1
|
He D, Tang H, Yang X, Liu X, Zhang Y, Shi J. Elaboration and validation of a prognostic signature associated with disulfidoptosis in lung adenocarcinoma, consolidated with integration of single-cell RNA sequencing and bulk RNA sequencing techniques. Front Immunol 2023; 14:1278496. [PMID: 37965333 PMCID: PMC10641741 DOI: 10.3389/fimmu.2023.1278496] [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: 08/16/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023] Open
Abstract
Background Lung adenocarcinoma (LUAD), the predominant subtype of non-small cell lung cancer (NSCLC), remains a pervasive global public health concern. Disulfidoptosis, a nascent form of regulated cell death (RCD), presents an emerging field of inquiry. Currently, investigations into disulfidoptosis are in their initial stages. Our undertaking sought to integrate single-cell RNA sequencing (scRNA-seq) in conjunction with traditional bulk RNA sequencing (bulk RNA-seq) methodologies, with the objective of delineating genes associated with disulfidoptosis and subsequently prognosticating the clinical outcomes of LUAD patients. Methods Initially, we conducted an in-depth examination of the cellular composition disparities existing between LUAD and normal samples using scRNA-seq data sourced from GSE149655. Simultaneously, we scrutinized the expression patterns of disulfidoptosis-associated gene sets across diverse cell types. Subsequently, leveraging the bulk RNA-seq data, we formulated disulfidoptosis-related prognostic risk signatures (DRPS) employing LASSO-Cox regression. This was accomplished by focusing on genes implicated in disulfidoptosis that exhibited differential expression within endothelial cells (ECs). Sequentially, the robustness and precision of the DRPS model were rigorously verified through both internal and external validation datasets. In parallel, we executed single-cell trajectory analysis to delve into the differentiation dynamics of ECs. Concluding our study, we undertook a comprehensive investigation encompassing various facets. These included comparative assessments of enrichment pathways, clinicopathological parameters, immune cell abundance, immune response-associated genes, impacts of immunotherapy, and drug predictions among distinct risk cohorts. Results The scrutiny of scRNA-seq data underscored discernible disparities in cellular composition between LUAD and normal samples. Furthermore, disulfidoptosis-associated genes exhibited marked discrepancies within endothelial cells (ECs). Consequently, we formulated the Disulfidoptosis-Related Prognostic Signature (DRPS) to facilitate prognostic prediction. The prognostic nomogram based on the risk score effectively demonstrated DRPS's robust capacity to prognosticate survival outcomes. This assertion was corroborated by rigorous assessments utilizing both internal and external validation sets, thus affirming the commendable predictive accuracy and enduring stability of DRPS. Functional enrichment analysis shed light on the significant correlation of DRPS with pathways intrinsic to the cell cycle. Subsequent analysis unveiled correlations between DRPS and gene mutations characteristic of LUAD, as well as indications of an immunosuppressive status. Through drug prediction, we explored potential therapeutic agents for low-risk patients. Concluding our investigation, qRT-PCR experiments confirmed the heightened expression levels of EPHX1, LDHA, SHC1, MYO6, and TLE1 in lung cancer cell lines.
Collapse
Affiliation(s)
- Dabao He
- Department of Laboratory Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Hengfeng Tang
- Department of Laboratory Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Xiaoling Yang
- Department of Laboratory Medicine, Shenzhen Baoan District Songgang People’s Hospital, Shenzhen, China
| | - Xiaohong Liu
- Department of Oncology, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Yipeng Zhang
- Department of Laboratory Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Junzhu Shi
- Department of Laboratory Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, China
| |
Collapse
|
2
|
Zhao M, Ma J, Li M, Zhu W, Zhou W, Shen L, Wu H, Zhang N, Wu S, Fu C, Li X, Yang K, Tang T, Shen R, He L, Huai C, Qin S. Different responses to risperidone treatment in Schizophrenia: a multicenter genome-wide association and whole exome sequencing joint study. Transl Psychiatry 2022; 12:173. [PMID: 35484098 PMCID: PMC9050705 DOI: 10.1038/s41398-022-01942-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/15/2022] [Accepted: 04/20/2022] [Indexed: 12/11/2022] Open
Abstract
Risperidone is routinely used in the clinical management of schizophrenia, but the treatment response is highly variable among different patients. The genetic underpinnings of the treatment response are not well understood. We performed a pharmacogenomic study of the treatment response to risperidone in patients with schizophrenia by using a SNP microarray -based genome-wide association study (GWAS) and whole exome sequencing (WES)-based GWAS. DNA samples were collected from 189 patients for the GWAS and from 222 patients for the WES after quality control in multiple centers of China. Antipsychotic response phenotypes of patients who received eight weeks of risperidone treatment were quantified with percentage change on the Positive and Negative Syndrome Scale (PANSS). The GWAS revealed a significant association between several SNPs and treatment response, such as three GRM7 SNPs (rs141134664, rs57521140, and rs73809055). Gene-based analysis in WES revealed 13 genes that were associated with antipsychotic response, such as GPR12 and MAP2K3. We did not identify shared loci or genes between GWAS and WES, but association signals tended to cluster into the GPCR gene family and GPCR signaling pathway, which may play an important role in the treatment response etiology. This study may provide a research paradigm for pharmacogenomic research, and these data provide a promising illustration of our potential to identify genetic variants underlying antipsychotic responses and may ultimately facilitate precision medicine in schizophrenia.
Collapse
Affiliation(s)
- Mingzhe Zhao
- grid.16821.3c0000 0004 0368 8293Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030 China ,grid.16821.3c0000 0004 0368 8293School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Jingsong Ma
- grid.494629.40000 0004 8008 9315School of Engineering, Westlake University, 18 Shilongshan Road, Hangzhou, 310024 Zhejiang Province China ,grid.494629.40000 0004 8008 9315Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024 Zhejiang Province China
| | - Mo Li
- grid.16821.3c0000 0004 0368 8293Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030 China ,grid.16821.3c0000 0004 0368 8293School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Wenli Zhu
- The Fourth People’s Hospital of Wuhu, No.1 East Wuxiashan Road, Wuhu, 241003 China
| | - Wei Zhou
- grid.16821.3c0000 0004 0368 8293Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030 China ,grid.16821.3c0000 0004 0368 8293School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Lu Shen
- grid.16821.3c0000 0004 0368 8293Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030 China ,grid.16821.3c0000 0004 0368 8293School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Hao Wu
- grid.16821.3c0000 0004 0368 8293Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030 China ,grid.16821.3c0000 0004 0368 8293School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Na Zhang
- grid.16821.3c0000 0004 0368 8293Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030 China ,grid.16821.3c0000 0004 0368 8293School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Shaochang Wu
- The Second People’s Hospital of Lishui, No.69 Beihua Road, Lishui, 323020 China
| | - Chunpeng Fu
- The Third People’s Hospital of Shangrao, No.1 Fenghuang East Avenue, Taokan Road, Shangrao, 334000 China
| | - Xianxi Li
- Shanghai Yangpu district mental health center, No.585 Jungong Road, Yangpu District, Shanghai, 900093 China
| | - Ke Yang
- grid.16821.3c0000 0004 0368 8293Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030 China ,grid.16821.3c0000 0004 0368 8293School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Tiancheng Tang
- grid.16821.3c0000 0004 0368 8293Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030 China ,grid.16821.3c0000 0004 0368 8293School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Ruoxi Shen
- grid.16821.3c0000 0004 0368 8293Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030 China ,grid.16821.3c0000 0004 0368 8293School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Lin He
- grid.16821.3c0000 0004 0368 8293Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030 China ,grid.16821.3c0000 0004 0368 8293School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Cong Huai
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China. .,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China. .,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| |
Collapse
|
3
|
A Lipid Metabolism-Based Seven-Gene Signature Correlates with the Clinical Outcome of Lung Adenocarcinoma. JOURNAL OF ONCOLOGY 2022; 2022:9913206. [PMID: 35186082 PMCID: PMC8856807 DOI: 10.1155/2022/9913206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 01/04/2022] [Indexed: 12/13/2022]
Abstract
Background. Herein, we tried to develop a prognostic prediction model for patients with LUAD based on the expression profiles of lipid metabolism-related genes (LMRGs). Methods. Molecular subtypes were identified by non-negative matrix factorization (NMF) clustering. The overall survival (OS) predictive gene signature was developed and validated internally and externally based on online data sets. Time-dependent receiver operating characteristic (ROC) curve, Kaplan–Meier curve, nomogram, restricted mean survival time (EMST), and decision curve analysis (DCA) were used to assess the performance of the gene signature. Results. We identified three molecular subtypes in LUAD with distinct characteristics on immune cells infiltration and clinical outcomes. Moreover, we confirmed a seven-gene signature as an independent prognostic factor for patients with LUAD. Calibration and DCA analysis plots indicated the excellent predictive performance of the prognostic nomogram constructed based on the gene signature. In addition, the nomogram showed higher robustness and clinical usability compared with four previously reported prognostic gene signatures. Conclusions. Findings in the present study shed new light on the characteristics of lipid metabolism within LUAD, and the established seven-gene signature can be utilized as a new prognostic marker for predicting survival in patients with LUAD.
Collapse
|
4
|
Hong K, Dong S, Xu X, Zhang Z, Shi T, Yuan H, Xu X, Hu W. Enantioselective Intermolecular Mannich-Type Interception of Phenolic Oxonium Ylide for the Direct Assembly of Chiral 2,2-Disubstituted Dihydrobenzofurans. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01321] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Kemiao Hong
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Shanliang Dong
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xinxin Xu
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhijing Zhang
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Taoda Shi
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Haoxuan Yuan
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xinfang Xu
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Wenhao Hu
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| |
Collapse
|