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Shi H, Yuan M, Cai J, Shi J, Li Y, Qian Q, Dong Z, Pan G, Zhu S, Wang W, Zhou J, Zhou X, Liu J. Exploring personalized treatment for cardiac graft rejection based on a four-archetype analysis model and bioinformatics analysis. Sci Rep 2024; 14:6529. [PMID: 38499711 PMCID: PMC10948767 DOI: 10.1038/s41598-024-57097-9] [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: 10/22/2023] [Accepted: 03/14/2024] [Indexed: 03/20/2024] Open
Abstract
Heart transplantation is the gold standard for treating patients with advanced heart failure. Although improvements in immunosuppressive therapies have significantly reduced the frequency of cardiac graft rejection, the incidences of T cell-mediated rejection (TCMR) and antibody-mediated rejection remain almost unchanged. A four-archetype analysis (4AA) model, developed by Philip F. Halloran, illustrated this problem well. It provided a new dimension to improve the accuracy of diagnoses and an independent system for recalibrating the histology guidelines. However, this model was based on the invasive method of endocardial biopsy, which undoubtedly increased the postoperative risk of heart transplant patients. Currently, little is known regarding the associated genes and specific functions of the different phenotypes. We performed bioinformatics analysis (using machine-learning methods and the WGCNA algorithm) to screen for hub-specific genes related to different phenotypes, based Gene Expression Omnibus accession number GSE124897. More immune cell infiltration was observed with the ABMR, TCMR, and injury phenotypes than with the stable phenotype. Hub-specific genes for each of the four archetypes were verified successfully using an external test set (accession number GSE2596). Logistic-regression models based on TCMR-specific hub genes and common hub genes were constructed with accurate diagnostic utility (area under the curve > 0.95). RELA, NFKB1, and SOX14 were identified as transcription factors important for TCMR/injury phenotypes and common genes, respectively. Additionally, 11 Food and Drug Administration-approved drugs were chosen from the DrugBank Database for each four-archetype model. Tyrosine kinase inhibitors may be a promising new option for transplant rejection treatment. KRAS signaling in cardiac transplant rejection is worth further investigation. Our results showed that heart transplant rejection subtypes can be accurately diagnosed by detecting expression of the corresponding specific genes, thereby enabling precise treatment or medication.
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Affiliation(s)
- Hongjie Shi
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
- Hubei Provincial Engineering Research Center of Minimally Invasive Cardiovascular Surgery, Wuhan, 430071, China
- Wuhan Clinical Research Center for Minimally Invasive Treatment of Structural Heart Disease, Wuhan, 430071, China
| | - Ming Yuan
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
- Hubei Provincial Engineering Research Center of Minimally Invasive Cardiovascular Surgery, Wuhan, 430071, China
- Wuhan Clinical Research Center for Minimally Invasive Treatment of Structural Heart Disease, Wuhan, 430071, China
| | - Jie Cai
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
- Hubei Provincial Engineering Research Center of Minimally Invasive Cardiovascular Surgery, Wuhan, 430071, China
- Wuhan Clinical Research Center for Minimally Invasive Treatment of Structural Heart Disease, Wuhan, 430071, China
| | - Jiajun Shi
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
- Hubei Provincial Engineering Research Center of Minimally Invasive Cardiovascular Surgery, Wuhan, 430071, China
- Wuhan Clinical Research Center for Minimally Invasive Treatment of Structural Heart Disease, Wuhan, 430071, China
| | - Yang Li
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
- Hubei Provincial Engineering Research Center of Minimally Invasive Cardiovascular Surgery, Wuhan, 430071, China
- Wuhan Clinical Research Center for Minimally Invasive Treatment of Structural Heart Disease, Wuhan, 430071, China
| | - Qiaofeng Qian
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
- Hubei Provincial Engineering Research Center of Minimally Invasive Cardiovascular Surgery, Wuhan, 430071, China
- Wuhan Clinical Research Center for Minimally Invasive Treatment of Structural Heart Disease, Wuhan, 430071, China
| | - Zhe Dong
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
- Hubei Provincial Engineering Research Center of Minimally Invasive Cardiovascular Surgery, Wuhan, 430071, China
- Wuhan Clinical Research Center for Minimally Invasive Treatment of Structural Heart Disease, Wuhan, 430071, China
| | - Gaofeng Pan
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
- Hubei Provincial Engineering Research Center of Minimally Invasive Cardiovascular Surgery, Wuhan, 430071, China
- Wuhan Clinical Research Center for Minimally Invasive Treatment of Structural Heart Disease, Wuhan, 430071, China
| | - Shaoping Zhu
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
- Hubei Provincial Engineering Research Center of Minimally Invasive Cardiovascular Surgery, Wuhan, 430071, China
- Wuhan Clinical Research Center for Minimally Invasive Treatment of Structural Heart Disease, Wuhan, 430071, China
| | - Wei Wang
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
- Hubei Provincial Engineering Research Center of Minimally Invasive Cardiovascular Surgery, Wuhan, 430071, China
- Wuhan Clinical Research Center for Minimally Invasive Treatment of Structural Heart Disease, Wuhan, 430071, China
| | - Jianliang Zhou
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
- Hubei Provincial Engineering Research Center of Minimally Invasive Cardiovascular Surgery, Wuhan, 430071, China
- Wuhan Clinical Research Center for Minimally Invasive Treatment of Structural Heart Disease, Wuhan, 430071, China
| | - Xianwu Zhou
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China.
- Hubei Provincial Engineering Research Center of Minimally Invasive Cardiovascular Surgery, Wuhan, 430071, China.
- Wuhan Clinical Research Center for Minimally Invasive Treatment of Structural Heart Disease, Wuhan, 430071, China.
| | - Jinping Liu
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China.
- Hubei Provincial Engineering Research Center of Minimally Invasive Cardiovascular Surgery, Wuhan, 430071, China.
- Wuhan Clinical Research Center for Minimally Invasive Treatment of Structural Heart Disease, Wuhan, 430071, China.
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Sun X, Dong M, Li J, Sun Y, Gao Y, Wang Y, Du L, Liu Y, Ji K, He N, Wang J, Zhang M, Song H, Xu C, Liu Q. NRF2 promotes radiation resistance by cooperating with TOPBP1 to activate the ATR-CHK1 signaling pathway. Theranostics 2024; 14:681-698. [PMID: 38169561 PMCID: PMC10758056 DOI: 10.7150/thno.88899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024] Open
Abstract
Background: Radiation resistance is the main limitation of the application of radiotherapy. Ionizing radiation (IR) kills cancer cells mainly by causing DNA damage, particularly double-strand breaks (DSBs). Radioresistant cancer cells have developed the robust capability of DNA damage repair to survive IR. Nuclear factor erythroid 2-related factor 2 (NRF2) has been correlated with radiation resistance. We previously reported a novel function of NRF2 as an ATR activator in response to DSBs. However, little is known about the mechanism that how NRF2 regulates DNA damage repair and radiation resistance. Methods: The TCGA database and tissue microarray were used to analyze the correlation between NRF2 and the prognosis of lung cancer patients. The radioresistant lung cancer cells were constructed, and the role of NRF2 in radiation resistance was explored by in vivo and in vitro experiments. Immunoprecipitation, immunofluorescence and extraction of chromatin fractions were used to explore the underlying mechanisms. Results: In this study, the TCGA database and clinical lung cancer samples showed that high expression of NRF2 was associated with poor prognosis in lung cancer patients. We established radioresistant lung cancer cells expressing NRF2 at high levels, which showed increased antioxidant and DNA repair abilities. In addition, we found that NRF2 can be involved in the DNA damage response independently of its antioxidant function. Mechanistically, we demonstrated that NRF2 promoted the phosphorylation of replication protein A 32 (RPA32), and DNA topoisomerase 2-binding protein 1 (TOPBP1) was recruited to DSB sites in an NRF2-dependent manner. Conclusion: This study explored the novel role of NRF2 in promoting radiation resistance by cooperating with RPA32 and TOPBP1 to activate the ATR-CHK1 signaling pathway. In addition, the findings of this study not only provide novel insights into the molecular mechanisms underlying the radiation resistance of lung cancer cells but also validate NRF2 as a potential target for radiotherapy.
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Affiliation(s)
| | | | | | | | | | | | - Liqing Du
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | | | | | | | | | | | | | - Chang Xu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - Qiang Liu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
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Iliadi C, Verset L, Bouchart C, Martinive P, Van Gestel D, Krayem M. The current understanding of the immune landscape relative to radiotherapy across tumor types. Front Immunol 2023; 14:1148692. [PMID: 37006319 PMCID: PMC10060828 DOI: 10.3389/fimmu.2023.1148692] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
Radiotherapy is part of the standard of care treatment for a great majority of cancer patients. As a result of radiation, both tumor cells and the environment around them are affected directly by radiation, which mainly primes but also might limit the immune response. Multiple immune factors play a role in cancer progression and response to radiotherapy, including the immune tumor microenvironment and systemic immunity referred to as the immune landscape. A heterogeneous tumor microenvironment and the varying patient characteristics complicate the dynamic relationship between radiotherapy and this immune landscape. In this review, we will present the current overview of the immunological landscape in relation to radiotherapy in order to provide insight and encourage research to further improve cancer treatment. An investigation into the impact of radiation therapy on the immune landscape showed in several cancers a common pattern of immunological responses after radiation. Radiation leads to an upsurge in infiltrating T lymphocytes and the expression of programmed death ligand 1 (PD-L1) which can hint at a benefit for the patient when combined with immunotherapy. In spite of this, lymphopenia in the tumor microenvironment of 'cold' tumors or caused by radiation is considered to be an important obstacle to the patient's survival. In several cancers, a rise in the immunosuppressive populations is seen after radiation, mainly pro-tumoral M2 macrophages and myeloid-derived suppressor cells (MDSCs). As a final point, we will highlight how the radiation parameters themselves can influence the immune system and, therefore, be exploited to the advantage of the patient.
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Affiliation(s)
- Chrysanthi Iliadi
- Department of Radiation Oncology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (H.U.B), Brussels, Belgium
- Laboratory of Clinical and Experimental Oncology (LOCE), Institut Jules Bordet, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (H.U.B), Brussels, Belgium
| | - Laurine Verset
- Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (H.U.B), Brussels, Belgium
| | - Christelle Bouchart
- Department of Radiation Oncology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (H.U.B), Brussels, Belgium
| | - Philippe Martinive
- Department of Radiation Oncology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (H.U.B), Brussels, Belgium
| | - Dirk Van Gestel
- Department of Radiation Oncology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (H.U.B), Brussels, Belgium
| | - Mohammad Krayem
- Department of Radiation Oncology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (H.U.B), Brussels, Belgium
- Laboratory of Clinical and Experimental Oncology (LOCE), Institut Jules Bordet, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (H.U.B), Brussels, Belgium
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Zhang E, Ding C, Li S, Zhou X, Aikemu B, Fan X, Sun J, Zheng M, Yang X. Roles and mechanisms of tumour-infiltrating B cells in human cancer: a new force in immunotherapy. Biomark Res 2023; 11:28. [PMID: 36890557 PMCID: PMC9997025 DOI: 10.1186/s40364-023-00460-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/28/2023] [Indexed: 03/10/2023] Open
Abstract
Immune checkpoint inhibitors (ICIs) targeting PD-1 or PD-L1 have emerged as a revolutionary treatment strategy for human cancer patients. However, as the response rate to ICI therapy varies widely among different types of tumours, we are beginning to gain insight into the mechanisms as well as biomarkers of therapeutic response and resistance. Numerous studies have highlighted the dominant role of cytotoxic T cells in determining the treatment response to ICIs. Empowered by recent technical advances, such as single-cell sequencing, tumour-infiltrating B cells have been identified as a key regulator in several solid tumours by affecting tumour progression and the response to ICIs. In the current review, we summarized recent advances regarding the role and underlying mechanisms of B cells in human cancer and therapy. Some studies have shown that B-cell abundance in cancer is positively associated with favourable clinical outcomes, while others have indicated that they are tumour-promoting, implying that the biological function of B cells is a complex landscape. The molecular mechanisms involved multiple aspects of the functions of B cells, including the activation of CD8+ T cells, the secretion of antibodies and cytokines, and the facilitation of the antigen presentation process. In addition, other crucial mechanisms, such as the functions of regulatory B cells (Bregs) and plasma cells, are discussed. Here, by summarizing the advances and dilemmas of recent studies, we depicted the current landscape of B cells in cancers and paved the way for future research in this field.
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Affiliation(s)
- Enkui Zhang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chengsheng Ding
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Shuchun Li
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xueliang Zhou
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Batuer Aikemu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaodong Fan
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jing Sun
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Minhua Zheng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Department of General Surgery & Carson International Cancer Research Center, Shenzhen University General Hospital and Shenzhen University Clinical Medical Academy, Shenzhen, 518055, China.
| | - Xiao Yang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Shanghai Minimally Invasive Surgery Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Department of General Surgery & Carson International Cancer Research Center, Shenzhen University General Hospital and Shenzhen University Clinical Medical Academy, Shenzhen, 518055, China.
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5
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Zhang D, Zhao Y. Identification of natural killer cell associated subtyping and gene signature to predict prognosis and drug sensitivity of lung adenocarcinoma. Front Genet 2023; 14:1156230. [PMID: 37091780 PMCID: PMC10119412 DOI: 10.3389/fgene.2023.1156230] [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: 02/01/2023] [Accepted: 03/20/2023] [Indexed: 04/25/2023] Open
Abstract
Introduction: This research explored the immune characteristics of natural killer (NK) cells in lung adenocarcinoma (LUAD) and their predictive role on patient survival and immunotherapy response. Material and methods: Molecular subtyping of LUAD samples was performed by evaluating NK cell-associated pathways and genes in The Cancer Genome Atlas (TCGA) dataset using consistent clustering. 12 programmed cell death (PCD) patterns were acquired from previous study. Riskscore prognostic models were constructed using Least absolute shrinkage and selection operator (Lasso) and Cox regression. The model stability was validated in Gene Expression Omnibus database (GEO). Results: We classified LUAD into three different molecular subgroups based on NK cell-related genes, with the worst prognosis in C1 patients and the optimal in C3. Homologous Recombination Defects, purity and ploidy, TMB, LOH, Aneuploidy Score, were the most high-expressed in C1 and the least expressed in C3. ImmuneScore was the highest in C3 type, suggesting greater immune infiltration in C3 subtype. C1 subtypes had higher TIDE scores, indicating that C1 subtypes may benefit less from immunotherapy. Generally, C3 subtype presented highest PCD patterns scores. With four genes, ANLN, FAM83A, RHOV and PARP15, we constructed a LUAD risk prediction model with significant differences in immune cell composition, cell cycle related pathways between the two risk groups. Samples in C1 and high group were more sensitive to chemotherapy drug. The score of PCD were differences in high- and low-groups. Finally, we combined Riskscore and clinical features to improve the performance of the prediction model, and the calibration curve and decision curve verified that the great robustness of the model. Conclusion: We identified three stable molecular subtypes of LUAD and constructed a prognostic model based on NK cell-related genes, maybe have a greater potential for application in predicting immunotherapy response and patient prognosis.
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Affiliation(s)
- Dexin Zhang
- Respiratory Department of the Second Affiliated Hospital of Xi’an Jiaotong University Medical College, Xi’an, China
- *Correspondence: Dexin Zhang,
| | - Yujie Zhao
- Regional Marketing Department, Yuce Biotechnology Co, Ltd., Dabaihui Center, Shenzhen, China
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Zhao T, Gao P, Li Y, Tian H, Ma D, Sun N, Chen C, Zhang Y, Qi X. Investigating the role of FADS family members in breast cancer based on bioinformatic analysis and experimental validation. Front Immunol 2023; 14:1074242. [PMID: 37122728 PMCID: PMC10130515 DOI: 10.3389/fimmu.2023.1074242] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Breast cancer (BC) is the most common malignant tumor in women worldwide. Emerging evidence indicates the significance of fatty acid metabolism in BC. Fatty acid desaturase (FADS) is closely associated with cancer occurrence and development. Here, bioinformatic analysis and experimental validation were applied to investigate the potential functions of FADS in BC. Several public databases, including TCGA, GEO, HPA, Kaplan-Meier plotter, STRING, DAVID, cBioPortal, TIMER, TRRUST, and LinkedOmics were used to determine mRNA/protein expression levels, prognostic significance, functional enrichment, genetic alterations, association with tumor-infiltrating immune cells, and related transcription factors and kinases. BC tissues showed higher and lower mRNA expression of FADS2/6/8 and FADS3/4/5, respectively. FADS1/2/6 and FADS3/4/5 showed higher and lower protein expression levels, respectively, in BC tissues. Moreover, FADS1/7 up- and FADS3/8 down-regulation predicted poor overall and recurrence-free survival, while FADS2/5 up- and FADS4 down-regulation were associated with poor recurrence-free survival. Receiver operating characteristic curves revealed that FADS2/3/4/8 were indicative diagnostic markers. FADS family members showing differential expression levels were associated with various clinical subtypes, clinical stages, lymph node metastasis status, copy number variants, DNA methylation, and miRNA regulation in BC. The mRNA expression level of FADS1/2/3/4/5/7/8 was observed to be significantly negatively correlated with DNA methylation. FADS1/2 upregulation was significantly correlated with clinical stages. FADS1/4 expression was obviously lower in BC patients with higher lymph node metastasis than lower lymph node metastasis, while FADS7/8 expression was obviously higher in BC patients with higher lymph node metastasis than lower lymph node metastasis. FADS family members showed varying degrees of genetic alterations, and Gene Ontology and KEGG pathway enrichment analyses suggested their involvement in lipid metabolism. Their expression level was correlated with immune cell infiltration levels. FADS2 was chosen for further validation analyses. We found FADS2 to be significantly over-expressed in clinical BC tissue samples. The proliferation, migration, and invasion abilities of MDA-MB-231 and BT474 cells were significantly reduced after FADS2 knockdown. Furthermore, FADS2 may promote the occurrence and development of BC cells via regulating the epithelial-mesenchymal transition (EMT) pathway. Altogether, our results suggest that FADS1/2/3/4 can serve as potential therapeutic targets, prognostic indicators, and diagnostic markers in patients with BC.
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Affiliation(s)
- Tingting Zhao
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Pingping Gao
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Yanling Li
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Hao Tian
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Dandan Ma
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Na Sun
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Ceshi Chen
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
- Academy of Biomedical Engineering, Kunming Medical University, Kunming, China
- Yunnan Cancer Hospital & The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Center, Kunming, China
- *Correspondence: Xiaowei Qi, ; Yi Zhang, ; Ceshi Chen,
| | - Yi Zhang
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
- *Correspondence: Xiaowei Qi, ; Yi Zhang, ; Ceshi Chen,
| | - Xiaowei Qi
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
- *Correspondence: Xiaowei Qi, ; Yi Zhang, ; Ceshi Chen,
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Immunotherapeutic Value of Transcription Factor 19 (TCF19) Associated with Renal Clear Cell Carcinoma: A Comprehensive Analysis of 33 Human Cancer Cases. JOURNAL OF ONCOLOGY 2022; 2022:1488165. [PMID: 36111242 PMCID: PMC9470357 DOI: 10.1155/2022/1488165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 06/30/2022] [Accepted: 07/06/2022] [Indexed: 12/04/2022]
Abstract
Background We aimed to study the relationship between transcription factor 19 (TCF19) and cancer immunotherapy in the 33 types of human cancers. Methods The Cancer Genome Atlas database was analyzed to obtain the gene expression data and clinical characteristics for the cases of 33 types of cancers. GSE67501, GSE78220, and IMvigor 210 were included in the immunotherapy cohorts. Relevant data were obtained by analyzing the gene expression database. The prognostic value of TCF19 was determined by analyzing various clinical parameters, such as survival duration, age, the stage of the tumor, and sex of the patients. The single-sample gene set enrichment analysis method was used to determine the activity of TCF19 and the method was also used to assess the differences between the TCF19 transcriptome and protein levels. The correlation between TCF19 and various immune processes and elements such as immunosuppressants, stimulants, and major histocompatibility complexes were analyzed to gain insights into the role of TCF19. The coherent paths associated with the process of TCF19 signal transduction and the influence of TCF19 on immunotherapy biomarkers have also been discussed herein. Finally, three independent immunotherapy methods were used to understand the relationship between TCF19 and immunotherapy response. Results It was observed that TCF19 was not significantly influenced by the age (5/33), sex (3/33), or tumor stage (3/21) of cancer patients. But the results revealed that TCF19 exhibited a potential prognostic value and could predict the survival rate of the patients. In some cases of this study, the activity and expression of TCF19 were taken at the same level (7/33). Conclusion TCF19 is strongly related to immune cell infiltration, immunomodulators, and immunotherapy markers. Our study demonstrated that high expression levels of TCF19 are strongly linked with the immune-related pathways. Nevertheless, it is noteworthy that TCF19 is not significantly associated with immunotherapy response.
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Abstract
The tumor microenvironment (TME) is a heterogeneous, complex organization composed of tumor, stroma, and endothelial cells that is characterized by cross talk between tumor and innate and adaptive immune cells. Over the last decade, it has become increasingly clear that the immune cells in the TME play a critical role in controlling or promoting tumor growth. The function of T lymphocytes in this process has been well characterized. On the other hand, the function of B lymphocytes is less clear, although recent data from our group and others have strongly indicated a critical role for B cells in antitumor immunity. There are, however, a multitude of populations of B cells found within the TME, ranging from naive B cells all the way to terminally differentiated plasma cells and memory B cells. Here, we characterize the role of B cells in the TME in both animal models and patients, with an emphasis on dissecting how B cell heterogeneity contributes to the immune response to cancer.
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Affiliation(s)
- Stephanie M Downs-Canner
- Department of Surgery, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Jeremy Meier
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA;
| | - Benjamin G Vincent
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA; .,Bioinformatics and Computational Biology Program, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Jonathan S Serody
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA; .,Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
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Han L, Shi H, Ma S, Luo Y, Sun W, Li S, Zhang N, Jiang X, Gao Y, Huang Z, Xie C, Gong Y. Agrin Promotes Non-Small Cell Lung Cancer Progression and Stimulates Regulatory T Cells via Increasing IL-6 Secretion Through PI3K/AKT Pathway. Front Oncol 2022; 11:804418. [PMID: 35111682 PMCID: PMC8801576 DOI: 10.3389/fonc.2021.804418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/23/2021] [Indexed: 01/04/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) has high mortality rates worldwide. Agrin contributes to immune synapse information and is involved in tumor metastasis. However, its roles in NSCLC and tumor immune microenvironment remain unclear. This study examined the effects and the underlying mechanisms of Agrin in NSCLC and tumor-infiltrated immune cells. Clinical tissue samples were used to confirm the bioinformatic predictions. NSCLC cells were used to investigate the effects of Agrin on cell cycle and proliferation, as well as invasion and migration. Tumor xenograft mouse model was used to confirm the effects of Agrin on NSCLC growth and tumor-infiltrated regulatory T cells (Tregs) in vivo. Agrin levels in NSCLC cells were closely related to tumor progression and metastasis, and its function was enriched in the PI3K/AKT pathway. In vitro assays demonstrated that Agrin knockdown suppressed NSCLC cell proliferation and metastasis, while PI3K/AKT activators reversed the inhibitory effects of Agrin deficiency on NSCLC cell behaviors. Agrin expression was negatively associated with immunotherapy responses in NSCLC patients. Agrin knockdown suppressed Tregs, as well as interleukin (IL)-6 expression and secretion, while PI3K/AKT activators and exogenous IL-6 rescued the inhibitory effects. In the mouse model, Agrin downregulation alleviated NSCLC cell growth and Treg infiltration in vivo. Our results indicated that Agrin promotes tumor cell growth and Treg infiltration via increasing IL-6 expression and secretion through PI3K/AKT pathway in NSCLC. Our studies suggested Agrin as a therapeutically potential target to increase the efficacy of immunotherapy in NSCLC patients.
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Affiliation(s)
- Linzhi Han
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hongjie Shi
- Department of Thoracic and Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shijing Ma
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yuan Luo
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wenjie Sun
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shuying Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Nannan Zhang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xueping Jiang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yanping Gao
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhengrong Huang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yan Gong
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
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10
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Genova C, Dellepiane C, Carrega P, Sommariva S, Ferlazzo G, Pronzato P, Gangemi R, Filaci G, Coco S, Croce M. Therapeutic Implications of Tumor Microenvironment in Lung Cancer: Focus on Immune Checkpoint Blockade. Front Immunol 2022; 12:799455. [PMID: 35069581 PMCID: PMC8777268 DOI: 10.3389/fimmu.2021.799455] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022] Open
Abstract
In the last decade, the treatment of non-small cell lung cancer (NSCLC) has been revolutionized by the introduction of immune checkpoint inhibitors (ICI) directed against programmed death protein 1 (PD-1) and its ligand (PD-L1), or cytotoxic T lymphocyte antigen 4 (CTLA-4). In spite of these improvements, some patients do not achieve any benefit from ICI, and inevitably develop resistance to therapy over time. Tumor microenvironment (TME) might influence response to immunotherapy due to its prominent role in the multiple interactions between neoplastic cells and the immune system. Studies investigating lung cancer from the perspective of TME pointed out a complex scenario where tumor angiogenesis, soluble factors, immune suppressive/regulatory elements and cells composing TME itself participate to tumor growth. In this review, we point out the current state of knowledge involving the relationship between tumor cells and the components of TME in NSCLC as well as their interactions with immunotherapy providing an update on novel predictors of benefit from currently employed ICI or new therapeutic targets of investigational agents. In first place, increasing evidence suggests that TME might represent a promising biomarker of sensitivity to ICI, based on the presence of immune-modulating cells, such as Treg, myeloid derived suppressor cells, and tumor associated macrophages, which are known to induce an immunosuppressive environment, poorly responsive to ICI. Consequently, multiple clinical studies have been designed to influence TME towards a pro-immunogenic state and subsequently improve the activity of ICI. Currently, the mostly employed approach relies on the association of "classic" ICI targeting PD-1/PD-L1 and novel agents directed on molecules, such as LAG-3 and TIM-3. To date, some trials have already shown promising results, while a multitude of prospective studies are ongoing, and their results might significantly influence the future approach to cancer immunotherapy.
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Affiliation(s)
- Carlo Genova
- UO Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Dipartimento di Medicina Interna e Specialità Mediche (DIMI), Università degli Studi di Genova, Genova, Italy
| | - Chiara Dellepiane
- Lung Cancer Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Paolo Carrega
- Dipartimento di Patologia Umana, University of Messina, Messina, Italy
| | - Sara Sommariva
- SuPerconducting and Other INnovative Materials and Devices Institute, Consiglio Nazionale delle Ricerche (CNR-SPIN), Genova, Italy
- Life Science Computational Laboratory (LISCOMP), IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Guido Ferlazzo
- Dipartimento di Patologia Umana, University of Messina, Messina, Italy
| | - Paolo Pronzato
- UO Oncologia Medica 2, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Rosaria Gangemi
- UO Bioterapie, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Gilberto Filaci
- Dipartimento di Medicina Interna e Specialità Mediche (DIMI), Università degli Studi di Genova, Genova, Italy
- UO Bioterapie, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Simona Coco
- Lung Cancer Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Michela Croce
- UO Bioterapie, IRCCS Ospedale Policlinico San Martino, Genova, Italy
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11
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Sha H, Gan Y, Zou R, Wu J, Feng J. Research Advances in the Role of the Poly ADP Ribose Polymerase Family in Cancer. Front Oncol 2022; 11:790967. [PMID: 34976832 PMCID: PMC8716401 DOI: 10.3389/fonc.2021.790967] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/24/2021] [Indexed: 12/27/2022] Open
Abstract
Poly ADP ribose polymerases (PARPs) catalyze the modification of acceptor proteins, DNA, or RNA with ADP-ribose, which plays an important role in maintaining genomic stability and regulating signaling pathways. The rapid development of PARP1/2 inhibitors for the treatment of ovarian and breast cancers has advanced research on other PARP family members for the treatment of cancer. This paper reviews the role of PARP family members (except PARP1/2 and tankyrases) in cancer and the underlying regulatory mechanisms, which will establish a molecular basis for the clinical application of PARPs in the future.
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Affiliation(s)
- Huanhuan Sha
- Department of Chemotherapy, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yujie Gan
- Department of Chemotherapy, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Renrui Zou
- Department of Chemotherapy, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jianzhong Wu
- Research Center of Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jifeng Feng
- Department of Chemotherapy, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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12
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Lue JK, Downs-Canner S, Chaudhuri J. The role of B cells in the development, progression, and treatment of lymphomas and solid tumors. Adv Immunol 2022; 154:71-117. [PMID: 36038195 DOI: 10.1016/bs.ai.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
B cells are integral components of the mammalian immune response as they have the ability to generate antibodies against an almost infinite array of antigens. Over the past several decades, significant scientific progress has been made in understanding that this enormous B cell diversity contributes to pathogen clearance. However, our understanding of the humoral response to solid tumors and to tumor-specific antigens is unclear. In this review, we first discuss how B cells interact with other cells in the tumor microenvironment and influence the development and progression of various solid tumors. The ability of B lymphocytes to generate antibodies against a diverse repertoire of antigens and subsequently tailor the humoral immune response to specific pathogens relies on their ability to undergo genomic alterations during their development and differentiation. We will discuss key transforming events that lead to the development of B cell lymphomas. Overall, this review provides a foundation for innovative therapeutic interventions for both lymphoma and solid tumor malignancies.
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Affiliation(s)
- Jennifer K Lue
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
| | - Stephanie Downs-Canner
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
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13
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Benvenuto M, Focaccetti C, Ciuffa S, Fazi S, Bei A, Miele MT, Albonici L, Cifaldi L, Masuelli L, Bei R. Polyphenols affect the humoral response in cancer, infectious and allergic diseases and autoimmunity by modulating the activity of T H1 and T H2 cells. Curr Opin Pharmacol 2021; 60:315-330. [PMID: 34520942 DOI: 10.1016/j.coph.2021.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 12/25/2022]
Abstract
Polyphenols are a wide class of natural substances, pleiotropic molecules capable of modulating several processes, involved in the humoral and cellular immune response. The activation, differentiation of B cells, and production of antibodies to protein antigens by plasma cells depend on T helper (TH) CD4+ cells and secreted cytokines. Cancer, infectious, allergic, and autoimmune diseases are characterized by an imbalance of TH1/TH2 immunity and abnormal activation of the humoral response. Accordingly, polyphenols modulate the TH1/TH2 ratio, the secretion of multiple cytokines, the levels of antibodies, and therefore could contribute to recovering the state of health in these diseases. In this review, we summarize the current knowledge on the effects of polyphenols in modulating the humoral response in cancer, infectious and allergic diseases and in autoimmunity by affecting the activity of TH1 and TH2 cells.
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Affiliation(s)
- Monica Benvenuto
- Saint Camillus International University of Health and Medical Sciences, Via di Sant'Alessandro 8, 00131 Rome, Italy; Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
| | - Chiara Focaccetti
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy; Department of Human Science and Promotion of the Quality of Life, San Raffaele University Rome, Via di Val Cannuta 247, 00166 Rome, Italy
| | - Sara Ciuffa
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
| | - Sara Fazi
- Department of Experimental Medicine, University of Rome "Sapienza", Viale Regina Elena 324, 00161 Rome, Italy
| | - Arianna Bei
- Medical School, University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Martino Tony Miele
- Department of Experimental Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
| | - Loredana Albonici
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
| | - Loredana Cifaldi
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy; Academic Department of Pediatrics (DPUO), Ospedale Pediatrico Bambino Gesù, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - Laura Masuelli
- Department of Experimental Medicine, University of Rome "Sapienza", Viale Regina Elena 324, 00161 Rome, Italy
| | - Roberto Bei
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy.
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14
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Construction of an immune-related lncRNA signature as a novel prognosis biomarker for LUAD. Aging (Albany NY) 2021; 13:20684-20697. [PMID: 34438369 PMCID: PMC8436904 DOI: 10.18632/aging.203455] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/11/2021] [Indexed: 12/23/2022]
Abstract
The tumor immune microenvironment of lung cancer is associated with prognosis and immunotherapy efficacy. Long noncoding RNAs are identified as prognostic biomarkers associated with immune functions. We constructed a signature comprising differentially expressed immune-related lncRNAs to predict the prognosis of patients with lung adenocarcinoma. We established the immune-related lncRNA signature by pairing immune-related lncRNAs regardless of expression level and lung adenocarcinoma patients were divided into high- and low-risk groups. The prognosis of patients in the two groups was significantly different; The immune-related lncRNA signature could serve as an independent lung adenocarcinoma prognostic indicator. The signature correlated negatively with B cell, CD4+ T cell, M2 macrophage, neutrophil, and monocyte immune infiltration. Patients with low risk scores had a higher abundance of immune cells and stromal cells around the tumor. Gene set enrichment analysis showed that samples from low-risk group were more active in the IgA production in intestinal immune network and the T and B cell receptor signaling pathway. High-risk groups had significant involvement of the cell cycle, DNA replication, adherens junction, actin cytoskeleton regulation, pathways in cancer, and TGF-β signaling pathways. High risk scores correlated significantly negatively with high CTLA-4 and HAVCR2 expression and higher median inhibitory concentration of common anti-tumor chemotherapeutics (e.g., cisplatin, paclitaxel, gemcitabine) and targeted therapy (e.g., erlotinib and gefitinib). We identified a reliable immune-related lncRNA lung adenocarcinoma prognosis model, and the immune-related lncRNA signature showed promising clinical prediction value.
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15
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Wu G, Yan Y, Cai Y, Peng B, Li J, Huang J, Xu Z, Zhou J. ALKBH1-8 and FTO: Potential Therapeutic Targets and Prognostic Biomarkers in Lung Adenocarcinoma Pathogenesis. Front Cell Dev Biol 2021; 9:633927. [PMID: 34150745 PMCID: PMC8209387 DOI: 10.3389/fcell.2021.633927] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 05/03/2021] [Indexed: 02/05/2023] Open
Abstract
The AlkB family consists of Fe(II)- and α-ketoglutarate-dependent dioxygenases that can catalyze demethylation on a variety of substrates, such as RNA and DNA, subsequently affecting tumor progression and prognosis. However, their detailed functional roles in lung adenocarcinoma (LUAD) have not been clarified in a comprehensive manner. In this study, several bioinformatics databases, such as ONCOMINE, TIMER, and DiseaseMeth, were used to evaluate the expression profiles and prognostic significance of the AlkB family (ALKBH1-8 and FTO) in LUAD. The expression levels of ALKBH1/2/4/5/7/8 were significantly increased in LUAD tissues, while the expression levels of ALKBH3/6 and FTO were decreased. The main functions of differentially expressed AlkB homologs are related to the hematopoietic system and cell adhesion molecules. We also found that the expression profiles of the AlkB family are highly correlated with infiltrating immune cells (i.e., B cells, CD8 + T cells, CD4 + T cells, macrophages, neutrophils and dendritic cells). In addition, DNA methylation analysis indicated that the global methylation levels of ALKBH1/2/4/5/6/8 and FTO were decreased, while the global methylation levels of ALKBH3/7 were increased. In addition, the patients with upregulated ALKBH2 have significantly poor overall survival (OS) and post-progressive survival (PPS). Taken together, our work could provide insightful information about aberrant AlkB family members as potential biomarkers for the diagnostic and prognostic evaluation of LUAD. Especially, ALKBH2 could be served as a therapeutic candidate for treating LUAD.
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Affiliation(s)
- Geting Wu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Juanni Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN, United States
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jianhua Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
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16
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Yu P, Tong L, Song Y, Qu H, Chen Y. Systematic profiling of invasion-related gene signature predicts prognostic features of lung adenocarcinoma. J Cell Mol Med 2021; 25:6388-6402. [PMID: 34060213 PMCID: PMC8256358 DOI: 10.1111/jcmm.16619] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/17/2022] Open
Abstract
Due to the high heterogeneity of lung adenocarcinoma (LUAD), molecular subtype based on gene expression profiles is of great significance for diagnosis and prognosis prediction in patients with LUAD. Invasion-related genes were obtained from the CancerSEA database, and LUAD expression profiles were downloaded from The Cancer Genome Atlas. The ConsensusClusterPlus was used to obtain molecular subtypes based on invasion-related genes. The limma software package was used to identify differentially expressed genes (DEGs). A multi-gene risk model was constructed by Lasso-Cox analysis. A nomogram was also constructed based on risk scores and meaningful clinical features. 3 subtypes (C1, C2 and C3) based on the expression of 97 invasion-related genes were obtained. C3 had the worst prognosis. A total of 669 DEGs were identified among the subtypes. Pathway enrichment analysis results showed that the DEGs were mainly enriched in the cell cycle, DNA replication, the p53 signalling pathway and other tumour-related pathways. A 5-gene signature (KRT6A, MELTF, IRX5, MS4A1 and CRTAC1) was identified by using Lasso-Cox analysis. The training, validation and external independent cohorts proved that the model was robust and had better prediction ability than other lung cancer models. The gene expression results showed that the expression levels of MS4A1 and KRT6A in tumour tissues were higher than in normal tissues, while CRTAC1 expression in tumour tissues was lower than in normal tissues. The 5-gene signature prognostic stratification system based on invasion-related genes could be used to assess prognostic risk in patients with LUAD.
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Affiliation(s)
- Ping Yu
- Department of Medical OncologyThe First Hospital of China Medical UniversityShenyangChina
- Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning ProvinceThe First Hospital of China Medical UniversityShenyangChina
- Liaoning Province Clinical Research Center for CancerShenyangChina
| | - Linlin Tong
- Department of Medical OncologyThe First Hospital of China Medical UniversityShenyangChina
- Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning ProvinceThe First Hospital of China Medical UniversityShenyangChina
- Liaoning Province Clinical Research Center for CancerShenyangChina
| | - Yujia Song
- Department of Medical OncologyThe First Hospital of China Medical UniversityShenyangChina
| | - Hui Qu
- Department of Medical OncologyThe First Hospital of China Medical UniversityShenyangChina
| | - Ying Chen
- Department of Medical OncologyThe First Hospital of China Medical UniversityShenyangChina
- Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning ProvinceThe First Hospital of China Medical UniversityShenyangChina
- Liaoning Province Clinical Research Center for CancerShenyangChina
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