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Mao Y, Zhang H, He X, Chen J, Xi L, Chen Y, Zeng Y. A four-gene signature predicts overall survival of patients with esophageal adenocarcinoma. Transl Cancer Res 2024; 13:1382-1393. [PMID: 38617513 PMCID: PMC11009802 DOI: 10.21037/tcr-23-1798] [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: 12/15/2023] [Accepted: 01/23/2024] [Indexed: 04/16/2024]
Abstract
Background Esophageal adenocarcinoma (EAC) is an aggressive cancer with poor prognosis. Thus, this study aimed to identify a prognostic molecular signature to predict the overall survival (OS) of patients with EAC. Methods The mRNA microarray data sets GSE13898 and GSE26886 were downloaded from the Gene Expression Omnibus (GEO) database. RNA sequencing profile and clinical data of EAC patients were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed genes (DEGs) between EAC tissues and adjacent non-cancerous tissues were obtained using R software. DEGs associated with prognosis of OS were assessed by univariate Cox analysis, and a prognostic signature was built using stepwise multivariate Cox analysis. Time-dependent receiver operating characteristic (ROC) analysis and stratification analysis were conducted to evaluate its predictive performance. Functional enrichment analysis was performed for genes co-expressed with the signature to explore its biological functions in EAC. Results A total of 336 genes were identified to be differentially expressed between EAC tissues and adjacent non-cancerous tissues. After univariate and multivariate Cox regression analysis, four genes (ALAD, ABLIM3, IL17RB and IFI6) were screened out to construct a prognostic signature. According to this signature, patients could be assigned into high-risk and low-risk group with significantly different OS (P=4.92e-05<0.0001). Multivariate Cox regression analysis suggested that the four-gene signature served as an independent factor in OS prediction. In the time-dependent ROC analysis, the areas under the curves (AUCs) were 0.804, 0.792 and 0.695 for 1-, 3- and 5-year survival prediction, respectively, suggesting a good performance. Functional enrichment analysis showed that the signature was mainly clustered in cell proliferation related biological processes or pathways. Conclusions The four-gene signature identified in the current study may be a potential prognostic factor for predicting OS of EAC patients.
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Affiliation(s)
- Yanmei Mao
- Department of Pharmacy, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Haibo Zhang
- Department of Pharmacy, Hangzhou Women’s Hospital, Hangzhou, China
| | - Xin He
- Department of Pharmacy, The Third Hospital of Changsha, Changsha, China
| | - Jing Chen
- Department of Pharmacy, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Lanyan Xi
- Department of Pharmacy, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Yanping Chen
- Department of Pharmacy, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Ying Zeng
- Department of Pharmacy, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
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Zeng X, Han Z, Chen K, Zeng P, Tang Y, Li L. Single-Cell Analyses Reveal Necroptosis's Potential Role in Neuron Degeneration and Show Enhanced Neuron-Immune Cell Interaction in Parkinson's Disease Progression. PARKINSON'S DISEASE 2023; 2023:5057778. [PMID: 38149092 PMCID: PMC10751163 DOI: 10.1155/2023/5057778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/09/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023]
Abstract
Parkinson's disease (PD) is a common neuron degenerative disease among the old, characterized by uncontrollable movements and an impaired posture. Although widely investigated on its pathology and treatment, the disease remains incompletely understood. Single-cell RNA sequencing (scRNA-seq) has been applied to the area of PD, providing valuable data for related research. However, few works have taken deeper insights into the causes of neuron death and cell-cell interaction between the cell types in the brain. Our bioinformatics analyses revealed necroptosis-related genes (NRGs) enrichment in neuron degeneration and selecting the cells by NRGs levels showed two subtypes within the main degenerative cell types in the midbrain. NRG-low subtype was largely replaced by NRG-high subtype in the patients, indicating the striking change of cell state related to necroptosis in PD progression. Moreover, we carried out cell-cell interaction analyses between cell types and found that microglia (MG)'s interaction strength with glutamatergic neuron (GLU), GABAergic neuron (GABA), and dopaminergic neuron (DA) was significantly upregulated in PD. Also, MG show much stronger interaction with NRG-high subtypes and a stronger cell killing function in PD samples. Additionally, we identified CLDN11 as a novel interaction pattern specific to necroptosis neurons and MG. We also found LEF1 and TCF4 as key transcriptional regulators in neuron degeneration. These findings suggest that MG were significantly overactivated in PD patients to clear abnormal neurons, especially the NRG-high cells, explaining the neuron inflammation in PD. Our analyses provide insights into the causes of neuron death and inflammation in PD from single-cell resolution, which could be seriously considered in clinical trials.
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Affiliation(s)
- Xiaomei Zeng
- Rehabilitation Medicine Center and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Rehabilitation Medicine in Sichuan Province, Sichuan University, Chengdu, China
| | - Zhifen Han
- Department of Ultrasound, Affiliated Hospital of Chengdu University of Traditional Chinese Medicine, Sichuan, Chengdu, China
| | - Kehan Chen
- Rehabilitation Medicine Center and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Rehabilitation Medicine in Sichuan Province, Sichuan University, Chengdu, China
| | - Peng Zeng
- Rehabilitation Medicine Center and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Rehabilitation Medicine in Sichuan Province, Sichuan University, Chengdu, China
| | - Yidan Tang
- Rehabilitation Medicine Center and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Rehabilitation Medicine in Sichuan Province, Sichuan University, Chengdu, China
| | - Lijuan Li
- Rehabilitation Medicine Center and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Rehabilitation Medicine in Sichuan Province, Sichuan University, Chengdu, China
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Liu J, Wang Y, Zhao Z, Ge Y. Bioinformatics analysis and experimental validation of tumorigenic role of PPIA in gastric cancer. Sci Rep 2023; 13:19116. [PMID: 37926757 PMCID: PMC10625987 DOI: 10.1038/s41598-023-46508-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: 02/08/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023] Open
Abstract
Gastric cancer (GC) is a malignant tumor with high incidence rate and mortality. Due to the lack of effective diagnostic indicators, most patients are diagnosed in late stage and have a poor prognosis. An increasing number of studies have proved that Peptidylprolyl isomerase A (PPIA) can play an oncogene role in various cancer types. However, the precise mechanism of PPIA in GC is still unclear. Herein, we analyzed the mRNA levels of PPIA in pan-cancer. The prognostic value of PPIA on GC was also evaluated using multiple databases. Additionally, the relationship between PPIA expression and clinical factors in GC was also examined. We further confirmed that PPIA expression was not affected by genetic alteration and DNA methylation. Moreover, the upstream regulator miRNA and lncRNA of PPIA were identified, which suggested that LINC10232/miRNA-204-5p/PPIA axis might act as a potential biological pathway in GC. Finally, this study revealed that PPIA was negatively correlated with immune checkpoint expression, immune cell biomarkers, and immune cell infiltration in GC.
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Affiliation(s)
- Jichao Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Henan, China
| | - Yanjun Wang
- Department of Vascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Henan, China
| | - Zhiwei Zhao
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Henan, China
| | - Yanhui Ge
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Henan, China.
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Jiang R, Sun Y, Li Y, Tang X, Hui B, Ma S, Zhang J, Sun C, Tan J, Zhou B, Lei J, Jiang T. Cuproptosis-related gene PDHX and heat stress-related HSPD1 as potential key drivers associated with cell stemness, aberrant metabolism and immunosuppression in esophageal carcinoma. Int Immunopharmacol 2023; 117:109942. [PMID: 36889194 DOI: 10.1016/j.intimp.2023.109942] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/10/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023]
Abstract
BACKGROUND Heat stress is fundamental to esophageal carcinoma (ESCA) oncogenesis and progression. Heat stress damages epithelial structure, causing aberrant 'cell death-repair' patterns of esophagus cells and thereby driving tumor occurrence and progression. However, due to the distinctive functions and crosstalk of regulatory cell death (RCD) patterns, the specific cell deaths in ESCA malignancy are still unclear. METHODS We analyzed the key regulatory cell death genes involved in heat stress and ESCA progression by using The Cancer Genome Atlas-ESCA database. The least absolute shrinkage and selection operator (LASSO) algorithm was used to filter the key genes. The one-class logistic regression (OCLR) and quanTIseq methods were used to evaluate the cell stemness and immune cell infiltration in ESCA samples. Cell counting kit-8 (CCK8) and wound healing assays were performed to assess the proliferation and migration of cells. RESULTS We found that cuproptosis may be a potential risk factor of heat stress-related ESCA. Two interrelated genes, HSPD1 and PDHX, were associated with heat stress and cuproptosis and played a role in cell survival, proliferation, migration, metabolism and immunosuppression. CONCLUSIONS We found that cuproptosis promoted ESCA related to heat stress, offering a new therapeutic opportunity to treat this malignant disorder.
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Affiliation(s)
- Runmin Jiang
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Ying Sun
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Yan Li
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China; Department of Radiation Oncology, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Xuefei Tang
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Bengang Hui
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Shouzheng Ma
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Jiao Zhang
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Chun Sun
- Student Major Team 3, School of Basic Medicine, Fourth Military Medical University, Xi'an, China
| | - Jiyi Tan
- Student Major Team 3, School of Basic Medicine, Fourth Military Medical University, Xi'an, China
| | - Boyan Zhou
- Student Major Team 3, School of Basic Medicine, Fourth Military Medical University, Xi'an, China
| | - Jie Lei
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China.
| | - Tao Jiang
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China.
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