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Hutarew G, Alinger-Scharinger B, Sotlar K, Kraus TFJ. Genome-Wide Methylation Analysis in Two Wild-Type Non-Small Cell Lung Cancer Subgroups with Negative and High PD-L1 Expression. Cancers (Basel) 2024; 16:1841. [PMID: 38791918 PMCID: PMC11119885 DOI: 10.3390/cancers16101841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/25/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
We conducted a pilot study to analyze the differential methylation status of 20 primary acinar adenocarcinomas of the lungs. These adenocarcinomas had to be wild type in mutation analysis and had either high (TPS > 50%; n = 10) or negative (TPS < 1%; n = 10) PD-L1 status to be integrated into our study. To examine the methylation of 866,895 specific sites, we utilized the Illumina Infinium EPIC bead chip array. Both hypermethylation and hypomethylation play significant roles in tumor development, progression, and metastasis. They also impact the formation of the tumor microenvironment, which plays a decisive role in tumor differentiation, epigenetics, dissemination, and immune evasion. The gained methylation patterns were correlated with PD-L1 expression. Our analysis has identified distinct methylation patterns in lung adenocarcinomas with high and negative PD-L1 expression. After analyzing the correlation between the methylation results of genes and promoters with their pathobiology, we found that tumors with high expression of PD-L1 tend to exhibit oncogenic effects through hypermethylation. On the other hand, tumors with negative PD-L1 expression show loss of their suppressor functions through hypomethylation. The suppressor functions of hypermethylated genes and promoters are ineffective compared to simultaneously activated dominant oncogenic mechanisms. The tumor microenvironment supports tumor growth in both groups.
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Affiliation(s)
- Georg Hutarew
- Institute of Pathology, University Hospital Salzburg, Paracelsus Medical University, Müllner Hauptstr. 48, A-5020 Salzburg, Austria; (B.A.-S.); (K.S.); (T.F.J.K.)
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Arnhold J. Inflammation-Associated Cytotoxic Agents in Tumorigenesis. Cancers (Basel) 2023; 16:81. [PMID: 38201509 PMCID: PMC10778456 DOI: 10.3390/cancers16010081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Chronic inflammatory processes are related to all stages of tumorigenesis. As inflammation is closely associated with the activation and release of different cytotoxic agents, the interplay between cytotoxic agents and antagonizing principles is highlighted in this review to address the question of how tumor cells overcome the enhanced values of cytotoxic agents in tumors. In tumor cells, the enhanced formation of mitochondrial-derived reactive species and elevated values of iron ions and free heme are antagonized by an overexpression of enzymes and proteins, contributing to the antioxidative defense and maintenance of redox homeostasis. Through these mechanisms, tumor cells can even survive additional stress caused by radio- and chemotherapy. Through the secretion of active agents from tumor cells, immune cells are suppressed in the tumor microenvironment and an enhanced formation of extracellular matrix components is induced. Different oxidant- and protease-based cytotoxic agents are involved in tumor-mediated immunosuppression, tumor growth, tumor cell invasion, and metastasis. Considering the special metabolic conditions in tumors, the main focus here was directed on the disturbed balance between the cytotoxic agents and protective mechanisms in late-stage tumors. This knowledge is mandatory for the implementation of novel anti-cancerous therapeutic approaches.
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Affiliation(s)
- Jürgen Arnhold
- Institute of Medical Physics and Biophysics, Medical Faculty, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany
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Kitamura K, Yamamoto T, Ochi H, Suzuki M, Suzuki N, Igawa T, Yoshida T, Futakuchi M, Ogino H, Michiue T. Identification of tumor-related genes via RNA sequencing of tumor tissues in Xenopus tropicalis. Sci Rep 2023; 13:13214. [PMID: 37580380 PMCID: PMC10425369 DOI: 10.1038/s41598-023-40193-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/06/2023] [Indexed: 08/16/2023] Open
Abstract
Cancer treatment is still challenging because the disease is often caused by multiple mutations. Although genomic studies have identified many oncogenes and tumor suppressor genes, gene sets involved in tumorigenesis remain poorly understood. Xenopus, a genus of aquatic frogs, is a useful model to identify gene sets because it can be genetically and experimentally analyzed. Here, we analyzed gene expression in tumor tissues of three individuals in Xenopus tropicalis and identified 55 differentially expressed genes (DEGs). Gene ontology (GO) analysis showed that the upregulated genes in the tumor tissues were enriched in GO terms related to the extracellular matrix and collagen fibril organization. Hierarchical clustering showed that the gene expression patterns of tumor tissues in X. tropicalis were comparable to those of human connective, soft, and subcutaneous tissue-derived cancers. Additionally, pathway analysis revealed that these DEGs were associated with multiple pathways, including the extracellular matrix, collagen fibril organization, MET signaling, and keratan sulfate. We also found that the expression tendency of some DEGs that have not been well analyzed in the cancer field clearly determines the prognosis of human cancer patients. This study provides a remarkable reference for future experimental work on X. tropicalis to identify gene sets involved in human cancer.
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Affiliation(s)
- Kazuki Kitamura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan
| | - Takayoshi Yamamoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan
| | - Haruki Ochi
- Institute for Promotion of Medical Science Research, Faculty of Medicine, Yamagata University, 2-2-2 Iida-Nishi, Yamagata City, Yamagata, 990-9585, Japan
| | - Makoto Suzuki
- Amphibian Research Center, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
| | - Nanoka Suzuki
- Amphibian Research Center, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
| | - Takeshi Igawa
- Amphibian Research Center, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
| | - Tadashi Yoshida
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan
| | - Mitsuru Futakuchi
- Department of Pathology, Faculty of Medicine, Yamagata University, 2-2-2 Iida-Nishi, Yamagata City, Yamagata, 990-9585, Japan
| | - Hajime Ogino
- Amphibian Research Center, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
| | - Tatsuo Michiue
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan.
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan.
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Zhang H, Wang Y, Wang K, Ding Y, Li X, Zhao S, Jia X, Sun D. Prognostic analysis of lung adenocarcinoma based on cancer-associated fibroblasts genes using scRNA-sequencing. Aging (Albany NY) 2023; 15:6774-6797. [PMID: 37437244 PMCID: PMC10415565 DOI: 10.18632/aging.204838] [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: 03/21/2023] [Accepted: 06/09/2023] [Indexed: 07/14/2023]
Abstract
Cancer-associated fibroblasts (CAFs) are an important component of the tumor microenvironment (TME). CAFs can promote tumor occurrence and metastasis by promoting cancer cell proliferation, angiogenesis, extracellular matrix (ECM) remodeling, and drug resistance. Nevertheless, how CAFs are related to Lung adenocarcinoma (LUAD) has not yet been revealed, especially since the CAFs-related prediction model has yet to be established. We combined Single-cell RNA-sequencing (scRNA-seq) and Bulk-RNA data to develop a predictive model of 8 CAFs-associated genes. Our model predicted LUAD prognosis and immunotherapy efficacy. TME, mutation landscape and drug sensitivity differences were also systematically analyzed between the LUAD patients of high- and low-risk. Moreover, the model prognostic performance was validated in four independent validation cohorts in the Gene expression omnibus (GEO) and the IMvigor210 immunotherapy cohort.
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Affiliation(s)
- Han Zhang
- Clinical School of Thoracic, Tianjin Medical University, Tianjin, China
| | - Yuhang Wang
- Clinical School of Thoracic, Tianjin Medical University, Tianjin, China
| | - Kai Wang
- Department of Thoracic Surgery, Tianjin Chest Hospital of Tianjin University, Tianjin, China
| | - Yun Ding
- Clinical School of Thoracic, Tianjin Medical University, Tianjin, China
| | - Xin Li
- Department of Thoracic Surgery, Tianjin Chest Hospital of Tianjin University, Tianjin, China
| | - Shuai Zhao
- Department of Thoracic Surgery, Tianjin Chest Hospital of Tianjin University, Tianjin, China
| | - Xiaoteng Jia
- Clinical School of Thoracic, Tianjin Medical University, Tianjin, China
| | - Daqiang Sun
- Department of Thoracic Surgery, Tianjin Chest Hospital of Tianjin University, Tianjin, China
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