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Lavoro A, Falzone L, Gattuso G, Conti GN, Caltabiano R, Madonna G, Capone M, McCubrey JA, Ascierto PA, Libra M, Candido S. Identification of SLC22A17 DNA methylation hotspot as a potential biomarker in cutaneous melanoma. J Transl Med 2024; 22:887. [PMID: 39358721 PMCID: PMC11445995 DOI: 10.1186/s12967-024-05622-9] [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: 06/05/2024] [Accepted: 08/18/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Cancer onset and progression are driven by genetic and epigenetic alterations leading to oncogene activation and the silencing of tumor suppressor genes. Among epigenetic mechanisms, DNA methylation (methDNA) is gaining growing interest in cancer. Promoter hypomethylation is associated with oncogene activation while intragenic methDNA can be involved in transcriptional elongation, alternative spicing, and the activation of cryptic start sites. Several genes involved in the modulation of the tumor microenvironment are regulated by methDNA, including the Solute Carrier Family 22 Member 17 (SLC22A17), which is involved in iron trafficking and extracellular matrix remodeling cooperating with the Gelatinase-Associated Lipocalin (NGAL) ligand. However, the exact role of intragenic methDNA in cancer has not been fully investigated. Therefore, the aim of the present study is to explore the role of methDNA in the regulation of SLC22A17 in cutaneous melanoma (CM), used as a tumor model. METHODS Correlation and differential analyses between SLC22A17 expression and methDNA were performed using the data contained in The Cancer Genome Atlas and Gene Expression Omnibus databases. Functional studies on melanoma cell lines treated with 5-Azacytidine (5-Aza) were conducted to assess the correlation between methDNA and SLC22A17 expression. A validation study on the diagnostic potential of the in silico-identified SLC22A17 methDNA hotspot was finally performed by analyzing tissue samples obtained from CM patients and healthy controls. RESULTS The computational analyses revealed that SLC22A17 was significantly downregulated in CM, and its expression was related to promoter hypomethylation and intragenic hypermethylation. Moreover, SLC22A17 overexpression and hypermethylation of two intragenic methDNA hotspots were associated with a better clinical outcome in CM patients. The correlation between SLC22A17 methDNA and expression was confirmed in 5-Aza-treated cells. In agreement with in silico analyses, the SLC22A17 promoter methylation hotspot showed higher methDNA levels in CM samples compared to nevi. In addition, the methDNA levels of this hotspot were positively correlated with advanced CM. CONCLUSIONS The SLC22A17 methDNA hotspot could represent a promising biomarker for CM, highlighting the regulatory role of methDNA on SLC22A17 expression. These results pave the way for the identification of novel epigenetic biomarkers and therapeutic targets for the management of CM patients.
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Affiliation(s)
- Alessandro Lavoro
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, I-95123, Italy
| | - Luca Falzone
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, I-95123, Italy.
| | - Giuseppe Gattuso
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, I-95123, Italy
| | - Giuseppe N Conti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, I-95123, Italy
| | - Rosario Caltabiano
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", University of Catania, Catania, I-95123, Italy
| | - Gabriele Madonna
- Melanoma Cancer Immunotherapy and Innovative Therapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, I-80131, Italy
| | - Mariaelena Capone
- Melanoma Cancer Immunotherapy and Innovative Therapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, I-80131, Italy
| | - James A McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, 27858, USA
| | - Paolo A Ascierto
- Melanoma Cancer Immunotherapy and Innovative Therapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, I-80131, Italy
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, I-95123, Italy.
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, Catania, I- 95123, Italy.
| | - Saverio Candido
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, I-95123, Italy
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, Catania, I- 95123, Italy
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Shao L, Yu H, Wang M, Chen L, Ji B, Wu T, Teng X, Su M, Han X, Shi W, Hu X, Wang Z, He H, Han G, Zhang Y, Wu Q. DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression. Cell Death Dis 2024; 15:566. [PMID: 39107271 PMCID: PMC11303742 DOI: 10.1038/s41419-024-06915-z] [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: 02/21/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 08/09/2024]
Abstract
Super-enhancers are a class of DNA cis-regulatory elements that can regulate cell identity, cell fate, stem cell pluripotency, and even tumorigenesis. Increasing evidence shows that epigenetic modifications play an important role in the pathogenesis of various types of cancer. However, the current research is far from enough to reveal the complex mechanism behind it. This study found a super-enhancer enriched with abnormally active histone modifications in pancreatic ductal adenocarcinoma (PDAC), called DKK1-super-enhancer (DKK1-SE). The major active component of DKK1-SE is component enhancer e1. Mechanistically, AP1 induces chromatin remodeling in component enhancer e1 and activates the transcriptional activity of DKK1. Moreover, DKK1 was closely related to the malignant clinical features of PDAC. Deletion or knockdown of DKK1-SE significantly inhibited the proliferation, colony formation, motility, migration, and invasion of PDAC cells in vitro, and these phenomena were partly mitigated upon rescuing DKK1 expression. In vivo, DKK1-SE deficiency not only inhibited tumor proliferation but also reduced the complexity of the tumor microenvironment. This study identifies that DKK1-SE drives DKK1 expression by recruiting AP1 transcription factors, exerting oncogenic effects in PDAC, and enhancing the complexity of the tumor microenvironment.
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Affiliation(s)
- Lan Shao
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Haoran Yu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Mengyun Wang
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Lu Chen
- Department of Pathology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Boshu Ji
- Department of Pathology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Xiangqi Teng
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Mu Su
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Xiao Han
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Weikai Shi
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Xin Hu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Ziwen Wang
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Hongjuan He
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Guiping Han
- Department of Pathology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yan Zhang
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Qiong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China.
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Ye Z, Xu J, Zhang X, Zhang Y, Ivanova D, Lu W, Zhang J, Li F, Chen X, Wang Y, Wang M, Xie B. Identification and Validation of Tumor Microenvironment-Associated Signature in Clear-Cell Renal Cell Carcinoma through Integration of DNA Methylation and Gene Expression. Int J Mol Sci 2024; 25:6792. [PMID: 38928496 PMCID: PMC11203551 DOI: 10.3390/ijms25126792] [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: 05/17/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
The tumor microenvironment (TME) is crucial in tumor development, metastasis, and response to immunotherapy. DNA methylation can regulate the TME without altering the DNA sequence. However, research on the methylation-driven TME in clear-cell renal cell carcinoma (ccRCC) is still lacking. In this study, integrated DNA methylation and RNA-seq data were used to explore methylation-driven genes (MDGs). Immune scores were calculated using the ESTIMATE, which was employed to identify TME-related genes. A new signature connected with methylation-regulated TME using univariate, multivariate Cox regression and LASSO regression analyses was developed. This signature consists of four TME-MDGs, including AJAP1, HOXB9, MYH14, and SLC6A19, which exhibit high methylation and low expression in tumors. Validation was performed using qRT-PCR which confirmed their downregulation in ccRCC clinical samples. Additionally, the signature demonstrated stable predictive performance in different subtypes of ccRCC. Risk scores are positively correlated with TMN stages, immune cell infiltration, tumor mutation burden, and adverse outcomes of immunotherapy. Interestingly, the expression of four TME-MDGs are highly correlated with the sensitivity of first-line drugs in ccRCC treatment, especially pazopanib. Molecular docking indicates a high affinity binding between the proteins and pazopanib. In summary, our study elucidates the comprehensive role of methylation-driven TME in ccRCC, aiding in identifying patients sensitive to immunotherapy and targeted therapy, and providing new therapeutic targets for ccRCC treatment.
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Affiliation(s)
- Zijian Ye
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China (J.X.); (X.Z.); (Y.Z.); (W.L.); (J.Z.)
- Department of Biostatistics, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Jialiang Xu
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China (J.X.); (X.Z.); (Y.Z.); (W.L.); (J.Z.)
- Joint International Research Laboratory of Reproduction, Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China; (F.L.); (X.C.); (Y.W.)
| | - Xin Zhang
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China (J.X.); (X.Z.); (Y.Z.); (W.L.); (J.Z.)
| | - Yifan Zhang
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China (J.X.); (X.Z.); (Y.Z.); (W.L.); (J.Z.)
- Department of Biostatistics, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Deyana Ivanova
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
| | - Weiyu Lu
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China (J.X.); (X.Z.); (Y.Z.); (W.L.); (J.Z.)
| | - Jianning Zhang
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China (J.X.); (X.Z.); (Y.Z.); (W.L.); (J.Z.)
- Department of Biostatistics, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Fangfang Li
- Joint International Research Laboratory of Reproduction, Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China; (F.L.); (X.C.); (Y.W.)
| | - Xuemei Chen
- Joint International Research Laboratory of Reproduction, Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China; (F.L.); (X.C.); (Y.W.)
| | - Yingxiong Wang
- Joint International Research Laboratory of Reproduction, Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China; (F.L.); (X.C.); (Y.W.)
| | - Meijiao Wang
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China (J.X.); (X.Z.); (Y.Z.); (W.L.); (J.Z.)
- Joint International Research Laboratory of Reproduction, Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing 400016, China; (F.L.); (X.C.); (Y.W.)
| | - Biao Xie
- Department of Biostatistics, School of Public Health, Chongqing Medical University, Chongqing 400016, China
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Tang Y, Cui G, Liu H, Han Y, Cai C, Feng Z, Shen H, Zeng S. Converting "cold" to "hot": epigenetics strategies to improve immune therapy effect by regulating tumor-associated immune suppressive cells. Cancer Commun (Lond) 2024; 44:601-636. [PMID: 38715348 PMCID: PMC11194457 DOI: 10.1002/cac2.12546] [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: 11/13/2023] [Revised: 04/09/2024] [Accepted: 04/18/2024] [Indexed: 06/26/2024] Open
Abstract
Significant developments in cancer treatment have been made since the advent of immune therapies. However, there are still some patients with malignant tumors who do not benefit from immunotherapy. Tumors without immunogenicity are called "cold" tumors which are unresponsive to immunotherapy, and the opposite are "hot" tumors. Immune suppressive cells (ISCs) refer to cells which can inhibit the immune response such as tumor-associated macrophages (TAMs), myeloid-derived suppressor cells (MDSCs), regulatory T (Treg) cells and so on. The more ISCs infiltrated, the weaker the immunogenicity of the tumor, showing the characteristics of "cold" tumor. The dysfunction of ISCs in the tumor microenvironment (TME) may play essential roles in insensitive therapeutic reaction. Previous studies have found that epigenetic mechanisms play an important role in the regulation of ISCs. Regulating ISCs may be a new approach to transforming "cold" tumors into "hot" tumors. Here, we focused on the function of ISCs in the TME and discussed how epigenetics is involved in regulating ISCs. In addition, we summarized the mechanisms by which the epigenetic drugs convert immunotherapy-insensitive tumors into immunotherapy-sensitive tumors which would be an innovative tendency for future immunotherapy in "cold" tumor.
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Affiliation(s)
- Yijia Tang
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Guangzu Cui
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Haicong Liu
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Ying Han
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Changjing Cai
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Ziyang Feng
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
| | - Hong Shen
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
- National Clinical Resaerch Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangshaHunanChina
| | - Shan Zeng
- Department of OncologyXiangya HospitalCentral South UniversityChangshaHunanP. R. China
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Malavasi E, Adamo M, Zamprogno E, Vella V, Giamas G, Gagliano T. Decoding the Tumour Microenvironment: Molecular Players, Pathways, and Therapeutic Targets in Cancer Treatment. Cancers (Basel) 2024; 16:626. [PMID: 38339377 PMCID: PMC10854614 DOI: 10.3390/cancers16030626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/16/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
The tumour microenvironment (TME) is a complex and constantly evolving collection of cells and extracellular components. Cancer cells and the surrounding environment influence each other through different types of processes. Characteristics of the TME include abnormal vasculature, altered extracellular matrix, cancer-associated fibroblast and macrophages, immune cells, and secreted factors. Within these components, several molecules and pathways are altered and take part in the support of the tumour. Epigenetic regulation, kinases, phosphatases, metabolic regulators, and hormones are some of the players that influence and contribute to shaping the tumour and the TME. All these characteristics contribute significantly to cancer progression, metastasis, and immune escape, and may be the target for new approaches for cancer treatment.
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Affiliation(s)
- Eleonora Malavasi
- Cancer Cell Signalling Laboratory, Department of Medicine, University of Udine, 33100 Udine, Italy; (E.M.); (M.A.); (E.Z.)
| | - Manuel Adamo
- Cancer Cell Signalling Laboratory, Department of Medicine, University of Udine, 33100 Udine, Italy; (E.M.); (M.A.); (E.Z.)
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK;
| | - Elisa Zamprogno
- Cancer Cell Signalling Laboratory, Department of Medicine, University of Udine, 33100 Udine, Italy; (E.M.); (M.A.); (E.Z.)
| | - Viviana Vella
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK;
| | - Georgios Giamas
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK;
| | - Teresa Gagliano
- Cancer Cell Signalling Laboratory, Department of Medicine, University of Udine, 33100 Udine, Italy; (E.M.); (M.A.); (E.Z.)
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Li L, Li S, Zhang X, Mei L, Fu X, Dai M, Wei N. Establishing the role of BRCA1 in the diagnosis, prognosis and immune infiltrates of breast invasive cancer by bioinformatics analysis and experimental validation. Aging (Albany NY) 2024; 16:1077-1095. [PMID: 38224491 PMCID: PMC10866431 DOI: 10.18632/aging.205366] [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: 09/08/2023] [Accepted: 11/16/2023] [Indexed: 01/17/2024]
Abstract
BACKGROUND Breast cancer susceptibility gene 1 (BRCA1) is a well-known gene that acts a vital role in suppressing the growth of tumors. Previous studies have primarily focused on the genetic mutations of BRCA1 and its association with hereditary breast invasive carcinoma (BRCA). However, little research has been done to investigate the relationship between BRCA1 and immune infiltrates and prognosis in BRCA. METHODS We obtained the expression profiles and clinical information of patients with BRCA from the Cancer Genome Atlas (TCGA) database. The levels of the BRCA1 gene between BRCA tissues and normal breast tissues were compared through the Wilcoxon rank-sum test. Additionally, we performed WB and RT-qPCR techniques to detect the expression of BRCA1. We conducted functional enrichment analyses. Furthermore, we assessed immune cell infiltration using a single-sample gene set enrichment analysis. The methylation status of the BRCA1 gene was analyzed using the UALCAN and MethSurv databases. The Cox regression analysis and (KM) Kaplan-Meier method were employed to determine the prognostic value of BRCA1. In order to provide a practical tool for predicting the overall survival rates at different time points, we also constructed a nomogram. RESULTS Our analysis revealed that the expression of BRCA1 was significantly higher in BRCA tissues compared to normal tissues. Furthermore, this increased level of BRCA1 was found to be associated with specific BRCA subtypes, including T2, stage II, ER positive, ect. Importantly, the overexpression of BRCA1 was shown to be a negative prognostic marker for the overall survival rates of BRCA patients. Moreover, low methylation status of the BRCA1 gene was related to a poorer prognosis. Furthermore, our results indicated that high levels of BRCA1 are related to a decrease in level of killer immune cells, such as natural killer (NK) cells, macrophages, CD8+ T cells, and plasma-like dendritic cells (pDCs) within the tumor microenvironment. CONCLUSIONS Our study is the first to provide evidence indicating that the presence of BRCA1 can serve as a reliable marker for both diagnosing and determining the prognosis of BRCA. Moreover, BRCA1 acts as a crucial indicator of the cancer's potential to infiltrate and invade the immune system, which has important implications for developing targeted therapies in BRCA.
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Affiliation(s)
- Leilei Li
- Department of Pathology, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Shuangyan Li
- Department of Oncology, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Xuyang Zhang
- Department of Hepatobiliary, Second Affiliated Hospital of Zunyi Medical University, Zunyi 563000, Guizhou, China
| | - Liying Mei
- Department of Breast Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, Guizhou, China
| | - Xueqin Fu
- Department of Breast Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, Guizhou, China
| | - Min Dai
- Department of Breast Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, Guizhou, China
| | - Na Wei
- Department of Breast Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, Guizhou, China
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Wang T, Li P, Qi Q, Zhang S, Xie Y, Wang J, Liu S, Ma S, Li S, Gong T, Xu H, Xiong M, Li G, You C, Luo Z, Li J, Du L, Wang C. A multiplex blood-based assay targeting DNA methylation in PBMCs enables early detection of breast cancer. Nat Commun 2023; 14:4724. [PMID: 37550304 PMCID: PMC10406825 DOI: 10.1038/s41467-023-40389-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/21/2023] [Indexed: 08/09/2023] Open
Abstract
The immune system can monitor tumor development, and DNA methylation is involved in the body's immune response to tumors. In this work, we investigate whether DNA methylation alterations in peripheral blood mononuclear cells (PBMCs) could be used as markers for early detection of breast cancer (BC) from the perspective of tumor immune alterations. We identify four BC-specific methylation markers by combining Infinium 850 K BeadChips, pyrosequencing and targeted bisulfite sequencing. Based on the four methylation markers in PBMCs of BC, we develop an efficient and convenient multiplex methylation-specific quantitative PCR assay for the detection of BC and validate its diagnostic performance in a multicenter cohort. This assay was able to distinguish early-stage BC patients from normal controls, with an AUC of 0.940, sensitivity of 93.2%, and specificity of 90.4%. More importantly, this assay outperformed existing clinical diagnostic methods, especially in the detection of early-stage and minimal tumors.
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Affiliation(s)
- Tiantian Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China
| | - Peilong Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China
| | - Qiuchen Qi
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China
| | - Shujun Zhang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China
| | - Yan Xie
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China
| | - Jing Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China
| | - Shibiao Liu
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China
| | - Suhong Ma
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China
| | - Shijun Li
- Clinical Laboratory, The First Hospital of Dalian Medical University, Dalian, 116011, P. R. China
| | - Tingting Gong
- Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, P. R. China
| | - Huiting Xu
- Departmemt of Clinical Laboratory Medicine, Affiliated Tumor Hospital of Nantong University, 226361, Jiangsu, China; Medical School of Nantong University, Nantong, 226001, P. R. China
| | - Mengqiu Xiong
- Clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, P. R. China
| | - Guanghua Li
- Department of clinical laboratory, Guangdong Provincial People's Hospital/Guangdong Academy of Medical Sciences, Guangzhou, 510000, P. R. China
| | - Chongge You
- Laboratory Medicine Center, Lanzhou University Second Hospital, the Second Clinical Medical College of Lanzhou University, Lanzhou, 730000, P. R. China
| | - Zhaofan Luo
- Department of Clinical Laboratory, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, 518107, P. R. China
| | - Juan Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China.
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China.
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Provincial Key Laboratory of Innovation Technology in Laboratory Medicine, Jinan, 250012, P. R. China.
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China.
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, China.
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, China.
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Fan Z, Wu S, Sang H, Li Q, Cheng S, Zhu H. Identification of GPD1L as a Potential Prognosis Biomarker and Associated with Immune Infiltrates in Lung Adenocarcinoma. Mediators Inflamm 2023; 2023:9162249. [PMID: 37035759 PMCID: PMC10079383 DOI: 10.1155/2023/9162249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/01/2022] [Accepted: 03/18/2023] [Indexed: 04/03/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is one of the most prevalent pathological kinds of lung cancer, which is a common form of cancer that has a high death rate. Over the past several years, growing studies have indicated that GPD1L was involved in the advancement of a number of different cancers. However, its clinical significance in LUAD has not been investigated. In this study, following an examination of the TGCA datasets, we found that GPD1L displayed a dysregulated state in a wide variety of cancers; this led us to believe that GPD1L is an essential regulator in the progression of malignancies. In addition, we found that the expression of GPD1L was much lower in LUAD tissues when compared with nontumor specimens. According to the findings of ROC tests, GPD1L was able to effectively identify LUAD specimens from nontumor samples with an AUC value of 0.828 (95% confidence interval: 0.793 to 0.863). On the basis of the clinical study, a low expression of GPD1L was clearly related with both the N stage and the clinical stage. Moreover, based on the findings of a Kaplan-Meier survival study, elevated GPD1L expression was a strong indicator of considerably improved overall survival (OS) and disease-specific survival (DSS). GPD1L expression and clinical stages were found to be independent prognostic indicators for overall survival and disease-free survival in LUAD patients, according to multivariate analyses. Based on multivariate analysis, the C-indexes and calibration plots of the nomogram demonstrated an effective prediction performance for LUAD patients. Besides, the expression of GPD1L was positively related to mast cells, eosinophils, Tcm, TFH, iDC, DC, and macrophages, while negatively associated with Th2 cells, NK CD56dim cells, Tgd, Treg, and neutrophils. Finally, qRT-PCR was able to demonstrate that GPD1L had a significant amount of expression in LUAD. Additionally, according to the results of functional tests, overexpression of GPD1L had a significant inhibiting effect on the proliferation of LUAD cells. In general, the results of our study suggested that GPD1L had the potential to serve as a diagnostic and prognostic marker for LUAD.
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Song Y, Gao N, Yang Z, Zhang S, Fan T, Zhang B. COX7B Is a New Prognostic Biomarker and Correlates with Tumor Immunity in Esophageal Carcinoma. Mediators Inflamm 2023. [DOI: 10.1155/2023/6831695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
Esophageal carcinoma (ESCA) refers to the most common type of malignant tumor, which reveals that it occurs often all over the world. ESCA is also correlated with an advanced stage and low survival rates. Thus, the development of new prognostic biomarkers is an absolute necessity. In this study, the aim was to investigate the potential of COX7B as a brand-new predictive biomarker for ESCA patients. COX7B expression in pancancer was examined using TIMER2. The statistical significance of the predictive value of COX7B expression was explored. The relationship between COX7B expression and tumor-infiltrating immune cells in ESCA was analyzed by using ssGSEA. In this study, the result indicated that several types of cancers had an abnormally high amount of COX7B. COX7B expression in samples from patients with ESCA was considerably higher than in nontumor tissues. A more advanced clinical stage may be anticipated from higher COX7B expression. According to the findings of Kaplan-Meier survival curves, patients with low COX7B levels had a more favorable prognosis than those with high COX7B levels. The result of multivariate analysis suggested that COX7B expression was a standalone prognostic factor for the overall survival of ESCA patients. A prognostic nomogram including gender, clinical stage, and COX7B expression was constructed, and TCGA-based calibration plots indicated its excellent predictive performance. An analysis of immune infiltration revealed that COX7B expression has a negative correlation with TFH, Tcm, NK cells, and mast cells. COX7B may serve as an immunotherapy target and as a biomarker for ESCA diagnosis and prognosis.
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10
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Co-Targeting Luminal B Breast Cancer with S-Adenosylmethionine and Immune Checkpoint Inhibitor Reduces Primary Tumor Growth and Progression, and Metastasis to Lungs and Bone. Cancers (Basel) 2022; 15:cancers15010048. [PMID: 36612044 PMCID: PMC9818024 DOI: 10.3390/cancers15010048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BCa) is the most prevalent cancer in females and has a high rate of mortality, especially due to increased metastasis to skeletal and non-skeletal sites. Despite the marked clinical accomplishment of immune checkpoint inhibitor (CPI) therapy in patients with several cancers, it has had limited success in luminal subtypes of BCa. Accordingly, recent efforts have focused on combination therapy with CPI, including epigenetic modulators, to increase response rates of CPI in luminal BCa. We have previously shown that S-adenosylmethionine (SAM), the ubiquitous methyl donor, has strong anti-cancer effects in various cancers, including all subtypes of BCa. In the current study, we took a novel approach and examined the effect of CPI alone and in combination with SAM on tumor growth and metastasis in a syngeneic mouse model of luminal B BCa. We showed that SAM decreases cell proliferation, colony-formation (survival), and invasion of luminal B BCa cell lines (Eo771, R221A) in vitro. In in vivo studies, in Eo771 tumor-bearing mice, either SAM or anti-PD-1 antibody treatment alone significantly reduced tumor growth and progression, while the SAM+anti-PD-1 combination treatment had the highest anti-cancer efficacy of all groups. The SAM+anti-PD-1 combination reduced the percentage of animals with lung metastasis, as well as total metastatic lesion area, compared to control. Additionally, the SAM+anti-PD-1 combination significantly reduced the skeletal lesion area and protected tibial integrity to a greater extent than the monotherapies in an Eo771 bone metastasis model. Transcriptome analysis of Eo771 primary tumors revealed significant downregulation of pro-metastatic genes, including Matrix metalloproteinases (MMPs) and related pathways. On the other hand, CD8+ T cell infiltration, CD8+ T cell cytotoxicity (elevated granzymes), and immunostimulatory genes and pathways were significantly upregulated by the combination treatment. The results presented point to a combination of SAM with CPI as a possible treatment for luminal B BCa that should be tested in clinical studies.
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11
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The cell-free DNA methylome captures distinctions between localized and metastatic prostate tumors. Nat Commun 2022; 13:6467. [PMID: 36309516 PMCID: PMC9617856 DOI: 10.1038/s41467-022-34012-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
Metastatic prostate cancer remains a major clinical challenge and metastatic lesions are highly heterogeneous and difficult to biopsy. Liquid biopsy provides opportunities to gain insights into the underlying biology. Here, using the highly sensitive enrichment-based sequencing technology, we provide analysis of 60 and 175 plasma DNA methylomes from patients with localized and metastatic prostate cancer, respectively. We show that the cell-free DNA methylome can capture variations beyond the tumor. A global hypermethylation in metastatic samples is observed, coupled with hypomethylation in the pericentromeric regions. Hypermethylation at the promoter of a glucocorticoid receptor gene NR3C1 is associated with a decreased immune signature. The cell-free DNA methylome is reflective of clinical outcomes and can distinguish different disease types with 0.989 prediction accuracy. Finally, we show the ability of predicting copy number alterations from the data, providing opportunities for joint genetic and epigenetic analysis on limited biological samples.
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12
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Cao L, Wu W, Deng X, Peng Y, Chen Y, Guo H, Wang L, Li X, Zhang Z, Shao Z. Systematic pan-cancer analysis of the nicotinamide n-methyltransferase in human cancer. Front Genet 2022; 13:1000515. [DOI: 10.3389/fgene.2022.1000515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022] Open
Abstract
In several tumors, Nicotinamide N-Methyltransferase (NNMT) was identified as a bridge between methylation metabolism and tumorigenesis and was associated with a poor prognosis. This research aims is to study the prognostic value of NNMT in cancer, its relationship with DNA methylation, and the immune microenvironment. On the basis of the Cancer Genome Atlas and the Cancer Cell Line Encyclopedia, Genotype Tissue-Expression, cBioPortal, Cellminer, Gene Expression Profiling Interactive Analysis, Human Protein Atlas and Clinical Proteomic Tumor Analysis Consortium, we used a series of bioinformatics strategies to investigate the potential carcinogenicity of NNMT, including the relationship between NNMT expression and prognosis, tumor mutational burden, microsatellite instability, and sensitivity analysis of anticancer drugs. The GeneMANIA, STRING, and BioGRID databases were examined for protein-protein interactions, and Gene Ontology and the Kyoto Encyclopedia of Genes were used to infer the signal pathway. The results indicated that NNMT was significantly expressed in several tumor tissues compared to the matching non-tumor tissues. Increased NNMT expression was linked to reduced OS, DSS, and DFI. In addition, there was a link between NNMT expression and TMB and MSI in 18 cancer types, and between NNMT expression and DNA methylation in 23 cancer types. Further study of NNMT gene alteration data revealed that deletion was the most prevalent form of NNMT mutation, and that there was a significant negative association between NNMT expression and mismatch repair genes. In addition, there was a strong positive connection between NNMT and immune infiltration in 28 types of tumors, and the immune cells that infiltrated the tumors displayed a characteristic NNMT pattern. According to the enrichment study, cell migration, cell motility, and cell adhesion were highly enriched in biological processes, and NNMT may be associated with the PI3K-Akt signaling pathway. By downregulating gene methylation or impacting the immunological microenvironment widely, NNMT may drive carcinogenesis and cause a poor prognosis. Our research showed that NNMT could be used as a biomarker of tumor immune infiltration and poor prognosis, thus providing a unique strategy for cancer therapy.
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Luo H, Ye M, Hu Y, Wu M, Cheng M, Zhu X, Huang K. DNA methylation regulator-mediated modification patterns and tumor microenvironment characterization in glioma. Aging (Albany NY) 2022; 14:7824-7850. [PMID: 36152044 PMCID: PMC9596205 DOI: 10.18632/aging.204291] [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: 06/16/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022]
Abstract
Growing evidences indicate DNA methylation plays a crucial regulatory role in inflammation, innate immunity, and immunotherapy. However, the overall landscape of various DNA methylation regulatory genes and their relationship with the infiltration of immune cells into the tumor microenvironment (TME) as well as the response to immunotherapy in gliomas is still not clear. Therefore, we comprehensively analyzed the correlation between DNA methylation regulator patterns, infiltration of immune cell-types, and tumor immune response status in gather glioma cohorts. Furthermore, we calculated the DNA methylation score (DMS) for individual glioma samples, then evaluated the relationship between DMS, clinicopathological characteristics, and overall survival (OS) in patients with gliomas. Our results showed three distinct DNA methylation regulator patterns among the glioma patients which correlated with three distinct tumor immune response phenotypes, namely, immune-inflamed, immune-excluded, and immune desert. We then calculated DMS for individual glioma samples based on the expression of DNA methylation-related gene clusters. Furthermore, DMS, tumor mutation burden (TMB), programmed death 1 (PD-1) expression, immune cell infiltration status in the TME, and Tumor Immune Dysfunction and Exclusion (TIDE) scores were associated with survival outcomes and clinical responses to immune checkpoint blockade therapy. We also validated the predictive value of DMS in two independent immunotherapy cohorts. In conclusion, our results demonstrated that three DNA methylation regulator patterns that correlated with three tumor immune response phenotypes. Moreover, we demonstrated that DMS was an independent predictive biomarker that correlated with survival outcomes of glioma patients and their responses to immunotherapy therapeutic regimens.
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Affiliation(s)
- Haitao Luo
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi Province, China
| | - Minhua Ye
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi Province, China
| | - Yan Hu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China.,East China Institute of Digital Medical Engineering, Shangrao, Jiangxi Province, China
| | - Miaojing Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China
| | - Mengqi Cheng
- Department of Obstetrics and Gynecology, Suizhou Central Hospital, Hubei University of Medicine, Suizhou, Hubei Province, China
| | - Xingen Zhu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi Province, China
| | - Kai Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China.,Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang, Jiangxi Province, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi Province, China
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Zhao X, Bao Y, Meng B, Xu Z, Li S, Wang X, Hou R, Ma W, Liu D, Zheng J, Shi M. From rough to precise: PD-L1 evaluation for predicting the efficacy of PD-1/PD-L1 blockades. Front Immunol 2022; 13:920021. [PMID: 35990664 PMCID: PMC9382880 DOI: 10.3389/fimmu.2022.920021] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Developing biomarkers for accurately predicting the efficacy of immune checkpoint inhibitor (ICI) therapies is conducive to avoiding unwanted side effects and economic burden. At the moment, the quantification of programmed cell death ligand 1 (PD-L1) in tumor tissues is clinically used as one of the combined diagnostic assays of response to anti-PD-1/PD-L1 therapy. However, the current assays for evaluating PD-L1 remain imperfect. Recent studies are promoting the methodologies of PD-L1 evaluation from rough to precise. Standardization of PD-L1 immunohistochemistry tests is being promoted by using optimized reagents, platforms, and cutoff values. Combining novel in vivo probes with PET or SPECT will probably be of benefit to map the spatio-temporal heterogeneity of PD-L1 expression. The dynamic change of PD-L1 in the circulatory system can also be realized by liquid biopsy. Consider PD-L1 expressed on non-tumor (immune and non-immune) cells, and optimized combination detection indexes are further improving the accuracy of PD-L1 in predicting the efficacy of ICIs. The combinations of artificial intelligence with novel technologies are conducive to the intelligence of PD-L1 as a predictive biomarker. In this review, we will provide an overview of the recent progress in this rapidly growing area and discuss the clinical and technical challenges.
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Affiliation(s)
- Xuan Zhao
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Yulin Bao
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Bi Meng
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Zijian Xu
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Sijin Li
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Xu Wang
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Rui Hou
- College of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Wen Ma
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Dan Liu
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Dan Liu, ; Junnian Zheng, ; Ming Shi,
| | - Junnian Zheng
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Dan Liu, ; Junnian Zheng, ; Ming Shi,
| | - Ming Shi
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Dan Liu, ; Junnian Zheng, ; Ming Shi,
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15
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SNHG3 Affects Gastric Cancer Development by Regulating SEPT9 Methylation. JOURNAL OF ONCOLOGY 2022; 2022:3433406. [PMID: 35528235 PMCID: PMC9071877 DOI: 10.1155/2022/3433406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/18/2022] [Accepted: 03/24/2022] [Indexed: 11/17/2022]
Abstract
Background Gastric cancer (GC) is a common malignancy that can be formed by methylation-induced deactivation of tumor silencer genes, which is one of the key mechanisms of tumorigenesis. SEPT9 methylation, a symptomatic marker for tumors, can downregulate gene expression. Long noncoding RNA small nucleolar host gene 3 (lncRNA SNHG3) is a new type of lncRNA related to cancer. Our study investigated the mechanism of SNHG3 regulation of SEPT9 methylation and its effects on the growth, metastasis, and spread of gastric cancer cells. Methods Quantitative real-time PCR (qRT–PCR) was used to detect SNHG3 and miR-448 in gastric cancer, and a dual-luciferase experiment verified the effects of SNHG3, miR-448, and DNMT1. After abnormally expressing SNHG3, miR-448, and DNMT1 alone or together, methylation-specific PCR was performed to determine the methylation of SEPT9, Western blotting was performed to detect the expression of DNA methyltransferase 1 (DNMT1) and SEPT9, and Transwell, scratch, and CCK-8 assays were performed to reveal the invasion, migration, and cell growth of gastric cancer cells. Results We found that SNHG3 was upregulated in gastric cancer and that SNHG3 knockdown or miR-448 overexpression inhibited SEP9 methylation and therefore increased its expression, thereby inhibiting the growth, metastasis, and spread of gastric cancer cells. Conclusion Our study indicates that SNHG3 regulates SEPT9 methylation by targeting miR-448/DNMT1 and subsequently affecting the occurrence and development of gastric cancer.
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16
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McGuire MH, Dasari SK, Yao H, Wen Y, Mangala LS, Bayraktar E, Ma W, Ivan C, Shoshan E, Wu SY, Jonasch E, Bar-Eli M, Wang J, Baggerly KA, Sood AK. Gene Body Methylation of the Lymphocyte-Specific Gene CARD11 Results in Its Overexpression and Regulates Cancer mTOR Signaling. Mol Cancer Res 2021; 19:1917-1928. [PMID: 34348992 PMCID: PMC8568653 DOI: 10.1158/1541-7786.mcr-20-0753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 06/16/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022]
Abstract
Investigations into the function of nonpromoter DNA methylation have yielded new insights into epigenetic regulation of gene expression. Previous studies have highlighted the importance of distinguishing between DNA methylation in discrete functional regions; however, integrated nonpromoter DNA methylation and gene expression analyses across a wide number of tumor types and corresponding normal tissues have not been performed. Through integrated analysis of gene expression and DNA methylation profiles, we examined 32 tumor types and identified 57 tumor suppressors and oncogenes out of 260 genes exhibiting a correlation of > 0.5 between gene body methylation and gene expression in at least one tumor type. The lymphocyte-specific gene CARD11 exhibits robust association between gene body methylation and expression across 19 of 32 tumor types examined. It is significantly overexpressed in kidney renal cell carcinoma (KIRC) and lung adenocarcinoma (LUAD) tumor tissues in comparison with respective control samples; and is significantly associated with lower overall survival in KIRC. Contrary to its canonical function in lymphocyte NFκB activation, CARD11 activates the mTOR pathway in KIRC and LUAD, resulting in suppressed autophagy. Furthermore, demethylation of a CpG island within the gene body of CARD11 decreases gene expression. Collectively, our study highlights how DNA methylation outside the promoter region can impact tumor progression. IMPLICATIONS: Our study describes a novel regulatory role of gene body DNA methylation-dependent CARD11 expression on mTOR signaling and its impact on tumor progression.
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Affiliation(s)
- Michael H McGuire
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Santosh K Dasari
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hui Yao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yunfei Wen
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lingegowda S Mangala
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Emine Bayraktar
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wencai Ma
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Einav Shoshan
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sherry Y Wu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Eric Jonasch
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Menashe Bar-Eli
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Keith A Baggerly
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas
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17
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Wang G, Jia Y, Ye Y, Kang E, Chen H, Wang J, He X. Identification of key methylation differentially expressed genes in posterior fossa ependymoma based on epigenomic and transcriptome analysis. J Transl Med 2021; 19:174. [PMID: 33902636 PMCID: PMC8077736 DOI: 10.1186/s12967-021-02834-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/13/2021] [Indexed: 02/06/2023] Open
Abstract
Background Posterior fossa ependymoma (EPN-PF) can be classified into Group A posterior fossa ependymoma (EPN-PFA) and Group B posterior fossa ependymoma (EPN-PFB) according to DNA CpG island methylation profile status and gene expression. EPN-PFA usually occurs in children younger than 5 years and has a poor prognosis. Methods Using epigenome and transcriptome microarray data, a multi-component weighted gene co-expression network analysis (WGCNA) was used to systematically identify the hub genes of EPN-PF. We downloaded two microarray datasets (GSE66354 and GSE114523) from the Gene Expression Omnibus (GEO) database. The Limma R package was used to identify differentially expressed genes (DEGs), and ChAMP R was used to analyze the differential methylation genes (DMGs) between EPN-PFA and EPN-PFB. GO and KEGG enrichment analyses were performed using the Metascape database. Results GO analysis showed that enriched genes were significantly enriched in the extracellular matrix organization, adaptive immune response, membrane raft, focal adhesion, NF-kappa B pathway, and axon guidance, as suggested by KEGG analysis. Through WGCNA, we found that MEblue had a significant correlation with EPN-PF (R = 0.69, P = 1 × 10–08) and selected the 180 hub genes in the blue module. By comparing the DEGs, DMGs, and hub genes in the co-expression network, we identified five hypermethylated, lower expressed genes in EPN-PFA (ATP4B, CCDC151, DMKN, SCN4B, and TUBA4B), and three of them were confirmed by IHC. Conclusion ssGSEA and GSVA analysis indicated that these five hub genes could lead to poor prognosis by inducing hypoxia, PI3K-Akt-mTOR, and TNFα-NFKB pathways. Further study of these dysmethylated hub genes in EPN-PF and the pathways they participate in may provides new ideas for EPN-PF treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02834-1.
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Affiliation(s)
- Guanyi Wang
- Department of Neurosurgery, Xijing Hospital, Airforce Military Medical University (Fourth Military Medical University), Xi'an, 710032, China
| | - Yibin Jia
- Department of Neurosurgery, Xijing Hospital, Airforce Military Medical University (Fourth Military Medical University), Xi'an, 710032, China
| | - Yuqin Ye
- Department of Neurosurgery, Xijing Hospital, Airforce Military Medical University (Fourth Military Medical University), Xi'an, 710032, China.,Department of Neurosurgery, PLA 163Rd Hospital (Second Affiliated Hospital of Hunan Normal University), Changsha, 410000, China
| | - Enming Kang
- Department of Neurosurgery, Xijing Hospital, Airforce Military Medical University (Fourth Military Medical University), Xi'an, 710032, China
| | - Huijun Chen
- Department of Neurosurgery, Xijing Hospital, Airforce Military Medical University (Fourth Military Medical University), Xi'an, 710032, China
| | - Jiayou Wang
- Department of Neurosurgery, Xijing Hospital, Airforce Military Medical University (Fourth Military Medical University), Xi'an, 710032, China
| | - Xiaosheng He
- Department of Neurosurgery, Xijing Hospital, Airforce Military Medical University (Fourth Military Medical University), Xi'an, 710032, China.
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18
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Gu Y, Wu X, Zhang J, Fang Y, Pan Y, Shu Y, Ma P. The evolving landscape of N 6-methyladenosine modification in the tumor microenvironment. Mol Ther 2021; 29:1703-1715. [PMID: 33839323 DOI: 10.1016/j.ymthe.2021.04.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/22/2021] [Accepted: 04/06/2021] [Indexed: 12/15/2022] Open
Abstract
The tumor microenvironment (TME), controlled by intrinsic mechanisms of carcinogenesis and epigenetic modifications, has, in recent years, become a heavily researched topic. The TME can be described in terms of hypoxia, metabolic dysregulation, immune escape, and chronic inflammation. RNA methylation, an epigenetic modification, has recently been found to have a pivotal role in shaping the TME. The N6-methylation of adenosine (m6A) modification is the most common type of RNA methylation that occurs in the N6-position of adenosine, which is the primary internal modification of eukaryotic mRNA. Compelling evidence has demonstrated that m6A regulates transcriptional and protein expression through splicing, translation, degradation, and export, thereby mediating the biological processes of cancer cells and/or stromal cells and characterizing the TME. The TME also has a crucial role in the complicated regulatory network of m6A modifications and, subsequently, influences tumor initiation, progression, and therapy responses. In this review, we describe the features of the TME and how the m6A modification modulates and interacts with it. We also focus on various factors and pathways involved in m6A methylation. Finally, we discuss potential therapeutic strategies and prognostic biomarkers with respect to the TME and m6A modification.
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Affiliation(s)
- Yunru Gu
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Xi Wu
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Jingxin Zhang
- Department of General Surgery, The Affiliated People's Hospital of Jiangsu University, Zhenjiang Clinic School of Nanjing Medical University, Zhenjiang 212002, People's Republic of China
| | - Yuan Fang
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Yutian Pan
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Yongqian Shu
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China.
| | - Pei Ma
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China.
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Genome-wide analysis of the hypoxia-related DNA methylation-driven genes in lung adenocarcinoma progression. Biosci Rep 2021; 40:222062. [PMID: 32031203 PMCID: PMC7033312 DOI: 10.1042/bsr20194200] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/01/2020] [Accepted: 02/04/2020] [Indexed: 12/15/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is a common type of lung cancer with high incidence and poor prognosis. Hypoxia and DNA methylation play important regulatory roles in cancer progression. The purpose of the present study was to explore the relationship between hypoxia and DNA methylation, and to identify key genes for hypoxia-regulated LUAD progression. Hypoxia score (HS) was calculated using the GSVA algorithm. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and protein-protein interaction (PPI) analysis were performed using clusterProfile package, STRING database and Cytoscape software. Kaplan-Meier curves of overall survival (OS) and disease-free survival (DFS) were drawn using R software. Smoking status and cancer stages were significantly associated with LUAD hypoxia, and hypoxia is a poor prognostic factor for LUAD. Compared with HS-low group, 1803 aberrantly methylated DEGs were identified in HS-high group. KEGG analysis showed that the 1803 genes were enriched in the metabolic pathways associated with hypoxia stress, angiogenesis and cancer progression. FAM20C, MYLIP and COL7A1 were identified as the hypoxia-related key genes in LUAD progression, which were regulated by DNA methylation. Hypoxia in LUAD tumor cells led to changes in DNA methylation patterns. In-depth study of the relationship between hypoxia and DNA methylation is helpful to elucidate the mechanism of tumorigenesis, and provides new ideas for LUAD treatment.
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20
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Polano M, Fabbiani E, Adreuzzi E, Cintio FD, Bedon L, Gentilini D, Mongiat M, Ius T, Arcicasa M, Skrap M, Dal Bo M, Toffoli G. A New Epigenetic Model to Stratify Glioma Patients According to Their Immunosuppressive State. Cells 2021; 10:cells10030576. [PMID: 33807997 PMCID: PMC8001235 DOI: 10.3390/cells10030576] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/27/2021] [Accepted: 02/28/2021] [Indexed: 01/02/2023] Open
Abstract
Gliomas are the most common primary neoplasm of the central nervous system. A promising frontier in the definition of glioma prognosis and treatment is represented by epigenetics. Furthermore, in this study, we developed a machine learning classification model based on epigenetic data (CpG probes) to separate patients according to their state of immunosuppression. We considered 573 cases of low-grade glioma (LGG) and glioblastoma (GBM) from The Cancer Genome Atlas (TCGA). First, from gene expression data, we derived a novel binary indicator to flag patients with a favorable immune state. Then, based on previous studies, we selected the genes related to the immune state of tumor microenvironment. After, we improved the selection with a data-driven procedure, based on Boruta. Finally, we tuned, trained, and evaluated both random forest and neural network classifiers on the resulting dataset. We found that a multi-layer perceptron network fed by the 338 probes selected by applying both expert choice and Boruta results in the best performance, achieving an out-of-sample accuracy of 82.8%, a Matthews correlation coefficient of 0.657, and an area under the ROC curve of 0.9. Based on the proposed model, we provided a method to stratify glioma patients according to their epigenomic state.
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Affiliation(s)
- Maurizio Polano
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy; (F.D.C.); (L.B.); (M.D.B.); (G.T.)
- Correspondence:
| | - Emanuele Fabbiani
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, 27100 Pavia, Italy;
| | - Eva Adreuzzi
- Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Division of Molecular Oncology, 33081 Aviano, Italy; (E.A.); (M.M.)
| | - Federica Di Cintio
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy; (F.D.C.); (L.B.); (M.D.B.); (G.T.)
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Luca Bedon
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy; (F.D.C.); (L.B.); (M.D.B.); (G.T.)
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Davide Gentilini
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, 20095 Cusano Milanino, Italy;
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Maurizio Mongiat
- Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Division of Molecular Oncology, 33081 Aviano, Italy; (E.A.); (M.M.)
| | - Tamara Ius
- Neurosurgery Unit, Department of Neuroscience, Santa Maria della Misericordia University Hospital, 33100 Udine, Italy; (T.I.); (M.S.)
| | - Mauro Arcicasa
- Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Department of Radiotherapy, 33081 Aviano, Italy;
| | - Miran Skrap
- Neurosurgery Unit, Department of Neuroscience, Santa Maria della Misericordia University Hospital, 33100 Udine, Italy; (T.I.); (M.S.)
| | - Michele Dal Bo
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy; (F.D.C.); (L.B.); (M.D.B.); (G.T.)
| | - Giuseppe Toffoli
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy; (F.D.C.); (L.B.); (M.D.B.); (G.T.)
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21
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Mehdi A, Rabbani SA. Role of Methylation in Pro- and Anti-Cancer Immunity. Cancers (Basel) 2021; 13:cancers13030545. [PMID: 33535484 PMCID: PMC7867049 DOI: 10.3390/cancers13030545] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/09/2021] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
DNA and RNA methylation play a vital role in the transcriptional regulation of various cell types including the differentiation and function of immune cells involved in pro- and anti-cancer immunity. Interactions of tumor and immune cells in the tumor microenvironment (TME) are complex. TME shapes the fate of tumors by modulating the dynamic DNA (and RNA) methylation patterns of these immune cells to alter their differentiation into pro-cancer (e.g., regulatory T cells) or anti-cancer (e.g., CD8+ T cells) cell types. This review considers the role of DNA and RNA methylation in myeloid and lymphoid cells in the activation, differentiation, and function that control the innate and adaptive immune responses in cancer and non-cancer contexts. Understanding the complex transcriptional regulation modulating differentiation and function of immune cells can help identify and validate therapeutic targets aimed at targeting DNA and RNA methylation to reduce cancer-associated morbidity and mortality.
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Affiliation(s)
- Ali Mehdi
- Department of Human Genetics, McGill University, Montreal, QC H3A 2B4, Canada;
- Department of Medicine, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Shafaat A. Rabbani
- Department of Human Genetics, McGill University, Montreal, QC H3A 2B4, Canada;
- Department of Medicine, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Correspondence: ; Tel.: +1-514-843-1632
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22
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Zhang J, Zuo T, Yang J, Hu Z, Wang Z, Xu R, Ma S, Wei Y, Shen Q. Hierarchically Releasing Bio-Responsive Nanoparticles for Complete Tumor Microenvironment Modulation via TGF-β Pathway Inhibition and TAF Reduction. ACS APPLIED MATERIALS & INTERFACES 2021; 13:2256-2268. [PMID: 33423468 DOI: 10.1021/acsami.0c18545] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The aggressive progression of breast cancer is impacted significantly by the tumor microenvironment (TME). The current chemotherapy normally causes cytotoxicity to tumor cells, while does not effectively modulate the TME. Thus, the chemotherapy effect of breast cancer is usually dissatisfactory. In this study, a kind of hierarchically releasing bio-responsive nanoparticles (R(D)/H(S) NPs), constructed by β-cyclodextrin-grafted heparin and pH-sensitive pseudorotaxane, were investigated to enhance the breast cancer chemotherapeutic efficacy through TME modulation. Doxorubicin (DOX) and transforming growth factor-β (TGF-β) receptor inhibitor (SB431542) loaded onto R(D)/H(S) NPs were released rapidly for the respective response to low pH in endosomes/lysosomes and heparanase (HPSE) in TME. Our results showed that R(D)/H(S) NPs effectively inhibited the formation of tumor-associated fibroblasts (TAFs) and reduced TGF-β and collagen I secretion. Besides, the immunosuppressive microenvironment was effectively reversed into immunogenic, characterized by increased CD8+ and CD4+ T cell infiltration, which distinctly inhibited breast cancer metastasis. Therefore, R(D)/H(S) NPs remodeled the TME by downregulating TAFs, TGF-β, and collagen I; activating the immune microenvironment; and then amplifying the chemotherapeutic efficacy of DOX.
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Affiliation(s)
- Jun Zhang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Tiantian Zuo
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jie Yang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zongwei Hu
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zhihua Wang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Rui Xu
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Siyu Ma
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yawen Wei
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Qi Shen
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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23
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Hassona MM, Naguib M, Radwan EM, Abdel-Samiee M, Estaphan S, Abdelsameea E. DNA Methyltransferases as Potential Biomarkers for HCV Related Hepatocellular Carcinoma. Asian Pac J Cancer Prev 2020; 21:3357-3363. [PMID: 33247696 PMCID: PMC8033121 DOI: 10.31557/apjcp.2020.21.11.3357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/19/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a major health concern in many countries including Egypt. The alteration in DNA methylation that was observed in HCC patients suggests a possible role of DNA methyltransferases (DNMTs) in the disease pathogenesis in addition to potential role as a disease biomarker. AIM To study the change in DNMTs expression in chronic HCV infected patients as potential non- invasive biomarker for diagnosis of hepatocellular carcinoma. METHODS 26 patients with HCC, 45 patients with liver cirrhosis, 20 chronic HCV patients and 20 apparently healthy individuals as a control group were enrolled in this study. Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) was performed for all study participants. RESULTS A significant difference in DNMTs expression was observed among the studied groups. Receiver operating characteristics (ROC) curve analysis revealed that with a cutoff value of 3.16 for DNMT 3A expression, sensitivity and specificity were 80.8 and 95.6% respectively and area under curve (AUC) was 0.958, p < 0.001 for discriminating hepatocellular carcinoma among post hepatitis C cirrhotic patients. Besides DNMT 3B relative expression cutoff value of 3.10 showed 84.6% sensitivity and 77.8% specificity and AUC was 0.888, p < 0.001. On the other hand, cutoff value 0.65 for DNMT1 relative expression showed 92.3% sensitivity and 44.4% specificity and AUC was 0.72, p= 0.002. DNMT1, DNMT 3A and DNMT 3B have significant positive correlation with the level of AFP (p-value = 0.003, 0.004 and 0.008 respectively). The relative expression of DNMT3B was significantly correlated to focal lesion size (p-value = 0.015). High DNMTs expression was significantly associated with the presence of multiple focal lesions but not with the Child Pugh grade (p> 0.05). CONCLUSION The mRNA levels of DNMTs could be a potential biomarker for early detection of HCC development. .
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Affiliation(s)
- Mona M Hassona
- Department of Clinical and Chemical Pathology, National Liver Institute, Menoufia University, Shebeen El-Kom, Egypt.
| | - Mary Naguib
- Department of Clinical and Chemical Pathology, National Liver Institute, Menoufia University, Shebeen El-Kom, Egypt.
| | - Enas M Radwan
- Department of Clinical pathology, National Cancer Institute, Cairo University, Cairo, Egypt.
| | - Mohamed Abdel-Samiee
- Hepatology and Gastroenterology, National Liver Institute, Clinical Pathology, Menoufia University, Shebeen El-Kom, Egypt.
| | - Suzanne Estaphan
- Department of Physiology, Faculty of Medicine, Cairo University, Cairo, Egypt.
| | - Eman Abdelsameea
- Department of Physiology, Faculty of Medicine, Cairo University, Cairo, Egypt.
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24
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Zeng H, Luo M, Chen L, Ma X, Ma X. Machine learning analysis of DNA methylation in a hypoxia-immune model of oral squamous cell carcinoma. Int Immunopharmacol 2020; 89:107098. [PMID: 33091815 DOI: 10.1016/j.intimp.2020.107098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/15/2020] [Accepted: 10/10/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Hypoxia status and immunity are related with the development and prognosis of oral squamous cell carcinoma (OSCC). Here, we constructed a hypoxia-immune model to explore its upstream mechanism and identify potential CpG sites. METHODS The hypoxia-immune model was developed and validated by the iCluster algorithm. The LASSO, SVM-RFE and GA-ANN were performed to screen CpG sites correlated to the hypoxia-immune microenvironment. RESULTS We found seven hypoxia-immune related CpG sites. Lasso had the best classification performance among three machine learning algorithms. CONCLUSION We explored the clinical significance of the hypoxia-immune model and found seven hypoxia-immune related CpG sites by multiple machine learning algorithms. This model and candidate CpG sites may have clinical applications to predict the hypoxia-immune microenvironment.
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Affiliation(s)
- Hao Zeng
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Meng Luo
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Linyan Chen
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Xinyu Ma
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Xuelei Ma
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, China.
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25
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Blecua P, Martinez‐Verbo L, Esteller M. The DNA methylation landscape of hematological malignancies: an update. Mol Oncol 2020; 14:1616-1639. [PMID: 32526054 PMCID: PMC7400809 DOI: 10.1002/1878-0261.12744] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 06/04/2020] [Indexed: 12/17/2022] Open
Abstract
The rapid advances in high-throughput sequencing technologies have made it more evident that epigenetic modifications orchestrate a plethora of complex biological processes. During the last decade, we have gained significant knowledge about a wide range of epigenetic changes that crucially contribute to some of the most aggressive forms of leukemia, lymphoma, and myelodysplastic syndromes. DNA methylation is a key epigenetic player in the abnormal initiation, development, and progression of these malignancies, often acting in synergy with other epigenetic alterations. It also contributes to the acquisition of drug resistance. In this review, we summarize the role of DNA methylation in hematological malignancies described in the current literature. We discuss in detail the dual role of DNA methylation in normal and aberrant hematopoiesis, as well as the involvement of this type of epigenetic change in other aspects of the disease. Finally, we present a comprehensive overview of the main clinical implications, including a discussion of the therapeutic strategies that regulate or reverse aberrant DNA methylation patterns in hematological malignancies, including their combination with (chemo)immunotherapy.
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Affiliation(s)
- Pedro Blecua
- Cancer Epigenetics GroupJosep Carreras Leukaemia Research Institute (IJC)BarcelonaSpain
| | - Laura Martinez‐Verbo
- Cancer Epigenetics GroupJosep Carreras Leukaemia Research Institute (IJC)BarcelonaSpain
| | - Manel Esteller
- Cancer Epigenetics GroupJosep Carreras Leukaemia Research Institute (IJC)BarcelonaSpain
- Centro de Investigación Biomedica en Red Cancer (CIBERONC)MadridSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
- Physiological Sciences DepartmentSchool of Medicine and Health SciencesUniversity of BarcelonaSpain
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26
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Izzi V, Koivunen J, Rappu P, Heino J, Pihlajaniemi T. Integration of Matrisome Omics: Towards System Biology of the Tumor Matrisome. EXTRACELLULAR MATRIX OMICS 2020. [DOI: 10.1007/978-3-030-58330-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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27
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Xue G, Cui ZJ, Zhou XH, Zhu YX, Chen Y, Liang FJ, Tang DN, Huang BY, Zhang HY, Hu ZH, Yuan XY, Xiong J. DNA Methylation Biomarkers Predict Objective Responses to PD-1/PD-L1 Inhibition Blockade. Front Genet 2019; 10:724. [PMID: 31475034 PMCID: PMC6707807 DOI: 10.3389/fgene.2019.00724] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/10/2019] [Indexed: 12/11/2022] Open
Abstract
Immune checkpoint inhibitor (ICI) treatment could bring long-lasting clinical benefits to patients with metastatic cancer. However, only a small proportion of patients respond to PD-1/PD-L1 blockade, so predictive biomarkers are needed. Here, based on DNA methylation profiles and the objective response rates (ORRs) of PD-1/PD-L1 inhibition therapy, we identified 269 CpG sites and developed an initial CpG-based model by Lasso to predict ORRs. Notably, as measured by the area under the receiver operating characteristic curve (AUC), our model can produce better performance (AUC = 0.92) than both a model based on tumor mutational burden (TMB) (AUC = 0.77) and a previously reported TMB model (AUC = 0.71). In addition, most CpGs also have additional synergies with TMB, which can achieve a higher prediction accuracy when joined with TMB. Furthermore, we identified CpGs that are associated with TMB at the individual level. DNA methylation modules defined by protein networks, Kyoto Encylopedia of Genes and Genomes (KEGG) pathways, and ligand-receptor gene pairs are also associated with ORRs. This method suggested novel immuno-oncology targets that might be beneficial when combined with PD-1/PD-L1 blockade. Thus, DNA methylation studies might hold great potential for individualized PD1/PD-L1 blockade or combinatory therapy.
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Affiliation(s)
- Gang Xue
- SPACEnter Space Science and Technology Institute, Shenzhen, China.,College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Ze-Jia Cui
- College of Informatics, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Xiong-Hui Zhou
- College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Yue-Xing Zhu
- SPACEnter Space Science and Technology Institute, Shenzhen, China
| | - Ying Chen
- SPACEnter Space Science and Technology Institute, Shenzhen, China
| | - Feng-Ji Liang
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Da-Nian Tang
- Gastro-Intestinal Surgery Department, Beijing Hospital, Beijing, China
| | - Bing-Yang Huang
- Department of Cardiothoracic Surgery, Strategic Support Force Medical Center of PLA. No. 9, Beijing, China
| | - Hong-Yu Zhang
- College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Zhi-Huang Hu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xi-Yu Yuan
- Department of General Surgery, Dongguan People's Hospital affiliated to Southern Medical University, Dongguan, China
| | - Jianghui Xiong
- SPACEnter Space Science and Technology Institute, Shenzhen, China.,State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
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28
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Lamprecht S, Sigal-Batikoff I, Shany S, Abu-Freha N, Ling E, Delinasios GJ, Moyal-Atias K, Delinasios JG, Fich A. Teaming Up for Trouble: Cancer Cells, Transforming Growth Factor-β1 Signaling and the Epigenetic Corruption of Stromal Naïve Fibroblasts. Cancers (Basel) 2018; 10:cancers10030061. [PMID: 29495500 PMCID: PMC5876636 DOI: 10.3390/cancers10030061] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 01/28/2018] [Accepted: 02/21/2018] [Indexed: 12/22/2022] Open
Abstract
It is well recognized that cancer cells subvert the phenotype of stromal naïve fibroblasts and instruct the neighboring cells to sustain their growth agenda. The mechanisms underpinning the switch of fibroblasts to cancer-associated fibroblasts (CAFs) are the focus of intense investigation. One of the most significant hallmarks of the biological identity of CAFs is that their tumor-promoting phenotype is stably maintained during in vitro and ex vivo propagation without the continual interaction with the adjacent cancer cells. In this review, we discuss robust evidence showing that the master cytokine Transforming Growth Factor-β1 (TGFβ-1) is a prime mover in reshaping, via epigenetic switches, the phenotype of stromal fibroblasts to a durable state. We also examine, in detail, the pervasive involvement of TGFβ-1 signaling from both cancer cells and CAFs in fostering cancer development, taking colorectal cancer (CRC) as a paradigm of human neoplasia. Finally, we review the stroma-centric anticancer therapeutic approach focused on CAFs—the most abundant cell population of the tumor microenvironment (TME)—as target cells.
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Affiliation(s)
- Sergio Lamprecht
- Department of Clinical Biochemistry and Pharmacology, Ben Gurion University of the Negev, Beersheva 8410500, Israel.
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beersheva 8410500, Israel.
- Institute of Gastroenterology and Hepatology, Soroka University Medical Center, Beersheva 8410100, Israel.
| | - Ina Sigal-Batikoff
- Department of Clinical Biochemistry and Pharmacology, Ben Gurion University of the Negev, Beersheva 8410500, Israel.
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beersheva 8410500, Israel.
- Institute of Gastroenterology and Hepatology, Soroka University Medical Center, Beersheva 8410100, Israel.
| | - Shraga Shany
- Department of Clinical Biochemistry and Pharmacology, Ben Gurion University of the Negev, Beersheva 8410500, Israel.
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beersheva 8410500, Israel.
| | - Naim Abu-Freha
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beersheva 8410500, Israel.
- Institute of Gastroenterology and Hepatology, Soroka University Medical Center, Beersheva 8410100, Israel.
| | - Eduard Ling
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beersheva 8410500, Israel.
- Pediatrics Department B, Soroka University Medical Center, Beersheva 8410100, Israel.
| | - George J Delinasios
- International Institute of Anticancer Research, Kapandriti, Athens 19014, Greece.
| | - Keren Moyal-Atias
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beersheva 8410500, Israel.
- Institute of Gastroenterology and Hepatology, Soroka University Medical Center, Beersheva 8410100, Israel.
| | - John G Delinasios
- International Institute of Anticancer Research, Kapandriti, Athens 19014, Greece.
| | - Alexander Fich
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beersheva 8410500, Israel.
- Institute of Gastroenterology and Hepatology, Soroka University Medical Center, Beersheva 8410100, Israel.
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29
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Utaijaratrasmi P, Vaeteewoottacharn K, Tsunematsu T, Jamjantra P, Wongkham S, Pairojkul C, Khuntikeo N, Ishimaru N, Sirivatanauksorn Y, Pongpaibul A, Thuwajit P, Thuwajit C, Kudo Y. The microRNA-15a-PAI-2 axis in cholangiocarcinoma-associated fibroblasts promotes migration of cancer cells. Mol Cancer 2018; 17:10. [PMID: 29347950 PMCID: PMC5773154 DOI: 10.1186/s12943-018-0760-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 01/04/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Cholangiocarcinoma (CCA) has an abundance of tumor stroma which plays an important role in cancer progression via tumor-promoting signals. This study aims to explore the microRNA (miRNA) profile of CCA-associated fibroblasts (CCFs) and the roles of any identified miRNAs in CCA progression. METHODS miRNA expression profiles of CCFs and normal skin fibroblasts were compared by microarray. Identified downregulated miRNAs and their target genes were confirmed by real-time PCR. Their binding was confirmed by a luciferase reporter assay. The effects of conditioned-media (CM) of miRNA mimic- and antagonist-transfected CCFs were tested in CCA migration in wound healing assays. Finally, the levels of miRNA and their target genes were examined by real-time PCR and immunohistochemistry in clinical CCA samples. RESULTS miR-15a was identified as a downregulated miRNA in CCFs. Moreover, PAI-2 was identified as a novel target gene of miR-15a. Recombinant PAI-2 promoted migration of CCA cells. Moreover, CM from miR-15a mimic-transfected CCFs suppressed migration of CCA cells. Lower expression of miR-15a and higher expression of PAI-2 were observed in human CCA samples compared with normal liver tissues. Importantly, PAI-2 expression correlated with poor prognosis in CCA patients. CONCLUSIONS These findings highlight the miR-15a/PAI-2 axis as a potential therapeutic target in CCA patients.
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Affiliation(s)
- Penkhae Utaijaratrasmi
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kulthida Vaeteewoottacharn
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Takaaki Tsunematsu
- Department of Oral Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Pranisa Jamjantra
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sopit Wongkham
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Chawalit Pairojkul
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Narong Khuntikeo
- Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Naozumi Ishimaru
- Department of Oral Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Yongyut Sirivatanauksorn
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ananya Pongpaibul
- Department of Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Peti Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chanitra Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
| | - Yasusei Kudo
- Department of Oral Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan.
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