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Zhang C, Tan H, Xu H, Ding J, Chen H, Liu X, Sun F. Pan-cancer identified ARPC1B as a promising target for tumor immunotherapy and prognostic biomarker, particularly in READ. Heliyon 2024; 10:e28005. [PMID: 38689995 PMCID: PMC11059418 DOI: 10.1016/j.heliyon.2024.e28005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 05/02/2024] Open
Abstract
ARPC1B encodes the protein known as actin-related protein 2/3 complex subunit 1 B (ARPC1B), which controls actin polymerization in the human body. Although ARPC1B has been linked to several human malignancies, its function in these cancers remains unclear. TCGA, GTEx, CCLE, Xena, CellMiner, TISIDB, and molecular signature databases were used to analyze ARPC1B expression in cancers. Visualization of data was primarily achieved using R language, version 4.0. Nineteen tumors exhibited high levels of ARPC1B expression, which were associated with different tumor stages and significantly affected the prognosis of various cancers. The level of ARPC1B expression substantially connected the narrative of ARPC1B expression with several TMB cancers and showed significant changes in MSI. Additionally, tolerance to numerous anticancer medications has been linked to high ARPC1B gene expression. Using Gene Set Variation Analysis/Gene Set Enrichment Analysisanalysis and concentrating on Rectum adenocarcinoma (READ), we thoroughly examined the molecular processes of the ARPC1B gene in pan-cancer. Using WGCNA, we examined the co-expression network of READ and ARPC1B. Meanwhile, ten specimens were selected for immunohistochemical examination, which showed high expression of ARPC1B in READ. Human pan-cancer samples show higher ARPC1B expression than healthy tissues. In many malignancies, particularly READ, ARPC1B overexpression is associated with immune cell infiltration and a poor prognosis. These results imply that the molecular biomarker ARPC1B may be used to assess the prognosis and immune infiltration of patients with READ.
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Affiliation(s)
- Chenxiong Zhang
- Department of Proctology, Yubei Hospital of Traditional Chinese Medicine, Chongqing Yubei District, Chongqing, 401120, China
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510403, China
| | - Hao Tan
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510403, China
| | - Han Xu
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510403, China
| | - Jiaming Ding
- Zhongshan Hospital of Traditional Chinese Medicine, Zhongshan, 528400, China
| | - Huijuan Chen
- Department of Proctology, Yubei Hospital of Traditional Chinese Medicine, Chongqing Yubei District, Chongqing, 401120, China
| | - Xiaohong Liu
- Department of Proctology, Yubei Hospital of Traditional Chinese Medicine, Chongqing Yubei District, Chongqing, 401120, China
| | - Feng Sun
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, 510403, China
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Redmer T, Schumann E, Peters K, Weidemeier ME, Nowak S, Schroeder HWS, Vidal A, Radbruch H, Lehmann A, Kreuzer-Redmer S, Jürchott K, Radke J. MET receptor serves as a promising target in melanoma brain metastases. Acta Neuropathol 2024; 147:44. [PMID: 38386085 PMCID: PMC10884227 DOI: 10.1007/s00401-024-02694-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/23/2024]
Abstract
The development of brain metastases hallmarks disease progression in 20-40% of melanoma patients and is a serious obstacle to therapy. Understanding the processes involved in the development and maintenance of melanoma brain metastases (MBM) is critical for the discovery of novel therapeutic strategies. Here, we generated transcriptome and methylome profiles of MBM showing high or low abundance of infiltrated Iba1high tumor-associated microglia and macrophages (TAMs). Our survey identified potential prognostic markers of favorable disease course and response to immune checkpoint inhibitor (ICi) therapy, among them APBB1IP and the interferon-responsive gene ITGB7. In MBM with high ITGB7/APBB1IP levels, the accumulation of TAMs correlated significantly with the immune score. Signature-based deconvolution of MBM via single sample GSEA revealed enrichment of interferon-response and immune signatures and revealed inflammation, stress and MET receptor signaling. MET receptor phosphorylation/activation maybe elicited by inflammatory processes in brain metastatic melanoma cells via stroma cell-released HGF. We found phospho-METY1234/1235 in a subset of MBM and observed a marked response of brain metastasis-derived cell lines (BMCs) that lacked druggable BRAF mutations or developed resistance to BRAF inhibitors (BRAFi) in vivo to MET inhibitors PHA-665752 and ARQ197 (tivantinib). In summary, the activation of MET receptor in brain colonizing melanoma cells by stromal cell-released HGF may promote tumor self-maintenance and expansion and might counteract ICi therapy. Therefore, therapeutic targeting of MET possibly serves as a promising strategy to control intracranial progressive disease and improve patient survival.
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Affiliation(s)
- Torben Redmer
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria.
- Institute of Pathology, Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, Vienna, Austria.
| | - Elisa Schumann
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, CCCC (Campus Mitte), Berlin, Germany
| | - Kristin Peters
- Institute of Pathology, University Medicine Greifswald, Greifswald, Germany
| | - Martin E Weidemeier
- Department of Neurosurgery, University Medicine Greifswald, Greifswald, Germany
| | - Stephan Nowak
- Department of Neurosurgery, University Medicine Greifswald, Greifswald, Germany
| | - Henry W S Schroeder
- Department of Neurosurgery, University Medicine Greifswald, Greifswald, Germany
| | - Anna Vidal
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Helena Radbruch
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Annika Lehmann
- Institute of Pathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Susanne Kreuzer-Redmer
- Nutrigenomics Unit, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Karsten Jürchott
- Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Josefine Radke
- Institute of Pathology, University Medicine Greifswald, Greifswald, Germany.
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Xue X, Feng Q, Hong X, Lin Z, Luo Y, Li Y, Yao G, Wang N, Chen L. Comprehensive analysis of ALG3 in pan-cancer and validation of ALG3 as an onco-immunological biomarker in breast cancer. Aging (Albany NY) 2024; 16:2320-2339. [PMID: 38329424 PMCID: PMC10911369 DOI: 10.18632/aging.205483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/14/2023] [Indexed: 02/09/2024]
Abstract
ALG3 has significant modulatory function in the process of tumor development. Yet how ALG3 involves in the advancement of different malignancies isn't fully understood. We performed a pan-cancer assessment on ALG3 utilizing datasets from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) to examine its tumor-related roles across malignancies and its link to particular molecules and cells in the tumor microenvironment (TME). Furthermore, we focused on breast cancer to examine the influence of ALG3-mediated signaling pathways and intercellular interactions in the advancement of tumors. The biological effects of ALG3 were verified by breast cancer cells. Enhanced ALG3 expression was discovered to be substantially linked to patients' grim prognoses in a number of malignancies. Furthermore, the expression of ALG3 in the TME was linked to the infiltration of stromal and immune cells, and ALG3-related immune checkpoints, TMB, and MSI were also discovered. We also discovered that cancer patients having a high level of ALG3 exhibited a lower probability of benefiting from immunotherapy. Furthermore, our research found that KEGG enrichment, single-cell RNA and spatial sequencing analyses were effective in identifying key signaling pathways in ALG3-associated tumor growth. In vitro, knockdown of ALG3 could decrease the proliferation of breast cancer cells. In summary, our research offers a comprehensive insight into the advancement of tumors under the mediation of ALG3. ALG3 appears to be intimately associated with tumor development in the TME. ALG3 might be a viable treatment target for cancer therapy, particularly in the case of breast cancer.
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Affiliation(s)
- Xiaolei Xue
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Qiaoli Feng
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Xi Hong
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Zhousheng Lin
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Yingrui Luo
- Basic Medical Academy, Cancer Research Institute, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Yingshi Li
- Basic Medical Academy, Cancer Research Institute, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Guangyu Yao
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Nisha Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Lujia Chen
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
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Lin Z, Ji X, Tian N, Gan Y, Ke L. APOB is a potential prognostic biomarker in hepatocellular carcinoma. Discov Oncol 2024; 15:28. [PMID: 38310202 PMCID: PMC10838261 DOI: 10.1007/s12672-024-00877-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/30/2024] [Indexed: 02/05/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is significantly associated with adverse prognostic outcomes. The development and progression of different types of human tumors are significantly influenced by APOB. Nevertheless, the significance and pathomechanisms of APOB in HCC have not been conclusively determined. We assessed APOB expression levels in HCC using three publicly available databases of TIMER2.0, UALCAN and Human Protein Atlas. To identify the biological function of APOB, we conducted enrichment analysis via LinkedOmics. Moreover, UALCAN was employed to assess the relationship between APOB expression and clinicopathological features among HCC patients. Additionally, the Kaplan-Meier plotter was utilized to investigate the prognostic relevance of APOB in HCC. To explore potential regulatory ncRNAs that could bind to APOB, we utilized StarBase and GEPIA. Furthermore, the correlation between APOB expression and immune cell infiltration, as well as immune checkpoint genes, was investigated using Spearman's correlation analysis in TISIDB, GEPIA, and TIMER2.0. The findings of our investigation showed a notable decrease in the expression levels of APOB among individuals diagnosed with HCC. Moreover, a noteworthy correlation was observed between the expression of APOB and immune checkpoint genes, alongside the occurrence of immune cell infiltration. The levels of APOB expression in HCC tissues also showed correlations with various clinicopathological features. According to Cox regression analysis, decreased APOB expression emerged as a potential autonomous predictor for OS, RFS, DSS, and PFS among HCC patients. Furthermore, we identified six potential pathways associated with non-coding RNA (ncRNA) as the most promising pathway for APOB in HCC. Our results illuminate the possible involvement of APOB in HCC and offer understanding into its governing mechanisms and medical importance.
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Affiliation(s)
- Zhifeng Lin
- Department of Medical Record; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Xiaohui Ji
- Department of Obstetrics and Gynaecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Nana Tian
- Department of Medical Record, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yu Gan
- Department of Medical Record, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Ke
- Department of Medical Record; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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Wang Y, Guan L, Zhao Y, Yang Y, Wang Y, Feng S, Zou A, Li Y, Zhou B, Zhang D, Che W, Liu F. A Comprehensive Pan-cancer Analysis of the Biological Immunomodulatory Function and Clinical Value of CD27. J Cancer 2024; 15:508-525. [PMID: 38169519 PMCID: PMC10758032 DOI: 10.7150/jca.85446] [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: 04/20/2023] [Accepted: 09/26/2023] [Indexed: 01/05/2024] Open
Abstract
Background: CD27 is an immunological checkpoint gene, plays a critical function inInhibition or activation of cancer immunity. The CD27/CD27L axis is its pathway of action. Therefore, our goal was to examine the predictive role of CD27 in the clinical prognosis of 33 cancer types and its functions in cancer progression, as well as explore the link between pan-cancer CD27 gene expression and immune infiltration. Methods: By comprehensive use of datasets and methods from TCGA, cBioPortal, GTEx, HPA, KM-plotter, Spearman, CellMinerTM, R packages and RT-qPCR, we delved deeper into the potential impact of the CD27 on cancer development. These include expression differences, immune infiltration, matrix infiltration, gene mutations, DNA methylation, signaling pathways, TMB, MSI, and prognosis. Also, we explored CD27 interactions with different drugs. Results: The results showed that, mutated CD27 was highly expressed in most cancers. The CD27 showed strong diagnostic value in 4 cancers and marked a positive prognosis for CESC, intracervical adenocarcinoma, HNSC, and endometrial cancer, and a poor prognosis for UVM. In addition, CD27 affects multiple immune and inflammatory signaling pathways and is positively correlated with immune cell infiltration, T cell differentiation, macrophage M1 polarization, stromal infiltration, and drug sensitivity. DNA methylation is involved in CD27 expression in cancer. Conclusion: CD27, which is mutated in cancers and appears widely highly expressed and altered tumor immune invasion and stromal invasion by affecting multiple immune-related and inflammation signaling pathways, plays a significant role in CESC, HNSC, UCEC and UVM, and may be used as a therapeutic target for related cancers.
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Affiliation(s)
- Yongfeng Wang
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, 730000, China
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, Gansu, 730000, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Gansu 730000, China
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China
| | - Ling Guan
- School of Stomatology, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Yanzong Zhao
- School of Stomatology, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Yanling Yang
- College of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yitong Wang
- School of Stomatology, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Shengjiao Feng
- School of Stomatology, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Anqi Zou
- School of Stomatology, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Yawei Li
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, Gansu, 730000, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Gansu 730000, China
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China
| | - Botao Zhou
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, Gansu, 730000, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Gansu 730000, China
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China
| | - Dongzhi Zhang
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China
| | - Weiqi Che
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Fangyu Liu
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, 730000, China
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Urbiola-Salvador V, Jabłońska A, Miroszewska D, Huang Q, Duzowska K, Drężek-Chyła K, Zdrenka M, Śrutek E, Szylberg Ł, Jankowski M, Bała D, Zegarski W, Nowikiewicz T, Makarewicz W, Adamczyk A, Ambicka A, Przewoźnik M, Harazin-Lechowicz A, Ryś J, Filipowicz N, Piotrowski A, Dumanski JP, Li B, Chen Z. Plasma protein changes reflect colorectal cancer development and associated inflammation. Front Oncol 2023; 13:1158261. [PMID: 37228491 PMCID: PMC10203952 DOI: 10.3389/fonc.2023.1158261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/05/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction Colorectal cancer (CRC) is the third most common malignancy and the second leading cause of death worldwide. Efficient non-invasive blood-based biomarkers for CRC early detection and prognosis are urgently needed. Methods To identify novel potential plasma biomarkers, we applied a proximity extension assay (PEA), an antibody-based proteomics strategy to quantify the abundance of plasma proteins in CRC development and cancer-associated inflammation from few μL of plasma sample. Results Among the 690 quantified proteins, levels of 202 plasma proteins were significantly changed in CRC patients compared to age-and-sex-matched healthy subjects. We identified novel protein changes involved in Th17 activity, oncogenic pathways, and cancer-related inflammation with potential implications in the CRC diagnosis. Moreover, the interferon γ (IFNG), interleukin (IL) 32, and IL17C were identified as associated with the early stages of CRC, whereas lysophosphatidic acid phosphatase type 6 (ACP6), Fms-related tyrosine kinase 4 (FLT4), and MANSC domain-containing protein 1 (MANSC1) were correlated with the late-stages of CRC. Discussion Further study to characterize the newly identified plasma protein changes from larger cohorts will facilitate the identification of potential novel diagnostic, prognostic biomarkers for CRC.
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Affiliation(s)
- Víctor Urbiola-Salvador
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Poland
| | - Agnieszka Jabłońska
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Poland
| | - Dominika Miroszewska
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Poland
| | - Qianru Huang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Respiratory and Critical Care Medicine of Ruijin Hospital, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | | | - Marek Zdrenka
- Department of Tumor Pathology and Pathomorphology, Oncology Center−Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Ewa Śrutek
- Department of Tumor Pathology and Pathomorphology, Oncology Center−Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Łukasz Szylberg
- Department of Tumor Pathology and Pathomorphology, Oncology Center−Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
- Department of Obstetrics, Gynaecology and Oncology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Michał Jankowski
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in ToruńSurgical Oncology, Ludwik Rydygier’s Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
- Department of Surgical Oncology, Oncology Center−Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Dariusz Bała
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in ToruńSurgical Oncology, Ludwik Rydygier’s Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
- Department of Surgical Oncology, Oncology Center−Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Wojciech Zegarski
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in ToruńSurgical Oncology, Ludwik Rydygier’s Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
- Department of Surgical Oncology, Oncology Center−Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Tomasz Nowikiewicz
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in ToruńSurgical Oncology, Ludwik Rydygier’s Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Toruń, Poland
- Department of Breast Cancer and Reconstructive Surgery, Oncology Center−Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Wojciech Makarewicz
- Clinic of General and Oncological Surgery, Specialist Hospital of Kościerzyna, Kościerzyna, Poland
| | - Agnieszka Adamczyk
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Aleksandra Ambicka
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Marcin Przewoźnik
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Agnieszka Harazin-Lechowicz
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Janusz Ryś
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | | | | | - Jan P. Dumanski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Gdańsk, Poland
| | - Bin Li
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Respiratory and Critical Care Medicine of Ruijin Hospital, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi Chen
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Gdańsk, Poland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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7
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Zhang L, Wei Y, He Y, Wang X, Huang Z, Sun L, Chen J, Zhu Q, Zhou X. Clinical implication and immunological landscape analyses of ANLN in pan-cancer: A new target for cancer research. Cancer Med 2023; 12:4907-4920. [PMID: 36030492 PMCID: PMC9972146 DOI: 10.1002/cam4.5177] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 08/02/2022] [Accepted: 08/14/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Anillin is a F-actin binding protein (ANLN) mainly involved in the process of cytokinesis and known to be dysregulated in diverse cancers. However, the role of ANLN in pan-cancer prognosis and tumor immunity remains unclear. METHODS Gene expression profiles of 31 solid tumors were downloaded from The Cancer Genome Atlas (TCGA) database. ANLN mRNA and protein expression were quantified using quantitative real-time PCR (qRT-PCR) and immunohistochemistry (IHC). Protein expression of ANLN was further confirmed in Human Protein Atlas (HPA) database. Cox regression and Kaplan-Meier analysis were utilized to assess the prognostic value of ANLN in pan-cancer. The correlation between ANLN and different immune gene markers and infiltration cells was analyzed via ESTIMATE and CIBERSORT. A BLCA immunotherapy cohort: IMvigor (210) was used to confirm the role of ANLN in immune response. RESULTS ANLN upregulation was detected in 21 types of cancers and was associated with poor overall survival (OS), disease-free interval (DFI), and progression-free interval (PFI) in most cancers except in THYM (Thymoma). Additionally, correlation analysis revealed a significantly positive association between ANLN expression and tumor mutation burden (TMB), microsatellite instability (MSI), immune cells infiltration. and immune checkpoint genes in various cancers. The BLCA immunotherapy cohort confirmed that patients with higher ANLN level had better immune responses and longer OS. CONCLUSION ANLN may serve as a prognostic biomarker for pan-cancer. ANLN upregulation is associated with higher TMB, MSI, and immune cell infiltration in multiple types of tumors, shedding new light for cancer treatment.
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Affiliation(s)
- Lan Zhang
- Department of Radiation Oncology, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China
| | - Yong Wei
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yan He
- Department of Radiotherapy & Oncology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Xiaping Wang
- Department of Pathology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zebo Huang
- Department of Oncology, The Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Libing Sun
- Department of Pathology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Jie Chen
- Department of Radiation Oncology, Dushu Lake Hospital Affiliated to Soochow University (Medical Center of Soochow University), Suzhou, China.,State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Qingyi Zhu
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xin Zhou
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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8
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Li Z, Jin C, Lu X, Zhang Y, Zhang Y, Wen J, Liu Y, Liu X, Li J. Construction of a novel mRNAsi-related risk model for predicting prognosis and immunotherapy response in osteosarcoma. ANNALS OF TRANSLATIONAL MEDICINE 2023; 11:61. [PMID: 36819514 PMCID: PMC9929782 DOI: 10.21037/atm-22-6011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/06/2023] [Indexed: 01/31/2023]
Abstract
Background Targeting cancer stem cells (CSC) may represent a future therapeutic direction for osteosarcoma (OS), which mainly relies on the identification of CSC markers. This study aimed to classify OS based on messenger ribonucleic acid (mRNA) stemness indices (mRNAsi) and construct a mRNAsi-related risk model to predict the prognosis of OS. Methods The one-class logistic regression (OCLR) algorithm was applied to the RNA- sequencing (seq) data of human embryonic stem cells (hESC) and induced pluripotent stem cell (iPSC) lines to calculate mRNAsi. Weighted gene co-expression network analysis (WGCNA) was performed on data obtained from the TARGET database to screen the mRNAsi-related genes. Univariate Cox regression analysis was implemented to screen mRNAsi-related genes with prognostic significance for consensus clustering of OS. The least absolute shrinkage and selection operator (LASSO) and COX regression analysis were conducted to construct a risk model based on mRNAsi-related genes. Results Six gene modules were identified in the TARGET database. The yellow module showed the strongest negative correlation with mRNAsi and the strongest significant positive correlation with the immune score and stromal score. OS was divided into three molecular subtypes with significant survival differences based on 73 mRNAsi-related genes with prognostic value for OS. The survival rate was ranked as C3 < C1 < C2 from low to high. The levels of immune components in C2 was significantly higher than those in C1 and C3. HSD11B2, GBP1, RNF130, APBB1IP, and NPC2 in the yellow module were used as variables for building the mRNAsi-related risk model. The survival rate of the high-risk group (as defined by this model) was significantly higher than that of the low-risk group, and it had significant survival prediction ability in 28 types of cancer. In addition, the mRNAsi-related risk model was superior to the Tumor Immune Dysfunction and Exclusion (TIDE) model in predicting the prognosis and immunotherapy response in all three immunotherapy cohorts. Conclusions This study classified OS and constructed a mRNAsi-related risk model based on mRNAsi-related genes, which provides a potential tool for more accurate risk stratification of OS and prediction of immunotherapy response.
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Affiliation(s)
- Zhe Li
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chi Jin
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinchang Lu
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yan Zhang
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yi Zhang
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jia Wen
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongkui Liu
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoting Liu
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiazhen Li
- Department of Orthopaedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Wei L, Li H, Xiao M, Zhou C, Liu J, Weng S, Wei R. CCNF is a potential pancancer biomarker and immunotherapy target. Front Oncol 2023; 13:1109378. [PMID: 37168372 PMCID: PMC10164972 DOI: 10.3389/fonc.2023.1109378] [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: 11/27/2022] [Accepted: 04/11/2023] [Indexed: 05/13/2023] Open
Abstract
Background CCNF catalyzes the transfer of ubiquitin molecules from E2 ubiquitin-conjugating enzymes to target proteins, thereby regulating the G1/S or G2/M transition of tumor cells. Thus far, CCNF expression and its potential as a pancancer biomarker and immunotherapy target have not been reported. Methods TCGA datasets and the R language were used to analyze the pancancer gene expression, protein expression, and methylation levels of CCNF; the relationship of CCNF expression with overall survival (OS), recurrence-free survival (RFS), immune matrix scores, sex and race; and the mechanisms for posttranscriptional regulation of CCNF. Results CCNF expression analysis showed that CCNF mRNA expression was higher in cancer tissues than in normal tissues in the BRCA, CHOL, COAD, ESCA, HNSC, LUAD, LUSC, READ, STAD, and UCEC; CCNF protein expression was also high in many cancer tissues, indicating that it could be an important predictive factor for OS and RFS. CCNF overexpression may be caused by CCNF hypomethylation. CCNF expression was also found to be significantly different between patients grouped based on sex and race. Overexpression of CCNF reduces immune and stromal cell infiltration in many cancers. Posttranscriptional regulation analysis showed that miR-98-5p negatively regulates the expression of the CCNF gene. Conclusion CCNF is overexpressed across cancers and is an adverse prognostic factor in terms of OS and RFS in many cancers; this phenomenon may be related to hypomethylation of the CCNF gene, which could lead to cancer progression and worsen prognosis. In addition, CCNF expression patterns were significantly different among patients grouped by sex and race. Its overexpression reduces immune and stromal cell infiltration. miR-98-5p negatively regulates CCNF gene expression. Hence, CCNF is a potential pancancer biomarker and immunotherapy target.
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Affiliation(s)
- Lifang Wei
- Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Huiming Li
- Department of Preventive Medicine, Medical School of Yichun University, Yichun, China
| | - Mengjun Xiao
- Oncology Department, Shenzhen Overseas Chinese Hospital Affiliated to Jinan University, Shenzhen, China
| | - Cuiling Zhou
- Oncology Department, Shenzhen Overseas Chinese Hospital Affiliated to Jinan University, Shenzhen, China
| | - Jiliang Liu
- Oncology Department, Shenzhen Overseas Chinese Hospital Affiliated to Jinan University, Shenzhen, China
| | - Shilian Weng
- Oncology Department, Shenzhen Overseas Chinese Hospital Affiliated to Jinan University, Shenzhen, China
- *Correspondence: Ruda Wei, ; Shilian Weng,
| | - Ruda Wei
- Oncology Department, Shenzhen Overseas Chinese Hospital Affiliated to Jinan University, Shenzhen, China
- *Correspondence: Ruda Wei, ; Shilian Weng,
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10
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Cai W, Li Y, Cao W. Prognostic value and immunological role of Kruppel-like transcription factor 9 gene in pan-carcinoma. Medicine (Baltimore) 2022; 101:e32027. [PMID: 36550808 PMCID: PMC9771293 DOI: 10.1097/md.0000000000032027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE To investigate the correlation between the expression of Kruppel-like transcription factor 9 (KLF9) and the prognostic value of tumors as well as its relationship with tumor immune invasion. METHODS A series of bioinformatics methods were used to analyze the relationship between KLF9 and tumor prognosis, tumor mutation burden, microsatellite instability (MSI), and immune cell infiltration in multiple carcinomas. RESULTS In multiple tumor tissues, the expression of KLF9 was lower compared with paracancerous tissues. Therefore, KLF9 can serve as a protective factor to improve the prognosis of carcinoma patients with certain tumor types. KLF9 was closely related to the clinical staging of various carcinomas. The expression of KLF9 was not only associated with tumor mutation burden and MSI in some tumor types, but also positively correlated with immune and stromal cells in multiple tumors. Further studies have found that, the level of immune cell infiltration was significantly related to the expression of KLF9. CONCLUSION KLF9 can affect the prognosis of pan-carcinoma, which is related to immune invasion. Therefore, KLF9 can be used as a potential biomarker for the prognosis of pan-carcinoma.
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Affiliation(s)
- Weichao Cai
- Department of Plastic Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, China
| | - Yecheng Li
- Department of General Surgery, Second Affiliated Hospital of Soochow University, Suzhou, P. R. China
- *Correspondence: Weihong Cao, Department of Plastic Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, No. 150 XiMen Road, Taizhou, Zhejiang 317000, China (e-mail: ) and Yecheng Li, Department of General Surgery, Second Affiliated Hospital of Soochow University, No. 1055 Sanxiang Road, Suzhou, Jiangsu 215004, P. R. China (e-mail: )
| | - Weihong Cao
- Department of Plastic Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, China
- *Correspondence: Weihong Cao, Department of Plastic Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, No. 150 XiMen Road, Taizhou, Zhejiang 317000, China (e-mail: ) and Yecheng Li, Department of General Surgery, Second Affiliated Hospital of Soochow University, No. 1055 Sanxiang Road, Suzhou, Jiangsu 215004, P. R. China (e-mail: )
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Liu B, Pang K, Feng C, Liu Z, Li C, Zhang H, Liu P, Li Z, He S, Tu C. Comprehensive analysis of a novel cuproptosis-related lncRNA signature associated with prognosis and tumor matrix features to predict immunotherapy in soft tissue carcinoma. Front Genet 2022; 13:1063057. [PMID: 36568384 PMCID: PMC9768346 DOI: 10.3389/fgene.2022.1063057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
Background: A crucial part of the malignant processes of soft tissue sarcoma (STS) is played by cuproptosis and lncRNAs. However, the connection between cuproptosis-related lncRNAs (CRLs) and STS is nevertheless unclear. As a result, our objective was to look into the immunological activity, clinical significance, and predictive accuracy of CRLs in STS. Methods: The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases, respectively, provided information on the expression patterns of STS patients and the general population. Cuproptosis-related lncRNA signature (CRLncSig) construction involved the univariate, multivariate, and least absolute shrinkage and selection operator Cox regression analysis. The predictive performance of the CRLncSig was evaluated using a serial analysis. Further research was done on the connections between the CRLncSig and the tumor immune milieu, somatic mutation, immunotherapy response, and chemotherapeutic drug susceptibility. Notably, an in vitro investigation served to finally validate the expression of the hallmark CRLs. Results: A novel efficient CRLncSig composed of seven CRLs was successfully constructed. Additionally, the low-CRLncSig group's prognosis was better than that of the high-CRLncSig group's based on the new CRLncSig. The innovative CRLncSig then demonstrated outstanding, consistent, and independent prognostic and predictive usefulness for patients with STS, according to the evaluation and validation data. The low-CRLncSig group's patients also displayed improved immunoreactivity phenotype, increased immune infiltration abundance and checkpoint expression, and superior immunotherapy response, whereas those in the high-CRLncSig group with worse immune status, increased tumor stemness, and higher collagen levels in the extracellular matrix. Additionally, there is a noticeable disparity in the sensitivity of widely used anti-cancer drugs amongst various populations. What's more, the nomogram constructed based on CRLncSig and clinical characteristics of patients also showed good predictive ability. Importantly, Real-Time Quantitative Polymerase Chain Reaction (RT-qPCR) demonstrated that the signature CRLs exhibited a significantly differential expression level in STS cell lines. Conclusion: In summary, this study revealed the novel CRLncSig could be used as a promising predictor for prognosis prediction, immune activity, tumor immune microenvironment, immune response, and chemotherapeutic drug susceptibility in patients with STS. This may provide an important direction for the clinical decision-making and personalized therapy of STS.
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Affiliation(s)
- Binfeng Liu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ke Pang
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Chengyao Feng
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhongyue Liu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Chenbei Li
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Haixia Zhang
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ping Liu
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhihong Li
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Shasha He
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,*Correspondence: Shasha He, ; Chao Tu,
| | - Chao Tu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,*Correspondence: Shasha He, ; Chao Tu,
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Yi W, Qiao T, Yang Z, Hu L, Sun M, Fan H, Xu Y, Lv Z. The regulation role and diagnostic value of fibrinogen-like protein 1 revealed by pan-cancer analysis. Mater Today Bio 2022; 17:100470. [PMID: 36345363 PMCID: PMC9636576 DOI: 10.1016/j.mtbio.2022.100470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/07/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Although the role of fibrinogen-like protein 1 (FGL1) in tumorigenesis is well known, a pan-cancer analysis of FGL1 lacks. We used bioinformatics techniques to analyze cancer data from publicly available datasets from The Cancer Genome Atlas, UALCAN, TIMER, Gene Expression Profiling Interactive Analysis, cBioPortal, Search Tool for the Retrieval of Interacting Genes, and DAVID. FGL1 expression was significantly regulated in various common tumors than in normal tissues; it was increased in lung adenocarcinoma and decreased in colon adenocarcinoma. Cox regression analysis demonstrated that the upregulation of FGL1 expression was correlated with poor overall survival (OS) and disease-free survival (DFS) in stomach adenocarcinoma, brain low-grade glioma, cervical squamous cell carcinoma, and endocervical adenocarcinoma. Decreased FGL1 methylation levels were observed in majority of tumor types. FGL1 expression was significantly associated with the levels of immune cell subtypes and immune checkpoint genes. Deep deletion was the most common genetic mutation in FGL1 that led to frame-shift mutations, which was closely associated with poor progression-free interval, disease-specific survival, and OS in patients with FGL1 mutations. Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that FGL1-related genes participate in diverse pathways. Ubiquitin-mediated proteolysis is significantly correlated to the function of FGL1, which was identified for the first time in the present study. This pan-cancer study provides a deep understanding of the functions of FGL1 in progression of many tumors and demonstrates that FGL1 may be a potential biomarker for the diagnosis, prognosis, and immune infiltration in cancer.
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Affiliation(s)
- Wanwan Yi
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Yanchang Middle Road 301, Shanghai, 200072, China
| | - Tingting Qiao
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Yanchang Middle Road 301, Shanghai, 200072, China
| | - Ziyu Yang
- Department of Integrated Chinese and Western Medicine, The Eastern Hepatobiliary Surgery Hospital, Navy Medical University (Second Military Medical University), Shanghai, 200438, China
| | - Lei Hu
- Department of Hepatic Surgery, The Eastern Hepatobiliary Surgery Hospital, Navy Medical University (Second Military Medical University), Shanghai, 200438, China
| | - Mingming Sun
- Department of Hepatic Surgery, The Eastern Hepatobiliary Surgery Hospital, Navy Medical University (Second Military Medical University), Shanghai, 200438, China
| | - Hengwei Fan
- Department of Hepatic Surgery, The Eastern Hepatobiliary Surgery Hospital, Navy Medical University (Second Military Medical University), Shanghai, 200438, China
- Corresponding author.
| | - Yanping Xu
- School of Life Sciences and Technology, Tongji University, No.1239 SiPing Road, Yangpu District, Shanghai, 200092, China
- Corresponding author.
| | - Zhongwei Lv
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Yanchang Middle Road 301, Shanghai, 200072, China
- Corresponding author.
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Liu Z, Zhang L, Zhong Y. Characterization of osteosarcoma subtypes mediated by macrophage-related genes and creation and validation of a risk score system to quantitatively assess the prognosis of osteosarcoma and reflect the tumor microenvironment. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1318. [PMID: 36660647 PMCID: PMC9843337 DOI: 10.21037/atm-22-5613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Background Macrophages are the main immune components in the microenvironment of osteosarcoma. The treatment strategy centered on macrophages has become a hot topic to improve cancer treatment. However, the research on the role of macrophages in the treatment of osteosarcoma is still in its infancy. Methods The data of osteosarcoma samples were downloaded from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and GSE21257 datasets, and the macrophage enrichment fraction of osteosarcoma samples in TARGET was calculated by single-sample gene set enrichment analysis (ssGSEA) method to screen macrophage-related genes for consensus clustering. Differential expression analysis, univariable Cox, and least absolute shrinkage and selection operator (LASSO) regression were conducted to select reliable predictors and create a risk score system. The GSE21257 dataset was used as a verification set to verify the accuracy of risk score system. Results We identified 2 osteosarcoma clusters mediated by 22 macrophage score-related genes, namely cluster 1 (C1) and cluster 2 (C2). Compared with C2, C1 had a significant advantage in prognosis, and the degree of immune cell infiltration in tumor microenvironment (TME) was significantly higher, the expression of immune checkpoint molecules was significantly enhanced, and the Tumor Immune Dysfunction and Exclusion (TIDE) score was also significantly down-regulated. A robust risk score system was presented and validated, which demonstrated accuracy and independence in assessing the risk of death of osteosarcoma. The risk score system could also monitor TME infiltration in osteosarcoma samples and showed a close relationship with osteosarcoma biology, including metastasis and immunity. Conclusions We identified 2 types of clusters mediated by macrophage-related genes and helped to analyze the cluster suitable for immunotherapy. A new prognostic risk score system was created to quantitatively evaluate the prognosis and TME of osteosarcoma, and to provide a new entry point for the design of personalized treatment.
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Affiliation(s)
- Zhe Liu
- Department of Orthopedics, Jiangxi Cancer Hospital, Nanchang, China
| | - Lei Zhang
- Department of Orthopedics, Jiangxi Cancer Hospital, Nanchang, China
| | - Yun Zhong
- Department of Lymphohematology and Oncology, Jiangxi Cancer Hospital, Nanchang, China
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Gong Y, Liu X, Sahu A, Reddy AV, Wang H. Exploration of hub genes, lipid metabolism, and the immune microenvironment in stomach carcinoma and cholangiocarcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:834. [PMID: 36034995 PMCID: PMC9403925 DOI: 10.21037/atm-22-3530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/02/2022] [Indexed: 01/11/2023]
Abstract
Background Gastric cancer (GC) is the 5th most common cause of cancer in the world and the 3rd largest cause of cancer-related death. It is usually associated with a variety of cancers, of which cholangiocarcinoma (CCA) combined with GC accounts for about 1.6%. This study sought to examine the hub genes and role of lipid metabolism in the development and diagnosis of GC and CCA. Methods To screen potential hub genes, The Cancer Genome Atlas (TCGA) data sets, including the GC (STAD, dataset of GC) and CCA (CHOL, dataset of CCA) data sets, were used to conduct a differentially expressed gene (DEG) analysis and an enrichment analysis of the DEGs. A weighted-gene co-expression network analysis (WGCNA) was conducted to identify the significant gene module and then find the hub genes in the module. To verify the 4 hub genes, we conducted a differentiation analysis of the 4 genes in GC and CCA and found that there were differences. A survival analysis of the hub genes was performed and mutations were mapped. Additionally, tumor immune microenvironment (TIME) and immune analyses were performed to evaluate how lipid metabolism affects the development of GC with CCA. Results The principal component analysis showed that both GC and CCA had distinct up-regulated and down-regulated genes, which are involved in a variety of metabolic processes. Upon WGCNA, the turquoise and blue modules were meaningful, and the hub genes were identified from these 2 modules. Four hub genes were identified: amyloid beta precursor protein binding family B member 1 (APBB1), Homo sapiens armadillo repeat containing X-linked 1 (ARMCX1), DAZ interacting zinc finger protein 1 (DZIP1), and methionine sulfoxide reductase B3 (MSRB3). In survival analysis, increased expression of the 4 hub genes was associated with inferior survival outcomes, with variations in all 4 genes. Additionally, we demonstrated that genes related to lipid metabolism had an effect on immune function. Conclusions APBB1, ARMCX1, DZIP1, and MSRB3 affect the development of GC and CCA and can be used as biomarkers. The expression of lipid metabolism genes is related to the TIME of patients with GC and CCA.
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Affiliation(s)
- Yuda Gong
- Department of General Surgery, Fudan University Zhongshan Hospital, Shanghai, China
| | - Xuan Liu
- Department of General Surgery, Fudan University Zhongshan Hospital, Shanghai, China
| | - Arvind Sahu
- Department of Oncology, Goulburn Valley Health, Shepparton, Victoria, Australia
| | - Abhinav V Reddy
- Department of Radiation Oncology & Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Sidney Kimmel Cancer Center, Baltimore, MD, USA
| | - Haiyu Wang
- Department of General Surgery, Fudan University Zhongshan Hospital, Shanghai, China
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Comprehensive Analysis of RELL2 as a Potential Biomarker Associated with Tumor Immune Infiltrating Cells in a Pan-Cancer Analysis. DISEASE MARKERS 2022; 2022:5009512. [PMID: 35634441 PMCID: PMC9132657 DOI: 10.1155/2022/5009512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 04/12/2022] [Indexed: 11/17/2022]
Abstract
Background Receptor expressed in lymphoid tissues-like 2 (RELL2), which is a member of RELT family, is closely associated with the plasma membrane and acts as a modulator for RELT signaling. Overexpression of RELL2 induces the activation of MAPK14/p38 cascade and apoptosis. However, whether RELL2 contributes to cancers remains unclear. Here, we examined its role in cancer patient prognosis and various tumors. Methods We used several bioinformatics methods, specifically gene set enrichment analysis (GSEA), ScanNeo, and ESTIMATE, to analyze the CCLE dataset, GTEx dataset, and TCGA dataset. We investigated the possible association of RELL2 with the microsatellite instability (MSI) of various tumors, tumor mutational burden (TMB), immune checkpoint, immune neoantigens, immune microenvironment, and patient prognosis. Result RELL2 is highly expressed in cancer compared with normal tissues. RELL2 expression is linked with worse progression-free interval and overall survival in numerous cancers. In most cancers, high RELL2 expression was related to a poor prognosis. RELL2 expression was significantly associated with the tumor microenvironment, MSI, and TMB. RELL2 expression is strongly associated with phenotypes that are of major clinical significance, particularly those associated with immune neoantigens and the expression profiles of immune checkpoint genes in pan-cancer. RELL2 expression strongly linked with the expressions of methyltransferases and DNA repair genes. It also significantly correlated with multiple signaling pathways through gene set enrichment analysis. Conclusion RELL2 may be a prognostic biomarker in pan-cancer and may have an important function in tumorigenesis and progression.
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Yu Y, Sun X, Chen F, Liu M. Genetic Alteration, Prognostic and Immunological Role of Acyl-CoA Synthetase Long-Chain Family Member 4 in a Pan-Cancer Analysis. Front Genet 2022; 13:812674. [PMID: 35126480 PMCID: PMC8811308 DOI: 10.3389/fgene.2022.812674] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/03/2022] [Indexed: 12/26/2022] Open
Abstract
Acyl-CoA Synthetase long-chain family member 4 (ACSL4) is a member of acyl-CoA synthetase protein long-chain family, which is associated with amino acid synthesis, lipid synthesis and lipid peroxidation dependent iron death. However, the role of ACSL4 in generalized carcinoma remains unclear. We aim to analyze the expression and prognostic value of ACSL4 in pan-cancer, and further explore the correlation between ACSL4 and immune infiltration. Through ONCOMINE, TIMER (Tumor Immune Estimation Resource), GEPIA (Gene expression Profiling Interactive), UALCAN and HPA, ACSL4 expression patterns of in pan-cancer were analyzed. The prognostic value of ACSL4 was analyzed using PrognoScan and Kaplan-Meier Plotter databases. Furthermore, gene variation and epigenetic modification of ACSL4 were analyzed by cBioPortal and GSCA databases. Meanwhile, GEPIA and TIMER databases applied to evaluate the relationship between ACSL4 expression and immune infiltration. These results indicate that ACSL4 expression is down-regulated and associated with prognosis in most tumors. In general, lower ACSL4 expression shows more beneficial prognosis. The most common genetic alteration of ACSL4 is point mutation. ACSL4 is negatively correlated with DNA methylation levels in most cancers. ACSL4 mutations or hypomethylation are associated with poor prognosis. In addition, ACSL4 is positively correlated with immune infiltration in cancers. ACSL4 and immune infiltration are strongly associated with prognosis in BRCA (Breast invasive carcinoma) and SKCM (Skin Cutaneous Melanoma). ACSL4 mutation caused significant changes of immune infiltration in UCEC (Uterine Corpus Endometrial Carcinoma) and SARC (Sarcoma). ACSL4 may be a promising prognostic biomarker for pan-cancer and is closely associated with immune infiltration in the tumor microenvironment.
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Affiliation(s)
- Yongsheng Yu
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xuepu Sun
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fei Chen
- Department of General Surgery, Linyi Traditional Chinese Medicine Hospital, Linyi, China
| | - Miao Liu
- Department of Pathology, Beidahuang Industry Group General Hospital, Harbin, China
- *Correspondence: Miao Liu,
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Huang D, Shen J, Zhai L, Chen H, Fei J, Zhu X, Zhou J. Insights Into the Prognostic Value and Immunological Role of NAAA in Pan-Cancer. Front Immunol 2022; 12:812713. [PMID: 35069601 PMCID: PMC8772335 DOI: 10.3389/fimmu.2021.812713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/06/2021] [Indexed: 11/23/2022] Open
Abstract
N-Acylethanolamine Acid Amidase (NAAA) is an N-terminal cysteine hydrolase and plays a vital physiological role in inflammatory response. However, the roles of NAAA in tumor immunity are still unclear. By using a series of bioinformatics approaches, we study combined data from different databases, including the Cancer Genome Atlas, the Cancer Cell Line Encyclopedia, Genotype Tissue-Expression, cBioPortal, Human Protein Atlas, TIMER, and ImmuCellAI to investigate the role of NAAA expression in prognosis and tumor immunity response. We would like to reveal the potential correlations between NAAA expression and gene alterations, tumor mutational burden (TMB), microsatellite instability (MSI), DNA methylation, tumor microenvironment (TME), immune infiltration levels, and various immune-related genes across different cancers. The results show that NAAA displayed abnormal expression within most malignant tumors, and overexpression of NAAA was associated with the poor prognosis of tumor patients. Through gene set enrichment analysis (GSEA), we found that NAAA was significantly associated with cell cycle and immune regulation-related signaling pathways, such as in innate immune system, adaptive immune system, neutrophil degranulation, and Toll-like receptor signaling pathways (TLRs). Further, the expression of NAAA was also confirmed to be correlated with tumor microenvironment and diverse infiltration of immune cells, especially tumor-associated macrophage (TAM). In addition to this, we found that NAAA is co-expressed with genes encoding major histocompatibility complex (MHC), immune activation, immune suppression, chemokine, and chemokine receptors. Meanwhile, we demonstrate that NAAA expression was correlated with TMB in 4 cancers and with MSI in 10 cancers. Our study reveals that NAAA plays an important role in tumorigenesis and cancer immunity, which may be used to function as a prognostic biomarker and potential target for cancer immunotherapy.
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Affiliation(s)
- Da Huang
- Department of Gynecology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiayu Shen
- Department of Obstetrics, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lingyun Zhai
- Department of Gynecology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Huanhuan Chen
- Department of Gynecology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jing Fei
- Department of Gynecology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaoqing Zhu
- Department of Gynecology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jianwei Zhou
- Department of Gynecology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Pan-Cancer Analysis Reveals FH as a Potential Prognostic and Immunological Biomarker in Lung Adenocarcinoma. DISEASE MARKERS 2021; 2021:8554844. [PMID: 34737838 PMCID: PMC8563123 DOI: 10.1155/2021/8554844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/11/2021] [Indexed: 02/07/2023]
Abstract
Fumarate hydratase (FH) is an important enzymatic component in the tricarboxylic acid cycle. Studies have reported that FH plays an important role in hereditary leiomyomatosis and renal cell cancer (HLRCC). However, the role of FH in human different cancers remains unknown. This study is aimed at analyzing the prognostic value of FH and demonstrating the correlation between FH expression and tumor immunity. Results showed that FH was mutated or copy number varied in 27 types of cancer. FH mRNA was abnormally upregulated across various cancers. Survival analysis suggested high expression of FH was associated with poor prognosis in many cancer types, including lung adenocarcinoma (LUAD). Additionally, FH expression was associated with immune infiltration, including B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells, especially in liver hepatocellular carcinoma (LIHC), LUAD, and lung squamous cell carcinoma (LUSC). Moreover, FH expression showed a strong correlation with immune checkpoint markers in LUAD and testicular germ cell tumors (TGCT). These results indicate that FH is an immunotherapeutic target and a potential prognostic biomarker in LUAD.
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