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Chen L, Wan Y, Yang T, Zhang Q, Zeng Y, Zheng S, Ling Z, Xiao Y, Wan Q, Liu R, Yang C, Huang G, Zeng Q. Bibliometric and visual analysis of single-cell sequencing from 2010 to 2022. Front Genet 2024; 14:1285599. [PMID: 38274109 PMCID: PMC10808606 DOI: 10.3389/fgene.2023.1285599] [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: 09/04/2023] [Accepted: 12/31/2023] [Indexed: 01/27/2024] Open
Abstract
Background: Single-cell sequencing (SCS) is a technique used to analyze the genome, transcriptome, epigenome, and other genetic data at the level of a single cell. The procedure is commonly utilized in multiple fields, including neurobiology, immunology, and microbiology, and has emerged as a key focus of life science research. However, a thorough and impartial analysis of the existing state and trends of SCS-related research is lacking. The current study aimed to map the development trends of studies on SCS during the years 2010-2022 through bibliometric software. Methods: Pertinent papers on SCS from 2010 to 2022 were obtained using the Web of Science Core Collection. Research categories, nations/institutions, authors/co-cited authors, journals/co-cited journals, co-cited references, and keywords were analyzed using VOSviewer, the R package "bibliometric", and CiteSpace. Results: The bibliometric analysis included 9,929 papers published between 2010 and 2022, and showed a consistent increase in the quantity of papers each year. The United States was the source of the highest quantity of articles and citations in this field. The majority of articles were published in the periodical Nature Communications. Butler A was the most frequently quoted author on this topic, and his article "Integrating single-cell transcriptome data across diverse conditions, technologies, and species" has received numerous citations to date. The literature and keyword analysis showed that studies involving single-cell RNA sequencing (scRNA-seq) were prominent in this discipline during the study period. Conclusion: This study utilized bibliometric techniques to visualize research in SCS-related domains, which facilitated the identification of emerging patterns and future directions in the field. Current hot topics in SCS research include COVID-19, tumor microenvironment, scRNA-seq, and neuroscience. Our results are significant for scholars seeking to identify key issues and generate new research ideas.
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Affiliation(s)
- Ling Chen
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yantong Wan
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of BasicMedical Sciences, Southern Medical University, Guangzhou, China
| | - Tingting Yang
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Qi Zhang
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Yuting Zeng
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Shuqi Zheng
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Zhishan Ling
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Yupeng Xiao
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Qingyi Wan
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Ruili Liu
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Chun Yang
- Dongguan Key Laboratory of Stem Cell and Regenerative Tissue Engineering, Guangdong Medical University, Dongguan, China
| | - Guozhi Huang
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
| | - Qing Zeng
- Department of Rehabilitation Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Medicine, Southern Medical University, Guangzhou, China
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Hou Z, Lin J, Ma Y, Fang H, Wu Y, Chen Z, Lin X, Lu F, Wen S, Yu X, Huang H, Pan Y. Single-cell RNA sequencing revealed subclonal heterogeneity and gene signatures of gemcitabine sensitivity in pancreatic cancer. Front Pharmacol 2023; 14:1193791. [PMID: 37324492 PMCID: PMC10267405 DOI: 10.3389/fphar.2023.1193791] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction: Resistance to gemcitabine is common and critically limits its therapeutic efficacy in pancreatic ductal adenocarcinoma (PDAC). Methods: We constructed 17 patient-derived xenograft (PDX) models from PDAC patient samples and identified the most notable responder to gemcitabine by screening the PDX sets in vivo. To analyze tumor evolution and microenvironmental changes pre- and post-chemotherapy, single-cell RNA sequencing (scRNA-seq) was performed. Results: ScRNA-seq revealed that gemcitabine promoted the expansion of subclones associated with drug resistance and recruited macrophages related to tumor progression and metastasis. We further investigated the particular drug-resistant subclone and established a gemcitabine sensitivity gene panel (GSGP) (SLC46A1, PCSK1N, KRT7, CAV2, and LDHA), dividing PDAC patients into two groups to predict the overall survival (OS) in The Cancer Genome Atlas (TCGA) training dataset. The signature was successfully validated in three independent datasets. We also found that 5-GSGP predicted the sensitivity to gemcitabine in PDAC patients in the TCGA training dataset who were treated with gemcitabine. Discussion and conclusion: Our study provides new insight into the natural selection of tumor cell subclones and remodeling of tumor microenvironment (TME) cells induced by gemcitabine. We revealed a specific drug resistance subclone, and based on the characteristics of this subclone, we constructed a GSGP that can robustly predict gemcitabine sensitivity and prognosis in pancreatic cancer, which provides a theoretical basis for individualized clinical treatment.
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Affiliation(s)
- Zelin Hou
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Jiajing Lin
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yuan Ma
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Haizhong Fang
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yuwei Wu
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Zhijiang Chen
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Xianchao Lin
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Fengchun Lu
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shi Wen
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | | | - Heguang Huang
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yu Pan
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, China
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