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Ahmad F, Muhmood T. Clinical translation of nanomedicine with integrated digital medicine and machine learning interventions. Colloids Surf B Biointerfaces 2024; 241:114041. [PMID: 38897022 DOI: 10.1016/j.colsurfb.2024.114041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024]
Abstract
Nanomaterials based therapeutics transform the ways of disease prevention, diagnosis and treatment with increasing sophistications in nanotechnology at a breakneck pace, but very few could reach to the clinic due to inconsistencies in preclinical studies followed by regulatory hinderances. To tackle this, integrating the nanomedicine discovery with digital medicine provide technologies as tools of specific biological activity measurement. Hence, overcome the redundancies in nanomedicine discovery by the on-site data acquisition and analytics through integrating intelligent sensors and artificial intelligence (AI) or machine learning (ML). Integrated AI/ML wearable sensors directly gather clinically relevant biochemical information from the subject's body and process data for physicians to make right clinical decision(s) in a time and cost-effective way. This review summarizes insights and recommend the infusion of actionable big data computation enabled sensors in burgeoning field of nanomedicine at academia, research institutes, and pharmaceutical industries, with a potential of clinical translation. Furthermore, many blind spots are present in modern clinically relevant computation, one of which could prevent ML-guided low-cost new nanomedicine development from being successfully translated into the clinic was also discussed.
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Affiliation(s)
- Farooq Ahmad
- State Key Laboratory of Chemistry and Utilization of Carbon Based Energy Resources, College of Chemistry, Xinjiang University, Urumqi 830017, China.
| | - Tahir Muhmood
- International Iberian Nanotechnology Laboratory (INL), Avenida Mestre José Veiga, Braga 4715-330, Portugal.
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Ye QW, Liu YJ, Li JQ, Han M, Bian ZR, Chen TY, Li JP, Liu SL, Zou X. GJA4 expressed on cancer associated fibroblasts (CAFs)-A 'promoter' of the mesenchymal phenotype. Transl Oncol 2024; 46:102009. [PMID: 38833783 PMCID: PMC11190749 DOI: 10.1016/j.tranon.2024.102009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 05/09/2024] [Accepted: 05/25/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the third most common cancer worldwide. Connexin is a transmembrane protein involved in gap junctions (GJs) formation. Our previous study found that connexin 37 (Cx37), encoded by gap junction protein alpha 4 (GJA4), expressed on fibroblasts acts as a promoter of CRC and is closely related to epithelial-mesenchymal transition (EMT) and tumor immune microenvironment. However, to date, the mechanism concerning the malignancy of GJA4 in tumor stroma has not been studied. METHODS Hematoxylin-eosin (HE) and immunohistochemical (IHC) staining were used to validate the expression and localization of GJA4. Using single-cell analysis, enrichment analysis, spatial transcriptomics, immunofluorescence staining (IF), Sirius red staining, wound healing and transwell assays, western blotting (WB), Cell Counting Kit-8 (CCK8) assay and in vivo experiments, we investigated the possible mechanisms of GJA4 in promoting CRC. RESULTS We discovered that in CRC, GJA4 on fibroblasts is involved in promoting fibroblast activation and promoting EMT through a fibroblast-dependent pathway. Furthermore, GJA4 may act synergistically with M2 macrophages to limit T cell infiltration by stimulating the formation of an immune-excluded desmoplasic barrier. Finally, we found a significantly correlation between GJA4 and pathological staging (P < 0.0001) or D2 dimer (R = 0.03, P < 0.05). CONCLUSION We have identified GJA4 expressed on fibroblasts is actually a promoter of the tumor mesenchymal phenotype. Our findings suggest that the interaction between GJA4+ fibroblasts and M2 macrophages may be an effective target for enhancing tumor immunotherapy.
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Affiliation(s)
- Qian-Wen Ye
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, PR China; No.1 Clinical Medicial College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, PR China
| | - Yuan-Jie Liu
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, PR China; No.1 Clinical Medicial College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, PR China
| | - Jia-Qi Li
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, PR China; No.1 Clinical Medicial College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, PR China
| | - Mei Han
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, PR China
| | - Ze-Ren Bian
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, PR China; No.1 Clinical Medicial College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, PR China
| | - Tian-Yuan Chen
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, PR China; No.1 Clinical Medicial College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, PR China
| | - Jie-Pin Li
- Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, Nanjing, Jiangsu, PR China
| | - Shen-Lin Liu
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, PR China.
| | - Xi Zou
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, Nanjing, Jiangsu, PR China.
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Ye Z, Huang N, Fu Y, Tian R, Wang L, Huang W. Tumor purity-related genes for predicting the prognosis and drug sensitivity of DLBCL patients. eLife 2024; 13:RP92841. [PMID: 38980810 PMCID: PMC11233133 DOI: 10.7554/elife.92841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024] Open
Abstract
Background Diffuse large B-cell lymphoma (DLBCL) is the predominant type of malignant B-cell lymphoma. Although various treatments have been developed, the limited efficacy calls for more and further exploration of its characteristics. Methods Datasets from the Gene Expression Omnibus (GEO) database were used for identifying the tumor purity of DLBCL. Survival analysis was employed for analyzing the prognosis of DLBCL patients. Immunohistochemistry was conducted to detect the important factors that influenced the prognosis. Drug-sensitive prediction was performed to evaluate the value of the model. Results VCAN, CD3G, and C1QB were identified as three key genes that impacted the outcome of DLBCL patients both in GEO datasets and samples from our center. Among them, VCAN and CD3G+ T cells were correlated with favorable prognosis, and C1QB was correlated with worse prognosis. The ratio of CD68 + macrophages and CD8 + T cells was associated with better prognosis. In addition, CD3G+T cells ratio was significantly correlated with CD68 + macrophages, CD4 + T cells, and CD8 +T cells ratio, indicating it could play an important role in the anti-tumor immunity in DLBCL. The riskScore model constructed based on the RNASeq data of VCAN, C1QB, and CD3G work well in predicting the prognosis and drug sensitivity. Conclusions VCAN, CD3G, and C1QB were three key genes that influenced the tumor purity of DLBCL, and could also exert certain impact on drug sensitivity and prognosis of DLBCL patients. Funding This work is supported by the Shenzhen High-level Hospital Construction Fund and CAMS Innovation Fund for Medical Sciences (CIFMS) (2022-I2M-C&T-B-062).
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MESH Headings
- Humans
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/mortality
- Lymphoma, Large B-Cell, Diffuse/immunology
- Prognosis
- Female
- Male
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Drug Resistance, Neoplasm/genetics
- Gene Expression Regulation, Neoplastic
- Middle Aged
- Survival Analysis
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Affiliation(s)
- Zhenbang Ye
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ning Huang
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongliang Fu
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rongle Tian
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liming Wang
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenting Huang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
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Wei J, Wang M, Wu Y. A disulfidptosis-related lncRNAs cluster to forecast the prognosis and immune landscapes of ovarian cancer. Front Genet 2024; 15:1397011. [PMID: 39045330 PMCID: PMC11263023 DOI: 10.3389/fgene.2024.1397011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/11/2024] [Indexed: 07/25/2024] Open
Abstract
Objective Disulfidptosis is a newly recognized form of regulated cell death that has been linked to cancer progression and prognosis. Despite this association, the prognostic significance, immunological characteristics and treatment response of disulfidptosis-related lncRNAs (DRLs) in ovarian cancer have not yet been elucidated. Methods The lncRNA data and clinical information for ovarian cancer and normal samples were obtained from the UCSC XENA. Differential expression analysis and Pearson analysis were utilized to identify core DRLs, followed by LASSO algorithm. Random Survival Forest was used to construct a prognostic model. The relationships between risk scores, RNA methylation, immune cell infiltration, mutation, responses to immunotherapy and drug sensitivity analysis were further examined. Additionally, qRT-PCR experiments were conducted to validate the expression of the core DRLs in human ovarian cancer cells and normal ovarian cells and the scRNA-seq data of the core DRLs were obtained from the GEO dataset, available in the TISCH database. Results A total of 8 core DRLs were obtained to construct a prognostic model for ovarian cancer, categorizing all patients into low-risk and high-risk groups using an optimal cutoff value. The AUC values for 1-year, 3-year and 5-year OS in the TCGA cohort were 0.785, 0.810 and 0.863 respectively, proving a strong predictive capability of the model. The model revealed the high-risk group patients exhibited lower overall survival rates, higher TIDE scores and lower TMB levels compared to the low-risk group. Variations in immune cell infiltration and responses to therapeutic drugs were observed between the high-risk and low-risk groups. Besides, our study verified the correlations between the DRLs and RNA methylation. Additionally, qRT-PCR experiments and single-cell RNA sequencing data analysis were conducted to confirm the significance of the core DRLs at both cellular and scRNA-seq levels. Conclusion We constructed a reliable and novel prognostic model with a DRLs cluster for ovarian cancer, providing a foundation for further researches in the management of this disease.
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Zhao Y, Chen C, Chen K, Sun Y, He N, Zhang X, Xu J, Shen A, Zhao S. Multi-omics analysis of macrophage-associated receptor and ligand reveals a strong prognostic signature and subtypes in hepatocellular carcinoma. Sci Rep 2024; 14:12163. [PMID: 38806553 PMCID: PMC11133315 DOI: 10.1038/s41598-024-62668-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 05/20/2024] [Indexed: 05/30/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a significant contributor to morbidity and mortality worldwide. The interaction between receptors and ligands is the primary mode of intercellular signaling and plays a vital role in the progression of HCC. This study aimed to identify the macrophage-related receptor ligand marker genes associated with HCC and further explored the molecular immune mechanisms attributed to altered biomarkers. Single-cell RNA sequencing data containing primary and recurrent samples were downloaded from the China National GeneBank. Cell types were first identified to explore differences between immune cells from different sample sources. CellChat analysis was used to infer and analyze intercellular communication networks quantitatively. Three molecular subtypes were constructed based on the screened twenty macrophage-associated receptor ligand genes. Bulk RNA-Seq data were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus databases. After the screening, the minor absolute shrinkage and selection operator (LASSO) regression model was employed to identify key markers. After collecting peripheral blood and clinical information from patients, an enzyme-linked immunosorbent assay (ELISA) was used to detect the correlation between key markers and IL-10, one of the macrophage markers. After developing a new HCC risk adjustment model and conducting analysis, it was found that there were significant differences in immune status and gene mutations between the high-risk and low-risk groups of patients based on macrophage-associated receptor and ligand genes. This study identified SPP1, ANGPT2, and NCL as key biological targets for HCC. The drug-gene interaction network analysis identified wortmannin, ribavirin, and tarnafloxin as potential therapeutic drugs for the three key markers. In a clinical cohort study, patients with immune checkpoint inhibitor (ICI) resistance had significantly higher expression levels of OPN, ANGPT2, NCL, and IL-10 than patients with ICI-responsiveness. These three key markers were positively correlated with the expression level of IL-10. The signature based on macrophage-associated receptor and ligand genes can accurately predict the prognosis of patients with HCC and the sensitivity to immunotherapy. These results may help guide the development of targeted prevention and personalized treatment of HCC.
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Affiliation(s)
- Yulou Zhao
- Medical School, Nantong University, Nantong, China
| | - Cong Chen
- Department of Interventional and Vascular Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Kang Chen
- Department of Interventional and Vascular Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Yanjun Sun
- The Sixth People's Hospital of Yancheng City, Yancheng, China
| | - Ning He
- Department of Interventional and Vascular Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Xiubing Zhang
- Department of Medical Oncology, Nantong Second People's Affiliated Hospital of Nantong University, Nantong, China
| | - Jian Xu
- Department of Medical Oncology, Nantong Second People's Affiliated Hospital of Nantong University, Nantong, China
| | - Aiguo Shen
- Cancer Research Center Nantong, Affiliated Tumor Hospital of Nantong University, Nantong, China.
| | - Suming Zhao
- Department of Interventional and Vascular Surgery, Affiliated Hospital of Nantong University, Nantong, China.
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Sun X, He W, Lin B, Huang W, Ye D. Defining three ferroptosis-based molecular subtypes and developing a prognostic risk model for high-grade serous ovarian cancer. Aging (Albany NY) 2024; 16:9106-9126. [PMID: 38795391 PMCID: PMC11164503 DOI: 10.18632/aging.205857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 04/08/2024] [Indexed: 05/27/2024]
Abstract
BACKGROUND As a newly defined regulated cell death, ferroptosis is a potential biomarker in ovarian cancer (OV). However, its underlying mechanism in tumor microenvironment (TME) and clinical prediction significance in OV remained to be elucidated. METHODS The transcriptome data of high-grade serous OV from The Cancer Genome Atlas (TCGA) database were downloaded. Molecular subtypes were classified based on ferroptosis-correlated genes from the FerrDb database by performing consensus clustering analysis. The associations between the subtypes and clinicopathologic characteristics, mutation, regulatory pathways and immune landscape were assessed. A ferroptosis-related prognostic model was constructed and verified using International Cancer Genome Consortium (ICGC) cohort and GSE70769. RESULTS Three molecular subtypes of OV were defined. Patients in subtype C3 tended to have the most favorable prognosis, while subtype C1 showing more mesenchymal cells, increased immune infiltration of Macrophages_M2, lower tumor purity, and epithelial-to-mesenchymal transition (EMT) features had the poorest prognosis. A ferroptosis-related risk model was constructed using 8 genes (PDP1, FCGBP, EPHA4, GAS1, SLC7A11, BLOC1S1, SPOCK2, and CXCL9) and manifested a strong prediction performance. High-risk patients had enriched EMT pathways, more Macrophages_M2, less plasma cells and CD8 cell infiltration, greater tendency of immune escape and worse prognosis. The risk score has negatively correlated relation with LAG3, TIGIT, CTLA4, IDO1, CD27, ICOS, and IL2RB but positively correlated with PVR, CD276, and CD28. Moreover, low-risk patients were more sensitive to Cisplatin and Gefitinib, Gemcitabine. CONCLUSIONS Our results could improve the understanding of ferroptosis in OV, providing promising insights for the clinical targeted therapy for the cancer.
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Affiliation(s)
- Xiang Sun
- Department of Obstetrics and Gynecology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Wenbin He
- Department of Otolaryngology, Lanzhou University Second Hospital, Gansu 730030, China
| | - Baohua Lin
- Department of Obstetrics and Gynecology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Weiming Huang
- Department of Obstetrics and Gynecology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
| | - Danping Ye
- Department of Obstetrics and Gynecology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong 510623, China
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Pei J, Gao Y, Wu A. An inflammation-related subtype classification for analyzing tumor microenvironment and clinical prognosis in colorectal cancer. Front Immunol 2024; 15:1369726. [PMID: 38742117 PMCID: PMC11089903 DOI: 10.3389/fimmu.2024.1369726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Background The inflammatory response plays an essential role in the tumor microenvironment (TME) of colorectal cancer (CRC) by modulating tumor growth, progression, and response to therapy through the recruitment of immune cells, production of cytokines, and activation of signaling pathways. However, the molecular subtypes and risk score prognostic model based on inflammatory response remain to be further explored. Methods Inflammation-related genes were collected from the molecular signature database and molecular subtypes were identified using nonnegative matrix factorization based on the TCGA cohort. We compared the clinicopathological features, immune infiltration, somatic mutation profile, survival prognosis, and drug sensitivity between the subtypes. The risk score model was developed using LASSO and multivariate Cox regression in the TCGA cohort. The above results were independently validated in the GEO cohort. Moreover, we explored the biological functions of the hub gene, receptor interacting protein kinase 2 (RIPK2), leveraging proteomics data, in vivo, and in vitro experiments. Results We identified two inflammation-related subtypes (inflammation-low and inflammation-high) and have excellent internal consistency and stability. Inflammation-high subtype showed higher immune cell infiltration and increased sensitivity to common chemotherapeutic drugs, while inflammation-low subtype may be more suitable for immunotherapy. Besides, the two subtypes differ significantly in pathway enrichment and biological functions. In addition, the 11-gene signature prognostic model constructed from inflammation-related genes showed strong prognostic assessment power and could serve as a novel prognostic marker to predict the survival of CRC patients. Finally, RIPK2 plays a crucial role in promoting malignant proliferation of CRC cell validated by experiment. Conclusions This study provides new insights into the heterogeneity of CRC and provides novel opportunities for treatment development and clinical decision making.
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Affiliation(s)
| | | | - Aiwen Wu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Unit III, Gastrointestinal Cancer Center, Peking University Cancer Hospital and Institute, Beijing, China
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Sun JR, Kong CF, Ye YX, Wang Q, Qu XK, Jia LQ, Wu S. Integrated analysis of single-cell and bulk RNA-sequencing reveals a novel signature based on NK cell marker genes to predict prognosis and immunotherapy response in gastric cancer. Sci Rep 2024; 14:7648. [PMID: 38561388 PMCID: PMC10985121 DOI: 10.1038/s41598-024-57714-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
Natural killer (NK) cells play essential roles in the tumor development, diagnosis, and prognosis of tumors. In this study, we aimed to establish a reliable signature based on marker genes in NK cells, thus providing a new perspective for assessing immunotherapy and the prognosis of patients with gastric cancer (GC). We analyzed a total of 1560 samples retrieved from the public database. We performed a comprehensive analysis of single-cell RNA-sequencing (scRNA-seq) data of gastric cancer and identified 377 marker genes for NK cells. By performing Cox regression analysis, we established a 12-gene NK cell-associated signature (NKCAS) for the Cancer Genome Atlas (TCGA) cohort, that assigned GC patients into a low-risk group (LRG) or a high-risk group (HRG). In the TCGA cohort, the areas under curve (AUC) value were 0.73, 0.81, and 0.80 at 1, 3, and 5 years. External validation of the predictive ability for the signature was then validated in the Gene Expression Omnibus (GEO) cohorts (GSE84437). The expression levels of signature genes were measured and validated in GC cell lines by real-time PCR. Moreover, NKCAS was identified as an independent prognostic factor by multivariate analysis. We combined this with a variety of clinicopathological characteristics (age, M stage, and tumor grade) to construct a nomogram to predict the survival outcomes of patients. Moreover, the LRG showed higher immune cell infiltration, especially CD8+ T cells and NK cells. The risk score was negatively associated with inflammatory activities. Importantly, analysis of the independent immunotherapy cohort showed that the LRG had a better prognosis and immunotherapy response when compared with the HRG. The identification of NK cell marker genes in this study suggests potential therapeutic targets. Additionally, the developed predictive signatures and nomograms may aid in the clinical management of GC.
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Affiliation(s)
- Jian-Rong Sun
- School of Clinical Medicine, Beijing University of Chinese Medicine, No. 11, North 3rd East Road, Beijing, 100029, Chaoyang, People's Republic of China
| | - Chen-Fan Kong
- Department of Urology, The affiliated Shenzhen Hospital of Shanghai University of Traditional Chinese Medicine, No. 16, Liantangxiantong Road, Shenzhen, 518009, Luohu, People's Republic of China
| | - Yi-Xiang Ye
- School of Clinical Medicine, Beijing University of Chinese Medicine, No. 11, North 3rd East Road, Beijing, 100029, Chaoyang, People's Republic of China
| | - Qin Wang
- School of Clinical Medicine, Beijing University of Chinese Medicine, No. 11, North 3rd East Road, Beijing, 100029, Chaoyang, People's Republic of China
| | - Xiang-Ke Qu
- School of Clinical Medicine, Beijing University of Chinese Medicine, No. 11, North 3rd East Road, Beijing, 100029, Chaoyang, People's Republic of China
| | - Li-Qun Jia
- School of Clinical Medicine, Beijing University of Chinese Medicine, No. 11, North 3rd East Road, Beijing, 100029, Chaoyang, People's Republic of China.
| | - Song Wu
- Department of Urology, The affiliated Shenzhen Hospital of Shanghai University of Traditional Chinese Medicine, No. 16, Liantangxiantong Road, Shenzhen, 518009, Luohu, People's Republic of China.
- Department of Urology, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, 518116, People's Republic of China.
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Ding Z, Ding Q, Li H. The prognostic biomarker TPGS2 is correlated with immune infiltrates in pan-cancer: a bioinformatics analysis. Transl Cancer Res 2024; 13:1458-1478. [PMID: 38617524 PMCID: PMC11009813 DOI: 10.21037/tcr-23-113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 10/20/2023] [Indexed: 04/16/2024]
Abstract
Background Tubulin polyglutamylase complex subunit 2 (TPGS2) is an element of the neuronal polyglutamylase complex that plays a role in the post-translational addition of glutamate residues to C-terminal tubulin tails. Recent research has shown that TPGS2 is associated with some tumors, but the roles of TPGS2 in tumor immunity remain unclear. Methods The research data were mainly sourced from The Cancer Genome Atlas. The data were analyzed to identify potential correlations between TPGS2 expression and survival, gene alterations, the tumor mutational burden (TMB), microsatellite instability (MSI), immune infiltration, and various immune-related genes across various cancers. The Wilcoxon rank-sum test was used to identify the significance. A log-rank test and univariate Cox regression analysis were performed to assess the survival state of the patients. Spearman's correlation coefficients were used to show the correlations. Results TPGS2 exhibited abnormal expression patterns in most types of cancers, and has promising prognostic potential in adrenocortical carcinoma and liver hepatocellular carcinoma. Further, TPGS2 expression was significantly correlated with molecular and immune subtypes. Moreover, the single-cell analyses showed that the expression of TPGS2 was associated with the cell cycle, metastasis, invasion, inflammation, and DNA damage. In addition, the immune cell infiltration analysis and gene-set enrichment analysis demonstrated that a variety of immune cells and immune processes were associated with TPGS2 expression in various cancers. Further, immune regulators, including immunoinhibitors, immunostimulators, the major histocompatibility complex, chemokines, and chemokine receptors, were correlated with TPGS2 expression in different cancer types. Finally, the TMB and MSI, which have been identified as powerful predictors of immunotherapy, were shown to be correlated with the expression of TPGS2 across human cancers. Conclusions TPGS2 is aberrantly expressed in most cancer tissues and might be associated with immune cell infiltration in the tumor microenvironment. TPGS2 could serve not only as a biomarker for predicting clinical outcomes, but also as a promising biomarker for evaluating and developing new approaches to immunotherapy in many types of cancers, especially colon adenocarcinoma and stomach adenocarcinoma.
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Affiliation(s)
- Zujun Ding
- Department of General Surgery, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Qing Ding
- Department of Pharmacy, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hang Li
- Department of General Surgery, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
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Ma X, Liu H, Shi C, Zhao Y, Wang H, Han Z. Bioinformatics analysis and clinical significance of NRP-1 in triple-negative breast cancer. Heliyon 2024; 10:e27368. [PMID: 38495206 PMCID: PMC10943386 DOI: 10.1016/j.heliyon.2024.e27368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Purpose This study aimed to investigate the diagnostic and prognostic values of neuropilin-1 (NRP-1) in triple-negative breast cancer (TNBC) and analyze its immune function in the tumor microenvironment. Methods Based on The Cancer Genome Atlas (TCGA), Gene Expression Omnibus, Genotype Tissue Expression, Immune Cell Abundance Identifier (ImmuCellAI), Reactome, and Genomics of Drug Sensitivity in Cancer databases, the cancer tissues from 50 patients with TNBC and corresponding adjacent noncancerous tissues from 10 patients (tissue microarrays were purchased from Shanghai Xinchao Biotechnology Co., Ltd.) were collected for validation. Bioinformatics combined with immunohistochemistry was used to analyze the relationship among NRP-1 expression, prognosis, tumor immune cell infiltration, immune genes, and drug resistance so as to investigate the role of NRP-1 in the development of TNBC. Results A significant difference in NRP-1 gene expression was found between the cancerous and noncancerous tissues (p-value < 0.05); NRP-1 expression was high in carcinoma. No significant correlation was found between NRP-1 protein expression levels and each stage in the TCGA database. Prognostic expression survival analysis showed that the survival probability of patients with high NRP-1 expression was significantly lower than that of patients with low NRP-1 expression (p-value < 0.05), suggesting that the gene might be a pro-oncogene. The data from 50 clinical samples also confirmed that the NRP-1 expression was significantly higher in triple-negative breast cancer (TNBC) tissues than in adjacent noncancerous tissues. The NRP-1 expression significantly correlated with the tumor diameter and pathological grade (p-value < 0.05), but not with age, stage, and ki67 (p-value > 0.05). The Kaplan-Meier survival curves suggested that the median overall survival was significantly shorter in patients with high NRP-1 expression than in those with low NRP-1 expression (13.6 months vs 15.2 months, p-value < 0.05). The 300 genes most significantly positively associated with this gene were selected for Gene Ontology (including Biological Process, Molecular Function, and Cellular Component groups) and Kyoto Encyclopedia of Genes and Genomics enrichment analysis. The findings showed that NRP-1 was involved in immune regulation in TNBC. In addition, the NRP-1 expression in TNBC positively correlated with a variety of immune cells and checkpoints. Conclusion NRP-1 can be used as a potential biomarker and therapeutic target in TNBC.
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Affiliation(s)
- Xiao Ma
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China
| | - Haonan Liu
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China
| | - Congcong Shi
- Department of Gastroenterology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China
| | - Yang Zhao
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China
| | - Hongmei Wang
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China
| | - Zhengxiang Han
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China
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11
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Nie J, Yang H, Liu X, Deng W, Fu B. Identification and validation of shared gene signature of kidney renal clear cell carcinoma and COVID-19. PeerJ 2024; 12:e16927. [PMID: 38464749 PMCID: PMC10921934 DOI: 10.7717/peerj.16927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/22/2024] [Indexed: 03/12/2024] Open
Abstract
Background COVID-19 is a severe infectious disease caused by the SARS-CoV-2 virus, and previous studies have shown that patients with kidney renal clear cell carcinoma (KIRC) are more susceptible to SARS-CoV-2 infection than the general population. Nevertheless, their co-pathogenesis remains incompletely elucidated. Methods We obtained shared genes between these two diseases based on public datasets, constructed a prognostic risk model consisting of hub genes, and validated the accuracy of the model using internal and external validation sets. We further analyzed the immune landscape of the prognostic risk model, investigated the biological functions of the hub genes, and detected their expression in renal cell carcinoma cells using qPCR. Finally, we searched the candidate drugs associated with hub gene-related targets from DSigDB and CellMiner databases. Results We obtained 156 shared genes between KIRC and COVID-19 and constructed a prognostic risk model consisting of four hub genes. Both shared genes and hub genes were highly enriched in immune-related functions and pathways. Hub genes were significantly overexpressed in COVID-19 and KIRC. ROC curves, nomograms, etc., showed the reliability and robustness of the risk model, which was validated in both internal and external datasets. Moreover, patients in the high-risk group showed a higher proportion of immune cells, higher expression of immune checkpoint genes, and more active immune-related functions. Finally, we identified promising drugs for COVID-19 and KIRC, such as etoposide, fulvestrant, and topotecan. Conclusion This study identified and validated four shared genes for KIRC and COVID-19. These genes are associated with immune functions and may serve as potential prognostic biomarkers for KIRC. The shared pathways and genes may provide new insights for further mechanistic research and treatment of comorbidities.
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Affiliation(s)
- Jianqiang Nie
- First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hailang Yang
- First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaoqiang Liu
- First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Institute of Urology, Nanchang, China
| | - Wen Deng
- First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Institute of Urology, Nanchang, China
| | - Bin Fu
- First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Institute of Urology, Nanchang, China
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12
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Yu N, Huang S, Zhang Z, Huang M, Wang Y, Zhang W, Zhang X, Zhu X, Sheng X, Yu K, Chen Z, Guo W. A prospective phase II single-arm study and predictive factor analysis of irinotecan as third-line treatment in patients with metastatic gastric cancer. Ther Adv Med Oncol 2024; 16:17588359241229433. [PMID: 38425987 PMCID: PMC10903192 DOI: 10.1177/17588359241229433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/03/2024] [Indexed: 03/02/2024] Open
Abstract
Background Currently, there is no recommended standard third-line chemotherapy for metastatic gastric cancer. Objectives In this study, we aimed to evaluate irinotecan's efficacy and safety in treating metastatic gastric cancer after the failure of first- and second-line chemotherapy. Design Prospective single-arm, two-center, phase II trial. Methods Patients were aged 18-70 years, with histologically confirmed gastric adenocarcinoma and an Eastern Cooperative Oncology Group performance status of 0-1, progressed during or within 3 months following the last administration of second-line chemotherapy and had no other severe hematologic, cardiac, pulmonary, hepatic, or renal functional abnormalities or immunodeficiency diseases. Eligible patients received 28-day cycles of irinotecan (180 mg/m2 intravenously, days 1 and 15) and were assessed according to the RECIST 1.1 criteria every two cycles. Patients who discontinued treatment for any reason were followed up every 2 months until death. The primary endpoint was overall survival (OS), and the secondary endpoints were progression-free survival (PFS), objective response rate (ORR), disease control rate (DCR), and toxicity. Results A total of 98 eligible patients were enrolled in this study. In the intention-to-treat population, the median OS was 7.17 months, the median PFS was 3.47 months, and the ORR and DCR were 4.08% and 47.96%, respectively. In the per-protocol population, the median OS was 7.77 months, the median PFS was 3.47 months, and the ORR and DCR were 4.82% and 50.60%, respectively. The incidence of grade 3 or 4 hematological and non-hematological toxicities was 19.4%, and none of the patients died owing to adverse events. Cox regression analysis revealed neutropenia and baseline thrombocyte levels were independently correlated with PFS and OS. Conclusion Irinotecan monotherapy is an efficient, well-tolerated, and economical third-line treatment for patients with metastatic gastric cancer as a third-line treatment. Trial registration ClinicalTrials.gov identifier: NCT02662959.
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Affiliation(s)
- Nuoya Yu
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Sha Huang
- Department of Medical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Zhe Zhang
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Mingzhu Huang
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yusheng Wang
- Department of Digestive, Shanxi Province Cancer Hospital, Taiyuan, Shanxi, China
| | - Wen Zhang
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaowei Zhang
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaodong Zhu
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xuedan Sheng
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kaiyue Yu
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiyu Chen
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, No. 270, Dongan Road, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Weijian Guo
- Department of Gastrointestinal Medical Oncology, Fudan University Shanghai Cancer Center, No. 270, Dongan Road, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
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13
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Wu Y, Zhao S, Guo W, Liu Y, Requena Mullor MDM, Rodrìguez RA, Wei R. Systematic analysis of the prognostic value and immunological function of LTBR in human cancer. Aging (Albany NY) 2024; 16:129-152. [PMID: 38175686 PMCID: PMC10817409 DOI: 10.18632/aging.205356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 11/15/2023] [Indexed: 01/05/2024]
Abstract
Lymphotoxin beta receptor (LTBR) is a positive T cell proliferation regulator gene. It is closely associated with the tumor immune microenvironment. However, its role in cancer and immunotherapy is unclear. Firstly, the expression level and prognostic value of LTBR were analyzed. Secondly, the expression of LTBR in clinical stages, immune subtypes, and molecular subtypes was analyzed. The correlation between LTBR and immune regulatory genes, immune checkpoint genes, and RNA modification genes was then analyzed. Correlations between LTBR and immune cells, scores, cancer-related functional status, tumor stemness index, mismatch repair (MMR) genes, and DNA methyltransferase were also analyzed. In addition, we analyzed the role of LTBR in DNA methylation, mutational status, tumor mutation burden (TMB), and microsatellite instability (MSI). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were used to explore the role of LTBR in pan-cancer. Finally, the drugs associated with LTBR were analyzed. The expression of LTBR was confirmed using quantitative real-time PCR and Western blot. LTBR is significantly overexpressed in most cancers and is associated with low patient survival. In addition, LTBR expression was strongly correlated with immune cells, score, cancer-related functional status, tumor stemness index, MMR genes, DNA methyltransferase, DNA methylation, mutational status, TMB, and MSI. Enrichment analysis revealed that LTBR was associated with apoptosis, necroptosis, and immune-related pathways. Finally, multiple drugs targeting LTBR were identified. LTBR is overexpressed in several tumors and is associated with a poor prognosis. It is related to immune-related genes and immune cell infiltration.
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Affiliation(s)
- Yinteng Wu
- Department of Orthopedic and Trauma Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Shijian Zhao
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Wenliang Guo
- Department of Rehabilitation Medicine, The Eighth Affiliated Hospital of Guangxi Medical University, Guigang, Guangxi 537100, China
| | - Ying Liu
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | | | | | - Ruqiong Wei
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
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14
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Lin W, Zhou J, Ma Y, Ge L, Luo Y, Wang Y, Zhou S. Prognostic value of mitochondrial CKMT2 in Pan-cancer and its tumor immune correlation analysis. Sci Rep 2024; 14:342. [PMID: 38172162 PMCID: PMC10764887 DOI: 10.1038/s41598-023-46468-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/01/2023] [Indexed: 01/05/2024] Open
Abstract
Mitochondrial metabolism has been shown to play a key role in immune cell survival and function, but mitochondrial creatine kinase 2 (CKMT2) has been relatively little studied about tumor immunity. We aimed to explore the prognostic value of CKMT2 in 33 cancer types and investigate its potential immune function. We used a range of bioinformatics approaches to explore the potential carcinogenic role of CKMT2 in multiple cancers. CKMT2 was lowly expressed in 14 tumor tissues and highly expressed in 4 tumor tissues. Immunohistochemical assays showed overexpression of CKMT2 in colon cancer and rectal cancer. CKMT2 overexpression was positively correlated with the prognosis of lung adenocarcinoma and prostate cancer. CKMT2 overexpression is mainly enriched in the adaptive immune system and immune regulatory pathways of immunoglobulins. Seven cancers were positively correlated with low CKMT2 expression in tumor microenvironment analysis. Among the five cancers, low expression of CKMT2 resulted in better immunotherapy treatment outcomes. There was a strong correlation between CKMT2 and most immune-related genes in specific cancer types. CKMT2 plays an important role in tumorigenesis and cancer immunity and can be used as a prognostic biomarker and potential target for cancer immunotherapy.
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Affiliation(s)
- Wei Lin
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jiamin Zhou
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Yili Ma
- Department of Pathology, Affiliated Cancer Hospital of Guangxi Medical University, Nanning, China
| | - Liuxing Ge
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Yiling Luo
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Yaobin Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Sufang Zhou
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China.
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Chen Z, Zeng L, Chen Z, Xu J, Zhang X, Ying H, Zeng Y, Yu F. Combined OLA1 and CLEC3B Gene Is a Prognostic Signature for Hepatocellular Carcinoma and Impact Tumor Progression. Technol Cancer Res Treat 2024; 23:15330338241241935. [PMID: 38564315 PMCID: PMC11007312 DOI: 10.1177/15330338241241935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/26/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Hepatocellular carcinoma (HCC), partly because of its complexity and high heterogeneity, has a poor prognosis and an extremely high mortality rate. In this study, mRNA sequencing expression profiles and relevant clinical data of HCC patients were gathered from different public databases. Kaplan-Meier survival curves as well as ROC curves validated that OLA1|CLEC3B was an independent predictor with better predictive capability of HCC prognosis compared to OLA1 and CLEC3B separately. Further, the cell transfection experiment verified that knockdown of OLA1 inhibited cell proliferation, facilitated apoptosis, and improved sensitivity of HCC cells to gemcitabine. In this study, the prognostic model of HCC composed of OLA1/CLEC3B genes was constructed and verified, and the prediction ability was favorable. A higher level of OLA1 along with a lower level of CEC3B is a sign of poor prognosis in HCC. We revealed a novel gene pair OLA1|CLEC3B overexpressed in HCC patients, which may serve as a promising independent predictor of HCC survival and an approach for innovative diagnostic and therapeutic strategies.
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Affiliation(s)
- Zhoufeng Chen
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Liuwei Zeng
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhuoyan Chen
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jun Xu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiangting Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Huiya Ying
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuan Zeng
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Fujun Yu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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16
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Wang J, Shu J. Construction of RNA Methylation Modification-immune-related lncRNA Molecular Subtypes and Prognostic Scoring System in Lung Adenocarcinoma. Curr Med Chem 2024; 31:1539-1560. [PMID: 37680151 DOI: 10.2174/0929867331666230901110629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/13/2023] [Accepted: 08/07/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND RNA methylation modification is not only intimately interrelated with cancer development and progression but also actively influences immune cell infiltration in the tumor microenvironment (TME). RNA methylation modification genes influence the therapeutic progression of lung adenocarcinoma (LUAD), and mining RNA methylation modification prognosis-related markers in LUAD is crucial for its precise prognosis. METHODS RNA-Seq data and Gene sets were collected from online databases or published literature. Genomic variation analysis was conducted by the Maftools package. RNA methylation-immune-related lncRNAs were obtained by Pearson correlation analysis. Then, Consistent clustering analysis was performed to obtain RNA methylation modification- immune molecular subtypes (RMM-I Molecular subtypes) in LUAD based on selected lncRNAs. COX and random survival forest analysis were carried out to construct the RMM-I Score. The receiver operating characteristic (ROC) curve and Kaplan Meier survival analysis were used to assess survival differences. Tumor immune microenvironment was assessed through related gene signatures and CIBERSORT algorithm. In addition, drug sensitivity analysis was executed by the pRRophetic package. RESULTS Four RNA methylation modified-immune molecular subtypes (RMM-I1, RMM- I2, RMM-I3, RMM-I4) were presented in LUAD. Patients in RMM-I4 exhibited excellent survival advantages and immune activity. HAVCR2, CD274, and CTLA-4 expression were activated in RMM-I4, which might be heat tumors and a potential beneficial group for immunotherapy. OGFRP1, LINC01116, DLGAP1-AS2, CRNDE, LINC01137, MIR210HG, and CYP1B1-AS1 comprised the RMM-I Score. The RMM-I Score exhibited excellent accuracy in the prognostic assessment of LUAD, as patients with a low RMM- I Score exhibited remarkable survival advantage. Patients with a low RMM-I score might be more sensitive to treatment with Docetaxel, Vinorelbine, Paclitaxel, Cisplatin, and immunotherapy. CONCLUSION The RMM-I molecular subtype constituted the novel molecular characteristic subtype of LUAD, which complemented the existing pathological typing. More refined and accurate molecular subtypes provide help to reveal the mechanism of LUAD development. In addition, the RMM-I score offers a reliable tool for accurate prognosis of LUAD.
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Affiliation(s)
- Jiajing Wang
- Department of Clinical Laboratory, Beilun People's Hospital, Ningbo, 315000, China
| | - Jianfeng Shu
- Huamei Hospital, University of Chinese Academy of Sciences, Ningbo, 315000, China
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Bae SH, Hwang T, Han MR. Unraveling the hypoxia modulating potential of VEGF family genes in pan-cancer. Genomics Inform 2023; 21:e44. [PMID: 37852616 PMCID: PMC10788353 DOI: 10.5808/gi.23061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/20/2023] Open
Abstract
Tumor hypoxia, oxygen deprivation state, occurs in most cancers and promotes angiogenesis, enhancing the potential for metastasis. The vascular endothelial growth factor (VEGF) family genes play crucial roles in tumorigenesis by promoting angiogenesis. To investigate the malignant processes triggered by hypoxia-induced angiogenesis across pan-cancers, we comprehensively analyzed the relationships between the expression of VEGF family genes and hypoxic microenvironment based on integrated bioinformatics methods. Our results suggest that the expression of VEGF family genes differs significantly among various cancers, highlighting their heterogeneity effect on human cancers. Across the 33 cancers, VEGFB and VEGFD showed the highest and lowest expression levels, respectively. The survival analysis showed that VEGFA and placental growth factor (PGF) were correlated with poor prognosis in many cancers, including kidney renal cell and liver hepatocellular carcinoma. VEGFC expression was positively correlated with glioma and stomach cancer. VEGFA and PGF showed distinct positive correlations with hypoxia scores in most cancers, indicating a potential correlation with tumor aggressiveness. The expression of miRNAs targeting VEGF family genes, including hsa-miR-130b-5p and hsa-miR-940, was positively correlated with hypoxia. In immune subtypes analysis, VEGFC was highly expressed in C3 (inflammatory) and C6 (transforming growth factor β dominant) across various cancers, indicating its potential role as a tumor promotor. VEGFC expression exhibited positive correlations with immune infiltration scores, suggesting low tumor purity. High expression of VEGFA and VEGFC showed favorable responses to various drugs, including BLU-667, which abrogates RET signaling, an oncogenic driver in liver and thyroid cancers. Our findings suggest potential roles of VEGF family genes in malignant processes related with hypoxia-induced angiogenesis.
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Affiliation(s)
- So-Hyun Bae
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea
| | - Taewon Hwang
- Department of Electrical and Electronic Engineering, Yonsei University, Seoul 03722, Korea
| | - Mi-Ryung Han
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea
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Wu G, Zhou J, Ren H, Qin Y, Qian D, Hu Q, Xu P, Yu T, Ma H, Chen H, He M, Shi J. Unraveling the molecular crosstalk and immune landscape between COVID-19 infections and ischemic heart failure comorbidity: New insights into diagnostic biomarkers and therapeutic approaches. Cell Signal 2023; 112:110909. [PMID: 37777104 DOI: 10.1016/j.cellsig.2023.110909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19), resulting from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), remains a persistent global health concern. Evidence has highlighted a significant association between COVID-19 and ischemic heart failure (IHF), contributing to disease progression and increased mortality. This study identified diagnostic biomarkers for these comorbidities and elucidated disease progression's molecular mechanisms. METHODS We retrieved differentially expressed gene (DEG) data for COVID-19 and IHF from publicly available microarray and RNA-Seq datasets to investigate the underlying mechanisms and potential pathways associated with the co-occurrence of COVID-19 and IHF. By intersecting the results from the two diseases, we obtained diagnostic biomarkers using SVM-RFE and LASSO algorithms. Animal experiments and immunological analyses were conducted to help understand the association between SARS-CoV-2 and IHF in patients, enabling early diagnosis of disease progression. Finally, we analyzed the regulatory network of critical genes and identified potential drug compounds that could target the genetic links identified in our study. RESULTS 1974 common DEGs were identified between COVID-19 and IHF, contributing to disease progression and potential cancer risk by participating in immune and cancer-related pathways. In addition, we identified six hub genes (VDAC3, EIF2AK2, CHMP5, FTL, VPS4A, and CHMP4B) associated with the co-morbidity, and their diagnostic potential was confirmed through validation using relevant datasets and a mouse model. Functional enrichment analysis and examination of immune cell infiltration revealed immune dysregulation after disease progression. The comorbid hub genes exhibited outstanding immunomodulatory capacities. We also constructed regulatory networks tightly linked to both disorders, including transcription factors (TFs), miRNAs, and genes at both transcriptional and post-transcriptional levels. Finally, we identified 92 potential drug candidates to enhance the precision of anti-comorbidity treatment strategies. CONCLUSION Our study reveals a shared pathogenesis between COVID-19 and IHF, demonstrating that their coexistence exacerbates disease severity. By identifying and consolidating hub genes as pivotal diagnostic biomarkers for COVID-19 and IHF comorbidity, we have made significant advancements in understanding the underlying mechanisms of these conditions. Moreover, our study highlights dysregulated immunity and increased cancer risk in the advanced stages of disease progression. These findings offer novel perspectives for diagnosing and treating IHF progression during SARS-CoV-2 infection.
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Affiliation(s)
- Gujie Wu
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China; Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jiabin Zhou
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China
| | - Hefei Ren
- Department of Laboratory Medicine, Changzheng Hospital, Naval Medical University, Shanghai 200032, China
| | - Yiran Qin
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Diandian Qian
- Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Geriatrics, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Center for Evidence Based Medicine and Clinical Epidemiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Qin Hu
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China; Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Peng Xu
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China
| | - Tao Yu
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China; Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Huiyun Ma
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China
| | - Hongyu Chen
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China
| | - Min He
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China
| | - Jiayu Shi
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China.
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Su Q, Zhu Y, He B, Dai B, Mu W, Tian J. A novel tumor purity and immune infiltration-related model for predicting distant metastasis-free survival in prostate cancer. Eur J Med Res 2023; 28:545. [PMID: 38017548 PMCID: PMC10683297 DOI: 10.1186/s40001-023-01522-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 11/09/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND umor cells, immune cells and stromal cells jointly modify tumor development and progression. We aim to explore the potential effects of tumor purity on the immune microenvironment, genetic landscape and prognosis in prostate cancer (PCa). METHODS Tumor purity of prostate cancer patients was extracted from The cancer genome atlas (TCGA). Immune cellular proportions were calculated by the CIBERSORT. To identify critical modules related to tumor purity, we used weighted gene co-expression network analysis (WGCNA). Using STRING and Cytoscape, protein-protein interaction (PPI) networks were constructed and analyzed. A Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, Disease Ontology (DO), and Gene Set Enrichment Analysis (GSEA) enrichment analysis of identified modules was conducted. To identify the expression of key genes at protein levels, we used the Human Protein Atlas (HPA) platform. RESULTS A model of tumor purity score (TPS) was constructed in the gene expression omnibus series (GSE) 116,918 cohort. TCGA cohort served as a validation set and was employed to validate the TPS. TPS model, as an independent prognostic factor of distant metastasis-free survival (DMFS) in PCa. Patients had higher tumor purity and better prognosis in the low-TPS group. Tumor purity was related to the infiltration of mast cells and macrophage cells positively, whereas related to the infiltration of dendritic cells, T cells and B cells negatively in PCa. The nomogram based on TPS, Age, Gleason score and T stage had a good predictive value and could evaluate the prognosis of PCa metastasis. GO and KEGG enrichment analyses showed that hub genes mainly participate in T cell activation and T-helper lymphocytes (TH) differentiation. Hub genes were mainly enriched in primary immunodeficiency disease, according to DO analysis. SLAMF8 was identified as the most critical gene by Cytoscape and HPA analysis. CONCLUSIONS Dynamic changes in the immune microenvironment associated with tumor purity could correlate with a poor DMFS of low-purity PCa. The TPS can predict the DMFS of PCa. In addition, prostate cancer metastases may be related to immunosuppression caused by a disorder of the immune microenvironment.
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Affiliation(s)
- Qiang Su
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, People's Republic of China, Beijing, 100191, China
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
| | - Yongbei Zhu
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, People's Republic of China, Beijing, 100191, China
| | - Bingxi He
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, People's Republic of China, Beijing, 100191, China
| | - Bin Dai
- Neurosurgery department, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
| | - Wei Mu
- School of Engineering Medicine, Beihang University, Beijing, 100191, China.
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, People's Republic of China, Beijing, 100191, China.
| | - Jie Tian
- School of Engineering Medicine, Beihang University, Beijing, 100191, China.
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, People's Republic of China, Beijing, 100191, China.
- CAS Key Laboratory of Molecular Imaging, Beijing Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, 100190, China.
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20
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Liu S, Zhai J, Li D, Peng Y, Wang Y, Dai B. Identification and validation of molecular subtypes' characteristics in bladder urothelial carcinoma based on autophagy-dependent ferroptosis. Heliyon 2023; 9:e21092. [PMID: 37920516 PMCID: PMC10618552 DOI: 10.1016/j.heliyon.2023.e21092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 09/11/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023] Open
Abstract
Background Nowadays, more evidences indicated that autophagy-dependent ferroptosis regulatory molecules (ADFRMs) may be closely related to various tumors. In current study, we intended to establish a prognostic ADFRMs signature and investigated its potential roles in bladder urothelial carcinoma (BLCA). Methods Two distinct clusters were determined by consensus clustering with expression of 119 identified ADFRMs in BLCA. The tumor microenvironment was investigated through "CIBERSORT" algorithm, and enrichment analyses were utilized to seek molecular characteristics of differentially expressed genes (DEGs) between clusters. Moreover, a 2-ADFRMs prognostic signature including TRIB3 and WIPI1 was identified in TCGA cohort and further evaluated in the GSE13507 cohort. The qRT-PCR was conducted to examine the expression of prognostic genes. Further, the risk score was gained through calculating the level of TRIB3 and WIPI1 expression through the coefficient. The correlations between risk score with clinicopathologica features, tumor microenvironment, and drug sensitivity were explored. Results Patients in TCGA-BLCA were grouped into two clusters with different expression patterns of ADFRMs. And the overall survival, tumor microenvironment and biological functions were significant different between two clusters. Moreover, a 2-ADFRMs model was constructed, and patients were separated into a low-risk and high-risk group. Survival analysis indicated patients with low risk promised a good prognosis, suggesting the risk score determined with ADFRMs signature exhibited an acceptable capacity for survival prediction in BLCA. Correlation analysis demonstrated risk score had close ties with age, stage, and tumor microenvironment. In vivo, the expression of prognostic genes was identified to be up-regulated in BLCA cell line T24. Conclusion The constructed 2-ADFRMs signature was a promising model to predict prognosis and correlated with tumor microenvironment, which had latent clinical value in the intervention for BLCA.
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Affiliation(s)
- Shiwei Liu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Jing Zhai
- Department of Urology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Deng Li
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Yu Peng
- Department of Urology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Yi Wang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu Province, China
| | - Bo Dai
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
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Huang J, Zhang J, Zhang F, Lu S, Guo S, Shi R, Zhai Y, Gao Y, Tao X, Jin Z, You L, Wu J. Identification of a disulfidptosis-related genes signature for prognostic implication in lung adenocarcinoma. Comput Biol Med 2023; 165:107402. [PMID: 37657358 DOI: 10.1016/j.compbiomed.2023.107402] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/24/2023] [Accepted: 08/26/2023] [Indexed: 09/03/2023]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the most prevalent subtype of non-small cell lung cancer. Additionally, disulfidptosis, a newly discovered type of cell death, has been found to be closely associated with the onset and progression of tumors. METHODS The study first identified genes related to disulfidptosis through correlation analysis. These genes were then screened using univariate cox regression and LASSO regression, and a prognostic model was constructed through multivariate cox regression. A nomogram was also created to predict the prognosis of LUAD. The model was validated in three independent data sets: GSE72094, GSE31210, and GSE37745. Next, patients were grouped based on their median risk score, and differentially expressed genes between the two groups were analyzed. Enrichment analysis, immune infiltration analysis, and drug sensitivity evaluation were also conducted. RESULTS In this study, we examined 21 genes related to disulfidptosis and developed a gene signature that was found to be associated with a poorer prognosis in LUAD. Our model was validated using three independent datasets and showed AUC values greater than 0.5 at 1, 3, and 5 years. Enrichment analysis revealed that the disulfidptosis-related genes signature had a multifaceted impact on LUAD, particularly in relation to tumor development, proliferation, and metastasis. Patients in the high-risk group exhibited higher tumor purity and lower stromal score, ESTIMATE score, and Immune score. CONCLUSION This study constructed a gene signature related to disulfidptosis in lung adenocarcinoma and analyzed its impact on the disease and its association with the tumor microenvironment. The findings of this research provide valuable insights into the understanding of lung adenocarcinoma and could potentially lead to the development of new treatment strategies.
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Affiliation(s)
- Jiaqi Huang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Jingyuan Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Fanqin Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Shan Lu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Siyu Guo
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Rui Shi
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Yiyan Zhai
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Yifei Gao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xiaoyu Tao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Zhengsen Jin
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Leiming You
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Jiarui Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China.
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Huang Y, Xu J, Xie C, Liao Y, Lin R, Zeng Y, Yu F. A Novel Gene Pair CSTF2/DPE2A Impacts Prognosis and Cell Cycle of Hepatocellular Carcinoma. J Hepatocell Carcinoma 2023; 10:1639-1657. [PMID: 37791068 PMCID: PMC10544262 DOI: 10.2147/jhc.s413935] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC), one of the commonest cancers at present, possesses elevated mortality. This study explored the predictive value of CSTF2/PDE2A for HCC prognosis. Methods In this study, clinical information and RNA sequencing expression profiles of HCC patients were acquired from common databases. Kaplan-Meier curve compound with time-dependent ROC curve, nomogram model, and univariate/multivariate Cox analysis were carried out to access the prediction capacity of CSTF2/PDE2A. The immune status, tumor microenvironment, drug sensitivity, biological function and pathway between HCC and adjacent non-tumorous tissue were analyzed and compared. Finally, RT-qPCR, Western blot, and apoptosis assays were performed to verify the effect on HCC cells of CSTF2/PDE2A. Results The optimal cut-off value of CSTF2, PDE2A and CSTF2/PDE2A was 6.95, 0.95 and 3.63, respectively. In TCGA and ICGC cohorts, the high group of CSTF2/PDE2A presented higher OS compared to low group. The area under the curve (AUC) for OS at 1-, 2-, and 3-years predicted by CSTF2/PDE2A were 0.731/0.695, 0.713/0.732 and 0.689/0.755, higher than the counterparts of the single gene CSTF2 and PDE2A. Multivariate Cox analysis revealed that CSTF2/PDE2A (HR = 1.860/3.236, 95% CI = 1.265-2.733/1.575-6.645) was an independent prognostic factor for HCC. The OS nomogram model created according to five independent factors including CSTF2/PDE2A showed excellent capacity for HCC prognosis. Furthermore, the immune status of the CSTF2/PDE2A high group was deleted, cell cycle-related genes and chemotherapy resistance were increased. Finally, cell experiments revealed distinct differences in the proliferation, apoptosis, protein and mRNA expression of HCC cells after si-CSTF2 transfection compared with the negative control. Conclusion Taken together, the gene pair CSTF2/PDE2A is able to forecast the prognosis of HCC and regulates cell cycle, which is promising as a novel prognostic predictor of HCC.
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Affiliation(s)
- Yangjin Huang
- Department of Gastroenterology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People’s Republic of China
| | - Jun Xu
- Department of Gastroenterology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People’s Republic of China
| | - Chunming Xie
- Department of Gastroenterology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People’s Republic of China
| | - Yuejuan Liao
- Department of Gastroenterology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People’s Republic of China
| | - Rong Lin
- Department of Gastroenterology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People’s Republic of China
| | - Yuan Zeng
- Department of Gastroenterology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People’s Republic of China
| | - Fujun Yu
- Department of Gastroenterology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People’s Republic of China
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Zohair B, Chraa D, Rezouki I, Benthami H, Razzouki I, Elkarroumi M, Olive D, Karkouri M, Badou A. The immune checkpoint adenosine 2A receptor is associated with aggressive clinical outcomes and reflects an immunosuppressive tumor microenvironment in human breast cancer. Front Immunol 2023; 14:1201632. [PMID: 37753093 PMCID: PMC10518422 DOI: 10.3389/fimmu.2023.1201632] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/21/2023] [Indexed: 09/28/2023] Open
Abstract
Background The crosstalk between the immune system and cancer cells has aroused considerable interest over the past decades. To escape immune surveillance cancer cells evolve various strategies orchestrating tumor microenvironment. The discovery of the inhibitory immune checkpoints was a major breakthrough due to their crucial contribution to immune evasion. The A2AR receptor represents one of the most essential pathways within the TME. It is involved in several processes such as hypoxia, tumor progression, and chemoresistance. However, its clinical and immunological significance in human breast cancer remains elusive. Methods The mRNA expression and protein analysis were performed by RT-qPCR and immunohistochemistry. The log-rank (Mantel-Cox) test was used to estimate Kaplan-Meier analysis for overall survival. Using large-scale microarray data (METABRIC), digital cytometry was conducted to estimate cell abundance. Analysis was performed using RStudio software (7.8 + 2023.03.0) with EPIC, CIBERSORT, and ImmuneCellAI algorithms. Tumor purity, stromal and immune scores were calculated using the ESTIMATE computational method. Finally, analysis of gene set enrichment (GSEA) and the TISCH2 scRNA-seq database were carried out. Results Gene and protein analysis showed that A2AR was overexpressed in breast tumors and was significantly associated with high grade, elevated Ki-67, aggressive molecular and histological subtypes, as well as poor survival. On tumor infiltrating immune cells, A2AR was found to correlate positively with PD-1 and negatively with CTLA-4. On the other hand, our findings disclosed more profuse infiltration of protumoral cells such as M0 and M2 macrophages, Tregs, endothelial and exhausted CD8+ T cells within A2ARhigh tumors. According to the Single-Cell database, A2AR is expressed in malignant, stromal and immune cells. Moreover, it is related to tumor purity, stromal and immune scores. Our results also revealed that CD8+T cells from A2ARhigh patients exhibited an exhausted functional profile. Finally, GSEA analysis highlighted the association of A2AR with biological mechanisms involved in tumor escape and progression. Conclusion The present study is the first to elucidate the clinical and immunological relevance of A2AR in breast cancer patients. In light of these findings, A2AR could be deemed a promising therapeutic target to overcome immune evasion prevailing within the TME of breast cancer patients.
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Affiliation(s)
- Basma Zohair
- Immuno-Genetics and Human Pathology Laboratory (LIGEP), Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Dounia Chraa
- Team Immunity and Cancer, The Cancer Research Center of Marseille (CRCM), Inserm, 41068, CNRS, UMR7258, Paoli-Calmettes Institute, Aix-Marseille University, UM 105, Marseille, France
| | - Ibtissam Rezouki
- Immuno-Genetics and Human Pathology Laboratory (LIGEP), Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Hamza Benthami
- Immuno-Genetics and Human Pathology Laboratory (LIGEP), Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Ibtissam Razzouki
- Department of Pathological Anatomy, Ibn Rochd University Hospital Center, Casablanca, Morocco
| | - Mohamed Elkarroumi
- Mohamed VI Oncology Center, Ibn Rochd University Hospital Center, Casablanca, Morocco
| | - Daniel Olive
- Team Immunity and Cancer, The Cancer Research Center of Marseille (CRCM), Inserm, 41068, CNRS, UMR7258, Paoli-Calmettes Institute, Aix-Marseille University, UM 105, Marseille, France
| | - Mehdi Karkouri
- Department of Pathological Anatomy, Ibn Rochd University Hospital Center, Casablanca, Morocco
| | - Abdallah Badou
- Immuno-Genetics and Human Pathology Laboratory (LIGEP), Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
- Mohammed VI Center for Research & Innovation, Rabat, Morocco and Mohammed VI University of Sciences and Health, Casablanca, Morocco
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Wu G, Dong Y, Hu Q, Ma H, Xu Q, Xu K, Chen H, Yang Z, He M. HGH1 and the immune landscape: a novel prognostic marker for immune-desert tumor microenvironment identification and immunotherapy outcome prediction in human cancers. Cell Cycle 2023; 22:1969-1985. [PMID: 37811868 PMCID: PMC10761050 DOI: 10.1080/15384101.2023.2260163] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
HGH1 homolog, a protein-coding gene, plays a crucial role in human growth and development. However, its role in human cancer remains unclear. For the first time, this study comprehensively evaluated the potential involvement of HGH1 in cancer prognosis and immunological function. To achieve this, data from various databases, including The Cancer Genome Atlas, Genotype Tissue Expression, Cancer Cell Lineage Encyclopedia, Human Protein Atlas, cBioPortal, Tumor Immune Estimation Resource and Immune Cell Abundance Identifier, were collated, as well as from one large clinical study, three immunotherapy cohorts and in vitro experiments. This study aims to elucidate the role of HGH1 expression in cancer prognosis and immune response. Our findings revealed a significant association between increased HGH1 expression and a worse prognosis across various cancer types. Predominantly, copy number variations were identified as the most common genetic mutations. Additionally, HGH1 was observed to not only regulate cell cycle-related functions to promote cell proliferation but also influence autoimmunity-related functions within both the innate and adaptive immune systems, along with other relevant immune-related signaling pathways. Gene set enrichment analysis and gene set variation analysis were used to substantiate these findings. HGH1 overexpression contributed to an immune-deficient (immune-desert) tumor microenvironment, which was characterized by a significant expression of immune-related features such as immune-related gene and pathway expression and the number of immune-infiltrating cells. Furthermore, the correlation between HGH1 expression and tumor mutational burden in four cancers and microsatellite instability in eight cancers was observed. This suggests that HGH1 has potential as an immunotherapeutic target. Immunotherapy data analysis supports this notion, demonstrating that patients with low HGH1 expression treated with immune checkpoint inhibitors exhibit improved survival rates and a higher likelihood of responding to immunotherapy than patients with high HGH1 expression. Collectively, these findings highlight the significant role of HGH1 in human cancers, illuminating its involvement in tumorigenesis and cancer immunity. Elevated HGH1 expression was identified to be indicative of an immune-desert tumor microenvironment. Consequently, the targeting of HGH1, particularly in combination with immune checkpoint inhibitor therapy, holds promise for enhancing therapeutic outcomes in patients with cancer.
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Affiliation(s)
- Gujie Wu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
- Shanghai Medical College, Fudan University, Shanghai, China
| | - Yipeng Dong
- School of Medicine, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qin Hu
- Shanghai Medical College, Fudan University, Shanghai, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Huiyun Ma
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Qun Xu
- School of Medicine, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Kun Xu
- Department of Chemotherapy, Jiangsu Cancer Hospital, Nanjing Medical University, Nanjing, China
| | - Hongyu Chen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng Yang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Min He
- Shanghai Medical College, Fudan University, Shanghai, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
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25
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Zhao Y, Xu X, Wang Y, Wu LD, Luo RL, Xia RP. Tumor purity-associated genes influence hepatocellular carcinoma prognosis and tumor microenvironment. Front Oncol 2023; 13:1197898. [PMID: 37434985 PMCID: PMC10330704 DOI: 10.3389/fonc.2023.1197898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/16/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction Tumor purity takes on critical significance to the progression of solid tumors. The aim of this study was at exploring potential prognostic genes correlated with tumor purity in hepatocellular carcinoma (HCC) by bioinformatics analysis. Methods The ESTIMATE algorithm was applied for determining the tumor purity of HCC samples from The Cancer Genome Atlas (TCGA). The tumor purity-associated genes with differential expression (DEGs) were identified based on overlap analysis, weighted gene co-expression network analysis (WGCNA), and differential expression analysis. The prognostic genes were identified in terms of the prognostic model construction based on the Kaplan-Meier (K-M) survival analysis and Least Absolute Shrinkage and Selection Operator (LASSO) regression analyses. The expression of the above-described genes was further validated by the GSE105130 dataset from the Gene Expression Omnibus (GEO) database. We also characterized the clinical and immunophenotypes of prognostic genes. Gene set enrichment analysis (GSEA) was carried out for exploring the biological signaling pathway. Results A total of 26 tumor purity-associated DEGs were identified, which were involved in biological processes such as immune/inflammatory responses and fatty acid elongation. Ultimately, we identified ADCK3, HK3, and PPT1 as the prognostic genes for HCC. Moreover, HCC patients exhibiting higher ADCK3 expression and lower HK3 and PPT1 expressions had a better prognosis. Furthermore, high HK3 and PPT1 expressions and low ADCK3 expression resulted in high tumor purity, high immune score, high stromal score, and high ESTIMATE score. GSEA showed that the abovementioned prognostic genes showed a significant correlation with immune-inflammatory response, tumor growth, and fatty acid production/degradation. Discussion In conclusion, this study identified novel predictive biomarkers (ADCK3, HK3, and PPT1) and studied the underlying molecular mechanisms of HCC pathology initially.
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Affiliation(s)
- Yan Zhao
- Department of Organ Transplantation, Kunming Medical University First Affiliated Hospital, Kunming, China
| | - Xu Xu
- Department of Urology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Yue Wang
- Department of Organ Transplantation, Kunming Medical University First Affiliated Hospital, Kunming, China
| | - Lin D. Wu
- Department of Organ Transplantation, Kunming Medical University First Affiliated Hospital, Kunming, China
| | - Rui L. Luo
- Department of Urology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Ren P. Xia
- Department of Organ Transplantation, Kunming Medical University First Affiliated Hospital, Kunming, China
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Wei F, Li T, Li J, Zhang Y, Liu T, Zhao Z, Zhu W, Guo H, Yang R. Prognostic and Immunological Role of Asporin across Cancers and Exploration in Bladder Cancer. Gene 2023:147573. [PMID: 37336272 DOI: 10.1016/j.gene.2023.147573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND Asporin (ASPN) has been identified as a player in tumorigenesis, but its precise roles and modulatory function are largely unknown. METHODS In the present study, ASPN expression was first explored, followed by a prognostic evaluation of ASPN and a comprehensive investigation of the connections between ASPN and immunomodulation, immune cell infiltration and potential compounds on a pancancer level. Finally, ASPN expression was validated in bladder urothelial carcinoma (BLCA) tissues, and the potential function of ASPN, including its effects on migration and invasion capabilities, was investigated in tumor cells. RESULTS The expression of ASPN exhibited significant variation across cancers and was found to be associated with patient prognosis. In addition, the expression level of APSN was markedly correlated with the abundances of infiltrating immune cells and cancer-associated fibroblasts and the expression levels of immunomodulatory genes based on the results of pancancer analysis. Metastasis and immune-associated signaling pathways were identified in enrichment analysis based on ASPN expression. Finally, we confirmed that ASPN expression increased with the degree of malignancy in BLCA tissues and cell lines and that low expression of ASPN hindered the migration and invasion of cells. CONCLUSIONS ASPN has the potential to be a biomarker of cancer prognosis and a therapeutic target, and it also has predictive capability for the progression of BLCA.
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Affiliation(s)
- Fayun Wei
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China; Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Tianhang Li
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China; Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Jiazheng Li
- Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China; Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China; Department of Urology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Yulin Zhang
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China; Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Tianyao Liu
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China; Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zihan Zhao
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China; Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Wenjie Zhu
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China; Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Hongqian Guo
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China; Department of Urology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China.
| | - Rong Yang
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China; Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China; Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China; Department of Urology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China.
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27
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Sarfaty M, Golkaram M, Funt SA, Al-Ahmadie H, Kaplan S, Song F, Regazzi A, Makarov V, Kuo F, Ostrovnaya I, Seshan V, Zhao C, Greenbaum B, Liu L, Rosenberg JE, Chan TA. Novel Genetic Subtypes of Urothelial Carcinoma With Differential Outcomes on Immune Checkpoint Blockade. J Clin Oncol 2023; 41:3225-3235. [PMID: 36927002 PMCID: PMC10256354 DOI: 10.1200/jco.22.02144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 02/09/2023] [Indexed: 03/18/2023] Open
Abstract
PURPOSE Immune checkpoint blockade (ICB) therapy has significantly improved clinical outcomes in bladder cancer. Identification of correlates of benefit is critical to select appropriate therapy for individual patients. METHODS To reveal genetic variables associated with benefit from ICB, we performed whole-exome sequencing on tumor specimens from 88 patients with advanced bladder cancer treated with ICB. RESULTS We identified several genetic factors that correlated with progression-free and overall survival after ICB therapy including ARID1A mutation, tumor mutational burden, intratumoral heterogeneity, the ratio of nonsynonymous to synonymous mutations in the immunopeptidome (immune dN/dS), and tumor cell purity. In addition, we noted that neutrophil-to-lymphocyte ratio and smoking history were negatively associated with overall survival. These genetic characteristics define four molecular subtypes demonstrating differential sensitivity to ICB. We validated the association of these four subtypes with clinical benefit from ICB in an independent cohort (IMvigor210). Finally, we showed that these molecular subtypes also correlate with outcome, although with distinct relationships, among patients not treated with ICB using The Cancer Genome Atlas (TCGA) bladder cancer cohort. Using parallel RNA sequencing data, the subtypes were also shown to correlate with immune infiltration and inflammation, respectively, in the IMvigor210 and TCGA cohorts. CONCLUSION Together, our study defines molecular subgroups of bladder cancer that influence benefit from ICB.
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Affiliation(s)
- Michal Sarfaty
- Genitourinary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Samuel A. Funt
- Genitourinary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hikmat Al-Ahmadie
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Ashley Regazzi
- Genitourinary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vladimir Makarov
- Center for Immunotherapy and Precision-Immuno-Oncology, Cleveland Clinic, Cleveland, OH
| | - Fengshen Kuo
- Department of Urology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Venkatraman Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Benjamin Greenbaum
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Li Liu
- Illumina, Inc, San Diego, CA
| | - Jonathan E. Rosenberg
- Genitourinary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Timothy A. Chan
- Center for Immunotherapy and Precision-Immuno-Oncology, Cleveland Clinic, Cleveland, OH
- National Center for Regenerative Medicine, Cleveland Clinic, Cleveland, OH
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28
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Xu L, Wu P, Rong A, Li K, Xiao X, Zhang Y, Wu H. Systematic pan-cancer analysis identifies cuproptosis-related gene DLAT as an immunological and prognostic biomarker. Aging (Albany NY) 2023; 15:4269-4287. [PMID: 37199628 PMCID: PMC10258010 DOI: 10.18632/aging.204728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 05/03/2023] [Indexed: 05/19/2023]
Abstract
Lipoylated dihydrolipoamide S-acetyltransferase (DLAT), the component E2 of the multi-enzyme pyruvate dehydrogenase complex, is one of the key molecules of cuproptosis. However, the prognostic value and immunological role of DLAT in pan-cancer are still unclear. Using a series of bioinformatics approaches, we studied combined data from different databases, including the Cancer Genome Atlas, Genotype Tissue-Expression, the Cancer Cell Line Encyclopedia, Human Protein Atlas, and cBioPortal to investigate the role of DLAT expression in prognosis and tumor immunity response. We also reveal the potential correlations between DLAT expression and gene alterations, DNA methylation, copy number variation (CNV), tumor mutational burden (TMB), microsatellite instability (MSI), tumor microenvironment (TME), immune infiltration levels, and various immune-related genes across different cancers. The results show that DLAT displays abnormal expression within most malignant tumors. Through gene set enrichment analysis (GSEA), we found that DLAT was significantly associated with immune-related pathways. Further, the expression of DLAT was also confirmed to be correlated with the tumor microenvironment and diverse infiltration of immune cells, especially tumor-associated macrophages (TAMs). In addition, we found that DLAT is co-expressed with genes encoding major histocompatibility complex (MHC), immunostimulators, immune inhibitors, chemokines, and chemokine receptors. Meanwhile, we demonstrate that DLAT expression is correlated with TMB in 10 cancers and MSI in 11 cancers. Our study reveals that DLAT plays an essential role in tumorigenesis and cancer immunity, which may be used to function as a prognostic biomarker and potential target for cancer immunotherapy.
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Affiliation(s)
- Lidong Xu
- Department of Gastroenterology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450000, China
- Medical Key Laboratory for Diagnosis and Treatment of Colorectal Cancer in Henan Province, Zhengzhou 450000, China
- Zhengzhou Key Laboratory for Diagnosis, Treatment and Research of Colorectal Cancer, Zhengzhou 450000, China
| | - Peipei Wu
- Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou 450000, China
| | - Aimei Rong
- Department of Gastroenterology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450000, China
- Medical Key Laboratory for Diagnosis and Treatment of Colorectal Cancer in Henan Province, Zhengzhou 450000, China
- Zhengzhou Key Laboratory for Diagnosis, Treatment and Research of Colorectal Cancer, Zhengzhou 450000, China
| | - Kunkun Li
- Department of Gastroenterology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450000, China
- Medical Key Laboratory for Diagnosis and Treatment of Colorectal Cancer in Henan Province, Zhengzhou 450000, China
- Zhengzhou Key Laboratory for Diagnosis, Treatment and Research of Colorectal Cancer, Zhengzhou 450000, China
| | - Xingguo Xiao
- Department of Gastroenterology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450000, China
- Medical Key Laboratory for Diagnosis and Treatment of Colorectal Cancer in Henan Province, Zhengzhou 450000, China
- Zhengzhou Key Laboratory for Diagnosis, Treatment and Research of Colorectal Cancer, Zhengzhou 450000, China
| | - Yong Zhang
- Department of Gastroenterology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450000, China
- Medical Key Laboratory for Diagnosis and Treatment of Colorectal Cancer in Henan Province, Zhengzhou 450000, China
- Zhengzhou Key Laboratory for Diagnosis, Treatment and Research of Colorectal Cancer, Zhengzhou 450000, China
| | - Huili Wu
- Department of Gastroenterology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450000, China
- Medical Key Laboratory for Diagnosis and Treatment of Colorectal Cancer in Henan Province, Zhengzhou 450000, China
- Zhengzhou Key Laboratory for Diagnosis, Treatment and Research of Colorectal Cancer, Zhengzhou 450000, China
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Weng S, Li M, Deng J, Xu H, Ren Y, Zhou Z, Wang L, Zhang Y, Xing Z, Li L, Liu Z, Han X. Epigenetically regulated gene expression profiles decipher four molecular subtypes with prognostic and therapeutic implications in gastric cancer. Clin Epigenetics 2023; 15:64. [PMID: 37061743 PMCID: PMC10105476 DOI: 10.1186/s13148-023-01478-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/31/2023] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND Gastric cancer (GC) is one of the most common malignant tumors of the digestive tract which seriously endangers the health of human beings worldwide. Transcriptomic deregulation by epigenetic mechanisms plays a crucial role in the heterogeneous progression of GC. This study aimed to investigate the impact of epigenetically regulated genes on the prognosis, immune microenvironment, and potential treatment of GC. RESULTS Under the premise of verifying significant co-regulation of the aberrant frequencies of microRNA (miRNA) correlated (MIRcor) genes and DNA methylation-correlated (METcor) genes. Four GC molecular subtypes were identified and validated by comprehensive clustering of MIRcor and METcor GEPs in 1521 samples from five independent multicenter GC cohorts: cluster 1 was characterized by up-regulated cell proliferation and transformation pathways, with good prognosis outcomes, driven by mutations, and was sensitive to 5-fluorouracil and paclitaxel; cluster 2 performed moderate prognosis and benefited more from apatinib and cisplatin; cluster 3 was featured by an up-regulated ligand-receptor formation-related pathways, poor prognosis, an immunosuppression phenotype with low tumor purity, resistant to chemotherapy (e.g., 5-fluorouracil, paclitaxel, and cisplatin), and targeted therapy drug (apatinib) and sensitive to dasatinib; cluster 4 was characterized as an immune-activating phenotype, with advanced tumor stages, benefit more from immunotherapy and displayed worst prognosis. CONCLUSIONS According to the epigenetically regulated GEPs, we developed four robust GC molecular subtypes, which facilitated the understanding of the epigenetic mechanisms underlying GC heterogeneity, offering an optimized decision-making and surveillance platform for GC patients.
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Affiliation(s)
- Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, 450052, Henan, China
| | - Minghao Li
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jinhai Deng
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer and Pharmaceutical Sciences, King's College London, London, SE1 1UL, UK
| | - Hui Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, 450052, Henan, China
| | - Yuqing Ren
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhaokai Zhou
- Department of Urologic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Libo Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, 450052, Henan, China
| | - Zhe Xing
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Henan, China
| | - Lifeng Li
- Medical School, Huanghe Science and Technology University, 666 Zi Jing Shan Road, Zhengzhou, 450000, Henan, China.
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, 450052, Henan, China.
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, 450052, Henan, China.
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30
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Kumari S, Kumar P. Design and Computational Analysis of an MMP9 Inhibitor in Hypoxia-Induced Glioblastoma Multiforme. ACS OMEGA 2023; 8:10565-10590. [PMID: 36969457 PMCID: PMC10035023 DOI: 10.1021/acsomega.3c00441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The main therapeutic difficulties in treating hypoxia-induced glioblastoma multiforme (GBM) are toxicity of current treatments and the resistance brought on by the microenvironment. More effective therapeutic alternatives are urgently needed to reduce tumor lethality. Hence, we screened plant-based natural product panels intending to identify novel drugs without elevating drug resistance. We explored GEO for the hypoxia GBM model and compared hypoxic genes to non-neoplastic brain cells. A total of 2429 differentially expressed genes expressed exclusively in hypoxia were identified. The functional enrichment analysis demonstrated genes associated with GBM, further PPI network was constructed, and biological pathways associated with them were explored. Seven webtools, including GEPIA2.0, TIMER2.0, TCGA-GBM, and GlioVis, were used to validate 32 hub genes discovered using Cytoscape tool in GBM patient samples. Four GBM-specific hypoxic hub genes, LYN, MMP9, PSMB9, and TIMP1, were connected to the tumor microenvironment using TIMER analysis. 11 promising hits demonstrated positive drug-likeness with nontoxic characteristics and successfully crossed blood-brain barrier and ADMET analyses. Top-ranking hits have stable intermolecular interactions with the MMP9 protein according to molecular docking, MD simulation, MM-PBSA, PCA, and DCCM analyses. Herein, we have reported flavonoids, 7,4'-dihydroxyflavan, (3R)-3-(4-hydroxybenzyl)-6-hydroxy-8-methoxy-3,4-dihydro-2H-1-benzopyran, and 4'-hydroxy-7-methoxyflavan, to inhibit MMP9, a novel hypoxia gene signature that could serve as a promising predictor in various clinical applications, including GBM diagnosis, prognosis, and targeted therapy.
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31
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Chang J, Wu H, Wu J, Liu M, Zhang W, Hu Y, Zhang X, Xu J, Li L, Yu P, Zhu J. Constructing a novel mitochondrial-related gene signature for evaluating the tumor immune microenvironment and predicting survival in stomach adenocarcinoma. J Transl Med 2023; 21:191. [PMID: 36915111 PMCID: PMC10012538 DOI: 10.1186/s12967-023-04033-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/03/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND The incidence and mortality of gastric cancer ranks fifth and fourth worldwide among all malignancies, respectively. Accumulating evidences have revealed the close relationship between mitochondrial dysfunction and the initiation and progression of stomach cancer. However, rare prognostic models for mitochondrial-related gene risk have been built up in stomach cancer. METHODS In current study, the expression and prognostic value of mitochondrial-related genes in stomach adenocarcinoma (STAD) patients were systematically analyzed to establish a mitochondrial-related risk model based on available TCGA and GEO databases. The tumor microenvironment (TME), immune cell infiltration, tumor mutation burden, and drug sensitivity of gastric adenocarcinoma patients were also investigated using R language, GraphPad Prism 8 and online databases. RESULTS We established a mitochondrial-related risk prognostic model including NOX4, ALDH3A2, FKBP10 and MAOA and validated its predictive power. This risk model indicated that the immune cell infiltration in high-risk group was significantly different from that in the low-risk group. Besides, the risk score was closely related to TME signature genes and immune checkpoint molecules, suggesting that the immunosuppressive tumor microenvironment might lead to poor prognosis in high-risk groups. Moreover, TIDE analysis demonstrated that combined analysis of risk score and immune score, or stromal score, or microsatellite status could more effectively predict the benefit of immunotherapy in STAD patients with different stratifications. Finally, rapamycin, PD-0325901 and dasatinib were found to be more effective for patients in the high-risk group, whereas AZD7762, CEP-701 and methotrexate were predicted to be more effective for patients in the low-risk group. CONCLUSIONS Our results suggest that the mitochondrial-related risk model could be a reliable prognostic biomarker for personalized treatment of STAD patients.
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Affiliation(s)
- Jingjia Chang
- Department of Cell Biology and Medical Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan, 030001, China
| | - Hao Wu
- Department of Cell Biology and Medical Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan, 030001, China
| | - Jin Wu
- Department of Pathology, Laboratory of Translational Medicine Research, Deyang People's Hospital, Deyang, China.,Key Laboratory of Tumor Molecular Research of Deyang, Deyang, China.,Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14263, USA
| | - Ming Liu
- Department of Cell Biology and Medical Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan, 030001, China
| | - Wentao Zhang
- Department of Cell Biology and Medical Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan, 030001, China
| | - Yanfen Hu
- Department of Cell Biology and Medical Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan, 030001, China
| | - Xintong Zhang
- Department of Cell Biology and Medical Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan, 030001, China
| | - Jing Xu
- Department of Cell Biology and Medical Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan, 030001, China
| | - Li Li
- Department of Cell Biology and Medical Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan, 030001, China
| | - Pengfei Yu
- Department of Gastrointestinal Surgery, Xijing Hospital, Air Force Military Medical University, Xi'an, 710032, Shaanxi, China.
| | - Jianjun Zhu
- Department of Cell Biology and Medical Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan, 030001, China.
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A comprehensive analysis of PANoptosome to prognosis and immunotherapy response in pan-cancer. Sci Rep 2023; 13:3877. [PMID: 36890219 PMCID: PMC9995449 DOI: 10.1038/s41598-023-30934-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 03/03/2023] [Indexed: 03/10/2023] Open
Abstract
PANoptosis, a programmed cell death, shares key characteristics of apoptosis, pyroptosis, and necroptosis. Accumulating evidence suggests that PANoptosis plays a crucial role in tumorigenesis. However, the respective regulation mechanisms in cancer are so far unclear. Using various bioinformatic approaches, we comprehensively analyzed the expression patterns, genetic alterations, prognostic value, and immunological role of PANoptosis genes in pan-cancer. Expression of the PANoptosis gene, PYCARD, was validated based on the Human Protein Atlas database and real-time quantitative reverse transcription polymerase chain reaction (RT-PCR). We found that PANoptosis genes were aberrantly expressed in most cancer types, which was consistent with the validation of PYCARD expression. Concurrently, PANoptosis genes and PANoptosis scores were significantly associated with patient survival in 21 and 14 cancer types, respectively. Pathway analysis showed that PANoptosis score was positively correlated with pathways linked to immune and inflammatory responses in pan-cancer, such as IL6-JAK-STAT3 signaling, the interferon-gamma response, and IL2-STAT5 signaling. In addition, the PANoptosis score was significantly correlated with the tumor microenvironment, the infiltration levels of most immune cells (i.e.NK cells, CD8+ T cells, CD4+ T cells, DC cells), and immune-related genes. Furthermore, it was a predictive indicator of immunotherapy response in patients with tumors. These insights substantially improve our understanding of PANoptosis components in cancers and may inspire the discovery of novel prognostic and immunotherapy response biomarkers.
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Xu C, Li F, Liu Z, Yan C, Xiao J. Pan-cancer analysis of the prognostic and immunological role of SNX29: a potential target for survival and immunotherapy. BMC Med Genomics 2023; 16:34. [PMID: 36829159 PMCID: PMC9951530 DOI: 10.1186/s12920-023-01466-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND There is growing evidence that the SNX family is critical for clinical prognosis, immune infiltration and drug sensitivity in many types of tumors. The relationships between the SNX29 gene and clinical prognosis as well as pan-cancer cell infiltration and drug sensitivity have not been fully elucidated. METHODS In the current study, we explored the correlation between SNX29 expression and 33 types of malignancies via TCGA and GTEx. The relationship between SNX29 expression and prognostic outcome in the pan-caner cohort was also analyzed. Immune infiltration, microsatellite instability, tumor mutational burden and potential therapeutic targets of SNX29 were investigated by analyzing public databases. RESULTS The expression of SNX29 was found to be significantly upregulated in most tumor tissues compared to normal tissues. SNX29 expression was associated with prognosis and clinical stage. In the immune infiltration analysis, a significant relationship was found between SNX29 expression and the level of immune infiltration. In addition, we found associations between the SNX29 gene and tumor mutation burden, microsatellite instability, immunoinhibition-related genes and autophagy-related genes. Finally, the expression of SNX29 was significantly associated with the sensitivity of various tumor cell lines to 8 antitumor drugs. These results suggest that SNX29 expression is important in determining the progression, immune infiltration and drug sensitivity of various cancers. CONCLUSION This study provides novel insights into the potential pan-cancer targets of SNX29.
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Affiliation(s)
- Chengfei Xu
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China.,School of Clinical Medicine, Chengdu Medical College, Chengdu, 610500, People's Republic of China.,First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China
| | - Fanghan Li
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China.,School of Clinical Medicine, Chengdu Medical College, Chengdu, 610500, People's Republic of China
| | - Zilin Liu
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China.,School of Clinical Medicine, Chengdu Medical College, Chengdu, 610500, People's Republic of China.,First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China
| | - Chuanjing Yan
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China. .,School of Clinical Medicine, Chengdu Medical College, Chengdu, 610500, People's Republic of China. .,First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China.
| | - Jiangwei Xiao
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China. .,School of Clinical Medicine, Chengdu Medical College, Chengdu, 610500, People's Republic of China. .,First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China.
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Sun JR, Kong CF, Qu XK, Sun AT, Zhao KP, Sun JH. An immune-related prognostic signature associated with immune landscape and therapeutic responses in gastric cancer. Aging (Albany NY) 2023; 15:1074-1106. [PMID: 36812479 PMCID: PMC10008502 DOI: 10.18632/aging.204534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/13/2023] [Indexed: 02/24/2023]
Abstract
Immune-related genes (IRGs) have attracted attention in recent years as therapeutic targets in various tumors. However, the role of IRGs in gastric cancer (GC) has not been clearly elucidated. This study presents a comprehensive analysis exploring the clinical, molecular, immune, and drug response features characterizing the IRGs in GC. Data were acquired from the TCGA and GEO databases. The Cox regression analyses were performed to develop a prognostic risk signature. The genetic variants, immune infiltration, and drug responses associated with the risk signature were explored using bioinformatics methods. Lastly, the expression of the IRS was verified by qRT-PCR in cell lines. In this manner, an immune-related signature (IRS) was established based on 8 IRGs. According to the IRS, patients were divided into the low-risk group (LRG) and high-risk group (HRG). Compared with the HRG, the LRG was characterized by a better prognosis, high genomic instability, more CD8+ T cell infiltration, greater sensitivity to chemotherapeutic drugs, and greater likelihood of benefiting from the immunotherapy. Moreover, the expression result showed good consistency between the qRT-PCR and TCGA cohort. Our findings provide insights into the specific clinical and immune features underlying the IRS, which may be important for patient treatment.
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Affiliation(s)
- Jian-Rong Sun
- School of Clinical Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Chen-Fan Kong
- School of Clinical Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xiang-Ke Qu
- School of Clinical Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - An-Tao Sun
- Department of Hematology, Guang’anmen Hospital, Beijing 100053, China
| | - Kun-Peng Zhao
- School of Traditional Chinese Medicine, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Jin-Hui Sun
- Department of Gastroenterology, Beijing University of Chinese Medicine Affiliated Dongzhimen Hospital, Beijing 100700, China
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Ding J, Sun Y, Sulaiman Z, Li C, Cheng Z, Liu S. Comprehensive Analysis Reveals Distinct Immunological and Prognostic Characteristics of CD276/B7-H3 in Pan-Cancer. Int J Gen Med 2023; 16:367-391. [PMID: 36756390 PMCID: PMC9901449 DOI: 10.2147/ijgm.s395553] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/23/2023] [Indexed: 02/04/2023] Open
Abstract
Background CD276 (also known as B7-H3), a newly discovered immunoregulatory protein that belongs to the B7 family, is a significant and attractive target for cancer immunotherapy. Existing evidence demonstrates its pivotal role in the tumorigenesis of some cancers. However, there still lacks a systematic and comprehensive pan-cancer analysis of the role of CD276 in tumor immunology and prognosis. Methods We explored and validated the mRNA and protein expression levels of CD276 in multiple tumors through public databases and clinical tissues specimens. The Univariate Cox regression analysis and Kaplan-Meier analysis were applied to assess the prognostic value of CD276. The correlation between CD276 expression and clinical characteristics and immunological features in diverse tumors was also explored. GSEA was performed to illuminate the biological function and involved pathways of CD276. Moreover, the CellMiner database was used to interpret the relationship between CD276 and multiple chemotherapeutic agents. CCK-8 assay was performed to validate the biological function of CD276 in vitro. Results In general, CD276 was differentially expressed between most tumor tissues and their corresponding normal tissues. Higher expression levels of CD276 were associated with poorer survival outcomes in most tumor cohorts from TCGA. There was a close correlation between CD276 expression and clinical features, the infiltration levels of specific immune cells, immune subtypes, TMB, MSI, MMR, recognized immunoregulatory genes and drug sensitivity across diverse human cancers. The scRNA-seq data analysis further revealed that CD276 was mainly expressed on the tumor infiltrating macrophages. Additionally, in vitro experiments showed that knockdown of CD276 inhibited the proliferation of ovarian cancer (OV) and cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) cell lines. Conclusion CD276 is a potent biomarker for predicting the prognosis and immunological features in some tumors, and it may play a critical role in the tumor immune microenvironment (TIME) through macrophage-associated signaling.
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Affiliation(s)
- Jinye Ding
- Department of Obstetrics and Gynecology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Yaoqi Sun
- Department of Obstetrics and Gynecology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Zubaidan Sulaiman
- Department of Obstetrics and Gynecology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Caixia Li
- Department of Obstetrics and Gynecology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China,Institute of Gynecological Minimally Invasive Medicine, School of Medicine, Tongji University, Shanghai, People’s Republic of China
| | - Zhongping Cheng
- Department of Obstetrics and Gynecology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China,Institute of Gynecological Minimally Invasive Medicine, School of Medicine, Tongji University, Shanghai, People’s Republic of China,Correspondence: Zhongping Cheng; Shupeng Liu, Email ;
| | - Shupeng Liu
- Department of Obstetrics and Gynecology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, People’s Republic of China,Institute of Gynecological Minimally Invasive Medicine, School of Medicine, Tongji University, Shanghai, People’s Republic of China
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36
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Ji T, Gao X, Li D, Huai S, Chi Y, An X, Ji W, Yang S, Li J. Identification and validation of signature for prognosis and immune microenvironment in gastric cancer based on m6A demethylase ALKBH5. Front Oncol 2023; 12:1079402. [PMID: 36686788 PMCID: PMC9853004 DOI: 10.3389/fonc.2022.1079402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/07/2022] [Indexed: 01/07/2023] Open
Abstract
Background N6-methyladenosine (m6A) RNA regulators play important roles in cancers, but their functions and mechanism have not been demonstrated clearly in gastric cancer (GC). Methods In this study, the GC samples with clinical information and RNA transcriptome were downloaded from The Cancer Genome Atlas database. The different expression genes were compared by the absolute value and median ± standard deviation. Samples with complete information were randomly divided into a training dataset and a test dataset. The differential expression genes (DEGs) between ALKBH5-low and ALKBH5-high subgroups were identified in the training dataset and constructed a risk model by Cox and least absolute shrinkage and selection operator regression. The model was testified in test datasets, overall survival (OS) was compared with the Kaplan-Meier method, and immune cell infiltration was calculated by the CIBERSORT algorithm in the low-risk and high-risk subgroups based on the model. The protein levels of ALKBH5 were detected with immunohistochemistry. The relative expression of messenger-ribonucleic acid (mRNA) was detected with quantitative polymerase chain reaction. Results ALKBH5 was the only regulator whose expression was lower in tumor samples than that in normal samples. The low expression of ALKBH5 led to the poor OS of GC patients and seemed to be an independent protective factor. The model based on ALKBH5-regulated genes was validated in both datasets (training/test) and displayed a potential capacity to predict a clinical prognosis. Gene Ontology analysis implied that the DEGs were involved in the immune response; CIBERSORT results indicated that ALKBH5 and its related genes could alter the immune microenvironment of GC. The protein levels of ALKBH5 were verified as lowly expressed in GC tissues. SLC7A2 and CGB3 were downregulated with ALKBH5 knockdown. Conclusions In this study, we found that ALKBH5 might be a suppressor of GC; ALKBH5 and its related genes were latent biomarkers and immunotherapy targets.
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Affiliation(s)
- Tiannan Ji
- Medical School of Chinese PLA, Beijing, China,Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Xiaohui Gao
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China,Department of Clinical Medicine, Graduate School of Hebei North University, Zhangjiakou, Hebei, China
| | - Dan Li
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Siyuan Huai
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Yajing Chi
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China,School of Medicine, Nankai University, Tianjin, China
| | - Xian An
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Wenyu Ji
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China,Department of Clinical Medicine, Graduate School of Hebei North University, Zhangjiakou, Hebei, China
| | - Siming Yang
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Jianxiong Li
- Department of Radiotherapy, Senior Department of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, China,*Correspondence: Jianxiong Li,
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Usman M, Hameed Y, Ahmad M, Iqbal MJ, Maryam A, Mazhar A, Naz S, Tanveer R, Saeed H, Bint-E-Fatima, Ashraf A, Hadi A, Hameed Z, Tariq E, Aslam AS. SHMT2 is Associated with Tumor Purity, CD8+ T Immune Cells Infiltration, and a Novel Therapeutic Target in Four Different Human Cancers. Curr Mol Med 2023; 23:161-176. [PMID: 35023455 DOI: 10.2174/1566524022666220112142409] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 11/15/2021] [Accepted: 11/25/2021] [Indexed: 12/16/2022]
Abstract
AIMS This study was launched to identify the SHMT2 associated Human Cancer subtypes. BACKGROUND Cancer is the 2nd leading cause of death worldwide. Previous reports revealed the limited involvement of SHMT2 in human cancer. In the current study, we comprehensively analyzed the role of SHMT2 in 24 major subtypes of human cancers using in silico approach and identified a few subtypes that are mainly associated with SHMT2. OBJECTIVE We aim to comprehensively analyze the role of SHMT2 in 24 major subtypes of human cancers using in silico approach and identified a few subtypes that are mainly associated with SHMT2. Earlier, limited knowledge exists in the medical literature regarding the involvement of Serine Hydroxymethyltransferase 2 (SHMT2) in human cancer. METHODS In the current study, we comprehensively analyzed the role of SHMT2 in 24 major subtypes of human cancers using in silico approach and identified a few subtypes that are mainly associated with SHMT2. Pan-cancer transcriptional expression profiling of SHMT2 was done using UALCAN while further validation was performed using GENT2. For translational profiling of SHMT2, we utilized Human Protein Atlas (HPA) platform. Promoter methylation, genetic alteration, and copy number variations (CNVs) profiles were analyzed through MEXPRESS and cBioPortal. Survival analysis was carried out through Kaplan-Meier (KM) plotter platform. Pathway enrichment analysis of SHMT2 was performed using DAVID, while the gene-drug network was drawn through CTD and Cytoscape. Furthermore, in the tumor microenvironment, a correlation between tumor purity, CD8+ T immune cells infiltration, and SHMT2 expression was accessed using TIMER. RESULTS SHMT2 was found overexpressed in 24 different subtypes of human cancers and its overexpression was significantly associated with the reduced Overall survival (OS) and Relapse-free survival durations of Breast cancer (BRCA), Kidney renal papillary cell carcinoma (KIRP), Liver hepatocellular carcinoma (LIHC), and Lung adenocarcinoma (LUAD) patients. This implies that SHMT2 plays a significant role in the development and progression of these cancers. We further noticed that SHMT2 was also up-regulated in BRCA, KIRP, LIHC, and LUAD patients of different clinicopathological features. Pathways enrichment analysis revealed the involvement of SHMT2 enriched genes in five diverse pathways. Furthermore, we also explored some interesting correlations between SHMT2 expression and promoter methylation, genetic alterations, CNVs, tumor purity, and CD8+ T immune cell infiltrates. CONCLUSION Our results suggested that overexpressed SHMT2 is correlated with the reduced OS and RFS of the BRCA, KIRP, LIHC, and LUAD patients and can be a potential diagnostic and prognostic biomarker for these cancers.
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Affiliation(s)
- Muhammad Usman
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Yasir Hameed
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mukhtiar Ahmad
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | | | - Aghna Maryam
- Department of Biochemistry, Quaid-i-Azam University Islamabad, Pakistan
| | - Afshan Mazhar
- Department of Biochemistry, Quaid-i-Azam University Islamabad, Pakistan
| | - Saima Naz
- Department of zoology, Government Sadiq College Women University Bahawalpur, Bahawalpur, Pakistan
| | - Rida Tanveer
- University College of Conventional Medicine, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Hina Saeed
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Bint-E-Fatima
- Department of Biotechnology, University of Gujrat, Gujrat, Pakistan
| | - Aneela Ashraf
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Alishba Hadi
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Zahid Hameed
- Department of Bioinformatics and Biotechnology, International Islamic University Islamabad, Islamabad, Pakistan
| | - Eman Tariq
- Department of Chemistry, The University of Swabi, Swabi, Pakistan
| | - Alia Sumyya Aslam
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
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Zhu Z, Shi L, Dong Y, Zhang Y, Yang F, Wei J, Huo M, Li P, Liu X. Effect of crosstalk among conspirators in tumor microenvironment on niche metastasis of gastric cancer. Am J Cancer Res 2022; 12:5375-5402. [PMID: 36628284 PMCID: PMC9827080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 11/16/2022] [Indexed: 01/12/2023] Open
Abstract
In Traditional Chinese medicine, the metaphoric views of the human body are based on observations of nature guided by the theory of "Yin-Yang". The direct meanings of yin and yang are the bright and dark sides of an object, which often represent a wider range of opposite properties. When we shifted our view to gastric cancer (GC), we found that there are more distinctive Yin and Yang features in the mechanism of GC development and metastasis, which is observed in many mechanisms such as GC metastasis, immune escape, and stem cell homing. When illustrating this process from the yin-yang perspective, categorizing different cells in the tumor microenvironment enables new and different perspectives to be put forward on the mechanism and treatment of GC metastasis.
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Affiliation(s)
- Zhongbo Zhu
- Key Laboratory of Gansu Provincial Prescription Mining and Innovative Translational Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China,Gansu Provincial Traditional Chinese Medicine New Product Creation Engineering Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China
| | - Lijuan Shi
- Key Laboratory of Gansu Provincial Prescription Mining and Innovative Translational Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China,Gansu Provincial Traditional Chinese Medicine New Product Creation Engineering Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China
| | - Yawei Dong
- Key Laboratory of Gansu Provincial Prescription Mining and Innovative Translational Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China,Gansu Provincial Traditional Chinese Medicine New Product Creation Engineering Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China
| | - Yanmei Zhang
- Key Laboratory of Gansu Provincial Prescription Mining and Innovative Translational Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China,Gansu Provincial Traditional Chinese Medicine New Product Creation Engineering Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China
| | - Fan Yang
- Key Laboratory of Gansu Provincial Prescription Mining and Innovative Translational Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China,Gansu Provincial Traditional Chinese Medicine New Product Creation Engineering Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China
| | - Jingjing Wei
- Key Laboratory of Gansu Provincial Prescription Mining and Innovative Translational Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China,Gansu Provincial Traditional Chinese Medicine New Product Creation Engineering Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China
| | - Minfeng Huo
- Key Laboratory of Gansu Provincial Prescription Mining and Innovative Translational Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China,Gansu Provincial Traditional Chinese Medicine New Product Creation Engineering Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China
| | - Peiqing Li
- Key Laboratory of Gansu Provincial Prescription Mining and Innovative Translational Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China,Gansu Provincial Traditional Chinese Medicine New Product Creation Engineering Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China
| | - Xiping Liu
- Key Laboratory of Gansu Provincial Prescription Mining and Innovative Translational Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China,Gansu Provincial Traditional Chinese Medicine New Product Creation Engineering Laboratory, Gansu University of Chinese MedicineLanzhou 730000, Gansu, P. R. China
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Immune infiltration could predict the efficacy of short-term radiotherapy in patients with cervical cancer. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2022; 25:1353-1367. [PMID: 36510039 DOI: 10.1007/s12094-022-03033-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
Radiotherapy is the main treatment for cervical cancer. It is usually applied alone or in combination with surgery and/or chemotherapy. To explore the association between immune microenvironment of cervical cancer and radiotherapy response, we collected 20 paired cervical cancer tumor samples before and after radiotherapy and partial clinical information. With paired-end RNA-seq, we quantified the immune infiltration and tumor purity of these samples, and obtained 6350 differentially expressed genes before and after radiotherapy. With the help of R language, the function enrichment analysis and 22 immune cells infiltration analysis were carried out. Moreover, we built a random forest model based on the immune microenvironment to predict the short-term efficacy of radiotherapy. We found that the effect of radiotherapy on the immune microenvironment of stage III and IV cervical cancer patients was weaker than that of stage I and II cervical cancer patients. Radiotherapy can significantly reduce the tumor purity and increase immune infiltration. The proportions of the immune infiltrating cells are predictive of the radiotherapy efficacy. In addition, the local mucositis caused by radiotherapy can improve the curative effect of radiotherapy.
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Sun X, Zhang Z, Wang Z, Xie R, Yi C, Liu H, Chi X, Li T, Liu H, Han Y, Pang X, Cui Y, Liu Z. The role of Angiogenesis and remodeling (AR) associated signature for predicting prognosis and clinical outcome of immunotherapy in pan-cancer. Front Immunol 2022; 13:1033967. [PMID: 36479101 PMCID: PMC9719961 DOI: 10.3389/fimmu.2022.1033967] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/03/2022] [Indexed: 11/22/2022] Open
Abstract
Background Angiogenesis and remodeling (AR) is necessary for the growth and metastasis of cancers. Although AR related genes involved in this process are reported, the correlation between AR and clinical outcome, immune cell infiltration, and immunotherapy is still unknown in diverse cancers. This study aimed to investigate the role of AR in the tumor immune microenvironment (TIME) in pan-cancer, and explore its values in prognostic prediction and therapeutic responses. Methods Firstly, AR genes (including angiogenesis genes and blood vessel remodeling genes) are collected from MsigDB database. The differential expression, and prognostic value of AR genes were studied in 33 tumor types based on TCGA and GTEx data. The AR score of each sample was calculated using the "ssGSEA" function of R package "GSVA" in pan-cancer. The correlation of the AR score with TIME index, such as the amount of stromal and immune components and the immune cell infiltration, was evaluated via integrating multiple computational methods. And we also utilized IMvigor210 and GSE78220 data to explore the prediction value of the AR score on the immunotherapy response. Results Significant differences in AR gene expression between tumors and adjacent normal tissues were found in most cancer types. The AR score varied depending on the types of tumors, and high score was related to worse survival in various tumors, such as pancreatic and stomach adenocarcinoma and so on. Moreover, the AR score was further explored to be positively correlated with proportions and pathways of immune and stromal in TIME. And the AR score was positively correlated with immunosuppressive cells, including TAMs and iTregs, while negatively with CD8+ T cells. Further analysis revealed that patients with high AR had worse therapy efficacy and survival status in bladder cancer and melanomas. Conclusions Our systematic analysis revealed that AR is closely associated TIME, and prognosis, and clinical characteristics in multiple cancers. Targeting AR genes may activate immune microenvironment and increase the efficacy of immunotherapy.
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Affiliation(s)
- Xiaojiao Sun
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Health Science Center, Peking University, Beijing, China
| | - Zhuo Zhang
- Department of Pharmacy, Peking University First Hospital, Beijing, China,Institute of Clinical Pharmacology, Peking University, Beijing, China
| | - Zhiqi Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Health Science Center, Peking University, Beijing, China
| | - Ran Xie
- Department of Pharmacy, Peking University First Hospital, Beijing, China
| | - Chuxiao Yi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Health Science Center, Peking University, Beijing, China
| | - Huiyu Liu
- Departments of Otorhinolaryngology-Head and Neck Surgery, Peking University First Hospital, Beijing, China
| | - Xiaowei Chi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Health Science Center, Peking University, Beijing, China
| | - Tiancheng Li
- Departments of Otorhinolaryngology-Head and Neck Surgery, Peking University First Hospital, Beijing, China
| | - Haitao Liu
- Institute of Clinical Pharmacology, Peking University, Beijing, China
| | - Yi Han
- Department of Thoracic Surgery, Beijing Thoracic Hospital, Beijing, China
| | - Xiaocong Pang
- Department of Pharmacy, Peking University First Hospital, Beijing, China,Institute of Clinical Pharmacology, Peking University, Beijing, China,*Correspondence: Xiaocong Pang, ; Yimin Cui, ; Zhenming Liu,
| | - Yimin Cui
- Department of Pharmacy, Peking University First Hospital, Beijing, China,Institute of Clinical Pharmacology, Peking University, Beijing, China,*Correspondence: Xiaocong Pang, ; Yimin Cui, ; Zhenming Liu,
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Health Science Center, Peking University, Beijing, China,*Correspondence: Xiaocong Pang, ; Yimin Cui, ; Zhenming Liu,
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Li R, Tong R, Zhang Z, Deng M, Wang T, Hou G. Single-cell sequencing analysis and transcriptome analysis constructed the macrophage related gene-related signature in lung adenocarcinoma and verified by an independent cohort. Genomics 2022; 114:110520. [PMID: 36372305 DOI: 10.1016/j.ygeno.2022.110520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Recent studies have emphasized the close relationship between macrophages and tumor immunity, and the prognosis of lung adenocarcinoma (LUAD) patients is intimately linked to this. Nonetheless, the prognostic signature and classification of different immune patterns in LUAD patients based on the macrophages is largely unexplored. METHODS Two sc-RNAseq datasets of LUAD patients were collected and reprocessed. The differentially expressed genes (DEGs) related to macrophages between LUAD tissues and normal lung tissues were then identified. Based upon the above genes, three distinct immune patterns in the TCGA-LUAD cohort were identified. The ssGSEA and CIBERSORT were applied for immune profiling and characterization of different subtypes. A four-gene prognostic signature for LUAD patients was established based on the DEGs between the subtypes using stepwise multi-Cox regression. TCGA-LUAD cohort was used as training set. Five GEO-LUAD datasets and an independent cohort containing 112 LUAD samples were used for validation. TIDE (tumor immune dysfunction and exclusion) and drug sensitivity analyses were also performed. RESULTS Macrophage-related differentially expressed genes were found out using the publicly available scRNA-seq data of LUAD. Three different immune patterns which were proved to have distinct immune infiltration characteristics in the TCGA-LUAD cohort were recognized based on the above macrophage-related genes. Thereafter, 174 DEGs among the above three different immune patterns were figured out; on the basis of this, a four-gene prognostic signature was constructed. This signature distinguished the prognosis of LUAD patients well in various GSE datasets as well as our independent cohort. Further analyses revealed that patients which had a higher risk score also accompanied with a lower immune infiltration level and a worse response to several immunotherapy biomarkers. CONCLUSION This study highlighted that macrophage were significantly associated with TME diversity and complexity. The four-gene prognostic signature could be used for predicting outcomes and immune landscapes for patients with LUAD.
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Affiliation(s)
- Ruixia Li
- Department of Pulmonary and Critical Care Medicine, First Hospital of China Medical University, Shenyang 110001, China
| | - Run Tong
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing 100029, China; National Center for Respiratory Medicine, Beijing 100029, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing 100029, China; National Clinical Research Center for Respiratory Diseases, Beijing 100029, China
| | - Zhe Zhang
- Department of Pathology, Shengjing Hospital of China Medical University, Shenyang 110001, China
| | - Mingming Deng
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing 100029, China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100029, China; National Center for Respiratory Medicine, Beijing 100029, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing 100029, China; National Clinical Research Center for Respiratory Diseases, Beijing 100029, China
| | - Tao Wang
- Department of Pathology, Shenyang KingMed Center for Clinical Laboratory Co., Ltd., Shenyang 110001, China
| | - Gang Hou
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing 100029, China; National Center for Respiratory Medicine, Beijing 100029, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing 100029, China; National Clinical Research Center for Respiratory Diseases, Beijing 100029, China.
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Chen C, Li Y, Miao P, Xu Y, Xie Y, Chen Z, Qian S. Tumor immune cell infiltration score based model predicts prognosis in multiple myeloma. Sci Rep 2022; 12:17082. [PMID: 36224246 PMCID: PMC9556830 DOI: 10.1038/s41598-022-21763-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/30/2022] [Indexed: 01/10/2023] Open
Abstract
The tumor microenvironment plays an important role in various processes, including tumorigenesis, cancer progression, and metastasis. Immune signatures have been identified and verified for use in diagnosis and prognosis prediction. We used single-sample Gene Set Enrichment Analysis to evaluate tumor immune cell infiltration score (TIICs) and verify their prognostic significance in both training and validation cohorts and using this information to build a prognostic model. A total of 1281 samples were obtained for further evaluation of the immune enrichment scores of 28 immune cells, showing that Th17 cell contributed most significantly to survival. Using the median TIICs as a cutoff to divide the samples into two groups, we found that the high-TIICs group was associated with favorable outcomes in both the training and validation sets. We then constructed a prognostic model to predict the 6, 8, and 10-year survival outcomes. Further analysis showed that immune score and tumor purity were higher in the high-TIICs group, while the matrix score was lower in this group. Forty-two differentially expressed genes were identified between the two groups. This new prognostic model based on immune cell infiltration indicates the potential for TIICs in predicting prognosis and as targets for treatment.
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Affiliation(s)
- Can Chen
- grid.13402.340000 0004 1759 700XDepartment of Hematology, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, 216 Huansha Road, Hangzhou, 310006 Zhejiang China
| | - Yiwei Li
- grid.13402.340000 0004 1759 700XDepartment of Critical Care Medicine, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, 216 Huansha Road, Hangzhou, 310006 Zhejiang China
| | - Peiwen Miao
- grid.268505.c0000 0000 8744 8924Department of Hematology, Affiliated Hangzhou First People’s Hospital, Zhejiang Chinese Medical University, 216 Huansha Road, Hangzhou, 310006 Zhejiang China
| | - Ying Xu
- grid.13402.340000 0004 1759 700XDepartment of Hematology, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, 216 Huansha Road, Hangzhou, 310006 Zhejiang China
| | - Yaping Xie
- grid.13402.340000 0004 1759 700XDepartment of Hematology, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, 216 Huansha Road, Hangzhou, 310006 Zhejiang China
| | - Zhenzhen Chen
- grid.13402.340000 0004 1759 700XDepartment of Hematology, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, 216 Huansha Road, Hangzhou, 310006 Zhejiang China
| | - Shenxian Qian
- grid.13402.340000 0004 1759 700XDepartment of Hematology, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, 216 Huansha Road, Hangzhou, 310006 Zhejiang China
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Lin L, Zeng X, Liang S, Wang Y, Dai X, Sun Y, Wu Z. Construction of a co-expression network and prediction of metastasis markers in colorectal cancer patients with liver metastasis. J Gastrointest Oncol 2022; 13:2426-2438. [PMID: 36388701 PMCID: PMC9660078 DOI: 10.21037/jgo-22-965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/18/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a common global malignancy associated with high invasiveness, high metastasis, and poor prognosis. CRC commonly metastasizes to the liver, where the treatment of metastasis is both difficult and an important topic in current CRC management. METHODS Microarrays data of human CRC with liver metastasis (CRCLM) were downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database to identify potential key genes. Differentially expressed (DE) genes (DEGs) and DEmiRNAs of primary CRC tumor tissues and metastatic liver tissues were identified. Microenvironment Cell Populations (MCP)-counter was used to estimate the abundance of immune cells in the tumor micro-environment (TME), and weighted gene correlation network analysis (WGCNA) was used to construct the co-expression network analysis. Gene Ontology and Kyoto Encyclopaedia of Gene and Genome (KEGG) pathway enrichment analyses were conducted, and the protein-protein interaction (PPI) network for the DEGs were constructed and gene modules were screened. RESULTS Thirty-five pairs of matched colorectal primary cancer and liver metastatic gene expression profiles were screened, and 610 DEGs (265 up-regulated and 345 down-regulated) and 284 DEmiRNAs were identified. The DEGs were mainly enriched in the complement and coagulation cascade pathways and renin secretion. Immune infiltrating cells including neutrophils, monocytic lineage, and cancer-associated fibroblasts (CAFs) differed significantly between primary tumor tissues and metastatic liver tissues. WGCN analysis obtained 12 modules and identified 62 genes with significant interactions which were mainly related to complement and coagulation cascade and the focal adhesion pathway. The best subset regression analysis and backward stepwise regression analysis were performed, and eight genes were determined, including F10, FGG, KNG1, MBL2, PROC, SERPINA1, CAV1, and SPP1. Further analysis showed four genes, including FGG, KNG1, CAV1, and SPP1 were significantly associated with CRCLM. CONCLUSIONS Our study implies complement and coagulation cascade and the focal adhesion pathway play a significant role in the development and progression of CRCLM, and FGG, KNG1, CAV1, and SPP1 may be metastatic markers for its early diagnosis.
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Affiliation(s)
- Lihong Lin
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Xiuxiu Zeng
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Shanyan Liang
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Yunzhi Wang
- School of Health Sciences, University of Sydney, Lidcombe, NSW, Australia
| | - Xiaoyu Dai
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Yuechao Sun
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China;,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Zhou Wu
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
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Prognostic and Immunological Role of STK38 across Cancers: Friend or Foe? Int J Mol Sci 2022; 23:ijms231911590. [PMID: 36232893 PMCID: PMC9570386 DOI: 10.3390/ijms231911590] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 12/24/2022] Open
Abstract
Although STK38 (serine-threonine kinase 38) has been proven to play an important role in cancer initiation and progression based on a series of cell and animal experiments, no systemic assessment of STK38 across human cancers is available. We firstly performed a pan-cancer analysis of STK38 in this study. The expression level of STK38 was significantly different between tumor and normal tissues in 15 types of cancers. Meanwhile, a prognosis analysis showed that a distinct relationship existed between STK38 expression and the clinical prognosis of cancer patients. Furthermore, the expression of STK38 was related to the infiltration of immune cells, such as NK cells, memory CD4+ T cells, mast cells and cancer-associated fibroblasts in a few cancers. There were three immune-associated signaling pathways involved in KEGG analysis of STK38. In general, STK38 shows a significant prognostic value in different cancers and is closely associated with cancer immunity.
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Feng D, Zhu W, You J, Shi X, Han P, Wei W, Wei Q, Yang L. Mitochondrial Aldehyde Dehydrogenase 2 Represents a Potential Biomarker of Biochemical Recurrence in Prostate Cancer Patients. Molecules 2022; 27:6000. [PMID: 36144737 PMCID: PMC9500792 DOI: 10.3390/molecules27186000] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND We aimed to explore the role of mitochondrial aldehyde dehydrogenase 2 (ALDH2) in prostate cancer (PCa) patients and provide insights into the tumor immune microenvironment (TME) for those patients undergoing radical radiotherapy. METHODS We performed all analyses using R version 3.6.3 and its suitable packages. Cytoscape 3.8.2 was used to establish network of competing endogenous RNAs (ceRNAs). RESULTS Downregulation of ADLH2 was significantly associated with higher risk of BCR-free survival (HR: 0.40, 95%CI: 0.24-0.68, p = 0.001) and metastasis-free survival (HR: 0.21, 95%CI: 0.09-0.49, p = 0.002). Additionally, ALDH2 repression contributed to significantly shorter BCR-free survival in the TCGA database (HR: 0.55, 95%CI: 0.33-0.93, p = 0.027). For immune checkpoints, patients that expressed a higher level of CD96 had a higher risk of BCR than their counterparts (HR: 1.79, 95%CI: 1.06-3.03, p = 0.032), as well as NRP1 (HR: 2.18, 95%CI: 1.29-3.69, p = 0.005). In terms of the TME parameters, the spearman analysis showed that ALDH was positively associated with B cells (r: 0.13), CD8+ T cells (r: 0.19), neutrophils (r: 0.13), and macrophages (r: 0.17). Patients with higher score of neutrophils (HR: 1.75, 95%CI: 1.03-2.95, p = 0.038), immune score (HR: 1.92, 95%CI: 1.14-3.25, p = 0.017), stromal score (HR: 2.52, 95%CI: 1.49-4.26, p = 0.001), and estimate score (HR: 1.81, 95%CI: 1.07-3.06, p = 0.028) had higher risk of BCR than their counterparts. Our ceRNA network found that PART1 might regulate the expression of ALDH via has-miR-578 and has-miR-6833-3p. Besides, PHA-793887, PI-103, and piperlongumine had better correlations with ALDH2. CONCLUSIONS We found that ALDH2 might serve as a potential biomarker predicting biochemical recurrence for PCa patients.
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Affiliation(s)
| | | | | | | | | | | | - Qiang Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lu Yang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
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Xin S, Mao J, Cui K, Li Q, Chen L, Li Q, Tu B, Liu X, Wang T, Wang S, Liu J, Song X, Song W. A cuproptosis-related lncRNA signature identified prognosis and tumour immune microenvironment in kidney renal clear cell carcinoma. Front Mol Biosci 2022; 9:974722. [PMID: 36188220 PMCID: PMC9515514 DOI: 10.3389/fmolb.2022.974722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Kidney renal clear cell carcinoma (KIRC) is a heterogeneous malignant tumor with high incidence, metastasis, and mortality. The imbalance of copper homeostasis can produce cytotoxicity and cause cell damage. At the same time, copper can also induce tumor cell death and inhibit tumor transformation. The latest research found that this copper-induced cell death is different from the known cell death pathway, so it is defined as cuproptosis. We included 539 KIRC samples and 72 normal tissues from the Cancer Genome Atlas (TCGA) in our study. After identifying long non-coding RNAs (lncRNAs) significantly associated with cuproptosis, we clustered 526 KIRC samples based on the prognostic lncRNAs and obtained two different patterns (Cuproptosis.C1 and C2). C1 indicated an obviously worse prognostic outcome and possessed a higher immune score and immune cell infiltration level. Moreover, a prognosis signature (CRGscore) was constructed to effectively and accurately evaluate the overall survival (OS) of KIRC patients. There were significant differences in tumor immune microenvironment (TIME) and tumor mutation burden (TMB) between CRGscore-defined groups. CRGscore also has the potential to predict medicine efficacy.
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Affiliation(s)
- Sheng Xin
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Jiaquan Mao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Kai Cui
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Qian Li
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Liang Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Qinyu Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Bocheng Tu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Xiaming Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Tao Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Shaogang Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Jihong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Xiaodong Song
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- *Correspondence: Xiaodong Song, ; Wen Song,
| | - Wen Song
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- *Correspondence: Xiaodong Song, ; Wen Song,
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Sang Q, Dai W, Yu J, Chen Y, Fan Z, Liu J, Li F, Li J, Wu X, Hou J, Yu B, Feng H, Zhu ZG, Su L, Li YY, Liu B. Identification of prognostic gene expression signatures based on the tumor microenvironment characterization of gastric cancer. Front Immunol 2022; 13:983632. [PMID: 36032070 PMCID: PMC9411533 DOI: 10.3389/fimmu.2022.983632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/20/2022] [Indexed: 12/02/2022] Open
Abstract
Increasing evidence has elucidated that the tumor microenvironment (TME) shows a strong association with tumor progression and therapeutic outcome. We comprehensively estimated the TME infiltration patterns of 111 gastric cancer (GC) and 21 normal stomach mucosa samples based on bulk transcriptomic profiles based on which GC could be clustered as three subtypes, TME-Stromal, TME-Mix, and TME-Immune. The expression data of TME-relevant genes were utilized to build a GC prognostic model—GC_Score. Among the three GC TME subtypes, TME-Stomal displayed the worst prognosis and the highest GC_Score, while TME-Immune had the best prognosis and the lowest GC_Score. Connective tissue growth factor (CTGF), the highest weighted gene in the GC_Score, was found to be overexpressed in GC. In addition, CTGF exhibited a significant correlation with the abundance of fibroblasts. CTGF has the potential to induce transdifferentiation of peritumoral fibroblasts (PTFs) to cancer-associated fibroblasts (CAFs). Beyond characterizing TME subtypes associated with clinical outcomes, we correlated TME infiltration to molecular features and explored their functional relevance, which helps to get a better understanding of carcinogenesis and therapeutic response and provide novel strategies for tumor treatments.
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Affiliation(s)
- Qingqing Sang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wentao Dai
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical and Pharmaceutical Technologies), Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai, China
| | - Junxian Yu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunqin Chen
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical and Pharmaceutical Technologies), Fudan University, Shanghai, China
| | - Zhiyuan Fan
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jixiang Liu
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical and Pharmaceutical Technologies), Fudan University, Shanghai, China
| | - Fangyuan Li
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianfang Li
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiongyan Wu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junyi Hou
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Beiqin Yu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haoran Feng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zheng-Gang Zhu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liping Su
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuan-Yuan Li
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical and Pharmaceutical Technologies), Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai, China
- *Correspondence: Bingya Liu, ; Yuan-Yuan Li,
| | - Bingya Liu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Bingya Liu, ; Yuan-Yuan Li,
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Li Q, Zhang P, Hu H, Huang H, Pan D, Mao G, Hu B. The DDR-related gene signature with cell cycle checkpoint function predicts prognosis, immune activity, and chemoradiotherapy response in lung adenocarcinoma. Respir Res 2022; 23:190. [PMID: 35840978 PMCID: PMC9288070 DOI: 10.1186/s12931-022-02110-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/09/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND As a DNA surveillance mechanism, cell cycle checkpoint has recently been discovered to be closely associated with lung adenocarcinoma (LUAD) prognosis. It is also an essential link in the process of DNA damage repair (DDR) that confers resistance to radiotherapy. Whether genes that have both functions play a more crucial role in LUAD prognosis remains unclear. METHODS In this study, DDR-related genes with cell cycle checkpoint function (DCGs) were selected to investigate their effects on the prognosis of LUAD. The TCGA-LUAD cohort and two GEO external validation cohorts (GSE31210 and GSE42171) were performed to construct a prognosis model based on the least absolute shrinkage and selection operator (LASSO) regression. Patients were divided into high-risk and low-risk groups based on the model. Subsequently, the multivariate COX regression was used to construct a prognostic nomogram. The ssGSEA, CIBERSORT algorithm, TIMER tool, CMap database, and IC50 of chemotherapeutic agents were used to analyze immune activity and responsiveness to chemoradiotherapy. RESULTS 4 DCGs were selected as prognostic signatures, and patients in the high-risk group had a lower overall survival (OS). The lower infiltration levels of immune cells and the higher expression levels of immune checkpoints appeared in the high-risk group. The damage repair pathways were upregulated, and chemotherapeutic agent sensitivity was poor in the high-risk group. CONCLUSIONS The 4-DCGs signature prognosis model we constructed could predict the survival rate, immune activity, and chemoradiotherapy responsiveness of LUAD patients.
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Affiliation(s)
- Quan Li
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China.,Zhejiang Provincial Key Laboratory of Watershed Sciences and Health, Wenzhou Medical University, Wenzhou, 325035, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou Medical University, Wenzhou, 325035, China.,Department of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Pan Zhang
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China.,Zhejiang Provincial Key Laboratory of Watershed Sciences and Health, Wenzhou Medical University, Wenzhou, 325035, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou Medical University, Wenzhou, 325035, China.,Department of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Huixiao Hu
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China.,Zhejiang Provincial Key Laboratory of Watershed Sciences and Health, Wenzhou Medical University, Wenzhou, 325035, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou Medical University, Wenzhou, 325035, China.,Department of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Hang Huang
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China.,Zhejiang Provincial Key Laboratory of Watershed Sciences and Health, Wenzhou Medical University, Wenzhou, 325035, China.,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou Medical University, Wenzhou, 325035, China.,Department of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Dong Pan
- Department of Dermatology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Guangyun Mao
- Department of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China
| | - Burong Hu
- Department of Radiation Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, 325035, China. .,Zhejiang Provincial Key Laboratory of Watershed Sciences and Health, Wenzhou Medical University, Wenzhou, 325035, China. .,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou Medical University, Wenzhou, 325035, China.
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Zhang L, Ding D, Liu J, Liu J, Wang N, Liu J. Identification of prognostic and immunotherapy-related eRNA ID2-AS1 in bladder cancer. Medicine (Baltimore) 2022; 101:e29759. [PMID: 35776987 PMCID: PMC9239636 DOI: 10.1097/md.0000000000029759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
AbstractEnhancer RNAs (eRNAs) can participate in enhancer regulation and target gene transcription, thus affecting the occurrence and development of tumors. In this study, we identified eRNAs closely related to bladder cancer (BLCA). Gene expression profiles and clinical information from The Cancer Genome Atlas (TCGA) database were used in this study. The Atlas of Noncoding RNAs in Cancer (TANRIC) co-expression data was also studied to evaluate correlations between the inferred levels of eRNA and its predicted target genes. Moreover, we evaluated differences in tumor microenvironment between high and low ID2-AS1 expression groups, and predicted the response of high- and low-expression groups to immune checkpoint inhibitor (ICI) treatment. Finally, we analyzed the prognostic value of ID2-AS1 in different tumors. ID2-AS1 and ID2 were identified as eRNAs and target genes related to the prognosis of BLCA. Low ID2-AS1 levels were associated with advanced age, low overall survival, high histological grade, and late BLCA staging. ID2-AS1 appeared to regulate epithelial mesenchymal transition, mitotic spindle assembly, and angiogenesis, thereby affecting BLCA progression. The ID2-AS1 high-expression group had better ICI treatment response. In addition, ID2-AS1 also had prognostic value in other cancers. ID2-AS1 helps predict prognostic and immunotherapeutic effects in BLCA.
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Affiliation(s)
- Lei Zhang
- Department of Urology, Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, China
| | - Degang Ding
- Department of Urology, Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, China
| | - Jianjun Liu
- Department of Urology, Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, China
| | - Junfeng Liu
- Department of Urology, Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, China
| | - Ning Wang
- Department of Urology, Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, China
| | - Jie Liu
- Department of Urology, Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, China
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50
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Analysis of CFTR gene expression as an immunological and prognostic biomarker in pan-cancers. Comput Biol Med 2022; 146:105614. [DOI: 10.1016/j.compbiomed.2022.105614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/23/2022]
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