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Chen M, Chen F, Gao Z, Li X, Hu L, Yang S, Zhao S, Song Z. CAFs and T cells interplay: The emergence of a new arena in cancer combat. Biomed Pharmacother 2024; 177:117045. [PMID: 38955088 DOI: 10.1016/j.biopha.2024.117045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/11/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
The interaction between the immune system and the tumor matrix has a huge impact on the progression and treatment of cancer. This paper summarizes and discusses the crosstalk between T cells and cancer-associated fibroblasts (CAFs). CAFs can also produce inhibitors that counteract the function of T cells and promote tumor immune escape, while T cells can also engage in complex two-way interactions with CAFs through direct cell contact, the exchange of soluble factors such as cytokines, and the remodeling of the extracellular matrix. Precise targeted intervention can effectively reverse tumor-promoting crosstalk between T cells and CAFs, improve anti-tumor immune response, and provide a new perspective for cancer treatment. Therefore, it is important to deeply understand the mechanism of crosstalk between T cells and CAFs. This review aims to outline the underlying mechanisms of these interactions and discuss potential therapeutic strategies that may become fundamental tools in the treatment of cancer, especially hard-to-cure cancers.
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Affiliation(s)
- Minjie Chen
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Fei Chen
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Zhaofeng Gao
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Xiaoping Li
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Lingyu Hu
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Shuying Yang
- Department of intensive medicine, The Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China.
| | - Siqi Zhao
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China.
| | - Zhengwei Song
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China.
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Li Y, Yue L, Zhang S, Wang X, Zhu YN, Liu J, Ren H, Jiang W, Wang J, Zhang Z, Liu T. Proteomic, single-cell and bulk transcriptomic analysis of plasma and tumor tissues unveil core proteins in response to anti-PD-L1 immunotherapy in triple negative breast cancer. Comput Biol Med 2024; 176:108537. [PMID: 38744008 DOI: 10.1016/j.compbiomed.2024.108537] [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] [Revised: 04/18/2024] [Accepted: 04/28/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND Anti-PD-1/PD-L1 treatment has achieved durable responses in TNBC patients, whereas a fraction of them showed non-sensitivity to the treatment and the mechanism is still unclear. METHODS Pre- and post-treatment plasma samples from triple negative breast cancer (TNBC) patients treated with immunotherapy were measured by tandem mass tag (TMT) mass spectrometry. Public proteome data of lung cancer and melanoma treated with immunotherapy were employed to validate the findings. Blood and tissue single-cell RNA sequencing (scRNA-seq) data of TNBC patients treated with or without immunotherapy were analyzed to identify the derivations of plasma proteins. RNA-seq data from IMvigor210 and other cancer types were used to validate plasma proteins in predicting response to immunotherapy. RESULTS A random forest model constructed by FAP, LRG1, LBP and COMP could well predict the response to immunotherapy. The activation of complement cascade was observed in responders, whereas FAP and COMP showed a higher abundance in non-responders and negative correlated with the activation of complements. scRNA-seq and bulk RNA-seq analysis suggested that FAP, COMP and complements were derived from fibroblasts of tumor tissues. CONCLUSIONS We constructe an effective plasma proteomic model in predicting response to immunotherapy, and find that FAP+ and COMP+ fibroblasts are potential targets for reversing immunotherapy resistance.
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Affiliation(s)
- Yingpu Li
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, 150000, China; NHC Key Laboratory of Cell Transplantation, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, 150001, China
| | - Liang Yue
- Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, 310030, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, 310030, China; Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310030, China
| | - Sifan Zhang
- Department of Neurobiology, Harbin Medical University, Harbin, 150081, Heilongjiang Province, China
| | - Xinxuan Wang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, 150000, China
| | - Yu-Nan Zhu
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, 150000, China
| | - Jianyu Liu
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, 150000, China
| | - He Ren
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, 150000, China
| | - Wenhao Jiang
- Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, 310030, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, 310030, China; Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310030, China
| | - Jingxuan Wang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, 150000, China.
| | - Zhiren Zhang
- NHC Key Laboratory of Cell Transplantation, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, 150001, China; Institute of Metabolic Disease, Heilongjiang Academy of Medical Science, Heilongjiang Key Laboratory for Metabolic Disorder and Cancer Related Cardiovascular Diseases, Harbin, 150001, China.
| | - Tong Liu
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province, 150000, China; NHC Key Laboratory of Cell Transplantation, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, 150001, China.
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Wang Z, Ji X, Zhang Y, Yang F, Su H, Zhang H, Li Z, Zhang W, Sun W. Interactions between LAMP3+ dendritic cells and T-cell subpopulations promote immune evasion in papillary thyroid carcinoma. J Immunother Cancer 2024; 12:e008983. [PMID: 38816233 PMCID: PMC11141193 DOI: 10.1136/jitc-2024-008983] [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] [Accepted: 05/13/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND The incidence of papillary thyroid cancer (PTC) continues to rise all over the world, 10-15% of the patients have a poor prognosis. Although immunotherapy has been applied in clinical practice, its therapeutic efficacy remains far from satisfactory, necessitating further investigation of the mechanism of PTC immune remodeling and exploration of novel treatment targets. METHODS This study conducted a single-cell RNA sequencing (scRNA-seq) analysis using 18 surgical tissue specimens procured from 14 patients diagnosed with adjacent tissues, non-progressive PTC or progressive PTC. Key findings were authenticated through spatial transcriptomics RNA sequencing, immunohistochemistry, multiplex immunohistochemistry, and an independent bulk RNA-seq data set containing 502 samples. RESULTS A total of 151,238 individual cells derived from 18 adjacent tissues, non-progressive PTC and progressive PTC specimens underwent scRNA-seq analysis. We found that progressive PTC exhibits the following characteristics: a significant decrease in overall immune cells, enhanced immune evasion of tumor cells, and disrupted antigen presentation function. Moreover, we identified a subpopulation of lysosomal associated membrane protein 3 (LAMP3+) dendritic cells (DCs) exhibiting heightened infiltration in progressive PTC and associated with advanced T stage and poor prognosis of PTC. LAMP3+ DCs promote CD8+ T cells exhaustion (mediated by NECTIN2-TIGIT) and increase infiltration abundance of regulatory T cells (mediated by chemokine (C-C motif) ligand 17 (CCL17)-chemokine (C-C motif) receptor 4 (CCR4)) establishing an immune-suppressive microenvironment. Ultimately, we unveiled that progressive PTC tumor cells facilitate the retention of LAMP3+ DCs within the tumor microenvironment through NECTIN3-NECTIN2 interactions, thereby rendering tumor cells more susceptible to immune evasion. CONCLUSION Our findings expound valuable insights into the role of the interaction between LAMP3+ DCs and T-cell subpopulations and offer new and effective ideas and strategies for immunotherapy in patients with progressive PTC.
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Affiliation(s)
- Zhiyuan Wang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Xiaoyu Ji
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Ye Zhang
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Fan Yang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Hongyue Su
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Hao Zhang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Zhendong Li
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Wenqian Zhang
- Department of Head and Neck Surgery, Cancer Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Wei Sun
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
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Lujano Olazaba O, Farrow J, Monkkonen T. Fibroblast heterogeneity and functions: insights from single-cell sequencing in wound healing, breast cancer, ovarian cancer and melanoma. Front Genet 2024; 15:1304853. [PMID: 38525245 PMCID: PMC10957653 DOI: 10.3389/fgene.2024.1304853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
Cancer has been described as the wound that does not heal, in large part due to fibroblast involvement. Activation of cancer-associated fibroblasts (CAFs) contributes to critical features of the tumor microenvironment, including upregulation of key marker proteins, recruitment of immune cells, and deposition of extracellular matrix (ECM)-similar to fibroblast activation in injury-induced wound healing. Prior to the widespread availability of single-cell RNA sequencing (scRNA seq), studies of CAFs or fibroblasts in wound healing largely relied on models guided by individual fibroblast markers, or methods with less resolution to unravel the heterogeneous nature of CAFs and wound healing fibroblasts (especially regarding scarring outcome). Here, insights from the enhanced resolution provided by scRNA sequencing of fibroblasts in normal wound healing, breast cancer, ovarian cancer, and melanoma are discussed. These data have revealed differences in expression of established canonical activation marker genes, epigenetic modifications, fibroblast lineages, new gene and proteins of clinical interest for further experimentation, and novel signaling interactions with other cell types that include spatial information.
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Affiliation(s)
| | | | - Teresa Monkkonen
- Department of Biology, San Diego State University, San Diego, CA, United States
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Kang H, Hwang S, Kang H, Jo A, Lee JM, Choi JK, An HJ, Lee H. Altered tumor signature and T-cell profile after chemotherapy reveal new therapeutic opportunities in high-grade serous ovarian carcinoma. Cancer Sci 2024; 115:989-1000. [PMID: 38226451 PMCID: PMC10921005 DOI: 10.1111/cas.16074] [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: 09/15/2023] [Revised: 12/30/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
Chemotherapy combined with debulking surgery is the standard treatment protocol for high-grade serous ovarian carcinoma (HGSOC). Nonetheless, a significant number of patients encounter relapse due to the development of chemotherapy resistance. To better understand and address this resistance, we conducted a comprehensive study investigating the transcriptional alterations at the single-cell resolution in tissue samples from patients with HGSOC, using single-cell RNA sequencing and T-cell receptor sequencing techniques. Our analyses unveiled notable changes in the tumor signatures after chemotherapy, including those associated with epithelial-mesenchymal transition and cell cycle arrest. Within the immune compartment, we observed alterations in the T-cell profiles, characterized by naïve or pre-exhausted populations following chemotherapy. This phenotypic change was further supported by the examination of adjoining T-cell receptor clonotypes in paired longitudinal samples. These findings underscore the profound impact of chemotherapy on reshaping the tumor landscape and the immune microenvironment. This knowledge may provide clues for the development of future therapeutic strategies to combat treatment resistance in HGSOC.
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Affiliation(s)
- Huiram Kang
- Department of Microbiology, College of MedicineThe Catholic University of KoreaSeoulKorea
- Department of Biomedicine and Health Sciences, Graduate SchoolThe Catholic University of KoreaSeoulKorea
| | - Sohyun Hwang
- Department of Pathology, CHA Bundang Medical CenterCHA UniversitySeongnam‐siKorea
- Department of CHA Future Medicine Research InstituteCHA Bundang Medical CenterSeongnam‐siGyeonggi‐doSouth Korea
| | - Haeyoun Kang
- Department of Pathology, CHA Bundang Medical CenterCHA UniversitySeongnam‐siKorea
| | - Areum Jo
- Department of Microbiology, College of MedicineThe Catholic University of KoreaSeoulKorea
- Department of Biomedicine and Health Sciences, Graduate SchoolThe Catholic University of KoreaSeoulKorea
| | - Ji Min Lee
- Department of CHA Future Medicine Research InstituteCHA Bundang Medical CenterSeongnam‐siGyeonggi‐doSouth Korea
| | | | - Hee Jung An
- Department of Pathology, CHA Bundang Medical CenterCHA UniversitySeongnam‐siKorea
- Department of CHA Future Medicine Research InstituteCHA Bundang Medical CenterSeongnam‐siGyeonggi‐doSouth Korea
| | - Hae‐Ock Lee
- Department of Microbiology, College of MedicineThe Catholic University of KoreaSeoulKorea
- Department of Biomedicine and Health Sciences, Graduate SchoolThe Catholic University of KoreaSeoulKorea
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Yang S, Zhou X. SRT-Server: powering the analysis of spatial transcriptomic data. Genome Med 2024; 16:18. [PMID: 38279156 PMCID: PMC10811909 DOI: 10.1186/s13073-024-01288-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
BACKGROUND Spatial resolved transcriptomics (SRT) encompasses a rapidly developing set of technologies that enable the measurement of gene expression in tissue while retaining spatial localization information. SRT technologies and the enabled SRT studies have provided unprecedent insights into the structural and functional underpinnings of complex tissues. As SRT technologies have advanced and an increasing number of SRT studies have emerged, numerous sophisticated statistical and computational methods have been developed to facilitate the analysis and interpretation of SRT data. However, despite the growing popularity of SRT studies and the widespread availability of SRT analysis methods, analysis of large-scale and complex SRT datasets remains challenging and not easily accessible to researchers with limited statistical and computational backgrounds. RESULTS Here, we present SRT-Server, the first webserver designed to carry out comprehensive SRT analyses for a wide variety of SRT technologies while requiring minimal prior computational knowledge. Implemented with cutting-edge web development technologies, SRT-Server is user-friendly and features multiple analytic modules that can perform a range of SRT analyses. With a flowchart-style interface, these different analytic modules on the SRT-Server can be dragged into the main panel and connected to each other to create custom analytic pipelines. SRT-Server then automatically executes the desired analyses, generates corresponding figures, and outputs results-all without requiring prior programming knowledge. We demonstrate the advantages of SRT-Server through three case studies utilizing SRT data collected from two common platforms, highlighting its versatility and values to researchers with varying analytic expertise. CONCLUSIONS Overall, SRT-Server presents a user-friendly, efficient, effective, secure, and expandable solution for SRT data analysis, opening new doors for researchers in the field. SRT-Server is freely available at https://spatialtranscriptomicsanalysis.com/ .
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Affiliation(s)
- Sheng Yang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, China.
| | - Xiang Zhou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA.
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
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Zhai Z, Mu T, Zhao L, Zhu D, Zhong X, Li Y, Liang C, Li W, Zhou Q. Stachydrine represses the proliferation and enhances cell cycle arrest and apoptosis of breast cancer cells via PLA2G2A/DCN axis. Chem Biol Drug Des 2024; 103:e14429. [PMID: 38230769 DOI: 10.1111/cbdd.14429] [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: 08/14/2023] [Revised: 12/03/2023] [Accepted: 12/11/2023] [Indexed: 01/18/2024]
Abstract
Considering the therapeutic efficacy of Stachydrine on breast cancer (BC), this study aims to decipher the relevant mechanism. The effects of Stachydrine on BC cell viability, proliferation and apoptosis were firstly investigated. Then, Bioinformatics was applied to sort out the candidate interacting with Stachydrine as well as its expression and downstream target in BC. Relative expressions of genes of interest as well as proliferation- and apoptosis-related factors in BC cells were quantified through quantitative reverse-transcription PCR and western blot as appropriate. As a result, Stachydrine inhibited the proliferation, down-regulated the expressions of proliferating cell nuclear antigen and CyclinD1, enhanced cell cycle arrest and apoptosis, and up-regulated the levels of Cleaved caspase-3 and Cleaved caspase-9 in BC cells. Phospholipase A2 Group IIA (PLA2G2A) was predicted as the candidate interacting with Stachydrine and to be lowly expressed in BC. PLA2G2A silencing reversed while PLA2G2A overexpression reinforced the effects of Stachydrine. Decorin (DCN) was the downstream target of PLA2G2A and also lowly expressed in BC. PLA2G2A silencing counteracted yet overexpressed PLA2G2A strengthened the promoting effects of Stachydrine on DCN level. Collectively, Stachydrine inhibits the growth of BC cells to promote cell cycle arrest and apoptosis via PLA2G2A/DCN axis.
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Affiliation(s)
- Zhen Zhai
- Mammary Department, Dongfang Hospital Beijing University of Chinese Medicine, Beijing, China
| | - Tianlong Mu
- Pathology Department, Dongfang Hospital Beijing University of Chinese Medicine, Beijing, China
| | - Lina Zhao
- Mammary Department, Dongfang Hospital Beijing University of Chinese Medicine, Beijing, China
| | - Dongsheng Zhu
- Mammary Department, Dongfang Hospital Beijing University of Chinese Medicine, Beijing, China
| | - Xin Zhong
- Mammary Department, Dongfang Hospital Beijing University of Chinese Medicine, Beijing, China
| | - Yiliang Li
- Mammary Department, Dongfang Hospital Beijing University of Chinese Medicine, Beijing, China
| | - Chen Liang
- Mammary Department, Dongfang Hospital Beijing University of Chinese Medicine, Beijing, China
| | - Wei Li
- Mammary Department, Dongfang Hospital Beijing University of Chinese Medicine, Beijing, China
| | - Qingyuan Zhou
- Mammary Department, Dongfang Hospital Beijing University of Chinese Medicine, Beijing, China
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Chen C, Guo Q, Liu Y, Hou Q, Liao M, Guo Y, Zang Y, Wang F, Liu H, Luan X, Liang Y, Guan Z, Li Y, Liu H, Dong X, Zhang X, Liu J, Xu Q. Single-cell and spatial transcriptomics reveal POSTN + cancer-associated fibroblasts correlated with immune suppression and tumour progression in non-small cell lung cancer. Clin Transl Med 2023; 13:e1515. [PMID: 38115703 PMCID: PMC10731139 DOI: 10.1002/ctm2.1515] [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: 06/01/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Cancer-associated fibroblasts (CAFs) are potential targets for cancer therapy. Due to the heterogeneity of CAFs, the influence of CAF subpopulations on the progression of lung cancer is still unclear, which impedes the translational advances in targeting CAFs. METHODS We performed single-cell RNA sequencing (scRNA-seq) on tumour, paired tumour-adjacent, and normal samples from 16 non-small cell lung cancer (NSCLC) patients. CAF subpopulations were analyzed after integration with published NSCLC scRNA-seq data. SpaTial enhanced resolution omics-sequencing (Stereo-seq) was applied in tumour and tumour-adjacent samples from seven NSCLC patients to map the architecture of major cell populations in tumour microenvironment (TME). Immunohistochemistry (IHC) and multiplexed IHC (mIHC) were used to validate marker gene expression and the association of CAFs with immune infiltration in TME. RESULTS A subcluster of myofibroblastic CAFs, POSTN+ CAFs, were significantly enriched in advanced tumours and presented gene expression signatures related to extracellular matrix remodeling, tumour invasion pathways and immune suppression. Stereo-seq and mIHC demonstrated that POSTN+ CAFs were in close localization with SPP1+ macrophages and were associated with the exhausted phenotype and lower infiltration of T cells. POSTN expression or the abundance of POSTN+ CAFs were associated with poor prognosis of NSCLC. CONCLUSIONS Our study identified a myofibroblastic CAF subpopulation, POSTN+ CAFs, which might associate with SPP1+ macrophages to promote the formation of desmoplastic architecture and participate in immune suppression. Furthermore, we showed that POSTN+ CAFs associated with cancer progression and poor clinical outcomes and may provide new insights on the treatment of NSCLC.
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Affiliation(s)
- Chao Chen
- Department of Thoracic SurgeryPeking University Shenzhen HospitalShenzhen Peking University‐The Hong Kong University of Science and Technology Medical CenterShenzhenChina
| | - Qiang Guo
- BGI ResearchHangzhouChina
- BGI ResearchShenzhenChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yang Liu
- BGI ResearchHangzhouChina
- BGI ResearchShenzhenChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Qinghua Hou
- Department of Thoracic SurgeryPeking University Shenzhen HospitalShenzhen Peking University‐The Hong Kong University of Science and Technology Medical CenterShenzhenChina
| | - Mengying Liao
- Department of PathologyPeking University Shenzhen HospitalShenzhenChina
| | - Yanying Guo
- BGI ResearchHangzhouChina
- BGI ResearchShenzhenChina
| | - Yupeng Zang
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | | | - Huanyu Liu
- Department of PathologyPeking University Shenzhen HospitalShenzhenChina
| | - Xinyu Luan
- Department of Thoracic SurgeryPeking University Shenzhen HospitalShenzhen Peking University‐The Hong Kong University of Science and Technology Medical CenterShenzhenChina
| | - Yanling Liang
- BGI ResearchShenzhenChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Zhuojue Guan
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yanling Li
- Central Laboratory of Peking University Shenzhen HospitalShenzhenChina
| | - Haozhen Liu
- Department of Thoracic SurgeryPeking University Shenzhen HospitalShenzhen Peking University‐The Hong Kong University of Science and Technology Medical CenterShenzhenChina
| | - Xuan Dong
- BGI ResearchHangzhouChina
- BGI ResearchShenzhenChina
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of GenomicsBGI ResearchShenzhenChina
| | - Xiuqing Zhang
- BGI ResearchShenzhenChina
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of GenomicsBGI ResearchShenzhenChina
| | - Jixian Liu
- Department of Thoracic SurgeryPeking University Shenzhen HospitalShenzhen Peking University‐The Hong Kong University of Science and Technology Medical CenterShenzhenChina
| | - Qumiao Xu
- BGI ResearchHangzhouChina
- BGI ResearchShenzhenChina
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of GenomicsBGI ResearchShenzhenChina
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Huang H, Li N, Liang Y, Li R, Tong X, Xiao J, Tang H, Jiang D, Xie K, Fang C, Chen S, Li G, Wang B, Wang J, Luo H, Guo L, Ma H, Jiang W, Feng Y. Multi-omics analyses reveal spatial heterogeneity in primary and metastatic oesophageal squamous cell carcinoma. Clin Transl Med 2023; 13:e1493. [PMID: 38009315 PMCID: PMC10679972 DOI: 10.1002/ctm2.1493] [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: 07/17/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/28/2023] Open
Abstract
BACKGROUND Biopsies obtained from primary oesophageal squamous cell carcinoma (ESCC) guide diagnosis and treatment. However, spatial intra-tumoral heterogeneity (ITH) influences biopsy-derived information and patient responsiveness to therapy. Here, we aimed to elucidate the spatial ITH of ESCC and matched lymph node metastasis (LNmet ). METHODS Primary tumour superficial (PTsup ), deep (PTdeep ) and LNmet subregions of patients with locally advanced resectable ESCC were evaluated using whole-exome sequencing (WES), whole-transcriptome sequencing and spatially resolved digital spatial profiling (DSP). To validate the findings, immunohistochemistry was conducted and a single-cell transcriptomic dataset was analysed. RESULTS WES revealed 15.72%, 5.02% and 32.00% unique mutations in PTsup , PTdeep and LNmet , respectively. Copy number alterations and phylogenetic trees showed spatial ITH among subregions both within and among patients. Driver mutations had a mixed intra-tumoral clonal status among subregions. Transcriptome data showed distinct differentially expressed genes among subregions. LNmet exhibited elevated expression of immunomodulatory genes and enriched immune cells, particularly when compared with PTsup (all P < .05). DSP revealed orthogonal support of bulk transcriptome results, with differences in protein and immune cell abundance between subregions in a spatial context. The integrative analysis of multi-omics data revealed complex heterogeneity in mRNA/protein levels and immune cell abundance within each subregion. CONCLUSIONS This study comprehensively characterised spatial ITH in ESCC, and the findings highlight the clinical significance of unbiased molecular classification based on multi-omics data and their potential to improve the understanding and management of ESCC. The current practices for tissue sampling are insufficient for guiding precision medicine for ESCC, and routine profiling of PTdeep and/or LNmet should be systematically performed to obtain a more comprehensive understanding of ESCC and better inform treatment decisions.
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Affiliation(s)
- Haitao Huang
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Na Li
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and TherapyYuceBio Technology Co., LtdShenzhenChina
| | - Yingkuan Liang
- Department of Thoracic SurgeryNanjing Medical University Affiliated Cancer HospitalNanjingChina
| | - Rutao Li
- Department of Thoracic SurgeryDushu Lake Hospital Affiliated to Soochow UniversitySuzhouChina
| | - Xing Tong
- Department of Pathologythe First Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Jinyuan Xiao
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and TherapyYuceBio Technology Co., LtdShenzhenChina
| | - Hongzhen Tang
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and TherapyYuceBio Technology Co., LtdShenzhenChina
| | - Dong Jiang
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Kai Xie
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Chen Fang
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Shaomu Chen
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Guangbin Li
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Bin Wang
- Department of Thoracic SurgeryDushu Lake Hospital Affiliated to Soochow UniversitySuzhouChina
| | - Jiaqian Wang
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and TherapyYuceBio Technology Co., LtdShenzhenChina
| | - Haitao Luo
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and TherapyYuceBio Technology Co., LtdShenzhenChina
| | - Lingchuan Guo
- Department of Pathologythe First Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Haitao Ma
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Department of Thoracic SurgeryDushu Lake Hospital Affiliated to Soochow UniversitySuzhouChina
| | - Wei Jiang
- Department of Thoracic SurgeryDushu Lake Hospital Affiliated to Soochow UniversitySuzhouChina
| | - Yu Feng
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
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10
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Viúdez-Pareja C, Kreft E, García-Caballero M. Immunomodulatory properties of the lymphatic endothelium in the tumor microenvironment. Front Immunol 2023; 14:1235812. [PMID: 37744339 PMCID: PMC10512957 DOI: 10.3389/fimmu.2023.1235812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/08/2023] [Indexed: 09/26/2023] Open
Abstract
The tumor microenvironment (TME) is an intricate complex and dynamic structure composed of various cell types, including tumor, stromal and immune cells. Within this complex network, lymphatic endothelial cells (LECs) play a crucial role in regulating immune responses and influencing tumor progression and metastatic dissemination to lymph node and distant organs. Interestingly, LECs possess unique immunomodulatory properties that can either promote or inhibit anti-tumor immune responses. In fact, tumor-associated lymphangiogenesis can facilitate tumor cell dissemination and metastasis supporting immunoevasion, but also, different molecular mechanisms involved in LEC-mediated anti-tumor immunity have been already described. In this context, the crosstalk between cancer cells, LECs and immune cells and how this communication can shape the immune landscape in the TME is gaining increased interest in recent years. In this review, we present a comprehensive and updated report about the immunomodulatory properties of the lymphatic endothelium within the TME, with special focus on primary tumors and tumor-draining lymph nodes. Furthermore, we outline emerging research investigating the potential therapeutic strategies targeting the lymphatic endothelium to enhance anti-tumor immune responses. Understanding the intricate mechanisms involved in LEC-mediated immune modulation in the TME opens up new possibilities for the development of innovative approaches to fight cancer.
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Affiliation(s)
- Cristina Viúdez-Pareja
- Department of Molecular Biology and Biochemistry, Faculty of Sciences, Andalucía Tech, University of Málaga, Málaga, Spain
- IBIMA (Biomedical Research Institute of Málaga)-Plataforma BIONAND, Málaga, Spain
| | - Ewa Kreft
- Department of Molecular Biology and Biochemistry, Faculty of Sciences, Andalucía Tech, University of Málaga, Málaga, Spain
- IBIMA (Biomedical Research Institute of Málaga)-Plataforma BIONAND, Málaga, Spain
| | - Melissa García-Caballero
- Department of Molecular Biology and Biochemistry, Faculty of Sciences, Andalucía Tech, University of Málaga, Málaga, Spain
- IBIMA (Biomedical Research Institute of Málaga)-Plataforma BIONAND, Málaga, Spain
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11
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Peng H, Wu X, Liu S, He M, Tang C, Wen Y, Xie C, Zhong R, Li C, Xiong S, Liu J, Zheng H, He J, Lu X, Liang W. Cellular dynamics in tumour microenvironment along with lung cancer progression underscore spatial and evolutionary heterogeneity of neutrophil. Clin Transl Med 2023; 13:e1340. [PMID: 37491740 PMCID: PMC10368809 DOI: 10.1002/ctm2.1340] [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: 04/13/2023] [Revised: 06/21/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND The cellular dynamics in the tumour microenvironment (TME) along with non-small cell lung cancer (NSCLC) progression remain unclear. METHODS Multiplex immunofluorescence test detecting 10 immune-related markers on 553 primary tumour (PT) samples of NSCLC was conducted and spatial information in TME was assessed by the StarDist depth learning model. The single-cell transcriptomic atlas of PT (n = 4) and paired tumour-draining lymph nodes (TDLNs) (n = 5 for tumour-invaded, n = 3 for tumour-free) microenvironment was profiled. Various bioinformatics analyses based on Gene Expression Omnibus, TCGA and Array-Express databases were also used to validate the discoveries. RESULTS Spatial distances of CD4+ T cells-CD38+ T cells, CD4+ T cells-neutrophils and CD38+ T cells-neutrophils prolonged and they were replaced by CD163+ macrophages in PT along with tumour progression. Neutrophils showed unique stage and location-dependent prognostic effects. A high abundance of stromal neutrophils improved disease-free survival in the early-stage, whereas high intratumoural neutrophil infiltrates predicted poor prognosis in the mid-to-late-stage. Significant molecular and functional reprogramming in PT and TDLN microenvironments was observed. Diverse interaction networks mediated by neutrophils were found between positive and negative TDLNs. Five phenotypically and functionally heterogeneous subtypes of tumour-associated neutrophil (TAN) were further identified by pseudotime analysis, including TAN-0 with antigen-presenting function, TAN-1 with strong expression of interferon (IFN)-stimulated genes, the pro-tumour TAN-2 subcluster, the classical subset (TAN-3) and the pro-inflammatory subtype (TAN-4). Loss of IFN-stimulated signature and growing angiogenesis activity were discovered along the transitional trajectory. Eventually, a robust six neutrophil differentiation relevant genes-based model was established, showing that low-risk patients had longer overall survival time and may respond better to immunotherapy. CONCLUSIONS The cellular composition, spatial location, molecular and functional changes in PT and TDLN microenvironments along with NSCLC progression were deciphered, highlighting the immunoregulatory roles and evolutionary heterogeneity of TANs.
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Affiliation(s)
- Haoxin Peng
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Deparment of Clinical MedicineNanshan SchoolGuangzhou Medical UniversityGuangzhouChina
- Department of OncologyPeking University Cancer Hospital & InstitutePeking University Health Science Center, Peking UniversityBeijingChina
| | - Xiangrong Wu
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Deparment of Clinical MedicineNanshan SchoolGuangzhou Medical UniversityGuangzhouChina
- Department of OncologyShanghai Medical College, Fudan UniversityShanghaiChina
| | - Shaopeng Liu
- Department of Computer ScienceGuangdong Polytechnic Normal UniversityGuangzhouChina
- Department of Artificial Intelligence ResearchPazhou LabGuangzhouChina
| | - Miao He
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Deparment of Clinical MedicineNanshan SchoolGuangzhou Medical UniversityGuangzhouChina
| | - Chenshuo Tang
- Department of Computer ScienceGuangdong Polytechnic Normal UniversityGuangzhouChina
| | - Yaokai Wen
- Deparment of Clinical MedicineTongji UniversityShanghaiChina
- Department of Medical OncologyShanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University, School of MedicineShanghaiChina
| | - Chao Xie
- Department of Computer ScienceGuangdong Polytechnic Normal UniversityGuangzhouChina
| | - Ran Zhong
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Caichen Li
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Shan Xiong
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Jun Liu
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Hongbo Zheng
- Medical DepartmentGenecast Biotechnology Co., LtdBeijingChina
| | - Jianxing He
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Xu Lu
- Department of Computer ScienceGuangdong Polytechnic Normal UniversityGuangzhouChina
- Department of Artificial Intelligence ResearchPazhou LabGuangzhouChina
| | - Wenhua Liang
- Department of Thoracic Oncology and Surgery, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Diseasethe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Medical OncologyThe First People's Hospital of ZhaoqingZhaoqingChina
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12
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Wang Z, Wang X, Jin R, Liu F, Rao H, Wei L, Chen H, Feng B. LAMP3 expression in the liver is involved in T cell activation and adaptive immune regulation in hepatitis B virus infection. Front Immunol 2023; 14:1127572. [PMID: 37006307 PMCID: PMC10060507 DOI: 10.3389/fimmu.2023.1127572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
BackgroundThe disease burden caused by chronic hepatitis B virus (HBV) infection is still heavy, and the current treatment scheme has not achieved a complete cure. Changes in natural and adaptive immunity usually accompany chronic HBV infection. As a marker expressed on dendritic cells (DCs), whether lysosome-associated membrane glycoprotein 3 (LAMP3) participates in chronic HBV infection deserves further analysis.MethodsWe retrieved chronic HBV infection transcriptional information from the Gene Expression Omnibus (GEO) database. The LAMP3 expression in the liver of patients with chronic hepatitis B (CHB) was analyzed in three GEO datasets and confirmed in our validation cohort (27 patients with CHB). Differentially expressed genes were obtained from one CHB cohort by comparing LAMP3high and LAMP3low expression subgroups. These genes underwent Gene Ontology, Kyoto Encyclopedia of Genes and Genomes analysis, and Gene Set Enrichment Analysis to decipher the influence of LAMP3 on the biological process and immunity changes in HBV infection. Furthermore, we investigated the potential relationship between LAMP3 levels, the abundance of infiltrating immune cells, and liver dysfunction.ResultsCompared to healthy controls, LAMP3 expression was upregulated in the transcriptional profiles of the liver in patients with CHB. The high LAMP3 expression was related to T cell activation and the chemokine signaling pathway. The LAMP3 gene was positively linked to marker sets of infiltrating activated regulatory T cells (Treg), T cell exhaustion, monocytes, and DCs. Moreover, CHB patients with high LAMP3 expression had unfavorable liver dysfunction.ConclusionsLAMP3 is a gene related to HBV infection, which might be involved in HBV infection by regulating T cell activation and adaptive immune response.
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Affiliation(s)
- Zilong Wang
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China
| | - Xiaoxiao Wang
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China
| | - Rui Jin
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China
| | - Feng Liu
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China
| | - Huiying Rao
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China
| | - Lai Wei
- Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing, China
| | - Hongsong Chen
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China
| | - Bo Feng
- Peking University People’s Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on NAFLD Diagnosis, Beijing, China
- *Correspondence: Bo Feng,
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13
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Li M, Quintana A, Alberts E, Hung MS, Boulat V, Ripoll MM, Grigoriadis A. B Cells in Breast Cancer Pathology. Cancers (Basel) 2023; 15:1517. [PMID: 36900307 PMCID: PMC10000926 DOI: 10.3390/cancers15051517] [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: 12/22/2022] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
B cells have recently become a focus in breast cancer pathology due to their influence on tumour regression, prognosis, and response to treatment, besides their contribution to antigen presentation, immunoglobulin production, and regulation of adaptive responses. As our understanding of diverse B cell subsets in eliciting both pro- and anti-inflammatory responses in breast cancer patients increases, it has become pertinent to address the molecular and clinical relevance of these immune cell populations within the tumour microenvironment (TME). At the primary tumour site, B cells are either found spatially dispersed or aggregated in so-called tertiary lymphoid structures (TLS). In axillary lymph nodes (LNs), B cell populations, amongst a plethora of activities, undergo germinal centre reactions to ensure humoral immunity. With the recent approval for the addition of immunotherapeutic drugs as a treatment option in the early and metastatic settings for triple-negative breast cancer (TNBC) patients, B cell populations or TLS may resemble valuable biomarkers for immunotherapy responses in certain breast cancer subgroups. New technologies such as spatially defined sequencing techniques, multiplex imaging, and digital technologies have further deciphered the diversity of B cells and the morphological structures in which they appear in the tumour and LNs. Thus, in this review, we comprehensively summarise the current knowledge of B cells in breast cancer. In addition, we provide a user-friendly single-cell RNA-sequencing platform, called "B singLe cEll rna-Seq browSer" (BLESS) platform, with a focus on the B cells in breast cancer patients to interrogate the latest publicly available single-cell RNA-sequencing data collected from diverse breast cancer studies. Finally, we explore their clinical relevance as biomarkers or molecular targets for future interventions.
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Affiliation(s)
- Mengyuan Li
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, UK
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, UK
| | | | - Elena Alberts
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, UK
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, UK
- Immunity and Cancer Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Miu Shing Hung
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, UK
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, UK
| | - Victoire Boulat
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, UK
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, UK
- Immunity and Cancer Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Mercè Martí Ripoll
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
- Biosensing and Bioanalysis Group, Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Anita Grigoriadis
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, UK
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, UK
- Breast Cancer Now Unit, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, UK
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14
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Liu Y, Ge J, Chen Y, Liu T, Chen L, Liu C, Ma D, Chen Y, Cai Y, Xu Y, Shao Z, Yu K. Combined Single-Cell and Spatial Transcriptomics Reveal the Metabolic Evolvement of Breast Cancer during Early Dissemination. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205395. [PMID: 36594618 PMCID: PMC9951304 DOI: 10.1002/advs.202205395] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 12/10/2022] [Indexed: 06/17/2023]
Abstract
Breast cancer is now the most frequently diagnosed malignancy, and metastasis remains the leading cause of death in breast cancer. However, little is known about the dynamic changes during the evolvement of dissemination. In this study, 65 968 cells from four patients with breast cancer and paired metastatic axillary lymph nodes are profiled using single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics. A disseminated cancer cell cluster with high levels of oxidative phosphorylation (OXPHOS), including the upregulation of cytochrome C oxidase subunit 6C and dehydrogenase/reductase 2, is identified. The transition between glycolysis and OXPHOS when dissemination initiates is noticed. Furthermore, this distinct cell cluster is distributed along the tumor's leading edge. The findings here are verified in three different cohorts of breast cancer patients and an external scRNA-seq dataset, which includes eight patients with breast cancer and paired metastatic axillary lymph nodes. This work describes the dynamic metabolic evolvement of early disseminated breast cancer and reveals a switch between glycolysis and OXPHOS in breast cancer cells as the early event during lymph node metastasis.
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Affiliation(s)
- Yi‐Ming Liu
- Department of Breast SurgeryShanghai Cancer Center and Cancer InstituteFudan UniversityShanghai200032P. R. China
- Shanghai Medical CollegeFudan UniversityShanghai200032P. R. China
| | - Jing‐Yu Ge
- Shanghai Medical CollegeFudan UniversityShanghai200032P. R. China
| | - Yu‐Fei Chen
- Shanghai Medical CollegeFudan UniversityShanghai200032P. R. China
| | - Tong Liu
- Department of Breast SurgeryHarbin Medical University Cancer HospitalHarbinHeilongjiang150081P. R. China
| | - Lie Chen
- Shanghai Medical CollegeFudan UniversityShanghai200032P. R. China
| | - Cui‐Cui Liu
- Department of Breast SurgeryShanghai Cancer Center and Cancer InstituteFudan UniversityShanghai200032P. R. China
| | - Ding Ma
- Department of Breast SurgeryShanghai Cancer Center and Cancer InstituteFudan UniversityShanghai200032P. R. China
| | - Yi‐Yu Chen
- Shanghai Medical CollegeFudan UniversityShanghai200032P. R. China
| | - Yu‐Wen Cai
- Shanghai Medical CollegeFudan UniversityShanghai200032P. R. China
| | - Ying‐Ying Xu
- Department of Breast SurgeryThe First Affiliated Hospital of China Medical UniversityShenyangLiaoning110000P. R. China
| | - Zhi‐Ming Shao
- Department of Breast SurgeryShanghai Cancer Center and Cancer InstituteFudan UniversityShanghai200032P. R. China
- Key Laboratory of Breast Cancer in ShanghaiShanghai200032P. R. China
| | - Ke‐Da Yu
- Department of Breast SurgeryShanghai Cancer Center and Cancer InstituteFudan UniversityShanghai200032P. R. China
- Shanghai Medical CollegeFudan UniversityShanghai200032P. R. China
- Key Laboratory of Breast Cancer in ShanghaiShanghai200032P. R. China
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15
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Proietto M, Crippa M, Damiani C, Pasquale V, Sacco E, Vanoni M, Gilardi M. Tumor heterogeneity: preclinical models, emerging technologies, and future applications. Front Oncol 2023; 13:1164535. [PMID: 37188201 PMCID: PMC10175698 DOI: 10.3389/fonc.2023.1164535] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Heterogeneity describes the differences among cancer cells within and between tumors. It refers to cancer cells describing variations in morphology, transcriptional profiles, metabolism, and metastatic potential. More recently, the field has included the characterization of the tumor immune microenvironment and the depiction of the dynamics underlying the cellular interactions promoting the tumor ecosystem evolution. Heterogeneity has been found in most tumors representing one of the most challenging behaviors in cancer ecosystems. As one of the critical factors impairing the long-term efficacy of solid tumor therapy, heterogeneity leads to tumor resistance, more aggressive metastasizing, and recurrence. We review the role of the main models and the emerging single-cell and spatial genomic technologies in our understanding of tumor heterogeneity, its contribution to lethal cancer outcomes, and the physiological challenges to consider in designing cancer therapies. We highlight how tumor cells dynamically evolve because of the interactions within the tumor immune microenvironment and how to leverage this to unleash immune recognition through immunotherapy. A multidisciplinary approach grounded in novel bioinformatic and computational tools will allow reaching the integrated, multilayered knowledge of tumor heterogeneity required to implement personalized, more efficient therapies urgently required for cancer patients.
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Affiliation(s)
- Marco Proietto
- Next Generation Sequencing Core, The Salk Institute for Biological Studies, La Jolla, CA, United States
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Martina Crippa
- Vita-Salute San Raffaele University, Milan, Italy
- Experimental Imaging Center, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale San Raffaele, Milan, Italy
| | - Chiara Damiani
- Infrastructure Systems Biology Europe /Centre of Systems Biology (ISBE/SYSBIO) Centre of Systems Biology, Milan, Italy
- Department of Biotechnology and Biosciences, School of Sciences, University of Milano-Bicocca, Milan, Italy
| | - Valentina Pasquale
- Infrastructure Systems Biology Europe /Centre of Systems Biology (ISBE/SYSBIO) Centre of Systems Biology, Milan, Italy
- Department of Biotechnology and Biosciences, School of Sciences, University of Milano-Bicocca, Milan, Italy
| | - Elena Sacco
- Infrastructure Systems Biology Europe /Centre of Systems Biology (ISBE/SYSBIO) Centre of Systems Biology, Milan, Italy
- Department of Biotechnology and Biosciences, School of Sciences, University of Milano-Bicocca, Milan, Italy
| | - Marco Vanoni
- Infrastructure Systems Biology Europe /Centre of Systems Biology (ISBE/SYSBIO) Centre of Systems Biology, Milan, Italy
- Department of Biotechnology and Biosciences, School of Sciences, University of Milano-Bicocca, Milan, Italy
- *Correspondence: Marco Vanoni, ; Mara Gilardi,
| | - Mara Gilardi
- NOMIS Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA, United States
- Salk Cancer Center, The Salk Institute for Biological Studies, La Jolla, CA, United States
- *Correspondence: Marco Vanoni, ; Mara Gilardi,
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Jihad M, Yet İ. Multiomics Integration at Single-Cell Resolution Using Bayesian Networks: A Case Study in Hepatocellular Carcinoma. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:24-33. [PMID: 36602810 DOI: 10.1089/omi.2022.0170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Multiomics data integration is one of the leading frontiers of complex disease research and integrative biology. The advances in single-cell sequencing technologies offer yet another crucial dimension in multiomics research. The single-cell studies enable the study and integration of multiomics data simultaneously in the same cell. We report in this study multiomics data integration in single-cell resolution using Bayesian networks (BNs) in a case study of hepatocellular carcinoma (HCC). A BN encodes the conditional dependencies/independencies of variables using a graphical model with an accompanying joint probability. RNA-seq and Reduced Representation Bisulfite Sequencing data were analyzed separately, and copy number variations were estimated by the hidden Markov model method. Several BN models were constructed to reveal omics' causal and associational relationships. These methods were subjected to a validation study using an independent data set. We show the heterogeneity of the multiple cellular layers of HCC at single-cell omics resolution by identifying best-fitted BN models of 295 genes. We also provide novel insights into the multiomics mechanistic relationships in the human lymphocyte antigen class I genes in HCC. To the best of our knowledge, this is the first study to focus on integrating omics data using a machine learning algorithm, BNs, at the single-cell resolution using a case study of HCC.
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Affiliation(s)
- Muntadher Jihad
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey
| | - İdil Yet
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey
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