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Zhou S, Lin N, Yu L, Su X, Liu Z, Yu X, Gao H, Lin S, Zeng Y. Single-cell multi-omics in the study of digestive system cancers. Comput Struct Biotechnol J 2024; 23:431-445. [PMID: 38223343 PMCID: PMC10787224 DOI: 10.1016/j.csbj.2023.12.007] [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: 08/04/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 01/16/2024] Open
Abstract
Digestive system cancers are prevalent diseases with a high mortality rate, posing a significant threat to public health and economic burden. The diagnosis and treatment of digestive system cancer confront conventional cancer problems, such as tumor heterogeneity and drug resistance. Single-cell sequencing (SCS) emerged at times required and has developed from single-cell RNA-seq (scRNA-seq) to the single-cell multi-omics era represented by single-cell spatial transcriptomics (ST). This article comprehensively reviews the advances of single-cell omics technology in the study of digestive system tumors. While analyzing and summarizing the research cases, vital details on the sequencing platform, sample information, sampling method, and key findings are provided. Meanwhile, we summarize the commonly used SCS platforms and their features, as well as the advantages of multi-omics technologies in combination. Finally, the development trends and prospects of the application of single-cell multi-omics technology in digestive system cancer research are prospected.
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Affiliation(s)
- Shuang Zhou
- The Second Clinical Medical School of Fujian Medical University, Quanzhou, Fujian Province, China
- The Clinical Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Nanfei Lin
- The Clinical Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Liying Yu
- The Clinical Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Xiaoshan Su
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China
| | - Zhenlong Liu
- Lady Davis Institute for Medical Research, Jewish General Hospital, & Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC, Canada
| | - Xiaowan Yu
- Clinical Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Hongzhi Gao
- The Clinical Center of Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Shu Lin
- Centre of Neurological and Metabolic Research, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia
| | - Yiming Zeng
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Fujian Medical University, Respirology Medicine Centre of Fujian Province, Quanzhou, China
- Fujian Provincial Key Laboratory of Lung Stem Cells, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong Province, China
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2
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Zhao M, Cheng Y, Gao J, Zhou F. Single-cell mass cytometry in immunological skin diseases. Front Immunol 2024; 15:1401102. [PMID: 39081313 PMCID: PMC11286489 DOI: 10.3389/fimmu.2024.1401102] [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: 03/14/2024] [Accepted: 07/01/2024] [Indexed: 08/02/2024] Open
Abstract
Immune-related skin diseases represent a collective of dermatological disorders intricately linked to dysfunctional immune system processes. These conditions are primarily characterized by an immoderate activation of the immune system or deviant immune responses, involving diverse immune components including immune cells, antibodies, and inflammatory mediators. However, the precise molecular dysregulation underlying numerous individual cases of these diseases and unique subsets respond under disease conditions remains elusive. Comprehending the mechanisms and determinants governing the homeostasis and functionality of diseases could offer potential therapeutic opportunities for intervention. Mass cytometry enables precise and high-throughput quantitative measurement of proteins within individual cells by utilizing antibodies labeled with rare heavy metal isotopes. Imaging mass cytometry employs mass spectrometry to obtain spatial information on cell-to-cell interactions within tissue sections, simultaneously utilizing more than 40 markers. The application of single-cell mass cytometry presents a unique opportunity to conduct highly multiplexed analysis at the single-cell level, thereby revolutionizing our understanding of cell population heterogeneity and hierarchy, cellular states, multiplexed signaling pathways, proteolysis products, and mRNA transcripts specifically in the context of many autoimmune diseases. This information holds the potential to offer novel approaches for the diagnosis, prognostic assessment, and monitoring responses to treatment, thereby enriching our strategies in managing the respective conditions. This review summarizes the present-day utilization of single-cell mass cytometry in studying immune-related skin diseases, highlighting its advantages and limitations. This technique will become increasingly prevalent in conducting extensive investigations into these disorders, ultimately yielding significant contributions to their accurate diagnosis and efficacious therapeutic interventions.
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Affiliation(s)
- Mingming Zhao
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Yuqi Cheng
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Jinping Gao
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Fusheng Zhou
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
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Vitale S, Calapà F, Colonna F, Luongo F, Biffoni M, De Maria R, Fiori ME. Advancements in 3D In Vitro Models for Colorectal Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2405084. [PMID: 38962943 DOI: 10.1002/advs.202405084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Indexed: 07/05/2024]
Abstract
The process of drug discovery and pre-clinical testing is currently inefficient, expensive, and time-consuming. Most importantly, the success rate is unsatisfactory, as only a small percentage of tested drugs are made available to oncological patients. This is largely due to the lack of reliable models that accurately predict drug efficacy and safety. Even animal models often fail to replicate human-specific pathologies and human body's complexity. These factors, along with ethical concerns regarding animal use, urge the development of suitable human-relevant, translational in vitro models.
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Affiliation(s)
- Sara Vitale
- Department of Oncology and Molecular Medicine (OMM), Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, 00161, Italy
| | - Federica Calapà
- Dipartimento di Medicina e Chirurgia traslazionale, Università Cattolica del Sacro Cuore, Largo F. Vito 1, Rome, Italy
| | - Francesca Colonna
- Department of Oncology and Molecular Medicine (OMM), Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, 00161, Italy
| | - Francesca Luongo
- Dipartimento di Medicina e Chirurgia traslazionale, Università Cattolica del Sacro Cuore, Largo F. Vito 1, Rome, Italy
| | - Mauro Biffoni
- Department of Oncology and Molecular Medicine (OMM), Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, 00161, Italy
| | - Ruggero De Maria
- Dipartimento di Medicina e Chirurgia traslazionale, Università Cattolica del Sacro Cuore, Largo F. Vito 1, Rome, Italy
- Fondazione Policlinico Universitario "A. Gemelli" - IRCCS, Largo F. Vito 1, Rome, Italy
| | - Micol E Fiori
- Department of Oncology and Molecular Medicine (OMM), Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, 00161, Italy
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Ouyang Y, Shen R, Chu L, Fu C, Hu W, Huang H, Zhang Z, Jiang M, Chen X. Combining single-cell and bulk RNA sequencing, NK cell marker genes reveal a prognostic and immune status in pancreatic ductal adenocarcinoma. Sci Rep 2024; 14:15037. [PMID: 38951569 PMCID: PMC11217423 DOI: 10.1038/s41598-024-65917-1] [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: 07/19/2023] [Accepted: 06/25/2024] [Indexed: 07/03/2024] Open
Abstract
The NK cell is an important component of the tumor microenvironment of pancreatic ductal adenocarcinoma (PDAC), also plays a significant role in PDAC development. This study aimed to explore the relationship between NK cell marker genes and prognosis, immune response of PDAC patients. By scRNA-seq data, we found the proportion of NK cells were significantly downregulated in PDAC and 373 NK cell marker genes were screened out. By TCGA database, we enrolled 7 NK cell marker genes to construct the signature for predicting prognosis in PDAC patients. Cox analysis identified the signature as an independent factor for pancreatic cancer. Subsequently, the predictive power of signature was validated by 6 GEO datasets and had an excellent evaluation. Our analysis of relationship between the signature and patients' immune status revealed that the signature has a strong correlation with immunocyte infiltration, inflammatory reaction, immune checkpoint inhibitors (ICIs) response. The NK cell marker genes are closely related to the prognosis and immune capacity of PDAC patients, and they have potential value as a therapeutic target.
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Affiliation(s)
- Yonghao Ouyang
- Research Institute of General Surgery, Jinling Hospital, Nanjing University Medical School, 305 Zhong Shan East Road, Nanjing, 210002, China.
- Nanchang University, 461 Bayi Avenue, Nanchang, 330006, Jiangxi, China.
| | - Rongxi Shen
- Research Institute of General Surgery, Jinling Hospital, Nanjing University Medical School, 305 Zhong Shan East Road, Nanjing, 210002, China.
| | - Lihua Chu
- Jinggangshan University, Ji'an, 334000, China
| | - Chengchao Fu
- Nanchang University, 461 Bayi Avenue, Nanchang, 330006, Jiangxi, China
| | - Wang Hu
- Nanchang University, 461 Bayi Avenue, Nanchang, 330006, Jiangxi, China
| | - Haoxuan Huang
- Nanchang University, 461 Bayi Avenue, Nanchang, 330006, Jiangxi, China
| | - Zhicheng Zhang
- Nanchang University, 461 Bayi Avenue, Nanchang, 330006, Jiangxi, China
| | - Ming Jiang
- Nanchang University, 461 Bayi Avenue, Nanchang, 330006, Jiangxi, China
| | - Xin Chen
- Jiangxi University of Chinese Medicine, Nanchang, 330000, China
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5
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Chang X, Zheng Y, Xu K. Single-Cell RNA Sequencing: Technological Progress and Biomedical Application in Cancer Research. Mol Biotechnol 2024; 66:1497-1519. [PMID: 37322261 PMCID: PMC11217094 DOI: 10.1007/s12033-023-00777-0] [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: 03/09/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023]
Abstract
Single-cell RNA-seq (scRNA-seq) is a revolutionary technology that allows for the genomic investigation of individual cells in a population, allowing for the discovery of unusual cells associated with cancer and metastasis. ScRNA-seq has been used to discover different types of cancers with poor prognosis and medication resistance such as lung cancer, breast cancer, ovarian cancer, and gastric cancer. Besides, scRNA-seq is a promising method that helps us comprehend the biological features and dynamics of cell development, as well as other disorders. This review gives a concise summary of current scRNA-seq technology. We also explain the main technological steps involved in implementing the technology. We highlight the present applications of scRNA-seq in cancer research, including tumor heterogeneity analysis in lung cancer, breast cancer, and ovarian cancer. In addition, this review elucidates potential applications of scRNA-seq in lineage tracing, personalized medicine, illness prediction, and disease diagnosis, which reveals that scRNA-seq facilitates these events by producing genetic variations on the single-cell level.
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Affiliation(s)
- Xu Chang
- Department of Otolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Yunxi Zheng
- Department of Otolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Kai Xu
- Department of Otolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China.
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Nishide M, Shimagami H, Kumanogoh A. Single-cell analysis in rheumatic and allergic diseases: insights for clinical practice. Nat Rev Immunol 2024:10.1038/s41577-024-01043-3. [PMID: 38914790 DOI: 10.1038/s41577-024-01043-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 06/26/2024]
Abstract
Since the advent of single-cell RNA sequencing (scRNA-seq) methodology, single-cell analysis has become a powerful tool for exploration of cellular networks and dysregulated immune responses in disease pathogenesis. Advanced bioinformatics tools have enabled the combined analysis of scRNA-seq data and information on various cell properties, such as cell surface molecular profiles, chromatin accessibility and spatial information, leading to a deeper understanding of pathology. This Review provides an overview of the achievements in single-cell analysis applied to clinical samples of rheumatic and allergic diseases, including rheumatoid arthritis, systemic lupus erythematosus, systemic sclerosis, allergic airway diseases and atopic dermatitis, with an expanded scope beyond peripheral blood cells to include local diseased tissues. Despite the valuable insights that single-cell analysis has provided into disease pathogenesis, challenges remain in translating single-cell findings into clinical practice and developing personalized treatment strategies. Beyond understanding the atlas of cellular diversity, we discuss the application of data obtained in each study to clinical practice, with a focus on identifying biomarkers and therapeutic targets.
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Affiliation(s)
- Masayuki Nishide
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
- Department of Immunopathology, World Premier International Research Center Initiative (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan.
- Department of Advanced Clinical and Translational Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
| | - Hiroshi Shimagami
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center Initiative (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
- Department of Advanced Clinical and Translational Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
- Department of Immunopathology, World Premier International Research Center Initiative (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan.
- Center for Infectious Diseases for Education and Research (CiDER), Osaka University, Suita, Osaka, Japan.
- Center for Advanced Modalities and DDS (CAMaD), Osaka University, Suita, Osaka, Japan.
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Xin S, Zhang Y, Zhang Z, Li Z, Sun X, Liu X, Jin L, Li W, Tang C, Mei W, Cao Q, Wang H, Wei Z, Zhou Z, Li R, Wen X, Yang G, Chen W, Zheng J, Ye L. ScRNA-seq revealed the tumor microenvironment heterogeneity related to the occurrence and metastasis in upper urinary tract urothelial carcinoma. Cancer Gene Ther 2024:10.1038/s41417-024-00779-3. [PMID: 38877164 DOI: 10.1038/s41417-024-00779-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 06/16/2024]
Abstract
Metastasis is the greatest clinical challenge for UTUCs, which may have distinct molecular and cellular characteristics from earlier cancers. Herein, we provide single-cell transcriptome profiles of UTUC para cancer normal tissue, primary tumor lesions, and lymphatic metastases to explore possible mechanisms associated with UTUC occurrence and metastasis. From 28,315 cells obtained from normal and tumor tissues of 3 high-grade UTUC patients, we revealed the origin of UTUC tumor cells and the homology between metastatic and primary tumor cells. Unlike the immunomicroenvironment suppression of other tumors, we found no immunosuppression in the tumor microenvironment of UTUC. Moreover, it is imperative to note that stromal cells are pivotal in the advancement of UTUC. This comprehensive single-cell exploration enhances our comprehension of the molecular and cellular dynamics of metastatic UTUCs and discloses promising diagnostic and therapeutic targets in cancer-microenvironment interactions.
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Affiliation(s)
- Shiyong Xin
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Department of Urology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471000, China
| | - Yanwei Zhang
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Zhenhua Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ziyao Li
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Xianchao Sun
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Xiang Liu
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Liang Jin
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Weiyi Li
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Chaozhi Tang
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Wangli Mei
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Qiong Cao
- Department of Pathology, The Third Affiliated Hospital of Henan University of Science and Technology, Luoyang, 471003, China
| | - Haojie Wang
- Department of Central Laboratory, Zhengzhou University, Luoyang Central Hospital, Luoyang, 471003, China
| | - Zhihao Wei
- Department of Pathology, Yiluo Hospital of Luoyang, The Teaching Hospital of Henan University of Science and Technology, Luoyang, China
| | - Zhen Zhou
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Rongbing Li
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Xiaofei Wen
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Guosheng Yang
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Weihua Chen
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China.
| | - Junhua Zheng
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
| | - Lin Ye
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China.
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Zhu J, Zhang K, Chen Y, Ge X, Wu J, Xu P, Yao J. Progress of single-cell RNA sequencing combined with spatial transcriptomics in tumour microenvironment and treatment of pancreatic cancer. J Transl Med 2024; 22:563. [PMID: 38867230 PMCID: PMC11167806 DOI: 10.1186/s12967-024-05307-3] [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: 11/27/2023] [Accepted: 05/16/2024] [Indexed: 06/14/2024] Open
Abstract
In recent years, single-cell analyses have revealed the heterogeneity of the tumour microenvironment (TME) at the genomic, transcriptomic, and proteomic levels, further improving our understanding of the mechanisms of tumour development. Single-cell RNA sequencing (scRNA-seq) technology allow analysis of the transcriptome at the single-cell level and have unprecedented potential for exploration of the characteristics involved in tumour development and progression. These techniques allow analysis of transcript sequences at higher resolution, thereby increasing our understanding of the diversity of cells found in the tumour microenvironment and how these cells interact in complex tumour tissue. Although scRNA-seq has emerged as an important tool for studying the tumour microenvironment in recent years, it cannot be used to analyse spatial information for cells. In this regard, spatial transcriptomics (ST) approaches allow researchers to understand the functions of individual cells in complex multicellular organisms by understanding their physical location in tissue sections. In particular, in related research on tumour heterogeneity, ST is an excellent complementary approach to scRNA-seq, constituting a new method for further exploration of tumour heterogeneity, and this approach can also provide unprecedented insight into the development of treatments for pancreatic cancer (PC). In this review, based on the methods of scRNA-seq and ST analyses, research progress on the tumour microenvironment and treatment of pancreatic cancer is further explained.
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Affiliation(s)
- Jie Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Northern Jiangsu People's Hospital Affiliated Yangzhou University, Jiangsu Province, China
| | - Ke Zhang
- Dalian Medical University, Dalian, China
| | - Yuan Chen
- Department of Hepatobiliary and Pancreatic Surgery, Northern Jiangsu People's Hospital Affiliated Yangzhou University, Jiangsu Province, China
| | - Xinyu Ge
- Dalian Medical University, Dalian, China
| | - Junqing Wu
- Department of Hepatobiliary and Pancreatic Surgery, Northern Jiangsu People's Hospital Affiliated Yangzhou University, Jiangsu Province, China
| | - Peng Xu
- Department of Hepatobiliary and Pancreatic Surgery, Northern Jiangsu People's Hospital Affiliated Yangzhou University, Jiangsu Province, China.
| | - Jie Yao
- Department of Hepatobiliary and Pancreatic Surgery, Northern Jiangsu People's Hospital Affiliated Yangzhou University, Jiangsu Province, China.
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9
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Wu J, Li W, Su J, Zheng J, Liang Y, Lin J, Xu B, Liu Y. Integration of single-cell sequencing and bulk RNA-seq to identify and develop a prognostic signature related to colorectal cancer stem cells. Sci Rep 2024; 14:12270. [PMID: 38806611 PMCID: PMC11133358 DOI: 10.1038/s41598-024-62913-3] [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: 01/08/2024] [Accepted: 05/22/2024] [Indexed: 05/30/2024] Open
Abstract
The prognosis for patients with colorectal cancer (CRC) remains worse than expected due to metastasis, recurrence, and resistance to chemotherapy. Colorectal cancer stem cells (CRCSCs) play a vital role in tumor metastasis, recurrence, and chemotherapy resistance. However, there are currently no prognostic markers based on CRCSCs-related genes available for clinical use. In this study, single-cell transcriptome sequencing was employed to distinguish cancer stem cells (CSCs) in the CRC microenvironment and analyze their properties at the single-cell level. Subsequently, data from TCGA and GEO databases were utilized to develop a prognostic risk model for CRCSCs-related genes and validate its diagnostic performance. Additionally, functional enrichment, immune response, and chemotherapeutic drug sensitivity of the relevant genes in the risk model were investigated. Lastly, the key gene RPS17 in the risk model was identified as a potential prognostic marker and therapeutic target for further comprehensive studies. Our findings provide new insights into the prognostic treatment of CRC and offer novel perspectives for a systematic and comprehensive understanding of CRC development.
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Affiliation(s)
- Jiale Wu
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Wanyu Li
- Well Lead Medical Co., Ltd., Guangzhou, 511434, Guangdong, China
| | - Junyu Su
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Jiamin Zheng
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Yanwen Liang
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Jiansuo Lin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangdong Medical University, Dongguan, 523808, Guangdong, China
| | - Bilian Xu
- School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China.
| | - Yi Liu
- School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China.
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10
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Tang X, Wu Q, Shang L, Liu K, Ge Y, Liang P, Li B. Raman cell sorting for single-cell research. Front Bioeng Biotechnol 2024; 12:1389143. [PMID: 38832129 PMCID: PMC11145634 DOI: 10.3389/fbioe.2024.1389143] [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: 02/21/2024] [Accepted: 04/08/2024] [Indexed: 06/05/2024] Open
Abstract
Cells constitute the fundamental units of living organisms. Investigating individual differences at the single-cell level facilitates an understanding of cell differentiation, development, gene expression, and cellular characteristics, unveiling the underlying laws governing life activities in depth. In recent years, the integration of single-cell manipulation and recognition technologies into detection and sorting systems has emerged as a powerful tool for advancing single-cell research. Raman cell sorting technology has garnered attention owing to its non-labeling, non-destructive detection features and the capability to analyze samples containing water. In addition, this technology can provide live cells for subsequent genomics analysis and gene sequencing. This paper emphasizes the importance of single-cell research, describes the single-cell research methods that currently exist, including single-cell manipulation and single-cell identification techniques, and highlights the advantages of Raman spectroscopy in the field of single-cell analysis by comparing it with the fluorescence-activated cell sorting (FACS) technique. It describes various existing Raman cell sorting techniques and introduces their respective advantages and disadvantages. The above techniques were compared and analyzed, considering a variety of factors. The current bottlenecks include weak single-cell spontaneous Raman signals and the requirement for a prolonged total cell exposure time, significantly constraining Raman cell sorting technology's detection speed, efficiency, and throughput. This paper provides an overview of current methods for enhancing weak spontaneous Raman signals and their associated advantages and disadvantages. Finally, the paper outlines the detailed information related to the Raman cell sorting technology mentioned in this paper and discusses the development trends and direction of Raman cell sorting.
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Affiliation(s)
- Xusheng Tang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Chinese Academy of Sciences, State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qingyi Wu
- Key Laboratory of Optical System Advanced Manufacturing Technology, Chinese Academy of Sciences, State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lindong Shang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Chinese Academy of Sciences, State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kunxiang Liu
- Key Laboratory of Optical System Advanced Manufacturing Technology, Chinese Academy of Sciences, State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Ge
- Key Laboratory of Optical System Advanced Manufacturing Technology, Chinese Academy of Sciences, State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Liang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Chinese Academy of Sciences, State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
- Hooke Instruments Ltd., Changchun, China
| | - Bei Li
- Key Laboratory of Optical System Advanced Manufacturing Technology, Chinese Academy of Sciences, State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
- Hooke Instruments Ltd., Changchun, China
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Auxillos J, Crouigneau R, Li YF, Dai Y, Stigliani A, Tavernaro I, Resch-Genger U, Sandelin A, Marie R, Pedersen SF. Spatially resolved analysis of microenvironmental gradient impact on cancer cell phenotypes. SCIENCE ADVANCES 2024; 10:eadn3448. [PMID: 38701211 PMCID: PMC11068013 DOI: 10.1126/sciadv.adn3448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/02/2024] [Indexed: 05/05/2024]
Abstract
Despite the physiological and pathophysiological significance of microenvironmental gradients, e.g., for diseases such as cancer, tools for generating such gradients and analyzing their impact are lacking. Here, we present an integrated microfluidic-based workflow that mimics extracellular pH gradients characteristic of solid tumors while enabling high-resolution live imaging of, e.g., cell motility and chemotaxis, and preserving the capacity to capture the spatial transcriptome. Our microfluidic device generates a pH gradient that can be rapidly controlled to mimic spatiotemporal microenvironmental changes over cancer cells embedded in a 3D matrix. The device can be reopened allowing immunofluorescence analysis of selected phenotypes, as well as the transfer of cells and matrix to a Visium slide for spatially resolved analysis of transcriptional changes across the pH gradient. This workflow is easily adaptable to other gradients and multiple cell types and can therefore prove invaluable for integrated analysis of roles of microenvironmental gradients in biology.
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Affiliation(s)
- Jamie Auxillos
- Section for Computational and RNA biology, Department of Biology, University of Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Denmark
| | - Roxane Crouigneau
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Denmark
| | - Yan-Fang Li
- Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Yifan Dai
- Section for Computational and RNA biology, Department of Biology, University of Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Denmark
| | - Arnaud Stigliani
- Section for Computational and RNA biology, Department of Biology, University of Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Denmark
| | - Isabella Tavernaro
- Division Biophotonics, Bundesanstalt für Materialforschung und -prüfung, Richard-Willstaetter Str. 11, 12489, Berlin, Germany
| | - Ute Resch-Genger
- Division Biophotonics, Bundesanstalt für Materialforschung und -prüfung, Richard-Willstaetter Str. 11, 12489, Berlin, Germany
| | - Albin Sandelin
- Section for Computational and RNA biology, Department of Biology, University of Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Denmark
| | - Rodolphe Marie
- Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Stine F. Pedersen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Denmark
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Chen Q, Luo J, Liu J, Yu H, Zhou M, Yu L, Chen Y, Zhang S, Mo Z. Integrating single-cell and spatial transcriptomics to elucidate the crosstalk between cancer-associated fibroblasts and cancer cells in hepatocellular carcinoma with spleen-deficiency syndrome. J Tradit Complement Med 2024; 14:321-334. [PMID: 38707923 PMCID: PMC11068993 DOI: 10.1016/j.jtcme.2023.11.008] [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: 04/11/2023] [Revised: 09/24/2023] [Accepted: 11/20/2023] [Indexed: 05/07/2024] Open
Abstract
Background and aim Most patients with hepatocellular carcinoma (HCC) in China have been diagnosed with spleen deficiency syndrome (SDS), which accelerates the progression of HCC by disrupting the tumor microenvironment homeostasis. This study aimed to investigate the intercellular crosstalk in HCC with SDS. Experimental procedure An HCC-SDS mouse model was established using orthotopic HCC transplantation based on reserpine-induced SDS. Single-cell data analysis and cancer cell prediction were conducted using Seurat and CopyKAT package, respectively. Intercellular interactions were explored using CellPhoneDB and CellChat and subsequently validated using co-culture assays, ELISA and histological staining. We performed pathway activity analysis using gene set variation analysis and the Seurat package. The extracellular matrix (ECM) remodeling was assessed using a gel contraction assay, atomic force microscopy, and Sirius red staining. The deconvolution of the spatial transcriptomics data using the "CARD" package based on single-cell data. Results and conclusion We successfully established the HCC-SDS mouse model. Twenty-nine clusters were identified. The interactions between cancer cells and cancer-associated fibroblasts (CAFs) were significantly enhanced via platelet-derived growth factor (PDGF) signaling in HCC-SDS. CAFs recruited in HCC-SDS lead to ECM remodeling and the activation of TGF-β signaling pathway. Deconvolution of the spatial transcriptome data revealed that CAFs physically surround cancer cells in HCC-SDS. This study reveals that the crosstalk of CAFs-cancer cells is crucial for the tumor-promoting effect of SDS. CAFs recruited by HCC via PDGFA may lead to ECM remodeling through activation of the TGF-β pathway, thereby forming a physical barrier to block immune cell infiltration under SDS.
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Affiliation(s)
- Qiuxia Chen
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, 510080, China
| | - Jin Luo
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, 510080, China
| | - Jiahui Liu
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, 510080, China
| | - He Yu
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, 510080, China
| | - Meiling Zhou
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, 510080, China
| | - Ling Yu
- Department of Critical Care Medicine, The Second Clinical College to Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Yan Chen
- Department of Traditional Chinese Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, 510630, China
| | - Shijun Zhang
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, 510080, China
| | - Zhuomao Mo
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang Province, 311113, China
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Zhou H, Shen Y, Zheng G, Zhang B, Wang A, Zhang J, Hu H, Lin J, Liu S, Luan X, Zhang W. Integrating single-cell and spatial analysis reveals MUC1-mediated cellular crosstalk in mucinous colorectal adenocarcinoma. Clin Transl Med 2024; 14:e1701. [PMID: 38778448 PMCID: PMC11111627 DOI: 10.1002/ctm2.1701] [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: 11/28/2023] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Mucinous colorectal adenocarcinoma (MCA) is a distinct subtype of colorectal cancer (CRC) with the most aggressive pattern, but effective treatment of MCA remains a challenge due to its vague pathological characteristics. An in-depth understanding of transcriptional dynamics at the cellular level is critical for developing specialised MCA treatment strategies. METHODS We integrated single-cell RNA sequencing and spatial transcriptomics data to systematically profile the MCA tumor microenvironment (TME), particularly the interactome of stromal and immune cells. In addition, a three-dimensional bioprinting technique, canonical ex vivo co-culture system, and immunofluorescence staining were further applied to validate the cellular communication networks within the TME. RESULTS This study identified the crucial intercellular interactions that engaged in MCA pathogenesis. We found the increased infiltration of FGF7+/THBS1+ myofibroblasts in MCA tissues with decreased expression of genes associated with leukocyte-mediated immunity and T cell activation, suggesting a crucial role of these cells in regulating the immunosuppressive TME. In addition, MS4A4A+ macrophages that exhibit M2-phenotype were enriched in the tumoral niche and high expression of MS4A4A+ was associated with poor prognosis in the cohort data. The ligand-receptor-based intercellular communication analysis revealed the tight interaction of MUC1+ malignant cells and ZEB1+ endothelial cells, providing mechanistic information for MCA angiogenesis and molecular targets for subsequent translational applications. CONCLUSIONS Our study provides novel insights into communications among tumour cells with stromal and immune cells that are significantly enriched in the TME during MCA progression, presenting potential prognostic biomarkers and therapeutic strategies for MCA. KEY POINTS Tumour microenvironment profiling of MCA is developed. MUC1+ tumour cells interplay with FGF7+/THBS1+ myofibroblasts to promote MCA development. MS4A4A+ macrophages exhibit M2 phenotype in MCA. ZEB1+ endotheliocytes engage in EndMT process in MCA.
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Affiliation(s)
- Haiyang Zhou
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
- Department of Colorectal SurgeryChangzheng HospitalNaval Medical UniversityShanghaiChina
| | - Yiwen Shen
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Guangyong Zheng
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Beibei Zhang
- Department of DermatologyTongren HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Anqi Wang
- Department of Colorectal SurgeryChangzheng HospitalNaval Medical UniversityShanghaiChina
| | - Jing Zhang
- Department of PathologyChangzheng HospitalNaval Medical UniversityShanghaiChina
| | - Hao Hu
- Department of PathologyChanghai HospitalNaval Medical UniversityShanghaiChina
| | - Jiayi Lin
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Sanhong Liu
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Xin Luan
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Weidong Zhang
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- School of PharmacyNaval Medical UniversityShanghaiChina
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14
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He Y, Qi W, Xie X, Jiang H. Identification and validation of a novel predictive signature based on hepatocyte-specific genes in hepatocellular carcinoma by integrated analysis of single-cell and bulk RNA sequencing. BMC Med Genomics 2024; 17:103. [PMID: 38654290 DOI: 10.1186/s12920-024-01871-1] [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: 09/12/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma represents a significant global burden in terms of cancer-related mortality, posing a substantial risk to human health. Despite the availability of various treatment modalities, the overall survival rates for patients with hepatocellular carcinoma remain suboptimal. The objective of this study was to explore the potential of novel biomarkers and to establish a novel predictive signature utilizing multiple transcriptome profiles. METHODS The GSE115469 and CNP0000650 cohorts were utilized for single cell analysis and gene identification. The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) datasets were utilized in the development and evaluation of a predictive signature. The expressions of hepatocyte-specific genes were further validated using the GSE135631 cohort. Furthermore, immune infiltration results, immunotherapy response prediction, somatic mutation frequency, tumor mutation burden, and anticancer drug sensitivity were analyzed based on various risk scores. Subsequently, functional enrichment analysis was performed on the differential genes identified in the risk model. Moreover, we investigated the expression of particular genes in chronic liver diseases utilizing datasets GSE135251 and GSE142530. RESULTS Our findings revealed hepatocyte-specific genes (ADH4, LCAT) with notable alterations during cell maturation and differentiation, leading to the development of a novel predictive signature. The analysis demonstrated the efficacy of the model in predicting outcomes, as evidenced by higher risk scores and poorer prognoses in the high-risk group. Additionally, a nomogram was devised to forecast the survival rates of patients at 1, 3, and 5 years. Our study demonstrated that the predictive model may play a role in modulating the immune microenvironment and impacting the anti-tumor immune response in hepatocellular carcinoma. The high-risk group exhibited a higher frequency of mutations and was more likely to benefit from immunotherapy as a treatment option. Additionally, we confirmed that the downregulation of hepatocyte-specific genes may indicate the progression of hepatocellular carcinoma and aid in the early diagnosis of the disease. CONCLUSION Our research findings indicate that ADH4 and LCAT are genes that undergo significant changes during the differentiation of hepatocytes into cancer cells. Additionally, we have created a unique predictive signature based on genes specific to hepatocytes.
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Affiliation(s)
- Yujian He
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, Shijiazhuang, Hebei, China
| | - Wei Qi
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, Shijiazhuang, Hebei, China
| | - Xiaoli Xie
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, Shijiazhuang, Hebei, China
| | - Huiqing Jiang
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Hebei Key Laboratory of Gastroenterology, Hebei Institute of Gastroenterology, Hebei Clinical Research Center for Digestive Diseases, Shijiazhuang, Hebei, China.
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15
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Ci Y, Zhang Y, Zhang X. Methylated lncRNAs suppress apoptosis of gastric cancer stem cells via the lncRNA-miRNA/protein axis. Cell Mol Biol Lett 2024; 29:51. [PMID: 38600465 PMCID: PMC11005211 DOI: 10.1186/s11658-024-00568-8] [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: 11/21/2023] [Accepted: 03/28/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) play essential roles in the tumorigenesis of gastric cancer. However, the influence of lncRNA methylation on gastric cancer stem cells (GCSCs) remains unclear. METHODS The N6-methyladenosine (m6A) levels of lncRNAs in gastric cancer stem cells were detected by methylated RNA immunoprecipitation sequencing (MeRIP-seq), and the results were validated by MeRIP-quantitative polymerase chain reaction (qPCR). Specific sites of m6A modification on lncRNAs were detected by single-base elongation- and ligation-based qPCR amplification (SELECT). By constructing and transfecting the plasmid expressing methyltransferase-like 3 (METTL3) fused with catalytically inactivated Cas13 (dCas13b) and guide RNA targeting specific methylation sites of lncRNAs, we obtained gastric cancer stem cells with site-specific methylation of lncRNAs. Reverse transcription (RT)-qPCR and Western blot were used for detecting the stemness of treated gastric cancer stem cells. RESULTS The site-specific methylation of PSMA3-AS1 and MIR22HG suppressed apoptosis and promoted stemness of GCSCs. LncRNA methylation enhanced the stability of PSMA3-AS1 and MIR22HG to suppress apoptosis of GCSCs via the PSMA3-AS1-miR-411-3p- or MIR22HG-miR-24-3p-SERTAD1 axis. Simultaneously, the methylated lncRNAs promoted the interaction between PSMA3-AS1 and the EEF1A1 protein or MIR22HG and the LRPPRC protein, stabilizing the proteins and leading to the suppression of apoptosis. The in vivo data revealed that the methylated PSMA3-AS1 and MIR22HG triggered tumorigenesis of GCSCs. CONCLUSIONS Our study revealed the requirement for site-specific methylation of lncRNAs in the tumorigenesis of GCSCs, contributing novel insights into cancer development.
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Affiliation(s)
- Yuan Ci
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao), Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Yuan Zhang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao), Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xiaobo Zhang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao), Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou, 310058, People's Republic of China.
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16
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Yang S, Wang Y, Jia J, Fang Y, Yang Y, Yuan W, Hu J. Advances in Engineered Macrophages: A New Frontier in Cancer Immunotherapy. Cell Death Dis 2024; 15:238. [PMID: 38561367 PMCID: PMC10985090 DOI: 10.1038/s41419-024-06616-7] [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: 12/29/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
Macrophages, as pivotal cells within the tumour microenvironment, significantly influence the impact of and reactions to treatments for solid tumours. The rapid evolution of bioengineering technology has revealed the vast potential of engineered macrophages in immunotherapy, disease diagnosis, and tissue engineering. Given this landscape, the goal of harnessing and innovating macrophages as a novel strategy for solid tumour immunotherapy cannot be overstated. The diverse strategies for engineered macrophages in the realm of cancer immunotherapy, encompassing macrophage drug delivery systems, chimeric antigen receptor macrophage therapy, and synergistic treatment approaches involving bacterial outer membrane vesicles and macrophages, are meticulously examined in this review. These methodologies are designed to enhance the therapeutic efficacy of macrophages against solid tumours, particularly those that are drug-resistant and metastatic. Collectively, these immunotherapies are poised to supplement and refine current solid tumour treatment paradigms, thus heralding a new frontier in the fight against malignant tumours.
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Affiliation(s)
- Shuaixi Yang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, 450000, China
| | - Yuhang Wang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, 450000, China
| | - Jiachi Jia
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, 450000, China
| | - Yingshuai Fang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, 450000, China
| | - Yabing Yang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, 450000, China
| | - Weitang Yuan
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, 450000, China.
| | - Junhong Hu
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, 450000, China.
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Weng KQ, Liu JY, Li H, She LL, Qiu JL, Qi H, Qi HY, Li YS, Dai YB. Identification of Treg-related prognostic molecular subtypes and individualized characteristics in clear cell renal cell carcinoma through single-cell transcriptomes and bulk RNA sequencing. Int Immunopharmacol 2024; 130:111746. [PMID: 38442575 DOI: 10.1016/j.intimp.2024.111746] [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: 01/03/2024] [Accepted: 02/20/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND In clear cell renal cell carcinoma (ccRCC), the role of Regulatory T cells (Treg cells) as prognostic and immunotherapy response predictors is not fully explored. METHODS Analyzing renal clear cell carcinoma datasets from TISCH, TCGA, and GEO, we focused on 8 prognostic Treg genes to study patient subtypes in ccRCC. We assessed Treg subtypes in relation to patient prognosis, tumor microenvironment, metabolism. Using Cox regression and principal component analysis, we devised Treg scores for individual patient characterization and explored the molecular role of C1QL1, a critical gene in the Treg model, through in vivo and in vitro studies. RESULTS Eight Treg-associated prognostic genes were identified, classifying ccRCC patients into cluster A and B. Cluster A patients showed poorer prognosis with distinct clinical and molecular profiles, potentially benefiting more from immunotherapy. Low Treg scores correlated with worse outcomes and clinical progression. Low scores also suggested that patients might respond better to immunotherapy and targeted therapies. In ccRCC, C1QL1 knockdown reduced tumor proliferation and invasion via NF-kb-EMT pathways and decreased Treg cell infiltration, enhancing immune efficacy. CONCLUSIONS The molecular subtype and Treg score in ccRCC, based on Treg cell marker genes, are crucial in personalizing ccRCC treatment and underscore C1QL1's potential as a tumor biomarker and target for immunotherapy.
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Affiliation(s)
- Kang Qiang Weng
- Department of Urology, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong, China.
| | - Jin Yu Liu
- The Affiliated Hospital of Putian University, 999 DongZhen East Rd, Putian 351100, Fujian, China.
| | - Hu Li
- Department of Urology, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong, China.
| | - Lin Lu She
- Department of Urology, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong, China.
| | - Jun Liang Qiu
- Department of Urology, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong, China.
| | - Hao Qi
- Department of Urology, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong, China.
| | - Hui Yue Qi
- Department of Urology, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong, China.
| | - Yong Sheng Li
- Department of Urology, Fujian Province, Fujian Medical University Union Hospital, Gulou District, 29 Xin-quan Road, Fuzhou, China.
| | - Ying Bo Dai
- Department of Urology, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong, China.
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Li Y, Jiang B, Chen B, Zou Y, Wang Y, Liu Q, Song B, Yu B. Integrative analysis of bulk and single-cell RNA-seq reveals the molecular characterization of the immune microenvironment and oxidative stress signature in melanoma. Heliyon 2024; 10:e28244. [PMID: 38560689 PMCID: PMC10979206 DOI: 10.1016/j.heliyon.2024.e28244] [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: 09/30/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
Background The immune microenvironment and oxidative stress of melanoma show significant heterogeneity, which affects tumor growth, invasion and treatment response. Single-cell and bulk RNA-seq data were used to explore the heterogeneity of the immune microenvironment and oxidative stress of melanoma. Methods The R package Seurat facilitated the analysis of the single-cell dataset, while Harmony, another R package, was employed for batch effect correction. Cell types were classified using Uniform Manifold Approximation and Projection (UMAP). The Secreted Signaling algorithm from CellChatDB.human was applied to elucidate cell-to-cell communication patterns within the single-cell data. Consensus clustering analysis for the skin cutaneous melanoma (SKCM) samples was executed with the R package ConsensusClusterPlus. To quantify immune infiltrating cells, we utilized CIBERSORT, ESTIMATE, and TIMERxCell algorithms provided by the R package Immuno-Oncology Biological Research (IOBR). Single nucleotide variant (SNV) analysis was conducted using Maftools, an R package specifically designed for this purpose. Subsequently, the expression levels of PXDN and PAPSS2 genes were assessed in melanoma tissues compared to adjacent normal tissues. Furthermore, in vitro experiments were conducted to evaluate the proliferation and reactive oxygen species expression in melanoma cells following transfection with siRNA targeting PXDN and PAPSS2. Results Malignant tumor cell populations were reclassified based on a comprehensive single-cell dataset analysis, which yielded six distinct tumor subsets. The specific marker genes identified for these subgroups were then used to interrogate the Cancer Genome Atlas Skin Cutaneous Melanoma (TCGA-SKCM) cohort, derived from bulk RNA sequencing data, resulting in the delineation of two immune molecular subtypes. Notably, patients within the cluster2 (C2) subtype exhibited a significantly more favorable prognosis compared to those in the cluster1 (C1) subtype. An alignment of immune characteristics was observed between the C2 subtype and unique immune functional tumor cell subsets. Genes differentially expressed across these subtypes were subsequently leveraged to construct a predictive risk model. In vitro investigations further revealed elevated expression levels of PXDN and PAPSS2 in melanoma tissue samples. Functional assays indicated that modulation of PXDN and PAPSS2 expression could influence the production of reactive oxygen species (ROS) and the proliferative capacity of melanoma cells. Conclusion The constructed six-gene signature can be used as an immune response and an oxidative stress marker to guide the clinical diagnosis and treatment of melanoma.
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Affiliation(s)
- Yaling Li
- Department of Dermatology, Institute of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
- Institute of Biomedical and Health Engineering, Shen Zhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen, 518055, Guangdong, China
- Department of Dermatology, the First Hospital of China Medical University, Shenyang, 110001, Liaoning, China
| | - Bin Jiang
- Department of Dermatology, Institute of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
| | - Bancheng Chen
- Department of Dermatology, Institute of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
| | - Yanfen Zou
- Department of Dermatology, Institute of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
| | - Yan Wang
- Institute of Biomedical and Health Engineering, Shen Zhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen, 518055, Guangdong, China
| | - Qian Liu
- Institute of Biomedical and Health Engineering, Shen Zhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen, 518055, Guangdong, China
| | - Bing Song
- Institute of Biomedical and Health Engineering, Shen Zhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen, 518055, Guangdong, China
- Department of Dermatology, the First Hospital of China Medical University, Shenyang, 110001, Liaoning, China
| | - Bo Yu
- Department of Dermatology, Institute of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
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Busarello E, Biancon G, Lauria F, Ibnat Z, Ramirez C, Tomè G, Aass KR, VanOudenhove J, Standal T, Viero G, Halene S, Tebaldi T. Interpreting single-cell messages in normal and aberrant hematopoiesis with the Cell Marker Accordion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584053. [PMID: 38559181 PMCID: PMC10979856 DOI: 10.1101/2024.03.08.584053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Single-cell technologies offer a unique opportunity to explore cellular heterogeneity in hematopoiesis, reveal malignant hematopoietic cells with clinically significant features and measure gene signatures linked to pathological pathways. However, reliable identification of cell types is a crucial bottleneck in single-cell analysis. Available databases contain dissimilar nomenclature and non-concurrent marker sets, leading to inconsistent annotations and poor interpretability. Furthermore, current tools focus mostly on physiological cell types, lacking extensive applicability in disease. We developed the Cell Marker Accordion, a user-friendly platform for the automatic annotation and biological interpretation of single-cell populations based on consistency weighted markers. We validated our approach on peripheral blood and bone marrow single-cell datasets, using surface markers and expert-based annotation as the ground truth. In all cases, we significantly improved the accuracy in identifying cell types with respect to any single source database. Moreover, the Cell Marker Accordion can identify disease-critical cells and pathological processes, extracting potential biomarkers in a wide variety of contexts in human and murine single-cell datasets. It characterizes leukemia stem cell subtypes, including therapy-resistant cells in acute myeloid leukemia patients; it identifies malignant plasma cells in multiple myeloma samples; it dissects cell type alterations in splicing factor-mutant cells from myelodysplastic syndrome patients; it discovers activation of innate immunity pathways in bone marrow from mice treated with METTL3 inhibitors. The breadth of these applications elevates the Cell Marker Accordion as a flexible, faithful and standardized tool to annotate and interpret hematopoietic populations in single-cell datasets focused on the study of hematopoietic development and disease.
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Affiliation(s)
- Emma Busarello
- Laboratory of RNA and Disease Data Science, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Italy
| | - Zuhairia Ibnat
- Laboratory of RNA and Disease Data Science, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Christian Ramirez
- Laboratory of RNA and Disease Data Science, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Gabriele Tomè
- Laboratory of RNA and Disease Data Science, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Institute of Biophysics, CNR Unit at Trento, Italy
| | - Kristin R Aass
- Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jennifer VanOudenhove
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Therese Standal
- Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Toma Tebaldi
- Laboratory of RNA and Disease Data Science, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
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20
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Zhao K, Li Q, Li P, Liu T, Liu X, Zhu F, Zhang L. Single-cell transcriptome sequencing provides insight into multiple chemotherapy resistance in a patient with refractory DLBCL: a case report. Front Immunol 2024; 15:1303310. [PMID: 38533514 PMCID: PMC10963401 DOI: 10.3389/fimmu.2024.1303310] [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: 09/27/2023] [Accepted: 02/21/2024] [Indexed: 03/28/2024] Open
Abstract
Relapsed and refractory diffuse large B-cell lymphoma (DLBCL) is associated with poor prognosis. As such, a comprehensive analysis of intratumoral components, intratumoral heterogeneity, and the immune microenvironment is essential to elucidate the mechanisms driving the progression of DLBCL and to develop new therapeutics. Here, we used single-cell transcriptome sequencing and conventional bulk next-generation sequencing (NGS) to understand the composite tumor landscape of a single patient who had experienced multiple tumor recurrences following several chemotherapy treatments. NGS revealed several key somatic mutations that are known to contribute to drug resistance. Based on gene expression profiles at the single-cell level, we identified four clusters of malignant B cells with distinct transcriptional signatures, showing high intra-tumoral heterogeneity. Among them, heterogeneity was reflected in activating several key pathways, human leukocyte antigen (HLA)-related molecules' expression, and key oncogenes, which may lead to multi-drug resistance. In addition, FOXP3+ regulatory CD4+ T cells and exhausted cytotoxic CD8+ T cells were identified, accounted for a significant proportion, and showed highly immunosuppressive properties. Finally, cell communication analysis indicated complex interactions between malignant B cells and T cells. In conclusion, this case report demonstrates the value of single-cell RNA sequencing for visualizing the tumor microenvironment and identifying potential therapeutic targets in a patient with treatment-refractory DLBCL. The combination of NGS and single-cell RNA sequencing may facilitate clinical decision-making and drug selection in challenging DLBCL cases.
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Affiliation(s)
| | | | | | | | | | | | - Liling Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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21
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Christ SM, Pohl K, Willmann J, Heesen P, Heusel A, Ahmadsei M, Kühnis A, Vlaskou Badra E, Muehlematter UJ, Mayinger M, Balermpas P, Andratschke N, Zaorsky N, Huellner M, Guckenberger M. Patterns of metastatic spread and tumor burden in unselected cancer patients using PET imaging: Implications for the oligometastatic spectrum theory. Clin Transl Radiat Oncol 2024; 45:100724. [PMID: 38288311 PMCID: PMC10823052 DOI: 10.1016/j.ctro.2024.100724] [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: 07/22/2023] [Revised: 12/08/2023] [Accepted: 01/07/2024] [Indexed: 01/31/2024] Open
Abstract
Introduction and background Metastatic disease has been proposed as a continuum, with no clear cut-off between oligometastatic and polymetastatic disease. This study aims to quantify tumor burden and patterns of spread in unselected metastatic cancer patients referred for PET-based staging, response assessment of restaging. Materials and methods All oncological fluorodeoxyglucose (FDG-) and prostate-specific membrane antigen (PSMA-) positron emission tomography (PET) scans conducted at a single academic center in 2020 were analyzed. Imaging reports of all patients with metastatic disease were reviewed and assessed. Results For this study, 7,000 PET scans were screened. One third of PET scans (n = 1,754; 33 %) from 1,155 unique patients showed presence of metastatic disease from solid malignancies, of which 601 (52 %) and 554 (48 %) were classified as oligometastatic (maximum 5 metastases) and polymetastatic (>5 metastases), respectively. Lung and pleural cancer, skin cancer, and breast cancer were the most common primary tumor histologies with 132 (23.8 %), 88 (15.9 %), and 72 (13.0 %) cases, respectively. Analysis of the number of distant metastases showed a strong bimodal distribution of the metastatic burden with 26 % of patients having one solitary metastasis and 43 % of patients harboring >10 metastases. Yet, despite 43 % of polymetastatic patients having >10 distant metastases, their pattern of distribution was restricted to one or two organs in about two thirds of patients, and there was no association between the number of distant metastases and the number of involved organs. Conclusion The majority of metastatic cancer patients are characterized by either a solitary metastasis or a high tumor burden with >10 metastases, the latter was often associated with affecting a limited number of organs. These findings support both the spectrum theory of metastasis and the seed and soil hypothesis and can support in designing the next generation of clinical trials in the field of oligometastatic disease.
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Affiliation(s)
- Sebastian M. Christ
- Department of Radiation Oncology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Kaspar Pohl
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Jonas Willmann
- Department of Radiation Oncology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center for Proton Therapy, Paul Scherrer Institute, ETH Domain, Villigen, Switzerland
| | - Philip Heesen
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Astrid Heusel
- Department of Radiation Oncology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Maiwand Ahmadsei
- Department of Radiation Oncology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Anja Kühnis
- Department of Radiation Oncology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Eugenia Vlaskou Badra
- Department of Radiation Oncology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Urs J. Muehlematter
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michael Mayinger
- Department of Radiation Oncology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Panagiotis Balermpas
- Department of Radiation Oncology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Nicolaus Andratschke
- Department of Radiation Oncology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Nicholas Zaorsky
- Department of Radiation Oncology, University Hospitals Seidman Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Martin Huellner
- Department of Nuclear Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Matthias Guckenberger
- Department of Radiation Oncology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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22
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You Y, Chen Z, Hu WW. The role of microglia heterogeneity in synaptic plasticity and brain disorders: Will sequencing shed light on the discovery of new therapeutic targets? Pharmacol Ther 2024; 255:108606. [PMID: 38346477 DOI: 10.1016/j.pharmthera.2024.108606] [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: 10/31/2023] [Revised: 01/05/2024] [Accepted: 02/02/2024] [Indexed: 02/18/2024]
Abstract
Microglia play a crucial role in interacting with neuronal synapses and modulating synaptic plasticity. This function is particularly significant during postnatal development, as microglia are responsible for removing excessive synapses to prevent neurodevelopmental deficits. Dysregulation of microglial synaptic function has been well-documented in various pathological conditions, notably Alzheimer's disease and multiple sclerosis. The recent application of RNA sequencing has provided a powerful and unbiased means to decipher spatial and temporal microglial heterogeneity. By identifying microglia with varying gene expression profiles, researchers have defined multiple subgroups of microglia associated with specific pathological states, including disease-associated microglia, interferon-responsive microglia, proliferating microglia, and inflamed microglia in multiple sclerosis, among others. However, the functional roles of these distinct subgroups remain inadequately characterized. This review aims to refine our current understanding of the potential roles of heterogeneous microglia in regulating synaptic plasticity and their implications for various brain disorders, drawing from recent sequencing research and functional studies. This knowledge may aid in the identification of pathogenetic biomarkers and potential factors contributing to pathogenesis, shedding new light on the discovery of novel drug targets. The field of sequencing-based data mining is evolving toward a multi-omics approach. With advances in viral tools for precise microglial regulation and the development of brain organoid models, we are poised to elucidate the functional roles of microglial subgroups detected through sequencing analysis, ultimately identifying valuable therapeutic targets.
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Affiliation(s)
- Yi You
- Department of Pharmacology and Department of Pharmacy of the Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhong Chen
- Department of Pharmacology and Department of Pharmacy of the Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China; Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Wei-Wei Hu
- Department of Pharmacology and Department of Pharmacy of the Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou 310058, China.
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23
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Chen JP, Diekmann C, Wu H, Chen C, Della Chiara G, Berrino E, Georgiadis KL, Bouwman BAM, Virdi M, Harbers L, Bellomo SE, Marchiò C, Bienko M, Crosetto N. scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells. Nat Commun 2024; 15:1768. [PMID: 38409079 PMCID: PMC10897160 DOI: 10.1038/s41467-024-45972-y] [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: 03/07/2023] [Accepted: 02/08/2024] [Indexed: 02/28/2024] Open
Abstract
Extrachromosomal circular DNAs (eccDNAs) have emerged as important intra-cellular mobile genetic elements that affect gene copy number and exert in trans regulatory roles within the cell nucleus. Here, we describe scCircle-seq, a method for profiling eccDNAs and unraveling their diversity and complexity in single cells. We implement and validate scCircle-seq in normal and cancer cell lines, demonstrating that most eccDNAs vary largely between cells and are stochastically inherited during cell division, although their genomic landscape is cell type-specific and can be used to accurately cluster cells of the same origin. eccDNAs are preferentially produced from chromatin regions enriched in H3K9me3 and H3K27me3 histone marks and are induced during replication stress conditions. Concomitant sequencing of eccDNAs and RNA from the same cell uncovers the absence of correlation between eccDNA copy number and gene expression levels, except for a few oncogenes, including MYC, contained within a large eccDNA in colorectal cancer cells. Lastly, we apply scCircle-seq to one prostate cancer and two breast cancer specimens, revealing cancer-specific eccDNA landscapes and a higher propensity of eccDNAs to form in amplified genomic regions. scCircle-seq is a scalable tool that can be used to dissect the complexity of eccDNAs across different cell and tissue types, and further expands the potential of eccDNAs for cancer diagnostics.
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Affiliation(s)
- Jinxin Phaedo Chen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
| | - Constantin Diekmann
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Honggui Wu
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, PR China
- School of Life Sciences, Peking University, Beijing, PR China
| | - Chong Chen
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | | | - Enrico Berrino
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Konstantinos L Georgiadis
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Britta A M Bouwman
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Mohit Virdi
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy
| | - Luuk Harbers
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Sara Erika Bellomo
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Magda Bienko
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy.
| | - Nicola Crosetto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy.
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24
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Liang Y, Zhong D, Yang Q, Tang Y, Qin Y, Su Y, Huang X, Shang J. Single-Cell RNA Sequencing Revealed That the Enrichment of TPI1 + Malignant Hepatocytes Was Linked to HCC Metastasis and Immunosuppressive Microenvironment. J Hepatocell Carcinoma 2024; 11:373-383. [PMID: 38410699 PMCID: PMC10896104 DOI: 10.2147/jhc.s453249] [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: 12/04/2023] [Accepted: 02/18/2024] [Indexed: 02/28/2024] Open
Abstract
Background Tumor metastasis is the leading cause of high mortality in hepatocellular carcinoma (HCC). The metastasis-related HCC microenvironment is characterized by high heterogeneity. Single-cell RNA sequencing (scRNA-seq) may aid in determining specific cell clusters involved in regulating the immune microenvironment of HCC. Methods The scRNA-seq data of 10 HCC samples were collected from the Gene Expression Omnibus (GEO) database GSE124395. Correlations between key gene expression and clinicopathological data were determined using public databases. HCC tissues and matched tumor-adjacent and normal tissue samples were obtained by surgical resection at Sichuan Cancer Hospital. Immune cell infiltration analysis was performed and verified by immunohistochemistry and immunofluorescent staining. Results Nine malignant hepatocyte clusters with different marker genes and biological functions were identified. C3_Hepatocyte-SERF2 and C6_Hepatocyte-IL13RA2 were mainly involved in the regulation of the immune microenvironment, which was also a significant pathway in regulating HCC metastasis. Key genes in malignant hepatocyte clusters that associated with HCC metastasis were further screened by LASSO regression analysis. TPI1, a key gene in C6_Hepatocyte-IL13RA2 and HCC metastasis, could participate in regulating the HCC immune microenvironment in The Cancer Genome Atlas (TCGA) and Tumor Immune Estimation Resource (TIMER) databases. Moreover, immunohistochemistry analysis demonstrated that TPI1 expression was positively correlated with HCC metastasis and poor prognosis, while negatively correlated with CD8+ T cell infiltration. The negative correlation between TPI1 expression and CD8+ T cell infiltration was further confirmed by immunofluorescence staining. Conclusion In summary, a cluster of TPI1+ malignant hepatocytes was associated with the suppression of CD8+ T cell infiltration and HCC metastasis, providing novel insights into potential biomarkers for immunotherapy in HCC.
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Affiliation(s)
- Yuxin Liang
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Deyuan Zhong
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Qinyan Yang
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Yuan Tang
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Yingying Qin
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau, SAR, People's Republic of China
| | - Yuhao Su
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Xiaolun Huang
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Jin Shang
- Liver Transplantation Center and HBP Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
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25
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Zang D, Dong Z, Liu Y, Chen Q. Single-cell RNA sequencing of anaplastic ependymoma and H3K27M-mutant diffuse midline glioma. BMC Neurol 2024; 24:74. [PMID: 38383423 PMCID: PMC10880286 DOI: 10.1186/s12883-024-03558-7] [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: 07/31/2023] [Accepted: 02/01/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Anaplastic ependymoma and H3K27M-mutant diffuse midline glioma are two common subtypes of brain tumors with poor long-term prognosis. The present study analyzed and compared the differences in cell types between two tumors by single-cell RNA sequencing (scRNA-seq) technology. METHODS ScRNA-seq was performed to profile cells from cancer tissue from anaplastic ependymoma patient and H3K27M-mutant diffuse midline glioma patient. Cell clustering, marker gene identification, cell type annotation, copy number variation analysis and function analysis of differentially expressed genes were then performed. RESULTS A total of 11,219 cells were obtained from anaplastic ependymoma and H3K27M mutant diffuse midline glioma, and these cells categorized into 12 distinct clusters. Each cell cluster could be characterized with specific cell markers to indicate cellular heterogeneity. Five cell types were annotated in each sample, including astrocyte, oligodendrocytes, microglial cell, neural progenitor cell and immune cell. The cluster types and proportion of cell types were not consistent between the two brain tumors. Functional analyses suggest that these cell clusters are involved in tumor-associated pathways, with slight differences in the cells of origin between the two tumors. In addition, cell communication analysis showed that the NRG3-ERBB4 pair is a key Ligand-receptor pair for anaplastic ependymoma, while in H3K27M-mutant diffuse midline glioma it is the PTN-PTPRZ1 pair that establishes contact with other cells. CONCLUSION There was intratumor heterogeneity in anaplastic ependymoma and H3K27M mutant diffuse midline glioma, and that the subtype differences may be due to differences in the origin of the cells.
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Affiliation(s)
- Dongdong Zang
- Department of Neurosurgery, Shenzhen Children's Hospital, 7019 Yitian Road, Futian District, Shenzhen, Guangdong, China
| | - Zilong Dong
- Department of Neurosurgery, Shenzhen Children's Hospital, 7019 Yitian Road, Futian District, Shenzhen, Guangdong, China
| | - Yuecheng Liu
- Department of Neurosurgery, Shenzhen Children's Hospital, 7019 Yitian Road, Futian District, Shenzhen, Guangdong, China
| | - Qian Chen
- Department of Neurosurgery, Shenzhen Children's Hospital, 7019 Yitian Road, Futian District, Shenzhen, Guangdong, China.
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26
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Qin F, Cai G, Amos CI, Xiao F. A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data. Genome Res 2024; 34:85-93. [PMID: 38290978 PMCID: PMC10903939 DOI: 10.1101/gr.278098.123] [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: 05/15/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
The availability of single-cell sequencing (SCS) enables us to assess intra-tumor heterogeneity and identify cellular subclones without the confounding effect of mixed cells. Copy number aberrations (CNAs) have been commonly used to identify subclones in SCS data using various clustering methods, as cells comprising a subpopulation are found to share a genetic profile. However, currently available methods may generate spurious results (e.g., falsely identified variants) in the procedure of CNA detection, thereby diminishing the accuracy of subclone identification within a large, complex cell population. In this study, we developed a subclone clustering method based on a fused lasso model, referred to as FLCNA, which can simultaneously detect CNAs in single-cell DNA sequencing (scDNA-seq) data. Spike-in simulations were conducted to evaluate the clustering and CNA detection performance of FLCNA, benchmarking it against existing copy number estimation methods (SCOPE, HMMcopy) in combination with commonly used clustering methods. Application of FLCNA to a scDNA-seq data set of breast cancer revealed different genomic variation patterns in neoadjuvant chemotherapy-treated samples and pretreated samples. We show that FLCNA is a practical and powerful method for subclone identification and CNA detection with scDNA-seq data.
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Affiliation(s)
- Fei Qin
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Guoshuai Cai
- Department of Environmental Health Science, Arnold School of Public Health, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Christopher I Amos
- Department of Quantitative Sciences, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Feifei Xiao
- Department of Biostatistics, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, Florida 32603, USA
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27
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Tavares V, Marques IS, Melo IGD, Assis J, Pereira D, Medeiros R. Paradigm Shift: A Comprehensive Review of Ovarian Cancer Management in an Era of Advancements. Int J Mol Sci 2024; 25:1845. [PMID: 38339123 PMCID: PMC10856127 DOI: 10.3390/ijms25031845] [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: 12/31/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Ovarian cancer (OC) is the female genital malignancy with the highest lethality. Patients present a poor prognosis mainly due to the late clinical presentation allied with the common acquisition of chemoresistance and a high rate of tumour recurrence. Effective screening, accurate diagnosis, and personalised multidisciplinary treatments are crucial for improving patients' survival and quality of life. This comprehensive narrative review aims to describe the current knowledge on the aetiology, prevention, diagnosis, and treatment of OC, highlighting the latest significant advancements and future directions. Traditionally, OC treatment involves the combination of cytoreductive surgery and platinum-based chemotherapy. Although more therapeutical approaches have been developed, the lack of established predictive biomarkers to guide disease management has led to only marginal improvements in progression-free survival (PFS) while patients face an increasing level of toxicity. Fortunately, because of a better overall understanding of ovarian tumourigenesis and advancements in the disease's (epi)genetic and molecular profiling, a paradigm shift has emerged with the identification of new disease biomarkers and the proposal of targeted therapeutic approaches to postpone disease recurrence and decrease side effects, while increasing patients' survival. Despite this progress, several challenges in disease management, including disease heterogeneity and drug resistance, still need to be overcome.
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Affiliation(s)
- Valéria Tavares
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP), Pathology and Laboratory Medicine Department, Clinical Pathology SV/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Centre (Porto.CCC), 4200-072 Porto, Portugal
- Faculty of Medicine, University of Porto, 4200-072 Porto, Portugal
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar, University of Porto, 4050-313 Porto, Portugal
| | - Inês Soares Marques
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP), Pathology and Laboratory Medicine Department, Clinical Pathology SV/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Centre (Porto.CCC), 4200-072 Porto, Portugal
- Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Inês Guerra de Melo
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP), Pathology and Laboratory Medicine Department, Clinical Pathology SV/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Centre (Porto.CCC), 4200-072 Porto, Portugal
- Faculty of Medicine, University of Porto, 4200-072 Porto, Portugal
| | - Joana Assis
- Clinical Research Unit, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal
| | - Deolinda Pereira
- Oncology Department, Portuguese Institute of Oncology of Porto (IPOP), 4200-072 Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP), Pathology and Laboratory Medicine Department, Clinical Pathology SV/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Centre (Porto.CCC), 4200-072 Porto, Portugal
- Faculty of Medicine, University of Porto, 4200-072 Porto, Portugal
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- Faculty of Health Sciences, Fernando Pessoa University, 4200-150 Porto, Portugal
- Research Department, Portuguese League Against Cancer (NRNorte), 4200-172 Porto, Portugal
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Yan N, Xie W, Wang D, Fang Q, Guo J, Chen Y, Li X, Gong L, Wang J, Guo W, Zhang X, Zhang Y, Gu J, Li C. Single-cell transcriptomic analysis reveals tumor cell heterogeneity and immune microenvironment features of pituitary neuroendocrine tumors. Genome Med 2024; 16:2. [PMID: 38167466 PMCID: PMC10759356 DOI: 10.1186/s13073-023-01267-3] [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: 03/10/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Pituitary neuroendocrine tumors (PitNETs) are one of the most common types of intracranial tumors. Currently, the cellular characteristics of normal pituitary and various other types of PitNETs are still not completely understood. METHODS We performed single-cell RNA sequencing (scRNA-seq) on 4 normal samples and 24 PitNET samples for comprehensive bioinformatics analysis. Findings regarding the function of PBK in the aggressive tumor cells were validated by siRNA knockdown, overexpression, and transwell experiments. RESULTS We first constructed a reference cell atlas of the human pituitary. Subsequent scRNA-seq analysis of PitNET samples, representing major tumor subtypes, shed light on the intrinsic cellular heterogeneities of the tumor cells and tumor microenvironment (TME). We found that the expression of hormone-encoding genes defined the major variations of the PIT1-lineage tumor cell transcriptomic heterogeneities. A sub-population of TPIT-lineage tumor cells highly expressing GZMK suggested a novel subtype of corticotroph tumors. In immune cells, we found two clusters of tumor-associated macrophages, which were both highly enriched in PitNETs but with distinct functional characteristics. In PitNETs, the stress response pathway was significantly activated in T cells. While a majority of these tumors are benign, our study unveils a common existence of aggressive tumor cells in the studied samples, which highly express a set of malignant signature genes. The following functional experiments confirmed the oncogenic role of selected up-regulated genes. The over-expression of PBK could promote both tumor cell proliferation and migration, and it was also significantly associated with poor prognosis in PitNET patients. CONCLUSIONS Our data and analysis manifested the basic cell types in the normal pituitary and inherent heterogeneity of PitNETs, identified several features of the tumor immune microenvironments, and found a novel epithelial cell sub-population with aggressive signatures across all the studied cases.
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Affiliation(s)
- Nan Yan
- MOE Key Laboratory of Bioinformatics, Department of Automation, BNRIST Bioinformatics Division, Tsinghua University, Beijing, 100084, China
| | - Weiyan Xie
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Dongfang Wang
- Biomedical Pioneering Innovative Center, Peking University, Beijing, 100871, China
| | - Qiuyue Fang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Jing Guo
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Yiyuan Chen
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Xinqi Li
- MOE Key Laboratory of Bioinformatics, Department of Automation, BNRIST Bioinformatics Division, Tsinghua University, Beijing, 100084, China
| | - Lei Gong
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Jialin Wang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Wenbo Guo
- MOE Key Laboratory of Bioinformatics, Department of Automation, BNRIST Bioinformatics Division, Tsinghua University, Beijing, 100084, China
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics, Department of Automation, BNRIST Bioinformatics Division, Tsinghua University, Beijing, 100084, China
| | - Yazhuo Zhang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China.
- Department of Neurosurgery, Beijing Tiantan Hospital Affiliated to Capital Medical University, Beijing, 100070, China.
| | - Jin Gu
- MOE Key Laboratory of Bioinformatics, Department of Automation, BNRIST Bioinformatics Division, Tsinghua University, Beijing, 100084, China.
| | - Chuzhong Li
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China.
- Department of Neurosurgery, Beijing Tiantan Hospital Affiliated to Capital Medical University, Beijing, 100070, China.
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Zhang W, Wang J, Huang D, Liu Z, Lu T, Cui C, Li Z. Single-cell sequencing reveals SATB2/NOTCH1 signaling promotes the progression of malignancy of epithelial cells from papillary thyroid cancer. Mol Carcinog 2024; 63:22-33. [PMID: 37877736 DOI: 10.1002/mc.23631] [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: 04/12/2023] [Revised: 08/01/2023] [Accepted: 08/22/2023] [Indexed: 10/26/2023]
Abstract
Although most papillary thyroid cancers (PTCs) are deemed to have a favorable clinical course and outcome, some develop an aggressive biological behavior at diagnosis or during treatment. Single-cell RNA sequencing (scRNA-seq), which is based on quantifying the features of individual cells to resolve tumor tissue heterogeneity, was used to uncover gene regulatory relationships and trace the transcriptional trajectories underlying the malignant transformation. In this study, we performed single-cell sequencing on samples from four PTC patients and one benign thyroid tumor patient. These included two papillary thyroid microcarcinoma cancers (PTMC) patients, two age-matched advanced PTC patients with invading surrounding tissues, and one patient undergoing surgical treatment due to a benign thyroid tumor. We constructed a new PTC RNA spectrum using single-cell sequencing. Single-cell sequencing analysis indicated that there was a highly invasive subgroup in the PTC epithelial cells, the expression of SATB2 (special AT-rich binding protein-2) was related to the prognosis and clinical progress of PTC, and SATB2 could promote the proliferation, migration, and invasion of PTC cells. We found that NOTCH1 was the key target gene of SATB2, and the activation of the SATB2/NOTCH1 pathway was one of the reasons for the high carcinogenicity of this subgroup.
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Affiliation(s)
- Wenqian Zhang
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Shenyang, China
| | - Jing Wang
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Shenyang, China
| | - Dongning Huang
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Shenyang, China
| | - Zhu Liu
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Shenyang, China
| | - Tie Lu
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Shenyang, China
| | - Chen Cui
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Shenyang, China
| | - Zhendong Li
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Shenyang, China
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Guo ZH, Wu Y, Wang S, Zhang Q, Shi JM, Wang YB, Chen ZH. scInterpreter: a knowledge-regularized generative model for interpretably integrating scRNA-seq data. BMC Bioinformatics 2023; 24:481. [PMID: 38104057 PMCID: PMC10724984 DOI: 10.1186/s12859-023-05579-4] [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: 09/29/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND The rapid emergence of single-cell RNA-seq (scRNA-seq) data presents remarkable opportunities for broad investigations through integration analyses. However, most integration models are black boxes that lack interpretability or are hard to train. RESULTS To address the above issues, we propose scInterpreter, a deep learning-based interpretable model. scInterpreter substantially outperforms other state-of-the-art (SOTA) models in multiple benchmark datasets. In addition, scInterpreter is extensible and can integrate and annotate atlas scRNA-seq data. We evaluated the robustness of scInterpreter in a variety of situations. Through comparison experiments, we found that with a knowledge prior, the training process can be significantly accelerated. Finally, we conducted interpretability analysis for each dimension (pathway) of cell representation in the embedding space. CONCLUSIONS The results showed that the cell representations obtained by scInterpreter are full of biological significance. Through weight sorting, we found several new genes related to pathways in PBMC dataset. In general, scInterpreter is an effective and interpretable integration tool. It is expected that scInterpreter will bring great convenience to the study of single-cell transcriptomics.
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Affiliation(s)
- Zhen-Hao Guo
- College of Electronics and Information Engineering, Tongji University, Shanghai, 200000, China
- Department of Clinical Anesthesiology, Faculty of Anesthesiology, Second Military Medical University / Naval Medical University, Shanghai, 200433, China
| | - Yan Wu
- College of Electronics and Information Engineering, Tongji University, Shanghai, 200000, China.
| | - Siguo Wang
- EIT Institute for Advanced Study, Ningbo, 315201, Zhejiang, China
| | - Qinhu Zhang
- EIT Institute for Advanced Study, Ningbo, 315201, Zhejiang, China
- Big Data and Intelligent Computing Research Center, Guangxi Academy of Science, Nanning, 530007, China
| | - Jin-Ming Shi
- Department of Endocrinology, Aviation General Hospital, Beijing, 100000, China
| | - Yan-Bin Wang
- College of Computer Science and Technology, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Zhan-Heng Chen
- Department of Clinical Anesthesiology, Faculty of Anesthesiology, Second Military Medical University / Naval Medical University, Shanghai, 200433, China.
- Big Data and Intelligent Computing Research Center, Guangxi Academy of Science, Nanning, 530007, China.
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Liu F, Zheng J, Yang G, Pan L, Xie Y, Chen S, Tuo J, Su J, Ou X, Liu R. Unraveling the enigma of B cells in diffuse large B-cell lymphoma: unveiling cancer stem cell-like B cell subpopulation at single-cell resolution. Front Immunol 2023; 14:1310292. [PMID: 38149239 PMCID: PMC10750418 DOI: 10.3389/fimmu.2023.1310292] [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: 10/09/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023] Open
Abstract
Background Diffuse large B-cell lymphoma (DLBCL) represents the most prevalent form of aggressive non-Hodgkin lymphoma. Despite receiving standard treatment, a subset of patients undergoes refractory or recurrent cases, wherein the involvement of cancer stem cells (CSCs) could be significant. Methods We comprehensively characterized B cell subpopulations using single-cell RNA sequencing data from three DLBCL samples and one normal lymph tissue. The CopyKat R package was employed to assess the malignancy of B cell subpopulations based on chromosomal copy number variations. CIBERSORTx software was utilized to estimate the proportions of B cell subpopulations in 230 DLBCL tissues. Furthermore, we employed the pySCENIC to identify key transcription factors that regulate the functionality of B cell subpopulations. By employing CellphoneDB, we elucidated the interplay among tumor microenvironment components within the B cell subpopulations. Finally, we validated our findings through immunofluorescence experiments. Results Our analysis revealed a specific cancer stem cell-like B cell subpopulation exhibiting self-renewal and multilineage differentiation capabilities based on the exploration of B cell subpopulations in DLBCL and normal lymph tissues at the single-cell level. Notably, a high infiltration of cancer stem cell-like B cells correlated with a poor prognosis, potentially due to immune evasion mediated by low expression of major histocompatibility complex molecules. Furthermore, we identified key transcription factor regulatory networks regulated by HMGB3, SAP30, and E2F8, which likely played crucial roles in the functional characterization of the cancer stem cell-like B cell subpopulation. The existence of cancer stem cell-like B cells in DLBCL was validated through immunofluorescent staining. Finally, cell communication between B cells and tumor-infiltrating T cell subgroups provided further insights into the functional characterization of the cancer stem cell-like B cell subpopulation. Conclusions Our research provides a systematic description of a specific cancer stem cell-like B cell subpopulation associated with a poor prognosis in DLBCL. This study enhances our understanding of CSCs and identifies potential therapeutic targets for refractory or recurrent DLBCL patients.
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Affiliation(s)
- Fengling Liu
- Department of Hematology, The first Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jie Zheng
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - Gaohui Yang
- Department of Hematology, The first Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Lin Pan
- Department of Hematology, The first Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yanni Xie
- Department of Hematology, The first Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Siyu Chen
- Department of Hematology, The first Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jinwei Tuo
- Department of Hematology, The first Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jinxia Su
- Department of Hematology, The first Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiuyi Ou
- Department of Hematology, The first Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Rongrong Liu
- Department of Hematology, The first Affiliated Hospital of Guangxi Medical University, Nanning, China
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32
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Zhu Q, Zhao X, Zhang Y, Li Y, Liu S, Han J, Sun Z, Wang C, Deng D, Wang S, Tang Y, Huang Y, Jiang S, Tian C, Chen X, Yuan Y, Li Z, Yang T, Lai T, Liu Y, Yang W, Zou X, Zhang M, Cui H, Liu C, Jin X, Hu Y, Chen A, Xu X, Li G, Hou Y, Liu L, Liu S, Fang L, Chen W, Wu L. Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines. Nat Commun 2023; 14:8170. [PMID: 38071219 PMCID: PMC10710513 DOI: 10.1038/s41467-023-43991-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Human cancer cell lines have long served as tools for cancer research and drug discovery, but the presence and the source of intra-cell-line heterogeneity remain elusive. Here, we perform single-cell RNA-sequencing and ATAC-sequencing on 42 and 39 human cell lines, respectively, to illustrate both transcriptomic and epigenetic heterogeneity within individual cell lines. Our data reveal that transcriptomic heterogeneity is frequently observed in cancer cell lines of different tissue origins, often driven by multiple common transcriptional programs. Copy number variation, as well as epigenetic variation and extrachromosomal DNA distribution all contribute to the detected intra-cell-line heterogeneity. Using hypoxia treatment as an example, we demonstrate that transcriptomic heterogeneity could be reshaped by environmental stress. Overall, our study performs single-cell multi-omics of commonly used human cancer cell lines and offers mechanistic insights into the intra-cell-line heterogeneity and its dynamics, which would serve as an important resource for future cancer cell line-based studies.
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Affiliation(s)
- Qionghua Zhu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Xin Zhao
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuanhang Zhang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yanping Li
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Shang Liu
- BGI Research, 518083, Shenzhen, China
| | - Jingxuan Han
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Zhiyuan Sun
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Chunqing Wang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Daqi Deng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Yisen Tang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Siyuan Jiang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Chi Tian
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Xi Chen
- BGI Research, 518083, Shenzhen, China
| | - Yue Yuan
- BGI Research, 518083, Shenzhen, China
| | - Zeyu Li
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Tao Yang
- China National GeneBank, 518120, Shenzhen, China
| | - Tingting Lai
- China National GeneBank, 518120, Shenzhen, China
| | - Yiqun Liu
- China National GeneBank, 518120, Shenzhen, China
| | - Wenzhen Yang
- China National GeneBank, 518120, Shenzhen, China
| | - Xuanxuan Zou
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | | | - Huanhuan Cui
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Xin Jin
- BGI Research, 518083, Shenzhen, China
| | - Yuhui Hu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Ao Chen
- BGI Research, 518083, Shenzhen, China
- JFL-BGI STOmics Center, Jinfeng Laboratory, 401329, Chongqing, China
- The Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong, China
| | - Xun Xu
- BGI Research, 518083, Shenzhen, China
| | - Guipeng Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Yong Hou
- BGI Research, 518083, Shenzhen, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, 518100, Shenzhen, China
| | - Longqi Liu
- BGI Research, 518083, Shenzhen, China.
- BGI Research, 310012, Hangzhou, China.
- Shenzhen Bay Laboratory, 518000, Shenzhen, China.
| | - Shiping Liu
- BGI Research, 518083, Shenzhen, China.
- The Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong, China.
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, 518100, Shenzhen, China.
- BGI Research, 310012, Hangzhou, China.
- Shenzhen Bay Laboratory, 518000, Shenzhen, China.
| | - Liang Fang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Wei Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Liang Wu
- BGI Research, 518083, Shenzhen, China.
- JFL-BGI STOmics Center, Jinfeng Laboratory, 401329, Chongqing, China.
- BGI Research, 401329, Chongqing, China.
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Nale V, Chiodi A, Di Nanni N, Cifola I, Moscatelli M, Cocola C, Gnocchi M, Piscitelli E, Sula A, Zucchi I, Reinbold R, Milanesi L, Mezzelani A, Pelucchi P, Mosca E. scMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis. BMC Bioinformatics 2023; 24:445. [PMID: 38012590 PMCID: PMC10680269 DOI: 10.1186/s12859-023-05563-y] [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: 06/01/2022] [Accepted: 11/08/2023] [Indexed: 11/29/2023] Open
Abstract
INTRODUCTION Single-cell (SC) gene expression analysis is crucial to dissect the complex cellular heterogeneity of solid tumors, which is one of the main obstacles for the development of effective cancer treatments. Such tumors typically contain a mixture of cells with aberrant genomic and transcriptomic profiles affecting specific sub-populations that might have a pivotal role in cancer progression, whose identification eludes bulk RNA-sequencing approaches. We present scMuffin, an R package that enables the characterization of cell identity in solid tumors on the basis of a various and complementary analyses on SC gene expression data. RESULTS scMuffin provides a series of functions to calculate qualitative and quantitative scores, such as: expression of marker sets for normal and tumor conditions, pathway activity, cell state trajectories, Copy Number Variations, transcriptional complexity and proliferation state. Thus, scMuffin facilitates the combination of various evidences that can be used to distinguish normal and tumoral cells, define cell identities, cluster cells in different ways, link genomic aberrations to phenotypes and identify subtle differences between cell subtypes or cell states. We analysed public SC expression datasets of human high-grade gliomas as a proof-of-concept to show the value of scMuffin and illustrate its user interface. Nevertheless, these analyses lead to interesting findings, which suggest that some chromosomal amplifications might underlie the invasive tumor phenotype and the presence of cells that possess tumor initiating cells characteristics. CONCLUSIONS The analyses offered by scMuffin and the results achieved in the case study show that our tool helps addressing the main challenges in the bioinformatics analysis of SC expression data from solid tumors.
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Affiliation(s)
- Valentina Nale
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Alice Chiodi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Noemi Di Nanni
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Ingrid Cifola
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Marco Moscatelli
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Cinzia Cocola
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Matteo Gnocchi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Eleonora Piscitelli
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Ada Sula
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Ileana Zucchi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Rolland Reinbold
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Luciano Milanesi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Alessandra Mezzelani
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Paride Pelucchi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy.
| | - Ettore Mosca
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy.
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Mi K, Zeng L, Chen Y, Yang S. Integrative Analysis of Single-Cell and Bulk RNA Sequencing Reveals Prognostic Characteristics of Macrophage Polarization-Related Genes in Lung Adenocarcinoma. Int J Gen Med 2023; 16:5031-5050. [PMID: 37942473 PMCID: PMC10629586 DOI: 10.2147/ijgm.s430408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023] Open
Abstract
Background Lung adenocarcinoma (LUAD) is a group of cancers with poor prognosis. The combination of single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (RNA-seq) can identify important genes involved in cancer development and progression from a broader perspective. Methods The scRNA-seq data and bulk RNA-seq data of LUAD were downloaded from the Gene Expression Omnibus (GEO) database and the Cancer Genome Atlas (TCGA) database. Analyzing scRNA-seq for core cells in the GSE131907 dataset, and the uniform manifold approximation and projection (UMAP) was used for dimensionality reduction and cluster identification. Macrophage polarization-associated subtypes were acquired from the TCGA-LUAD dataset after analysis, followed by further identification of differentially expressed genes (DEGs) in the TCGA-LUAD dataset (normal/LUAD tissue samples, two subtypes). Venn diagrams were utilized to visualize differentially expressed and highly variable macrophage polarization-related genes. Subsequently, a prognostic risk model for LUAD patients was constructed by univariate Cox and Least Absolute Shrinkage and Selection Operator (LASSO), and the model was investigated for stability in the external data GSE72094. After analyzing the correlation between the trait genes and significantly mutated genes, the immune infiltration between the high/low-risk groups was then examined. The Monocle package was applied to analyze the pseudo-temporal trajectory analysis of different cell clusters in macrophage clusters. Subsequently, cell clusters of data macrophages were selected as key cell clusters to explore the role of characteristic genes in different cell populations and to identify transcription factors (TFs) that affect signature genes. Finally, qPCR were employed to validate the expression levels of prognosis signature genes in LUAD. Results 424 macrophage highly variable genes, 3920 DEGs, and 9561 DEGs were obtained from macrophage clusters, the macrophage polarization-related subtypes, and normal/LUAD tissue samples, respectively. Twenty-eight differentially expressed and highly mutated MPRGs were obtained. A prognostic risk model with 7 DE-MPRGs (RGS13, ADRB2, DDIT4, MS4A2, ALDH2, CTSH, and PKM) was constructed. This prognostic model still has a good prediction effect in the GSE72094 dataset. ZNF536 and DNAH9 were mutated in the low-risk group, while COL11A1 was mutated in the high-risk group, and they were highly correlated with the characteristic genes. A total of 11 immune cells were significantly different in the high/low-risk groups. Five cell types were again identified in the macrophage cluster, and then NK cells: CD56hiCD62L+ differentiated earlier and were present mainly on 2 branches. While macrophages were present on 2 branches and differentiated later. It was found that the expression levels of BCLAF1 and MAX were higher in cluster 1, which might be the TFs affecting the expression of the characteristic genes. Moreover, qPCR confirmed that the expression of the prognosis genes was generally consistent with the results of the bioinformatic analysis. Conclusion Seven MPRGs (RGS13, ADRB2, DDIT4, MS4A2, ALDH2, CTSH, and PKM) were identified as prognostic genes for LUAD and revealed the mechanisms of MPRGs at the single-cell level.
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Affiliation(s)
- Ke Mi
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China
| | - Lizhong Zeng
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China
| | - Yang Chen
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China
| | - Shuanying Yang
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, People’s Republic of China
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Chen S, Zhou Z, Li Y, Du Y, Chen G. Application of single-cell sequencing to the research of tumor microenvironment. Front Immunol 2023; 14:1285540. [PMID: 37965341 PMCID: PMC10641410 DOI: 10.3389/fimmu.2023.1285540] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
Single-cell sequencing is a technique for detecting and analyzing genomes, transcriptomes, and epigenomes at the single-cell level, which can detect cellular heterogeneity lost in conventional sequencing hybrid samples, and it has revolutionized our understanding of the genetic heterogeneity and complexity of tumor progression. Moreover, the tumor microenvironment (TME) plays a crucial role in the formation, development and response to treatment of tumors. The application of single-cell sequencing has ushered in a new age for the TME analysis, revealing not only the blueprint of the pan-cancer immune microenvironment, but also the heterogeneity and differentiation routes of immune cells, as well as predicting tumor prognosis. Thus, the combination of single-cell sequencing and the TME analysis provides a unique opportunity to unravel the molecular mechanisms underlying tumor development and progression. In this review, we summarize the recent advances in single-cell sequencing and the TME analysis, highlighting their potential applications in cancer research and clinical translation.
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Affiliation(s)
| | | | | | | | - Guoan Chen
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China
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Zhang JT, Zhang J, Wang SR, Yan LX, Qin J, Yin K, Chu XP, Wang MM, Hong HZ, Lv ZY, Dong S, Jiang BY, Zhang XC, Liu X, Zhou Q, Wu YL, Zhong WZ. Spatial downregulation of CD74 signatures may drive invasive component development in part-solid lung adenocarcinoma. iScience 2023; 26:107699. [PMID: 37810252 PMCID: PMC10550719 DOI: 10.1016/j.isci.2023.107699] [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: 01/30/2023] [Revised: 05/23/2023] [Accepted: 08/18/2023] [Indexed: 10/10/2023] Open
Abstract
Pulmonary nodules with part-solid imaging features manifest during the progression from preinvasive to invasive lung adenocarcinoma. To define the spatial composition and evolutionary trajectories of early-stage lung adenocarcinoma, we combined spatial transcriptomics (ST) and pathological annotations from 20 part-solid nodules (PSNs), four of which were matched with single-cell RNA sequencing. Two malignant cell populations (MC1 and MC2) were identified, and a linear evolutionary relationship was observed. Compared to MC2, the pre-existing malignant MC1 exhibited a lower metastatic signature, corresponding to the preinvasive component (lepidic) on pathology and the ground glass component on PSN imaging. Higher immune infiltration was observed among MC1 regions in ST profiles, and further analysis revealed that macrophages may be involved in this process through the CD74 axis. This work provides deeper insights into the evolutionary process and spatial immune cell composition behind PSNs and highlights the mechanisms of immune escape behind this adenocarcinoma trajectory.
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Affiliation(s)
- Jia-Tao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | | | - Song-Rong Wang
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Li-Xu Yan
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Jing Qin
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Kai Yin
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Xiang-Peng Chu
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Meng-Min Wang
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Hui-Zhao Hong
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Zhi-Yi Lv
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Song Dong
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Ben-Yuan Jiang
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Xiang Liu
- Echo Biotech Co, Ltd, Beijing, China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Wen-Zhao Zhong
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
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Storrs EP, Chati P, Usmani A, Sloan I, Krasnick BA, Babbra R, Harris PK, Sachs CM, Qaium F, Chatterjee D, Wetzel C, Goedegebuure SP, Hollander T, Anthony H, Ponce J, Khaliq AM, Badiyan S, Kim H, Denardo DG, Lang GD, Cosgrove ND, Kushnir VM, Early DS, Masood A, Lim KH, Hawkins WG, Ding L, Fields RC, Das KK, Chaudhuri AA. High-dimensional deconstruction of pancreatic cancer identifies tumor microenvironmental and developmental stemness features that predict survival. NPJ Precis Oncol 2023; 7:105. [PMID: 37857854 PMCID: PMC10587349 DOI: 10.1038/s41698-023-00455-z] [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: 04/06/2023] [Accepted: 09/26/2023] [Indexed: 10/21/2023] Open
Abstract
Numerous cell states are known to comprise the pancreatic ductal adenocarcinoma (PDAC) tumor microenvironment (TME). However, the developmental stemness and co-occurrence of these cell states remain poorly defined. Here, we performed single-cell RNA sequencing (scRNA-seq) on a cohort of treatment-naive PDAC time-of-diagnosis endoscopic ultrasound-guided fine needle biopsy (EUS-FNB) samples (n = 25). We then combined these samples with surgical resection (n = 6) and publicly available samples to increase statistical power (n = 80). Following annotation into 25 distinct cell states, cells were scored for developmental stemness, and a customized version of the Ecotyper tool was used to identify communities of co-occurring cell states in bulk RNA-seq samples (n = 268). We discovered a tumor microenvironmental community comprised of aggressive basal-like malignant cells, tumor-promoting SPP1+ macrophages, and myofibroblastic cancer-associated fibroblasts associated with especially poor prognosis. We also found a developmental stemness continuum with implications for survival that is present in both malignant cells and cancer-associated fibroblasts (CAFs). We further demonstrated that high-dimensional analyses predictive of survival are feasible using standard-of-care, time-of-diagnosis EUS-FNB specimens. In summary, we identified tumor microenvironmental and developmental stemness characteristics from a high-dimensional gene expression analysis of PDAC using human tissue specimens, including time-of-diagnosis EUS-FNB samples. These reveal new connections between tumor microenvironmental composition, CAF and malignant cell stemness, and patient survival that could lead to better upfront risk stratification and more personalized upfront clinical decision-making.
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Affiliation(s)
- Erik P Storrs
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Prathamesh Chati
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Abul Usmani
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ian Sloan
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bradley A Krasnick
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Ramandeep Babbra
- Division of Hematology & Oncology, Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Peter K Harris
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Chloe M Sachs
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Faridi Qaium
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Deyali Chatterjee
- Division of Laboratory Medicine, Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Chris Wetzel
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - S Peter Goedegebuure
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Thomas Hollander
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Hephzibah Anthony
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jennifer Ponce
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Ateeq M Khaliq
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Shahed Badiyan
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Hyun Kim
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - David G Denardo
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Gabriel D Lang
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Natalie D Cosgrove
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Vladimir M Kushnir
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Dayna S Early
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Ashiq Masood
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kian-Huat Lim
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - William G Hawkins
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Li Ding
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Ryan C Fields
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Koushik K Das
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
| | - Aadel A Chaudhuri
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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Chen X, Liu X, Du S. Unveiling the Role of Tumor-Infiltrating T Cells and Immunotherapy in Hepatocellular Carcinoma: A Comprehensive Review. Cancers (Basel) 2023; 15:5046. [PMID: 37894413 PMCID: PMC10605632 DOI: 10.3390/cancers15205046] [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: 09/13/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a rapidly rising global health concern, ranking as the third-leading cause of cancer-related mortality. Despite medical advancements, the five-year survival rate remains a dismal 18%, with a daunting 70% recurrence rate within a five-year period. Current systematic treatments, including first-line sorafenib, yield an overall response rate (ORR) below 10%. In contrast, immunotherapies have shown promise by improving ORR to approximately 30%. The IMbravel150 clinical trial demonstrates that combining atezolizumab and bevacizumab surpasses sorafenib in terms of median progression-free survival (PFS) and overall survival (OS). However, the therapeutic efficacy for HCC patients remains unsatisfactory, highlighting the urgent need for a comprehensive understanding of antitumor responses and immune evasion mechanisms in HCC. In this context, understanding the immune landscape of HCC is of paramount importance. Tumor-infiltrating T cells, including cytotoxic T cells, regulatory T cells, and natural killer T cells, are key components in the antitumor immune response. This review aims to shed light on their intricate interactions within the immunosuppressive tumor microenvironment and explores potential strategies for revitalizing dysfunctional T cells. Additionally, current immune checkpoint inhibitor (ICI)-based trials, ICI-based combination therapies, and CAR-T- or TCR-T-cell therapies for HCC are summarized, which might further improve OS and transform the management of HCC in the future.
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Affiliation(s)
- Xiaokun Chen
- Department of Liver Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (X.C.); (X.L.)
- Graduate School, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiao Liu
- Department of Liver Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (X.C.); (X.L.)
| | - Shunda Du
- Department of Liver Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; (X.C.); (X.L.)
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Okonechnikov K, Joshi P, Sepp M, Leiss K, Sarropoulos I, Murat F, Sill M, Beck P, Chan KCH, Korshunov A, Sah F, Deng MY, Sturm D, DeSisto J, Donson AM, Foreman NK, Green AL, Robinson G, Orr BA, Gao Q, Darrow E, Hadley JL, Northcott PA, Gojo J, Kawauchi D, Hovestadt V, Filbin MG, von Deimling A, Zuckermann M, Pajtler KW, Kool M, Jones DTW, Jäger N, Kutscher LM, Kaessmann H, Pfister SM. Mapping pediatric brain tumors to their origins in the developing cerebellum. Neuro Oncol 2023; 25:1895-1909. [PMID: 37534924 PMCID: PMC10547518 DOI: 10.1093/neuonc/noad124] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Distinguishing the cellular origins of childhood brain tumors is key for understanding tumor initiation and identifying lineage-restricted, tumor-specific therapeutic targets. Previous strategies to map the cell-of-origin typically involved comparing human tumors to murine embryonal tissues, which is potentially limited due to species-specific differences. The aim of this study was to unravel the cellular origins of the 3 most common pediatric brain tumors, ependymoma, pilocytic astrocytoma, and medulloblastoma, using a developing human cerebellar atlas. METHODS We used a single-nucleus atlas of the normal developing human cerebellum consisting of 176 645 cells as a reference for an in-depth comparison to 4416 bulk and single-cell transcriptome tumor datasets, using gene set variation analysis, correlation, and single-cell matching techniques. RESULTS We find that the astroglial cerebellar lineage is potentially the origin for posterior fossa ependymomas. We propose that infratentorial pilocytic astrocytomas originate from the oligodendrocyte lineage and MHC II genes are specifically enriched in these tumors. We confirm that SHH and Group 3/4 medulloblastomas originate from the granule cell and unipolar brush cell lineages. Radiation-induced gliomas stem from cerebellar glial lineages and demonstrate distinct origins from the primary medulloblastoma. We identify tumor genes that are expressed in the cerebellar lineage of origin, and genes that are tumor specific; both gene sets represent promising therapeutic targets for future study. CONCLUSION Based on our results, individual cells within a tumor may resemble different cell types along a restricted developmental lineage. Therefore, we suggest that tumors can arise from multiple cellular states along the cerebellar "lineage of origin."
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Affiliation(s)
- Konstantin Okonechnikov
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Piyush Joshi
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mari Sepp
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Kevin Leiss
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ioannis Sarropoulos
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Florent Murat
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- INRAE, LPGP, Rennes, France
| | | | - Pengbo Beck
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kenneth Chun-Ho Chan
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrey Korshunov
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sah
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Maximilian Y Deng
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominik Sturm
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - John DeSisto
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Andrew M Donson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Nicholas K Foreman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado School of Medicine, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Adam L Green
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado School of Medicine, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Giles Robinson
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Brent A Orr
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Qingsong Gao
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Emily Darrow
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jennifer L Hadley
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Paul A Northcott
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Johannes Gojo
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - Daisuke Kawauchi
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Volker Hovestadt
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Andreas von Deimling
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marc Zuckermann
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands
| | - David T W Jones
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Lena M Kutscher
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Chen Y, Qi Y, Wang K. Neoadjuvant chemotherapy for breast cancer: an evaluation of its efficacy and research progress. Front Oncol 2023; 13:1169010. [PMID: 37854685 PMCID: PMC10579937 DOI: 10.3389/fonc.2023.1169010] [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: 02/18/2023] [Accepted: 09/14/2023] [Indexed: 10/20/2023] Open
Abstract
Neoadjuvant chemotherapy (NAC) for breast cancer is widely used in the clinical setting to improve the chance of surgery, breast conservation and quality of life for patients with advanced breast cancer. A more accurate efficacy evaluation system is important for the decision of surgery timing and chemotherapy regimen implementation. However, current methods, encompassing imaging techniques such as ultrasound and MRI, along with non-imaging approaches like pathological evaluations, often fall short in accurately depicting the therapeutic effects of NAC. Imaging techniques are subjective and only reflect macroscopic morphological changes, while pathological evaluation is the gold standard for efficacy assessment but has the disadvantage of delayed results. In an effort to identify assessment methods that align more closely with real-world clinical demands, this paper provides an in-depth exploration of the principles and clinical applications of various assessment approaches in the neoadjuvant chemotherapy process.
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Affiliation(s)
- Yushi Chen
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, Basic Medical School, Central South University, Changsha, Hunan, China
| | - Yu Qi
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, Basic Medical School, Central South University, Changsha, Hunan, China
| | - Kuansong Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, Basic Medical School, Central South University, Changsha, Hunan, China
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41
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Liu Y, Liu Z, Yang Y, Cui J, Sun J, Liu Y. The prognostic and biology of tumour-infiltrating lymphocytes in the immunotherapy of cancer. Br J Cancer 2023; 129:1041-1049. [PMID: 37452117 PMCID: PMC10539364 DOI: 10.1038/s41416-023-02321-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 05/04/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Tumour immunotherapy has achieved remarkable clinical success in many different types of cancer in the past two decades. The outcome of immune checkpoint inhibitors in cancer patients has been linked to the quality and magnitude of T cell, NK cell, and more recently, B cell within the tumour microenvironment, suggesting that the immune landscape of a tumour is highly connected to patient response and prognosis. It is critical to understanding tumour immune microenvironments for identifying immune modifiers of cancer progression and developing cancer immunotherapies. The infiltration of solid tumours by immune cells with anti-tumour activity is both a strong prognostic factor and a therapeutic goal. Recent approaches and applications of new technologies, especially single-cell mRNA analysis in dissecting tumour microenvironments have brought important insights into the biology of tumour-infiltrating immune cells, revealed a remarkable degree of cellular heterogeneity and distinct patterns of immune response. In this review, we will discuss recent advances in the understanding of tumour infiltrated lymphocytes, their prognostic benefit, and predictive value for immunotherapy.
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Affiliation(s)
- Yanbin Liu
- Grit Biotechnology Ltd., Building 25, Area C, Sangtian Island Biological Industrial Park, Suzhou Industrial Park, Suzhou, Jiangsu Province, China
| | - Zhenjiang Liu
- Grit Biotechnology Ltd., Building 24, 388 Shengrong Road, Pudong New Area, Shanghai, China
| | - Yixiao Yang
- Grit Biotechnology Ltd., Building 24, 388 Shengrong Road, Pudong New Area, Shanghai, China
| | - Jun Cui
- Grit Biotechnology Ltd., Building 24, 388 Shengrong Road, Pudong New Area, Shanghai, China
| | - Jingwei Sun
- Grit Biotechnology Ltd., Building 24, 388 Shengrong Road, Pudong New Area, Shanghai, China
| | - Yarong Liu
- Grit Biotechnology Ltd., Building 24, 388 Shengrong Road, Pudong New Area, Shanghai, China.
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42
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Abe Y. Follicular lymphoma microenvironment: insights provided by single-cell analysis. J Clin Exp Hematop 2023; 63:143-151. [PMID: 37635086 PMCID: PMC10628831 DOI: 10.3960/jslrt.23012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/17/2023] [Accepted: 06/19/2023] [Indexed: 08/29/2023] Open
Abstract
Follicular lymphoma (FL) is the most frequent indolent lymphoma and is characterized by the abundant infiltration of tumor microenvironment (TME) cells. The activity of TME cells reportedly plays an important role in the biology of FL. TME cells that reside within neoplastic follicles, such as T-follicular helper cells and follicular dendritic cells, have been shown to aid in FL development and progression through interactions with malignant B cells, whereas regulatory T cells have unexpectedly shown an apparently favorable prognostic impact in FL. Unfortunately, the understanding of the FL TME, particularly regarding minor cell subsets, has been hampered by unknown cell heterogeneity. As with other solid and hematologic cancers, novel single-cell analysis technologies have recently been applied to FL research and have uncovered previously unrecognized heterogeneities, not only in malignant B cells but also in TME cells. These reports have greatly increased the resolution of our understanding of the FL TME and, at the same time, raised questions about newly identified TME cells. This review provides an overview of the unique aspects of FL TME cells with a clinical viewpoint and highlights recent discoveries from single-cell analysis, while also suggesting potential future directions.
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Affiliation(s)
- Yoshiaki Abe
- Department of Hematology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
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43
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Sun Y, Yao L, Man C, Gao Z, He R, Fan Y. Development and validation of cuproptosis-related lncRNAs associated with pancreatic cancer immune microenvironment based on single-cell. Front Immunol 2023; 14:1220760. [PMID: 37822927 PMCID: PMC10563513 DOI: 10.3389/fimmu.2023.1220760] [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: 05/11/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023] Open
Abstract
Background Cuproptosis, a novel mode of cell death associated with the tricarboxylic acid (TCA) cycle, is relevant to the development of cancer. However, the impact of single-cell-based Cuproptosis-associated lncRNAs on the Tumor immune microenvironment (TIME) of Pancreatic adenocarcinoma (PAAD) and its potential value for individualized immunotherapy has not been clarified. Methods 14 immune-related CRGs were screened by exploring the interaction between differentially expressed Immune-Related Genes (IRGs) and Cuproptosis-Related Genes (CRGs) in PAAD. Next, the expression amount and expression distribution of CRGs in single-cell samples were analyzed by focusing on 7-CRGs with significant expressions. On the one hand, MAP2K2, SOD1, and VEGFA, which were significantly differentially expressed between PAAD sites and normal tissues adjacent to them, were subjected to immunohistochemical validation and immune landscape analysis. On the other hand, from these 7-CRGs, prognostic signatures of lncRNAs were established by co-expression and LASSO-COX regression analysis, and their prognostic value and immune relevance were assessed. In addition, this study not only validated the hub CRGs and the lncRNAs constituting the signature in a PAAD animal model treated with immunotherapy-based combination therapy using immunohistochemistry and qRT-PCR but also explored the potential value of the combination of targeted, chemotherapy and immunotherapy. Results Based on the screening of 7-CRGs significantly expressed in a PAAD single-cell cohort and their co-expressed Cuproptosis-Related lncRNAs (CRIs), this study constructed a prognostic signature of 4-CRIs named CIR-score. A Nomogram integrating the CIR-score and clinical risk factors was constructed on this basis to predict the individualized survival of patients. Moreover, high and low-risk groups classified according to the median of signatures exhibited significant differences in clinical prognosis, immune landscape, bioenrichment, tumor burden, and drug sensitivity. And the immunohistochemical and qRT-PCR results of different mouse PAAD treatment strategies were consistent with the trend of inter-group variability in drug sensitivity of hub CRGs and CIR-score. The combination of immunotherapy, targeted therapy, and chemotherapy exhibited a better tumor suppression effect. Conclusion CIR-score, as a Cuproptosis-related TIME-specific prognostic signature based on PAAD single cells, not only predicts the prognosis and immune landscape of PAAD patients but also provides a new strategy for individualized immunotherapy-based combination therapy.
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Affiliation(s)
- Yimeng Sun
- Cancer Institute, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Lin Yao
- Cancer Institute, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Changfeng Man
- Cancer Institute, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zhenjun Gao
- Department of Gastroenterology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Rong He
- Cancer Institute, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yu Fan
- Cancer Institute, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
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Volmer LL, Önder CE, Volz B, Singh AR, Brucker SY, Engler T, Hartkopf AD, Koch A. Microfluidic Isolation of Disseminated Tumor Cells from the Bone Marrow of Breast Cancer Patients. Int J Mol Sci 2023; 24:13930. [PMID: 37762233 PMCID: PMC10531360 DOI: 10.3390/ijms241813930] [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: 08/07/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Disseminated tumor cells (DTCs) in the bone marrow (BM) of breast cancer (BC) patients are putative precursors of metastatic disease, and their presence is associated with an adverse clinical outcome. To achieve the personalization of therapy on a clinical routine level, the characterization of DTCs and in vitro drug testing on DTCs are of great interest. Therefore, biobanking methods, as well as novel approaches to DTC isolation, need to be developed. In this study, we established a protocol for the biobanking of BM samples and evaluated a microfluidic-based separation system (Parsortix®) for the enrichment of cryopreserved DTCs. We were able to successfully isolate viable DTCs after the prior cryopreservation of BM samples. We calculated a significant increase of up to 90-fold in harvested DTCs with the proposed method compared to the current standard techniques, opening up new analysis possibilities for DTCs. Our advanced method further presents options for 3D DTC cultures, enabling the individualized testing of targeted therapies for BC patients. In conclusion, we present a novel approach for DTC enrichment, with possibilities for future clinical implications.
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Affiliation(s)
- Léa L. Volmer
- Research Institute for Women’s Health, University of Tübingen, 72076 Tübingen, Germany
- Department of Women’s Health, University of Tübingen, 72076 Tübingen, Germany
| | - Cansu E. Önder
- Research Institute for Women’s Health, University of Tübingen, 72076 Tübingen, Germany
| | - Barbara Volz
- Research Institute for Women’s Health, University of Tübingen, 72076 Tübingen, Germany
| | - Anjali R. Singh
- Research Institute for Women’s Health, University of Tübingen, 72076 Tübingen, Germany
| | - Sara Y. Brucker
- Department of Women’s Health, University of Tübingen, 72076 Tübingen, Germany
| | - Tobias Engler
- Department of Women’s Health, University of Tübingen, 72076 Tübingen, Germany
| | - Andreas D. Hartkopf
- Research Institute for Women’s Health, University of Tübingen, 72076 Tübingen, Germany
- Department of Women’s Health, University of Tübingen, 72076 Tübingen, Germany
| | - André Koch
- Research Institute for Women’s Health, University of Tübingen, 72076 Tübingen, Germany
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45
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Lyu P, Zhai Y, Li T, Qian J. CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server. Bioinformatics 2023; 39:btad521. [PMID: 37610325 PMCID: PMC10477937 DOI: 10.1093/bioinformatics/btad521] [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: 03/21/2023] [Revised: 07/17/2023] [Accepted: 08/22/2023] [Indexed: 08/24/2023] Open
Abstract
MOTIVATION Single-cell sequencing technology has become a routine in studying many biological problems. A core step of analyzing single-cell data is the assignment of cell clusters to specific cell types. Reference-based methods are proposed for predicting cell types for single-cell clusters. However, the scalability and lack of preprocessed reference datasets prevent them from being practical and easy to use. RESULTS Here, we introduce a reference-based cell annotation web server, CellAnn, which is super-fast and easy to use. CellAnn contains a comprehensive reference database with 204 human and 191 mouse single-cell datasets. These reference datasets cover 32 organs. Furthermore, we developed a cluster-to-cluster alignment method to transfer cell labels from the reference to the query datasets, which is superior to the existing methods with higher accuracy and higher scalability. Finally, CellAnn is an online tool that integrates all the procedures in cell annotation, including reference searching, transferring cell labels, visualizing results, and harmonizing cell annotation labels. Through the user-friendly interface, users can identify the best annotation by cross-validating with multiple reference datasets. We believe that CellAnn can greatly facilitate single-cell sequencing data analysis. AVAILABILITY AND IMPLEMENTATION The web server is available at www.cellann.io, and the source code is available at https://github.com/Pinlyu3/CellAnn_shinyapp.
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Affiliation(s)
- Pin Lyu
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Yijie Zhai
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Taibo Li
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21218, United States
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
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Cortés‐Llanos B, Jain V, Cooper‐Volkheimer A, Browne EP, Murdoch DM, Allbritton NL. Automated microarray platform for single-cell sorting and collection of lymphocytes following HIV reactivation. Bioeng Transl Med 2023; 8:e10551. [PMID: 37693052 PMCID: PMC10487311 DOI: 10.1002/btm2.10551] [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: 01/12/2023] [Revised: 04/29/2023] [Accepted: 05/04/2023] [Indexed: 09/12/2023] Open
Abstract
A promising strategy to cure HIV-infected individuals is to use latency reversing agents (LRAs) to reactivate latent viruses, followed by host clearance of infected reservoir cells. However, reactivation of latent proviruses within infected cells is heterogeneous and often incomplete. This fact limits strategies to cure HIV which may require complete elimination of viable virus from all cellular reservoirs. For this reason, understanding the mechanism(s) of reactivation of HIV within cellular reservoirs is critical to achieve therapeutic success. Methodologies enabling temporal tracking of single cells as they reactivate followed by sorting and molecular analysis of those cells are urgently needed. To this end, microraft arrays were adapted to image T-lymphocytes expressing mCherry under the control of the HIV long terminal repeat (LTR) promoter, in response to the application of LRAs (prostratin, iBET151, and SAHA). In response to prostratin, iBET151, and SAHA, 30.5%, 11.2%, and 12.1% percentage of cells, respectively. The arrays enabled large numbers of single cells (>25,000) to be imaged over time. mCherry fluorescence quantification identified cell subpopulations with differing reactivation kinetics. Significant heterogeneity was observed at the single-cell level between different LRAs in terms of time to reactivation, rate of mCherry fluorescence increase upon reactivation, and peak fluorescence attained. In response to prostratin, subpopulations of T lymphocytes with slow and fast reactivation kinetics were identified. Single T-lymphocytes that were either fast or slow reactivators were sorted, and single-cell RNA-sequencing was performed. Different genes associated with inflammation, immune activation, and cellular and viral transcription factors were found.
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Affiliation(s)
- Belén Cortés‐Llanos
- Department of BioengineeringUniversity of WashingtonWashingtonUSA
- Department of MedicineDuke UniversityNorth CarolinaUSA
| | - Vaibhav Jain
- Department of Molecular PhysiologyDuke UniversityNorth CarolinaUSA
| | | | - Edward P. Browne
- Department of MedicineUniversity of North CarolinaNorth CarolinaUSA
- Department of Microbiology and ImmunologyUniversity of North CarolinaNorth CarolinaUSA
- UNC HIV Cure CenterUniversity of North CarolinaNorth CarolinaUSA
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Kim J, Kim S, Yeom H, Song SW, Shin K, Bae S, Ryu HS, Kim JY, Choi A, Lee S, Ryu T, Choi Y, Kim H, Kim O, Jung Y, Kim N, Han W, Lee HB, Lee AC, Kwon S. Barcoded multiple displacement amplification for high coverage sequencing in spatial genomics. Nat Commun 2023; 14:5261. [PMID: 37644058 PMCID: PMC10465490 DOI: 10.1038/s41467-023-41019-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
Determining mutational landscapes in a spatial context is essential for understanding genetically heterogeneous cell microniches. Current approaches, such as Multiple Displacement Amplification (MDA), offer high genome coverage but limited multiplexing, which hinders large-scale spatial genomic studies. Here, we introduce barcoded MDA (bMDA), a technique that achieves high-coverage genomic analysis of low-input DNA while enhancing the multiplexing capabilities. By incorporating cell barcodes during MDA, bMDA streamlines library preparation in one pot, thereby overcoming a key bottleneck in spatial genomics. We apply bMDA to the integrative spatial analysis of triple-negative breast cancer tissues by examining copy number alterations, single nucleotide variations, structural variations, and kataegis signatures for each spatial microniche. This enables the assessment of subclonal evolutionary relationships within a spatial context. Therefore, bMDA has emerged as a scalable technology with the potential to advance the field of spatial genomics significantly.
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Affiliation(s)
- Jinhyun Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sungsik Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Huiran Yeom
- Division of Data Science, College of Information and Communication Technology, The University of Suwon, Hwaseong, 18323, Republic of Korea
| | - Seo Woo Song
- Basic Science and Engineering Initiative, Children's Heart Center, Stanford University, Stanford, CA, USA
| | - Kyoungseob Shin
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sangwook Bae
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Han Suk Ryu
- Cancer Research Institute, Seoul National University, Seoul, 03080, Republic of Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Ji Young Kim
- Biomedical Research Institute, Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Ahyoun Choi
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sumin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Meteor Biotech, Co. Ltd., Seoul, 08826, Republic of Korea
| | - Taehoon Ryu
- ATG Lifetech Inc., Seoul, 08507, Republic of Korea
| | - Yeongjae Choi
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Hamin Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Okju Kim
- ATG Lifetech Inc., Seoul, 08507, Republic of Korea
| | - Yushin Jung
- ATG Lifetech Inc., Seoul, 08507, Republic of Korea
| | - Namphil Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Wonshik Han
- Cancer Research Institute, Seoul National University, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, 03080, Republic of Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Han-Byoel Lee
- Cancer Research Institute, Seoul National University, Seoul, 03080, Republic of Korea.
- Biomedical Research Institute, Seoul National University Hospital, Seoul, 03080, Republic of Korea.
- Department of Surgery, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Amos C Lee
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.
- Meteor Biotech, Co. Ltd., Seoul, 08826, Republic of Korea.
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Biomedical Research Institute, Seoul National University Hospital, Seoul, 03080, Republic of Korea.
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.
- Inter-University Semiconductor Research Center, Seoul National University, Seoul, 08826, Republic of Korea.
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, 08826, Republic of Korea.
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Liao P, Huang Q, Zhang J, Su Y, Xiao R, Luo S, Wu Z, Zhu L, Li J, Hu Q. How single-cell techniques help us look into lung cancer heterogeneity and immunotherapy. Front Immunol 2023; 14:1238454. [PMID: 37671151 PMCID: PMC10475738 DOI: 10.3389/fimmu.2023.1238454] [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: 06/11/2023] [Accepted: 08/03/2023] [Indexed: 09/07/2023] Open
Abstract
Lung cancer patients tend to have strong intratumoral and intertumoral heterogeneity and complex tumor microenvironment, which are major contributors to the efficacy of and drug resistance to immunotherapy. From a new perspective, single-cell techniques offer an innovative way to look at the intricate cellular interactions between tumors and the immune system and help us gain insights into lung cancer and its response to immunotherapy. This article reviews the application of single-cell techniques in lung cancer, with focuses directed on the heterogeneity of lung cancer and the efficacy of immunotherapy. This review provides both theoretical and experimental information for the future development of immunotherapy and personalized treatment for the management of lung cancer.
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Affiliation(s)
- Pu Liao
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qi Huang
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, National Health Commission (NHC) Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jiwei Zhang
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Su
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, National Health Commission (NHC) Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Rui Xiao
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Pathophysiology, School of Basic Medicine; Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shengquan Luo
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Pathophysiology, School of Basic Medicine; Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zengbao Wu
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Liping Zhu
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Pathophysiology, School of Basic Medicine; Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiansha Li
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qinghua Hu
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Pathophysiology, School of Basic Medicine; Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Wang WJ, Chu LX, He LY, Zhang MJ, Dang KT, Gao C, Ge QY, Wang ZG, Zhao XW. Spatial transcriptomics: recent developments and insights in respiratory research. Mil Med Res 2023; 10:38. [PMID: 37592342 PMCID: PMC10433685 DOI: 10.1186/s40779-023-00471-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Abstract
The respiratory system's complex cellular heterogeneity presents unique challenges to researchers in this field. Although bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) have provided insights into cell types and heterogeneity in the respiratory system, the relevant specific spatial localization and cellular interactions have not been clearly elucidated. Spatial transcriptomics (ST) has filled this gap and has been widely used in respiratory studies. This review focuses on the latest iterative technology of ST in recent years, summarizing how ST can be applied to the physiological and pathological processes of the respiratory system, with emphasis on the lungs. Finally, the current challenges and potential development directions are proposed, including high-throughput full-length transcriptome, integration of multi-omics, temporal and spatial omics, bioinformatics analysis, etc. These viewpoints are expected to advance the study of systematic mechanisms, including respiratory studies.
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Affiliation(s)
- Wen-Jia Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Liu-Xi Chu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Li-Yong He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Ming-Jing Zhang
- Orthopaedic Bioengineering Research Group, Division of Surgery and Interventional Science, University College London, London, HA7 4LP, UK
| | - Kai-Tong Dang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Chen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Qin-Yu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Zhou-Guang Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| | - Xiang-Wei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
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Aslan Kamil M, Fourneaux C, Yilmaz A, Stavros S, Parmentier R, Paldi A, Gonin-Giraud S, deMello AJ, Gandrillon O. An image-guided microfluidic system for single-cell lineage tracking. PLoS One 2023; 18:e0288655. [PMID: 37527253 PMCID: PMC10393162 DOI: 10.1371/journal.pone.0288655] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/30/2023] [Indexed: 08/03/2023] Open
Abstract
Cell lineage tracking is a long-standing and unresolved problem in biology. Microfluidic technologies have the potential to address this problem, by virtue of their ability to manipulate and process single-cells in a rapid, controllable and efficient manner. Indeed, when coupled with traditional imaging approaches, microfluidic systems allow the experimentalist to follow single-cell divisions over time. Herein, we present a valve-based microfluidic system able to probe the decision-making processes of single-cells, by tracking their lineage over multiple generations. The system operates by trapping single-cells within growth chambers, allowing the trapped cells to grow and divide, isolating sister cells after a user-defined number of divisions and finally extracting them for downstream transcriptome analysis. The platform incorporates multiple cell manipulation operations, image processing-based automation for cell loading and growth monitoring, reagent addition and device washing. To demonstrate the efficacy of the microfluidic workflow, 6C2 (chicken erythroleukemia) and T2EC (primary chicken erythrocytic progenitors) cells are tracked inside the microfluidic device over two generations, with a cell viability rate in excess of 90%. Sister cells are successfully isolated after division and extracted within a 500 nL volume, which was demonstrated to be compatible with downstream single-cell RNA sequencing analysis.
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Affiliation(s)
- Mahmut Aslan Kamil
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Camille Fourneaux
- Laboratory of Biology and Modelling of the Cell, Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard, Lyon, France
| | | | - Stavrakis Stavros
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Romuald Parmentier
- Ecole Pratique des Hautes Etudes, St-Antoine Research Center, Inserm U938, PSL Research University, Paris, France
| | - Andras Paldi
- Ecole Pratique des Hautes Etudes, St-Antoine Research Center, Inserm U938, PSL Research University, Paris, France
| | - Sandrine Gonin-Giraud
- Laboratory of Biology and Modelling of the Cell, Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard, Lyon, France
| | - Andrew J deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Olivier Gandrillon
- Laboratory of Biology and Modelling of the Cell, Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard, Lyon, France
- Inria, France
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