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Yang W, Zhao X, Duan L, Niu L, Zhang Y, Zhou W, Li Y, Chen J, Fan A, Xie Q, Liu J, Han Y, Fan D, Hong L. Development and validation of a ligand-receptor pairs signature to predict outcome and provide a therapeutic strategy in gastric cancer. Expert Rev Mol Diagn 2023; 23:619-634. [PMID: 37248704 DOI: 10.1080/14737159.2023.2219843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
BACKGROUND An important factor in tumor development and progression is the tumor microenvironment (TME), which is heterogeneous. Previous studies have mainly investigated the expression profile and prognostic values of genes in gastric cancer (GC) at the cell population level but neglected the interactions and heterogeneity between cells. METHODS The pattern of ligand-receptor (LR) interactions was delineated on a scRNA-seq dataset containing 44,953 cells from nine GC patients and a fourth bulk RNA-seq dataset including data from 1159 GC patients. We then constructed an LR.Score scoring model to comprehensively evaluate the influence of LR-pairs on the TME, overall survival, and immunotherapy response in GC patients from several cohorts. RESULTS Cell communication network among 13 cell types was constructed based on the LR-pairs. We proposed a new molecular subtyping model for GC based on the LR-pairs and revealed the differences in prognosis, pathophysiologic features, mutation characteristics, function enrichment, and immunological characteristics among the three subtypes. Finally, an LR.Score model based on LR-pairs was developed and validated on several datasets. CONCLUSIONS Based on the selected LR-pairs, we successfully constructed a novel prediction model and observed its well performance on molecular subtyping, target and pathway screening, prognosis judging, and immunotherapy response predicting.
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Affiliation(s)
- Wanli Yang
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Xinhui Zhao
- Department of Thyroid and Breast Surgery, The Affiliated Hospital of Northwest University & Xi'an No.3 Hospital, Northwest University, Xi'an, Shaanxi Province, China
| | - Lili Duan
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Liaoran Niu
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Yujie Zhang
- Department of Histology and Embryology, School of Basic Medicine, Xi'an Medical University, Xi'an, Shaanxi Province, China
| | - Wei Zhou
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Yiding Li
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Junfeng Chen
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Aqiang Fan
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Qibin Xie
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Jinqiang Liu
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Yu Han
- Department of Otolaryngology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Daiming Fan
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Liu Hong
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province, China
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Worzfeld T, Pogge von Strandmann E, Huber M, Adhikary T, Wagner U, Reinartz S, Müller R. The Unique Molecular and Cellular Microenvironment of Ovarian Cancer. Front Oncol 2017; 7:24. [PMID: 28275576 PMCID: PMC5319992 DOI: 10.3389/fonc.2017.00024] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/07/2017] [Indexed: 12/13/2022] Open
Abstract
The reciprocal interplay of cancer cells and host cells is an indispensable prerequisite for tumor growth and progression. Cells of both the innate and adaptive immune system, in particular tumor-associated macrophages (TAMs) and T cells, as well as cancer-associated fibroblasts enter into a malicious liaison with tumor cells to create a tumor-promoting and immunosuppressive tumor microenvironment (TME). Ovarian cancer, the most lethal of all gynecological malignancies, is characterized by a unique TME that enables specific and efficient metastatic routes, impairs immune surveillance, and mediates therapy resistance. A characteristic feature of the ovarian cancer TME is the role of resident host cells, in particular activated mesothelial cells, which line the peritoneal cavity in huge numbers, as well as adipocytes of the omentum, the preferred site of metastatic lesions. Another crucial factor is the peritoneal fluid, which enables the transcoelomic spread of tumor cells to other pelvic and peritoneal organs, and occurs at more advanced stages as a malignancy-associated effusion. This ascites is rich in tumor-promoting soluble factors, extracellular vesicles and detached cancer cells as well as large numbers of T cells, TAMs, and other host cells, which cooperate with resident host cells to support tumor progression and immune evasion. In this review, we summarize and discuss our current knowledge of the cellular and molecular interactions that govern this interplay with a focus on signaling networks formed by cytokines, lipids, and extracellular vesicles; the pathophysiologial roles of TAMs and T cells; the mechanism of transcoelomic metastasis; and the cell type selective processing of signals from the TME.
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Affiliation(s)
- Thomas Worzfeld
- Institute of Pharmacology, Biochemical-Pharmacological Center (BPC), Philipps University, Marburg, Germany; Department of Pharmacology, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Elke Pogge von Strandmann
- Experimental Tumor Research, Clinic for Hematology, Oncology and Immunology, Center for Tumor Biology and Immunology, Philipps University , Marburg , Germany
| | - Magdalena Huber
- Institute of Medical Microbiology and Hygiene, Biomedical Research Center, Philipps University , Marburg , Germany
| | - Till Adhikary
- Institute of Molecular Biology and Tumor Research, Center for Tumor Biology and Immunology, Philipps University , Marburg , Germany
| | - Uwe Wagner
- Clinic for Gynecology, Gynecological Oncology and Gynecological Endocrinology, University Hospital of Giessen and Marburg (UKGM) , Marburg , Germany
| | - Silke Reinartz
- Clinic for Gynecology, Gynecological Oncology and Gynecological Endocrinology, Center for Tumor Biology and Immunology (ZTI), Philipps University , Marburg , Germany
| | - Rolf Müller
- Institute of Molecular Biology and Tumor Research, Center for Tumor Biology and Immunology, Philipps University , Marburg , Germany
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Finkernagel F, Reinartz S, Lieber S, Adhikary T, Wortmann A, Hoffmann N, Bieringer T, Nist A, Stiewe T, Jansen JM, Wagner U, Müller-Brüsselbach S, Müller R. The transcriptional signature of human ovarian carcinoma macrophages is associated with extracellular matrix reorganization. Oncotarget 2016; 7:75339-75352. [PMID: 27659538 PMCID: PMC5342745 DOI: 10.18632/oncotarget.12180] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022] Open
Abstract
Macrophages occur as resident cells of fetal origin or as infiltrating blood monocyte-derived cells. Despite the critical role of tumor-associated macrophages (TAMs) in tumor progression, the contribution of these developmentally and functionally distinct macrophage subsets and their alteration by the tumor microenvironment are poorly understood. We have addressed this question by comparing TAMs from human ovarian carcinoma ascites, resident peritoneal macrophages (pMPHs) and monocyte-derived macrophages (MDMs). Our study revealed striking a similarity between TAMs and pMPHs, which was considerably greater that the resemblance of TAMs and MDMs, including their transcriptomes, their inflammation-related activation state, the presence of receptors mediating immune functions and the expression of tumor-promoting mediators. Consistent with these results, TAMs phagocytized bacteria, presented peptide antigens and activated cytotoxic T cells within their pathophysiological environment. These observations support the notion that tumor-promoting properties of TAMs may reflect, at least to some extent, normal features of resident macrophages rather than functions induced by the tumor microenvironment. In spite of these surprising similarities between TAMs and pMPHs, bioinformatic analyses identified a TAM-selective signature of 30 genes that are upregulated relative to both pMPHs and MDMs. The majority of these genes is linked to extracellular matrix (ECM) remodeling, supporting a role for TAMs in cancer cell invasion and ovarian cancer progression.
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Affiliation(s)
- Florian Finkernagel
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Silke Reinartz
- Clinic for Gynecology, Gynecological Oncology and Gynecological Endocrinology, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Sonja Lieber
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Till Adhikary
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Annika Wortmann
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Nathalie Hoffmann
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Tim Bieringer
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Andrea Nist
- Genomics Core Facility, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Julia M. Jansen
- Clinic for Gynecology, Gynecological Oncology and Gynecological Endocrinology, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Uwe Wagner
- Clinic for Gynecology, Gynecological Oncology and Gynecological Endocrinology, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Sabine Müller-Brüsselbach
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Rolf Müller
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
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Reinartz S, Finkernagel F, Adhikary T, Rohnalter V, Schumann T, Schober Y, Nockher WA, Nist A, Stiewe T, Jansen JM, Wagner U, Müller-Brüsselbach S, Müller R. A transcriptome-based global map of signaling pathways in the ovarian cancer microenvironment associated with clinical outcome. Genome Biol 2016; 17:108. [PMID: 27215396 PMCID: PMC4877997 DOI: 10.1186/s13059-016-0956-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/15/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Soluble protein and lipid mediators play essential roles in the tumor environment, but their cellular origins, targets, and clinical relevance are only partially known. We have addressed this question for the most abundant cell types in human ovarian carcinoma ascites, namely tumor cells and tumor-associated macrophages. RESULTS Transcriptome-derived datasets were adjusted for errors caused by contaminating cell types by an algorithm using expression data derived from pure cell types as references. These data were utilized to construct a network of autocrine and paracrine signaling pathways comprising 358 common and 58 patient-specific signaling mediators and their receptors. RNA sequencing based predictions were confirmed for several proteins and lipid mediators. Published expression microarray results for 1018 patients were used to establish clinical correlations for a number of components with distinct cellular origins and target cells. Clear associations with early relapse were found for STAT3-inducing cytokines, specific components of WNT and fibroblast growth factor signaling, ephrin and semaphorin axon guidance molecules, and TGFβ/BMP-triggered pathways. An association with early relapse was also observed for secretory macrophage-derived phospholipase PLA2G7, its product arachidonic acid (AA) and signaling pathways controlled by the AA metabolites PGE2, PGI2, and LTB4. By contrast, the genes encoding norrin and its receptor frizzled 4, both selectively expressed by cancer cells and previously not linked to tumor suppression, show a striking association with a favorable clinical course. CONCLUSIONS We have established a signaling network operating in the ovarian cancer microenvironment with previously unidentified pathways and have defined clinically relevant components within this network.
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Affiliation(s)
- Silke Reinartz
- Clinic for Gynecology, Gynecological Oncology and Gynecological Endocrinology, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Florian Finkernagel
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Hans-Meerwein-Str. 3, Marburg, 35043, Germany
| | - Till Adhikary
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Hans-Meerwein-Str. 3, Marburg, 35043, Germany
| | - Verena Rohnalter
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Hans-Meerwein-Str. 3, Marburg, 35043, Germany
| | - Tim Schumann
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Hans-Meerwein-Str. 3, Marburg, 35043, Germany
| | - Yvonne Schober
- Metabolomics Core Facility and Institute of Laboratory Medicine and Pathobiochemistry, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - W Andreas Nockher
- Metabolomics Core Facility and Institute of Laboratory Medicine and Pathobiochemistry, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Andrea Nist
- Genomics Core Facility, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Julia M Jansen
- Clinic for Gynecology, Gynecological Oncology and Gynecological Endocrinology, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Uwe Wagner
- Clinic for Gynecology, Gynecological Oncology and Gynecological Endocrinology, Center for Tumor Biology and Immunology (ZTI), Philipps University, Marburg, Germany
| | - Sabine Müller-Brüsselbach
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Hans-Meerwein-Str. 3, Marburg, 35043, Germany
| | - Rolf Müller
- Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, Hans-Meerwein-Str. 3, Marburg, 35043, Germany.
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Ruggeri C, Eng KH. Inferring active and prognostic ligand-receptor pairs with interactions in survival regression models. Cancer Inform 2015; 13:67-75. [PMID: 25657571 PMCID: PMC4310509 DOI: 10.4137/cin.s16351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/20/2014] [Accepted: 10/23/2014] [Indexed: 01/29/2023] Open
Abstract
Modeling signal transduction in cancer cells has implications for targeting new therapies and inferring the mechanisms that improve or threaten a patient’s treatment response. For transcriptome-wide studies, it has been proposed that simple correlation between a ligand and receptor pair implies a relationship to the disease process. Statistically, a differential correlation (DC) analysis across groups stratified by prognosis can link the pair to clinical outcomes. While the prognostic effect and the apparent change in correlation are both biological consequences of activation of the signaling mechanism, a correlation-driven analysis does not clearly capture this assumption and makes inefficient use of continuous survival phenotypes. To augment the correlation hypothesis, we propose that a regression framework assuming a patient-specific, latent level of signaling activation exists and generates both prognosis and correlation. Data from these systems can be inferred via interaction terms in survival regression models allowing signal transduction models beyond one pair at a time and adjusting for other factors. We illustrate the use of this model on ovarian cancer data from the Cancer Genome Atlas (TCGA) and discuss how the finding may be used to develop markers to guide targeted molecular therapies.
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Affiliation(s)
- Christina Ruggeri
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Kevin H Eng
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
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