a scientific basis for the prevention, diagnosis, and treatment of CC, with the hope of improving patients' prognoses and quality of life. Method The present study acquired single-cell RNA sequencing data from ten CC tumor samples in the ArrayExpress database. Slingshot and AUCcell were utilized to infer and assess the differentiation trajectory and cell plasticity of MCs subpopulations. Differential expression analysis of MCs subpopulations in CC was performed, employing Gene Ontology, gene set enrichment analysis, and gene set variation analysis. CellChat software package was applied to predict cell communication between MCs subpopulations and CC cells. Cellular functional experiments validated the functionality of TNFRSF12A in HeLa and Caski cell lines. Additionally, a risk scoring model was constructed to evaluate the differences in clinical features, prognosis, immune infiltration, immune checkpoint, and functional enrichment across various risk scores. Copy number variation levels were computed using inference of copy number variations. Result The obtained 93,524 high-quality cells were classified into ten cell types, including T_NK cells, endothelial cells, fibroblasts, smooth muscle cells, epithelial cells, B cells, plasma cells, MCs, neutrophils, and myeloid cells. Furthermore, a total of 1,392 MCs were subdivided into seven subpopulations: C0 CTSG+ MCs, C1 CALR+ MCs, C2 ALOX5+ MCs, C3 ANXA2+ MCs, C4 MGP+ MCs, C5 IL32+ MCs, and C6 ADGRL4+ MCs. Notably, the C2 subpopulation showed close associations with tumor-related MCs, with Slingshot results indicating that C2 subpopulation resided at the intermediate-to-late stage of differentiation, potentially representing a crucial transition point in the benign-to-malignant transformation of CC. CNVscore and bulk analysis results further confirmed the transforming state of the C2 subpopulation. CellChat analysis revealed TNFRSF12A as a key receptor involved in the actions of C2 ALOX5+ MCs. Moreover, in vitro experiments indicated that downregulating the TNFRSF12A gene may partially inhibit the development of CC. Additionally, a prognosis model and immune infiltration analysis based on the marker genes of the C2 subpopulation provided valuable guidance for patient prognosis and clinical intervention strategies. Conclusions We first identified the transformative tumor-associated MCs subpopulation C2 ALOX5+ MCs within CC, which was at a critical stage of tumor differentiation and impacted the progression of CC. In vitro experiments confirmed the inhibitory effect of knocking down the TNFRSF12A gene on the development of CC. The prognostic model constructed based on the C2 ALOX5+MCs subset demonstrated excellent predictive value. These findings offer a fresh perspective for clinical decision-making in CC.
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Affiliation(s)
- Fu Zhao
- Department of Gynecological Radiotherapy, Zhejiang Cancer Hospital, Hangzhou, China
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Junjie Hong
- Department of Gynecological Oncology, Zhejiang Cancer Hospital, Hangzhou, China
| | - Guangyao Zhou
- Department of Lung Cancer, Tianjin Lung Cancer Center, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Tianjiao Huang
- The First School of Clinical Medicine, Heilongjiang University of Traditional Chinese Medicine, Harbin, China
| | - Zhiheng Lin
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yining Zhang
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Hangzhou, China
| | - Leilei Liang
- Department of Gynecological Radiotherapy, Zhejiang Cancer Hospital, Hangzhou, China
| | - Huarong Tang
- Department of Gynecological Radiotherapy, Zhejiang Cancer Hospital, Hangzhou, China
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Qiu Q, Song JR, Zheng XQ, Zheng H, Yi H. The impact of diabetes, hypercholesterolemia, and low-density lipoprotein (LDL) on the survival of cervical cancer patients. Discov Oncol 2024; 15:349. [PMID: 39143292 PMCID: PMC11324628 DOI: 10.1007/s12672-024-01224-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 08/06/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Cervical cancer is a prevalent malignancy and an important health concern worldwide. Recent research has highlighted the potential impact of metabolic factors, such as hyperlipidemia and diabetes, on cancer progression, increased mortality, and patient outcomes. However, insufficient data have been reported regarding their relationship with cervical cancer. This study aimed to investigate the relationships between metabolic disorders, including dyslipidemia, dysglycemia, and metabolic syndrome, and survival in patients with cervical cancer. METHODS We retrospectively analyzed demographic information, clinical characteristics, and metabolic health indicators of patients with cervical cancer. Patients were categorized into groups based on specific metabolic conditions: high triglyceride, high low-density lipoprotein, high cholesterol, and diabetes groups. Additionally, the presence of metabolic syndrome and other metabolic comorbidities was recorded. The log-rank test was used to compare survival rates between different patient groups and identify associated risk factors. Survival curves generated via the Cox proportional hazards model were used to evaluate the associations between metabolic parameters and survival. RESULTS The Cox proportional hazards model was used to analyze data from 840 patients with cervical cancer between 28 and 72 years old who underwent surgery. The hazard ratio (HR) of mortality was 1.804 (95% CI 1.394-2.333, p < 0.001) in the high-density lipoprotein group, 0.758 (95% CI 0.558 to 1.030, p < 0.001) in the high-triglyceride group, 1.794 (95% CI 1.304-2.470, p < 0.001) in the high low-density lipoprotein group, and 0.011 (95% CI 0.005-0.025, p < 0.001) in the diabetes group. These factors were significantly associated with reduced survival in patients with cervical cancer, and these associations persisted after adjusting for age, cancer stage, treatment type, and the presence of metabolic syndrome or other comorbidities. CONCLUSION This study highlights the importance of metabolic health and the significance of controlling metabolic disorders, including hyperlipidemia, diabetes, and metabolic syndrome, to improve survival outcomes in patients with cervical cancer. Future research should explore the impact of managing multiple metabolic conditions on the prognosis of these patients.
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Affiliation(s)
- Qian Qiu
- Department of Gynecological Oncology, Fujian Provincial Maternity and Children's Hospital, Fuzhou, Fujian, China
| | - Jian Rong Song
- Department of Gynecological Oncology, Fujian Provincial Maternity and Children's Hospital, Fuzhou, Fujian, China
| | - Xiang Qin Zheng
- Department of Gynecological Oncology, Fujian Provincial Maternity and Children's Hospital, Fuzhou, Fujian, China
| | - Hui Zheng
- Department of Gynecological Oncology, Fujian Provincial Maternity and Children's Hospital, Fuzhou, Fujian, China
| | - Huan Yi
- Department of Gynecological Oncology, Fujian Provincial Maternity and Children's Hospital, Fuzhou, Fujian, China.
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Feng K, Zhou S, Sheng Y, Lu K, Li C, Liu W, Kong H, Liu H, Mu Y, Zhang L, Zhang Q, Wang J. Disulfidptosis-Related LncRNA Signatures for Prognostic Prediction in Kidney Renal Clear Cell Carcinoma. Clin Genitourin Cancer 2024; 22:102095. [PMID: 38833825 DOI: 10.1016/j.clgc.2024.102095] [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: 02/16/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 06/06/2024]
Abstract
INTRODUCTION BACKGROUND Disulfidptosis is a prevalent apoptotic mechanism, intrinsically linked to cancer prognosis. However, the specific involvement of disulfidptosis-related long non-coding RNA (DRLncRNAs) in Kidney renal clear cell carcinoma (KIRC) remains incompletely understood. This study aims to elucidate the potential prognostic significance of disulfidptosis-related LncRNAs in KIRC. MATERIALS AND METHODS Expression profiles and clinical data of KIRC patients were retrieved from the TCGA database to discern differentially expressed DRLncRNAs correlated with overall survival. Cox univariate analysis, Lasso Regression, and Cox multivariate analysis were used to construct a clinical prediction model. RESULTS Six signatures, namely FAM83C.AS1, AC136475.2, AC121338.2, AC026401.3, AC254562.3, and AC000050.2, were established to evaluate overall survival (OS) in the context of Kidney renal clear cell carcinoma (KIRC) in this study. Survival analysis and ROC curves demonstrated the strong predictive performance of the associated signature. The nomogram exhibited accurate prognostic predictions for overall patient survival, offering substantial clinical utility. Gene set enrichment analysis revealed that risk signals were enriched in various immune-related pathways. Furthermore, the risk features exhibited significant correlations with immune cells, immune function, immune cell infiltration, and immune checkpoints. CONCLUSION This study has unveiled, for the first time, six disulfdptosis-related LncRNA signatures, laying a solid foundation for enhanced and precise prognostic predictions in KIRC.
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Affiliation(s)
- Kunlun Feng
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Shanshan Zhou
- Dongying People's Hospital (Dongying Hospital of Shandong Provincial Hospital Group), Dongying, Shandong, China
| | - Yawen Sheng
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Ke Lu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Chenghua Li
- International Office, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Wenhui Liu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Hui Kong
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Haoxiang Liu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Yu Mu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Lu Zhang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China.
| | - Qingxiang Zhang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China.
| | - Jingwen Wang
- The second affiliated hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China.
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Bozgeyik E, Elek A, Gocer Z, Bozgeyik I. The fate and function of non-coding RNAs during necroptosis. Epigenomics 2024; 16:901-915. [PMID: 38884366 PMCID: PMC11370912 DOI: 10.1080/17501911.2024.2354653] [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: 09/14/2023] [Accepted: 05/07/2024] [Indexed: 06/18/2024] Open
Abstract
Necroptosis is a novel form of cell death which is activated when apoptotic cell death signals are disrupted. Accumulating body of observations suggests that noncoding RNAs, which are the lately discovered mystery of the human genome, are significantly associated with necroptotic signaling circuitry. The fate and function of miRNAs have been well documented in human disease, especially cancer. Recently, lncRNAs have gained much attention due to their diverse regulatory functions. Although available studies are currently based on bioinformatic analysis, predicted interactions desires further attention, as these hold significant promise and should not be overlooked. In the light of these, here we comprehensively review and discuss noncoding RNA molecules that play significant roles during execution of necroptotic cell death.
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Affiliation(s)
- Esra Bozgeyik
- Department of Medical Services & Techniques, Vocational School of Health Services, Adiyaman University, Adiyaman, Turkey
| | - Alperen Elek
- Faculty of Medicine, Ege University, Izmir, Turkey
| | - Zekihan Gocer
- Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Ibrahim Bozgeyik
- Department of Medical Biology, Faculty of Medicine, Adiyaman University, Adiyaman, Turkey
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Qin Y, Sheng Y, Ren M, Hou Z, Xiao L, Chen R. Identification of necroptosis-related gene signatures for predicting the prognosis of ovarian cancer. Sci Rep 2024; 14:11133. [PMID: 38750159 PMCID: PMC11096311 DOI: 10.1038/s41598-024-61849-y] [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: 01/10/2024] [Accepted: 05/10/2024] [Indexed: 05/18/2024] Open
Abstract
Ovarian cancer (OC) is one of the most prevalent and fatal malignant tumors of the female reproductive system. Our research aimed to develop a prognostic model to assist inclinical treatment decision-making.Utilizing data from The Cancer Genome Atlas (TCGA) and copy number variation (CNV) data from the University of California Santa Cruz (UCSC) database, we conducted analyses of differentially expressed genes (DEGs), gene function, and tumor microenvironment (TME) scores in various clusters of OC samples.Next, we classified participants into low-risk and high-risk groups based on the median risk score, thereby dividing both the training group and the entire group accordingly. Overall survival (OS) was significantly reduced in the high-risk group, and two independent prognostic factors were identified: age and risk score. Additionally, three genes-C-X-C Motif Chemokine Ligand 10 (CXCL10), RELB, and Caspase-3 (CASP3)-emerged as potential candidates for an independent prognostic signature with acceptable prognostic value. In Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, pathways related to immune responses and inflammatory cell chemotaxis were identified. Cellular experiments further validated the reliability and precision of our findings. In conclusion, necroptosis-related genes play critical roles in tumor immunity, and our model introduces a novel strategy for predicting the prognosis of OC patients.
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Affiliation(s)
- Yuling Qin
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, No. 5, Beixiange Road, Xicheng District, Beijing, 100053, China
| | - Yawen Sheng
- Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, China
| | - Mengxue Ren
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, No. 5, Beixiange Road, Xicheng District, Beijing, 100053, China
| | - Zitong Hou
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, No. 5, Beixiange Road, Xicheng District, Beijing, 100053, China
| | - Lu Xiao
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, No. 5, Beixiange Road, Xicheng District, Beijing, 100053, China
| | - Ruixue Chen
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, No. 5, Beixiange Road, Xicheng District, Beijing, 100053, China.
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Zhu Z, Lu J. Development and assessment of an RNA editing-based risk model for the prognosis of cervical cancer patients. Medicine (Baltimore) 2024; 103:e38116. [PMID: 38728474 PMCID: PMC11081546 DOI: 10.1097/md.0000000000038116] [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: 01/26/2024] [Accepted: 04/12/2024] [Indexed: 05/12/2024] Open
Abstract
RNA editing, as an epigenetic mechanism, exhibits a strong correlation with the occurrence and development of cancers. Nevertheless, few studies have been conducted to investigate the impact of RNA editing on cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC). In order to study the connection between RNA editing and CESC patients' prognoses, we obtained CESC-related information from The Cancer Genome Atlas (TCGA) database and randomly allocated the patients into the training group or testing group. An RNA editing-based risk model for CESC patients was established by Cox regression analysis and least absolute shrinkage and selection operator (LASSO). According to the median score generated by this RNA editing-based risk model, patients were categorized into subgroups with high and low risks. We further constructed the nomogram by risk scores and clinical characteristics and analyzed the impact of RNA editing levels on host gene expression levels and adenosine deaminase acting on RNA. Finally, we also compared the biological functions and pathways of differentially expressed genes (DEGs) between different subgroups by enrichment analysis. In this risk model, we screened out 6 RNA editing sites with significant prognostic value. The constructed nomogram performed well in forecasting patients' prognoses. Furthermore, the level of RNA editing at the prognostic site exhibited a strong correlation with host gene expression. In the high-risk subgroup, we observed multiple biological functions and pathways associated with immune response, cell proliferation, and tumor progression. This study establishes an RNA editing-based risk model that helps forecast patients' prognoses and offers a new understanding of the underlying mechanism of RNA editing in CESC.
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Affiliation(s)
- Zihan Zhu
- Department of Biostatistics, School of Public Health, Nanjing Medical University 101 Longmian Avenue, Nanjing, P.R. China
| | - Jing Lu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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Hu J, Wang S, Li X. A comprehensive review of m 6A research in cervical cancer. Epigenomics 2024; 16:753-773. [PMID: 38639713 PMCID: PMC11318741 DOI: 10.2217/epi-2024-0002] [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: 01/03/2024] [Accepted: 03/27/2024] [Indexed: 04/20/2024] Open
Abstract
Cervical cancer (CC) remains one of the most common malignancies among women worldwide, posing a serious threat to women's health. N6-methyladenosine (m6A) modification, as the most abundant type of RNA methylation modification, and has been found to play a crucial role in various cancers. Current research suggests a close association between RNA m6A modification and the occurrence and progression of CC, encompassing disruptions in m6A levels and its regulatory machinery. This review summarizes the current status of m6A modification research in CC, explores the mechanisms underlying m6A levels and regulators (methyltransferases, demethylases, reader proteins) in CC and examines the application of small-molecule inhibitors of m6A regulators in disease treatment. The findings provide new insights into the future treatment of CC.
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Affiliation(s)
- Jing Hu
- Key Laboratory of Environmental Medicine & Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Shizhi Wang
- Key Laboratory of Environmental Medicine & Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Xiuting Li
- Department of Public Health, Jiangsu Health Vocational College, Nanjing, 210000, China
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Zhu S, Cheng Q, Zou M, Li C, Tang Y, Xia L, Jiang Y, Gong Z, Tang Z, Tang Y, Luo H, Peng N, Wang X, Dong X. Combining bulk and scRNA-seq to explore the molecular mechanisms governing the distinct efferocytosis activities of a macrophage subpopulation in PDAC. J Cell Mol Med 2024; 28:e18266. [PMID: 38501838 PMCID: PMC10949604 DOI: 10.1111/jcmm.18266] [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: 01/22/2024] [Revised: 02/25/2024] [Accepted: 03/11/2024] [Indexed: 03/20/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), a very aggressive tumour, is currently the third leading cause of cancer-related deaths. Unfortunately, many patients face the issue of inoperability at the diagnostic phase leading to a quite dismal prognosis. The onset of metastatic processes has a crucial role in the elevated mortality rates linked to PDAC. Individuals with metastatic advances receive only palliative therapy and have a grim prognosis. It is essential to carefully analyse the intricacies of the metastatic process to enhance the prognosis for individuals with PDAC. Malignancy development is greatly impacted by the process of macrophage efferocytosis. Our current knowledge about the complete range of macrophage efferocytosis activities in PDAC and their intricate interactions with tumour cells is still restricted. This work aims to resolve communication gaps and pinpoint the essential transcription factor that is vital in the immunological response of macrophage populations. We analysed eight PDAC tissue samples sourced from the gene expression omnibus. We utilized several software packages such as Seurat, DoubletFinder, Harmony, Pi, GSVA, CellChat and Monocle from R software together with pySCENIC from Python, to analyse the single-cell RNA sequencing (scRNA-seq) data collected from the PDAC samples. This study involved the analysis of a comprehensive sample of 22,124 cells, which were classified into distinct cell types. These cell types encompassed endothelial and epithelial cells, PDAC cells, as well as various immune cells, including CD4+ T cells, CD8+ T cells, NK cells, B cells, plasma cells, mast cells, monocytes, DC cells and different subtypes of macrophages, namely C0 macrophage TGM2+, C1 macrophage PFN1+, C2 macrophage GAS6+ and C3 macrophage APOC3+. The differentiation between tumour cells and epithelial cells was achieved by the implementation of CopyKat analysis, resulting in the detection and categorization of 1941 PDAC cells. The amplification/deletion patterns observed in PDAC cells on many chromosomes differ significantly from those observed in epithelial cells. The study of Pseudotime Trajectories demonstrated that the C0 macrophage subtype expressing TGM2+ had the lowest level of differentiation. Additionally, the examination of gene set scores related to efferocytosis suggested that this subtype displayed higher activity during the efferocytosis process compared to other subtypes. The most active transcription factors for each macrophage subtype were identified as BACH1, NFE2, TEAD4 and ARID3A. In conclusion, the examination of human PDAC tissue samples using immunofluorescence analysis demonstrated the co-localization of CD68 and CD11b within regions exhibiting the presence of keratin (KRT) and alpha-smooth muscle actin (α-SMA). This observation implies a spatial association between macrophages, fibroblasts, and epithelial cells. There is variation in the expression of efferocytosis-associated genes between C0 macrophage TGM2+ and other macrophage cell types. This observation implies that the diversity of macrophage cells might potentially influence the metastatic advancement of PDAC. Moreover, the central transcription factor of different macrophage subtypes offers a promising opportunity for targeted immunotherapy in the treatment of PDAC.
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Affiliation(s)
- Shaoliang Zhu
- Department of Hepatobiliary, Pancreas and Spleen SurgeryThe People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical SciencesNanningChina
| | - Quan Cheng
- Department of General SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Mengjie Zou
- Department of NephrologyThe People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical SciencesNanningChina
| | - Chunxing Li
- Department of Operating RoomThe People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical SciencesNanningChina
| | - Yi Tang
- Department of Hepatobiliary, Pancreas and Spleen SurgeryThe People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical SciencesNanningChina
| | - Longjie Xia
- Department of Cosmetology and Plastic Surgery CenterThe People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical SciencesNanningChina
| | - Yanming Jiang
- Department of GynecologyThe People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical SciencesNanningChina
| | - Zheng Gong
- Department of AnesthesiologyThe People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical SciencesNanningChina
| | - Zhenyong Tang
- Department of Hepatobiliary, Pancreas and Spleen SurgeryThe People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical SciencesNanningChina
| | - Yuntian Tang
- Department of Hepatobiliary, Pancreas and Spleen SurgeryThe People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical SciencesNanningChina
| | - Honglin Luo
- Institute of Oncology, The People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical SciencesNanningChina
| | - Ningfu Peng
- Department of Hepatobiliary SurgeryGuangxi Medical University Cancer HospitalNanningChina
| | - Xiaojing Wang
- Department of Rheumatology and Immunology, Tongren Hospital, School of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Xiaofeng Dong
- Department of Hepatobiliary, Pancreas and Spleen SurgeryThe People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical SciencesNanningChina
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Zhou W, Lin Z, Tan W. Deciphering the molecular landscape: integrating single-cell transcriptomics to unravel myofibroblast dynamics and therapeutic targets in clear cell renal cell carcinomas. Front Immunol 2024; 15:1374931. [PMID: 38562930 PMCID: PMC10982338 DOI: 10.3389/fimmu.2024.1374931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Background Clear cell renal cell carcinomas (ccRCCs) epitomize the most formidable clinical subtype among renal neoplasms. While the impact of tumor-associated fibroblasts on ccRCC progression is duly acknowledged, a paucity of literature exists elucidating the intricate mechanisms and signaling pathways operative at the individual cellular level. Methods Employing single-cell transcriptomic analysis, we meticulously curated UMAP profiles spanning substantial ccRCC populations, delving into the composition and intrinsic signaling pathways of these cohorts. Additionally, Myofibroblasts were fastidiously categorized into discrete subpopulations, with a thorough elucidation of the temporal trajectory relationships between these subpopulations. We further probed the cellular interaction pathways connecting pivotal subpopulations with tumors. Our endeavor also encompassed the identification of prognostic genes associated with these subpopulations through Bulk RNA-seq, subsequently validated through empirical experimentation. Results A notable escalation in the nFeature and nCount of Myofibroblasts and EPCs within ccRCCs was observed, notably enriched in oxidation-related pathways. This phenomenon is postulated to be closely associated with the heightened metabolic activities of Myofibroblasts and EPCs. The Myofibroblasts subpopulation, denoted as C3 HMGA1+ Myofibroblasts, emerges as a pivotal subset, displaying low differentiation and positioning itself at the terminal point of the temporal trajectory. Intriguingly, these cells exhibit a high degree of interaction with tumor cells through the MPZ signaling pathway network, suggesting that Myofibroblasts may facilitate tumor progression via this pathway. Prognostic genes associated with C3 were identified, among which TUBB3 is implicated in potential resistance to tumor recurrence. Finally, experimental validation revealed that the knockout of the key gene within the MPZ pathway, MPZL1, can inhibit tumor activity, proliferation, invasion, and migration capabilities. Conclusion This investigation delves into the intricate mechanisms and interaction pathways between Myofibroblasts and ccRCCs at the single-cell level. We propose that targeting MPZL1 and the oxidative phosphorylation pathway could serve as potential key targets for treating the progression and recurrence of ccRCC. This discovery paves the way for new directions in the treatment and prognosis diagnosis of ccRCC in the future.
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Affiliation(s)
- Wenqian Zhou
- Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhiheng Lin
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Wang Tan
- Xiangya Boai Rehabilitation Hospital, Changsha, Hunan, China
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13
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Liu P, Liu J, Liu J, Yu X. Investigating the mechanisms of drug resistance and prognosis in ovarian cancer using single-cell RNA sequencing and bulk RNA sequencing. Aging (Albany NY) 2024; 16:4736-4758. [PMID: 38461424 PMCID: PMC10968697 DOI: 10.18632/aging.205628] [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: 10/16/2023] [Accepted: 02/02/2024] [Indexed: 03/12/2024]
Abstract
Ovarian cancer stands as a prevalent malignancy within the realm of gynecology, and the emergence of resistance to chemotherapeutic agents remains a pivotal impediment to both prognosis and treatment. Through a single-cell level investigation, we scrutinize the drug resistance and mitotic activity of the core tumor cells in ovarian cancer. Our study revisits the interrelationships and temporal trajectories of distinct epithelial cells (EPCs) subpopulations, while identifying genes associated with ovarian cancer prognosis. Notably, our findings establish a strong association between the drug resistance of EPCs and oxidative phosphorylation pathways. Subsequently, through subpopulation and temporal trajectory analysis, we confirm the intermediate position of EPCs subpopulation C0. Furthermore, we delve into the immunological functions and differentially expressed genes associated with the prognosis of C0, shedding light on the potential for constructing novel ovarian cancer prognosis models and identifying new therapeutic targets.
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Affiliation(s)
- Pengfei Liu
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jinbao Liu
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jinxing Liu
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiao Yu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
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Liu P, Xing N, Xiahou Z, Yan J, Lin Z, Zhang J. Unraveling the intricacies of glioblastoma progression and recurrence: insights into the role of NFYB and oxidative phosphorylation at the single-cell level. Front Immunol 2024; 15:1368685. [PMID: 38510250 PMCID: PMC10950940 DOI: 10.3389/fimmu.2024.1368685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/19/2024] [Indexed: 03/22/2024] Open
Abstract
Background Glioblastoma (GBM), with its high recurrence and mortality rates, makes it the deadliest neurological malignancy. Oxidative phosphorylation is a highly active cellular pathway in GBM, and NFYB is a tumor-associated transcription factor. Both are related to mitochondrial function, but studies on their relationship with GBM at the single-cell level are still scarce. Methods We re-analyzed the single-cell profiles of GBM from patients with different subtypes by single-cell transcriptomic analysis and further subdivided the large population of Glioma cells into different subpopulations, explored the interrelationships and active pathways among cell stages and clinical subtypes of the populations, and investigated the relationship between the transcription factor NFYB of the key subpopulations and GBM, searching for the prognostic genes of GBM related to NFYB, and verified by experiments. Results Glioma cells and their C5 subpopulation had the highest percentage of G2M staging and rGBM, which we hypothesized might be related to the higher dividing and proliferating ability of both Glioma and C5 subpopulations. Oxidative phosphorylation pathway activity is elevated in both the Glioma and C5 subgroup, and NFYB is a key transcription factor for the C5 subgroup, suggesting its possible involvement in GBM proliferation and recurrence, and its close association with mitochondrial function. We also identified 13 prognostic genes associated with NFYB, of which MEM60 may cause GBM patients to have a poor prognosis by promoting GBM proliferation and drug resistance. Knockdown of the NFYB was found to contribute to the inhibition of proliferation, invasion, and migration of GBM cells. Conclusion These findings help to elucidate the key mechanisms of mitochondrial function in GBM progression and recurrence, and to establish a new prognostic model and therapeutic target based on NFYB.
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Affiliation(s)
- Pulin Liu
- Shandong University of Traditional Chinese Medicine, Jinan, China
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, Shanxi University of Chinese Medicine, Jinzhong, China
- National International Joint Research Center of Molecular Traditional Chinese Medicine, Shanxi University of Chinese Medicine, Jinzhong, China
| | - Naifei Xing
- Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Zhikai Xiahou
- China Institute of Sport and Health Science, Beijing Sport University, Beijing, China
| | - Jingwei Yan
- Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Zhiheng Lin
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Junlong Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, China
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, Shanxi University of Chinese Medicine, Jinzhong, China
- National International Joint Research Center of Molecular Traditional Chinese Medicine, Shanxi University of Chinese Medicine, Jinzhong, China
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15
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Cai HB, Zhao MY, Li XH, Li YQ, Yu TH, Wang CZ, Wang LN, Xu WY, Liang B, Cai YP, Zhang F, Hong WM. Single cell sequencing revealed the mechanism of CRYAB in glioma and its diagnostic and prognostic value. Front Immunol 2024; 14:1336187. [PMID: 38274814 PMCID: PMC10808695 DOI: 10.3389/fimmu.2023.1336187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Background We explored the characteristics of single-cell differentiation data in glioblastoma and established prognostic markers based on CRYAB to predict the prognosis of glioblastoma patients. Aberrant expression of CRYAB is associated with invasive behavior in various tumors, including glioblastoma. However, the specific role and mechanisms of CRYAB in glioblastoma are still unclear. Methods We assessed RNA-seq and microarray data from TCGA and GEO databases, combined with scRNA-seq data on glioma patients from GEO. Utilizing the Seurat R package, we identified distinct survival-related gene clusters in the scRNA-seq data. Prognostic pivotal genes were discovered through single-factor Cox analysis, and a prognostic model was established using LASSO and stepwise regression algorithms. Moreover, we investigated the predictive potential of these genes in the immune microenvironment and their applicability in immunotherapy. Finally, in vitro experiments confirmed the functional significance of the high-risk gene CRYAB. Results By analyzing the ScRNA-seq data, we identified 28 cell clusters representing seven cell types. After dimensionality reduction and clustering analysis, we obtained four subpopulations within the oligodendrocyte lineage based on their differentiation trajectory. Using CRYAB as a marker gene for the terminal-stage subpopulation, we found that its expression was associated with poor prognosis. In vitro experiments demonstrated that knocking out CRYAB in U87 and LN229 cells reduced cell viability, proliferation, and invasiveness. Conclusion The risk model based on CRYAB holds promise in accurately predicting glioblastoma. A comprehensive study of the specific mechanisms of CRYAB in glioblastoma would contribute to understanding its response to immunotherapy. Targeting the CRYAB gene may be beneficial for glioblastoma patients.
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Affiliation(s)
- Hua-Bao Cai
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Meng-Yu Zhao
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xin-Han Li
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Yu-Qing Li
- Department of Pathology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
| | - Tian-Hang Yu
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Cun-Zhi Wang
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Li-Na Wang
- School of Nursing, Anhui Medical University, Hefei, China
| | - Wan-Yan Xu
- School of Nursing, Anhui Medical University, Hefei, China
| | - Bo Liang
- Department of Dermatology and Venereology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yong-Ping Cai
- Department of Pathology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
| | - Fang Zhang
- School of Nursing, Anhui Medical University, Hefei, China
| | - Wen-Ming Hong
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
- Open Project of Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
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Ji L, Liang S, Cheng Y, Gao R, Yan W, Pang F, Zhang F. Identification of a novel necroptosis-related LncRNA signature for prognostic prediction and immune response in oral squamous cell carcinoma. Cancer Biomark 2024; 40:319-342. [PMID: 39213052 PMCID: PMC11380221 DOI: 10.3233/cbm-230407] [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] [Indexed: 09/04/2024]
Abstract
BACKGROUND Necroptosis is a caspase-independent regulated necrotic cell death modality that elicits strong adaptive immune responses, and has the potential to activate antitumor immunity. Long non-coding RNAs (lncRNAs) have critical effects on oral squamous cell carcinoma (OSCC), which are closely associated with the prognosis and immune regulation of OSCC patients. OBJECTIVE This study aimed to identify a novel necroptosis-related lncRNAs signature to predict the prognosis and immune response of OSCC patients and provide patients with anti-tumor drug selection through bioinformatics analysis and in vitro experiments. METHODS A series of analyses, including differential lncRNA screening, survival analysis, Cox regression analysis, ROC analysis, nomogram prediction, enrichment analysis, tumor-infiltrating immune cells, drug sensitivity analysis, and consensus cluster analysis, were performed to determine and validate the prognostic value of necroptosis-associated lncRNAs signature in OSCC. And real-time quantitative polymerase chain reaction (RT-qPCR) was used to determine the expression levels of these lncRNAs. RESULTS This signature including 5 lncRNAs (AC099850.3, StarD4-AS1, AC011978.1, LINC01503, CDKN2A-DT) in OSCC associated with necroptosis were established and verified by bioinformatics. Further, ROC, K-M, univariate/multivariate Cox regression, and nomogram analysis were used to evaluate the model's features for OSCC prognosis. Using multiple bioinformatics techniques, the levels of tumor-infiltrating immune cells, immune checkpoints and semi-inhibitory concentrations showed significant differences across risk subtypes. By consensus cluster analysis, there were significant differences between clusters in survival, immune checkpoint expression, clinicopathological correlation, and tumor immunity. RT-qPCR showed that AC099850.3, AC011978.1, LINC01503 were up-regulated, STARD4-AS1 and CDKN2A-DT were down-regulated in OSCC cell lines compared with human normal oral keratinoid cell line. CONCLUSION We established 5-NRLs markers, which is useful for assessing OSCC immune response and prognosis, recommending personalized antitumor drugs. The expression level of 5-NRLs in OSCC was identified in vitro, and the results preliminarily verified this model. And this study would generate new insights for future experimental research.
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Affiliation(s)
- Lanting Ji
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | - Shuang Liang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | | | - Ruifang Gao
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | - Wenpeng Yan
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | - Fang Pang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | - Fang Zhang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
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Kong X, Xiong Y. A novel necroptosis-related long non-coding RNA signature predicts prognosis and immune response in cervical cancer patients. J Cancer Res Clin Oncol 2023; 149:12947-12964. [PMID: 37466792 DOI: 10.1007/s00432-023-05158-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/09/2023] [Indexed: 07/20/2023]
Abstract
BACKGROUND Necroptosis has been linked to the development of tumors. Long non-coding RNAs (IncRNAs) have been identified as having a major role in numerous biological and pathological procedures. Despite this, the precise role that necroptosis-related lncRNAs (NRLs) have in cervical cancer (CC) and their potential for predicting its prognosis is still to a large extent unclear. METHODS Gene expression RNA-sequencing data, mutational data, and clinical profiles for 309 CC patients were obtained from the Cancer Genome Atlas (TCGA) database. The NRLs were then identified with Pearson correlation analysis followed by splitting of the patients into training and validation sets in a 3:2 ratio. Cox and LASSO regression models were performed to construct a cervical cancer prognostic signature based on NRLs. This 5-NRLs signature was then verified by Kaplan-Meier survival analysis, receiver operating characteristic (ROC) curve, and nomogram for prognostic prediction. Further, a correlation study between the risk score (RS) and immune cell infiltration, immune checkpoint molecules, tumor mutation burden (TMB), and the sensitivity of chemotherapy drug was conducted. To validate the 5-NRLs, a quantitative reverse transcription polymerase chain reaction (qRT-PCR) was finally performed. RESULTS The 5-NRLs signature was designed to accurately predict the prognosis of CC. It consists of AC092153.1, AC007686.3, LINC01281, AC009097.2, and RUSC1-AS1 and was found to be highly predictive using ROC and Kaplan-Meier curves. Furthermore, when analyzed through stratified survival analysis, it was confirmed to be an independent risk factor for prognosis. The nomogram and calibration curves further validated its clinical utility. Moreover, distinct differences between two risk groups were observed when examining immune cell infiltration, immune checkpoint molecules, somatic gene alterations and half-inhibitory concentration of anticancer drug. CONCLUSIONS The 5-NRLs signature is a novel and valuable tool for evaluating the prognosis of CC patients, providing clinicians with an informed decision-making framework to formulate tailored treatment plans for their patients.
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Affiliation(s)
- Xiaoyu Kong
- School of Public Health, Nanchang University, 330006, Nanchang, Jiangxi, China
| | - Yuanpeng Xiong
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, 330006, Nanchang, People's Republic of China.
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Chen J, Ye M, Bai J, Hu C, Lu F, Gu D, Yu P, Tang Q. Novel insights into the interplay between m6A modification and programmed cell death in cancer. Int J Biol Sci 2023; 19:1748-1763. [PMID: 37063421 PMCID: PMC10092764 DOI: 10.7150/ijbs.81000] [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: 11/18/2022] [Accepted: 03/08/2023] [Indexed: 04/18/2023] Open
Abstract
N6-methyladenosine (m6A) methylation, the most prevalent and abundant RNA modification in eukaryotes, has recently become a hot research topic. Several studies have indicated that m6A modification is dysregulated during the progression of multiple diseases, especially in cancer development. Programmed cell death (PCD) is an active and orderly method of cell death in the development of organisms, including apoptosis, autophagy, pyroptosis, ferroptosis, and necroptosis. As the study of PCD has become increasingly profound, accumulating evidence has revealed the mutual regulation of m6A modification and PCD, and their interaction can further influence the sensitivity of cancer treatment. In this review, we summarize the recent advances in m6A modification and PCD in terms of their interplay and potential mechanisms, as well as cancer therapeutic resistance. Our study provides promising insights and future directions for the examination and treatment of cancers.
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Affiliation(s)
| | | | | | | | | | | | | | - Qiyun Tang
- ✉ Corresponding author: Qiyun Tang, Department of Geriatric Gastroenterology, Neuroendocrine Tumor Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, Institute of Neuroendocrine Tumor, Nanjing Medical University, NO. 300 Guangzhou Road, Nanjing, China.
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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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