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Nicolau-Neto P, Peryassú BC, de Carvalho FN, Souza-Santos PT, Valverde P, Nascimento CM, Costa I, Dias FL, Pinto LFR. ALCAM is a biomarker of tumor aggressiveness and worse prognosis in glottic laryngeal squamous cell carcinoma. Head Neck 2024; 46:785-796. [PMID: 38196304 DOI: 10.1002/hed.27635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 12/01/2023] [Accepted: 12/24/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND Laryngeal squamous cell carcinoma (LSCC) is the second most frequent head and neck tumor. Prognosis of patients with LSCC has not improved in recent decades, showing a need for the identification of prognostic biomarkers and new therapeutic targets. Recently, we showed that ALCAM overexpression was associated with glottic LSCC prognosis. OBJECTIVES AND METHODS Aiming to validate the prognostic value of ALCAM, we evaluate the ALCAM protein levels by immunohistochemistry in 263 glottic LSCC surgically treated with neck dissection. RESULTS ALCAM was expressed in 48.7% and overexpressed in 36.5% of glottic LSCC samples. ALCAM overexpression was associated with lymph node metastasis (p = 0.030), lymphovascular involvement (p = 0.0002), high-grade tumors (p = 0.025), and tumor relapse (p = 0.043). Multivariate survival analyses showed an overfitting between ALCAM overexpression and lymph node metastasis as a prognostic variable. CONCLUSIONS High ALCAM expression was associated with an aggressive glottic LSCC profile.
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Affiliation(s)
- Pedro Nicolau-Neto
- Programa de Carcinogênese Molecular, Instituto Nacional de Câncer-INCA, Rio de Janeiro, Brazil
| | | | | | | | - Priscila Valverde
- Divisão de Patologia, Instituto Nacional de Câncer-INCA, Rio de Janeiro, Brazil
| | | | - Izabella Costa
- Seção de Cirurgia de Cabeça e Pescoço, Instituto Nacional de Câncer-INCA, Rio de Janeiro, Brazil
| | - Fernando L Dias
- Seção de Cirurgia de Cabeça e Pescoço, Instituto Nacional de Câncer-INCA, Rio de Janeiro, Brazil
| | - Luis Felipe Ribeiro Pinto
- Programa de Carcinogênese Molecular, Instituto Nacional de Câncer-INCA, Rio de Janeiro, Brazil
- Departamento de Bioquímica, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
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2
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Jiang X, Li W, Li R, Ning J. Addressing subject heterogeneity in time-dependent discrimination for biomarker evaluation. Stat Med 2024; 43:1341-1353. [PMID: 38287471 DOI: 10.1002/sim.10024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/29/2023] [Accepted: 01/12/2024] [Indexed: 01/31/2024]
Abstract
Accurate discrimination has been the central goal in identifying biomarkers for monitoring disease progression and early detection. Acknowledging the fact that discrimination accuracy of biomarkers for a time-to-event outcome often changes over time, local measures such as the time-dependent receiver operating characteristic curve and its area under the curve (AUC) are used to assess time-dependent predictive discrimination. However, such measures do not address subject heterogeneity, although the impact of covariates including demographics, disease-related characteristics, and other clinical information on the discriminatory performance of biomarkers needs to be investigated before their clinical use. We propose the covariate-specific time-dependent AUC, a measure for covariate-adjusted discrimination. We develop a regression model on the covariate-specific time-dependent AUC to understand how and in what magnitude the covariates influence biomarker performance. Then we construct a pseudo partial-likelihood for estimation and inference. This is followed by our establishing the asymptotic properties of the proposed estimators and provide variance estimation. The simulation studies and application to the AIDS Clinical Trials Group 175 data demonstrate that the proposed method offers an informative tool for inferring covariate-specific and time-dependent predictive discrimination.
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Affiliation(s)
- Xinyang Jiang
- Department of Biostatistics and Data Science, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Wen Li
- Department of Internal Medicine, The University of Texas McGovern Medical School, Houston, Texas, USA
| | - Ruosha Li
- Department of Biostatistics and Data Science, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Jing Ning
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Li H, Liu J, Wang S, Xu Y, Tang Q, Ying G. 4-Hydroxyphenylpyruvate Dioxygenase-Like predicts the prognosis and the immunotherapy response of cancers: a pan-cancer analysis. Aging (Albany NY) 2024; 16:4327-4347. [PMID: 38451188 DOI: 10.18632/aging.205591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/01/2023] [Indexed: 03/08/2024]
Abstract
The 4-Hydroxyphenylpyruvate Dioxygenase-Like (HPDL) protein plays a crucial role in safeguarding cells from oxidative stress by orchestrating metabolic reprogramming. New research suggests that HPDL is considerably increased in pancreatic ductal adenocarcinoma, although its impact on cancer immunotherapy is still unclear. Pancancer transcriptional data were obtained from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression datasets. The cBioPortal webtool was utilized to examine genomic changes in different cancer types. The prognostic significance of HPDL in pancancer was evaluated using univariate Cox regression analysis. Extensive utilization of the CTRP and PRISM databases was performed to forecast potential medications that specifically target HPDL in LUAD. In summary, studies were conducted to evaluate the impact of HPDL on the proliferation and movement of LUAD cells using loss-of-function experiments. HPDL is expressed excessively in a wide variety of cancer types, indicating its prognostic and predictive value. Moreover, we emphasized the strong correlation between HPDL and indicators of immune stimulation, infiltration of immune cells, and expression of immunoregulators. The remarkable finding of the HPDL was its capacity to precisely anticipate responses to cancer therapies using anti-PDL1 and anti-PD1 antibodies among individuals. Moreover, HPDL can function as a predictive marker for specific inhibitors in instances of cancer. Suppression of HPDL resulted in reduced growth and movement of LUAD cells. To summarize, our results suggest that HPDL acts as a prospective predictor of outcomes and a positive indication of response to immunotherapy in patients undergoing treatment with immune checkpoint inhibitors (ICIs).
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Affiliation(s)
- Huimin Li
- Laboratory of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, China
| | - Junzhi Liu
- Department of Otorhinolaryngology, Tianjin Medical University General Hospital, Tianjin 300070, China
| | - Shurui Wang
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yue Xu
- Laboratory of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, China
| | - Qiang Tang
- The Second Affiliated Hospital of Zhejiang University School Medicine, Hang Zhou 310000, China
| | - Guoguang Ying
- Laboratory of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, China
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Dai Y, Li J, Huang R, Yao Q, Shi Y, Guo S, Wang Y, Cheng J. Development of a novel head and neck squamous cell carcinoma prognostic signature by bulk/single-cell sequencing data integration. Oral Dis 2024; 30:128-139. [PMID: 36398480 DOI: 10.1111/odi.14443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/26/2022] [Accepted: 11/15/2022] [Indexed: 02/17/2024]
Abstract
BACKGROUND Identifying cell subpopulations conferring unfavorable prognosis in cancer holds clinical significance. Here, we sought to identify prognostic cell subsets and develop a novel, prognostic signature for head neck squamous cell carcinoma (HNSCC). METHODS Highly prognostic cell subpopulations in HNSCC were identified by integrating single-cell and bulk transcriptomic datasets. The prognostic signature and nomogram were developed by least absolute shrinkage and selection operator and multivariate Cox regression analyses based on significantly upregulated genes in this specific cell subpopulation, respectively. The qRT-PCR experiments were utilized for independent validation in our patient cohort. RESULTS A specific cancer cell subset associated with unfavorable prognoses was identified. Functional dissections revealed that its transcriptional programs were significantly enriched in E2F, epithelial-to-mesenchymal transition, and glycolysis. A novel prognostic signature comprising six genes was developed and further validated. Risk scores based on qRT-PCR data robustly stratified patients into subgroups with distinct prognoses. A nomogram integrated from this signature and clinical stage had superior performance. CONCLUSION Our model derived from integrative analyses of single-cell and bulk RNA-sequencing is a novel, robust prognostic biomarker for HNSCC.
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Affiliation(s)
- Yibin Dai
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Jin Li
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Rong Huang
- School of Medical Technology, Taizhou Polytechnic College, Taizhou, China
| | - Qin Yao
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Yawei Shi
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Songsong Guo
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Yanling Wang
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Jie Cheng
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
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Qin J, Fu J, Chen X. Comprehensive analysis of histone acetylation-related genes in glioblastoma and lower-grade gliomas: Insights into drug sensitivity, molecular subtypes, immune infiltration, and prognosis. J Gene Med 2024; 26:e3678. [PMID: 38500293 DOI: 10.1002/jgm.3678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/18/2024] [Accepted: 02/05/2024] [Indexed: 03/20/2024] Open
Abstract
OBJECTIVES The purpose of this research was to study the impact of histone acetylation on glioblastoma multiforme (GBM) and lower-grade gliomas (LGG) and its potential implications for patient prognosis. We aimed to assess the histone acetylation score (HAs) and its relationship with key genes involved in histone acetylation regulation. METHOD The TCGA-GBMLGG dataset, which provides comprehensive genomic and clinical information, was utilized for this study. We calculated the HAs by analyzing the expression levels of histone acetylation-related genes, including histone acetyltransferases and histone deacetylases, in GBM and LGG patients. Kaplan-Meier survival analysis was performed to evaluate the prognostic value of the HAs. Furthermore, correlation analysis and differential expression analysis were conducted to assess the relationship between the HAs and key genes involved in histone acetylation regulation, as well as the expression differences of immune checkpoint genes. RESULTS Our analysis revealed a significant association between the HAs and patient prognosis, with higher HAs correlating to poorer outcomes in GBM and LGG patients. We observed a positive correlation between the HAs and key genes involved in histone acetylation regulation, indicating their potential role in modulating histone acetylation levels. Moreover, we found significant expression differences for immune checkpoint genes between high and low HAs groups, suggesting a potential impact of histone acetylation on the immune response in GBM and LGG. CONCLUSION This study highlights the significance of histone acetylation in GBM and LGG. The HAs demonstrated prognostic value, indicating its potential as a clinically relevant biomarker. The correlation between the HAs and key genes involved in histone acetylation regulation provides insights into the underlying mechanisms driving histone acetylation dysregulation in GBM and LGG. Furthermore, the observed expression differences of immune checkpoint genes suggest a potential link between histone acetylation and the immune response. These findings contribute to our understanding of the molecular basis of GBM and LGG and have implications for personalized treatment approaches targeting histone acetylation and the immune microenvironment. Further validation and functional studies are needed to confirm these findings and explore potential therapeutic strategies.
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Affiliation(s)
- Jiajun Qin
- Department of Neurosurgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jin Fu
- Department of Neurosurgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xianzhen Chen
- Department of Neurosurgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
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Miao H, Bai Y, Shen S, Chu M, Miao C, Yang J, Li X, Li L, Shao S, Wang G, Dang E. Biological agent exerts therapeutic effects by reversing abnormalities in amino acid metabolic pathways in psoriasis. Exp Dermatol 2024; 33:e15059. [PMID: 38532578 DOI: 10.1111/exd.15059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/28/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024]
Abstract
Psoriasis is a common chronic inflammatory skin disease with a complex pathogenesis involving immune system dysregulation and inflammation. Previous studies have indicated that metabolic abnormalities are closely related to the development and occurrence of psoriasis. However, the specific involvement of amino acid metabolism in the pathogenesis of psoriasis remains unclear. In this study, we conducted a comprehensive analysis of amino acid metabolism pathway changes in psoriasis patients using transcriptome data, genome-wide association studies (GWASs) data, and single-cell data. Our findings revealed 11 significant alterations in amino acid metabolism pathways within psoriatic lesions, with notable restorative changes observed after biological therapy. Branched-chain amino acids, tyrosine and arginine metabolism have a causal relationship with the occurrence of psoriasis and may play a crucial role by promoting the proliferation and differentiation of the keratinocytes or immune-related pathways. Activation of phenylalanine, tyrosine and tryptophan biosynthesis suggests a favourable prognosis of psoriasis after treatment. Additionally, we identified the abnormal metabolic pathways in specific cell types and key gene sets that contribute to amino acid metabolic disorders in psoriasis. Overall, our study enhances understanding of the role of metabolism in the pathogenesis of psoriasis and provides potential targets for developing new therapeutic strategies for the disease.
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Affiliation(s)
- Haijun Miao
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Yaxing Bai
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Shengxian Shen
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Mengyang Chu
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Chang Miao
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Jundan Yang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Xia Li
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Liang Li
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Shuai Shao
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Gang Wang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | - Erle Dang
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
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Li Z, Li J, Wu Z, Zhu Y, Zhuo T, Nong J, Qian J, Peng H, Dai L, Wang Y, Chen M, Zeng X. Upregulation of POC1A in lung adenocarcinoma promotes tumour progression and predicts poor prognosis. J Cell Mol Med 2024; 28:e18135. [PMID: 38429900 PMCID: PMC10907829 DOI: 10.1111/jcmm.18135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 03/03/2024] Open
Abstract
Lung adenocarcinoma (LUAD) is characterized by a high incidence rate and mortality. Recently, POC1 centriolar protein A (POC1A) has emerged as a potential biomarker for various cancers, contributing to cancer onset and development. However, the association between POC1A and LUAD remains unexplored. We extracted The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) data sets to analyse the differential expression of POC1A and its relationship with clinical stage. Additionally, we performed diagnostic receiver operator characteristic (ROC) curve analysis and Kaplan-Meier (KM) survival analysis to assess the diagnostic and prognostic value of POC1A in LUAD. Furthermore, we investigated the correlation between POC1A expression and immune infiltration, tumour mutation burden (TMB), immune checkpoint expression and drug sensitivity. Finally, we verified POC1A expression using real-time quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry (IHC). Cell experiments were conducted to validate the effect of POC1A expression on the proliferation, migration and invasion of lung cancer cells. POC1A exhibited overexpression in most tumour tissues, and its overexpression in LUAD was significantly correlated with late-stage presentation and poor prognosis. The high POC1A expression group showed lower levels of immune infiltration but higher levels of immune checkpoint expression and TMB. Moreover, the high POC1A expression group demonstrated sensitivity to multiple drugs. In vitro experiments confirmed that POC1A knockdown led to decreased proliferation, migration, and invasion of lung cancer cells. Our findings suggest that POC1A may contribute to tumour development by modulating the cell cycle and immune cell infiltration. It also represents a potential therapeutic target and marker for the diagnosis and prognosis of LUAD.
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Affiliation(s)
- Zi‐Hao Li
- Department of Cardio‐Thoracic SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxiChina
| | - Jia‐Yi Li
- Geriatrics Department of Endocrinology and MetabolismThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxiChina
| | - Zuo‐Tao Wu
- Department of Cardio‐Thoracic SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxiChina
| | - Yong‐Jie Zhu
- Department of Cardio‐Thoracic SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxiChina
| | - Ting Zhuo
- Department of Respiratory MedicineThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxiChina
| | - Ju‐Sen Nong
- Department of Pediatric SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxiChina
| | - Jing Qian
- Department of Cardio‐Thoracic SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxiChina
| | - Hua‐Jian Peng
- Department of Cardio‐Thoracic SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxiChina
| | - Lei Dai
- Department of Cardio‐Thoracic SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxiChina
| | - Yong‐Yong Wang
- Department of Cardio‐Thoracic SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxiChina
| | - Ming‐Wu Chen
- Department of Cardio‐Thoracic SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxiChina
| | - Xiao‐Chun Zeng
- Department of Cardio‐Thoracic SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxiChina
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Liang C, Pan W, Zhou Z, Liu X. Identification of prognostic biomarkers of smoking-related lung cancer. J Thorac Dis 2024; 16:1438-1449. [PMID: 38505085 PMCID: PMC10944783 DOI: 10.21037/jtd-23-1890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024]
Abstract
Background The early diagnosis and effective prognostic treatment measures for lung cancer are still limited, leading to a 5-year survival rate of less than 15% for these patients. Smoking is one of the causes of lung cancer, but it is not the initial carcinogenic factor. It is not clear what specific mechanism cigarette induces lung cancer, and there is a lack of research on the relationship between related genes and the prognosis of patients with smoking lung cancer. The objective of this study was to provide new theoretical evidence and potential therapeutic targets for the mechanisms of smoking-related lung cancer formation. Methods The gene expression profile data from the GSE12428 dataset which includes 63 lung cancer and normal tissue pairs were downloaded from the Gene Expression Omnibus (GEO) database, and data from smokers with lung cancer [both lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC)] from The Cancer Genome Atlas (TCGA) database were analyzed. The differential genes in smokers with lung cancer were screened using the linear model for microarray data via R software. The differential gene enrichment analysis was performed using the online analysis software Database for Annotation, Visualization and Integrated Discovery (DAVID). The expression levels of differential genes and their correlation with patient tumor clinical stage were analyzed using gene expression profiling interactive analysis (GEPIA). The overall survival rate was analyzed using Kaplan-Meier curves. Results In the GSE12428 dataset, 225 upregulated genes and 565 downregulated genes were identified in cancer tissues; based on smoking status, 1 upregulated gene and 4 downregulated genes were identified. Among smokers who also had lung cancer, 4 genes were downregulated, namely CSH1, BPIFA1, SLPI, and SCGB3A1. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that these genes were mainly associated with biological functions such as antibacterial response, humoral immune response, and response to external stimuli. Among them, BPIFA1, SLPI, and SCGB3A1 expression was decreased in lung cancer tissues, with SCGB3A1 showing significant differences. Additionally, high expression of SCGB3A1 was associated with favorable prognosis in patients with lung cancer. Conclusions Three genes BPIFA1, SLPI and SCGB3A1, were identified as being associated with smokers with lung cancer, with SCGB3A1 showing a close correlation with patient prognosis. These findings provide potential new targets for the treatment of lung cancer. Certainly, this study needs to more investigate the mechanism of these genes regulation.
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Affiliation(s)
- Chen Liang
- School of Public Health, Fudan University, Shanghai, China
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai, China
| | - Wei Pan
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai, China
| | - Zhijun Zhou
- School of Public Health, Fudan University, Shanghai, China
| | - Xiaomin Liu
- School of Public Health, Fudan University, Shanghai, China
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai, China
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Li C, Zhao J, Kang B, Li S, Tang J, Dong D, Chen Y. Identification and validation of STAT4 as a prognostic biomarker in acute myeloid leukemia. Biosci Rep 2024; 44:BSR20231720. [PMID: 38294290 PMCID: PMC10861362 DOI: 10.1042/bsr20231720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/11/2024] [Accepted: 01/30/2024] [Indexed: 02/01/2024] Open
Abstract
Acute myelogenous leukemia (AML) is a common malignancy and is supposed to have the ability to escape host immune surveillance. The present study aimed to identify key genes in AML that may affect tumor immunity and to provide prognosis biomarkers of AML. The Cancer Genome Atlas (TCGA) dataset was screened for transcription factors (TFs) involved in immunity and influencing survival, combining Gene Expression Omnibus (GEO) data to validate the impact on patient survival. A prognostic signature was established using four transcription factors, and these genes play an important role in the immune system, with higher regulatory T cell (Treg) scores in high-risk patients compared with the low-risk group. Analysis of individual genes showed that STAT4 and Treg are closely related, which may be due to STAT4 transcribing related genes that affect immunity. STAT4 expression was positively correlated with the proportion of abnormal cells and promoted AML recurrence as verified by AML clinical patient samples. In addition, silencing of STAT4 significantly slowed down the proliferation capacity of HL60 cells. In conclusion, these findings suggest that STAT4 may be a potential biomarker for AML prognosis. As a key gene affecting the prognosis of AML patients, STAT4 has the potential to be a candidate diagnostic and prognostic biomarker for AML.
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Affiliation(s)
- Chenyu Li
- Department of Pharmacy, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- College of Pharmacy, Dalian Medical University, Dalian, China
| | - Jingyuan Zhao
- Stem Cell Clinical Research Center, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Bingyu Kang
- Department of Pharmacy, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- College of Pharmacy, Dalian Medical University, Dalian, China
| | - Shuai Li
- Department of Pharmacy, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jingya Tang
- Department of Pharmacy, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Deshi Dong
- Department of Pharmacy, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yanwei Chen
- Department of Pharmacy, The First Affiliated Hospital of Dalian Medical University, Dalian, China
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Ouyang L, Jing K, Zhu C, Wang R, Zheng P. The presence of autoantibodies as a potential prognostic biomarker for breast cancer. Scand J Immunol 2024:e13365. [PMID: 38436518 DOI: 10.1111/sji.13365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/28/2024] [Accepted: 02/18/2024] [Indexed: 03/05/2024]
Abstract
The presence of autoantibodies is closely associated with the occurrence and development of cancer. Autoantibodies can be used as biomarkers for early breast cancer diagnosis. However, the relationship between autoantibodies and the prognosis of breast cancer patients remains elusive. This retrospective study aimed to investigate the correlation between the presence of autoantibodies and outcomes in breast cancer patients. This study included a total of 155 patients from People's Hospital of Henan University (Zhengzhou, China) who were diagnosed with breast cancer from January 2017 to December 2021. The enrolled patients' clinicopathological features were collected, and 88 patients were ultimately involved in the analysis. Univariate and multivariate Cox regression analyses were performed to search for the risk factors related to the poor prognosis of breast cancer patients. The association between the presence of autoantibodies and patients' survival was analysed using Kaplan-Meier curves. After screening, there were 38 autoantibody-positive cases and 50 autoantibody-negative cases. Breast cancer patients with autoantibody-positive had a 57% lower risk of death compared with autoantibody-negative patients. Multivariate Cox regression analysis indicated that the presence of autoantibody could be a potential prognostic predictor for breast cancer, independent of age, histological grade, pathological classification, clinical stage, and the expression levels of hormonal receptors. In addition, autoantibody-positive breast cancer patients had longer progression-free survival and overall survival compared with autoantibody-negative cases. Positive autoantibody was found as an independent biomarker of better prognosis in breast cancer patients, providing a new strategy for the prognostic assessment of breast cancer patients.
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Affiliation(s)
- Libo Ouyang
- Department of Clinical Laboratory, People's Hospital of Henan University, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Henan University, Zhengzhou, Henan, China
| | - Keying Jing
- Department of Clinical Laboratory, People's Hospital of Henan University, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Henan University, Zhengzhou, Henan, China
| | - Chunkai Zhu
- Department of Clinical Laboratory, People's Hospital of Henan University, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Henan University, Zhengzhou, Henan, China
| | - Rong Wang
- Department of Clinical Laboratory, People's Hospital of Henan University, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Henan University, Zhengzhou, Henan, China
| | - Peiming Zheng
- Department of Clinical Laboratory, People's Hospital of Henan University, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Henan University, Zhengzhou, Henan, China
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Pashirzad M, Sahebkar A. The Prognostic Value and Clinical Significance of lncRNA SNHG5 Expression in Patients with Multiple Malignancies: A Bioinformatic and Meta-Analysis. Curr Cancer Drug Targets 2024; 24:CCDT-EPUB-138740. [PMID: 38409690 DOI: 10.2174/0115680096282865240111055640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 02/28/2024]
Abstract
BACKGROUND Long non-coding RNA small nucleolar RNA host gene 5 (lncRNA SNHG5) has been identified as both a promising target for treatment and a predictor of prognosis in diverse types of cancer. The objective of this study was to assess whether lncRNA SNHG5 expression can be utilized as a prognostic biomarker for human cancer. METHODS To ensure a thorough search of the literature for relevant English studies published before July 2023, several databases were searched, including PubMed, Web of Science, ProQuest, Cochrane Library, and Google Scholar. The study evaluated the impact of lncRNA SNHG5 on the overall survival (OS) of cancer by calculating the pooled hazard ratio (HR) and odds ratio (OR) with 95% confidence intervals (CIs). To further confirm the accuracy of the findings, the study investigated the expression profile and prognostic significance of lncRNA SNHG5 through the use of GenomicScape, OncoLnc, Kaplan-Meier plotter, and GEPIA databases. RESULTS In this study, 995 patients were examined across a total of fourteen original studies. The findings indicated that there was a significant relationship between heightened lncRNA SNHG5 expression and reduced OS, as evidenced by both univariate and multivariate analyses (HR = 1.89; 95% CI, 1.44-2.49; p < 0.001; HR = 3.97; 95% CI, 1.80-8.73; p < 0.001, respectively). Pooled OR analysis showed a significant association between over-expression of lncRNA SNHG5 with advanced histological grade (OR = 0.28; 95% CI, 0.11-0.71; p = 0.007), present lymph node metastasis (LNM; OR = 4.28; 95% CI, 2.47-7.43; p < 0.001), and smoking history (OR = 0.27; 95% CI, 0.15-0.49; p < 0.001). Bioinformatic databases confirmed that elevated SNHG5 expression was significantly linked to poor prognosis in cancer patients, including colorectal cancer (CRC), acute myeloid leukemia (AML), and esophageal adenocarcinoma (ESAD), and a longer OS in patients with uterine corpus endometrial carcinoma (UCEC). CONCLUSION These results suggest that lncRNA SNHG5 may serve as an adverse prognostic biomarker in several human cancers. Further investigations are needed to better understand the underlying mechanisms that link lncRNA SNHG5 to multiple malignancies.
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Affiliation(s)
- Mehran Pashirzad
- Department of Medical Biochemistry, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
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12
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Wang L, Li M, Yang H, Dai F, Xie N, Li L, Zhu M, Ding R. Subtype recognition and identification of a prognosis model characterized by antibody-dependent cell phagocytosis-related genes in breast cancer. Aging (Albany NY) 2024; 16:4014-4032. [PMID: 38393698 DOI: 10.18632/aging.205575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/23/2024] [Indexed: 02/25/2024]
Abstract
BACKGROUND Breast cancer (BC) is a heterogeneous tumor with a variety of etiology and clinical features. Antibody-dependent cell phagocytosis (ADCP) is the last step of immune checkpoint inhibition (ICI), and macrophages detect and recognize tumor cells, then destroy and engulf tumor cells. Despite the large number, negative regulators that inhibit phagocytic activity are still a key obstacle to the full efficacy of ICI. PATIENTS AND METHODS An ADCP-related risk score prognostic model for risk stratification as well as prognosis prediction was established in the Cancer Genome Atlas (TCGA) cohort. The predictive value of ADCP risk score in prognosis and immunotherapy was also further validated in the TCGA along with International Cancer Genome Consortium cohorts. To promote the clinical application of the risk score, a nomogram was established, with its effectiveness verified by different methods. RESULTS In this study, the genes collected from previous studies were defined as ADCP-related genes. In BC patients, two ADCP-related subtypes were identified. The immune characteristics and prognostic stratification were significant different between them. CONCLUSIONS We identified two subtypes associated with ADCP gene expression in breast cancer. They have significant differences in immune cells, molecular functions, HLA family genes, immune scores, stromal scores, and inflammatory gene expression, which have important guiding significance for the selection of clinical treatment methods. At the same time, we constructed a risk model based on ADCP, and the risk score can be used as a good indicator of prognosis, providing potential therapeutic advantages for chemotherapy and immunotherapy, thus helping the clinical decision-making of BC patients.
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Affiliation(s)
- Li Wang
- Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin 300060, China
| | - Menghan Li
- Acupuncture-Moxibustion Clinical Department, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 300381, China
| | - Hongyu Yang
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300381, China
| | - Fenghuan Dai
- Acupuncture-Moxibustion Clinical Department, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
| | - Ning Xie
- Acupuncture-Moxibustion Clinical Department, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300381, China
| | - Linhui Li
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin 300381, China
| | - Meiying Zhu
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300381, China
| | - Ran Ding
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, China
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13
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Chen J, Wu Y, Zhao H, Ruan G, Qin S. Ratio of hemoglobin to red cell distribution width: an inflammatory predictor of survival in AIDS-related DLBCL. Front Immunol 2024; 15:1354325. [PMID: 38426083 PMCID: PMC10901994 DOI: 10.3389/fimmu.2024.1354325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024] Open
Abstract
Background Despite the introduction of combined antiretroviral therapy, AIDS-related diffuse large B-cell lymphoma (AR-DLBCL) remains a prominent cancer among individuals living with HIV with a suboptimal prognosis. Identifying independent prognostic markers could improve risk stratification. Methods In this multicenter retrospective cohort study spanning years 2011 to 2019, 153 eligible patients with AR-DLBCL were examined. Overall survival (OS) factors were analyzed using Kaplan-Meier curves, and univariate and multivariate Cox proportional hazards models. The discriminatory ability of the risk score was evaluated by examining the area under the receiver operating characteristic curve. Results The study included 153 patients with a median age of 47 years (interquartile range [IQR] 39-58), 83.7% of whom were men. The median follow-up was 12.0 months (95% confidence interval [CI], 8.5-15.5), with an OS rate of 35.9%. Among the potential inflammatory markers examined, only the ratio of hemoglobin (g/dL) to red cell distribution width (%) (Hb/RDW) emerged as an independent prognostic parameter for OS in the training (hazard ratios [HR] = 2.645, 95% CI = 1.267-5.522, P = 0.010) and validation cohorts (HR = 2.645, 95% CI = 1.267-5.522, P = 0.010). A lower Hb/RDW ratio was strongly correlated with adverse clinical factors, including advanced Ann Arbor stage, increased extranodal sites, reduced CD4 count, elevated lactate dehydrogenase levels, poorer Eastern Cooperative Oncology Group performance status (ECOG PS), and a higher International Prognostic Index (IPI) score. The addition of the Hb/RDW ratio to the IPI produced a highly discriminatory prognostic composite score, termed Hb/RDW-IPI. Conclusion We identified a cost-effective and readily available inflammatory biomarker, the Hb/RDW ratio, as an independent predictor of outcomes in patients with AR-DLBCL. Its integration into the IPI score partially improves prognostic accuracy.
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Affiliation(s)
- Juanjuan Chen
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- State Key Laboratory of Organ Failure Research, Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Guangdong Institute of Hepatology, Guangzhou, China
| | - Yihua Wu
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- State Key Laboratory of Organ Failure Research, Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Guangdong Institute of Hepatology, Guangzhou, China
| | - Han Zhao
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- State Key Laboratory of Organ Failure Research, Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Guangdong Institute of Hepatology, Guangzhou, China
- Infectious Diseases Center, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Guangjing Ruan
- Guangxi AIDS Clinical Treatment Center, The Fourth People’s Hospital of Nanning, Nanning, China
| | - Shanfang Qin
- Guangxi AIDS Diagnosis and Treatment Quality Control Center, Chest Hospital of Guangxi Zhuang Autonomous Region, Liuzhou, China
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Murck H, Fava M, Cusin C, Fatt CC, Trivedi M. Brain ventricle and choroid plexus morphology as predictor of treatment response in major depression: Findings from the EMBARC study. Brain Behav Immun Health 2024; 35:100717. [PMID: 38186634 PMCID: PMC10767278 DOI: 10.1016/j.bbih.2023.100717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/09/2024] Open
Abstract
Recent observations suggest a role of the volume of the cerebral ventricle volume, corpus callosum (CC) segment volume, in particular that of the central-anterior part, and choroid plexus (CP) volume for treatment resistance of major depressive disorder (MDD). An increased CP volume has been associated with increased inflammatory activity and changes in the structure of the ventricles and corpus callosum. We attempt to replicate and confirm that these imaging markers are associated with clinical outcome in subjects from the EMBARC study, as implied by a recent pilot study. The EMBARC study is a placebo controlled randomized study comparing sertraline vs. placebo in patients with MDD to identify biological markers of therapy resistance. Association of baseline volumes of the lateral ventricles (LVV), choroid plexus volume (CPV) and volume of segments of the CC with treatment response after 4 weeks treatment was evaluated. 171 subjects (61 male, 110 female) completed the 4 week assessments; gender and age were taken into account for this analyses. As previously reported, no treatment effect of sertraline vs. placebo was observed, therefore the study characterized prognostic markers of response in the pooled population. Change in depression severity was identified by the ratio of the Hamilton-Depression rating scale 17 (HAMD-17) at week 4 divided by the HAMD-17 at baseline (HAMD-17 ratio). Volumes of the lateral ventricles and choroid plexi were positively correlated with the HAMD-17 ratio, indication worse outcome with larger ventricles and choroid plexus volumes, whereas the volume of the central-anterior corpus callosum was negatively correlated with the HAMD-17 ratio. Responders (n = 54) had significantly smaller volumes of the lateral ventricles and CP compared to non-responders (n = 117), whereas the volume of mid-anterior CC was significantly larger compared to non-responders (n = 117), confirming our previous findings. In an exploratory way associations between enlarged LVV and CPV and signs of lipid dysregulation were observed. In conclusion, we confirmed that volumes of lateral ventricles, choroid plexi and the mid-anterior corpus callosum are associated with clinical improvement of depression and may be indicators of metabolic/inflammatory activity.
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Affiliation(s)
- Harald Murck
- Dept. of Psychiatry and Psychotherapy, Philipps-University Marburg, Marburg, Germany
| | - Maurizio Fava
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cristina Cusin
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cherise Chin Fatt
- The University of Texas Southwestern Medical Center, Department of Psychiatry, Center for Depression Research and Clinical Care, Dallas, USA
| | - Madhukar Trivedi
- The University of Texas Southwestern Medical Center, Department of Psychiatry, Center for Depression Research and Clinical Care, Dallas, USA
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15
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Hamayal M, Khurshied S, Zahid MA, Khurshid N, Shahid W, Ali M, Ahmed H, Nisa M. Exploring the Significance of Vitamin D Levels as a Biomarker in Ear Diseases: A Narrative Review. Cureus 2024; 16:e54812. [PMID: 38529449 PMCID: PMC10962011 DOI: 10.7759/cureus.54812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2024] [Indexed: 03/27/2024] Open
Abstract
This narrative review examines the role of vitamin D as a biomarker in ear disorders, including benign paroxysmal positional vertigo (BPPV), otitis media, bell's palsy, Meniere's disease, and hearing loss. PubMed, The Cochrane Library, and Google Scholar were utilized to conduct a comprehensive literature search, and findings were combined from studies from 2014 to 2024. As highlighted in this review, there is a consistent association between vitamin D deficiency and an increased risk and recurrence of disease especially in BPPV and otitis media. Its importance as a prognostic biomarker is emphasized in Bell's palsy, where higher levels of deficiencies in vitamin D are associated with higher grades of severity on the House Brackmann grading system. Vitamin D deficiency can also lead to sensorineural hearing loss due to its receptors present in the inner ear or its effect on calcium metabolism. Serum levels of vitamin D have also been shown to influence treatment outcome of sensorineural hearing loss. The role of vitamin D in Meniere's disease is unclear as no cause has been identified for the increase in endolymphatic fluid. The findings of this review emphasize the importance of serum vitamin D as a biomarker in ear disorders and advocate for more studies to be conducted to assess the importance of optimal dosing of vitamin D for the progression and outcome of these diseases.
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Affiliation(s)
- Muhammad Hamayal
- Otorhinolaryngology, Pakistan Institute of Medical Sciences, Islamabad, PAK
| | - Saleh Khurshied
- Otorhinolaryngology, Pakistan Institute of Medical Sciences, Islamabad, PAK
| | | | - Nawal Khurshid
- Otorhinolaryngology, Pakistan Institute of Medical Sciences, Islamabad, PAK
| | - Warda Shahid
- Otorhinolaryngology, Federal Medical College, Islamabad, PAK
| | - Maesum Ali
- Otorhinolaryngology, Pakistan Institute of Medical Sciences, Islamabad, PAK
| | - Hammad Ahmed
- Paediatrics, Fauji Foundation Hospital, Rawalpindi, PAK
| | - Mehrun Nisa
- Medicine and Surgery, Pakistan Institute of Medical Sciences, Islamabad, PAK
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Mullen SA, Das D, Ziamiavaghi N, High R, Datta K, Teply BA. Association of plasma NRP2 and VEGF-C levels with prostate cancer disease severity. Prostate 2024; 84:277-284. [PMID: 37942701 PMCID: PMC10842186 DOI: 10.1002/pros.24648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
BACKGROUND Neuropilin 2 (NRP2) expression in tissue is an independent prognostic factor for aggressive prostate cancer. Since the NRP2 pathway activation is thought to occur in part through secondary resistance, quantification of NRP2 in initial tissue biopsy specimens collected at diagnosis may have limited utility in identifying patients at highest risk for morbidity and mortality. Given that metastatic tissue is only occasionally obtained for analysis, there is a need for development of a plasma biomarker indicative of NRP2 pathway activation to potentially inform prostate cancer prognosis. Therefore, we investigated if plasma levels of NRP2 or vascular endothelial growth factor C (VEGF-C), a known soluble ligand of NRP2, are prognostic for prostate cancer. We hypothesized that plasma NRP2 and VEGF-C would be associated with more advanced disease or relapsed disease. METHODS NRP2 and VEGF-C levels were quantified by enzyme-linked immunoassay in plasma samples obtained from 145 prostate cancer patients in an opportunistic biobank. These patients were either (1) newly diagnosed (N = 28), (2) in remission (N = 56), or (3) relapsed disease (N = 61). Plasma samples from 15 adult males without known malignancy served as a comparator cohort. Statistical analysis was performed to investigate the association of plasma NRP2/VEGF-C with patient outcomes, adjusting for age, race, prostate-specific antigen (PSA), Gleason score, and tumor stage at diagnosis. RESULTS Neither NRP2 nor VEGF-C levels were significantly different in cancer patients compared to noncancer controls. We observed no clear association between plasma NRP2 and disease severity. Increased plasma VEGF-C was significantly associated with disease remission and correlated with Stage I/II and intermediate-risk Gleason score. Neither NRP2 nor VEGF-C correlated with PSA level. CONCLUSIONS Although tissue NRP2 expression correlates with severe disease, this was not observed for plasma NRP2. Plasma NRP2 levels did not correlate with disease severity or relapse. VEGF-C was highest in patients in remission and with less severe disease. Future investigation is needed to identify noninvasive methods to assess tumor NRP2 status.
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Affiliation(s)
- Sarah A Mullen
- Department of Internal Medicine, Division of Hematology/Oncology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Dipanwita Das
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Negin Ziamiavaghi
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Robin High
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Kaustubh Datta
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Benjamin A Teply
- Department of Internal Medicine, Division of Hematology/Oncology, University of Nebraska Medical Center, Omaha, Nebraska, USA
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Sha Y, Liang W, Mo C, Hou X, Ou M. Multi‑dimensional analysis reveals NCKAP5L is a promising biomarker for the diagnosis and prognosis of human cancers, especially colorectal cancer. Oncol Lett 2024; 27:53. [PMID: 38192666 PMCID: PMC10773189 DOI: 10.3892/ol.2023.14186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/15/2023] [Indexed: 01/10/2024] Open
Abstract
The Nck-associated protein 5-like (NCKAP5L) gene, also known as Cep169, is associated with certain cancers. However, the diagnosis and prognosis value of NCKAP5L in several types of human cancer, including colorectal cancer, is not fully understood. In the present study, a comprehensive pan-cancer analysis of NCKAP5L was performed using several approaches, including gene expression and alteration, protein phosphorylation, immune infiltration, survival prognosis analyses and gene enrichment using the following: The University of California Santa Cruz Genome Browser Human Dec. 2013 (GRCh38/hg38) Assembly, Tumor Immune Estimation Resource (version 2), Human Protein Atlas, Gene Expression Profiling Interactive Analysis (version 2), University of Alabama at Birmingham Cancer Data Analysis portal, the Kaplan-Meier Plotter, cBioportal, Search Tool for the Retrieval of Interacting Genes/Proteins, Jvenn and the Metascape server. The role of NCKAP5L in colorectal cancer was further assessed by reverse transcription-quantitative PCR. The results demonstrated that NCKAP5L was upregulated in the majority of cancer types, including colorectal cancer. The high expression of NCKAP5L was significantly correlated with patient survival prognosis and immune infiltration of cancer-associated fibroblasts in numerous types of cancer, including colorectal cancer. Furthermore, Gene Ontology analysis identified that NCKAP5L may serve an important role in metabolic and cellular processes in human cancers. In summary, the data from the present study demonstrate that NCKAP5L is a potential tumor biomarker for the diagnosis and prognosis of human cancers, especially colorectal cancer.
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Affiliation(s)
- Yu Sha
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541199, P.R. China
| | - Wenken Liang
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541199, P.R. China
| | - Chune Mo
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541199, P.R. China
| | - Xianliang Hou
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541199, P.R. China
| | - Minglin Ou
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541199, P.R. China
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Chan DL, Hayes AR, Karfis I, Conner A, Mileva M, Bernard E, Schembri G, Navalkissoor S, Gnanasegaran G, Pavlakis N, Marin C, Vanderlinden B, Flamen P, Roach P, Caplin ME, Toumpanakis C, Bailey DL. [ 18F]FDG PET/CT-Avid Discordant Volume as a Biomarker in Patients with Gastroenteropancreatic Neuroendocrine Neoplasms: A Multicenter Study. J Nucl Med 2024; 65:185-191. [PMID: 38164579 PMCID: PMC10858377 DOI: 10.2967/jnumed.123.266346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/25/2023] [Indexed: 01/03/2024] Open
Abstract
[18F]FDG PET/CT and [68Ga]Ga-DOTATATE PET/CT are both used to predict tumor biology in neuroendocrine neoplasms. Although the presence of discordant ([18F]FDG-avid/non-[68Ga]Ga-DOTATATE-avid) disease predicts poor prognosis, the significance of the volume of such discordant disease remains undetermined. The aim of this study is to investigate discordant tumor volume as a potential biomarker in patients with advanced gastroenteropancreatic neuroendocrine neoplasms (GEPNENs). Methods: A multicenter retrospective study in patients with advanced GEPNENs and paired [18F]FDG and [68Ga]Ga-DOTATATE PET/CT no more than 85 d apart was conducted. Patients with discordant disease were identified by the NETPET score, and discordant lesions were contoured with a flat [18F]FDG SUV cutoff of 4. The primary variable of interest was the total discordant volume (TDV), which was the sum of the volumes of discordant lesions. Patients were dichotomized into high- and low-TDV cohorts by the median value. The primary endpoint was overall survival. Results: In total, 44 patients were included (50% men; median age, 60 y), with primary cancers in the pancreas (45%), small bowel (23%), colon (20%), and other (12%). Of the patients, 5% had grade 1 disease, 48% had grade 2 disease, and 48% had grade 3 disease (24% well differentiated, 67% poorly differentiated, 10% unknown within the grade 3 cohort). The overall median survival was 14.1 mo. Overall survival was longer in the low-TDV cohort than in the high-TDV cohort (median volume, 43.7 cm3; survival time, 23.8 mo vs. 9.4 mo; hazard ratio, 0.466 [95% CI, 0.229-0.948]; P = 0.0221). Patients with no more than 2 discordant intrahepatic lesions survived longer than those with 2 or more lesions (31.8 mo vs. 10.2 mo, respectively; hazard ratio, 0.389 [95% CI, 0.194-0.779]; P = 0.0049). Conclusion: TDV is a potential prognostic biomarker in GEPNENs and should be investigated in future neuroendocrine neoplasm trials.
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Affiliation(s)
- David L Chan
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia;
- Medical Oncology, ENETS Centre of Excellence, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Aimee R Hayes
- Neuroendocrine Tumour Unit, ENETS Centre of Excellence, Royal Free Hospital, London, United Kingdom
| | - Ioannis Karfis
- Nuclear Medicine Department, Institut Jules Bordet, ENETS Centre of Excellence, Hôpital Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | - Alice Conner
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Magdalena Mileva
- Nuclear Medicine Department, Institut Jules Bordet, ENETS Centre of Excellence, Hôpital Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | - Elizabeth Bernard
- Nuclear Medicine, ENETS Centre of Excellence, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Geoffrey Schembri
- Nuclear Medicine, ENETS Centre of Excellence, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Shaunak Navalkissoor
- Neuroendocrine Tumour Unit, ENETS Centre of Excellence, Royal Free Hospital, London, United Kingdom
- Nuclear Medicine, ENETS Centre of Excellence, Royal Free Hospital, London, United Kingdom; and
| | - Gopinath Gnanasegaran
- Neuroendocrine Tumour Unit, ENETS Centre of Excellence, Royal Free Hospital, London, United Kingdom
- Nuclear Medicine, ENETS Centre of Excellence, Royal Free Hospital, London, United Kingdom; and
| | - Nick Pavlakis
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
- Medical Oncology, ENETS Centre of Excellence, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Clémentine Marin
- Nuclear Medicine Department, Institut Jules Bordet, ENETS Centre of Excellence, Hôpital Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | - Bruno Vanderlinden
- Medical Physics Department, Institut Jules Bordet, ENETS Centre of Excellence, Hôpital Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | - Patrick Flamen
- Nuclear Medicine Department, Institut Jules Bordet, ENETS Centre of Excellence, Hôpital Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | - Paul Roach
- Nuclear Medicine, ENETS Centre of Excellence, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Martyn E Caplin
- Neuroendocrine Tumour Unit, ENETS Centre of Excellence, Royal Free Hospital, London, United Kingdom
| | - Christos Toumpanakis
- Neuroendocrine Tumour Unit, ENETS Centre of Excellence, Royal Free Hospital, London, United Kingdom
| | - Dale L Bailey
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
- Nuclear Medicine, ENETS Centre of Excellence, Royal North Shore Hospital, Sydney, New South Wales, Australia
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Xu B, Liang J, Fu L, Lin J, Wei J. A Novel Oncogenic Role of Disulfidptosis-related Gene SLC7A11 in Anti--tumor Immunotherapy Response to Human Cancers. Curr Cancer Drug Targets 2024; 24:CCDT-EPUB-138240. [PMID: 38303526 DOI: 10.2174/0115680096277818231229105732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/22/2023] [Accepted: 11/08/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND The protein Solute Carrier Family 7 Member 11 (SLC7A11) plays a pivotal role in cellular redox homeostasis by suppressing disulfidptosis, which restricts tumor growth. Yet, its relevance in prognosis, immunity, and cancer treatment efficacy is not well understood. METHODS We conducted a comprehensive analysis of the expression of SLC7A11 across 33 cancer types, employing datasets from public databases. Methods, such as Cox regression and survival analyses assessed its prognostic significance, while functional enrichment explored the biological processes tied to SLC7A11. The association between SLC7A11 expression, immune cell infiltration, and immune-related gene expression was also scrutinized. RESULTS Notably, SLC7A11 expression was more pronounced in cancerous compared to normal samples and correlated with higher tumor grades. Increased SLC7A11 expression was linked to poor outcomes, particularly in liver hepatocellular carcinoma (LIHC). This protein's expression also showcased significant relationships with diverse molecular and immune subtypes. Additionally, a prognostic nomogram was devised, integrating SLC7A11 expression and clinical variables. High SLC7A11 levels corresponded with cell growth and senescence pathways in various cancers and with lipid and cholesterol metabolism in LIHC. Furthermore, potential therapeutic compounds for LIHC with high SLC7A11 were identified. Real-time PCR (qPCR) and Western blot were conducted to explore the expression of SLC7A11 in tumor tissues and cancer cell lines. CONCLUSION In summation, this study emphasizes the prognostic and immunological importance of SLC7A11, spotlighting its potential as a therapeutic target in LIHC.
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Affiliation(s)
- Borui Xu
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Jiahua Liang
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Liangmin Fu
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China
- Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China
| | - Juan Lin
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China
| | - Jinhuan Wei
- Department of Pediatrics, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, People's Republic of China
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Zhang D, Zhao F, Liu H, Guo P, Li Z, Li S. FABP6 serves as a new therapeutic target in esophageal tumor. Aging (Albany NY) 2024; 16:1640-1662. [PMID: 38277205 PMCID: PMC10866426 DOI: 10.18632/aging.205448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/04/2023] [Indexed: 01/27/2024]
Abstract
BACKGROUND Esophageal cancer is one of the most common malignant tumors with high incidence and mortality rates. Despite the continuous development of treatment options, the prognosis for esophageal cancer patients remains poor. Therefore, there is an urgent need for new diagnostic and therapeutic targets in clinical practice to improve the survival of patients with esophageal cancer. METHODS In this study, we conducted a comprehensive scRNA-seq analysis of the tumor microenvironment in primary esophageal tumors to elucidate cell composition and heterogeneity. Using Seurat, we identified eight clusters, encompassing non-immune cells (fibroblasts, myofibroblasts, endothelial cells, and epithelial cells) and immunocytes (myeloid-derived cells, T cells, B cells, and plasma cells). Compared to normal tissues, tumors exhibited an increased proportion of epithelial cells and alterations in immune cell infiltration. Analysis of epithelial cells revealed a cluster (cluster 0) with a high differentiation score and early distribution, suggesting its importance as a precursor cell. RESULTS Cluster 0 was characterized by high expression of FABP6, indicating a potential role in fatty acid metabolism and tumor growth. T cell analysis revealed shifts in the balance between Treg and CD8+ effector T cells in tumor tissues. Cellular communication analysis identified increased interactions between FABP6+ tumor cells and T cells, with the involvement of the MIF-related pathway and the CD74-CD44 interaction. This study provides insights into the cellular landscape and immune interactions within esophageal tumors, contributing to a better understanding of tumor heterogeneity and potential therapeutic targets.
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Affiliation(s)
- Dengfeng Zhang
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, China
| | - Fangchao Zhao
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, China
| | - Haitao Liu
- College of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010031, China
| | - Pengfei Guo
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, China
| | - Zhirong Li
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, China
| | - Shujun Li
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, China
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21
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Zhang M, Chen F, Feng S, Liu X, Wang Z, Shen N, Meng L, Zhu D, Zhu Z. FBLN5 as One Presumably Prognostic Gene Potentially Modulating Tumor Immune Microenvironment for Renal Clear Cell Carcinoma in Children and Young Adults. Pharmgenomics Pers Med 2024; 17:27-40. [PMID: 38264064 PMCID: PMC10804877 DOI: 10.2147/pgpm.s442803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/13/2024] [Indexed: 01/25/2024] Open
Abstract
Objective To investigate the role of FBLN5in renal clear cell carcinoma (KIRC), in particular on the tumor's immune microenvironment, including children and young adults. Methods FBLN5 expression in tumor and normal samples was explored using SangerBox, TIMER2.0, GEPIA, UALCAN, HPA databases. The Linkedomics database was used to obtain FBLN5 co-expressed genes in KIRC tissue. SangerBox was also used to estimate immune infiltration of FBLN5 in KIRC. The Kaplan-Meier plotter was used to investigate the survival effects of FBLN5 expression in the presence of immune infiltration. We then collected 48 cases from 7 hospitals over a-20 year period to calculate the impact of FBLN5 on the prognosis of children and young adults with KIRC. Results FBLN5 expression was significantly reduced in KIRC tissue compared to normal adjacent tissue. FBLN5 was potentially involved in the immune-related biological processes. In addition, FBLN5 expression has been linked to a number of immune checkpoints, cytokines, chemokines and chemokine receptors in KIRC. At the same time, the expression of FBLN5 affected the survival rates differently in KIRC patients with high or low levels of immune infiltration. High expression of FBLN5 in children and young adults with KIRC was associated with a favorable prognosis. Conclusion This study shed light on the potential of FBLN5 as a prognostic marker in children and young adults with KIRC and as an immune-related target for clinical treatment.
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Affiliation(s)
- Ming Zhang
- Department of Pediatric Surgery, The First People’s Hospital of Lianyungang, Lianyungang, People’s Republic of China
| | - Feng Chen
- Department of Pediatric, Luodian Hospital, Shanghai, People’s Republic of China
| | - Shaoguang Feng
- Department of Pediatric Surgery, The Children’s Hospital of Hangzhou, Hangzhou, People’s Republic of China
| | - Xu Liu
- Department of Pediatric Surgery, The Children’s Hospital of Xuzhou, Xuzhou, People’s Republic of China
| | - Zhen Wang
- Department of Pediatric, the Maternal and Child Health Hospital of Zibo, Zibo, People’s Republic of China
| | - Nan Shen
- Department of Pediatrics, Suqian Hospital Affiliated to Xuzhou Medical University, Suqian, People’s Republic of China
| | - Lingjian Meng
- Department of Pediatrics, Hospital Affiliated to Xuzhou Medical University, Xuzhou, People’s Republic of China
| | - Dongsheng Zhu
- Department of Pediatric Surgery, The First People’s Hospital of Lianyungang, Lianyungang, People’s Republic of China
| | - Zhitao Zhu
- Department of Radiology, The Second People’s Hospital of Lianyungang, Lianyungang, People’s Republic of China
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22
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Lin S, Yu X, Yan H, Xu Y, Ma K, Wang X, Liu Y, Xie A, Yu Z. E2F7 serves as a potential prognostic biomarker for lung adenocarcinoma. Medicine (Baltimore) 2024; 103:e34342. [PMID: 38241554 PMCID: PMC10798722 DOI: 10.1097/md.0000000000034342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/23/2023] [Indexed: 01/21/2024] Open
Abstract
E2F transcription factors (E2Fs) are a family of transcription factors critical regulators of the cell cycle, apoptosis, and differentiation, thus influencing tumorigenesis. However, the specific roles of E2Fs in lung adenocarcinoma (LUAD) remain unclear. Data from The Cancer Genome Atlas (TCGA) were used. R version. 4.0.3 and multiple databases (TIMER, cBioportal, gene expression profile interaction analysis [GEPIA], LinkedOmics, and CancerSEA) were utilized to investigate mRNA expression, mutational analysis, prognosis, clinical correlations, co-expressed gene, pathway and network, and single-cell analyses. Immunohistochemistry (IHC) confirmed that E2F transcription factor 7 (E2F7) correlated with LUAD. Among the E2Fs, E2F7 was identified by constructing a prognostic model most significantly associated with overall survival (OS) in LUAD patients. The univariate and multivariate Cox regression analyses showed that E2F7, p-T stage, and p-TNM stage were closely related to OS and progression-free survival (PFS) (P < .05) in LUAD. E2F 7/8 were also identified as significantly associated with tumor stage in the GEPIA database. Compared with paracancerous tissues, E2F7 was up-regulated in LUAD by IHC, and E2F7 might be positively correlated with larger tumors and higher TNM stages. E2F7 may primarily regulate DNA repair, damage, and cell cycle processes and thus affect LUAD tumorigenesis, invasion, and metastasis by LinkedOmics and CancerSEA. E2F7 serves as a potential prognostic biomarker for LUAD.
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Affiliation(s)
- Shengcheng Lin
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Xiangyang Yu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Haojie Yan
- Translational Medicine Collaborative Innovation Center, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affifiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Basic Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
| | - Yafei Xu
- Department of Anesthesiology, Shunde Hospital of Southern Medical University (The First People’s Hospital of Shunde Foshan), Foshan, China
| | - Kai Ma
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Xiaoliang Wang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Yeqing Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Ahuan Xie
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Zhentao Yu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
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23
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Nelson ED, Benesch MGK, Wu R, Ishikawa T, Takabe K. High EIF4EBP1 expression reflects mTOR pathway activity and cancer cell proliferation and is a biomarker for poor breast cancer prognosis. Am J Cancer Res 2024; 14:227-242. [PMID: 38323277 PMCID: PMC10839327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 12/21/2023] [Indexed: 02/08/2024] Open
Abstract
Eukaryotic translation initiation factor 4E binding protein 1 (EIF4EBP1) is regulated by the mTOR (mammalian target of rapamycin) signaling pathway. Phosphorylated EIF4EBP1 protein leads to pathway activation and correlates with aggressive breast cancer features. However, the clinical relevance of EIF4EBP1 gene expression as a prognostic biomarker in bulk breast tumors is not understood. In this study, EIF4EBP1 expression was analyzed in over 5000 breast cancers from three large independent cohorts, TCGA, METABRIC, and SCAN-B (GSE96058), and expression was dichotomized into low and high groups by the median. We also performed gene set enrichment analysis (GSEA) and cell cybersorting via the xCell algorithm to investigate EIF4EBP1 biology and expression patterns within the tumor microenvironment (TME). We additionally confirmed EIF4EBP1 expression location in the TME via single cell RNA sequencing. EIF4EBP1 expression was highest in both triple negative and high-grade tumors (both P<0.001), and tumor mutational burden scores were highest in the high EIF4EBP1-expression groups (all P<0.001). High EIF4EBP1 expression significantly correlated to worse overall survival in all three cohorts (hazard ratios (HR) 1.4-1.9), and worse distant relapse-free survival in patients treated with neoadjuvant taxane-anthracycline chemotherapy (HR 2.4). GSEA demonstrated enriched mTOR and cell proliferation-related gene sets, including, MYC, G2M checkpoint, and E2F targets across all three bulk tumor and single cell RNA sequencing cohorts. Phenotypically, these pathways were reflected by increased Ki67 gene expression and signaling via pharmacologically-activated mTOR gene sets in EIF4EBP1 high-expressing tumors (all P<0.001). EIF4EBP1 expression was increased in whole breast tumors compared to normal breast tissue (P<0.001), and was expressed predominantly in cancer epithelial cells, particularly in basal epithelial cell subclasses. EIF4EBP1 expression did not correlate to a consistent immune system phenotype across all three cohorts. Overall, these findings support that high EIF4EBP1 gene expression in bulk breast tumors could represent a poor prognostic marker via mTOR signaling pathways activation and upregulation of cell cycling, ultimately leading to increased tumorigenesis.
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Affiliation(s)
- Erek D Nelson
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
| | - Matthew GK Benesch
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
| | - Rongrong Wu
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo 160-8402, Japan
| | - Takashi Ishikawa
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo 160-8402, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer CenterBuffalo, NY 14263, USA
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo 160-8402, Japan
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama 236-0004, Japan
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental SciencesNiigata 951-8520, Japan
- Department of Breast Surgery, Fukushima Medical University School of MedicineFukushima 960-1295, Japan
- Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, State University of New YorkBuffalo, NY 14263, USA
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Wang T, Guo K, Yang S, Zhang D, Cui H, Yin J, Yuan S, Wang Y, Qi Y, Wu W. Identification and validation of SLCO4C1 as a biological marker in hepatocellular carcinoma based on anoikis classification features. Aging (Albany NY) 2024; 16:1440-1462. [PMID: 38226966 PMCID: PMC10866452 DOI: 10.18632/aging.205438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/04/2023] [Indexed: 01/17/2024]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) exhibits a high degree of invasiveness and is closely associated with rapid disease progression. Multiple lines of evidence indicate a strong correlation between anoikis resistance and tumor progression, invasion, and metastasis. Nevertheless, the classification of anoikis in HCC and the investigation of novel biological target mechanisms in this context continue to pose challenges, requiring further exploration. METHODS Combined with HCC samples from TCGA, GEO and ICGC databases, cluster analysis was conducted on anoikis genes, revealing novel patterns among different subtypes. Significant gene analysis of different gene subtypes was performed using WCGNA. The anoikis prognostic risk model was established by Lasso-Cox. Go, KEGG, and GSEA were applied to investigate pathway enrichment primarily observed in risk groups. We compared the disparities in immune infiltration, TMB, tumor microenvironment (TME), and drug sensitivity between the two risk groups. RT-qPCR and Western blotting were performed to validate the expression levels of SLCO4C1 in HCC. The biological functions of SLCO4C1 in HCC cells were assessed through various experiments, including CCK8 assay, colony formation assay, invasion migration assay, wound healing assay, and flow cytometry analysis. RESULTS HCC was divided into 2 anoikis subtypes, and the subtypeB had a better prognosis. An anoikis prognostic model based on 12 (COPZ2, ACTG2, IFI27, SPP1, EPO, SLCO4C1, RAB26, STC2, RAC3, NQO1, MYCN, HSPA1B) risk genes is important for survival and prognosis. Significant differences were observed in immune cell infiltration, TME, and drug sensitivity analysis between the risk groups. SLCO4C1 was downregulated in HCC. SLCO4C1 downregulation promoted the proliferation, invasion, migration, and apoptosis of HCC cells. The tumor-suppressive role of SLCO4C1 in HCC has been confirmed. CONCLUSIONS Our study presents a novel anoikis classification method for HCC that reveals the association between anoikis features and HCC. The anoikis feature is a critical biomarker bridging tumor cell death and tumor immunity. In this study, we provided the first evidence of SLCO4C1 functioning as a tumor suppressor in HCC.
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Affiliation(s)
- Tianbing Wang
- Department of General Surgery, Anhui No. 2 Provincial People’s Hospital, Hefei 230000, China
| | - Kai Guo
- Department of General Surgery, Anhui No. 2 Provincial People’s Hospital, Hefei 230000, China
| | - Shoushan Yang
- Anhui No. 2 Provincial People’s Hospital Clinical College of Anhui Medical University, Hefei 230000, China
- Anhui No. 2 Provincial People’s Hospital, Hefei 230000, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei 230000, China
- Department of General Surgery, Luan Fourth People’s Hospital, Luan 237000, China
| | - Di Zhang
- Clinical Genomic Center, Hefei KingMed for Clinical Laboratory, Hefei 230000, China
| | - Haodong Cui
- Anhui No. 2 Provincial People’s Hospital Clinical College of Anhui Medical University, Hefei 230000, China
- Anhui No. 2 Provincial People’s Hospital, Hefei 230000, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei 230000, China
| | - Jimin Yin
- Anhui No. 2 Provincial People’s Hospital Clinical College of Anhui Medical University, Hefei 230000, China
- Anhui No. 2 Provincial People’s Hospital, Hefei 230000, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei 230000, China
| | - Shuhui Yuan
- Anhui Huaheng Biotechnology Co., Ltd., Hefei 230000, China
| | - Yong Wang
- Department of General Surgery, Anhui No. 2 Provincial People’s Hospital, Hefei 230000, China
| | - Yong Qi
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230000, China
| | - Wenyong Wu
- Anhui No. 2 Provincial People’s Hospital Clinical College of Anhui Medical University, Hefei 230000, China
- Anhui No. 2 Provincial People’s Hospital, Hefei 230000, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei 230000, China
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25
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Sun Y, Liu P, Zhang L, Lei S, Gao Q. Peripheral Blood CD8+T Cell as a Prognostic Biomarker for Hospitalised COVID-19 Patients Without Antiviral Treatment. Infect Drug Resist 2024; 17:109-117. [PMID: 38230269 PMCID: PMC10790588 DOI: 10.2147/idr.s432283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/14/2023] [Indexed: 01/18/2024] Open
Abstract
Background The status of T lymphocyte subset counts in patients with COVID-19 remains uncertain. This study aimed to assess alterations in peripheral blood CD3+CD8+T (CD8+T) cells among hospitalized COVID-19 patients who have not received antiviral treatment and to evaluate their prognostic value within this patient population. Methods A single-center, retrospective cohort study and a meta-analysis were conducted. The cohort study was performed at Xiangya Hospital from December 5, 2022, to January 31, 2023. We conducted a meta-analysis to explore the association between peripheral blood CD3+CD8+T cells and mortality in COVID-19 patients who did not receive antiviral therapy. All relevant studies in Embase, PubMed, Web of Science databases were systematically searched for meta-analysis. Results The retrospective cohort study included 201 patients. A significant decrease in peripheral blood CD8+ T cell count was found to be associated with an increased risk of mortality (adjusted odds ratio [aOR]: 13.88; 95% confidence interval [CI]: 3.15-61.23), after adjusting for gender, age, comorbidities, severity at admission, steroid therapy, and antibiotic therapy. The threshold value for CD8+T cell counts, determined by the receiver operating characteristic (ROC) curve analysis, was 145.5 (area under the curve [AUC]: 0.828, specificity: 90.3%, sensitivity: 72.9%, P<0.001). Additionally, A total of 7 studies with 2765 participants were included in the meta-analysis. The meta-analysis reveals a significant association between lower CD8+ T cell counts and mortality (odds ratio [OR] = 3.543, 95% CI: 1.726 to 7.272; I2=93%). Conclusion Peripheral blood CD8+ T cell can serve as a valuable prognostic biomarker for hospitalized patients who do not receive antiviral treatment.
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Affiliation(s)
- Yuming Sun
- Department of Plastic and Cosmetic Surgery, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
- National Engineering Research Centre of Personalized Diagnostic and Therapeutic Technology, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
- Furong Laboratory, Central South University, Changsha, People’s Republic of China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Centre of Skin Health and Disease, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
- National Clinical Research Centre for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Peilin Liu
- Clinical Laboratory Department, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Lifang Zhang
- Department of Plastic and Cosmetic Surgery, Changsha Mylike Cosmetic Hospital, Changsha, People’s Republic of China
| | - Shaorong Lei
- Department of Plastic and Cosmetic Surgery, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
| | - Qian Gao
- Clinical Laboratory Department, Xiangya Hospital, Central South University, Changsha, People’s Republic of China
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Hariri LP, Sharma A, Nandy S, Berigei SR, Yamamoto S, Raphaely RA, Flashner BM, Muniappan A, Auchincloss HG, Lanuti M, Hallowell RW, Shea BS, Keyes CM. Endobronchial Optical Coherence Tomography as a Novel Method for In Vivo Microscopic Assessment of Interstitial Lung Abnormalities. Am J Respir Crit Care Med 2024. [PMID: 38207094 DOI: 10.1164/rccm.202310-1871le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/10/2024] [Indexed: 01/13/2024] Open
Affiliation(s)
- Lida P Hariri
- Massachusetts General Hospital, Pathology, Boston, Massachusetts, United States;
| | - Amita Sharma
- Massachusetts General Hospital, Radiology, Boston, Massachusetts, United States
| | - Sreyankar Nandy
- Massachusetts General Hospital, Division of Pulmonary and Critical Care Medicine, Boston, Massachusetts, United States
| | - Sarita R Berigei
- Massachusetts General Hospital, 2348, Boston, Massachusetts, United States
| | - Satomi Yamamoto
- Massachusetts General Hospital, Division of Pulmonary and Critical Care Medicine, Boston, Massachusetts, United States
| | - Rebecca A Raphaely
- University of Washington, 7284, Division of Pulmonary and Critical Care Medicine, Seattle, Washington, United States
| | - Bess M Flashner
- Beth Israel Deaconess Medical Center, 1859, Internal Medicine, Boston, Massachusetts, United States
| | - Ashok Muniappan
- Massachusetts General Hospital, Thoracic Surgery, Boston, Massachusetts, United States
| | - Hugh G Auchincloss
- Massachusetts General Hospital, Thoracic Surgery, Boston, Massachusetts, United States
| | - Michael Lanuti
- Massachusetts General Hospital, Thoracic Surgery, Boston, Massachusetts, United States
| | - Robert W Hallowell
- Massachusetts General Hospital, 2348, Division of Pulmonary and Critical Care Medicine, Boston, Massachusetts, United States
| | - Barry S Shea
- Massachusetts General Hospital, 2348, Division of Pulmonary and Critical Care Medicine, Boston, Massachusetts, United States
| | - Colleen M Keyes
- Massachusetts General Hospital, Interventional Pulmonology, Boston, Massachusetts, United States
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27
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Dang Y, Huang J, Lin C, Xu S. Investigation of the association between the Toll-like receptor 1 rs4833095 variation and gastric adenocarcinoma recurrence. Ann Hum Genet 2024. [PMID: 38196279 DOI: 10.1111/ahg.12548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/10/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024]
Abstract
BACKGROUND Toll-like receptors (TLRs) are a family of transmembrane receptors that play key roles in identifying invading pathogens and activating innate immunity. TLR1 has been reported to be associated with the risk of gastric cancer (GC) but that was based on only a simple statistical analysis. METHODS We genotyped the TLR1 in 526 GC patients to investigate the association between the variation and gastric cancer survival by the multiplex polymerase chain reaction and sequencing method. The rs4833095 variation (chr4:38798089 [GRCh38. p14], T > C) in the TLR1 gene was genotyped in 526 patients who underwent GC resection. The associations between genotype, survival, and recurrence were investigated. The potential role of TLR1 in stomach cancer was investigated using clinical data from formalin-fixed, paraffin-embedded tissue samples. RESULTS Patients with the T/C and C/C genotypes of rs4833095 had a lower risk of recurrence than those with the T/T genotype. Recurrence-free periods were substantially longer in patients with the T/C or C/C genotypes (22.6 and 22.3 months, respectively) than in those with the T/T genotype (20.7 months). Patients with the T/C or C/C genotype, low expression levels of VEGF1, high expression levels of ERBB2 and ERCC1, the absence of cancer nodules, a tumor size of less than 5 cm, and poor differentiation had a considerably reduced risk of recurrence. CONCLUSIONS TLR1 rs4833095 was correlated with the postresection prognosis of patients with gastric cancer, suggesting that TLR1 may have a role in the onset or progression of gastric cancer.
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Affiliation(s)
- Yuan Dang
- Innovation Center for Cancer Research, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
- Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Jingyun Huang
- Innovation Center for Cancer Research, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
- Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Chen Lin
- Department of General Surgery, 900th Hospital of the Joint Logistics Support Force, Fuzhou, China
- Department of General Surgery, Fuzong Clinical Medical College, Fujian Medical University, Fuzhou, China
- Department of General Surgery, Dongfang Hospital of Xiamen University, School of Medicine, Xiamen University, Fuzhou, China
| | - Shaohua Xu
- Department of Hepatobiliary and Pancreatic Surgery, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
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Zhao M, Wang L, Wang X, He J, Yu K, Li D. Non-neoplastic cells as prognostic biomarkers in diffuse large B-cell lymphoma: A system review and meta-analysis. Tumori 2024:3008916231221636. [PMID: 38183180 DOI: 10.1177/03008916231221636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2024]
Abstract
The microenvironment of diffuse large B-cell lymphoma (DLBCL) is composed of various components, including immune cells and immune checkpoints, some of which have been correlated with the prognosis of DLBCL, but their results remain controversial. Therefore, we conducted a systematic review and meta-analysis to investigate the association between the microenvironment and prognosis in DLBCL. We searched PubMed, Web of Science, and EMBASE for relevant articles between 2001 and 2022. Twenty-five studies involving 4495 patients with DLBCL were included in the analysis. This meta-analysis confirmed that high densities of Foxp3+Tregs and PD-1+T cells are good indicators for overall survival (OS) in DLBCL, while high densities of programmed cell death protein ligand1(PD-L1)-positive expression cells and T-cell immunoglobulin-and mucin domain-3-containing molecule 3 (TIM-3)-positive expression tumor-infiltrating cells (TILs) play a contrary role in OS. Additionally, higher numbers of T-cell intracytoplasmic antigen-1(TIA-1)-positive expression T cells imply better OS and progression-free survival (PFS), while high numbers of lymphocyte activation gene(LAG)-positive expression TILs predict bad OS and PFS. Various non-tumoral cells in the microenvironment play important roles in the prognosis of DLBCL.
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Affiliation(s)
- Min Zhao
- Department of Pathology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Pathology, Chongqing Medical University, Chongqing, China
- Molecular Medicine Diagnostic and Testing Center of Chongqing Medical University, Chongqing, China
| | - Lixing Wang
- Department of Pathology, Chongqing Medical University, Chongqing, China
| | - Xingyu Wang
- Department of Pathology, Chongqing Medical University, Chongqing, China
| | - Juan He
- Department of Pathology, Chongqing Medical University, Chongqing, China
| | - Kuai Yu
- Department of Pathology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Molecular Medicine Diagnostic and Testing Center of Chongqing Medical University, Chongqing, China
- Department of Pathology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Dan Li
- Department of Pathology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Pathology, Chongqing Medical University, Chongqing, China
- Molecular Medicine Diagnostic and Testing Center of Chongqing Medical University, Chongqing, China
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Xi P, Zhang Z, Liu Y, Nie Y, Gong B, Liu J, Huang H, Liu Z, Sun T, Xie W. Multidimensional comprehensive and integrated analysis of the potential function of TMEM25 in renal clear cell carcinoma with low expression status. Aging (Albany NY) 2024; 16:367-388. [PMID: 38189809 PMCID: PMC10817401 DOI: 10.18632/aging.205372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND Transmembrane 25(TMEM25) stands out as a potential prognostic biomarker and therapeutic target in the realm of cancer, yet its precise mechanism of action within clear cell renal cell carcinoma (ccRCC) remains unclear. MATERIALS AND METHODS Gene expression data and clinically relevant information extracted from The Cancer Genome Atlas (TCGA) and Gene expression omnibus (GEO) databases unveil the expression patterns of TMEM25 within renal clear cell carcinoma, which reveals its prognostic and diagnostic significance. The protein expression data is available via the Human Protein Atlas (HPA) database. Further, qPCR experiments conducted on cells and tissues provide strong evidence of the gene's expression status. Additionally, they explore the correlations between TMEM25 expression and DNA methylation, gene mutations, immune cell infiltration, and drug sensitivity within this specific tumor context. RESULTS At both the RNA and protein levels, TMEM25 displays a noteworthy downregulation in expression, which is consistently linked to an unfavorable prognosis. Receiver Operating Characteristic (ROC) curve analysis, univariate and multivariate Cox regression analyses confirmed the ability of TMEM25 to diagnose and determine prognosis in ccRCC. Its expression related closely with various immune cell types, immune checkpoints, immune inhibitors, and MHC molecules. Within ccRCC tissues, TMEM25 DNA methylation levels are observed to be elevated, and this upregulation is observed across various conditions. TMEM25 mutations also have an impact on the prognosis of ccRCC patients and the results of drug sensitivity analyses are useful for clinical decision-making. CONCLUSIONS TMEM25 in ccRCC could potentially function as a tumor suppressor gene, holding substantial promise as a novel biomarker for diagnosing, treating, and prognosticating ccRCC patients.
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Affiliation(s)
- Ping Xi
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Zhicheng Zhang
- Department of Surgery, Fuzhou First People’s Hospital, Fuzhou 344000, Jiangxi Province, China
| | - Yifu Liu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Yechen Nie
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Binbin Gong
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Ji Liu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Hao Huang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Ziwen Liu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Ting Sun
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Wenjie Xie
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi Province, China
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Dong W, Li J, Zhuang Z. Deciphering the prognostic significance of anoikis-related lncRNAs in invasive breast cancer: from comprehensive bioinformatics analysis to functional experimental validation. Aging (Albany NY) 2024; 16:402-430. [PMID: 38189818 PMCID: PMC10817393 DOI: 10.18632/aging] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/06/2023] [Indexed: 12/15/2022]
Abstract
The global prevalence of breast cancer necessitates the development of innovative prognostic markers and therapeutic strategies. This study investigated the prognostic implications of anoikis-related long non-coding RNAs (ARLs) in invasive breast cancer (IBC), which is an area that has not been extensively explored. By integrating the RNA sequence transcriptome and clinical data from The Cancer Genome Atlas (TCGA) database and employing advanced regression analyses, we devised a novel prognostic model based on ARL scores. ARL scores correlated with diverse clinicopathological parameters, cellular pathways, distinct mutation patterns, and immune responses, thereby affecting both immune cell infiltration and anticipated responses to chemotherapy and immunotherapy. Additionally, the overexpression of a specific lncRNA, AL133467.1, significantly impeded the proliferation and migration, as well as possibly the anoikis resistance of breast cancer cells. These findings highlight the potential of the ARL signature as a robust prognostic tool and a promising basis for personalized IBC treatment strategies.
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Affiliation(s)
- Wenge Dong
- Department of Breast Surgery, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Jiejing Li
- Department of Breast Surgery, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Zhigang Zhuang
- Department of Breast Surgery, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
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Yuan J, Yu S. Comprehensive Analysis Reveals Prognostic and Therapeutic Immunity-Related Biomarkers for Pediatric Metastatic Osteosarcoma. Medicina (Kaunas) 2024; 60:95. [PMID: 38256356 PMCID: PMC10820594 DOI: 10.3390/medicina60010095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/15/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024]
Abstract
Background and Objectives: Osteosarcoma, the most prevalent malignant bone tumor in children and adolescents, presents a complex pathogenesis characterized by various genetic and epigenetic alterations. This study aims to identify key differentially expressed genes (DEGs) in pediatric osteosarcoma, with a focus on those influencing metastasis and patient survival. Materials and Methods: We utilized the GSE33382 dataset from the GEO database for a comprehensive bioinformatic analysis. This included a protein-protein interaction (PPI) network analysis, Cox regression, and Kaplan-Meier survival analysis to identify central DEGs associated with osteosarcoma metastasis and patient survival. Results: Our analysis identified 88 DEGs related to osteosarcoma metastasis. Among them, three survival-related central DEGs-C1QA, CD74, and HLA-DMA-were significantly linked to patient outcomes. Further correlation analysis established a strong relationship between these genes, tumor mutation burden (TMB), immune checkpoint gene expression, and overall survival. Notably, C1QA and CD74 exhibited higher expression in non-metastatic osteosarcoma cases, suggesting a potential role in disease progression. Conclusions: The identified DEGs, particularly C1QA, CD74, and HLA-DMA, may serve as critical biomarkers for pediatric osteosarcoma prognosis and potential targets for immunotherapy. These findings provide a deeper understanding of the molecular landscape of osteosarcoma and open new avenues for therapeutic intervention.
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Affiliation(s)
| | - Shengji Yu
- Department of Orthopedics, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 17 Nanli, Panjiayuan, Chaoyang District, Beijing 100021, China;
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Wu H, Fu Z, Li H, Fang F, He B, Ye Y, Wu H, Xu D, Zheng H, Zhang Q. TRIB3, as a robust prognostic biomarker for HNSC, is associated with poor immune infiltration and cancer cell immune evasion. Front Immunol 2024; 14:1290839. [PMID: 38235126 PMCID: PMC10791810 DOI: 10.3389/fimmu.2023.1290839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
Objective As a pseudokinase, Tribbles Pseudokinase 3 (TRIB3) is implicated in a wide array of biological processes, including cell signal transduction, metabolic regulation, stress responses, and immune regulation. While its significant role in the immune regulation of certain cancers is well-established, the specific functions and impact of TRIB3 in head and neck squamous cell carcinoma (HNSC) remain unclear. Methods The data of RNA-sequence was acquired from the TCGA database to analyze the expression patterns of TRIB3 and elucidate its prognostic value in HNSC patients. Furthermore, the correlation between TRIB3 and tumor mutation burden, clinical data, immune checkpoint genes, and immune cell infiltration was explored. Moreover, the TRIB3 location in tumor tissues and subcellular structures was identified via Tisch in the HPA database, and the potential protein interaction molecules for TRIB3 were elucidated in the STRING database. The potential TRIB3 gene function was assessed using gene set enrichment analysis (GSEA), whereas the TRIB3 expression levels in clinical HNSC samples were verified by RT-qPCR and immunohistochemistry. the role of TRIB3 in enhancing the malignant behavior of HNSC cells was validated in vitro through a series of methods including RT-qPCR, CCK8 assay, wound healing assay, and transwell assay. Results It was revealed that TRIB3 was significantly overexpressed in the nucleus and cytoplasm of HNSC. Furthermore, this overexpression markedly enhanced the migration ability of tumor cells. As an independent prognostic factor, TRIB3 was associated with advanced tumor T stage and was significantly involved with tumor mutation burden and immune cell infiltration in HNSC. Moreover, it was observed that TRIB3 was not a predicted factor for PD1/PDL1 and ATL4 inhibitor treatment; however, it was substantially correlated with various immune evasion-related genes in HNSC. Conclusion TRIB3 could serve as a potential prognostic marker for HNSC and might be a key gene mediating HNSC immune evasion.
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Affiliation(s)
- Huadong Wu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
- Department of Otolaryngology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Zhenzhen Fu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
| | - Hong Li
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
| | - Feifei Fang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
| | - Bin He
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
| | - Yujie Ye
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
| | - Heyong Wu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
| | - Dong Xu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
| | - Haoran Zheng
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
| | - Qiang Zhang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Jiangxi Medical college, Nanchang University, Nanchang, Jiangxi, China
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La Salvia A, Lens-Pardo A, López-López A, Carretero-Puche C, Capdevila J, Benavent M, Jiménez-Fonseca P, Castellano D, Alonso T, Teule A, Custodio A, Tafuto S, La Casta A, Spada F, Lopez-Gonzalvez A, Gil-Calderon B, Espinosa-Olarte P, Barbas C, Garcia-Carbonero R, Soldevilla B. Metabolomic profile of neuroendocrine tumors identifies methionine, porphyrin, and tryptophan metabolisms as key dysregulated pathways associated with patient survival. Eur J Endocrinol 2024; 190:62-74. [PMID: 38033321 DOI: 10.1093/ejendo/lvad160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/17/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
OBJECTIVE Metabolic profiling is a valuable tool to characterize tumor biology but remains largely unexplored in neuroendocrine tumors (NETs). Our aim was to comprehensively assess the metabolomic profile of NETs and identify novel prognostic biomarkers and dysregulated molecular pathways. DESIGN AND METHODS Multiplatform untargeted metabolomic profiling (GC-MS, CE-MS, and LC-MS) was performed in plasma from 77 patients with G1-2 extra-pancreatic NETs enrolled in the AXINET trial (NCT01744249) (study cohort) and from 68 non-cancer individuals (control). The prognostic value of each differential metabolite (n = 155) in NET patients (P < .05) was analyzed by univariate and multivariate analyses adjusted for multiple testing and other confounding factors. Related pathways were explored by Metabolite Set Enrichment Analysis (MSEA) and Metabolite Pathway Analysis (MPA). RESULTS Thirty-four metabolites were significantly associated with progression-free survival (PFS) (n = 16) and/or overall survival (OS) (n = 27). Thirteen metabolites remained significant independent prognostic factors in multivariate analysis, 3 of them with a significant impact on both PFS and OS. Unsupervised clustering of these 3 metabolites stratified patients in 3 distinct prognostic groups (1-year PFS of 71.1%, 47.7%, and 15.4% (P = .012); 5-year OS of 69.7%, 32.5%, and 27.7% (P = .003), respectively). The MSEA and MPA of the 13-metablolite signature identified methionine, porphyrin, and tryptophan metabolisms as the 3 most relevant dysregulated pathways associated with the prognosis of NETs. CONCLUSIONS We identified a metabolomic signature that improves prognostic stratification of NET patients beyond classical prognostic factors for clinical decisions. The enriched metabolic pathways identified reveal novel tumor vulnerabilities that may foster the development of new therapeutic strategies for these patients.
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Affiliation(s)
- Anna La Salvia
- Center of Experimental Oncology, Gastrointestinal and Neuroendrocrine Tumors Research Group, Research Institute Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Oncology Department, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- National Center for Drug Research and Evaluation, National Institute of Health (ISS), 00161 Rome, Italy
| | - Alberto Lens-Pardo
- Center of Experimental Oncology, Gastrointestinal and Neuroendrocrine Tumors Research Group, Research Institute Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
| | - Angel López-López
- Department of Chemistry and Biochemistry, Facultad de Farmacia, Centre for Metabolomics and Bioanalysis (CEMBIO), Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, 28925 Madrid, Spain
| | - Carlos Carretero-Puche
- Center of Experimental Oncology, Gastrointestinal and Neuroendrocrine Tumors Research Group, Research Institute Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
| | - Jaume Capdevila
- Vall Hebron University Hospital and Vall Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Marta Benavent
- Medical Oncology Department, Hospital Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS), 41013 Seville, Spain
| | - Paula Jiménez-Fonseca
- Medical Oncology Department, Hospital Universitario Central de Asturias, ISPA, 33011 Oviedo, Spain
| | - Daniel Castellano
- Oncology Department, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Teresa Alonso
- Medical Oncology, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - Alexandre Teule
- Institut Català d'Oncologia (ICO)-Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08908 L'Hospitalet del Llobregat, Barcelona, Spain
| | - Ana Custodio
- Department of Medical Oncology, Hospital Universitario La Paz, CIBERONC CB16/12/00398, 28046 Madrid, Spain
| | - Salvatore Tafuto
- Sarcomas and Rare Tumours Unit, Istituto Nazionale Tumori, IRCCS Fondazione G. Pascale, 80131 Naples, Italy
| | - Adelaida La Casta
- Department of Medical Oncology, Biodonostia Health Research Institute, Donostia University Hospital, University of the Basque Country (UPV/EHU), 20014 San Sebastián, Spain
| | - Francesca Spada
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Angeles Lopez-Gonzalvez
- Department of Chemistry and Biochemistry, Facultad de Farmacia, Centre for Metabolomics and Bioanalysis (CEMBIO), Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, 28925 Madrid, Spain
| | - Beatriz Gil-Calderon
- Center of Experimental Oncology, Gastrointestinal and Neuroendrocrine Tumors Research Group, Research Institute Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
| | - Paula Espinosa-Olarte
- Center of Experimental Oncology, Gastrointestinal and Neuroendrocrine Tumors Research Group, Research Institute Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Oncology Department, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Coral Barbas
- Department of Chemistry and Biochemistry, Facultad de Farmacia, Centre for Metabolomics and Bioanalysis (CEMBIO), Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte, 28925 Madrid, Spain
| | - Rocio Garcia-Carbonero
- Center of Experimental Oncology, Gastrointestinal and Neuroendrocrine Tumors Research Group, Research Institute Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Oncology Department, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
- Medicine Department, Complutense University of Madrid (UCM), 28040 Madrid, Spain
| | - Beatriz Soldevilla
- Center of Experimental Oncology, Gastrointestinal and Neuroendrocrine Tumors Research Group, Research Institute Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
- Genetics, Physiology and Microbiology Department, Complutense University of Madrid (UCM), 28040 Madrid, Spain
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Li P, Xu Q, Liu K, Ye J. CRYL1 is a Potential Prognostic Biomarker of Clear Cell Renal Cell Carcinoma Correlated with Immune Infiltration and Cuproptosis. Technol Cancer Res Treat 2024; 23:15330338241237439. [PMID: 38497139 PMCID: PMC10946081 DOI: 10.1177/15330338241237439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 03/19/2024] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is a widespread urogenital neoplasm. However, the therapeutic efficacy of these methods is unsatisfactory. In-depth screening of biomarkers could aid early diagnosis and therapy and predict patient prognosis. METHODS The GEO datasets were selected with specific criteria. Differentially expressed gene (DEG), weighted gene coexpression network analysis (WGCNA), protein-protein interaction, LASSO, random forest, and Cox regression analyses were applied to identify the independent prognostic biomarkers. Survival analysis, correlation with clinical features, gene set enrichment analysis (GSEA), GO enrichment, immune infiltration analysis, and correlation with cuproptosis-related genes were carried out to determine the prognostic value and possible molecular mechanisms of the TSVR. Wound healing assays, transwell assays, cell colony formation experiments, flow cytometry, and immunohistochemistry (IHC) analysis were used to validate the functional attributes of CRYL1. RESULTS Four GEO datasets were included to screen for hub genes. DEG combined with WGCNA showed a key module with 300 genes having the strongest correlation with "survival state" (R2 = -0.24 and P = 7e-8); six genes were identified by LASSO, random forest, and Cytoscape. Finally, CRYL1 (hazard ratio (HR) = 2.01, P < 0.001) was selected as an independent prognostic biomarker. The higher CRYL1 expression group had better DFS and overall survival (OS). GSEA demonstrated that the CRYL1-related DEGs were enriched mainly in the metabolism of sugar, fat, and amino acids. CRYL1 is positively correlated with FDX1 and the LIAS pathway, which are important molecule involved in cuproptosis. CRYL1 affects the infiltration abundance of four immune cells and can predict a positive OS. Wound healing, transwell, cell colony formation, and flow cytometry assays demonstrated that CRYL1 silencing enhances migration and proliferation and leads to a decreased apoptotic ratio. IHC analysis suggested that CRYL1 was highly expressed in adjacent tissues. CONCLUSIONS CRYL1 is a robust predictive marker for clinicopathological characteristics and survival status in ccRCC patients.
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Affiliation(s)
- Peng Li
- The 6th affiliated hospital of wenzhou medical university, Lishui city people's hospital, Lishui, Zhejiang, China
- Lishui city people's hospital, The first affiliated hospital of Lishui University, Lishui, Zhejiang, China
| | - Qiangqiang Xu
- The 6th affiliated hospital of wenzhou medical university, Lishui city people's hospital, Lishui, Zhejiang, China
- Lishui city people's hospital, The first affiliated hospital of Lishui University, Lishui, Zhejiang, China
| | - Ken Liu
- The 6th affiliated hospital of wenzhou medical university, Lishui city people's hospital, Lishui, Zhejiang, China
- Lishui city people's hospital, The first affiliated hospital of Lishui University, Lishui, Zhejiang, China
| | - Junjie Ye
- The 6th affiliated hospital of wenzhou medical university, Lishui city people's hospital, Lishui, Zhejiang, China
- Lishui city people's hospital, The first affiliated hospital of Lishui University, Lishui, Zhejiang, China
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Li Z, Wang Q, Huang X, Fu R, Wen X, Zhang L. Multi-omics analysis reveals that ferroptosis-related gene CISD2 is a prognostic biomarker of head and neck squamous cell carcinoma. J Gene Med 2024; 26:e3580. [PMID: 37581006 DOI: 10.1002/jgm.3580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/24/2023] [Accepted: 07/25/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is a prevalent malignancy, with high mortality rate and unavailability of accurate therapies. However, its early prevention remains a challenge. In the purview of predictive, preventive, and personalized medicine (PPPM), it is paramount to identify novel and powerful biomarkers. CISD2 is a crucial regulator of iron homeostasis and reactive oxygen species (ROS). Recent studies showed that the NEET protein (NAF-1) encoded by CISD2 is involved in regulating the proliferation and metastasis of tumor cells. Nevertheless, the prognostic value and immunological correlations of CISD2 remain unclear. METHODS Bioinformatics analyses conducted utilizing data from comprehensive databases The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). All statistical evaluations were executed employing R software. RESULTS Our investigation of biological function, enrichment pathway, and immune correlation revealed a discernable linkage between CISD2 and the immune response. Moreover, we found that the suppression of CISD2 is associated with immune cell infiltration and various immune signatures. CONCLUSIONS The present study successfully revealed the potential prognostic and biological function of CISD2 in HNSCC. High expression of CISD2 are linked to gender, race, grade, etc., can notably enhance the early detection, prognosis, and prediction for individuals afflicted with HNSCC.
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Affiliation(s)
- Zhengrui Li
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Research Institute of Stomatology, Shanghai, China
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Qi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Xufeng Huang
- Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - Rao Fu
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Research Institute of Stomatology, Shanghai, China
| | - Xutao Wen
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Research Institute of Stomatology, Shanghai, China
| | - Ling Zhang
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Research Institute of Stomatology, Shanghai, China
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Ding Y, Wang H, Wang Q, Jiang H, Li Z, Yu Z, Wang Q, Xu M. Pan-Cancer Analysis Reveals SOX2 as a Promising Prognostic and Immunotherapeutic Biomarker Across Various Cancer Types, Including Pancreatic Cancer. J Cancer 2024; 15:251-274. [PMID: 38164286 PMCID: PMC10751676 DOI: 10.7150/jca.88397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/15/2023] [Indexed: 01/03/2024] Open
Abstract
SOX2 is associated with the initiation, growth, and progression of various tumors and is related to stem cells. However, further studies of SOX2 in a pan-cancer context are warranted. In this study, we obtained pan-cancer and clinical data from TCGA, GTEx, STRING, and TISIDB databases and we analyzed the relationship between SOX2 expression levels and changes in gene diagnostics and survival prognosis. Additionally, we compared the expression levels of SOX2 in pancreatic cancer and healthy pancreatic tissues using Wilcoxon's rank-sum test. Functional enrichment analysis was conducted to identify potential signaling pathways and biological functions. To determine the prognostic value, we used the area under the curve (AUC) and Cox regression analysis. We further developed nomograms to predict overall survival at 1, 6, and 12 months after cancer diagnosis. Moreover, we assessed immune cell infiltration using single-sample gene set enrichment analysis. The methylation status of SOX2 was analyzed using the UALCAN and MethSurv databases. Furthermore, we verified the differential expression of SOX2 in pancreatic cancer cell lines by western blotting and quantitative polymerase chain reaction. We also confirmed the effect of SOX2 on the invasion and migration of pancreatic cancer cells using transwell and scratch assays. The biological effects were confirmed using a clone-formation assay. Our findings suggest that SOX2 is highly expressed in various tumor tissues and has potential clinical significance. It can be used as a new biomarker for pancreatic adenocarcinoma and plays a crucial role in immune infiltration.
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Affiliation(s)
- Yuntao Ding
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Huizhi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Qiaowei Wang
- Hematological Disease Institute of Jiangsu University, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, 212001, China
| | - Han Jiang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Zhangzuo Li
- Hematological Disease Institute of Jiangsu University, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, 212001, China
| | - Zhengyue Yu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Qi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
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Jadhav T, Malik A, Kashif AW, Shelly D, Mishra PS, Baranwal AK, Sahu R. Study of the association of the known prognostic variables with EGFR expression in head and neck squamous cell carcinomas. INDIAN J PATHOL MICR 2024; 67:36-45. [PMID: 38358186 DOI: 10.4103/ijpm.ijpm_833_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Context : Head and neck squamous cell carcinomas (HNSCCs) are the sixth most frequent malignancy in the world. Epidermal growth factor receptors (EGFRs) are members of Erb B family of receptors. EGFR is known to act as a driver of tumorigenesis in various carcinomas. Over expression of EGFR in HNSCC is associated with poor prognosis and resistance to radiotherapy. It is a useful prognostic marker, marker for response to therapy, and also a therapeutic target. Aim To study the association of the known prognostic variables with EGFR expression in HNSCCs and to correlate it with the clinical outcome. Settings and Design Cross-sectional observational study. Materials and Methods A total of 170 patients of HNSCC were evaluated for EGFR expression and followed up for at least two years, with correlation of EGFR expression with various histopathological factors and their clinical outcome. Statistical Analysis Used : Chi-square test. Results The expression of EGFR in HNSCC in this study population was 88.82%. Statistical significance was noted between EGFR reactivity and age of the patient, its histological grade and perineural invasion. Statistical significance was also noted between EGFR reactivity and recurrence of malignancy as well as the site of recurrence. Conclusion EGFR expression in patients with HNSCC is a poor prognostic biomarker and has a comparatively lower survival outcome as compared to non-EGFR expressing HNSCC cases. Hence, it will be helpful for all those patients diagnosed with HNSCC to ideally undergo an additional EGFR immunohistochemical evaluation, which, in turn, will help the oncologists in management of the tumor with anti-EGFR therapy combined with radiotherapy, to obtain a better response and a survival outcome.
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Affiliation(s)
- Toyaja Jadhav
- Department of Laboratory Sciences, 12 Airforce Hospital, Akash Vihar, Gorakhpur, Uttar Pradesh, India
| | - Ajay Malik
- Yashoda Hospital and Research Centre, Nehru Nagar, Ghaziabad, Uttar Pradesh, India
| | - Ahmed Waheed Kashif
- Department of Pathology, Armed Forces Medical College, Wanowrie, Pune, Maharashtra, India
| | - Divya Shelly
- Department of Pathology, INHS Asvini, Mumbai, Maharashtra, India
| | - Prabhashankar S Mishra
- Department of Pathology, Army Research and Referral (R&R) Hospital, Dhaula Kuan, Delhi, India
| | - Ajay Kumar Baranwal
- Department of Blood Transfusion and Immunohematology, Armed Forces Medical College, Wanowrie, Pune, Maharashtra, India
| | - Rajesh Sahu
- Department of Community Medicine, Armed Forces Medical College, Wanowrie, Pune, Maharashtra, India
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Yu Z, Lin X, Tian M, Chang W. [Retracted] microRNA‑196b promotes cell migration and invasion by targeting FOXP2 in hepatocellular carcinoma. Oncol Rep 2024; 51:1. [PMID: 37937660 PMCID: PMC10688451 DOI: 10.3892/or.2023.8660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/28/2017] [Indexed: 11/09/2023] Open
Abstract
Following the publication of the above paper, it was drawn to the Editor's attention by a concerned reader that the images showing metastatic nodules in the mouse lung in Fig. 4 on p. 735 had apparently previously been published a few years earlier in the following paper: Jia D, Yan M, Wang X, Hao X, Liang L, Liu L, Kong H, He X, Li J and Yao M: Development of a highly metastatic model that reveals a crucial role of fibronectin in lung cancer cell migration and invasion. BMC Cancer 10: 364, 2010. Moreover, among the cell migration and invasion assay data shown in Figs. 3B and D, and 6B and 7B, there were a number of overlaps noted among the data panels such that data which were intended to show results obtained under different experimental conditions were likely to have been derived from a smaller number of original sources. Owing to the fact that the contentious data in the above article had already been publihed prior to its submission to Oncology Reports, in addition the other features of concern regarding the data, the Editor has decided that this paper should be retracted from the Journal. The authors were asked for an explanation to account for these concerns, but the Editorial Office did not receive a reply. The Editor apologizes to the readership for any inconvenience caused. [Oncology Reports 39: 731‑738, 2018; DOI: 10.3892/or.2017.6130].
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Affiliation(s)
- Zhaoxiang Yu
- Department of General Surgery, The First Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi 710077, P.R. China
| | - Xiaobo Lin
- Department of General Surgery, The First Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi 710077, P.R. China
| | - Ming Tian
- Department of General Surgery, The First Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi 710077, P.R. China
| | - Weiping Chang
- Department of General Surgery, The First Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi 710077, P.R. China
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Wang J, Che F, Zhao Y, Wei L, Chen D, Dai C, Zhang B, Zhou X, Yang B, Chen Z. The Prognostic and Therapeutic Roles of ARL-6 Gene in Hepatocellular Carcinoma. Int J Med Sci 2024; 21:207-218. [PMID: 38169538 PMCID: PMC10758142 DOI: 10.7150/ijms.88039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/18/2023] [Indexed: 01/05/2024] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is one of the most prevalent human cancers. ARL-6, a member of the ADP ribosylation factor (like) (ARF) protein family, has gained attention as a potential therapeutic target in various malignancies and a prognostic biomarker. However, its specific roles in HCC, both prognostically and biochemically, remain largely unclear. Methods: To examine the functional relevance of ARL-6 in HCC, we acquired data from GEPIA, UALCAN, TIMER, TCGA, GeneMANIA, and Metascape databases. Then, we conducted immunohistochemistry on a replication sample comprising 26 HCC specimens to assess the efficacy of the ARL-6 gene. To unravel the mechanistic intricacies, we employed diverse assays such as the cell counting kit 8 (CCK8), flow cytometry, and transwell invasion assessment. Results: Our findings demonstrated the mRNA expression of ARL-6 was significantly upregulated in HCC compared to normal tissue, as evidenced by comprehensive database analysis. Immunohistochemistry further revealed that ARL-6 expression was remarkably higher in HCC than in para-carcinoma tissues. Moreover, ARL-6 expression exhibited noteworthy variations across diverse LIHC characteristics, including sample type, histological subtype, TP53 mutation status, nodal metastatic status, and cancer stage. In addition, high transcriptional levels of ARL-6 were correlated with diminished overall survival (OS) and disease-free survival (DFS) in HCC patients. Furthermore, our study indicated positive correlations between ARL-6 expression levels and the activities of tumor-infiltrating immune cells such as B cells, myeloid dendritic cells, macrophages, neutrophils, CD8+T cells, and CD4+T cells. Substantiating our findings, database analysis uncovered additional evidence of ARL-6 gene co-expression and its functional significance in HCC cases. Finally, we demonstrated the involvement of the ARL-6 gene in HCC cell invasion, proliferation, and apoptosis. Conclusions: In conclusion, our investigation sheds light on the pivotal role of ARL-6 in influencing HCC prognosis and treatment by modulating the biological activities of tumor cells. These discoveries hold promise for the development of predictive biomarkers and novel therapeutic avenues for affected patients.
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Affiliation(s)
- Jin Wang
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, China
- NHC Key Laboratory of Organ Transplantation, Wuhan, China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Fuheng Che
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, China
- NHC Key Laboratory of Organ Transplantation, Wuhan, China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Yuanyuan Zhao
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, China
- NHC Key Laboratory of Organ Transplantation, Wuhan, China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Lai Wei
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, China
- NHC Key Laboratory of Organ Transplantation, Wuhan, China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Dong Chen
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, China
- NHC Key Laboratory of Organ Transplantation, Wuhan, China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Chen Dai
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, China
- NHC Key Laboratory of Organ Transplantation, Wuhan, China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Bo Zhang
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, China
- NHC Key Laboratory of Organ Transplantation, Wuhan, China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Xi Zhou
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, China
- NHC Key Laboratory of Organ Transplantation, Wuhan, China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Bo Yang
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, China
- NHC Key Laboratory of Organ Transplantation, Wuhan, China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Zhishui Chen
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, China
- NHC Key Laboratory of Organ Transplantation, Wuhan, China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
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Hu M, Yang K, Wang J, Qiu RLJ, Roper J, Kahn S, Shu HK, Yang X. MGMT promoter methylation prediction based on multiparametric MRI via vision graph neural network. J Med Imaging (Bellingham) 2024; 11:014503. [PMID: 38370421 PMCID: PMC10869845 DOI: 10.1117/1.jmi.11.1.014503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 12/24/2023] [Accepted: 01/29/2024] [Indexed: 02/20/2024] Open
Abstract
Purpose Glioblastoma (GBM) is aggressive and malignant. The methylation status of the O 6 -methylguanine-DNA methyltransferase (MGMT) promoter in GBM tissue is considered an important biomarker for developing the most effective treatment plan. Although the standard method for assessing the MGMT promoter methylation status is via bisulfite modification and deoxyribonucleic acid (DNA) sequencing of biopsy or surgical specimens, a secondary automated method based on medical imaging may improve the efficiency and accuracy of those tests. Approach We propose a deep vision graph neural network (ViG) using multiparametric magnetic resonance imaging (MRI) to predict the MGMT promoter methylation status noninvasively. Our model was compared to the RSNA radiogenomic classification winners. The dataset includes 583 usable patient cases. Combinations of MRI sequences were compared. Our multi-sequence fusion strategy was compared with those using single MR sequences. Results Our best model [Fluid Attenuated Inversion Recovery (FLAIR), T1-weighted pre-contrast (T1w), T2-weighted (T2)] outperformed the winning models with a test area under the curve (AUC) of 0.628, an accuracy of 0.632, a precision of 0.646, a recall of 0.677, a specificity of 0.581, and an F1 score of 0.661. Compared to the winning models with single MR sequences, our ViG utilizing fused-MRI showed a significant improvement statistically in AUC scores, which are FLAIR (p = 0.042 ), T1w (p = 0.017 ), T1wCE (p = 0.001 ), and T2 (p = 0.018 ). Conclusions Our model is superior to challenge champions. A graph representation of the medical images enabled good handling of complexity and irregularity. Our work provides an automatic secondary check pipeline to ensure the correctness of MGMT methylation status prediction.
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Affiliation(s)
- Mingzhe Hu
- Emory University, Department of Radiation Oncology and Winship Cancer Institute, Atlanta, Georgia, United States
- Emory University, Department of Computer Science and Informatics, Atlanta, Georgia, United States
| | - Kailin Yang
- Cleveland Clinic, Taussig Cancer Center, Department of Radiation Oncology, Cleveland, Ohio, United States
| | - Jing Wang
- Emory University, Department of Radiation Oncology and Winship Cancer Institute, Atlanta, Georgia, United States
| | - Richard L. J. Qiu
- Emory University, Department of Radiation Oncology and Winship Cancer Institute, Atlanta, Georgia, United States
| | - Justin Roper
- Emory University, Department of Radiation Oncology and Winship Cancer Institute, Atlanta, Georgia, United States
| | - Shannon Kahn
- Emory University, Department of Radiation Oncology and Winship Cancer Institute, Atlanta, Georgia, United States
| | - Hui-Kuo Shu
- Emory University, Department of Radiation Oncology and Winship Cancer Institute, Atlanta, Georgia, United States
| | - Xiaofeng Yang
- Emory University, Department of Radiation Oncology and Winship Cancer Institute, Atlanta, Georgia, United States
- Emory University, Department of Computer Science and Informatics, Atlanta, Georgia, United States
- Georgia Institute of Technology and Emory University, Department of Biomedical Engineering, Atlanta, Georgia, United States
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Zhan M, Song H, Tian D, Wen Q, Shi X, Wang Y, Mao X, Wang J. Molecular features, biological behaviors and clinical implications of m 5C RNA methylation modification regulators in gastrointestinal cancers. Cancer Biol Ther 2023; 24:2223382. [PMID: 37332118 DOI: 10.1080/15384047.2023.2223382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023] Open
Abstract
Epitranscriptome studies have shown that critical RNA modifications drive tumorigenicity; however, the role of 5-methylcytosine (m5C) RNA methylation remains poorly understood. We extracted 17 m5C regulators and clustered distinct m5C modification patterns by consensus clustering analysis. Gene set variation and single-sample gene set enrichment analysis were applied to quantify functional analysis and immune infiltration. The least absolute shrinkage and selection operator was employed to develop a prognostic risk score. Kaplan-Meier with log-rank test was used for survival analysis. Differential expression analysis was performed with the "limma" R package. Wilcoxon signed ranked test or Kruskal-Wallis test was used to compare groups. We observed that m5C RNA methylation was commonly upregulated in gastrointestinal cancer and related to prognosis. Clusters were identified for m5C patterns, with distinct immune infiltrations and functional pathways. The risk scores of m5C regulators were independent risk factors. Differentially expressed mRNAs (DEmRNAs) in m5C clusters were involved in cancer-related pathways. The methylation-based m5Cscore showed a significant effect on the prognosis. Patients with a lower m5Cscore exhibited more therapeutic efficiency on anti-CTLA4 therapy in liver cancer, while the combination of anti-CTLA4 therapy and pd1 was more efficient for patients with a lower m5Cscore in pancreatic cancer. We uncovered dysregulations of m5C-related regulators in gastrointestinal cancer and their associations with overall survival. Some immune cells were differently infiltrated in distinct m5C modification patterns, indicating their potential impacts on gastrointestinal cancer cell-immune. Moreover, an m5Cscore, derived from DEmRNAs in specific clusters, can serve as a classifier for immunotherapy.
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Affiliation(s)
- Mengyao Zhan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Huan Song
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Occupational Health, Suzhou Center for Disease Control and Prevention, Suzhou, China
| | - Dan Tian
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qin Wen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xinling Shi
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuting Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xuhua Mao
- Department of Clinical Laboratory, Yixing People's Hospital, Wuxi, China
| | - Jianming Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
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Liang C, Chen Y, Chen S, She J, Shi Q, Wang P. KLRB1 is a novel prognostic biomarker in endometrial cancer and is associated with immune infiltration. Transl Cancer Res 2023; 12:3641-3652. [PMID: 38192989 PMCID: PMC10774036 DOI: 10.21037/tcr-23-697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/28/2023] [Indexed: 01/10/2024]
Abstract
Background Endometrial cancer (EC) has the characteristics of high mortality and poor prognosis in the advanced stage, which seriously threatens women's health. Killer cell lectin-like receptor B1 (KLRB1) is a promising immune checkpoint of which the expression level can regulate the killing effect on tumor cells of the immune system, thereby affecting the survival and prognosis of tumor patients. However, it is still unclear whether KLRB1 is associated with survival and prognosis in patients with EC. Therefore, our study focused on the relationship between KLRB1 and immune cells to explore the role of KLRB1 on the immune microenvironment, and to further explore its feasibility as a prognostic marker in EC. Methods In this study, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were used to analyze the messenger RNA (mRNA) expression level of KLRB1 in normal endometrial and EC tissues. The University of Alabama at Birmingham Cancer data analysis Portal (UALCAN) database was used to determine the correlation between KLRB1 mRNA expression and clinical features among the EC patients. KLRB1 expression levels were investigated in the Tumor IMmune Estimation Resource (TIMER) database to reveal its relationship with immune cell infiltration of EC. Finally, using the R package clusterProfiler, enrichment analysis was performed on KLRB1 to study its potential function. Results The results suggested that KLRB1 expression varied in different tumor tissues, and the EC group had lower mRNA expression levels than did the control group. It was also found that patients with high expression of KLRB1 had a better prognosis. According to further enrichment and immune infiltration analyses, KLRB1 expression had a closed relationship with the level of infiltration of some immune cell types, such as B cells memory, eosinophils, and Tregs, among others. Conclusions KLRB1 expression is associated with the infiltration of immune cells and can be used as a prognostic biomarker in EC.
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Affiliation(s)
- Chunyun Liang
- Third Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Department of Obstetrics and Gynecology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing, China
- Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
| | - Yue Chen
- Department of Obstetrics and Gynecology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing, China
- Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
| | - Si Chen
- Department of Obstetrics and Gynecology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing, China
- Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
| | - Jingyao She
- Third Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Department of Obstetrics and Gynecology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing, China
- Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
| | - Qiuyan Shi
- Third Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Department of Obstetrics and Gynecology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing, China
- Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
| | - Peijuan Wang
- Third Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Department of Obstetrics and Gynecology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing, China
- Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, China
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Foltyn-Dumitru M, Kessler T, Sahm F, Wick W, Heiland S, Bendszus M, Vollmuth P, Schell M. Cluster-based prognostication in glioblastoma: Unveiling heterogeneity based on diffusion and perfusion similarities. Neuro Oncol 2023:noad259. [PMID: 38153923 DOI: 10.1093/neuonc/noad259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Indexed: 12/30/2023] Open
Abstract
BACKGROUND While the association between diffusion and perfusion MRI and survival in glioblastoma is established, prognostic models for patients are lacking. This study employed clustering of functional imaging to identify distinct functional phenotypes in untreated glioblastomas, assessing their prognostic significance for overall survival. METHODS A total of 289 patients with glioblastoma who underwent preoperative multimodal MR imaging were included. Mean values of apparent diffusion coefficient (ADC) normalized relative cerebral blood volume (nrCBV), and relative cerebral blood flow (rCBF) were calculated for different tumor compartments and the entire tumor. Distinct imaging patterns were identified using Partition Around Medoids (PAM) clustering on the training dataset, and their ability to predict overall survival was assessed. Additionally, tree-based machine-learning models were trained to ascertain the significance of features pertaining to cluster membership. RESULTS Using the training dataset (231/289) we identified two stable imaging phenotypes through PAM clustering with significantly different overall survival (OS). Validation in an independent test set revealed a high-risk group with a median OS of 10.2 months and a low-risk group with a median OS of 26.6 months (p=0.012). Patients in the low-risk cluster had high diffusion and low perfusion values throughout, while the high-risk cluster displayed the reverse pattern. Including cluster membership in all multivariate Cox regression analyses improved performance (p≤ 0.004 each). CONCLUSIONS Our research demonstrates that data-driven clustering can identify clinically relevant, distinct imaging phenotypes, highlighting the potential role of diffusion and perfusion MRI in predicting survival rates of glioblastoma patients.
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Affiliation(s)
- Martha Foltyn-Dumitru
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, DE
- Section for Computational Neuroimaging, Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, DE
| | - Tobias Kessler
- Department of Neurology and Neurooncology Program, Heidelberg University Hospital, Heidelberg University, Heidelberg, DE
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, DE
| | - Felix Sahm
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, DE
| | - Wolfgang Wick
- Department of Neurology and Neurooncology Program, Heidelberg University Hospital, Heidelberg University, Heidelberg, DE
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, DE
| | - Sabine Heiland
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, DE
| | - Martin Bendszus
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, DE
| | - Philipp Vollmuth
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, DE
- Section for Computational Neuroimaging, Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, DE
| | - Marianne Schell
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, DE
- Section for Computational Neuroimaging, Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, DE
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Xiong YM, Zhou F, Zhou JW, Liu F, Zhou SQ, Li B, Liu ZJ, Qin Y. Aberrant Expressions of PSMD14 in Tumor Tissue are the Potential Prognostic Biomarkers for Hepatocellular Carcinoma after Curative Resection. Curr Genomics 2023; 24:368-384. [PMID: 38327651 PMCID: PMC10845065 DOI: 10.2174/0113892029277262231108105441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 02/09/2024] Open
Abstract
Introduction Hepatocellular carcinoma (HCC) has a high mortality rate, with curative resection being the primary treatment. However, HCC patients have a large possibility of recurrence within 5 years after curative resection. Methods Thus, identifying biomarkers to predict recurrence is crucial. In our study, we analyzed data from CCLE, GEO, and TCGA, identifying eight oncogenes associated with HCC. Subsequently, the expression of 8 genes was tested in 5 cases of tumor tissues and the adjacent non-tumor tissues. Then ATP6AP1, PSMD14 and HSP90AB1 were selected to verify the expression in 63 cases of tumor tissues and the adjacent non-tumor tissues. The results showed that ATP6AP1, PSMD14, HSP90AB1 were generally highly expressed in tumor tissues. A five-year follow-up of the 63 clinical cases, combined with Kaplan-Meier Plotter's relapse-free survival (RFS) analysis, found a significant correlation between PSMD14 expression and recurrence in HCC patients. Subsequently, we analyzed the PSMD14 mutations and found that the PSMD14 gene mutations can lead to a shorter disease-free survival time for HCC patients. Results The results of enrichment analysis indicated that the differentially expressed genes related to PSMD14 are mainly enriched in the signal release pathway. Conclusion In conclusion, our research showed that PSMD14 might be related to recurrence in HCC patients, and the expression of PSMD14 in tumor tissue might be a potential prognostic biomarker after tumor resection in HCC patients.
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Affiliation(s)
- Yi-Mei Xiong
- Department of Biochemistry and Molecular Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, 610 041, China
| | - Fang Zhou
- Department of Biochemistry and Molecular Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, 610 041, China
| | - Jia-Wen Zhou
- Department of Biochemistry and Molecular Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, 610 041, China
| | - Fei Liu
- Division of Liver Transplantation, Department of Surgery, West China Hospital, Sichuan University, Chengdu, 610 041, China
| | - Si-Qi Zhou
- Division of Liver Transplantation, Department of Surgery, West China Hospital, Sichuan University, Chengdu, 610 041, China
| | - Bo Li
- Division of Liver Transplantation, Department of Surgery, West China Hospital, Sichuan University, Chengdu, 610 041, China
| | - Zhong-Jian Liu
- Department of Biochemistry and Molecular Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, 610 041, China
| | - Yang Qin
- Department of Biochemistry and Molecular Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, 610 041, China
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Myo Min KK, Ffrench CB, McClure BJ, Ortiz M, Dorward EL, Samuel MS, Ebert LM, Mahoney MG, Bonder CS. Desmoglein-2 as a cancer modulator: friend or foe? Front Oncol 2023; 13:1327478. [PMID: 38188287 PMCID: PMC10766750 DOI: 10.3389/fonc.2023.1327478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Desmoglein-2 (DSG2) is a calcium-binding single pass transmembrane glycoprotein and a member of the large cadherin family. Until recently, DSG2 was thought to only function as a cell adhesion protein embedded within desmosome junctions designed to enable cells to better tolerate mechanical stress. However, additional roles for DSG2 outside of desmosomes are continuing to emerge, particularly in cancer. Herein, we review the current literature on DSG2 in cancer and detail its impact on biological functions such as cell adhesion, proliferation, migration, invasion, intracellular signaling, extracellular vesicle release and vasculogenic mimicry. An increased understanding of the diverse repertoire of the biological functions of DSG2 holds promise to exploit this cell surface protein as a potential prognostic biomarker and/or target for better patient outcomes. This review explores the canonical and non-canonical functions of DSG2, as well as the context-dependent impacts of DSG2 in the realm of cancer.
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Affiliation(s)
- Kay K. Myo Min
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Charlie B. Ffrench
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Barbara J. McClure
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Michael Ortiz
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Emma L. Dorward
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Michael S. Samuel
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- Basil Hetzel Institute, Queen Elizabeth Hospital, SA, Adelaide, Australia
| | - Lisa M. Ebert
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA, Australia
- Royal Adelaide Hospital, Adelaide, SA, Australia
| | - Mỹ G. Mahoney
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Claudine S. Bonder
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
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Zhou S, Huang H, Zheng Z, Zheng K, Xie L. MOGS promotes stemness acquisition and invasion via enhancing NOTCH1-glycosylation dependent NOTCH pathway in colorectal cancer. Am J Cancer Res 2023; 13:5996-6010. [PMID: 38187061 PMCID: PMC10767340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/22/2023] [Indexed: 01/09/2024] Open
Abstract
Colorectal cancer (CRC) ranks as the third most prevalent cancer globally, and about half of CRC patients eventually succumb to tumor metastasis. Despite this, treatment options for metastatic colon cancer remain severely limited, reflected by a 12% 5-year overall survival rate. Increasing evidence suggests that cancer stem cells (CSCs) are pivotal in driving CRC metastasis. Our study found a significant upregulation of MOGS in metastatic colorectal cancer, with high MOGS expression inversely correlating with patient prognosis. Additionally, MOGS enhances the NOTCH pathway, thus promoting stemness in CRC cells, both in vitro and in vivo. Mechanistically, MOGS may facilitate the maturation of NOTCH1 protein by promoting NOTCH1 glycosylation. Correspondingly, silencing MOGS markedly reduced invasion and stemness of CRC cells in vivo. In summary, our findings highlight the critical role of MOGS in fostering stemness and activating the NOTCH pathway in colorectal cancer cells. Disrupting the function of the MOGS/NOTCH could represent a feasible therapeutic strategy for CRC management.
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Affiliation(s)
- Shihai Zhou
- Department of Tumor Surgery, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
| | - Hongyun Huang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical CollegeBeijing 100730, China
| | - Zheng Zheng
- Department of Tumor Surgery, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
| | - Kehong Zheng
- Department of General Surgery, Zhujiang Hospital, Southern Medical UniversityGuangzhou 510280, Guangdong, China
| | - Lang Xie
- Department of General Surgery, Zhujiang Hospital, Southern Medical UniversityGuangzhou 510280, Guangdong, China
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Yoshimura J, Togami Y, Ebihara T, Matsumoto H, Mitsuyama Y, Sugihara F, Hirata H, Okuzaki D, Ogura H. Classification of patients with COVID-19 by blood RNA endotype: a prospective cohort study. Microbiol Spectr 2023; 11:e0264523. [PMID: 37966347 PMCID: PMC10715063 DOI: 10.1128/spectrum.02645-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/08/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE In this study, whole-blood RNAs (prolactin and toll-like receptor 3) involved in the prognosis of patients with COVID-19 were identified. The RNA endotypes classified by these important RNAs highlight the possibility of stratifying the COVID-19 patient population and the need for targeted therapy based on these phenotypes.
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Affiliation(s)
- Jumpei Yoshimura
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yuki Togami
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Takeshi Ebihara
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
| | - Hisatake Matsumoto
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
| | - Yumi Mitsuyama
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Japan
- Division of Trauma and Surgical Critical Care, Osaka General Medical Center, Osaka, Japan
| | - Fuminori Sugihara
- Core Instrumentation Facility, Immunology Frontier Research Center and Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Haruhiko Hirata
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Daisuke Okuzaki
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
- Laboratory of Human Immunology (Single Cell Genomics), WPI Immunology Research Center, Osaka University, Osaka, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Hiroshi Ogura
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
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Wu N, Chen J, Lin T, Zhong Z, Li M, Yu Y, Guo J, Yu W. Identification of AP002498.1 and LINC01871 as prognostic biomarkers and therapeutic targets for distant metastasis of colorectal adenocarcinoma. Cancer Med 2023; 13:e6823. [PMID: 38083905 PMCID: PMC10807603 DOI: 10.1002/cam4.6823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Increasing evidence suggests that lncRNA (Long non-coding RNA, lncRNA)-mediated ceRNA (competing endogenous RNA, ceRNA) networks are involved in the occurrence and progression of colorectal cancer (CRC). However, the roles of the lncRNA-miRNA-mRNA ceRNA network in distant metastasis of CRC are still unclear. METHODS In this study, we constructed a specific ceRNA network to identify potential biomarkers and therapeutic targets for distant metastasis of CRC. Specifically, RNA-Seq data from The Cancer Genome Atlas (TCGA) were used to screen for differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) related to metastasis. After validation and selection by qRT-PCR and univariate and multivariate analysis of the metastasis- and prognosis-related lncRNAs, the regulated microRNAs (miRNAs) and coexpressed mRNAs were used to construct a ceRNA network for distant metastasis of CRC. RESULTS Two key distant metastasis-related DElncRNAs, AP002498.1 and LINC01871, were identified by univariate and multivariate analysis in combination with analyses of clinical data and expression levels. Furthermore, lncRNA-associated ceRNA subnetworks were constructed from the predicted miRNAs and 13 coexpressed DEmRNAs (SERPINA1, ITLN1, REG4, L1TD1, IGFALS, MUC5B, CIITA, CXCL9, CXCL10, GBP4, GNLY, IDO1, and NOS2). The AP002498.1- and LINC01871-associated ceRNA subnetworks regulated the expression of the target genes SERPINA1 and MUC5B and GNLY, respectively, through the associated miRNAs. CONCLUSION The DElncRNA AP002498.1 and the LINC01871/miR-4644 and miR-185-5p/GNLY axes were identified as being closely associated with distant metastasis and could represent independent prognostic biomarkers or therapeutic targets in colorectal adenocarcinoma.
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Affiliation(s)
- Na Wu
- Department of Central Laboratory and Institute of Clinical Molecular BiologyPeking University People's HospitalBeijingChina
| | - Jingyi Chen
- Department of Central Laboratory and Institute of Clinical Molecular BiologyPeking University People's HospitalBeijingChina
- Department of GastroenterologyPeking University People's HospitalBeijingChina
| | - Tingru Lin
- Department of Central Laboratory and Institute of Clinical Molecular BiologyPeking University People's HospitalBeijingChina
- Department of GastroenterologyPeking University People's HospitalBeijingChina
| | - Zhaohui Zhong
- Department of General SurgeryPeking University People's HospitalBeijingChina
| | - Mei Li
- Department of Central Laboratory and Institute of Clinical Molecular BiologyPeking University People's HospitalBeijingChina
| | - Yimeng Yu
- Department of Central Laboratory and Institute of Clinical Molecular BiologyPeking University People's HospitalBeijingChina
| | - Jingzhu Guo
- Department of PediatricPeking University People's HospitalBeijingChina
| | - Weidong Yu
- Department of Central Laboratory and Institute of Clinical Molecular BiologyPeking University People's HospitalBeijingChina
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Tong Y, Tan Z, Wang P, Gao X. A Machine Learning Method for Predicting Biomarkers Associated with Prostate Cancer. FRONT BIOSCI-LANDMRK 2023; 28:333. [PMID: 38179769 DOI: 10.31083/j.fbl2812333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/12/2023] [Accepted: 10/24/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND Prostate cancer (PCa) is a prevalent form of malignant tumors affecting the prostate gland and is frequently diagnosed in males in Western countries. Identifying diagnostic and prognostic biomarkers is not only important for screening drug targets but also for understanding their pathways and reducing the cost of experimental verification of PCa. The objective of this study was to identify and validate promising diagnostic and prognostic biomarkers for PCa. METHODS This study implemented a machine learning technique to evaluate the diagnostic and prognostic biomarkers of PCa using protein-protein interaction (PPI) networks. In addition, multi-database validation and literature review were performed to verify the diagnostic biomarkers. To optimize the prognosis of our results, univariate Cox regression analysis was utilized to screen survival-related genes. This study employed stepwise multivariate Cox regression analysis to develop a prognostic risk model. Finally, receiver operating characteristic analysis confirmed that these predictive biomarkers demonstrated a substantial level of sensitivity and specificity when predicting the prognostic survival of patients. RESULTS The hub genes were UBE2C (Ubiquitin Conjugating Enzyme E2 C), CCNB1 (Cyclin B1), TOP2A (DNA Topoisomerase II Alpha), TPX2 (TPX2 Microtubule Nucleation Factor), CENPM (Centromere Protein M), F5 (Coagulation Factor V), APOE (Apolipoprotein E), NPY (Neuropeptide Y), and TRIM36 (Tripartite Motif Containing 36). All of these hub genes were validated by multiple databases. By validation in these databases, these 10 hub genes were significantly involved in significant pathways. The risk model was constructed by a four-gene-based prognostic factor that included TOP2A, UBE2C, MYL9, and FLNA. CONCLUSIONS The machine learning algorithm combined with PPI networks identified hub genes that can serve as diagnostic and prognostic biomarkers for PCa. This risk model will enable patients with PCa to be more accurately diagnosed and predict new drugs in clinical trials.
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Affiliation(s)
- Yanqiu Tong
- Laboratory of Forensic Medicine and Biomedical Informatics, Chongqing Medical University, 400016 Chongqing, China
- School of Tourism and Media, Chongqing Jiaotong University, 400074 Chongqing, China
| | - Zhongle Tan
- School of Traditional Chinese Medicine, Chongqing Three Gorges Medical College, 404120 Chongqing, China
| | - Pu Wang
- Department of Rehabilitation, Southwest Hospital, Third Military Medical University (Army Medical University), 400038 Chongqing, China
| | - Xi Gao
- Department of Traditional Chinese Medicine, University-Town Hospital, Chongqing Medical University, 400016 Chongqing, China
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50
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Wang T, Li C, Ma Y, Zhou H, Du X, Li Y, Long S, Ding Y, Lu G, Chen W, Zhou Y, Yu L, Wang J, Wang Y. Metabolomics of cerebrospinal fluid reveals prognostic biomarkers in pediatric status epilepticus. CNS Neurosci Ther 2023; 29:3925-3934. [PMID: 37381696 PMCID: PMC10651953 DOI: 10.1111/cns.14312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/03/2023] [Accepted: 06/05/2023] [Indexed: 06/30/2023] Open
Abstract
AIMS Status epilepticus (SE) is the most common neurological emergency in pediatric patients. This study aimed to screen for prognostic biomarkers of SE in the cerebrospinal fluid (CSF) using metabolomics. METHODS Ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry (UPLC-QTOF-MS) was conducted to identify prognostic biomarkers in CSF metabolomics by comparing the poor outcome group (N = 13) with the good outcome group (N = 15) of children with SE. Differentially expressed metabolites were identified using Mann-Whitney U test corrected by Benjamini-Hochberg and partial least squares discriminant analysis (PLS-DA). RESULTS The PLS-DA model identified and validated significant metabolic differences between the poor and good outcome groups of children with SE (PLS-DA with R2 Y = 0.992 and Q2 = 0.798). A total of 49 prognosis-related metabolites were identified. Of these metabolites, 20 including glutamyl-glutamine, 3-iodothyronamine, and L-fucose had an area under the curve (AUC) ≥ 80% in prognostic prediction of SE. The logistic regression model combining glutamyl-glutamine and 3-iodothyronamine produced an AUC value of 0.976, with a sensitivity of 0.863 and specificity of 0.956. Pathway analysis revealed that dysregulation of the citrate cycle (TCA) and arginine biosynthesis may contribute to poor SE prognosis. CONCLUSIONS This study highlighted the prognosis-related metabolomic disturbances in the CSF of children with SE and identified potential prognostic biomarkers. A prognostic prediction model combining glutamyl-glutamine and 3-iodothyronamine with high predictive value was established.
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Affiliation(s)
- Tianqi Wang
- Department of Neurology, National Children's Medical CenterChildren's Hospital of Fudan UniversityShanghaiChina
| | - Chunpei Li
- Department of Neurology, National Children's Medical CenterChildren's Hospital of Fudan UniversityShanghaiChina
| | - Yu Ma
- Department of Neurology, National Children's Medical CenterChildren's Hospital of Fudan UniversityShanghaiChina
| | - Hao Zhou
- Department of Developmental Behavioral Pediatrics, Guizhou Provincial People's HospitalMedical College of Guizhou UniversityGuiyangChina
| | - Xiaonan Du
- Department of Neurology, National Children's Medical CenterChildren's Hospital of Fudan UniversityShanghaiChina
| | - Yingfeng Li
- Department of Neurology, National Children's Medical CenterChildren's Hospital of Fudan UniversityShanghaiChina
| | - Shasha Long
- Department of Neurology, National Children's Medical CenterChildren's Hospital of Fudan UniversityShanghaiChina
| | - Yifeng Ding
- Department of Neurology, National Children's Medical CenterChildren's Hospital of Fudan UniversityShanghaiChina
| | - Guoping Lu
- Pediatric Intensive Care Unit, National Children's Medical CenterChildren's Hospital of Fudan UniversityShanghaiChina
| | - Weiming Chen
- Pediatric Intensive Care Unit, National Children's Medical CenterChildren's Hospital of Fudan UniversityShanghaiChina
| | - Yuanfeng Zhou
- Department of Neurology, National Children's Medical CenterChildren's Hospital of Fudan UniversityShanghaiChina
| | - Lifei Yu
- Department of Neurology, National Children's Medical CenterChildren's Hospital of Fudan UniversityShanghaiChina
| | - Ji Wang
- Department of Neurology, National Children's Medical CenterChildren's Hospital of Fudan UniversityShanghaiChina
| | - Yi Wang
- Department of Neurology, National Children's Medical CenterChildren's Hospital of Fudan UniversityShanghaiChina
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