151
|
Hu Y, Sun Y, Li T, Han W, Wang P. Identification of rat Vstm1 with conservative anti-inflammatory effect between rat and human homologs. Genomics 2024; 116:110774. [PMID: 38163574 DOI: 10.1016/j.ygeno.2023.110774] [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: 09/15/2023] [Revised: 11/17/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Human VSTM1 (also known as SIRL1) is an inhibitory immune checkpoint receptor involved in leukocyte activation. Identification of the homologous genes in other species, such as mice and rats, will undoubtedly contribute to functional studies and clinical applications. Here, we successfully cloned the Vstm1 gene in rats, as supported by high-throughput sequencing data. However, Vstm1 is degenerated to a pseudogene in the mouse genome. Rat Vstm1 mRNA contains a complete open reading frame (ORF) of 630 nucleotides encoding 209 amino acids. Rat Vstm1 is highly expressed in bone marrow, especially in granulocytes. The expression levels of Vstm1 gradually increase with the development of granulocytes in bone marrow but are downregulated in response to inflammatory stimuli. Rat VSTM1 does not have an immunoreceptor tyrosine-based inhibitory motif (ITIM), however, it shows a conservative function of inflammatory inhibition with human VSTM1, and both are anti-correlated with many inflammatory cytokines, such as IL-1α and TNF-α. In bone marrow-derived macrophages (BMDMs), either rat or human VSTM1 suppressed the secretion of inflammatory cytokines in response to LPS stimulation. Further analysis in lung cancer microenvironment revealed that VSTM1 is mainly expressed in myeloid cells, anti-correlated with inflammatory cytokines and associated with tumor development and metastasis.
Collapse
Affiliation(s)
- Yuzhe Hu
- Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; Peking University Center for Human Disease Genomics, Beijing, China
| | - Yingzhe Sun
- Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; Peking University Center for Human Disease Genomics, Beijing, China
| | - Ting Li
- Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; Peking University Center for Human Disease Genomics, Beijing, China
| | - Wenling Han
- Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; Peking University Center for Human Disease Genomics, Beijing, China.
| | - Pingzhang Wang
- Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China; Peking University Center for Human Disease Genomics, Beijing, China.
| |
Collapse
|
152
|
Galvez-Cancino F, Simpson AP, Costoya C, Matos I, Qian D, Peggs KS, Litchfield K, Quezada SA. Fcγ receptors and immunomodulatory antibodies in cancer. Nat Rev Cancer 2024; 24:51-71. [PMID: 38062252 DOI: 10.1038/s41568-023-00637-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/10/2023] [Indexed: 12/24/2023]
Abstract
The discovery of both cytotoxic T lymphocyte-associated antigen 4 (CTLA4) and programmed cell death protein 1 (PD1) as negative regulators of antitumour immunity led to the development of numerous immunomodulatory antibodies as cancer treatments. Preclinical studies have demonstrated that the efficacy of immunoglobulin G (IgG)-based therapies depends not only on their ability to block or engage their targets but also on the antibody's constant region (Fc) and its interactions with Fcγ receptors (FcγRs). Fc-FcγR interactions are essential for the activity of tumour-targeting antibodies, such as rituximab, trastuzumab and cetuximab, where the killing of tumour cells occurs at least in part due to these mechanisms. However, our understanding of these interactions in the context of immunomodulatory antibodies designed to boost antitumour immunity remains less explored. In this Review, we discuss our current understanding of the contribution of FcγRs to the in vivo activity of immunomodulatory antibodies and the challenges of translating results from preclinical models into the clinic. In addition, we review the impact of genetic variability of human FcγRs on the activity of therapeutic antibodies and how antibody engineering is being utilized to develop the next generation of cancer immunotherapies.
Collapse
Affiliation(s)
- Felipe Galvez-Cancino
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Alexander P Simpson
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Cristobal Costoya
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Ignacio Matos
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Danwen Qian
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Karl S Peggs
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| |
Collapse
|
153
|
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.
Collapse
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
| |
Collapse
|
154
|
van der Hoorn IAE, Martynova E, Subtil B, Meek J, Verrijp K, Textor J, Flórez-Grau G, Piet B, van den Heuvel MM, de Vries IJM, Gorris MAJ. Detection of dendritic cell subsets in the tumor microenvironment by multiplex immunohistochemistry. Eur J Immunol 2024; 54:e2350616. [PMID: 37840200 DOI: 10.1002/eji.202350616] [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: 06/19/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/17/2023]
Abstract
Dendritic cells (DCs) are essential in antitumor immunity. In humans, three main DC subsets are defined: two types of conventional DCs (cDC1s and cDC2s) and plasmacytoid DCs (pDCs). To study DC subsets in the tumor microenvironment (TME), it is important to correctly identify them in tumor tissues. Tumor-derived DCs are often analyzed in cell suspensions in which spatial information about DCs which can be important to determine their function within the TME is lost. Therefore, we developed the first standardized and optimized multiplex immunohistochemistry panel, simultaneously detecting cDC1s, cDC2s, and pDCs within their tissue context. We report on this panel's development, validation, and quantitative analysis. A multiplex immunohistochemistry panel consisting of CD1c, CD303, X-C motif chemokine receptor 1, CD14, CD19, a tumor marker, and DAPI was established. The ImmuNet machine learning pipeline was trained for the detection of DC subsets. The performance of ImmuNet was compared with conventional cell phenotyping software. Ultimately, frequencies of DC subsets within several tumors were defined. In conclusion, this panel provides a method to study cDC1s, cDC2s, and pDCs in the spatial context of the TME, which supports unraveling their specific roles in antitumor immunity.
Collapse
Affiliation(s)
- Iris A E van der Hoorn
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Pulmonary Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Evgenia Martynova
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Data Science, Institute for Computing and Information Sciences, Radboud University, Nijmegen, the Netherlands
| | - Beatriz Subtil
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jelena Meek
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Kiek Verrijp
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Division of Immunotherapy, Oncode Institute, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Johannes Textor
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Data Science, Institute for Computing and Information Sciences, Radboud University, Nijmegen, the Netherlands
| | - Georgina Flórez-Grau
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Berber Piet
- Department of Pulmonary Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Michel M van den Heuvel
- Department of Pulmonary Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - I Jolanda M de Vries
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mark A J Gorris
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Division of Immunotherapy, Oncode Institute, Radboud University Medical Center, Nijmegen, the Netherlands
| |
Collapse
|
155
|
Bi W, Xu Z, Liu F, Xie Z, Liu H, Zhu X, Zhong W, Zhang P, Tang X. Genome-wide analyses reveal the contribution of somatic variants to the immune landscape of multiple cancer types. PLoS Genet 2024; 20:e1011134. [PMID: 38241355 PMCID: PMC10829993 DOI: 10.1371/journal.pgen.1011134] [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: 09/06/2023] [Revised: 01/31/2024] [Accepted: 01/09/2024] [Indexed: 01/21/2024] Open
Abstract
It has been well established that cancer cells can evade immune surveillance by mutating themselves. Understanding genetic alterations in cancer cells that contribute to immune regulation could lead to better immunotherapy patient stratification and identification of novel immune-oncology (IO) targets. In this report, we describe our effort of genome-wide association analyses across 22 TCGA cancer types to explore the associations between genetic alterations in cancer cells and 74 immune traits. Results showed that the tumor microenvironment (TME) is shaped by different gene mutations in different cancer types. Out of the key genes that drive multiple immune traits, top hit KEAP1 in lung adenocarcinoma (LUAD) was selected for validation. It was found that KEAP1 mutations can explain more than 10% of the variance for multiple immune traits in LUAD. Using public scRNA-seq data, further analysis confirmed that KEAP1 mutations activate the NRF2 pathway and promote a suppressive TME. The activation of the NRF2 pathway is negatively correlated with lower T cell infiltration and higher T cell exhaustion. Meanwhile, several immune check point genes, such as CD274 (PD-L1), are highly expressed in NRF2-activated cancer cells. By integrating multiple RNA-seq data, a NRF2 gene signature was curated, which predicts anti-PD1 therapy response better than CD274 gene alone in a mixed cohort of different subtypes of non-small cell lung cancer (NSCLC) including LUAD, highlighting the important role of KEAP1-NRF2 axis in shaping the TME in NSCLC. Finally, a list of overexpressed ligands in NRF2 pathway activated cancer cells were identified and could potentially be targeted for TME remodeling in LUAD.
Collapse
Affiliation(s)
- Wenjian Bi
- Department of Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, People’s Republic of China
- Center for Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, People’s Republic of China
- Medicine Innovation Center for Fundamental Research on Major Immunology-related Diseases, Peking University, Beijing, People’s Republic of China
| | - Zhiyu Xu
- Regor Pharmaceuticals Inc., Cambridge, Massachusetts, United States of America
| | - Feng Liu
- Regor Pharmaceuticals Inc., Cambridge, Massachusetts, United States of America
| | - Zhi Xie
- Regor Pharmaceuticals Inc., Cambridge, Massachusetts, United States of America
| | - Hao Liu
- Regor Pharmaceuticals Inc., Cambridge, Massachusetts, United States of America
| | - Xiaotian Zhu
- Regor Pharmaceuticals Inc., Cambridge, Massachusetts, United States of America
| | - Wenge Zhong
- Regor Pharmaceuticals Inc., Cambridge, Massachusetts, United States of America
| | - Peipei Zhang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People’s Republic of China
- Key Laboratory for Neuroscience, Ministry of Education/National Health and Family Planning Commission, Peking University, Beijing, People’s Republic of China
| | - Xing Tang
- Regor Pharmaceuticals Inc., Cambridge, Massachusetts, United States of America
| |
Collapse
|
156
|
Ni Y, Jiang M, Wu Y, Xiao P, Wu A, Xia W, Tang C, Yang X, Tian K, Chen H, Huang R. Anoikis-related CTNND1 is associated with immuno-suppressive tumor microenvironment and predicts unfavorable immunotherapeutic outcome in non-small cell lung cancer. J Cancer 2024; 15:317-331. [PMID: 38169514 PMCID: PMC10758022 DOI: 10.7150/jca.89542] [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: 08/26/2023] [Accepted: 11/08/2023] [Indexed: 01/05/2024] Open
Abstract
Background: Immunotherapy has greatly changed the treatment of advanced non-small cell lung cancer (NSCLC). Anoikis is a programmed cell death process associated with cancer. However, the correlation between anoikis-related genes and the tumor microenvironment (TME) features and immunotherapeutic outcome in NSCLC has not been fully explored. Methods: The bulk and single-cell transcriptome data of NSCLC were downloaded from TCGA and GEO databases. The distribution of anoikis-related genes on different cell types at the single-cell level was analyzed, and these genes specifically expressed by tumor cells and immunotherapy-related were further extracted. Next, the candidate gene CTNND1 was identified and its correlations with the TME features and immunotherapeutic outcome in NSCLC were explored in multiple public cohorts. Finally, an in-house cohort was used to determine the CTNND1 expression and immuno-correlation in NSCLC. Results: At single-cell atlas, we found that anoikis-related genes expressed specifically in tumor cells of NSCLC. By intersecting anoikis-related genes, immunotherapy-associated genes, and the genes expressed in tumor cells, we obtained a special biomarker CTNND1. In addition, cell-cell communication analysis revealed that CTNND1+ tumor cells communicated with immune subpopulations frequently. Moreover, we found that high expression of CTNND1 was related to immuno-suppressive status of NSCLC. The expression of CTNND1 and its immuno-correlation were also validated, and the results showed that CTNND1 was highly expressed in NSCLC tissues and tumors with high CTNND1 expression accompanied with low CD8+ T cells infiltration. Conclusions: Overall, our study reported that CTNND1 can be considered as a novel biomarker for the predication of immunotherapeutic responses and a potential target for NSCLC therapy.
Collapse
Affiliation(s)
- Yingchen Ni
- Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Mengna Jiang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong 226019, China
| | - Yixuan Wu
- Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Pei Xiao
- Center for Non-Communicable Disease Management, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Anqi Wu
- Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Weiyi Xia
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong 226019, China
| | - Can Tang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong 226019, China
| | - Xu Yang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong 226019, China
| | - Kai Tian
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong 226019, China
| | - Hong Chen
- Department of Respiratory Medicine, Nantong Fourth People's Hospital, Nantong, 226000, China
| | - Rongrong Huang
- Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| |
Collapse
|
157
|
Chen C, Wan M, Peng X, Zhang Q, Liu Y. GPR37-centered ceRNA network contributes to metastatic potential in lung adenocarcinoma: Evidence from high-throughput sequencing. Transl Oncol 2024; 39:101819. [PMID: 37979558 PMCID: PMC10656721 DOI: 10.1016/j.tranon.2023.101819] [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: 06/11/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/20/2023] Open
Abstract
The competing endogenous RNA (ceRNA)-based profiling has been extensively studied in carcinogenesis of lung adenocarcinoma (LUAD), while it has seldomly been applied to investigate the metastatic potential of LUAD. This study aims to examine the function and in-depth mechanism of GPR37-centered ceRNA network in LUAD. Cancer tissues and adjacent normal tissues from three LUAD patients were collected for high-throughput sequencing to screen for differentially expressed genes. A PPI network was constructed to screen the key gene GPR37, followed by analysis for the functions and pathways. Clinical data from LUAD patients were integrated with gene expression data in TCGA-LUAD dataset for survival analysis. Based on the miRNAs targeting_GPR37 and lncRNAs targeting_miRNAs, a lncRNA-miRNA-mRNA ceRNA network was established. GPR37 was up-regulated in LUAD tissue samples, and it may be a key gene involved in LUAD progression. GPR37 in LUAD was mainly enriched in the mitosis-related pathways. High GPR37 expression corresponded to poor prognosis in LUAD patients. Meanwhile, GPR37 could be used as an independent factor to predict the prognosis in LUAD patients. LncRNA DLEU1, up-regulated in LUAD tissue samples, may competitively bind to miR-4458 to up-regulate the expression of the miR-4458 downstream target GPR37. DLEU1 was associated with poor prognosis and tumor metastasis in LUAD patients. Altogether, our findings reveal a novel ceRNA network of DLEU1/miR-4458/GPR37 in LUAD growth and metastasis.
Collapse
Affiliation(s)
- Chuanhui Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China
| | - Mengzhi Wan
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China
| | - Xiong Peng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China
| | - Qing Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China
| | - Yu Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China.
| |
Collapse
|
158
|
Ao YQ, Gao J, Jin C, Wang S, Zhang LC, Deng J, Chen ZW, Wang HK, Jiang JH, Ding JY. ASCC3 promotes the immunosuppression and progression of non-small cell lung cancer by impairing the type I interferon response via CAND1-mediated ubiquitination inhibition of STAT3. J Immunother Cancer 2023; 11:e007766. [PMID: 38148115 PMCID: PMC10753855 DOI: 10.1136/jitc-2023-007766] [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: 11/01/2023] [Indexed: 12/28/2023] Open
Abstract
BACKGROUND Activating signal cointegrator 3 (ASCC3) has been identified as an oncogenic factor that impairs host immune defense. However, the underlying mechanisms of carcinogenesis and its impact on the antitumor immune response remain unclear. In this study, we aimed to investigate the molecular mechanisms of ASCC3 in the progression of non-small cell lung cancer (NSCLC). METHODS Single-cell sequencing data from the Gene Expression Omnibus and gene expression profiles from The Cancer Genome Atlas database were analyzed. The expression, clinical relevance and biological functions of ASCC3 in NSCLC were explored. Then, RNA sequencing, immunoprecipitation, mass spectrometry, immunofluorescence, and flow cytometry analyses were conducted to explore the underlying molecular mechanisms. In addition, in vivo experiments in mouse models were conducted to explore the probability of ASCC3 knockdown to improve the efficacy of anti-Programmed Death-1 (PD-1) therapy in NSCLC. RESULTS ASCC3 was significantly upregulated in NSCLC and correlated with poor pathological characteristics and prognosis in patients with NSCLC. Overexpression of ASCC3 promoted malignant phenotypes of NSCLC cells and induced an immunosuppressive tumor microenvironment, which was characterized by a decrease in CD8+ T cells, natural killer cells and dendritic cells but an increase in regulatory T(Treg) cells. Mechanistically, ASCC3 stabilized signal transducer and activator of transcription (STAT)3 signaling by recruiting Cullin-associated and neddylation dissociated 1 (CAND1), which inhibited ubiquitin-mediated degradation of STAT3, thereby impairing the type I interferon response of tumor cells and promoting the immunosuppression and progression of NSCLC. Furthermore, high expression of ASCC3 impaired the efficacy of anti-PD-1 therapy, and an anti-PD-1 antibody combined with ASCC3 knockdown exerted promising synergistic efficacy in a preclinical mouse model. CONCLUSION ASCC3 could stabilize the STAT3 pathway via CAND1, reshaping the tumor microenvironment and inducing resistance to anti-PD-1 therapy, which promotes the progression of NSCLC. It is a reliable prognostic indicator and can be a target in combination therapy for NSCLC.
Collapse
Affiliation(s)
- Yong-Qiang Ao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
| | - Jian Gao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
| | - Chun Jin
- Department of Thoracic Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Shuai Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
| | - Li-Cheng Zhang
- School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jie Deng
- Institute of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zong-Wei Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
| | - Hai-Kun Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Beijing, China
| | - Jia-Hao Jiang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
| | - Jian-Yong Ding
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, Shanghai, China
| |
Collapse
|
159
|
Chen J, Tang Y, Qin D, Yu X, Tong H, Tang C, Tang Z. ALOX5 acts as a key role in regulating the immune microenvironment in intrahepatic cholangiocarcinoma, recruiting tumor-associated macrophages through PI3K pathway. J Transl Med 2023; 21:923. [PMID: 38124204 PMCID: PMC10734103 DOI: 10.1186/s12967-023-04804-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Intrahepatic cholangiocarcinoma (ICC) is poorly treated due to the presence of an inhibitory immune microenvironment. Tumor-associated macrophages (TAM) are an important component of TME. ALOX5 is an important lipid metabolism enzyme in cancer progression, but the mechanism by which it regulates TAM to promote ICC progression is unknown. The aim of this study was to investigate the potential mechanism of TAM regulation by ALOX5 and the translational effect of targeting ALOX5. METHODS In this study, we investigated the association between the spatial localization of epithelial cells and TAMs by combining scRNA-seq analysis with multiplex immunofluorescence analysis. Through bulk sequencing analysis and spatial analysis, lipid metabolism genes closely related to TAM infiltration were screened. In vitro co-culture model was constructed to verify that ALOX5 and its downstream metabolite LTB4 promote M2 macrophage migration. Bulk sequencing after co-culture combined with single-cell analysis was performed to identify key pathways for up-regulation of M2 macrophage migration. Finally, the effect of CSF1R inhibitor (PLX3397) combined with ALOX5 inhibitor (Zileuton) in vivo was investigated by by xenograft tumor formation experiment in nude mice. RESULTS ALOX5 in ICC cells was a key lipid metabolism gene affecting the infiltration of M2 macrophages in TME. Mechanically, LTB4, a metabolite downstream of ALOX5, recruited M2 macrophages to migrate around tumor cells by binding to BLT1/BLT2 and activating the PI3K pathway, which ultimately lead to the promotion of ICC progression. Targeting CSF1R in combination with ALOX5 inhibitor effectively reduced tumor volume and M2 macrophage infiltration abundance. CONCLUSION In ICC, LTB4, a metabolite secreted by ALOX5 of epithelial cells, binded to BLT1/BLT2 on TAM surface to activate PI3K pathway and promote TAM migration, thus promoting ICC progression. Targeting CSF1R in combination with ALOX5 inhibitor for ICC is a promising combination therapy modality.
Collapse
Affiliation(s)
- Jialu Chen
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200092, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Yue Tang
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200092, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Delong Qin
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200092, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Xiaopeng Yu
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200092, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Huanjun Tong
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200092, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Chengwei Tang
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200092, China
| | - Zhaohui Tang
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200092, China.
- Department of Blood Transfusion, Xinhua Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200092, China.
- Shanghai Key Laboratory of Biliary Tract Disease Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
| |
Collapse
|
160
|
Duan J, Zhang Y, Chen R, Liang L, Huo Y, Lu S, Zhao J, Hu C, Sun Y, Yang K, Chen M, Yu Y, Ying J, Huang R, Ma X, Leaw S, Bai F, Shen Z, Cai S, Gao D, Wang J, Wang Z. Tumor-immune microenvironment and NRF2 associate with clinical efficacy of PD-1 blockade combined with chemotherapy in lung squamous cell carcinoma. Cell Rep Med 2023; 4:101302. [PMID: 38052215 PMCID: PMC10772345 DOI: 10.1016/j.xcrm.2023.101302] [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: 09/30/2022] [Revised: 03/29/2023] [Accepted: 11/02/2023] [Indexed: 12/07/2023]
Abstract
The RATIONALE-307 study (ClinicalTrials.gov: NCT03594747) demonstrates prolonged progression-free survival (PFS) with first-line tislelizumab plus chemotherapy versus chemotherapy in advanced lung squamous cell carcinoma (LUSC; N = 360). Here we describe an immune-related gene expression signature (GES), composed of genes involved in both innate and adaptive immunity, that appears to differentiate tislelizumab plus chemotherapy PFS benefit versus chemotherapy. In contrast, a tislelizumab plus chemotherapy PFS benefit is observed regardless of programmed death ligand 1 (PD-L1) expression or tumor mutational burden (TMB). Genetic analysis reveals that NRF2 pathway activation is enriched in PD-L1positive and TMBhigh patients. NRF2 pathway activation is negatively associated with PFS, which affects efficacy outcomes associated with PD-L1 and TMB status, impairing their predictive potential. Mechanistic studies demonstrate that NRF2 directly mediates PD-L1 constitutive expression independent of adaptive PD-L1 regulation in LUSC. In summary, the GES is an immune signature that might identify LUSC patients likely to benefit from first-line tislelizumab plus chemotherapy.
Collapse
Affiliation(s)
- Jianchun Duan
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yun Zhang
- BeiGene (Beijing) Co., Ltd., Beijing 100022, China
| | - Ran Chen
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai 200090, China; Department of General Surgery, Yangpu Hospital, Tongji University School of Medicine, Shanghai 200090, China
| | - Liang Liang
- BeiGene (Beijing) Co., Ltd., Beijing 100022, China
| | - Yi Huo
- BeiGene (Beijing) Co., Ltd., Beijing 100022, China
| | - Shun Lu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Jun Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Department of Thoracic Medical Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Chunhong Hu
- Oncology Department, The Second Hospital of Central South University, Changsha 410011, China
| | - Yuping Sun
- Oncology Department, Jinan Central Hospital, Shandong 250013, China
| | - Kunyu Yang
- Union Hospital, Cancer Center, Tongji Medical College, Huazhong University of Science and Technology, Hubei 430074, China
| | - Mingwei Chen
- Department of Respiratory Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yan Yu
- Department of Respiratory Medicine, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Ruiqi Huang
- BeiGene (Shanghai) Co., Ltd., Shanghai 200040, China
| | - Xiaopeng Ma
- BeiGene (Beijing) Co., Ltd., Beijing 100022, China
| | | | - Fan Bai
- BeiGene (Shanghai) Co., Ltd., Shanghai 200040, China
| | - Zhirong Shen
- BeiGene (Beijing) Co., Ltd., Beijing 100022, China
| | - Shangli Cai
- Burning Rock Biotech, Guangzhou 510300, China
| | - Daming Gao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; School of Life Science, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou 310024, China
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| |
Collapse
|
161
|
Marcoux P, Hwang JW, Desterke C, Imeri J, Bennaceur-Griscelli A, Turhan AG. Modeling RET-Rearranged Non-Small Cell Lung Cancer (NSCLC): Generation of Lung Progenitor Cells (LPCs) from Patient-Derived Induced Pluripotent Stem Cells (iPSCs). Cells 2023; 12:2847. [PMID: 38132167 PMCID: PMC10742233 DOI: 10.3390/cells12242847] [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: 11/07/2023] [Revised: 12/03/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
REarranged during Transfection (RET) oncogenic rearrangements can occur in 1-2% of lung adenocarcinomas. While RET-driven NSCLC models have been developed using various approaches, no model based on patient-derived induced pluripotent stem cells (iPSCs) has yet been described. Patient-derived iPSCs hold great promise for disease modeling and drug screening. However, generating iPSCs with specific oncogenic drivers, like RET rearrangements, presents challenges due to reprogramming efficiency and genotypic variability within tumors. To address this issue, we aimed to generate lung progenitor cells (LPCs) from patient-derived iPSCs carrying the mutation RETC634Y, commonly associated with medullary thyroid carcinoma. Additionally, we established a RETC634Y knock-in iPSC model to validate the effect of this oncogenic mutation during LPC differentiation. We successfully generated LPCs from RETC634Y iPSCs using a 16-day protocol and detected an overexpression of cancer-associated markers as compared to control iPSCs. Transcriptomic analysis revealed a distinct signature of NSCLC tumor repression, suggesting a lung multilineage lung dedifferentiation, along with an upregulated signature associated with RETC634Y mutation, potentially linked to poor NSCLC prognosis. These findings were validated using the RETC634Y knock-in iPSC model, highlighting key cancerous targets such as PROM2 and C1QTNF6, known to be associated with poor prognostic outcomes. Furthermore, the LPCs derived from RETC634Y iPSCs exhibited a positive response to the RET inhibitor pralsetinib, evidenced by the downregulation of the cancer markers. This study provides a novel patient-derived off-the-shelf iPSC model of RET-driven NSCLC, paving the way for exploring the molecular mechanisms involved in RET-driven NSCLC to study disease progression and to uncover potential therapeutic targets.
Collapse
Affiliation(s)
- Paul Marcoux
- INSERM UMR-S-1310, Université Paris Saclay, 94800 Villejuif, France; (P.M.); (J.W.H.); (C.D.); (J.I.); (A.B.-G.)
- Faculty of Medicine, Paris-Saclay University, 94270 Le Kremlin Bicetre, France
| | - Jin Wook Hwang
- INSERM UMR-S-1310, Université Paris Saclay, 94800 Villejuif, France; (P.M.); (J.W.H.); (C.D.); (J.I.); (A.B.-G.)
- Faculty of Medicine, Paris-Saclay University, 94270 Le Kremlin Bicetre, France
| | - Christophe Desterke
- INSERM UMR-S-1310, Université Paris Saclay, 94800 Villejuif, France; (P.M.); (J.W.H.); (C.D.); (J.I.); (A.B.-G.)
- Faculty of Medicine, Paris-Saclay University, 94270 Le Kremlin Bicetre, France
| | - Jusuf Imeri
- INSERM UMR-S-1310, Université Paris Saclay, 94800 Villejuif, France; (P.M.); (J.W.H.); (C.D.); (J.I.); (A.B.-G.)
- Faculty of Medicine, Paris-Saclay University, 94270 Le Kremlin Bicetre, France
| | - Annelise Bennaceur-Griscelli
- INSERM UMR-S-1310, Université Paris Saclay, 94800 Villejuif, France; (P.M.); (J.W.H.); (C.D.); (J.I.); (A.B.-G.)
- Faculty of Medicine, Paris-Saclay University, 94270 Le Kremlin Bicetre, France
- APHP Paris Saclay, Department of Hematology, Hôpital Bicêtre, 94270 Le Kremlin Bicetre, France
- Center for IPSC Therapies, CITHERA, INSERM UMS-45, Genopole Campus, 91100 Evry, France
- APHP Paris Saclay, Department of Hematology, Hôpital Paul Brousse, 94800 Villejuif, France
| | - Ali G. Turhan
- INSERM UMR-S-1310, Université Paris Saclay, 94800 Villejuif, France; (P.M.); (J.W.H.); (C.D.); (J.I.); (A.B.-G.)
- Faculty of Medicine, Paris-Saclay University, 94270 Le Kremlin Bicetre, France
- APHP Paris Saclay, Department of Hematology, Hôpital Bicêtre, 94270 Le Kremlin Bicetre, France
- Center for IPSC Therapies, CITHERA, INSERM UMS-45, Genopole Campus, 91100 Evry, France
- APHP Paris Saclay, Department of Hematology, Hôpital Paul Brousse, 94800 Villejuif, France
| |
Collapse
|
162
|
Hwang SM, Awasthi D, Jeong J, Sandoval TA, Chae CS, Ramos Y, Tan C, Falco MM, McBain IT, Mishra B, Ivashkiv LB, Zamarin D, Cantillo E, Chapman-Davis E, Holcomb K, Morales DK, Rodriguez PC, Conejo-Garcia JR, Kaczocha M, Vähärautio A, Song M, Cubillos-Ruiz JR. Transgelin 2 guards T cell lipid metabolic programming and anti-tumor function. RESEARCH SQUARE 2023:rs.3.rs-3683989. [PMID: 38168227 PMCID: PMC10760247 DOI: 10.21203/rs.3.rs-3683989/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Mounting effective immunity against pathogens and tumors relies on the successful metabolic programming of T cells by extracellular fatty acids1-3. During this process, fatty-acid-binding protein 5 (FABP5) imports lipids that fuel mitochondrial respiration and sustain the bioenergetic requirements of protective CD8+ T cells4,5. Importantly, however, the mechanisms governing this crucial immunometabolic axis remain unexplored. Here we report that the cytoskeletal organizer Transgelin 2 (TAGLN2) is necessary for optimal CD8+ T cell fatty acid uptake, mitochondrial respiration, and anti-cancer function. We found that TAGLN2 interacts with FABP5, enabling the surface localization of this lipid importer on activated CD8+ T cells. Analysis of ovarian cancer specimens revealed that endoplasmic reticulum (ER) stress responses elicited by the tumor microenvironment repress TAGLN2 in infiltrating CD8+ T cells, enforcing their dysfunctional state. Restoring TAGLN2 expression in ER-stressed CD8+ T cells bolstered their lipid uptake, mitochondrial respiration, and cytotoxic capacity. Accordingly, chimeric antigen receptor T cells overexpressing TAGLN2 bypassed the detrimental effects of tumor-induced ER stress and demonstrated superior therapeutic efficacy in mice with metastatic ovarian cancer. Our study unveils the role of cytoskeletal TAGLN2 in T cell lipid metabolism and highlights the potential to enhance cellular immunotherapy in solid malignancies by preserving the TAGLN2-FABP5 axis.
Collapse
Affiliation(s)
- Sung-Min Hwang
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Deepika Awasthi
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Jieun Jeong
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Tito A. Sandoval
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Chang-Suk Chae
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Yusibeska Ramos
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
| | - Chen Tan
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Matías Marin Falco
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ian T. McBain
- Weill Cornell Graduate School of Medical Sciences. New York, NY 10065. USA
| | - Bikash Mishra
- Weill Cornell Graduate School of Medical Sciences. New York, NY 10065. USA
- HSS Research Institute and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
| | - Lionel B. Ivashkiv
- Weill Cornell Graduate School of Medical Sciences. New York, NY 10065. USA
- HSS Research Institute and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
| | - Dmitriy Zamarin
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Evelyn Cantillo
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Eloise Chapman-Davis
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Kevin Holcomb
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Diana K. Morales
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
| | - Paulo C. Rodriguez
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute. Tampa, FL, USA
| | - Jose R. Conejo-Garcia
- Department of Integrated Immunobiology, Duke School of Medicine, Durham, NC 27710, USA
- Duke Cancer Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Martin Kaczocha
- Department of Anesthesiology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, USA
- Stony Brook University Pain and Analgesia Research Center (SPARC), Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Anna Vähärautio
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Minkyung Song
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Juan R. Cubillos-Ruiz
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
- Weill Cornell Graduate School of Medical Sciences. New York, NY 10065. USA
| |
Collapse
|
163
|
Yu H, Liu Q, Jin M, Huang G, Cai Q. Comprehensive analysis of mitophagy-related genes in NSCLC diagnosis and immune scenery: based on bulk and single-cell RNA sequencing data. Front Immunol 2023; 14:1276074. [PMID: 38155968 PMCID: PMC10752969 DOI: 10.3389/fimmu.2023.1276074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/29/2023] [Indexed: 12/30/2023] Open
Abstract
Lung cancer is the main cause of cancer-related deaths, and non-small cell lung cancer (NSCLC) is the most common type. Understanding the potential mechanisms, prognosis, and treatment aspects of NSCLC is essential. This study systematically analyzed the correlation between mitophagy and NSCLC. Six mitophagy-related feature genes (SRC, UBB, PINK1, FUNDC1, MAP1LC3B, and CSNK2A1) were selected through machine learning and used to construct a diagnostic model for NSCLC. These feature genes are closely associated with the occurrence and development of NSCLC. Additionally, NSCLC was divided into two subtypes using unsupervised consensus clustering, and their differences in clinical characteristics, immune infiltration, and immunotherapy were systematically analyzed. Furthermore, the interaction between mitophagy-related genes (MRGs) and immune cells was analyzed using single-cell sequencing data. The findings of this study will contribute to the development of potential diagnostic biomarkers for NSCLC and the advancement of personalized treatment strategies.
Collapse
Affiliation(s)
- Haibo Yu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China
- School of Medical Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Qingtao Liu
- Department of Cardiothoracic Surgery, Xinhua Hospital Affiliated Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Mingming Jin
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China
- School of Medical Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Gang Huang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China
- School of Medical Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Qianqian Cai
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China
- School of Medical Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China
| |
Collapse
|
164
|
Lu H, Qian J, Cheng L, Shen Y, Chu T, Zhao C. Single-cell RNA-sequencing uncovers the dynamic changes of tumour immune microenvironment in advanced lung adenocarcinoma. BMJ Open Respir Res 2023; 10:e001878. [PMID: 38081768 PMCID: PMC10729175 DOI: 10.1136/bmjresp-2023-001878] [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: 06/08/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND The heterogeneity of lung adenocarcinoma (LUAD) plays a vital role in determining the development of cancer and therapeutic sensitivity and significantly hinders the clinical treatment of LUAD. OBJECTIVE To elucidate the cellular composition and reveal previously uncharacterised tumour microenvironment in LUAD using single-cell RNA-sequencing (scRNA-seq). METHODS Two scRNA-seq datasets with 106 829 high-quality cells from 34 patients including 11 normal, 9 early (stage I and II) and 14 advanced (stage III and IV) LUAD were integrated and clustered to explore diagnostic and therapeutic cell populations and their biomarkers for diverse stages of LUAD. Three independent bulk RNA-seq datasets were used to validate the results from scRNA-seq analysis. The expression of marker genes for specific cell types in early and advanced LUAD was verified by immunohistochemistry (IHC). RESULTS Comprehensive cluster analysis identified that S100P+ epithelial and SPP1+ macrophage, positively related to poor outcomes, were preferentially enriched in advanced stage. Although the accumulation of KLRB1+CD8+ T cell and IGHA1+/IGHG1+ plasma cell both significantly associated the favourable prognosis, we also found KLRB1+CD8+ T cell decreased in advanced stage while IGHA1+/IGHG1+ plasma cells were increased. Cell-cell communication analysis showed that SPP1+ macrophage could interact with most of CD8+ subclusters through SPP1-CD44 axis. Furthermore, based on three independent bulk RNA-seq datasets, we built risk model with nine marker genes for specific cell subtypes and conducted deconvolution analysis, both supporting our results from scRNA-seq data. We finally validated the expression of four marker genes in early and advanced LUAD by IHC. CONCLUSION Our analyses highlight the molecular dynamics of LUAD epithelial and microenvironment and provide new targets to improve LUAD therapy.
Collapse
Affiliation(s)
- Haijiao Lu
- Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jialin Qian
- Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Cheng
- Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yinchen Shen
- Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianqing Chu
- Department of Respiratory and Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chaoxian Zhao
- Shanghai Cancer Institute, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
165
|
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.
Collapse
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
| |
Collapse
|
166
|
Tang C, Fu S, Jin X, Li W, Xing F, Duan B, Cheng X, Chen X, Wang S, Zhu C, Li G, Chuai G, He Y, Wang P, Liu Q. Personalized tumor combination therapy optimization using the single-cell transcriptome. Genome Med 2023; 15:105. [PMID: 38041202 PMCID: PMC10691165 DOI: 10.1186/s13073-023-01256-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 11/13/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND The precise characterization of individual tumors and immune microenvironments using transcriptome sequencing has provided a great opportunity for successful personalized cancer treatment. However, the cancer treatment response is often characterized by in vitro assays or bulk transcriptomes that neglect the heterogeneity of malignant tumors in vivo and the immune microenvironment, motivating the need to use single-cell transcriptomes for personalized cancer treatment. METHODS Here, we present comboSC, a computational proof-of-concept study to explore the feasibility of personalized cancer combination therapy optimization using single-cell transcriptomes. ComboSC provides a workable solution to stratify individual patient samples based on quantitative evaluation of their personalized immune microenvironment with single-cell RNA sequencing and maximize the translational potential of in vitro cellular response to unify the identification of synergistic drug/small molecule combinations or small molecules that can be paired with immune checkpoint inhibitors to boost immunotherapy from a large collection of small molecules and drugs, and finally prioritize them for personalized clinical use based on bipartition graph optimization. RESULTS We apply comboSC to publicly available 119 single-cell transcriptome data from a comprehensive set of 119 tumor samples from 15 cancer types and validate the predicted drug combination with literature evidence, mining clinical trial data, perturbation of patient-derived cell line data, and finally in-vivo samples. CONCLUSIONS Overall, comboSC provides a feasible and one-stop computational prototype and a proof-of-concept study to predict potential drug combinations for further experimental validation and clinical usage using the single-cell transcriptome, which will facilitate and accelerate personalized tumor treatment by reducing screening time from a large drug combination space and saving valuable treatment time for individual patients. A user-friendly web server of comboSC for both clinical and research users is available at www.combosc.top . The source code is also available on GitHub at https://github.com/bm2-lab/comboSC .
Collapse
Affiliation(s)
- Chen Tang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Xuan Jin
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Wannian Li
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Bin Duan
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Xiaojie Cheng
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaohan Chen
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shuguang Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Chenyu Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Gaoyang Li
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Guohui Chuai
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yayi He
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, China.
| | - Ping Wang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, Tongji University, Shanghai, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, China.
- Tongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, Tongji University, Shanghai, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| |
Collapse
|
167
|
Lu Y, Chen QM, An L. Semi-reference based cell type deconvolution with application to human metastatic cancers. NAR Genom Bioinform 2023; 5:lqad109. [PMID: 38143958 PMCID: PMC10748484 DOI: 10.1093/nargab/lqad109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/01/2023] [Accepted: 12/13/2023] [Indexed: 12/26/2023] Open
Abstract
Bulk RNA-seq experiments, commonly used to discern gene expression changes across conditions, often neglect critical cell type-specific information due to their focus on average transcript abundance. Recognizing cell type contribution is crucial to understanding phenotype and disease variations. The advent of single-cell RNA sequencing has allowed detailed examination of cellular heterogeneity; however, the cost and analytic caveat prohibits such sequencing for a large number of samples. We introduce a novel deconvolution approach, SECRET, that employs cell type-specific gene expression profiles from single-cell RNA-seq to accurately estimate cell type proportions from bulk RNA-seq data. Notably, SECRET can adapt to scenarios where the cell type present in the bulk data is unrepresented in the reference, thereby offering increased flexibility in reference selection. SECRET has demonstrated superior accuracy compared to existing methods using synthetic data and has identified unknown tissue-specific cell types in real human metastatic cancers. Its versatility makes it broadly applicable across various human cancer studies.
Collapse
Affiliation(s)
- Yingying Lu
- Interdisciplinary Program in Statistics and Data Science, University of Arizona, Tucson, AZ, USA
| | - Qin M Chen
- College of Pharmacy, University of Arizona, Tucson, AZ, USA
- Cancer Biology Program, University of Arizona, Tucson, AZ, USA
| | - Lingling An
- Interdisciplinary Program in Statistics and Data Science, University of Arizona, Tucson, AZ, USA
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, USA
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ, USA
| |
Collapse
|
168
|
Yi M, Shi J, Tan X, Zhang X, Tao D, Yang Y, Liu Y. Integration and deconvolution methodology deciphering prognosis-related signatures in lung adenocarcinoma. J Cancer Res Clin Oncol 2023; 149:16441-16460. [PMID: 37710052 DOI: 10.1007/s00432-023-05403-9] [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: 08/04/2023] [Accepted: 09/04/2023] [Indexed: 09/16/2023]
Abstract
PURPOSE This study aims to establish a risk prediction model based on prognosis-related genes (PRGs) and clinicopathological factors, and investigate the biological activities of PRGs in lung adenocarcinoma (LUAD). METHODS Risk score signatures were developed by employing multiple algorithms and their amalgamations. A predictive model for overall survival was established through the integration of risk score signatures and several clinicopathological parameters. A comprehensive single-cell atlas, gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were used to investigate the biological activities of prognosis-related genes in LUAD. RESULTS A risk prediction model was established based on 16 PRGs, exhibiting robust performance in predicting overall survival. The single-cell analysis revealed that epithelial cells were primarily associated with worse survival of LUAD, and PRGs were predominantly enriched in malignant epithelial cells and influenced epithelial cell growth and progression. Furthermore, GSEA and GSVA analysis showed that PRGs were involved in tumor pathways such as epithelial-mesenchymal transition, hypoxia and KRAS_UP, and high GSVA scores are correlated with worse outcome in LUAD patients. CONCLUSIONS The constructed risk prediction model in this study offers clinicians a valuable tool for tailoring treatment strategies of LUAD and provides a comprehensive interpretation on the biological activities of PRGs in LUAD.
Collapse
Affiliation(s)
- Ming Yi
- Department of Medical Genetics and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jiaying Shi
- Department of Medical Genetics and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaolan Tan
- Department of Medical Genetics and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xinyue Zhang
- Department of Medical Genetics and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Dachang Tao
- Department of Medical Genetics and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuan Yang
- Department of Medical Genetics and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yunqiang Liu
- Department of Medical Genetics and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
| |
Collapse
|
169
|
Takatsu F, Suzawa K, Tomida S, Thu YM, Sakaguchi M, Toji T, Ohki M, Tsudaka S, Date K, Matsuda N, Iwata K, Zhu Y, Nakata K, Shien K, Yamamoto H, Nakayama A, Okazaki M, Sugimoto S, Toyooka S. Periostin secreted by cancer-associated fibroblasts promotes cancer progression and drug resistance in non-small cell lung cancer. J Mol Med (Berl) 2023; 101:1603-1614. [PMID: 37831111 DOI: 10.1007/s00109-023-02384-7] [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: 02/02/2023] [Revised: 09/19/2023] [Accepted: 10/05/2023] [Indexed: 10/14/2023]
Abstract
Cancer-associated fibroblasts (CAFs) are important components in the tumor microenvironment, and we sought to identify effective therapeutic targets in CAFs for non-small cell lung cancer (NSCLC). In this study, we established fibroblast cell lines from the cancerous and non-cancerous parts of surgical lung specimens from patients with NSCLC and evaluated the differences in behaviors towards NSCLC cells. RNA sequencing analysis was performed to investigate the differentially expressed genes between normal fibroblasts (NFs) and CAFs, and we identified that the expression of periostin (POSTN), which is known to be overexpressed in various solid tumors and promote cancer progression, was significantly higher in CAFs than in NFs. POSTN increased cell proliferation via NSCLC cells' ERK pathway activation and induced epithelial-mesenchymal transition (EMT), which improved migration in vitro. In addition, POSTN knockdown in CAFs suppressed these effects, and in vivo experiments demonstrated that the POSTN knockdown improved the sensitivity of EGFR-mutant NSCLC cells for osimertinib treatment. Collectively, our results showed that CAF-derived POSTN is involved in tumor growth, migration, EMT induction, and drug resistance in NSCLC. Targeting CAF-secreted POSTN could be a potential therapeutic strategy for NSCLC. KEY MESSAGES: • POSTN is significantly upregulated in CAFs compared to normal fibroblasts in NCSLC. • POSTN increases cell proliferation via activation of the NSCLC cells' ERK pathway. • POSTN induces EMT in NSCLC cells and improves the migration ability. • POSTN knockdown improves the sensitivity for osimertinib in EGFR-mutant NSCLC cells.
Collapse
Affiliation(s)
- Fumiaki Takatsu
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Ken Suzawa
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan.
| | - Shuta Tomida
- Center for Comprehensive Genomic Medicine, Okayama University Hospital, Okayama, Japan
| | - Yin Min Thu
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Masakiyo Sakaguchi
- Department of Cell Biology, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Tomohiro Toji
- Department of Pathology, Okayama University Hospital, Okayama, Japan
| | - Masayoshi Ohki
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Shimpei Tsudaka
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Keiichi Date
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Naoki Matsuda
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Kazuma Iwata
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Yidan Zhu
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Kentaro Nakata
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Kazuhiko Shien
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Hiromasa Yamamoto
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Akiko Nakayama
- Department of Pharmacology, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mikio Okazaki
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Seiichiro Sugimoto
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Shinichi Toyooka
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| |
Collapse
|
170
|
Liu X, Zhang L, Zhu B, Liu Y, Li L, Hou J, Qian M, Zheng N, Zeng Y, Chen C, Goel A, Wang X. Role of GSDM family members in airway epithelial cells of lung diseases: a systematic and comprehensive transcriptomic analysis. Cell Biol Toxicol 2023; 39:2743-2760. [PMID: 37462807 DOI: 10.1007/s10565-023-09799-5] [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: 10/12/2022] [Accepted: 03/05/2023] [Indexed: 12/03/2023]
Abstract
Gasdermin (GSDM) family, the key executioners of pyroptosis, play crucial roles in anti-pathogen and anti-tumor immunities, although little is known about the expression of GSDM in lung diseases at single-cell resolution, especially in lung epithelial cells. We comprehensively investigated the transcriptomic profiles of GSDM members in various lung tissues from healthy subjects or patients with different lung diseases at single cell level, e.g., chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), lung adenocarcinoma (LUAD), or systemic sclerosis (SSC). The expression of GSDM members varied among pulmonary cell types (immune cells, structural cells, and especially epithelial cells) and even across lung diseases. Regarding disease-associated specificities, we found that GSDMC or GSDMD altered significantly in ciliated epithelia of COPD or LUAD, GSDMD in mucous, club, and basal cells of LUAD and GSDMC in mucous epithelia of para-tumor tissue, as compared with the corresponding epithelia of other diseases. The phenomic specificity of GSDM in lung cancer subtypes was noticed by comparing with 15 non-pulmonary cancers and para-cancer samples. GSDM family gene expression changes were also observed in different lung epithelial cell lines (e.g., HBE, A549, H1299, SPC-1, or H460) in responses to external challenges, including lipopolysaccharide (LPS), lysophosphatidylcholine (lysoPC), cigarette smoking extract (CSE), cholesterol, and AR2 inhibitor at various doses or durations. GSDMA is rarely expressed in those cell lines, while GSDMB and GSDMC are significantly upregulated in human lung epithelia. Our data indicated that the heterogeneity of GSDM member expression exists at different cells, pathologic conditions, challenges, probably dependent upon cell biological phenomes, functions, and behaviors, upon cellular responses to external changes, and the nature and severity of lung disease. Thus, the deep exploration of GSDM phenomes may provide new insights into understanding the single-cell roles in the tissue, regulatory roles of the GSDM family in the pathogenesis, and potential values of biomarker identification and development.
Collapse
Affiliation(s)
- Xuanqi Liu
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai, China
- Shanghai Institute of Clinical Bioinformatics, Shanghai, China
- Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, China
| | - Linlin Zhang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai, China
| | - Bijun Zhu
- Shanghai Institute of Clinical Bioinformatics, Shanghai, China
- Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, China
| | - Yifei Liu
- Center of Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Liyang Li
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai, China
| | - Jiayun Hou
- Shanghai Institute of Clinical Bioinformatics, Shanghai, China
| | - Mengjia Qian
- Shanghai Institute of Clinical Bioinformatics, Shanghai, China
| | - Nannan Zheng
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai, China
| | - Yiming Zeng
- Center of Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
| | - Chengshui Chen
- Quzhou Hospital of Wenzhou Medical University, Quzhou, Zhejiang Province, China.
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
| | - Xiangdong Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai, China.
- Shanghai Institute of Clinical Bioinformatics, Shanghai, China.
- Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, China.
| |
Collapse
|
171
|
Ghaddar B, De S. Hierarchical and automated cell-type annotation and inference of cancer cell of origin with Census. Bioinformatics 2023; 39:btad714. [PMID: 38011649 PMCID: PMC10713118 DOI: 10.1093/bioinformatics/btad714] [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: 02/21/2023] [Revised: 10/26/2023] [Accepted: 11/25/2023] [Indexed: 11/29/2023] Open
Abstract
MOTIVATION Cell-type annotation is a time-consuming yet critical first step in the analysis of single-cell RNA-seq data, especially when multiple similar cell subtypes with overlapping marker genes are present. Existing automated annotation methods have a number of limitations, including requiring large reference datasets, high computation time, shallow annotation resolution, and difficulty in identifying cancer cells or their most likely cell of origin. RESULTS We developed Census, a biologically intuitive and fully automated cell-type identification method for single-cell RNA-seq data that can deeply annotate normal cells in mammalian tissues and identify malignant cells and their likely cell of origin. Motivated by the inherently stratified developmental programs of cellular differentiation, Census infers hierarchical cell-type relationships and uses gradient-boosted \decision trees that capitalize on nodal cell-type relationships to achieve high prediction speed and accuracy. When benchmarked on 44 atlas-scale normal and cancer, human and mouse tissues, Census significantly outperforms state-of-the-art methods across multiple metrics and naturally predicts the cell-of-origin of different cancers. Census is pretrained on the Tabula Sapiens to classify 175 cell-types from 24 organs; however, users can seamlessly train their own models for customized applications. AVAILABILITY AND IMPLEMENTATION Census is available at Zenodo https://zenodo.org/records/7017103 and on our Github https://github.com/sjdlabgroup/Census.
Collapse
Affiliation(s)
- Bassel Ghaddar
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, United States
| | - Subhajyoti De
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, United States
| |
Collapse
|
172
|
Huang Q, Wang F, Hao D, Li X, Li X, Lei T, Yue J, Liu C. Deciphering tumor-infiltrating dendritic cells in the single-cell era. Exp Hematol Oncol 2023; 12:97. [PMID: 38012715 PMCID: PMC10680280 DOI: 10.1186/s40164-023-00459-2] [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: 07/10/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023] Open
Abstract
Dendritic cells (DCs) serve as a pivotal link connecting innate and adaptive immunity by processing tumor-derived antigens and activating T cells. The advent of single-cell sequencing has revolutionized the categorization of DCs, enabling a high-resolution characterization of the previously unrecognized diversity of DC populations infiltrating the intricate tumor microenvironment (TME). The application of single-cell sequencing technologies has effectively elucidated the heterogeneity of DCs present in the tumor milieu, yielding invaluable insights into their subpopulation structures and functional diversity. This review provides a comprehensive summary of the current state of knowledge regarding DC subtypes in the TME, drawing from single-cell studies conducted across various human tumors. We focused on the categorization, functions, and interactions of distinct DC subsets, emphasizing their crucial roles in orchestrating tumor-related immune responses. Additionally, we delve into the potential implications of these findings for the identification of predictive biomarkers and therapeutic targets. Enhanced insight into the intricate interplay between DCs and the TME promises to advance our comprehension of tumor immunity and, in turn, pave the way for the development of more efficacious cancer immunotherapies.
Collapse
Affiliation(s)
- Qingyu Huang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China
| | - Fuhao Wang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China
| | - Di Hao
- The Second Clinical Medical College, Anhui Medical University, Hefei, 230032, China
| | - Xinyu Li
- The Second Clinical Medical College, Anhui Medical University, Hefei, 230032, China
| | - Xiaohui Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China
| | - Tianyu Lei
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Jinbo Yue
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China.
| | - Chao Liu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China.
| |
Collapse
|
173
|
Man HSJ, Moosa VA, Singh A, Wu L, Granton JT, Juvet SC, Hoang CD, de Perrot M. Unlocking the potential of RNA-based therapeutics in the lung: current status and future directions. Front Genet 2023; 14:1281538. [PMID: 38075698 PMCID: PMC10703483 DOI: 10.3389/fgene.2023.1281538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/06/2023] [Indexed: 02/12/2024] Open
Abstract
Awareness of RNA-based therapies has increased after the widespread adoption of mRNA vaccines against SARS-CoV-2 during the COVID-19 pandemic. These mRNA vaccines had a significant impact on reducing lung disease and mortality. They highlighted the potential for rapid development of RNA-based therapies and advances in nanoparticle delivery systems. Along with the rapid advancement in RNA biology, including the description of noncoding RNAs as major products of the genome, this success presents an opportunity to highlight the potential of RNA as a therapeutic modality. Here, we review the expanding compendium of RNA-based therapies, their mechanisms of action and examples of application in the lung. The airways provide a convenient conduit for drug delivery to the lungs with decreased systemic exposure. This review will also describe other delivery methods, including local delivery to the pleura and delivery vehicles that can target the lung after systemic administration, each providing access options that are advantageous for a specific application. We present clinical trials of RNA-based therapy in lung disease and potential areas for future directions. This review aims to provide an overview that will bring together researchers and clinicians to advance this burgeoning field.
Collapse
Affiliation(s)
- H. S. Jeffrey Man
- Temerty Faculty of Medicine, Institute of Medical Science, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Division of Respirology and Critical Care Medicine, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Vaneeza A. Moosa
- Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Division of Thoracic Surgery, Toronto General Hospital, Toronto, ON, Canada
| | - Anand Singh
- Thoracic Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Licun Wu
- Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Division of Thoracic Surgery, Toronto General Hospital, Toronto, ON, Canada
| | - John T. Granton
- Division of Respirology and Critical Care Medicine, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Stephen C. Juvet
- Temerty Faculty of Medicine, Institute of Medical Science, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Division of Respirology and Critical Care Medicine, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Chuong D. Hoang
- Thoracic Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Marc de Perrot
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Division of Thoracic Surgery, Toronto General Hospital, Toronto, ON, Canada
| |
Collapse
|
174
|
Yoon SH, Nam JW. Clustering malignant cell states using universally variable genes. Brief Bioinform 2023; 25:bbad460. [PMID: 38084922 PMCID: PMC10783859 DOI: 10.1093/bib/bbad460] [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: 08/09/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has revealed important insights into the heterogeneity of malignant cells. However, sample-specific genomic alterations often confound such analysis, resulting in patient-specific clusters that are difficult to interpret. Here, we present a novel approach to address the issue. By normalizing gene expression variances to identify universally variable genes (UVGs), we were able to reduce the formation of sample-specific clusters and identify underlying molecular hallmarks in malignant cells. In contrast to highly variable genes vulnerable to a specific sample bias, UVGs led to better detection of clusters corresponding to distinct malignant cell states. Our results demonstrate the utility of this approach for analyzing scRNA-seq data and suggest avenues for further exploration of malignant cell heterogeneity.
Collapse
Affiliation(s)
- Sang-Ho Yoon
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
- Hanyang Institute of Advanced BioConvergence, Hanyang University, Seoul 04763, Republic of Korea
- Hanyang Institute of Bioscience and Biotechnology, Bio-BigData Research Center, Hanyang University, Seoul 04763, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
- Hanyang Institute of Advanced BioConvergence, Hanyang University, Seoul 04763, Republic of Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Republic of Korea
- Hanyang Institute of Bioscience and Biotechnology, Bio-BigData Research Center, Hanyang University, Seoul 04763, Republic of Korea
| |
Collapse
|
175
|
Jiao D, Chen Y, Liu X, Tang X, Chen J, Liu Y, Jiang C, Chen Q. Targeting MET endocytosis or degradation to overcome HGF-induced gefitinib resistance in EGFR-sensitive mutant lung adenocarcinoma. Biochem Biophys Res Commun 2023; 682:371-380. [PMID: 37844446 DOI: 10.1016/j.bbrc.2023.10.037] [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: 08/04/2023] [Revised: 09/24/2023] [Accepted: 10/09/2023] [Indexed: 10/18/2023]
Abstract
The overexpression of hepatic growth factor(HGF) is one of the important reasons for the development of gefitinib resistance in EGFR-sensitive mutant lung adenocarcinoma cells. Targeting the HGF receptor MET through endocytosis inhibition or degradation induction has been proposed as a potential strategy to overcome this resistance. However, the effectiveness of this approach remains needs to be evaluated. In this study, we observed that MET receptors undergo persistent endocytosis but rarely enter the degradation pathway in HGF-overexpressing cells. We showed that MET endocytosis can be inhibited by using gene silence method or MET inhibitors. CHC or DNM2 gene silence slightly increases the sensitivity of resistant cells to gefitinib without affecting MET activity, while GRB2 gene silence can simultaneously inhibit MET endocytosis and reduce MET activity, resulting in a significant reversal effect of gefitinib resistance. Similarly, MET inhibitors significantly reverse drug resistance, accompanied by simultaneous inhibition of MET endocytosis and activity, highlighting the importance of both endocytosis and activity in HGF-induced gefitinib resistance. Additionally, we demonstrated that promoting MET degradation through deubiquitinase (USP8 or USP32) gene silence is another effective method for reversing drug resistance. Overall, our findings suggest that targeting MET receptor endocytosis and degradation is an attractive strategy for overcoming HGF-induced gefitinib resistance in EGFR-sensitive mutant lung adenocarcinoma.
Collapse
Affiliation(s)
- Demin Jiao
- Department of Respiratory and Critical Care Medicine, The 903rd Hospital of PLA (Xihu Hospital Affiliated to Hangzhou Medical College), Hangzhou, 310013, China
| | - Yu Chen
- Department of Respiratory and Critical Care Medicine, The 903rd Hospital of PLA (Xihu Hospital Affiliated to Hangzhou Medical College), Hangzhou, 310013, China
| | - Xiang Liu
- Department of Respiratory and Critical Care Medicine, The 903rd Hospital of PLA (Xihu Hospital Affiliated to Hangzhou Medical College), Hangzhou, 310013, China
| | - Xiali Tang
- Department of Respiratory and Critical Care Medicine, The 903rd Hospital of PLA (Xihu Hospital Affiliated to Hangzhou Medical College), Hangzhou, 310013, China
| | - Jun Chen
- Department of Respiratory and Critical Care Medicine, The 903rd Hospital of PLA (Xihu Hospital Affiliated to Hangzhou Medical College), Hangzhou, 310013, China
| | - Yongyang Liu
- The First Clinical Medical College, Wenzhou Medical University, Wenzhou, 325000, China
| | - Chunyan Jiang
- Department of Respiratory and Critical Care Medicine, The 903rd Hospital of PLA (Xihu Hospital Affiliated to Hangzhou Medical College), Hangzhou, 310013, China.
| | - Qingyong Chen
- Department of Respiratory and Critical Care Medicine, The 903rd Hospital of PLA (Xihu Hospital Affiliated to Hangzhou Medical College), Hangzhou, 310013, China; The First Clinical Medical College, Wenzhou Medical University, Wenzhou, 325000, China.
| |
Collapse
|
176
|
Wu L, Xia W, Hua Y, Fan K, Lu Y, Wang M, Jin Y, Zhang W, Pan S. Cellular crosstalk of macrophages and therapeutic implications in non-small cell lung cancer revealed by integrative inference of single-cell transcriptomics. Front Pharmacol 2023; 14:1295442. [PMID: 38044943 PMCID: PMC10690610 DOI: 10.3389/fphar.2023.1295442] [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: 09/16/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
Introduction: Non-small cell lung cancer (NSCLC) exhibits heterogeneity with diverse immune cell infiltration patterns that can influence tumor cell behavior and immunotherapy. A comprehensive characterization of the tumor microenvironment can guide precision medicine. Methods: Here, we generated a single-cell atlas of 398170 cells from 52 NSCLC patients, and investigated the imprinted genes and cellular crosstalk for macrophages. Subsequently, we evaluated the effect of tumor cells on macrophages and verified the expression of marker genes using co-culture experiments, flow cytometry and RT-qPCR assays. Results: Remarkable macrophage adaptability to NSCLC environment was observed, which contributed to generating tumor-associated macrophages (TAMs). We identified 5 distinct functional TAM subtypes, of which the majority were SELENOP-positive macrophages, with high levels of SLC40A1 and CCL13. The TAMs were also involved in mediating CD8+ T cell activity and form intercellular interaction with cancer cells, as indicated by receptor-ligand binding. Indirect coculture of tumor cells SPC-A1 and THP-1 monocytes, produced M2-like TAMs that highly expressed several markers of SELENOP-positive macrophages. The abundance of this type TAMs seemed to be associated with poorer overall survival rates [hazard ratio (HR) = 1.34, 95% confidence interval (CI) = 0.98-1.83, p = 0.068] based on deconvolution of TCGA-LUAD dataset. Discussion: In summary, we provided a high-resolution molecular resource of TAMs, and displayed the acquired properties in the tumor microenvironment. Dynamic crosstalk between TAMs and tumor cells via multiple ligand-receptor pairs were revealed, emphasizing its role in sustaining the pro-tumoral microenvironment and its implications for cancer therapy.
Collapse
Affiliation(s)
- Lei Wu
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Wenying Xia
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Yiting Hua
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Kun Fan
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Yanfei Lu
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Min Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Yuexinzi Jin
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Wei Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Shiyang Pan
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| |
Collapse
|
177
|
Wei J, Yu W, Wu L, Chen Z, Huang G, Hu M, Du H. Intercellular Molecular Crosstalk Networks within Invasive and Immunosuppressive Tumor Microenvironment Subtypes Associated with Clinical Outcomes in Four Cancer Types. Biomedicines 2023; 11:3057. [PMID: 38002057 PMCID: PMC10669098 DOI: 10.3390/biomedicines11113057] [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: 10/05/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Heterogeneity is a critical basis for understanding how the tumor microenvironment (TME) contributes to tumor progression. However, an understanding of the specific characteristics and functions of TME subtypes (subTMEs) in the progression of cancer is required for further investigations into single-cell resolutions. Here, we analyzed single-cell RNA sequencing data of 250 clinical samples with more than 200,000 cells analyzed in each cancer datum. Based on the construction of an intercellular infiltration model and unsupervised clustering analysis, four, three, three, and four subTMEs were revealed in breast, colorectal, esophageal, and pancreatic cancer, respectively. Among the subTMEs, the immune-suppressive subTME (subTME-IS) and matrix remodeling with malignant cells subTME (subTME-MRM) were highly enriched in tumors, whereas the immune cell infiltration subTME (subTME-ICI) and precancerous state of epithelial cells subTME (subTME-PSE) were less in tumors, compared with paracancerous tissues. We detected and compared genes encoding cytokines, chemokines, cytotoxic mediators, PD1, and PD-L1. The results showed that these genes were specifically overexpressed in different cell types, and, compared with normal tissues, they were upregulated in tumor-derived cells. In addition, compared with other subTMEs, the expression levels of PDCD1 and TGFB1 were higher in subTME-IS. The Cox proportional risk regression model was further constructed to identify possible prognostic markers in each subTME across four cancer types. Cell-cell interaction analysis revealed the distinguishing features in molecular pairs among different subTMEs. Notably, ligand-receptor gene pairs, including COL1A1-SDC1, COL6A2-SDC1, COL6A3-SDC1, and COL4A1-ITGA2 between stromal and tumor cells, associated with tumor invasion phenotypes, poor patient prognoses, and tumor advanced progression, were revealed in subTME-MRM. C5AR1-RPS19, LGALS9-HAVCR2, and SPP1-PTGER4 between macrophages and CD8+ T cells, associated with CD8+ T-cell dysfunction, immunosuppressive status, and tumor advanced progression, were revealed in subTME-IS. The spatial co-location information of cellular and molecular interactions was further verified by spatial transcriptome data from colorectal cancer clinical samples. Overall, our study revealed the heterogeneity within the TME, highlighting the potential pro-invasion and pro-immunosuppressive functions and cellular infiltration characteristics of specific subTMEs, and also identified the key cellular and molecular interactions that might be associated with the survival, invasion, immune escape, and classification of cancer patients across four cancer types.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (J.W.); (W.Y.); (L.W.); (Z.C.); (G.H.); (M.H.)
| |
Collapse
|
178
|
Wang Z, Yang L, Wang W, Zhou H, Chen J, Ma Z, Wang X, Zhang Q, Liu H, Zhou C, Guo Z, Zhang X. Comparative immunological landscape between pre- and early-stage LUAD manifested as ground-glass nodules revealed by scRNA and scTCR integrated analysis. Cell Commun Signal 2023; 21:325. [PMID: 37957625 PMCID: PMC10644515 DOI: 10.1186/s12964-023-01322-x] [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: 06/18/2023] [Accepted: 09/16/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Mechanism underlying the malignant progression of precancer to early-stage lung adenocarcinoma (LUAD) as well as their indolence nature remains elusive. METHODS Single-cell RNA sequencing (scRNA) with simultaneous T cell receptor (TCR) sequencing on 5 normal lung tissues, 3 precancerous and 4 early-stage LUAD manifested as pulmonary ground-glass nodules (GGNs) were performed. RESULTS Through this integrated analysis, we have delineated five key modules that drive the malignant progression of early-stage LUAD in a disease stage-dependent manner. These modules are related to cell proliferation and metabolism, immune response, mitochondria, cilia, and cell adhesion. We also find that the tumor micro-environment (TME) of early-stage LUAD manifested as GGN are featured with regulatory T (Tregs) cells accumulation with three possible origins, and loss-functional state (decreased clonal expansion and cytotoxicity) of CD8 + T cells. Instead of exhaustion, the CD8 + T cells are featured with a shift to memory phenotype, which is significantly different from the late stage LUAD. Furthermore, we have identified monocyte-derived macrophages that undergo a lipid-phenotype transition and may contribute to the suppressive TME. Intense interaction between stromal cells, myeloid cells including lipid associated macrophages and LAMP3 + DCs, and lymphocytes were also characterized. CONCLUSIONS Our work provides new insight into the molecular and cellular mechanism underlying malignant progression of LUAD manifested as GGN, and pave way for novel immunotherapies for GGN. Video Abstract.
Collapse
Affiliation(s)
- Ziqi Wang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Li Yang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Wenqiang Wang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Huanhuan Zhou
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Juan Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zeheng Ma
- Department of Thoracic Surgery Department, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Xiaoyan Wang
- Department of Pathological Department, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Quncheng Zhang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Haiyang Liu
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Chao Zhou
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Zhiping Guo
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China.
- Henan Provincial Key Laboratory of Chronic Diseases and Health Management, Zhengzhou, 450003, Henan, China.
| | - Xiaoju Zhang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China.
| |
Collapse
|
179
|
Jané P, Xu X, Taelman V, Jané E, Gariani K, Dumont RA, Garama Y, Kim F, Del Val Gomez M, Walter MA. The Imageable Genome. Nat Commun 2023; 14:7329. [PMID: 37957176 PMCID: PMC10643363 DOI: 10.1038/s41467-023-43123-3] [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: 04/25/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Understanding human disease on a molecular level, and translating this understanding into targeted diagnostics and therapies are central tenets of molecular medicine1. Realizing this doctrine requires an efficient adaptation of molecular discoveries into the clinic. We present an approach to facilitate this process by describing the Imageable Genome, the part of the human genome whose expression can be assessed via molecular imaging. Using a deep learning-based hybrid human-AI pipeline, we bridge individual genes and their relevance in human diseases with specific molecular imaging methods. Cross-referencing the Imageable Genome with RNA-seq data from over 60,000 individuals reveals diagnostic, prognostic and predictive imageable genes for a wide variety of major human diseases. Having both the critical size and focus to be altered in its expression during the development and progression of any human disease, the Imageable Genome will generate new imaging tools that improve the understanding, diagnosis and management of human diseases.
Collapse
Affiliation(s)
- Pablo Jané
- University of Geneva, Geneva, Switzerland
- Nuclear Medicine and Molecular Imaging Division, Geneva University Hospitals, Geneva, Switzerland
| | | | | | - Eduardo Jané
- Departamento de Matemática Aplicada a la Ingeniería Aeroespacial - ETSIAE, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - Karim Gariani
- Division of Endocrinology, Diabetes, Nutrition and Patient Therapeutic Education, Geneva University Hospitals, Geneva, Switzerland
| | | | | | | | - María Del Val Gomez
- Servicio de Medicina Nuclear, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Martin A Walter
- University of Lucerne, Lucerne, Switzerland.
- St. Anna Hospital, University of Lucerne, Lucerne, Switzerland.
| |
Collapse
|
180
|
Nakayama J, Yamamoto Y. Cancer-prone Phenotypes and Gene Expression Heterogeneity at Single-cell Resolution in Cigarette-smoking Lungs. CANCER RESEARCH COMMUNICATIONS 2023; 3:2280-2291. [PMID: 37910161 PMCID: PMC10637260 DOI: 10.1158/2767-9764.crc-23-0195] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/16/2023] [Accepted: 10/25/2023] [Indexed: 11/03/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) technologies have been broadly utilized to reveal molecular mechanisms of respiratory pathology and physiology at single-cell resolution. Here, we established single-cell meta-analysis (scMeta-analysis) by integrating data from eight public datasets, including 104 lung scRNA-seq samples with clinicopathologic information and designated a cigarette-smoking lung atlas. The atlas revealed early carcinogenesis events and defined the alterations of single-cell transcriptomics, cell population, and fundamental properties of biological pathways induced by smoking. In addition, we developed two novel scMeta-analysis methods: VARIED (Visualized Algorithms of Relationships In Expressional Diversity) and AGED (Aging-related Gene Expressional Differences). VARIED analysis revealed expressional diversity associated with smoking carcinogenesis. AGED analysis revealed differences in gene expression related to both aging and smoking status. The scMeta-analysis paves the way to utilize publicly-available scRNA-seq data and provide new insights into the effects of smoking and into cellular diversity in human lungs, at single-cell resolution. SIGNIFICANCE The atlas revealed early carcinogenesis events and defined the alterations of single-cell transcriptomics, cell population, and fundamental properties of biological pathways induced by smoking.
Collapse
Affiliation(s)
- Jun Nakayama
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Oncogenesis and Growth Regulation, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Yusuke Yamamoto
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo, Japan
| |
Collapse
|
181
|
Dong Q, Yu T, Chen B, Liu M, Sun X, Cao H, Liu K, Xu H, Wang Y, Zhuang S, Jin Z, Liang H, Hui Y, Gu Y. Mutant RB1 enhances therapeutic efficacy of PARPis in lung adenocarcinoma by triggering the cGAS/STING pathway. JCI Insight 2023; 8:e165268. [PMID: 37937640 PMCID: PMC10721263 DOI: 10.1172/jci.insight.165268] [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: 09/12/2022] [Accepted: 09/25/2023] [Indexed: 11/09/2023] Open
Abstract
Poly (ADP-ribose) polymerase inhibitors (PARPis) are approved for cancer therapy according to their synthetic lethal interactions, and clinical trials have been applied in non-small cell lung cancer. However, the therapeutic efficacy of PARPis in lung adenocarcinoma (LUAD) is still unknown. We explored the effect of a mutated retinoblastoma gene (RB1) on PARPi sensitivity in LUAD. Bioinformatic screening was performed to identify PARPi-sensitive biomarkers. Here, we showed that viability of LUAD cell lines with mutated RB1 was significantly decreased by PARPis (niraparib, rucaparib, and olaparib). RB1 deficiency induced genomic instability, prompted cytosolic double-stranded DNA (dsDNA) formation, activated the cGAS/STING pathway, and upregulated downstream chemokines CCL5 and CXCL10, triggering immune cell infiltration. Xenograft experiments indicated that PARPi treatment reduced tumorigenesis in RB1-KO mice. Additionally, single-cell RNA sequencing analysis showed that malignant cells with downregulated expression of RB1 had more communications with other cell types, exhibiting activation of specific signaling such as GAS, IFN response, and antigen-presenting and cytokine activities. Our findings suggest that RB1 mutation mediates the sensitivity to PARPis through a synthetic lethal effect by triggering the cGAS/STING pathway and upregulation of immune infiltration in LUAD, which may be a potential therapeutic strategy.
Collapse
Affiliation(s)
- Qi Dong
- Department of Systems Biology, College of Bioinformatics Science and Technology, and
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Tong Yu
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
- Shanghai Frontiers Science Research Center for Druggability of Cardiovascular noncoding RNA, Institute for Frontier Medical Technology, Shanghai University of Engineering Science, Shanghai, China
| | - Bo Chen
- Department of Systems Biology, College of Bioinformatics Science and Technology, and
| | - Mingyue Liu
- Department of Systems Biology, College of Bioinformatics Science and Technology, and
| | - Xiang Sun
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Huiying Cao
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Kaidong Liu
- Department of Systems Biology, College of Bioinformatics Science and Technology, and
| | - Huanhuan Xu
- Department of Systems Biology, College of Bioinformatics Science and Technology, and
| | - Yuquan Wang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Shuping Zhuang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Zixin Jin
- Department of Systems Biology, College of Bioinformatics Science and Technology, and
| | - Haihai Liang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yang Hui
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Yunyan Gu
- Department of Systems Biology, College of Bioinformatics Science and Technology, and
| |
Collapse
|
182
|
Wang X, Wen S, Du X, Zhang Y, Yang X, Zou R, Feng B, Fu X, Jiang F, Zhou G, Liu Z, Zhu W, Ma R, Feng J, Shen B. SAA suppresses α-PD-1 induced anti-tumor immunity by driving T H2 polarization in lung adenocarcinoma. Cell Death Dis 2023; 14:718. [PMID: 37925492 PMCID: PMC10625560 DOI: 10.1038/s41419-023-06198-w] [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: 05/22/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 11/06/2023]
Abstract
Cancer stem cells (CSCs) are believed to be crucial in the initiation, progression, and recurrence of cancer. CSCs are also known to be more resistant to cancer treatments. However, the interaction between CSCs and the immune microenvironment is complex and not fully understood. In current study we used single cell RNA sequence (scRNA-Seq, public dataset) technology to identify the characteristic of CSCs. We found that the lung adenocarcinoma cancer stem population is highly inflammatory and remodels the tumor microenvironment by secreting inflammatory factors, specifically the acute phase protein serum amyloid A (SAA). Next, we developed an ex-vivo autologous patient-derived organoids (PDOs) and peripheral blood mononuclear cells (PBMCs) co-culture model to evaluate the immune biological impact of SAA. We found that SAA not only promotes chemoresistance by inducing cancer stem transformation, but also restricts anti-tumor immunity and promotes tumor fibrosis by driving type 2 immunity, and α-SAA neutralization antibody could restrict treatment resistant and tumor fibrosis. Mechanically, we found that the malignant phenotype induced by SAA is dependent on P2X7 receptor. Our data indicate that cancer stem cells secreted SAA have significant biological impact to promote treatment resistant and tumor fibrosis by driving cancer stemness transformation and type 2 immunity polarization via P2X7 receptor. Notably, α-SAA neutralization antibody shows therapeutic potential by restricting these malignant phenotypes.
Collapse
Affiliation(s)
- Xin Wang
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Shaodi Wen
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Xiaoyue Du
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Yihan Zhang
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Xiao Yang
- Department of Clinical Laboratory, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Renrui Zou
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Bing Feng
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Xiao Fu
- Department of General Surgery, Nanjing Drum Tower Hospital, Nanjing, China
- Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Feng Jiang
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Guoren Zhou
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Zi Liu
- Nanjing Advanced Analysis Tech. (NAAT) Co., LTD, Nanjing, China
| | - Wei Zhu
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Rong Ma
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jifeng Feng
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.
| | - Bo Shen
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.
| |
Collapse
|
183
|
Zhu Y, Yang Y, Liu Y, Qian H, Qu G, Shi W, Liu J. A novel tetraspanin-related gene signature for predicting prognosis and immune invasion status of lung adenocarcinoma. J Cancer Res Clin Oncol 2023; 149:13631-13643. [PMID: 37516981 PMCID: PMC10590322 DOI: 10.1007/s00432-023-05176-1] [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: 06/03/2023] [Accepted: 07/10/2023] [Indexed: 08/01/2023]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD), the most common subtype of lung cancer, is the primary contributor to cancer-linked fatalities. Dysregulation in the proliferation of cells and death is primarily involved in its development. Recently, tetraspanins, a group of transmembrane proteins, have gained increasing attention for their potential role in the progression of LUAD. Hence, our endeavor involved the development of a novel tetraspanin-based model for the prognostication of lung cancer. METHODS A comprehensive set of bioinformatics tools was utilized to evaluate the expression of tetraspanin-related genes and assess their significance regarding prognosis. Hence, a robust risk signature was established through machine learning. The prognosis-predictive value of the signature was evaluated in terms of clinical application, functional enrichment, and the immune landscape. RESULTS The research first identified differential expression of tetraspanin genes in patients with LUAD via publicly available databases. The resulting data were indicative of the value that nine of them held regarding prognosis. Five distinct elements were utilized in the establishment of a tetraspanin-related model (TSPAN7, TSPAN11, TSPAN14, UPK1B, and UPK1A). Furthermore, as per the median risk scores, the participants were classified into high- and low-risk groups. The model was validated using inner and outer validation sets. Notably, consensus clustering and prognostic score grouping analysis revealed that tetraspanin-related features affect tumor prognosis by modulating tumor immunity. A nomogram based on the tetraspanin gene was constructed with the aim of enhancing the poor prognosis of high-risk groups and facilitating clinical application. CONCLUSION Through machine learning algorithms and in vitro experiments, a novel tetraspanin-associated signature was developed and validated for survival prediction in patients with LUAD that reflects tumor immune infiltration. This could potentially provide new and improved measures for diagnosis and therapeutic interventions for LUAD.
Collapse
Affiliation(s)
- Yindong Zhu
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Ying Yang
- Cancer Research Center Nantong, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Yuan Liu
- Cancer Research Center Nantong, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Hongyan Qian
- Cancer Research Center Nantong, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Ganlin Qu
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Weidong Shi
- Department of Thoracic Surgery, The Second People Hospital of Nantong, Nantong, China
| | - Jun Liu
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China.
| |
Collapse
|
184
|
Zhou W, Zeng W, Zheng D, Yang X, Qing Y, Zhou C, Liu X. Construction of a prognostic model for lung adenocarcinoma based on heat shock protein-related genes and immune analysis. Cell Stress Chaperones 2023; 28:821-834. [PMID: 37691069 PMCID: PMC10746678 DOI: 10.1007/s12192-023-01374-5] [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: 06/01/2023] [Revised: 08/07/2023] [Accepted: 08/20/2023] [Indexed: 09/12/2023] Open
Abstract
Lung adenocarcinoma (LUAD) represents a prevalent form of cancer, with low early diagnosis rates and high mortality rates, posing a global health challenge. Heat shock proteins (HSPs) assume a crucial role within the tumor immune microenvironment (TME) of LUAD. Here, a collection of 97 HSP-related genes (HSPGs) was assembled based on prior literature reports, of which 36 HSPGs were differentially expressed in LUAD. In The Cancer Genome Atlas (TCGA) cohort, we constructed a prognostic model for risk stratification and prognosis prediction by integrating 13 HSPGs. In addition, the prognostic significance and predictive efficacy of the HSP-related riskscore were examined and validated in the Gene Expression Omnibus (GEO) cohort. To facilitate the clinical use of this riskscore, we also established a nomogram scale by verifying its effectiveness through different methods. In light of these outcomes, we concluded a significant correlation between HSPs and TME in LUAD, and the riskscore can be a reliable prognostic indicator. Furthermore, this study evaluated the differences in immunophenoscore, tumor immune dysfunction and exclusion score, and sensitivity to several common chemotherapy drugs among LUAD individuals in different risk groups, which may aid in clinical decision-making for immune therapy and chemotherapy in LUAD individuals.
Collapse
Affiliation(s)
- Wangyan Zhou
- Department of Medical Record, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang City, 421001, Hunan Province, China
| | - Wei Zeng
- Department of Thoracic Surgery, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Jiefang Avenue 35, Hengyang City, 421001, Hunan Province, China
| | - Dayang Zheng
- Department of Thoracic Surgery, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Jiefang Avenue 35, Hengyang City, 421001, Hunan Province, China
| | - Xu Yang
- Department of Thoracic Surgery, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Jiefang Avenue 35, Hengyang City, 421001, Hunan Province, China
| | - Yongcheng Qing
- Department of Thoracic Surgery, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Jiefang Avenue 35, Hengyang City, 421001, Hunan Province, China
| | - Chunxiang Zhou
- Department of Thoracic Surgery, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Jiefang Avenue 35, Hengyang City, 421001, Hunan Province, China
| | - Xiang Liu
- Department of Thoracic Surgery, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Jiefang Avenue 35, Hengyang City, 421001, Hunan Province, China.
| |
Collapse
|
185
|
Qu X, Wang Y, Jiang Q, Ren T, Guo C, Hua K, Qiu J. Interactions of Indoleamine 2,3-dioxygenase-expressing LAMP3 + dendritic cells with CD4 + regulatory T cells and CD8 + exhausted T cells: synergistically remodeling of the immunosuppressive microenvironment in cervical cancer and therapeutic implications. Cancer Commun (Lond) 2023; 43:1207-1228. [PMID: 37794698 PMCID: PMC10631485 DOI: 10.1002/cac2.12486] [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: 04/07/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Cervical cancer (CC) is the fourth most common cancer in women worldwide. Although immunotherapy has been applied in clinical practice, its therapeutic efficacy remains far from satisfactory, necessitating further investigation of the mechanism of CC immune remodeling and exploration of novel treatment targets. This study aimed to investigate the mechanism of CC immune remodeling and explore potential therapeutic targets. METHODS We conducted single-cell RNA sequencing on a total of 17 clinical specimens, including normal cervical tissues, high-grade squamous intraepithelial lesions, and CC tissues. To validate our findings, we conducted multicolor immunohistochemical staining of CC tissues and constructed a subcutaneous tumorigenesis model in C57BL/6 mice using murine CC cell lines (TC1) to evaluate the effectiveness of combination therapy involving indoleamine 2,3-dioxygenase 1 (IDO1) inhibition and immune checkpoint blockade (ICB). We used the unpaired two-tailed Student's t-test, Mann-Whitney test, or Kruskal-Wallis test to compare continuous data between two groups and one-way ANOVA with Tukey's post hoc test to compare data between multiple groups. RESULTS Malignant cervical epithelial cells did not manifest noticeable signs of tumor escape, whereas lysosomal-associated membrane protein 3-positive (LAMP3+ ) dendritic cells (DCs) in a mature state with immunoregulatory roles were found to express IDO1 and affect tryptophan metabolism. These cells interacted with both tumor-reactive exhausted CD8+ T cells and CD4+ regulatory T cells, synergistically forming a vicious immunosuppressive cycle and mediating CC immune escape. Further validation through multicolor immunohistochemical staining showed co-localization of neoantigen-reactive T cells (CD3+ , CD4+ /CD8+ , and PD-1+ ) and LAMP3+ DCs (CD80+ and PD-L1+ ). Additionally, a combination of the IDO1 inhibitor with an ICB agent significantly reduced tumor volume in the mouse model of CC compared with an ICB agent alone. CONCLUSIONS Our study suggested that a combination treatment consisting of targeting IDO1 and ICB agent could improve the therapeutic efficacy of current CC immunotherapies. Additionally, our results provided crucial insights for designing drugs and conducting future clinical trials for CC.
Collapse
Affiliation(s)
- Xinyu Qu
- Department of GynecologyObstetrics and Gynecology HospitalFudan UniversityShanghaiP. R. China
- Shanghai Key Laboratory of Female Reproductive Endocrine‐Related DiseasesShanghaiP. R. China
| | - Yumeng Wang
- Department of GynecologyObstetrics and Gynecology HospitalFudan UniversityShanghaiP. R. China
- Shanghai Key Laboratory of Female Reproductive Endocrine‐Related DiseasesShanghaiP. R. China
| | - Qian Jiang
- Department of GynecologyObstetrics and Gynecology HospitalFudan UniversityShanghaiP. R. China
- Shanghai Key Laboratory of Female Reproductive Endocrine‐Related DiseasesShanghaiP. R. China
| | - Tingting Ren
- Department of GynecologyObstetrics and Gynecology HospitalFudan UniversityShanghaiP. R. China
- Shanghai Key Laboratory of Female Reproductive Endocrine‐Related DiseasesShanghaiP. R. China
| | - Chenyan Guo
- Department of GynecologyObstetrics and Gynecology HospitalFudan UniversityShanghaiP. R. China
- Shanghai Key Laboratory of Female Reproductive Endocrine‐Related DiseasesShanghaiP. R. China
| | - Keqin Hua
- Department of GynecologyObstetrics and Gynecology HospitalFudan UniversityShanghaiP. R. China
- Shanghai Key Laboratory of Female Reproductive Endocrine‐Related DiseasesShanghaiP. R. China
| | - Junjun Qiu
- Department of GynecologyObstetrics and Gynecology HospitalFudan UniversityShanghaiP. R. China
- Shanghai Key Laboratory of Female Reproductive Endocrine‐Related DiseasesShanghaiP. R. China
| |
Collapse
|
186
|
Daou B, Silvestri A, Lasa H, Mancino D, Prato M, Alegret N. Organic Functional Group on Carbon Nanotube Modulates the Maturation of SH-SY5Y Neuronal Models. Macromol Biosci 2023; 23:e2300173. [PMID: 37392465 DOI: 10.1002/mabi.202300173] [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: 04/21/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/03/2023]
Abstract
Carbon nanotubes (CNT) have proven to be excellent substrates for neuronal cultures, showing high affinity and greatly boosting their synaptic functionality. Therefore, growing cells on CNT offers an opportunity to perform a large variety of neuropathology studies in vitro. To date, the interactions between neurons and chemical functional groups have not been studied extensively. To this end, multiwalled CNT (f-CNT) is functionalized with various functional groups, including sulfonic (-SO3 H), nitro (-NO2 ), amino (-NH2 ), and oxidized moieties. f-CNTs are spray-coated onto untreated glass substrates and are used as substrates for the incubation of neuroblastoma cells (SH-SY5Y). After 7 d, its effect is evaluated in terms of cell attachment, survival, growth, and spontaneous differentiation. Cell viability assays show quite increased proliferation on various f-CNT substrates (CNTs-NO2 > ox-CNTs ≈ CNTs-SO3 H > CNTs ≈ CNTs-NH2 ). Additionally, SH-SY5Y cells show selectively better differentiation and maturation with -SO3 H substrates, where an increased expression of β-III tubulin is seen. In all cases, intricate cell-CNT networks are observed and the morphology of the cells adopts longer and thinner cellular processes, suggesting that the type of functionalization may have an effect of the length and thickness. Finally, a possible correlation is determined between conductivity of f-CNTs and cell-processes lengths.
Collapse
Affiliation(s)
- Bahaa Daou
- Center for Cooperative Research in Biomaterials (CIC BiomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, 20014, Spain
- Neuromuscular Diseases Group, Neurosciences Area, Biodonostia Health Research Institute, Donostia/San Sebastián, 20014, Spain
| | - Alessandro Silvestri
- Center for Cooperative Research in Biomaterials (CIC BiomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, 20014, Spain
| | - Haizpea Lasa
- Center for Cooperative Research in Biomaterials (CIC BiomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, 20014, Spain
- Neuromuscular Diseases Group, Neurosciences Area, Biodonostia Health Research Institute, Donostia/San Sebastián, 20014, Spain
| | - Donato Mancino
- Center for Cooperative Research in Biomaterials (CIC BiomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, 20014, Spain
| | - Maurizio Prato
- Center for Cooperative Research in Biomaterials (CIC BiomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, 20014, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain
- Department of Chemical and Pharmaceutical Sciences, Universitá Degli Studi di Trieste, Trieste, 34127, Italy
| | - Nuria Alegret
- Center for Cooperative Research in Biomaterials (CIC BiomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, 20014, Spain
| |
Collapse
|
187
|
Gottschlich A, Thomas M, Grünmeier R, Lesch S, Rohrbacher L, Igl V, Briukhovetska D, Benmebarek MR, Vick B, Dede S, Müller K, Xu T, Dhoqina D, Märkl F, Robinson S, Sendelhofert A, Schulz H, Umut Ö, Kavaka V, Tsiverioti CA, Carlini E, Nandi S, Strzalkowski T, Lorenzini T, Stock S, Müller PJ, Dörr J, Seifert M, Cadilha BL, Brabenec R, Röder N, Rataj F, Nüesch M, Modemann F, Wellbrock J, Fiedler W, Kellner C, Beltrán E, Herold T, Paquet D, Jeremias I, von Baumgarten L, Endres S, Subklewe M, Marr C, Kobold S. Single-cell transcriptomic atlas-guided development of CAR-T cells for the treatment of acute myeloid leukemia. Nat Biotechnol 2023; 41:1618-1632. [PMID: 36914885 PMCID: PMC7615296 DOI: 10.1038/s41587-023-01684-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 01/20/2023] [Indexed: 03/16/2023]
Abstract
Chimeric antigen receptor T cells (CAR-T cells) have emerged as a powerful treatment option for individuals with B cell malignancies but have yet to achieve success in treating acute myeloid leukemia (AML) due to a lack of safe targets. Here we leveraged an atlas of publicly available RNA-sequencing data of over 500,000 single cells from 15 individuals with AML and tissue from 9 healthy individuals for prediction of target antigens that are expressed on malignant cells but lacking on healthy cells, including T cells. Aided by this high-resolution, single-cell expression approach, we computationally identify colony-stimulating factor 1 receptor and cluster of differentiation 86 as targets for CAR-T cell therapy in AML. Functional validation of these established CAR-T cells shows robust in vitro and in vivo efficacy in cell line- and human-derived AML models with minimal off-target toxicity toward relevant healthy human tissues. This provides a strong rationale for further clinical development.
Collapse
Affiliation(s)
- Adrian Gottschlich
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Moritz Thomas
- Institute of AI for Health, Helmholtz Munich, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Ruth Grünmeier
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Stefanie Lesch
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Lisa Rohrbacher
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- Laboratory for Translational Cancer Immunology, Gene Center, LMU Munich, Munich, Germany
| | - Veronika Igl
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Daria Briukhovetska
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Mohamed-Reda Benmebarek
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Binje Vick
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Munich, German Research Center for Environmental Health (HMGU), Munich, Germany
- Department of Pediatrics, University Hospital, LMU Munich, Munich, Germany
| | - Sertac Dede
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany
| | - Katharina Müller
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany
| | - Tao Xu
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany
| | - Dario Dhoqina
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Florian Märkl
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Sophie Robinson
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | | | - Heiko Schulz
- Institute of Pathology, LMU Munich, Munich, Germany
| | - Öykü Umut
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Vladyslav Kavaka
- Institute of Clinical Neuroimmunology, University Hospital, LMU Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Christina Angeliki Tsiverioti
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Emanuele Carlini
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Sayantan Nandi
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Thaddäus Strzalkowski
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Theo Lorenzini
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Sophia Stock
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Philipp Jie Müller
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Janina Dörr
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Matthias Seifert
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Bruno L Cadilha
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Ruben Brabenec
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- Institute of AI for Health, Helmholtz Munich, Neuherberg, Germany
| | - Natalie Röder
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Felicitas Rataj
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Manuel Nüesch
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Franziska Modemann
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald University Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf Hamburg, Hamburg, Germany
| | - Jasmin Wellbrock
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald University Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Walter Fiedler
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald University Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Kellner
- Division of Transfusion Medicine, Cell Therapeutics and Haemostaseology, University Hospital, LMU Munich, Munich, Germany
| | - Eduardo Beltrán
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Institute of Clinical Neuroimmunology, University Hospital, LMU Munich, Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Dominik Paquet
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Munich, German Research Center for Environmental Health (HMGU), Munich, Germany
- Department of Pediatrics, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Louisa von Baumgarten
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
- Department of Neurosurgery, LMU Munich, Munich, Germany
| | - Stefan Endres
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
- Einheit für Klinische Pharmakologie (EKLiP), Helmholtz Munich, Research Center for Environmental Health (HMGU), Neuherberg, Germany
| | - Marion Subklewe
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- Laboratory for Translational Cancer Immunology, Gene Center, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Carsten Marr
- Institute of AI for Health, Helmholtz Munich, Neuherberg, Germany
| | - Sebastian Kobold
- Division of Clinical Pharmacology, University Hospital, LMU Munich, Member of the German Center for Lung Research (DZL), Munich, Germany.
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.
- Einheit für Klinische Pharmakologie (EKLiP), Helmholtz Munich, Research Center for Environmental Health (HMGU), Neuherberg, Germany.
| |
Collapse
|
188
|
Huang Q, Zhang N, Wang J, Xu H, Yao L, Yang Q, Yan D, Chen X, Xue Q, Xiao M, Wu J, Wu X, Liu Q, Tang D, Chen X, Li X, Liu J. Bilirubin inhibits lung carcinogenesis by up-regulating cystatin A expression in tumor-infiltrating macrophages. Genes Dis 2023; 10:2222-2225. [PMID: 37554191 PMCID: PMC10404995 DOI: 10.1016/j.gendis.2023.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/28/2023] [Accepted: 02/08/2023] [Indexed: 03/29/2023] Open
Affiliation(s)
- Qingtian Huang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
- Institute of Digestive Disease, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong 511518, China
| | - Na Zhang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Jiangtuan Wang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Hua Xu
- Department of Pathology, Dongguan People's Hospital Affiliated to Southern Medical University, Dongguan, Guangdong 523059, China
| | - Leyi Yao
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
- Institute of Digestive Disease, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong 511518, China
| | - Qianqian Yang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Ding Yan
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Xi Chen
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Qian Xue
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Min Xiao
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Jiawen Wu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Xueheng Wu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Qin Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xin Chen
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Xiaofen Li
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Jinbao Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, China
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
- Institute of Digestive Disease, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong 511518, China
| |
Collapse
|
189
|
Yoo H, Kim HS. Clinicopathological and Prognostic Values of Telomerase Reverse Transcriptase ( TERT) Promoter Mutations in Ovarian Clear Cell Carcinoma for Predicting Tumor Recurrence, Platinum Resistance and Survival. Cancer Genomics Proteomics 2023; 20:626-636. [PMID: 37889060 PMCID: PMC10614067 DOI: 10.21873/cgp.20411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND/AIM A small subset of patients with ovarian clear cell carcinoma (OCCC) harbors telomerase reverse transcriptase promoter (TERTp) mutations. We aimed to analyze the clinicopathological and molecular characteristics of TERTp-mutant OCCC and investigate whether TERTp mutations are associated with the clinicopathological characteristics and outcomes of patients with OCCC. PATIENTS AND METHODS We included 11 OCCC cases in our study. Targeted sequencing was performed with a thorough review of pathology slides and electronic medical records. RESULTS Eleven OCCCs harbored two hotspot TERTp mutations: c.1-146C>T (6/11) and c.1-124C>T (5/11). All patients (11/11) who underwent postoperative adjuvant chemotherapy experienced tumor recurrence, and eight of them were classified as platinum-resistant. TERTp-mutant OCCC showed significantly higher frequencies of postoperative recurrence and relapse within six months of chemotherapy. TERTp mutations significantly predicted disease-free survival (DFS) in patients with OCCC. CONCLUSION We demonstrate that TERTp mutations have significant prognostic value for predicting tumor recurrence, platinum resistance, and worse DFS in patients with OCCC.
Collapse
Affiliation(s)
- Hyunwoo Yoo
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyun-Soo Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| |
Collapse
|
190
|
Fu M, Shu S, Peng Z, Liu X, Chen X, Zeng Z, Yang Y, Cui H, Zhao R, Wang X, Du L, Wu M, Feng W, Song J. Single-Cell RNA Sequencing of Coronary Perivascular Adipose Tissue From End-Stage Heart Failure Patients Identifies SPP1+ Macrophage Subpopulation as a Target for Alleviating Fibrosis. Arterioscler Thromb Vasc Biol 2023; 43:2143-2164. [PMID: 37706320 PMCID: PMC10597444 DOI: 10.1161/atvbaha.123.319828] [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: 07/06/2023] [Accepted: 08/29/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND Perivascular adipose tissue (PVAT) is vital for vascular homeostasis, and PVAT dysfunction is associated with increased atherosclerotic plaque burden. But the mechanisms underlining coronary PVAT dysfunction in coronary atherosclerosis remain elusive. METHODS We performed single-cell RNA sequencing of the stromal vascular fraction of coronary PVAT from 3 groups of heart transplant recipients with end-stage heart failure, including 3 patients with nonobstructive coronary atherosclerosis, 3 patients with obstructive coronary artery atherosclerosis, and 4 nonatherosclerosis control subjects. Bioinformatics was used to annotate the cellular populations, depict the cellular developmental trajectories and interactions, and explore the differences among 3 groups of coronary PVAT at the cellular and molecular levels. Pathological staining, quantitative real-time polymerase chain reaction, and in vitro studies were performed to validate the key findings. RESULTS Ten cell types were identified among 67 936 cells from human coronary PVAT. Several cellular subpopulations, including SPP1+ (secreted phosphoprotein 1) macrophages and profibrotic fibroadipogenic progenitor cells, were accumulated in PVAT surrounding atherosclerotic coronary arteries compared with nonatherosclerosis coronary arteries. The fibrosis percentage was increased in PVAT surrounding atherosclerotic coronary arteries, and it was positively associated with the grade of coronary artery stenosis. Cellular interaction analysis suggested OPN (osteopontin) secreted by SPP1+ macrophages interacted with CD44 (cluster of differentiation 44)/integrin on fibroadipogenic progenitor cells. Strikingly, correlation analyses uncovered that higher level of SPP1 in PVAT correlates with a more severe fibrosis degree and a higher coronary stenosis grade. In vitro studies showed that conditioned medium from atherosclerotic coronary PVAT promoted the migration and proliferation of fibroadipogenic progenitor cells, while such effect was prevented by blocking CD44 or integrin. CONCLUSIONS SPP1+ macrophages accumulated in the PVAT surrounding atherosclerotic coronary arteries, and they promoted the migration and proliferation of fibroadipogenic progenitor cells via OPN-CD44/integrin interaction and thus aggravated the fibrosis of coronary PVAT, which was positively correlated to the coronary stenosis burden. Therefore, SPP1+ macrophages in coronary PVAT may participate in the progression of coronary atherosclerosis.
Collapse
Affiliation(s)
- Mengxia Fu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Galactophore Department, Galactophore Center, Beijing Shijitan Hospital (M.F., M.W.), Capital Medical University, China
| | - Songren Shu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- The Cardiomyopathy Research Group at Fuwai Hospital, China (S.S., X.L., X.C., H.C., R.Z., X.W., J.S.)
| | - Zhiming Peng
- Department of Orthopedics, Peking Union Medical College Hospital (Z.P.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaorui Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- The Cardiomyopathy Research Group at Fuwai Hospital, China (S.S., X.L., X.C., H.C., R.Z., X.W., J.S.)
| | - Xiao Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- The Cardiomyopathy Research Group at Fuwai Hospital, China (S.S., X.L., X.C., H.C., R.Z., X.W., J.S.)
| | - Zhiwei Zeng
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yicheng Yang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hao Cui
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- The Cardiomyopathy Research Group at Fuwai Hospital, China (S.S., X.L., X.C., H.C., R.Z., X.W., J.S.)
| | - Ruojin Zhao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- The Cardiomyopathy Research Group at Fuwai Hospital, China (S.S., X.L., X.C., H.C., R.Z., X.W., J.S.)
| | - Xiaohu Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- The Cardiomyopathy Research Group at Fuwai Hospital, China (S.S., X.L., X.C., H.C., R.Z., X.W., J.S.)
| | - Leilei Du
- Laboratory of Cardiovascular Science, Beijing Clinical Research Institute, Beijing Friendship Hospital (L.D.), Capital Medical University, China
| | - Min Wu
- Galactophore Department, Galactophore Center, Beijing Shijitan Hospital (M.F., M.W.), Capital Medical University, China
| | - Wei Feng
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Cardiovascular Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases (W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiangping Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases (M.F., S.S., X.L., X.C., Z.Z., Y.Y., H.C., R.Z., X.W., W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Cardiovascular Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases (W.F., J.S.), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- The Cardiomyopathy Research Group at Fuwai Hospital, China (S.S., X.L., X.C., H.C., R.Z., X.W., J.S.)
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, China (J.S.)
| |
Collapse
|
191
|
Guo J, Lin SD, Minervini F, Geraci TC, Kim JJ, Tong CY, Li XJ, Cao C. Neoadjuvant immunotherapy combined with chemotherapy in the treatment of stage III lung squamous cell carcinoma: a retrospective cohort study. J Thorac Dis 2023; 15:5658-5668. [PMID: 37969291 PMCID: PMC10636463 DOI: 10.21037/jtd-23-1175] [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: 07/27/2023] [Accepted: 08/31/2023] [Indexed: 11/17/2023]
Abstract
Background Neoadjuvant immunochemotherapy has been proven to be a successful therapeutic strategy for patients with locally advanced non-small cell lung cancer (NSCLC). Nevertheless, there is a paucity of information regarding surgical feasibility and safety as well as tumor response. The present study aimed to investigate the therapeutic and surgical outcomes for patients with stage III lung squamous cell carcinoma (LSCC). Methods Patients with stage III potentially resectable LSCC treated with neoadjuvant immunochemotherapy at The First Affiliated Hospital of Ningbo University between March 2020 and June 2022 were retrospectively included. Oncologic outcomes and intraoperative and postoperative variables were assessed. Results A total of 17 locally advanced LSCC patients were included in the study. Patients in stages IIIA and IIIB were represented by 10 (58.8%) and 7 (41.2%) cases, respectively. A minimally invasive procedure was successfully completed in 12 out of 17 cases (70.6%). A total of 10 patients (58.8%) had standard lobectomies performed, 1 (5.9%) had a bilobectomy, 3 (17.6%) had pneumonectomies, and 1 (5.9%) had a wedge resection. A total of 7 patients (41.2%) experienced postoperative complications, and there were no 30- or 90-day mortalities. The 2-year disease-free survival (DFS) and overall survival (OS) rates were 76.6% and 82.5%, respectively. The rate of major pathological response (MPR) was 70.6%. Conclusions Lung resection after immunochemotherapy for potentially resectable stage III LSCC is feasible and safe. This treatment strategy results in a significant pathologic response and promising rates of OS at 2 years.
Collapse
Affiliation(s)
- Jing Guo
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Shuai-Dong Lin
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Fabrizio Minervini
- Department of Thoracic Surgery, Cantonal Hospital Lucerne, Lucerne, Switzerland
| | - Travis C. Geraci
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, New York University Langone Health, New York, NY, USA
| | - Jae Jun Kim
- Department of Thoracic and Cardiovascular Surgery, Uijeongbu St. Mary’s Hospital, The Catholic University of Korea, College of Medicine, Seoul, Republic of Korea
| | - Chang-Yong Tong
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Xin-Jian Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Chao Cao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, China
| |
Collapse
|
192
|
Saqib J, Park B, Jin Y, Seo J, Mo J, Kim J. Identification of Niche-Specific Gene Signatures between Malignant Tumor Microenvironments by Integrating Single Cell and Spatial Transcriptomics Data. Genes (Basel) 2023; 14:2033. [PMID: 38002976 PMCID: PMC10671538 DOI: 10.3390/genes14112033] [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: 10/05/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
The tumor microenvironment significantly affects the transcriptomic states of tumor cells. Single-cell RNA sequencing (scRNA-seq) helps elucidate the transcriptomes of individual cancer cells and their neighboring cells. However, cell dissociation results in the loss of information on neighboring cells. To address this challenge and comprehensively assess the gene activity in tissue samples, it is imperative to integrate scRNA-seq with spatial transcriptomics. In our previous study on physically interacting cell sequencing (PIC-seq), we demonstrated that gene expression in single cells is affected by neighboring cell information. In the present study, we proposed a strategy to identify niche-specific gene signatures by harmonizing scRNA-seq and spatial transcriptomic data. This approach was applied to the paired or matched scRNA-seq and Visium platform data of five cancer types: breast cancer, gastrointestinal stromal tumor, liver hepatocellular carcinoma, uterine corpus endometrial carcinoma, and ovarian cancer. We observed distinct gene signatures specific to cellular niches and their neighboring counterparts. Intriguingly, these niche-specific genes display considerable dissimilarity to cell type markers and exhibit unique functional attributes independent of the cancer types. Collectively, these results demonstrate the potential of this integrative approach for identifying novel marker genes and their spatial relationships.
Collapse
Affiliation(s)
| | | | | | | | | | - Junil Kim
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-Ro, Dongjak-Gu, Seoul 06978, Republic of Korea; (J.S.); (Y.J.); (J.M.)
| |
Collapse
|
193
|
Pranoto IKA, Lee J, Kwon YV. The roles of the native cell differentiation program aberrantly recapitulated in Drosophila intestinal tumors. Cell Rep 2023; 42:113245. [PMID: 37837622 PMCID: PMC10872463 DOI: 10.1016/j.celrep.2023.113245] [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: 06/15/2022] [Revised: 06/11/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023] Open
Abstract
Many tumors recapitulate the developmental and differentiation program of their tissue of origin, a basis for tumor cell heterogeneity. Although stem-cell-like tumor cells are well studied, the roles of tumor cells undergoing differentiation remain to be elucidated. We employ Drosophila genetics to demonstrate that the differentiation program of intestinal stem cells is crucial for enabling intestinal tumors to invade and induce non-tumor-autonomous phenotypes. The differentiation program that generates absorptive cells is aberrantly recapitulated in the intestinal tumors generated by activation of the Yap1 ortholog Yorkie. Inhibiting it allows stem-cell-like tumor cells to grow but suppresses invasiveness and reshapes various phenotypes associated with cachexia-like wasting by altering the expression of tumor-derived factors. Our study provides insight into how a native differentiation program determines a tumor's capacity to induce advanced cancer phenotypes and suggests that manipulating the differentiation programs co-opted in tumors might alleviate complications of cancer, including cachexia.
Collapse
Affiliation(s)
| | - Jiae Lee
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Young V Kwon
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
194
|
Li Z, Yin Z, Luan Z, Zhang C, Wang Y, Zhang K, Chen F, Yang Z, Tian Y. Comprehensive analyses for the coagulation and macrophage-related genes to reveal their joint roles in the prognosis and immunotherapy of lung adenocarcinoma patients. Front Immunol 2023; 14:1273422. [PMID: 38022584 PMCID: PMC10644034 DOI: 10.3389/fimmu.2023.1273422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose This study aims to explore novel biomarkers related to the coagulation process and tumor-associated macrophage (TAM) infiltration in lung adenocarcinoma (LUAD). Methods The macrophage M2-related genes were obtained by Weighted Gene Co-expression Network Analysis (WGCNA) in bulk RNA-seq data, while the TAM marker genes were identified by analyzing the scRNA-seq data, and the coagulation-associated genes were obtained from MSigDB and KEGG databases. Survival analysis was performed for the intersectional genes. A risk score model was subsequently constructed based on the survival-related genes for prognosis prediction and validated in external datasets. Results In total, 33 coagulation and macrophage-related (COMAR) genes were obtained, 19 of which were selected for the risk score model construction. Finally, 10 survival-associated genes (APOE, ARRB2, C1QB, F13A1, FCGR2A, FYN, ITGB2, MMP9, OLR1, and VSIG4) were involved in the COMAR risk score model. According to the risk score, patients were equally divided into low- and high-risk groups, and the prognosis of patients in the high-risk group was significantly worse than that in the low-risk group. The ROC curve indicated that the risk score model had high sensitivity and specificity, which was validated in multiple external datasets. Moreover, the model also had high efficacy in predicting the clinical outcomes of LUAD patients who received anti-PD-1/PD-L1 immunotherapy. Conclusion The COMAR risk score model constructed in this study has excellent predictive value for the prognosis and immunotherapeutic clinical outcomes of patients with LUAD, which provides potential biomarkers for the treatment and prognostic prediction.
Collapse
Affiliation(s)
- Zhuoqi Li
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, China
- Radiotherapy Department, Shandong Second Provincial General Hospital, Shandong University, Jinan, China
| | - Zongxiu Yin
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Zupeng Luan
- Department of Radiation Oncology, Jinan Third People’s Hospital, Jinan, China
| | - Chi Zhang
- Department of Cardiology, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yuanyuan Wang
- Department of Oncology, The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Kai Zhang
- Generalsurgery Department, Wen-shang County People’s Hospital, Wenshang, China
| | - Feng Chen
- Department of Thoracic Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Zhensong Yang
- Department of Gastrointestinal Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
| | - Yuan Tian
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, China
- Radiotherapy Department, Shandong Second Provincial General Hospital, Shandong University, Jinan, China
| |
Collapse
|
195
|
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.
Collapse
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
| |
Collapse
|
196
|
Pulice JL, Meyerson M. Dosage amplification dictates oncogenic regulation by the NKX2-1 lineage factor in lung adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.563996. [PMID: 37994369 PMCID: PMC10664179 DOI: 10.1101/2023.10.26.563996] [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: 11/24/2023]
Abstract
Amplified oncogene expression is a critical and widespread driver event in cancer, yet our understanding of how amplification-mediated elevated dosage mediates oncogenic regulation is limited. Here, we find that the most significant focal amplification event in lung adenocarcinoma (LUAD) targets a lineage super-enhancer near the NKX2-1 lineage transcription factor. The NKX2-1 super-enhancer is targeted by focal and co-amplification with NKX2-1, and activation or repression controls NKX2-1 expression. We find that NKX2-1 is a widespread dependency in LUAD cell lines, where NKX2-1 pioneers enhancer accessibility to drive a lineage addicted state in LUAD, and NKX2-1 confers persistence to EGFR inhibitors. Notably, we find that oncogenic NKX2-1 regulation requires expression above a minimum dosage threshold-NKX2-1 dosage below this threshold is insufficient for cell viability, enhancer remodeling, and TKI persistence. Our data suggest that copy-number amplification can be a gain-of-function alteration, wherein amplification elevates oncogene expression above a critical dosage required for oncogenic regulation and cancer cell survival.
Collapse
Affiliation(s)
- John L. Pulice
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Cambridge, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Lead contact
| |
Collapse
|
197
|
Lin S, Zhou S, Han X, Yang Y, Zhou H, Chang X, Zhou Y, Ding Y, Lin H, Hu Q. Single-cell analysis reveals exosome-associated biomarkers for prognostic prediction and immunotherapy in lung adenocarcinoma. Aging (Albany NY) 2023; 15:11508-11531. [PMID: 37878007 PMCID: PMC10637798 DOI: 10.18632/aging.205140] [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: 07/12/2023] [Accepted: 10/03/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Exosomes play a crucial role in tumor initiation and progression, yet the precise involvement of exosome-related genes (ERGs) in lung adenocarcinoma (LUAD) remains unclear. METHODS We conducted a comprehensive investigation of ERGs within the tumor microenvironment (TME) of LUAD using single-cell RNA sequencing (scRNA-seq) analysis. Multiple scoring methods were employed to assess exosome activity (EA). Differences in cell communication were examined between high and low EA groups, utilizing the "CellChat" R package. Subsequently, we leveraged multiple bulk RNA-seq datasets to develop and validate exosome-associated signatures (EAS), enabling a multifaceted exploration of prognosis and immunotherapy outcomes between high- and low-risk groups. RESULTS In the LUAD TME, epithelial cells demonstrated the highest EA, with even more elevated levels observed in advanced LUAD epithelial cells. The high-EA group exhibited enhanced intercellular interactions. EAS were established through the analysis of multiple bulk RNA-seq datasets. Patients in the high-risk group exhibited poorer overall survival (OS), reduced immune infiltration, and decreased expression of immune checkpoint genes. Finally, we experimentally validated the high expression of SEC61G in LUAD cell lines and demonstrated that knockdown of SEC61G reduced the proliferative capacity of LUAD cells using colony formation assays. CONCLUSION The integration of single-cell and bulk RNA-seq analyses culminated in the development of the profound and significant EAS, which imparts invaluable insights for the clinical diagnosis and therapeutic management of LUAD patients.
Collapse
Affiliation(s)
- Shengrong Lin
- Department of Thoracic Surgery, Dongtai People’s Hospital, Dongtai 224299, China
| | - Shengjie Zhou
- Department of Thoracic Surgery, Dongtai People’s Hospital, Dongtai 224299, China
| | - Xin Han
- Department of Thoracic Surgery, Dongtai People’s Hospital, Dongtai 224299, China
| | - Yang Yang
- Department of Thoracic Surgery, Dongtai People’s Hospital, Dongtai 224299, China
| | - Hao Zhou
- Department of Thoracic Surgery, Dongtai People’s Hospital, Dongtai 224299, China
| | - Xuejiao Chang
- Department of Thoracic Surgery, Dongtai People’s Hospital, Dongtai 224299, China
| | - Yefeng Zhou
- Department of Thoracic Surgery, Dongtai People’s Hospital, Dongtai 224299, China
| | - Yuqin Ding
- Department of Thoracic Surgery, Dongtai People’s Hospital, Dongtai 224299, China
| | - Huihui Lin
- Department of Hematology, Dongtai People’s Hospital, Dongtai 224299, China
| | - Qing Hu
- Department of Thoracic Surgery, Dongtai People’s Hospital, Dongtai 224299, China
| |
Collapse
|
198
|
Fan G, Xie T, Tan Q, Lou N, Wang S, Han X, Shi Y. An immunosuppressive subtype of senescent tumor cells predicted worse immunotherapy response in lung adenocarcinoma. iScience 2023; 26:107894. [PMID: 37766998 PMCID: PMC10520875 DOI: 10.1016/j.isci.2023.107894] [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: 03/22/2023] [Revised: 08/14/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Senescent tumor cells (STCs) can induce immunosuppression, promoting tumor progression and therapy resistance. However, the specific characteristics of immunosuppressive STC have not been thoroughly investigated. This study aimed to characterize and elucidate the immunosuppressive phenotype of STC in lung adenocarcinoma by employing single-cell and bulk transcriptomics, as well as serum proteomics profiling. We identified senescence-related genes specific to tumors and identified Cluster10 of STC as the immunomodulatory subtype. Cluster10 exhibited a distinct secretome dominated by cytokines such as CXCL1, CXCL2, and CXCL8 and showed activation of transcription factors associated with cytokine secretion, including NFKB1, RELA, and STAT3. Notably, Cluster10 demonstrated the highest degree of intercellular communication among all cell types, with interactions as LGALS9-TIM3 and MIF-CD74. Furthermore, Cluster10 showed significant associations with poor prognosis and diminished response to immunotherapy. Analysis of serum proteomics data from our in-house cohort identified CXCL8 as a potential marker for predicting immunotherapeutic outcomes.
Collapse
Affiliation(s)
- Guangyu Fan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Tongji Xie
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Qiaoyun Tan
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, N0.109,Machang Road, Jianghan District, Wuhan 430024, China
| | - Ning Lou
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Shasha Wang
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Xiaohong Han
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe and Rare Diseases, NMPA Key Laboratory for Clinical Research and Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan, Dongcheng District, Beijing 100730, China
| | - Yuankai Shi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| |
Collapse
|
199
|
Chen S, Jiang W, Du Y, Yang M, Pan Y, Li H, Cui M. Single-cell analysis technologies for cancer research: from tumor-specific single cell discovery to cancer therapy. Front Genet 2023; 14:1276959. [PMID: 37900181 PMCID: PMC10602688 DOI: 10.3389/fgene.2023.1276959] [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: 08/13/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Single-cell sequencing (SCS) technology is changing our understanding of cellular components, functions, and interactions across organisms, because of its inherent advantage of avoiding noise resulting from genotypic and phenotypic heterogeneity across numerous samples. By directly and individually measuring multiple molecular characteristics of thousands to millions of single cells, SCS technology can characterize multiple cell types and uncover the mechanisms of gene regulatory networks, the dynamics of transcription, and the functional state of proteomic profiling. In this context, we conducted systematic research on SCS techniques, including the fundamental concepts, procedural steps, and applications of scDNA, scRNA, scATAC, scCITE, and scSNARE methods, focusing on the unique clinical advantages of SCS, particularly in cancer therapy. We have explored challenging but critical areas such as circulating tumor cells (CTCs), lineage tracing, tumor heterogeneity, drug resistance, and tumor immunotherapy. Despite challenges in managing and analyzing the large amounts of data that result from SCS, this technique is expected to reveal new horizons in cancer research. This review aims to emphasize the key role of SCS in cancer research and promote the application of single-cell technologies to cancer therapy.
Collapse
Affiliation(s)
- Siyuan Chen
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Weibo Jiang
- Department of Orthopaedic, The Second Hospital of Jilin University, Changchun, China
| | - Yanhui Du
- Department of Orthopaedics, Jilin Province People’s Hospital, Changchun, China
| | - Manshi Yang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yihan Pan
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Huan Li
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Mengying Cui
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| |
Collapse
|
200
|
Duan W, Xia S, Tang M, Lin M, Liu W, Wang Q. Targeting of endothelial cells in brain tumours. Clin Transl Med 2023; 13:e1433. [PMID: 37830128 PMCID: PMC10570772 DOI: 10.1002/ctm2.1433] [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: 04/17/2023] [Revised: 09/11/2023] [Accepted: 09/30/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND Aggressive brain tumours, whether primary gliomas or secondary metastases, are characterised by hypervascularisation and are fatal. Recent research has emphasised the crucial involvement of endothelial cells (ECs) in all brain tumour genesis and development events, with various patterns and underlying mechanisms identified. MAIN BODY Here, we highlight recent advances in knowledge about the contributions of ECs to brain tumour development, providing a comprehensive summary including descriptions of interactions between ECs and tumour cells, the heterogeneity of ECs and new models for research on ECs in brain malignancies. We also discuss prospects for EC targeting in novel therapeutic approaches. CONCLUSION Interventions targeting ECs, as an adjunct to other therapies (e.g. immunotherapies, molecular-targeted therapies), have shown promising clinical efficacy due to the high degree of vascularisation in brain tumours. Developing precise strategies to target tumour-associated vessels based on the heterogeneity of ECs is expected to improve anti-vascular efficacy.
Collapse
Affiliation(s)
- Wenzhe Duan
- Department of Respiratory MedicineThe Second HospitalDalian Medical UniversityDalianChina
| | - Shengkai Xia
- Department of Respiratory MedicineThe Second HospitalDalian Medical UniversityDalianChina
| | - Mengyi Tang
- Department of Respiratory MedicineThe Second HospitalDalian Medical UniversityDalianChina
| | - Manqing Lin
- Department of Respiratory MedicineThe Second HospitalDalian Medical UniversityDalianChina
| | - Wenwen Liu
- Cancer Translational Medicine Research CenterThe Second HospitalDalian Medical UniversityDalianChina
| | - Qi Wang
- Department of Respiratory MedicineThe Second HospitalDalian Medical UniversityDalianChina
- Cancer Translational Medicine Research CenterThe Second HospitalDalian Medical UniversityDalianChina
| |
Collapse
|