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Yang W, Zhao X, Duan L, Niu L, Zhang Y, Zhou W, Li Y, Chen J, Fan A, Xie Q, Liu J, Han Y, Fan D, Hong L. Development and validation of a ligand-receptor pairs signature to predict outcome and provide a therapeutic strategy in gastric cancer. Expert Rev Mol Diagn 2023; 23:619-634. [PMID: 37248704 DOI: 10.1080/14737159.2023.2219843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
BACKGROUND An important factor in tumor development and progression is the tumor microenvironment (TME), which is heterogeneous. Previous studies have mainly investigated the expression profile and prognostic values of genes in gastric cancer (GC) at the cell population level but neglected the interactions and heterogeneity between cells. METHODS The pattern of ligand-receptor (LR) interactions was delineated on a scRNA-seq dataset containing 44,953 cells from nine GC patients and a fourth bulk RNA-seq dataset including data from 1159 GC patients. We then constructed an LR.Score scoring model to comprehensively evaluate the influence of LR-pairs on the TME, overall survival, and immunotherapy response in GC patients from several cohorts. RESULTS Cell communication network among 13 cell types was constructed based on the LR-pairs. We proposed a new molecular subtyping model for GC based on the LR-pairs and revealed the differences in prognosis, pathophysiologic features, mutation characteristics, function enrichment, and immunological characteristics among the three subtypes. Finally, an LR.Score model based on LR-pairs was developed and validated on several datasets. CONCLUSIONS Based on the selected LR-pairs, we successfully constructed a novel prediction model and observed its well performance on molecular subtyping, target and pathway screening, prognosis judging, and immunotherapy response predicting.
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Affiliation(s)
- Wanli Yang
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Xinhui Zhao
- Department of Thyroid and Breast Surgery, The Affiliated Hospital of Northwest University & Xi'an No.3 Hospital, Northwest University, Xi'an, Shaanxi Province, China
| | - Lili Duan
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Liaoran Niu
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Yujie Zhang
- Department of Histology and Embryology, School of Basic Medicine, Xi'an Medical University, Xi'an, Shaanxi Province, China
| | - Wei Zhou
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Yiding Li
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Junfeng Chen
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Aqiang Fan
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Qibin Xie
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Jinqiang Liu
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Yu Han
- Department of Otolaryngology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Daiming Fan
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Liu Hong
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
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Wang YF, Hu YQ, Hu YN, Bai YC, Wang H, Zhang Q. Expression and clinical significance of DOK3 in renal clear cell carcinoma. J Int Med Res 2023; 51:3000605231174974. [PMID: 37235715 DOI: 10.1177/03000605231174974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
OBJECTIVES Docking Protein 3 (DOK3) is an adapter protein that has been implicated in various cellular processes relevant to diseases, such as cancer. In this study, we aimed to evaluate the role of DOK3 in kidney renal clear cell carcinoma (KIRC) by examining how its expression levels are correlated with patient characteristics and prognosis. METHODS We analyzed KIRC-related data from The Cancer Genome Atlas and used several bioinformatics tools, such as LinkedOmics and Oncomine, to evaluate DOK3 mRNA expression in KIRC. DOK3 protein expression was examined in 150 clinical KIRC samples and 100 non-cancerous renal tissues with immunohistochemistry assays. The prognostic value of DOK3 mRNA expression on patient overall survival was analyzed retrospectively using Kaplan-Meier survival and Cox regression analyses. RESULTS DOK3 mRNA expression was notably higher in KIRC samples compared with normal tissues. Significant correlations were found between DOK3 mRNA expression levels and tumor size, lymph node metastasis, distant metastasis, and pathological grade using the bioinformatics data. This was confirmed at the protein level with immunohistochemistry data. Survival analyses indicated that elevated DOK3 expression is linked to a lower overall survival rate in KIRC patients. CONCLUSIONS DOK3 is a potential biomarker for determining KIRC patient clinical prognosis.
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Affiliation(s)
- Yi-Fan Wang
- Urology & Nephrology Center, Department of Urology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
- Graduate Department, Bengbu Medical College, Bengbu, China
| | - Yu-Qi Hu
- Urology & Nephrology Center, Department of Urology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yu-Ning Hu
- Urology & Nephrology Center, Department of Urology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yu-Chen Bai
- Urology & Nephrology Center, Department of Urology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Heng Wang
- Urology & Nephrology Center, Department of Urology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Qi Zhang
- Urology & Nephrology Center, Department of Urology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
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Liu F, Wang P, Sun W, Jiang Y, Gong Q. Identification of Ligand-Receptor Pairs Associated With Tumour Characteristics in Clear Cell Renal Cell Carcinoma. Front Immunol 2022; 13:874056. [PMID: 35734169 PMCID: PMC9207243 DOI: 10.3389/fimmu.2022.874056] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
The tumour microenvironment (TME) of clear cell renal cell carcinoma (ccRCC) comprises multiple cell types, which promote tumour progression and modulate drug resistance and immune cell infiltrations via ligand-receptor (LR) interactions. However, the interactions, expression patterns, and clinical relevance of LR in the TME in ccRCC are insufficiently characterised. This study characterises the complex composition of the TME in ccRCC by analysing the single-cell sequencing (scRNA-seq) data of patients with ccRCC from the Gene expression omnibus database. On analysing the scRNA-seq data combined with the cancer genome atlas kidney renal clear cell carcinoma (TCGA-KIRC) dataset, 46 LR-pairs were identified that were significantly correlated and had prognostic values. Furthermore, a new molecular subtyping model was proposed based on these 46 LR-pairs. Molecular subtyping was performed in two ccRCC cohorts, revealing significant differences in prognosis between the subtypes of the two ccRCC cohorts. Different molecular subtypes exhibited different clinicopathological features, mutational, pathway, and immune signatures. Finally, the LR.score model that was constructed using ten essential LR-pairs that were identified based on LASSO Cox regression analysis revealed that the model could accurately predict the prognosis of patients with ccRCC. In addition, the differential expression of ten LR-pairs in tumour and normal cell lines was identified. Further functional experiments showed that CX3CL1 can exert anti-tumorigenic role in ccRCC cell line. Altogether, the effects of immunotherapy were connected to LR.scores, indicating that potential medications targeting these LR-pairs could contribute to the clinical benefit of immunotherapy. Therefore, this study identifies LR-pairs that could be effective biomarkers and predictors for molecular subtyping and immunotherapy effects in ccRCC. Targeting LR-pairs provides a new direction for immunotherapy regimens and prognostic evaluations in ccRCC.
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Affiliation(s)
- Fahui Liu
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Ping Wang
- Department of Dermatology, Fujian Provincial Geriatric Hospital, Fuzhou, China
| | - Wenjuan Sun
- Department of Internal Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Yan Jiang
- Guixi Key Laboratory for High Incidence Diseases, Youjiang Medical University for Nationalities, Baise, China
- *Correspondence: Qiming Gong, ; Yan Jiang,
| | - Qiming Gong
- Department of Nephrology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- *Correspondence: Qiming Gong, ; Yan Jiang,
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Xu Y, Du Y, Zheng Q, Zhou T, Ye B, Wu Y, Xu Q, Meng X. Identification of Ferroptosis-Related Prognostic Signature and Subtypes Related to the Immune Microenvironment for Breast Cancer Patients Receiving Neoadjuvant Chemotherapy. Front Immunol 2022; 13:895110. [PMID: 35603151 PMCID: PMC9115856 DOI: 10.3389/fimmu.2022.895110] [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: 03/13/2022] [Accepted: 04/06/2022] [Indexed: 12/20/2022] Open
Abstract
Purpose To identify molecular clusters associated with ferroptosis and to develop a ferroptosis-related signature for providing novel potential targets for the recurrence-free survival and treatment of breast cancer. Methods Ferroptosis-related gene (FRG) signature was constructed by univariate and multivariate Cox regression and least absolute shrinkage and selection operator (LASSO). Receiver operating characteristic curves, Kaplan–Meier survival analysis, principal component analysis, and univariate and multivariate Cox regression analyses in the training and test cohorts were used to evaluate the application of this signature. Quantitative reverse transcriptase–PCR (qRT-PCR) was employed to detect the expression of FRGs in the model. Furthermore, the correlations between the signature and immune microenvironment, somatic mutation, and chemotherapeutic drugs sensitivity were explored. Results Internal and external validations affirmed that relapse-free survival differed significantly between the high-risk and low-risk groups. Univariate and multivariate Cox regression analyses indicated that the riskScore was an independent prognostic factor for BRCA. The areas under the curve (AUCs) for predicting 1-, 2-, and 3-year survival in the training and test cohorts were satisfactory. Significant differences were also found in the immune microenvironment and IC50 of chemotherapeutic drugs between different risk groups. Furthermore, we divided patients into three clusters based on 18 FRGs to ameliorate the situation of immunotherapy failure in BRCA. Conclusions The FRG signature functions as a robust prognostic predictor of the immune microenvironment and therapeutic response, with great potential to guide individualized treatment strategies in the future.
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Affiliation(s)
- Yuhao Xu
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China.,General Surgery, Cancer Center, Department of Breast Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Yaoqiang Du
- Laboratory Medicine Center, Department of Transfusion Medicine, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Qinghui Zheng
- General Surgery, Cancer Center, Department of Breast Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Tao Zhou
- Hangzhou Medical College, Hangzhou, China
| | - Buyun Ye
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yihao Wu
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, China
| | - Qiuran Xu
- Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Xuli Meng
- General Surgery, Cancer Center, Department of Breast Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
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Dong K, Gu D, Shi J, Bao Y, Fu Z, Fang Y, Qu L, Zhu W, Jiang A, Wang L. Identification and Verification of m 7G Modification Patterns and Characterization of Tumor Microenvironment Infiltration via Multi-Omics Analysis in Clear Cell Renal Cell Carcinoma. Front Immunol 2022; 13:874792. [PMID: 35592316 PMCID: PMC9113293 DOI: 10.3389/fimmu.2022.874792] [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: 02/13/2022] [Accepted: 04/05/2022] [Indexed: 11/25/2022] Open
Abstract
The epigenetic modification of tumorigenesis and progression in neoplasm has been demonstrated in recent studies. Nevertheless, the underlying association of N7-methylguanosine (m7G) regulation with molecular heterogeneity and tumor microenvironment (TME) in clear cell renal cell carcinoma (ccRCC) remains unknown. We explored the expression profiles and genetic variation features of m7G regulators and identified their correlations with patient outcomes in pan-cancer. Three distinct m7G modification patterns, including MGCS1, MGCS2, and MGCS3, were further determined and systematically characterized via multi-omics data in ccRCC. Compared with the other two subtypes, patients in MGCS3 exhibited a lower clinical stage/grade and better prognosis. MGCS1 showed the lowest enrichment of metabolic activities. MGCS2 was characterized by the suppression of immunity. We then established and validated a scoring tool named m7Sig, which could predict the prognosis of ccRCC patients. This study revealed that m7G modification played a vital role in the formation of the tumor microenvironment in ccRCC. Evaluating the m7G modification landscape helps us to raise awareness and strengthen the understanding of ccRCC’s characterization and, furthermore, to guide future clinical decision making.
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Affiliation(s)
- Kai Dong
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Di Gu
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Jiazi Shi
- Department of Urology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yewei Bao
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Zhibin Fu
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yu Fang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Le Qu
- Department of Urology, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Wentong Zhu
- School of Chinese Medicine, Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Aimin Jiang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Linhui Wang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
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