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Li Z, Gu H, Xu X, Tian Y, Huang X, Du Y. Unveiling the novel immune and molecular signatures of ovarian cancer: insights and innovations from single-cell sequencing. Front Immunol 2023; 14:1288027. [PMID: 38022625 PMCID: PMC10654630 DOI: 10.3389/fimmu.2023.1288027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Ovarian cancer is a highly heterogeneous and lethal malignancy with limited treatment options. Over the past decade, single-cell sequencing has emerged as an advanced biological technology capable of decoding the landscape of ovarian cancer at the single-cell resolution. It operates at the level of genes, transcriptomes, proteins, epigenomes, and metabolisms, providing detailed information that is distinct from bulk sequencing methods, which only offer average data for specific lesions. Single-cell sequencing technology provides detailed insights into the immune and molecular mechanisms underlying tumor occurrence, development, drug resistance, and immune escape. These insights can guide the development of innovative diagnostic markers, therapeutic strategies, and prognostic indicators. Overall, this review provides a comprehensive summary of the diverse applications of single-cell sequencing in ovarian cancer. It encompasses the identification and characterization of novel cell subpopulations, the elucidation of tumor heterogeneity, the investigation of the tumor microenvironment, the analysis of mechanisms underlying metastasis, and the integration of innovative approaches such as organoid models and multi-omics analysis.
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Affiliation(s)
- Zhongkang Li
- Department of Obstetrics and Gynecology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Haihan Gu
- Department of Pharmacy, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xiaotong Xu
- Department of Obstetrics and Gynecology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yanpeng Tian
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xianghua Huang
- Department of Obstetrics and Gynecology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yanfang Du
- Department of Obstetrics and Gynecology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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Spencer TE, Wells KD, Lee K, Telugu BP, Hansen PJ, Bartol FF, Blomberg L, Schook LB, Dawson H, Lunney JK, Driver JP, Davis TA, Donovan SM, Dilger RN, Saif LJ, Moeser A, McGill JL, Smith G, Ireland JJ. Future of biomedical, agricultural, and biological systems research using domesticated animals. Biol Reprod 2022; 106:629-638. [PMID: 35094055 PMCID: PMC9189970 DOI: 10.1093/biolre/ioac019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 01/31/2023] Open
Abstract
Increased knowledge of reproduction and health of domesticated animals is integral to sustain and improve global competitiveness of U.S. animal agriculture, understand and resolve complex animal and human diseases, and advance fundamental research in sciences that are critical to understanding mechanisms of action and identifying future targets for interventions. Historically, federal and state budgets have dwindled and funding for the United States Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA) competitive grants programs remained relatively stagnant from 1985 through 2010. This shortage in critical financial support for basic and applied research, coupled with the underappreciated knowledge of the utility of non-rodent species for biomedical research, hindered funding opportunities for research involving livestock and limited improvements in both animal agriculture and animal and human health. In 2010, the National Institutes of Health and USDA NIFA established an interagency partnership to promote the use of agriculturally important animal species in basic and translational research relevant to both biomedicine and agriculture. This interagency program supported 61 grants totaling over $107 million with 23 awards to new or early-stage investigators. This article will review the success of the 9-year Dual Purpose effort and highlight opportunities for utilizing domesticated agricultural animals in research.
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Affiliation(s)
- Thomas E Spencer
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA,Correspondence: Division of Animal Sciences, University of Missouri, Columbia, MO, USA. Tel: +15738823467; E-mail:
| | - Kevin D Wells
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Kiho Lee
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Bhanu P Telugu
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Peter J Hansen
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - Frank F Bartol
- Department of Anatomy, Physiology and Pharmacology, Cellular and Molecular Biosciences Program, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - LeAnn Blomberg
- The Animal Biosciences and Biotechnology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705 USA
| | - Lawrence B Schook
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | - Harry Dawson
- USDA, ARS, Beltsville Human Nutrition Research Center, Diet, Genomics & Immunology Laboratory, Beltsville, MD 20705-2350, USA
| | - Joan K Lunney
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center (BARC), Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Beltsville, MD, USA
| | - John P Driver
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - Teresa A Davis
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Sharon M Donovan
- Department of Food Science and Human Nutrition, College of Agricultural, Consumer and Environmental Sciences, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Ryan N Dilger
- The Animal Biosciences and Biotechnology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705 USA
| | - Linda J Saif
- Center for Food Animal Health Research, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH, USA
| | - Adam Moeser
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Jodi L McGill
- Department of Veterinary Microbiology and Preventative Medicine, Iowa State University, Ames, IA, USA
| | - George Smith
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - James J Ireland
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
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Liang L, Yu J, Li J, Li N, Liu J, Xiu L, Zeng J, Wang T, Wu L. Integration of scRNA-Seq and Bulk RNA-Seq to Analyse the Heterogeneity of Ovarian Cancer Immune Cells and Establish a Molecular Risk Model. Front Oncol 2021; 11:711020. [PMID: 34621670 PMCID: PMC8490743 DOI: 10.3389/fonc.2021.711020] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/31/2021] [Indexed: 11/21/2022] Open
Abstract
Background Considerable evidence suggests that the heterogeneity of ovarian cancer (OC) is a major cause of treatment failure. Single-cell RNA sequencing (scRNA-seq) is a powerful tool to analyse the heterogeneity of the tumour at the single-cell level, leading to a better understanding of cell function at the genetic and cellular levels. Methods OC scRNA-seq data were extracted from the Gene Expression Omnibus (GEO) database and the FindCluster () package used for cell cluster analysis. The GSVA package was used for single-sample gene set enrichment analysis (ssGSEA) analysis to obtain a Hallmark gene set score and bulk RNA-seq data were used to analyse the key genes of OC-associated immune cell subsets. CIBERSORT was used to identify immune scores of cells and the “WGCNA” package for the weighted correlation network analysis (WGCNA). KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology) analyses of subtype groups were performed by GSEA. Then, univariate Cox and lasso regression were performed to further establish a signature. Finally, qPCR and immunohistochemistry staining were used to evaluate the expression of signature genes in OC. Results Two scRNA-seq (GSE154600 and GES158937) datasets were integrated to obtain 20 cell clusters. T cells or NK cells (cluster 5, 6, 7, 11), B cells (cluster 16, 19, 20) and myeloid cells (cluster 4, 9, 10) were clustered according to immune cell markers. The ssGSEA revealed that M1- and M2-like myeloid cell-related genes were significantly upregulated in P3 and P4 patients in the GSE154600 data. Immune cell analysis in TCGA-OC showed that a high abundance of M1-like tumour-associated macrophages (TAMS) predicts better survival. WGCNA, univariate Cox and lasso Cox regression established a two-gene signature (RiskScore=-0.059*CXCL13-0.034*IL26). Next, the TCGA-test and TCGA-OC were used to test the risk prediction ability of the signature, showing a good effect in the datasets. Moreover, the qPCR and immunohistochemistry staining revealed that the expression of CXCL13 and IL26 was reduced in OC tissues. Conclusion A two-gene signature prognostic stratification system (CXCL13 and IL26) was developed based on the heterogeneity of OC immune cells to accurately evaluate the prognostic risk.
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Affiliation(s)
- Leilei Liang
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Yu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jian Li
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ning Li
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Liu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Xiu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jia Zeng
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tiantian Wang
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lingying Wu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Kim K, Pröbstel AK, Baumann R, Dyckow J, Landefeld J, Kogl E, Madireddy L, Loudermilk R, Eggers EL, Singh S, Caillier SJ, Hauser SL, Cree BAC, Schirmer L, Wilson MR, Baranzini SE. Cell type-specific transcriptomics identifies neddylation as a novel therapeutic target in multiple sclerosis. Brain 2021; 144:450-461. [PMID: 33374005 DOI: 10.1093/brain/awaa421] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 08/18/2020] [Accepted: 09/23/2020] [Indexed: 11/13/2022] Open
Abstract
Multiple sclerosis is an autoimmune disease of the CNS in which both genetic and environmental factors are involved. Genome-wide association studies revealed more than 200 risk loci, most of which harbour genes primarily expressed in immune cells. However, whether genetic differences are translated into cell-specific gene expression profiles and to what extent these are altered in patients with multiple sclerosis are still open questions in the field. To assess cell type-specific gene expression in a large cohort of patients with multiple sclerosis, we sequenced the whole transcriptome of fluorescence-activated cell sorted T cells (CD4+ and CD8+) and CD14+ monocytes from treatment-naive patients with multiple sclerosis (n = 106) and healthy subjects (n = 22). We identified 479 differentially expressed genes in CD4+ T cells, 435 in monocytes, and 54 in CD8+ T cells. Importantly, in CD4+ T cells, we discovered upregulated transcripts from the NAE1 gene, a critical subunit of the NEDD8 activating enzyme, which activates the neddylation pathway, a post-translational modification analogous to ubiquitination. Finally, we demonstrated that inhibition of NEDD8 activating enzyme using the specific inhibitor pevonedistat (MLN4924) significantly ameliorated disease severity in murine experimental autoimmune encephalomyelitis. Our findings provide novel insights into multiple sclerosis-associated gene regulation unravelling neddylation as a crucial pathway in multiple sclerosis pathogenesis with implications for the development of tailored disease-modifying agents.
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Affiliation(s)
- Kicheol Kim
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Anne-Katrin Pröbstel
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA.,Neurologic Clinic and Policlinic, Departments of Medicine and Biomedicine, University Hospital of Basel, University of Basel, Basel, Switzerland
| | - Ryan Baumann
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Julia Dyckow
- Department of Neurology and Mannheim Center for Translational Neurosciences, Medical Faculty Mannheim, Interdisciplinary Center for Neurosciences, University of Heidelberg, Mannheim, Germany
| | - James Landefeld
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Elva Kogl
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Lohith Madireddy
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Rita Loudermilk
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Erica L Eggers
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Sneha Singh
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Stacy J Caillier
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Stephen L Hauser
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Bruce A C Cree
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | | | - Lucas Schirmer
- Department of Neurology and Mannheim Center for Translational Neurosciences, Medical Faculty Mannheim, Interdisciplinary Center for Neurosciences, University of Heidelberg, Mannheim, Germany
| | - Michael R Wilson
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Sergio E Baranzini
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, CA, USA.,Graduate Program in Bioinformatics, University of California, San Francisco, CA, USA
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Kim K, Park S, Park SY, Kim G, Park SM, Cho JW, Kim DH, Park YM, Koh YW, Kim HR, Ha SJ, Lee I. Single-cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti-PD-1 responses in human cancer. Genome Med 2020; 12:22. [PMID: 32111241 PMCID: PMC7048139 DOI: 10.1186/s13073-020-00722-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/09/2020] [Indexed: 02/06/2023] Open
Abstract
Background T cells exhibit heterogeneous functional states in the tumor microenvironment. Immune checkpoint inhibitors (ICIs) can reinvigorate only the stem cell-like progenitor exhausted T cells, which suggests that inhibiting the exhaustion progress will improve the efficacy of immunotherapy. Thus, regulatory factors promoting T cell exhaustion could serve as potential targets for delaying the process and improving ICI efficacy. Methods We analyzed the single-cell transcriptome data derived from human melanoma and non-small cell lung cancer (NSCLC) samples and classified the tumor-infiltrating (TI) CD8+ T cell population based on PDCD1 (PD-1) levels, i.e., PDCD1-high and PDCD1-low cells. Additionally, we identified differentially expressed genes as candidate factors regulating intra-tumoral T cell exhaustion. The co-expression of candidate genes with immune checkpoint (IC) molecules in the TI CD8+ T cells was confirmed by single-cell trajectory and flow cytometry analyses. The loss-of-function effect of the candidate regulator was examined by a cell-based knockdown assay. The clinical effect of the candidate regulator was evaluated based on the overall survival and anti-PD-1 responses. Results We retrieved many known factors for regulating T cell exhaustion among the differentially expressed genes between PDCD1-high and PDCD1-low subsets of the TI CD8+ T cells in human melanoma and NSCLC. TOX was the only transcription factor (TF) predicted in both tumor types. TOX levels tend to increase as CD8+ T cells become more exhausted. Flow cytometry analysis revealed a correlation between TOX expression and severity of intra-tumoral T cell exhaustion. TOX knockdown in the human TI CD8+ T cells resulted in downregulation of PD-1, TIM-3, TIGIT, and CTLA-4, which suggests that TOX promotes intra-tumoral T cell exhaustion by upregulating IC proteins in cancer. Finally, the TOX level in the TI T cells was found to be highly predictive of overall survival and anti-PD-1 efficacy in melanoma and NSCLC. Conclusions We predicted the regulatory factors involved in T cell exhaustion using single-cell transcriptome profiles of human TI lymphocytes. TOX promoted intra-tumoral CD8+ T cell exhaustion via upregulation of IC molecules. This suggested that TOX inhibition can potentially impede T cell exhaustion and improve ICI efficacy. Additionally, TOX expression in the TI T cells can be used for patient stratification during anti-tumor treatments, including anti-PD-1 immunotherapy.
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Affiliation(s)
- Kyungsoo Kim
- Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Seyeon Park
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Seong Yong Park
- Department of Thoracic and Cardiovascular Surgery, College of Medicine, Yonsei University, Seoul, 03722, Korea
| | - Gamin Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, College of Medicine, Yonsei University, Seoul, 03722, Korea
| | - Su Myeong Park
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, College of Medicine, Yonsei University, Seoul, 03722, Korea
| | - Jae-Won Cho
- Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Da Hee Kim
- Department of Otorhinolaryngology, College of Medicine, Yonsei University, Seoul, 03722, Korea
| | - Young Min Park
- Department of Otorhinolaryngology, College of Medicine, Yonsei University, Seoul, 03722, Korea
| | - Yoon Woo Koh
- Department of Otorhinolaryngology, College of Medicine, Yonsei University, Seoul, 03722, Korea
| | - Hye Ryun Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, College of Medicine, Yonsei University, Seoul, 03722, Korea
| | - Sang-Jun Ha
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, 03722, Korea.
| | - Insuk Lee
- Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul, 03722, Korea. .,Department of Biomedical Systems Informatics, College of Medicine, Yonsei University, Seoul, 03722, Korea.
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