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Yuan J, Yu S. Comprehensive Analysis Reveals Prognostic and Therapeutic Immunity-Related Biomarkers for Pediatric Metastatic Osteosarcoma. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:95. [PMID: 38256356 PMCID: PMC10820594 DOI: 10.3390/medicina60010095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/15/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024]
Abstract
Background and Objectives: Osteosarcoma, the most prevalent malignant bone tumor in children and adolescents, presents a complex pathogenesis characterized by various genetic and epigenetic alterations. This study aims to identify key differentially expressed genes (DEGs) in pediatric osteosarcoma, with a focus on those influencing metastasis and patient survival. Materials and Methods: We utilized the GSE33382 dataset from the GEO database for a comprehensive bioinformatic analysis. This included a protein-protein interaction (PPI) network analysis, Cox regression, and Kaplan-Meier survival analysis to identify central DEGs associated with osteosarcoma metastasis and patient survival. Results: Our analysis identified 88 DEGs related to osteosarcoma metastasis. Among them, three survival-related central DEGs-C1QA, CD74, and HLA-DMA-were significantly linked to patient outcomes. Further correlation analysis established a strong relationship between these genes, tumor mutation burden (TMB), immune checkpoint gene expression, and overall survival. Notably, C1QA and CD74 exhibited higher expression in non-metastatic osteosarcoma cases, suggesting a potential role in disease progression. Conclusions: The identified DEGs, particularly C1QA, CD74, and HLA-DMA, may serve as critical biomarkers for pediatric osteosarcoma prognosis and potential targets for immunotherapy. These findings provide a deeper understanding of the molecular landscape of osteosarcoma and open new avenues for therapeutic intervention.
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Affiliation(s)
| | - Shengji Yu
- Department of Orthopedics, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 17 Nanli, Panjiayuan, Chaoyang District, Beijing 100021, China;
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2
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Suzuki A, Nojima S, Tahara S, Motooka D, Kohara M, Okuzaki D, Hirokawa M, Morii E. Identification of invasive subpopulations using spatial transcriptome analysis in thyroid follicular tumors. J Pathol Transl Med 2024; 58:22-28. [PMID: 38229431 DOI: 10.4132/jptm.2023.11.21] [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: 10/27/2023] [Accepted: 11/21/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Follicular tumors include follicular thyroid adenomas and carcinomas; however, it is difficult to distinguish between the two when the cytology or biopsy material is obtained from a portion of the tumor. The presence or absence of invasion in the resected material is used to differentiate between adenomas and carcinomas, which often results in the unnecessary removal of the adenomas. If nodules that may be follicular thyroid carcinomas are identified preoperatively, active surveillance of other nodules as adenomas is possible, which reduces the risk of surgical complications and the expenses incurred during medical treatment. Therefore, we aimed to identify biomarkers in the invasive subpopulation of follicular tumor cells. METHODS We performed a spatial transcriptome analysis of a case of follicular thyroid carcinoma and examined the dynamics of CD74 expression in 36 cases. RESULTS We identified a subpopulation in a region close to the invasive area, and this subpopulation expressed high levels of CD74. Immunohistochemically, CD74 was highly expressed in the invasive and peripheral areas of the tumor. CONCLUSIONS Although high CD74 expression has been reported in papillary and anaplastic thyroid carcinomas, it has not been analyzed in follicular thyroid carcinomas. Furthermore, the heterogeneity of CD74 expression in thyroid tumors has not yet been reported. The CD74-positive subpopulation identified in this study may be useful in predicting invasion of follicular thyroid carcinomas.
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Affiliation(s)
- Ayana Suzuki
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Diagnostic Pathology and Cytology, Kuma Hospital, Kobe, Hyogo, Japan
| | - Satoshi Nojima
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Shinichiro Tahara
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Masaharu Kohara
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
| | - Mitsuyoshi Hirokawa
- Department of Diagnostic Pathology and Cytology, Kuma Hospital, Kobe, Hyogo, Japan
| | - Eiichi Morii
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
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3
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Perik-Zavodskaia O, Perik-Zavodskii R, Nazarov K, Volynets M, Alrhmoun S, Shevchenko J, Sennikov S. Murine Bone Marrow Erythroid Cells Have Two Branches of Differentiation Defined by the Presence of CD45 and a Different Immune Transcriptome Than Fetal Liver Erythroid Cells. Int J Mol Sci 2023; 24:15752. [PMID: 37958735 PMCID: PMC10650492 DOI: 10.3390/ijms242115752] [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: 09/16/2023] [Revised: 10/18/2023] [Accepted: 10/29/2023] [Indexed: 11/15/2023] Open
Abstract
Mouse erythropoiesis is a multifaceted process involving the intricate interplay of proliferation, differentiation, and maturation of erythroid cells, leading to significant changes in their transcriptomic and proteomic profiles. While the immunoregulatory role of murine erythroid cells has been recognized historically, modern investigative techniques have been sparingly applied to decipher their functions. To address this gap, our study sought to comprehensively characterize mouse erythroid cells through contemporary transcriptomic and proteomic approaches. By evaluating CD71 and Ter-119 as sorting markers for murine erythroid cells and employing bulk NanoString transcriptomics, we discerned distinctive gene expression profiles between bone marrow and fetal liver-derived erythroid cells. Additionally, leveraging flow cytometry, we assessed the surface expression of CD44, CD45, CD71, and Ter-119 on normal and phenylhydrazine-induced hemolytic anemia mouse bone marrow and splenic erythroid cells. Key findings emerged: firstly, the utilization of CD71 for cell sorting yielded comparatively impure erythroid cell populations compared to Ter-119; secondly, discernible differences in immunoregulatory molecule expression were evident between erythroid cells from mouse bone marrow and fetal liver; thirdly, two discrete branches of mouse erythropoiesis were identified based on CD45 expression: CD45-negative and CD45-positive, which had been altered differently in response to phenylhydrazine. Our deductions underscore (1) Ter-119's superiority over CD71 as a murine erythroid cell sorting marker, (2) the potential of erythroid cells in murine antimicrobial immunity, and (3) the importance of investigating CD45-positive and CD45-negative murine erythroid cells separately and in further detail in future studies.
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Affiliation(s)
| | | | | | | | | | | | - Sergey Sennikov
- Laboratory of Molecular Immunology, Federal State Budgetary Scientific Institution Research Institute of Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia; (O.P.-Z.); (R.P.-Z.); (K.N.); (M.V.); (S.A.)
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4
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Bedran G, Gasser HC, Weke K, Wang T, Bedran D, Laird A, Battail C, Zanzotto FM, Pesquita C, Axelson H, Rajan A, Harrison DJ, Palkowski A, Pawlik M, Parys M, O'Neill JR, Brennan PM, Symeonides SN, Goodlett DR, Litchfield K, Fahraeus R, Hupp TR, Kote S, Alfaro JA. The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I-Associated Peptides. Cancer Immunol Res 2023; 11:747-762. [PMID: 36961404 PMCID: PMC10236148 DOI: 10.1158/2326-6066.cir-22-0621] [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: 08/01/2022] [Revised: 11/25/2022] [Accepted: 03/16/2023] [Indexed: 03/25/2023]
Abstract
Tumor antigens can emerge through multiple mechanisms, including translation of noncoding genomic regions. This noncanonical category of tumor antigens has recently gained attention; however, our understanding of how they recur within and between cancer types is still in its infancy. Therefore, we developed a proteogenomic pipeline based on deep learning de novo mass spectrometry (MS) to enable the discovery of noncanonical MHC class I-associated peptides (ncMAP) from noncoding regions. Considering that the emergence of tumor antigens can also involve posttranslational modifications (PTM), we included an open search component in our pipeline. Leveraging the wealth of MS-based immunopeptidomics, we analyzed data from 26 MHC class I immunopeptidomic studies across 11 different cancer types. We validated the de novo identified ncMAPs, along with the most abundant PTMs, using spectral matching and controlled their FDR to 1%. The noncanonical presentation appeared to be 5 times enriched for the A03 HLA supertype, with a projected population coverage of 55%. The data reveal an atlas of 8,601 ncMAPs with varying levels of cancer selectivity and suggest 17 cancer-selective ncMAPs as attractive therapeutic targets according to a stringent cutoff. In summary, the combination of the open-source pipeline and the atlas of ncMAPs reported herein could facilitate the identification and screening of ncMAPs as targets for T-cell therapies or vaccine development.
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Affiliation(s)
- Georges Bedran
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Kenneth Weke
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Tongjie Wang
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Dominika Bedran
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Alexander Laird
- Urology Department, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Christophe Battail
- CEA, Grenoble Alpes University, INSERM, IRIG, Biosciences and Bioengineering for Health Laboratory (BGE) - UA13 INSERM-CEA-UGA, Grenoble, France
| | | | - Catia Pesquita
- LASIGE, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Håkan Axelson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Ajitha Rajan
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - David J. Harrison
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Aleksander Palkowski
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Maciej Pawlik
- Academic Computer Centre CYFRONET, AGH University of Science and Technology, Cracow, Poland
| | - Maciej Parys
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - J. Robert O'Neill
- Cambridge Oesophagogastric Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Paul M. Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Stefan N. Symeonides
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - David R. Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
- University of Victoria Genome BC Proteome Centre, Victoria, Canada
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Paris, France
| | - Ted R. Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Javier A. Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
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5
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Fan Z, Luo Y, Lu H, Wang T, Feng Y, Zhao W, Kim P, Zhou X. SPASCER: spatial transcriptomics annotation at single-cell resolution. Nucleic Acids Res 2023; 51:D1138-D1149. [PMID: 36243975 PMCID: PMC9825565 DOI: 10.1093/nar/gkac889] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/21/2022] [Accepted: 10/13/2022] [Indexed: 01/30/2023] Open
Abstract
In recent years, the explosive growth of spatial technologies has enabled the characterization of spatial heterogeneity of tissue architectures. Compared to traditional sequencing, spatial transcriptomics reserves the spatial information of each captured location and provides novel insights into diverse spatially related biological contexts. Even though two spatial transcriptomics databases exist, they provide limited analytical information. Information such as spatial heterogeneity of genes and cells, cell-cell communication activities in space, and the cell type compositions in the microenvironment are critical clues to unveil the mechanism of tumorigenesis and embryo differentiation. Therefore, we constructed a new spatial transcriptomics database, named SPASCER (https://ccsm.uth.edu/SPASCER), designed to help understand the heterogeneity of tissue organizations, region-specific microenvironment, and intercellular interactions across tissue architectures at multiple levels. SPASCER contains datasets from 43 studies, including 1082 sub-datasets from 16 organ types across four species. scRNA-seq was integrated to deconvolve/map spatial transcriptomics, and processed with spatial cell-cell interaction, gene pattern and pathway enrichment analysis. Cell-cell interactions and gene regulation network of scRNA-seq from matched spatial transcriptomics were performed as well. The application of SPASCER will provide new insights into tissue architecture and a solid foundation for the mechanistic understanding of many biological processes in healthy and diseased tissues.
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Affiliation(s)
- Zhiwei Fan
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yangyang Luo
- West China Hospital, Sichuan University, Chengdu 610041, China
| | - Huifen Lu
- West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tiangang Wang
- School of Life Science and Technology, Xidian University, Xi’an 710126, China
| | - YuZhou Feng
- West China Hospital, Sichuan University, Chengdu 610041, China
| | - Weiling Zhao
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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6
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Chen WW, Chu TSM, Xu L, Zhao CN, Poon WS, Leung GKK, Kong FM(S. Immune related biomarkers for cancer metastasis to the brain. Exp Hematol Oncol 2022; 11:105. [PMID: 36527157 PMCID: PMC9756766 DOI: 10.1186/s40164-022-00349-z] [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: 04/06/2022] [Accepted: 07/14/2022] [Indexed: 12/23/2022] Open
Abstract
Brain metastasis accounts for a large number of cancer-related deaths. The host immune system, involved at each step of the metastatic cascade, plays an important role in both the initiation of the brain metastasis and their treatment responses to various modalities, through either local and or systemic effect. However, few reliable immune biomarkers have been identified in predicting the development and the treatment outcome in patients with cancer brain metastasis. Here, we provide a focused perspective of immune related biomarkers for cancer metastasis to the brain and a thorough discussion of the potential utilization of specific biomarkers such as tumor mutation burden (TMB), genetic markers, circulating and tumor-infiltrating immune cells, cytokines, in predicting the brain disease progression and regression after therapeutic intervention. We hope to inspire the field to extend the research and establish practical guidelines for developing and validating immune related biomarkers to provide personalized treatment and improve treatment outcomes in patients with metastatic brain cancers.
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Affiliation(s)
- Wei-Wei Chen
- grid.194645.b0000000121742757Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, SAR China
| | - Timothy Shun Man Chu
- grid.419334.80000 0004 0641 3236Royal Victoria Infirmary, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Queen Victoria Road, Newcastle Upon Tyne, NE1 4LP UK ,grid.1006.70000 0001 0462 7212Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU UK
| | - LiangLiang Xu
- grid.440671.00000 0004 5373 5131Department of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Cai-Ning Zhao
- grid.194645.b0000000121742757Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, SAR China
| | - Wai-Sang Poon
- grid.440671.00000 0004 5373 5131Neuro-Medical Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China ,grid.194645.b0000000121742757Department of Surgery, School of Clinical Medicine,LKS Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, SAR China
| | - Gilberto Ka-Kit Leung
- grid.194645.b0000000121742757Department of Surgery, School of Clinical Medicine,LKS Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, SAR China
| | - Feng-Ming (Spring) Kong
- grid.194645.b0000000121742757Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, SAR China ,grid.440671.00000 0004 5373 5131Department of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
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7
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Zhao Y, Zhao J, Zhong M, Zhang Q, Yan F, Feng Y, Guo Y. The expression and methylation of PITX genes is associated with the prognosis of head and neck squamous cell carcinoma. Front Genet 2022; 13:982241. [PMID: 36204311 PMCID: PMC9530742 DOI: 10.3389/fgene.2022.982241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/07/2022] [Indexed: 12/24/2022] Open
Abstract
Background: The PITX gene family, comprising PITX1, PITX2, and PITX3, is critical in organogenesis and has been evolutionary conserved in animals. PITX genes are associated with the advanced progression and poor prognosis of multiple cancers. However, the relationship between the PITX genes and head and neck squamous cell carcinoma (HNSC) has not been reported. Methods: We used data from The Cancer Genome Atlas (TCGA) to analyze the association between PITX mRNA expression and clinicopathological parameters of patients with HNSC. The prognostic value of PITX genes was evaluated using the Kaplan-Meier plotter. Multivariate Cox analysis was used to screen out prognosis-associated genes to identify better prognostic indicators. The potential roles of PITX1 and PITX2 in HNSC prognosis were investigated using the protein-protein interaction (PPI) network, Gene Ontology (GO) analysis, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The correlation between PITX1 and PITX2 expression or methylation and immune cell infiltration was evaluated using the tumor-immune system interaction database (TISIDB). MethSurv was used to identify DNA methylation and its effect on HNSC prognosis. Results:PITX genes expression was correlated with different cancers. PITX1 and PITX2 expression was lower in the patients with HNSC. In HNSC, PITX1 expression was significantly related to the clinical stage, histologic grade, and N stage, while PITX2 expression was only significantly related to the histologic grade. The high expression of PITX3 was significantly related to the histologic grade, T stage, and N stage. Survival analysis revealed that PITX genes had prognostic value in HNSC, which was supported by multivariate Cox analysis. PPI network and enrichment analysis showed that the genes interacting with PITX1 and PITX2 belonged predominantly to signaling pathways associated with DNA binding and transcription. Of the CpG DNA methylation sites in PITX1 and PITX2, 28 and 22 were related to the prognosis of HNSC, respectively. Additionally, PITX1 and PITX2 expression and methylation was associated with tumor-infiltrating lymphocytes (TILs). Conclusion: The PITX genes were differentially expressed in patients with HNSC, highlighting their essential role in DNA methylation and tumor-infiltrating immune cell regulation, as well as overall prognostic value in HNSC.
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Affiliation(s)
- Yaqiong Zhao
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jie Zhao
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Mengmei Zhong
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Qian Zhang
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Fei Yan
- Hunan Key Laboratory of Oral Health Research and Hunan 3D Printing Engineering Research Center of Oral Care and Hunan Clinical Research Center of Oral Major Diseases and Oral Health and Xiangya Stomatological Hospital and Xiangya School of Stomatology, Central South University, Changsha, China
| | - Yunzhi Feng
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yue Guo
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Yue Guo,
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8
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Li T, Bou-Dargham MJ, Fultang N, Li X, Pear WS, Sun H, Chen YH. c-Rel-dependent monocytes are potent immune suppressor cells in cancer. J Leukoc Biol 2022; 112:845-859. [PMID: 35694784 PMCID: PMC9530019 DOI: 10.1002/jlb.1ma0422-518rr] [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: 11/02/2021] [Revised: 04/25/2022] [Indexed: 11/08/2022] Open
Abstract
Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of leukocytes that are important for tumorigenesis and tumor immunotherapy. They comprise up to 10% of leukocytes in the blood of tumor patients and their depletion may be required for successful tumor immunotherapy. However, the identity of MDSCs remains obscure, primarily due to their heterogeneity and lack of a known lineage-specific transcription factor specifying their differentiation. Using single-cell transcriptomics and gene knockout approaches, we now describe a subset of murine and human myeloid suppressor cells, named rel-dependent monocytes (rMos), which are programmed by the transcription factor c-Rel of the NF-κB family. Unlike MDSCs described previously, the c-Rel-dependent monocytes expressed a high amount of the proinflammatory cytokine IL-1β together with a low level of suppressive molecule arginase 1. Both in vitro and in tumor-bearing mice, these c-Rel+ IL-1βhi Arg1- monocytes promoted tumor growth by potently suppressing T cell function and showed a strong migratory phenotype, all of which were impaired by c-Rel deficiency or inhibition. Mechanistic studies revealed that c-Rel controlled the expression of monocyte signature genes through a unique transcriptional complex called the c-Rel enhanceosome, and IL-1β-CCL2 crosstalk between tumor cells and the rel-dependent monocytes maintained the suppressive tumor microenvironment. Thus, c-Rel specifies the development of a suppressive monocyte population and could be selectively targeted for treating cancer.
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Affiliation(s)
- Ting Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Mayassa J Bou-Dargham
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Norman Fultang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Xinyuan Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Warren S Pear
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Honghong Sun
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Youhai H Chen
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Faculty of Pharmaceutical Sciences, CAS Shenzhen Institute of Advanced Technology, Shenzhen, Guangdong, China
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9
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Wu T, Wei B, Lin H, Zhou B, Lin T, Liu Q, Sang H, Liu H, Huang W. Integral Analyses of Competing Endogenous RNA Mechanisms and DNA Methylation Reveal Regulatory Mechanisms in Osteosarcoma. Front Cell Dev Biol 2021; 9:763347. [PMID: 34957096 PMCID: PMC8696003 DOI: 10.3389/fcell.2021.763347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/26/2021] [Indexed: 12/21/2022] Open
Abstract
Background: Osteosarcoma (OS) is the most common primary malignant bone tumour in children and adolescents, with rapid growth, frequent metastasis, and a poor prognosis, but its pathogenesis has not been fully elucidated. Exploring the pathogenesis of OS is of great significance for improving diagnoses and finding new therapeutic targets. Methods: Differentially expressed circRNAs (DECs), miRNAs (DEMs), methylated DNA sites (DMSs), and mRNAs (DEGs) were identified between OS and control cell lines. GSEA of DEGs and functional enrichment analysis of methylated DEGs were carried out to further identify potential biological processes. Online tools were used to predict the miRNA binding sites of DECs and the mRNA binding sites of DEMs, and then construct a circRNA-miRNA-mRNA network. Next, an analysis of the interaction between methylated DEGs was performed with a protein-protein interaction (PPI) network, and hub gene identification and survival analysis were carried out. The expression pattern of circRNA-miRNA-mRNA was validated by real-time PCR. Results: GSEA and functional enrichment analysis indicated that DEGs and methylated DEGs are involved in important biological processes in cancer. Hsa_circ_0001753/has_miR_760/CD74 network was constructed and validated in cell lines. Low expression levels of CD74 are associated with poor overall survival times and show good diagnostic ability. Conclusion: Methylated DEGs may be involved in the development of OS, and the hsa_circ_0001753/has_miR_760/CD74 network may serve as a target for the early diagnosis of and targeted therapy for OS.
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Affiliation(s)
- Tingrui Wu
- Orthopaedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Bo Wei
- Orthopaedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Hao Lin
- Orthopaedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Boan Zhou
- Orthopaedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Tao Lin
- Orthopaedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Qianzheng Liu
- Orthopaedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Hongxun Sang
- Department of Orthopaedics, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Huan Liu
- Department of Orthopaedics, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China.,National Traditional Chinese Medicine Clinical Research Base, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Wenhua Huang
- Orthopaedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Medical Biomechanics, National Key Discipline of Human Anatomy, Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Medical Innovation Platform for Translation of 3D Printing Application, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
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10
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Sauerer T, Lischer C, Weich A, Berking C, Vera J, Dörrie J. Single-Molecule RNA Sequencing Reveals IFNγ-Induced Differential Expression of Immune Escape Genes in Merkel Cell Polyomavirus-Positive MCC Cell Lines. Front Microbiol 2021; 12:785662. [PMID: 35003017 PMCID: PMC8727593 DOI: 10.3389/fmicb.2021.785662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/18/2021] [Indexed: 12/15/2022] Open
Abstract
Merkel cell carcinoma (MCC) is a rare and highly aggressive cancer, which is mainly caused by genomic integration of the Merkel cell polyomavirus and subsequent expression of a truncated form of its large T antigen. The resulting primary tumor is known to be immunogenic and under constant pressure to escape immune surveillance. Because interferon gamma (IFNγ), a key player of immune response, is secreted by many immune effector cells and has been shown to exert both anti-tumoral and pro-tumoral effects, we studied the transcriptomic response of MCC cells to IFNγ. In particular, immune modulatory effects that may help the tumor evade immune surveillance were of high interest to our investigation. The effect of IFNγ treatment on the transcriptomic program of three MCC cell lines (WaGa, MKL-1, and MKL-2) was analyzed using single-molecule sequencing via the Oxford Nanopore platform. A significant differential expression of several genes was detected across all three cell lines. Subsequent pathway analysis and manual annotation showed a clear upregulation of genes involved in the immune escape of tumor due to IFNγ treatment. The analysis of selected genes on protein level underlined our sequencing results. These findings contribute to a better understanding of immune escape of MCC and may help in clinical treatment of MCC patients. Furthermore, we demonstrate that single-molecule sequencing can be used to assess characteristics of large eukaryotic transcriptomes and thus contribute to a broader access to sequencing data in the community due to its low cost of entry.
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Affiliation(s)
- Tatjana Sauerer
- RNA-based Immunotherapy, Hautklinik, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Christopher Lischer
- Systems Tumor Immunology, Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Adrian Weich
- Systems Tumor Immunology, Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Carola Berking
- Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Julio Vera
- Systems Tumor Immunology, Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Jan Dörrie
- RNA-based Immunotherapy, Hautklinik, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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HLA Class II Histocompatibility Antigen γ Chain (CD74) Expression Is Associated with Immune Cell Infiltration and Favorable Outcome in Breast Cancer. Cancers (Basel) 2021; 13:cancers13246179. [PMID: 34944801 PMCID: PMC8699420 DOI: 10.3390/cancers13246179] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 12/31/2022] Open
Abstract
Simple Summary CD74 is a transmembrane protein normally expressed in immune cells, and aberrantly expressed in cancer cells. Although CD74 overexpression is mostly associated with hematologic malignancies, some studies have also reported CD74 expression in breast cancer especially associated to the triple negative subtype and metastatic breast cancer. The triple-negative breast cancer is generally more aggressive and with a poorer prognosis than the other subtypes. Immunotherapy holds great promise in clinical management of breast cancer, and CD74 may play a regulatory role in immune system responses. Our results showed that CD74 is associated with expression of programmed cell death ligand 1 (PD-L1), which in turn is involved in preventing anticancer immune responses. Overall, our results indicate that CD74 may be a therapeutic target for the treatment of breast cancer patients, in particular in triple negative breast cancer and metastatic breast cancers, where CD74 is commonly overexpressed. Abstract The triple-negative breast cancer (TNBC) subtype, defined as negative for ER, PgR, and HER2, is biologically more aggressive and with a poorer prognosis than the other subtypes, in part due to the lack of suitable targeted therapies. Consequently, identification of any potential novel therapeutic option, predictive and/or prognostic biomarker, or any other relevant information that may impact the clinical management of this group of patients is valuable. The HLA class II histocompatibility antigen γ chain, or cluster of differentiation 74 (CD74), has been associated with TNBCs, and poorer survival. However, discordant results have been reported for immunohistochemical studies of CD74 expression in breast cancer. Here we report validation studies for use of a novel CD74 antibody, UMAb231. We used this antibody to stain a TMA including 640 human breast cancer samples, and found no association with the TNBC subtype, but did find a positive correlation with outcome. We also found associations between CD74 expression and immune cell infiltration, and expression of programmed death ligand 1 (PD-L1). Given that CD74 may play a role in innate immune system responses and the potential of immunotherapy as a viable treatment strategy for TNBCs, CD74 expression may have predictive value for immune checkpoint therapies.
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12
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Sharma M, Arora I, Chen M, Wu H, Crowley MR, Tollefsbol TO, Li Y. Therapeutic Effects of Dietary Soybean Genistein on Triple-Negative Breast Cancer via Regulation of Epigenetic Mechanisms. Nutrients 2021; 13:3944. [PMID: 34836197 PMCID: PMC8623013 DOI: 10.3390/nu13113944] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022] Open
Abstract
Consumption of dietary natural components such as genistein (GE) found in soy-rich sources is strongly associated with a lower risk of breast cancer. However, bioactive dietary component-based therapeutic strategies are largely understudied in breast cancer treatment. Our investigation sought to elucidate the potential mechanisms linking bioactive dietary GE to its breast cancer chemotherapeutic potential in a special subtype of aggressive breast cancer-triple-negative breast cancer (TNBC)-by utilizing two preclinical patient-derived xenograft (PDX) orthotopic mouse models: BCM-3204 and TM00091. Our study revealed that administration of GE resulted in a delay of tumor growth in both PDX models. With transcriptomics analyses in TNBC tumors isolated from BCM-3204 PDXs, we found that dietary soybean GE significantly influenced multiple tumor-regulated gene expressions. Further validation assessment of six candidate differentially expressed genes (DEGs)-Cd74, Lpl, Ifi44, Fzd9, Sat1 and Wwc1-demonstrated a similar trend at gene transcriptional and protein levels as observed in RNA-sequencing results. Mechanistically, GE treatment-induced Cd74 downregulation regulated the NF-κB/Bcl-xL/TAp63 signal pathway, which may contribute to soybean GE-mediated therapeutic effects on TNBC tumors. Additionally, our findings revealed that GE can modify expression levels of key epigenetic-associated genes such as DNA methyltransferases (Dnmt3b), ten-eleven translocation (Tet3) methylcytosine dioxygenases and histone deacetyltransferase (Hdac2), and their enzymatic activities as well as genomic DNA methylation and histone methylation (H3K9) levels. Collectively, our investigation shows high significance for potential development of a novel therapeutic approach by using bioactive soybean GE for TNBC patients who have few treatment options.
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Affiliation(s)
- Manvi Sharma
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.S.); (I.A.); (H.W.)
| | - Itika Arora
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.S.); (I.A.); (H.W.)
| | - Min Chen
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Huixin Wu
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.S.); (I.A.); (H.W.)
| | - Michael R. Crowley
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Trygve O. Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.S.); (I.A.); (H.W.)
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Integrative Center for Aging Research, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yuanyuan Li
- Department of Obstetrics, Gynecology & Women’s Heath, University of Missouri, Columbia, MO 65211, USA
- Department of Surgery, University of Missouri, Columbia, MO 65211, USA
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13
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Llinàs-Arias P, Íñiguez-Muñoz S, McCann K, Voorwerk L, Orozco JIJ, Ensenyat-Mendez M, Sesé B, DiNome ML, Marzese DM. Epigenetic Regulation of Immunotherapy Response in Triple-Negative Breast Cancer. Cancers (Basel) 2021; 13:4139. [PMID: 34439290 PMCID: PMC8394958 DOI: 10.3390/cancers13164139] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/13/2021] [Accepted: 08/13/2021] [Indexed: 12/24/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is defined by the absence of estrogen receptor and progesterone receptor and human epidermal growth factor receptor 2 (HER2) overexpression. This malignancy, representing 15-20% of breast cancers, is a clinical challenge due to the lack of targeted treatments, higher intrinsic aggressiveness, and worse outcomes than other breast cancer subtypes. Immune checkpoint inhibitors have shown promising efficacy for early-stage and advanced TNBC, but this seems limited to a subgroup of patients. Understanding the underlying mechanisms that determine immunotherapy efficiency is essential to identifying which TNBC patients will respond to immunotherapy-based treatments and help to develop new therapeutic strategies. Emerging evidence supports that epigenetic alterations, including aberrant chromatin architecture conformation and the modulation of gene regulatory elements, are critical mechanisms for immune escape. These alterations are particularly interesting since they can be reverted through the inhibition of epigenetic regulators. For that reason, several recent studies suggest that the combination of epigenetic drugs and immunotherapeutic agents can boost anticancer immune responses. In this review, we focused on the contribution of epigenetics to the crosstalk between immune and cancer cells, its relevance on immunotherapy response in TNBC, and the potential benefits of combined treatments.
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Affiliation(s)
- Pere Llinàs-Arias
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma, Spain; (P.L.-A.); (S.Í.-M.); (M.E.-M.); (B.S.)
| | - Sandra Íñiguez-Muñoz
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma, Spain; (P.L.-A.); (S.Í.-M.); (M.E.-M.); (B.S.)
| | - Kelly McCann
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA;
| | - Leonie Voorwerk
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands;
| | - Javier I. J. Orozco
- Saint John’s Cancer Institute, Providence Saint John’s Health Center, Santa Monica, CA 90404, USA;
| | - Miquel Ensenyat-Mendez
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma, Spain; (P.L.-A.); (S.Í.-M.); (M.E.-M.); (B.S.)
| | - Borja Sesé
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma, Spain; (P.L.-A.); (S.Í.-M.); (M.E.-M.); (B.S.)
| | - Maggie L. DiNome
- Department of Surgery, David Geffen School of Medicine, University California Los Angeles (UCLA), Los Angeles, CA 90024, USA;
| | - Diego M. Marzese
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma, Spain; (P.L.-A.); (S.Í.-M.); (M.E.-M.); (B.S.)
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14
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Loreth D, Schuette M, Zinke J, Mohme M, Piffko A, Schneegans S, Stadler J, Janning M, Loges S, Joosse SA, Lamszus K, Westphal M, Müller V, Glatzel M, Matschke J, Gebhardt C, Schneider SW, Belczacka I, Volkmer B, Greinert R, Yaspo ML, Harter PN, Pantel K, Wikman H. CD74 and CD44 Expression on CTCs in Cancer Patients with Brain Metastasis. Int J Mol Sci 2021; 22:ijms22136993. [PMID: 34209696 PMCID: PMC8268634 DOI: 10.3390/ijms22136993] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/15/2022] Open
Abstract
Up to 40% of advance lung, melanoma and breast cancer patients suffer from brain metastases (BM) with increasing incidence. Here, we assessed whether circulating tumor cells (CTCs) in peripheral blood can serve as a disease surrogate, focusing on CD44 and CD74 expression as prognostic markers for BM. We show that a size-based microfluidic approach in combination with a semi-automated cell recognition system are well suited for CTC detection in BM patients and allow further characterization of tumor cells potentially derived from BM. CTCs were found in 50% (7/14) of breast cancer, 50% (9/18) of non-small cell lung cancer (NSCLC) and 36% (4/11) of melanoma patients. The next-generation sequencing (NGS) analysis of nine single CTCs from one breast cancer patient revealed three different CNV profile groups as well as a resistance causing ERS1 mutation. CD44 and CD74 were expressed on most CTCs and their expression was strongly correlated, whereas matched breast cancer BM tissues were much less frequently expressing CD44 and CD74 (negative in 46% and 54%, respectively). Thus, plasticity of CD44 and CD74 expression during trafficking of CTCs in the circulation might be the result of adaptation strategies.
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Affiliation(s)
- Desiree Loreth
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (D.L.); (S.S.); (S.A.J.); (K.P.)
| | - Moritz Schuette
- Alacris Theranostics GmbH, Max-Planck-Straße 3, 12489 Berlin, Germany;
| | - Jenny Zinke
- Institute of Neurology (Edinger Institute), Goethe University, 60528 Frankfurt am Main, Germany; (J.Z.); (P.N.H.)
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), 60528 Frankfurt am Main, Germany
| | - Malte Mohme
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.M.); (A.P.); (K.L.); (M.W.)
| | - Andras Piffko
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.M.); (A.P.); (K.L.); (M.W.)
| | - Svenja Schneegans
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (D.L.); (S.S.); (S.A.J.); (K.P.)
| | - Julia Stadler
- Department of Dermatology and Venerology, University Hospital Hamburg-Eppendorf, 20246 Hamburg, Germany; (J.S.); (C.G.); (S.W.S.)
| | - Melanie Janning
- Division of Personalized Medical Oncology (A420), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (M.J.); (S.L.)
- Department of Personalized Oncology, University Hospital Mannheim, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Comprehensive Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sonja Loges
- Division of Personalized Medical Oncology (A420), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (M.J.); (S.L.)
- Department of Personalized Oncology, University Hospital Mannheim, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Comprehensive Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Simon A. Joosse
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (D.L.); (S.S.); (S.A.J.); (K.P.)
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.M.); (A.P.); (K.L.); (M.W.)
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.M.); (A.P.); (K.L.); (M.W.)
| | - Volkmar Müller
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Markus Glatzel
- Department of Neuropathology, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.G.); (J.M.)
| | - Jakob Matschke
- Department of Neuropathology, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.G.); (J.M.)
| | - Christoffer Gebhardt
- Department of Dermatology and Venerology, University Hospital Hamburg-Eppendorf, 20246 Hamburg, Germany; (J.S.); (C.G.); (S.W.S.)
| | - Stefan W. Schneider
- Department of Dermatology and Venerology, University Hospital Hamburg-Eppendorf, 20246 Hamburg, Germany; (J.S.); (C.G.); (S.W.S.)
| | - Iwona Belczacka
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; (I.B.); (M.-L.Y.)
| | - Beate Volkmer
- Association of Dermatological Prevention, Germany & Centre of Dermatology, Elbe Clinics, 21614 Buxtehude, Germany; (B.V.); (R.G.)
| | - Rüdiger Greinert
- Association of Dermatological Prevention, Germany & Centre of Dermatology, Elbe Clinics, 21614 Buxtehude, Germany; (B.V.); (R.G.)
| | - Marie-Laure Yaspo
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; (I.B.); (M.-L.Y.)
| | - Patrick N. Harter
- Institute of Neurology (Edinger Institute), Goethe University, 60528 Frankfurt am Main, Germany; (J.Z.); (P.N.H.)
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, 60528 Frankfurt am Main, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), 60528 Frankfurt am Main, Germany
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (D.L.); (S.S.); (S.A.J.); (K.P.)
| | - Harriet Wikman
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (D.L.); (S.S.); (S.A.J.); (K.P.)
- Correspondence: ; Tel.: +49-(407)-510-51913
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15
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Xiao N, Li K, Zhu X, Xu B, Liu X, Lei M, Sun HC. CD74 + macrophages are associated with favorable prognosis and immune contexture in hepatocellular carcinoma. Cancer Immunol Immunother 2021; 71:57-69. [PMID: 34009409 DOI: 10.1007/s00262-021-02962-z] [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: 01/06/2021] [Accepted: 05/06/2021] [Indexed: 10/21/2022]
Abstract
CD74 was initially thought to participate mainly in antigen presentation as an MHC class II chaperone. Recent studies have shown that CD74 plays an important role within the cell and throughout the immune system in a wide spectrum of neoplasms. However, the role of CD74 in hepatocellular carcinoma (HCC) remains elusive. In this study, HCC tissues from Zhongshan Hospital and data from The Cancer Genome Atlas (TCGA) were obtained and analyzed. Immunohistochemistry, flow cytometry, and single-cell RNA sequencing (scRNA-seq) were performed to detect the characteristics of CD74+ cells and explore their impact on the tumor microenvironment (TME) of HCC. Our data revealed that stromal CD74+ cell enrichment was associated with favorable prognosis in patients with HCC. CD74 was abundant in a large portion of HCC specimens and prominently distributed on stromal macrophages. scRNA-seq data also indicated that the pathways related to immune response were significantly upregulated in CD74+ macrophages. High infiltration of CD74+ macrophages was associated with increased infiltration of CD8+ cytotoxic T lymphocytes (CTLs) with enhanced effector functions in HCC. Besides, blocking CD74 weakened the antitumor activity and proliferation ability of CD8+ CTLs in HCC. Our findings highlight the critical role of CD74 in HCC. New drugs and antibodies targeting CD74 may be effective strategies for HCC therapy.
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Affiliation(s)
- Nan Xiao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, 200032, China
| | - Kangshuai Li
- Department of Hepatobiliary Surgery, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Xiaodong Zhu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, 200032, China
| | - Bin Xu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, 200032, China
| | - Xuefeng Liu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, 200032, China
| | - Ming Lei
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, 200032, China
| | - Hui-Chuan Sun
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, 200032, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, 200032, China.
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16
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Yang T, Hao L, Cui R, Liu H, Chen J, An J, Qi S, Li Z. Identification of an immune prognostic 11-gene signature for lung adenocarcinoma. PeerJ 2021; 9:e10749. [PMID: 33552736 PMCID: PMC7825366 DOI: 10.7717/peerj.10749] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/18/2020] [Indexed: 12/17/2022] Open
Abstract
Background The immunological tumour microenvironment (TME) has occupied a very important position in the beginning and progression of non-small cell lung cancer (NSCLC). Prognosis of lung adenocarcinoma (LUAD) remains poor for the local progression and widely metastases at the time of clinical diagnosis. Our objective is to identify a potential signature model to improve prognosis of LUAD. Methods With the aim to identify a novel immune prognostic signature associated with overall survival (OS), we analysed LUADs extracted from The Cancer Genome Atlas (TCGA). Immune scores and stromal scores of TCGA-LUAD were downloaded from Estimation of STromal and Immune cells in MAlignant Tumour tissues Expression using data (ESTIMATE). LASSO COX regression was applied to build the prediction model. Then, the prognostic gene signature was validated in the GSE68465 dataset. Results The data from TCGA datasets showed patients in stage I and stage II had higher stromal scores than patients in stage IV (P < 0.05), and for immune score patients in stage I were higher than patients in stage III and stage IV (P < 0.05). The improved overall survivals were observed in high stromal score and immune score groups. Patients in the high-risk group exhibited the inferior OS (P = 2.501e − 05). By validating the 397 LUAD patients from GSE68465, we observed a better OS in the low-risk group compared to the high-risk group, which is consistent with the results from the TCGA cohort. Nomogram results showed that practical and predicted survival coincided very well, especially for 3-year survival. Conclusion We obtained an 11 immune score related gene signature model as an independent element to effectively classify LUADs into different risk groups, which might provide a support for precision treatments. Moreover, immune score may play a potential valuable sole for estimating OS in LUADs.
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Affiliation(s)
- Tao Yang
- Department of Hematology and Oncology, Dongzhimen Hospital, the First Clinical Medical College of Beijing University of Chinese Medicine, Beijing, China
| | - Lizheng Hao
- Department of Hematology and Oncology, Dongzhimen Hospital, the First Clinical Medical College of Beijing University of Chinese Medicine, Beijing, China
| | - Renyun Cui
- Department of Hematology and Oncology, Dongzhimen Hospital, the First Clinical Medical College of Beijing University of Chinese Medicine, Beijing, China
| | - Huanyu Liu
- Department of Hematology and Oncology, Dongzhimen Hospital, the First Clinical Medical College of Beijing University of Chinese Medicine, Beijing, China
| | - Jian Chen
- Department of Hematology and Oncology, Dongzhimen Hospital, the First Clinical Medical College of Beijing University of Chinese Medicine, Beijing, China
| | - Jiongjun An
- Department of Hematology and Oncology, Dongzhimen Hospital, the First Clinical Medical College of Beijing University of Chinese Medicine, Beijing, China
| | - Shuo Qi
- Department of Thyroid, Dongzhimen Hospital, the First Clinical Medical College of Beijing University of Chinese Medicine, Beijing, China
| | - Zhong Li
- Department of Hematology and Oncology, Dongzhimen Hospital, the First Clinical Medical College of Beijing University of Chinese Medicine, Beijing, China
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17
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Braun Y, Filipski K, Bernatz S, Baumgarten P, Roller B, Zinke J, Zeiner PS, Ilina E, Senft C, Ronellenfitsch MW, Plate KH, Bähr O, Hattingen E, Steinbach JP, Mittelbronn M, Harter PN. Linking epigenetic signature and metabolic phenotype in IDH mutant and IDH wildtype diffuse glioma. Neuropathol Appl Neurobiol 2020; 47:379-393. [PMID: 33080075 DOI: 10.1111/nan.12669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/23/2020] [Accepted: 10/14/2020] [Indexed: 01/17/2023]
Abstract
AIMS Changes in metabolism are known to contribute to tumour phenotypes. If and how metabolic alterations in brain tumours contribute to patient outcome is still poorly understood. Epigenetics impact metabolism and mitochondrial function. The aim of this study is a characterisation of metabolic features in molecular subgroups of isocitrate dehydrogenase mutant (IDHmut) and isocitrate dehydrogenase wildtype (IDHwt) gliomas. METHODS We employed DNA methylation pattern analyses with a special focus on metabolic genes, large-scale metabolism panel immunohistochemistry (IHC), qPCR-based determination of mitochondrial DNA copy number and immune cell content using IHC and deconvolution of DNA methylation data. We analysed molecularly characterised gliomas (n = 57) for in depth DNA methylation, a cohort of primary and recurrent gliomas (n = 22) for mitochondrial copy number and validated these results in a large glioma cohort (n = 293). Finally, we investigated the potential of metabolic markers in Bevacizumab (Bev)-treated gliomas (n = 29). RESULTS DNA methylation patterns of metabolic genes successfully distinguished the molecular subtypes of IDHmut and IDHwt gliomas. Promoter methylation of lactate dehydrogenase A negatively correlated with protein expression and was associated with IDHmut gliomas. Mitochondrial DNA copy number was increased in IDHmut tumours and did not change in recurrent tumours. Hierarchical clustering based on metabolism panel IHC revealed distinct subclasses of IDHmut and IDHwt gliomas with an impact on patient outcome. Further quantification of these markers allowed for the prediction of survival under anti-angiogenic therapy. CONCLUSION A mitochondrial signature was associated with increased survival in all analyses, which could indicate tumour subgroups with specific metabolic vulnerabilities.
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Affiliation(s)
- Yannick Braun
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Katharina Filipski
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany.,German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt, Germany.,German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Simon Bernatz
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Peter Baumgarten
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany.,Department of Neurosurgery, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Bastian Roller
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Jenny Zinke
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Pia S Zeiner
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany.,Dr. Senckenberg Institute for Neurooncology, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Elena Ilina
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Christian Senft
- Department of Neurosurgery, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Michael W Ronellenfitsch
- German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt, Germany.,German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Dr. Senckenberg Institute for Neurooncology, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt, Germany
| | - Karl H Plate
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany.,German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt, Germany.,German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt, Germany
| | - Oliver Bähr
- Dr. Senckenberg Institute for Neurooncology, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Elke Hattingen
- Frankfurt Cancer Institute (FCI), Frankfurt, Germany.,Department of Neuroradiology, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Joachim P Steinbach
- German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt, Germany.,German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Dr. Senckenberg Institute for Neurooncology, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt, Germany
| | - Michel Mittelbronn
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany.,Luxembourg Centre of Neuropathology (LCNP), Luxembourg.,Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg.,National Centre of Pathology (NCP), Laboratoire national de santé (LNS), Luxembourg.,Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Luxembourg
| | - Patrick N Harter
- Neurological Institute (Edinger Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany.,German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt, Germany.,German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt, Germany
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18
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Ma J, Zhang JK, Yang D, Ma XX. Identification of novel prognosis-related genes in the endometrial cancer immune microenvironment. Aging (Albany NY) 2020; 12:22152-22173. [PMID: 33159014 PMCID: PMC7695382 DOI: 10.18632/aging.104083] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/31/2020] [Indexed: 12/11/2022]
Abstract
The incidence of endometrial cancer is increasing each year, and treatment effects are poor for patients with advanced and specific subtypes. Exploring immune infiltration-related factors in endometrial cancer can aid in the prognosis of patients and provide new immunotherapy targets. We downloaded immune metagene and functional data of patients with different subtypes of endometrial cancer from The Cancer Genome Atlas database and selected the lymphocyte-specific kinase (LCK) metagene as a representative genetic marker of the immune microenvironment in endometrial cancer. The results showed that LCK metagene expression is related to the prognosis of patients with endometrioid endometrial adenocarcinoma subtypes and highly correlated with the PTEN and PIK3CA mutational status. A search for LCK-related modules returned seven independent genetic predictors of survival in patients with endometrial cancer. The TIMER algorithm showed that the expression of these seven genes was positively correlated with the infiltration levels of six types of immune cells. The diagnostic value of these markers was validated using real-time quantitative PCR and immunohistochemical methods. Our results identified CD74, HLA-DRB5, CD52, HLA-DPB1 and HLA-DRB1 as possible valuable genetic markers for the diagnosis and prognosis of endometrial cancer and provided a theoretical basis for immunotherapy targets for its clinical treatment.
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Affiliation(s)
- Jian Ma
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Jing-Kai Zhang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Di Yang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Xiao-Xin Ma
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China
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19
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Zhang W, Wei Y, Zhang D, Xu EY. ZIAQ: a quantile regression method for differential expression analysis of single-cell RNA-seq data. Bioinformatics 2020; 36:3124-3130. [PMID: 32053182 DOI: 10.1093/bioinformatics/btaa098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/11/2020] [Accepted: 02/06/2020] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION Single-cell RNA sequencing (scRNA-seq) has enabled the simultaneous transcriptomic profiling of individual cells under different biological conditions. scRNA-seq data have two unique challenges that can affect the sensitivity and specificity of single-cell differential expression analysis: a large proportion of expressed genes with zero or low read counts ('dropout' events) and multimodal data distributions. RESULTS We have developed a zero-inflation-adjusted quantile (ZIAQ) algorithm, which is the first method to account for both dropout rates and complex scRNA-seq data distributions in the same model. ZIAQ demonstrates superior performance over several existing methods on simulated scRNA-seq datasets by finding more differentially expressed genes. When ZIAQ was applied to the comparison of neoplastic and non-neoplastic cells from a human glioblastoma dataset, the ranking of biologically relevant genes and pathways showed clear improvement over existing methods. AVAILABILITY AND IMPLEMENTATION ZIAQ is implemented in the R language and available at https://github.com/gefeizhang/ZIAQ. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Wenfei Zhang
- Department of Biostatistics and Programming, Sanofi, Framingham, MA 01701, USA
| | - Ying Wei
- Department of Biostatistics, Columbia University, New York, NY 10032, USA
| | - Donghui Zhang
- Department of Biostatistics and Programming, Sanofi, Framingham, MA 01701, USA
| | - Ethan Y Xu
- Translational Sciences, Sanofi, Framingham, MA 01701, USA
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20
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Li M, Jin X, Li H, Wu G, Wang S, Yang C, Deng S. Key genes with prognostic values in suppression of osteosarcoma metastasis using comprehensive analysis. BMC Cancer 2020; 20:65. [PMID: 31992246 PMCID: PMC6988291 DOI: 10.1186/s12885-020-6542-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 01/14/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Osteosarcoma is a primary malignant tumor originating from mesenchymal tissue, with a poor distant metastasis prognosis. The molecular mechanisms of osteosarcoma metastasis are extremely complicated. METHODS A public data series (GSE21257) was used to identify differentially expressed genes (DEGs) in osteosarcoma patients that did, or did not, develop metastases. Functional enrichment analysis, a protein-protein interaction network, and survival analysis of DEGs were performed. DEGs with a prognostic value were considered as candidate genes and their functional predictions, different expression in normal and malignant tissues, and immune infiltration were analyzed. RESULTS The DEGs were mainly enriched in the immune response. Three candidate genes (ALOX5AP, CD74, and FCGR2A) were found, all of which were expressed at higher levels in lungs and lymph nodes than in matched cancer tissues and were probably expressed in the microenvironment. CONCLUSIONS Candidate genes can help us understand the molecular mechanisms underlying osteosarcoma metastasis and provide targets for future research.
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Affiliation(s)
- Mi Li
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xin Jin
- Department of Digestive Surgical Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hao Li
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Gang Wu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Shanshan Wang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Caihong Yang
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Sisi Deng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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21
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Pocha K, Mock A, Rapp C, Dettling S, Warta R, Geisenberger C, Jungk C, Martins LR, Grabe N, Reuss D, Debus J, von Deimling A, Abdollahi A, Unterberg A, Herold-Mende CC. Surfactant Expression Defines an Inflamed Subtype of Lung Adenocarcinoma Brain Metastases that Correlates with Prolonged Survival. Clin Cancer Res 2020; 26:2231-2243. [PMID: 31953311 DOI: 10.1158/1078-0432.ccr-19-2184] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 12/09/2019] [Accepted: 01/14/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE To provide a better understanding of the interplay between the immune system and brain metastases to advance therapeutic options for this life-threatening disease. EXPERIMENTAL DESIGN Tumor-infiltrating lymphocytes (TIL) were quantified by semiautomated whole-slide analysis in brain metastases from 81 lung adenocarcinomas. Multi-color staining enabled phenotyping of TILs (CD3, CD8, and FOXP3) on a single-cell resolution. Molecular determinants of the extent of TILs in brain metastases were analyzed by transcriptomics in a subset of 63 patients. Findings in lung adenocarcinoma brain metastases were related to published multi-omic primary lung adenocarcinoma The Cancer Genome Atlas data (n = 230) and single-cell RNA-sequencing (scRNA-seq) data (n = 52,698). RESULTS TIL numbers within tumor islands was an independent prognostic marker in patients with lung adenocarcinoma brain metastases. Comparative transcriptomics revealed that expression of three surfactant metabolism-related genes (SFTPA1, SFTPB, and NAPSA) was closely associated with TIL numbers. Their expression was not only prognostic in brain metastasis but also in primary lung adenocarcinoma. Correlation with scRNA-seq data revealed that brain metastases with high expression of surfactant genes might originate from tumor cells resembling alveolar type 2 cells. Methylome-based estimation of immune cell fractions in primary lung adenocarcinoma confirmed a positive association between lymphocyte infiltration and surfactant expression. Tumors with a high surfactant expression displayed a transcriptomic profile of an inflammatory microenvironment. CONCLUSIONS The expression of surfactant metabolism-related genes (SFTPA1, SFTPB, and NAPSA) defines an inflamed subtype of lung adenocarcinoma brain metastases characterized by high abundance of TILs in close vicinity to tumor cells, a prolonged survival, and a tumor microenvironment which might be more accessible to immunotherapeutic approaches.
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Affiliation(s)
- Kolja Pocha
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas Mock
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Carmen Rapp
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Steffen Dettling
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Rolf Warta
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christoph Geisenberger
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Christine Jungk
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Leila R Martins
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ) Heidelberg, Heidelberg, Germany
| | - Niels Grabe
- Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, University of Heidelberg, Heidelberg, Germany
| | - David Reuss
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Juergen Debus
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Radiation Oncology, University of Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Amir Abdollahi
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Radiation Oncology, University of Heidelberg, Heidelberg, Germany
| | - Andreas Unterberg
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Christel C Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany
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22
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Chen J, Hou C, Wang P, Yang Y, Zhou D. Grade II/III Glioma Microenvironment Mining and Its Prognostic Merit. World Neurosurg 2019; 132:e76-e88. [PMID: 31518750 DOI: 10.1016/j.wneu.2019.08.253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 02/05/2023]
Abstract
OBJECTIVE The tumor microenvironment greatly influences tumor formation, invasion, and progression. The ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues) algorithm quantifies stromal and immune components in a tumor, reflecting the tumor microenvironment. This study aimed to explore key prognostic genes in a grade II/III glioma microenvironment. METHODS We obtained stromal/immune scores for the Cancer Genome Atlas (TCGA) grade II/III glioma cohort from the online ESTIMATE portal. The associations of stromal/immune scores with clinicopathologic characteristics and overall survival of patients with grade II/III glioma were assessed by the Mann-Whitney U test and the Kaplan-Meier method, respectively. Functional enrichment analysis and protein-protein interaction network assessments were employed to analyze differentially expressed genes (DEGs). The top 7 genes with 5 or more edges in the protein-protein interaction network were selected. For validation, CGGA grade II/III glioma data were analyzed. RESULTS The results showed that elevated stromal/immune/ESTIMATE score was significantly associated with poor survival of patients with TCGA grade II/III glioma. Functional enrichment analysis showed that DEGs were associated with immune cell regulation, extracellular matrix, cytokine activation, and receptor binding. The selected DEGs (interleukin-10, beta-2 microglobulin, C-C motif chemokine ligand 5, cluster of differentiation 74, human leukocyte antigen-DRA, lymphocyte cytosolic protein 2, and myxovirus resistance protein 1) showed prognostic values in patients with grade II/III glioma of the TCGA and CGGA database. CONCLUSIONS Stromal/immune/ESTIMATE scores have prognostic values in patients with grade II/III glioma. The selected DEGs, including interleukin-10, beta-2 microglobulin, C-C motif chemokine ligand 5, cluster of differentiation 74, human leukocyte antigen-DRA, lymphocyte cytosolic protein 2, and myxovirus resistance protein 1, associated with tumor immunity and microenvironment, have prognostic values in grade II/III glioma. Further investigation of these genes could provide novel insights into the tumor microenvironment of glioma.
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Affiliation(s)
- Jiawei Chen
- Department of Neurosurgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China; Shantou University Medical College, Shantou, Guangdong, China
| | - Chongxian Hou
- Department of Neurosurgery, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Peng Wang
- Department of Neurosurgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yong Yang
- Department of Neurosurgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Dong Zhou
- Department of Neurosurgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
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23
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Expressions of HLA Class II Genes in Cutaneous Melanoma Were Associated with Clinical Outcome: Bioinformatics Approaches and Systematic Analysis of Public Microarray and RNA-Seq Datasets. Diagnostics (Basel) 2019; 9:diagnostics9020059. [PMID: 31212865 PMCID: PMC6628136 DOI: 10.3390/diagnostics9020059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 12/24/2022] Open
Abstract
Major histocompatibility complex (MHC) class II molecules, encoded by human leukocyte antigen (HLA) class II genes, play important roles in antigen presentation and initiation of immune responses. However, the correlation between HLA class II gene expression level and patient survival and disease progression in cutaneous melanoma is still under investigation. In the present study, we analyzed microarray and RNA-Seq data of cutaneous melanoma from The Cancer Genome Atlas (TCGA) using different bioinformatics tools. Survival analysis revealed higher expression level of HLA class II genes in cutaneous melanoma, especially HLA-DP and -DR, was significantly associated with better overall survival. Furthermore, the expressions of HLA class II genes were most closely associated with survival in cutaneous melanoma as compared with other cancer types. The expression of HLA class II co-expressed genes, which were found to associate with antigen processing, immune response, and inflammatory response, was also positively associated with overall survival in cutaneous melanoma. Therefore, the results indicated that increased HLA class II expression may contribute to enhanced anti-tumor immunity and related inflammatory response via presenting tumor antigens to the immune system. The expression pattern of HLA class II genes may serve as a prognostic biomarker and therapeutic targets in cutaneous melanoma.
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24
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Thibodeau J, Moulefera MA, Balthazard R. On the structure–function of MHC class II molecules and how single amino acid polymorphisms could alter intracellular trafficking. Hum Immunol 2019; 80:15-31. [DOI: 10.1016/j.humimm.2018.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 12/01/2022]
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