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Shi Q, Song G, Song L, Wang Y, Ma J, Zhang L, Yuan E. Unravelling the function of prdm16 in human tumours: A comparative analysis of haematologic and solid tumours. Biomed Pharmacother 2024; 178:117281. [PMID: 39137651 DOI: 10.1016/j.biopha.2024.117281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 08/03/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
Extensive research has shown that PR domain 16 (PRDM16) plays a critical role in adipose tissue metabolism, including processes such as browning and thermogenesis of adipocytes, beigeing of adipocytes, and adipogenic differentiation of myoblasts. These functions have been associated with diseases such as obesity and diabetes. Additionally, PRDM16 has been correlated with various other conditions, including migraines, heterochromatin abnormalities, metabolic syndrome, cardiomyopathy, sarcopenia, nonsyndromic cleft lip, and essential hypertension, among others. However, there is currently no systematic or comprehensive conclusion regarding the mechanism of PRDM16 in human tumours, including haematologic and solid tumours. The aim of this review is to provide an overview of the research progress on PRDM16 in haematologic and solid tumours by incorporating recent literature findings. Furthermore, we explore the prospects of PRDM16 in the precise diagnosis and treatment of human haematologic and solid tumours.
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Affiliation(s)
- Qianqian Shi
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, Henan 450052, China; Tianjian Laboratory of Advanced Biomedical Sciences, Institute of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan 450000, China.
| | - Guangyong Song
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Liying Song
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, Henan 450052, China
| | - Yu Wang
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, Henan 450052, China
| | - Jun Ma
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, Henan 450052, China
| | - Linlin Zhang
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, Henan 450052, China; Tianjian Laboratory of Advanced Biomedical Sciences, Institute of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan 450000, China.
| | - Enwu Yuan
- Department of Laboratory Medicine, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, Henan 450052, China; Tianjian Laboratory of Advanced Biomedical Sciences, Institute of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou, Henan 450000, China.
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Herrington CS, Oswald AJ, Stillie LJ, Croy I, Churchman M, Hollis RL. Compartment-specific multiomic profiling identifies SRC and GNAS as candidate drivers of epithelial-to-mesenchymal transition in ovarian carcinosarcoma. Br J Cancer 2024; 130:327-335. [PMID: 38097740 PMCID: PMC10803731 DOI: 10.1038/s41416-023-02508-3] [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: 05/11/2023] [Revised: 11/05/2023] [Accepted: 11/14/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Ovarian carcinosarcoma (OCS) is an exceptionally aggressive and understudied ovarian cancer type harbouring distinct carcinomatous and sarcomatous compartments. Here, we seek to identify shared and compartment-specific events that may represent potential therapeutic targets and candidate drivers of sarcomatous compartment formation through epithelial-to-mesenchymal transition (EMT). METHODS We performed multiomic profiling (exome sequencing, RNA-sequencing, microRNA profiling) of paired carcinomatous and sarcomatous components in 12 OCS cases. RESULTS While paired sarcomatous and carcinomatous compartments demonstrate substantial genomic similarities, multiple loci are recurrently copy number-altered between components; regions containing GNAS and SRC are recurrently gained within the sarcomatous compartment. CCNE1 gain is a common event in OCS, occurring more frequently than in high grade serous ovarian carcinoma (HGSOC). Transcriptomic analysis suggests increased MAPK activity and subtype switching toward poor prognosis HGSOC-derived transcriptomic subtypes within the sarcomatous component. The two compartments show global differences in microRNA profiles, with differentially expressed microRNAs targeting EMT-related genes (SIRT1, ZEB2) and regulators of pro-tumourigenic pathways (TGFβ, NOTCH); chrX is a highly enriched target of these microRNAs and is also frequently deleted across samples. The sarcomatous component harbours significantly fewer CD8-positive cells, suggesting poorer immune engagement. CONCLUSION CCNE1 gain and chrX loss are frequent in OCS. SRC gain, increased GNAS expression and microRNA dysregulation represent potential mechanisms driving sarcomatous compartment formation.
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Affiliation(s)
- C Simon Herrington
- The Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ailsa J Oswald
- The Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Lorna J Stillie
- The Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Scotland Centre and Cancer Research UK Beatson Institute, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Ian Croy
- The Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Michael Churchman
- The Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Robert L Hollis
- The Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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Li A, Li M, Wang J, Zhou J, Yang T, Fan M, Zhang K, Gao H, Ren H, Chen M. MECOM: a bioinformatics and experimentally identified marker for the diagnosis and prognosis of lung adenocarcinoma. Biomark Med 2024; 18:79-91. [PMID: 38440890 DOI: 10.2217/bmm-2023-0600] [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] [Indexed: 03/06/2024] Open
Abstract
Objective: We aimed to explore the clinical value of MDS1 and EVI1 complex locus (MECOM) in lung adenocarcinoma (LUAD). Methods: Bioinformatics and experimental validation confirmed MECOM expression levels in LUAD. The value of MECOM was analyzed by receiver operating characteristic (ROC) curve and Cox regression analysis. Results: Serum MECOM levels were lower in LUAD and correlated with gender, TNM stage, tumor size, lymph node metastasis and distant metastasis. The ROC curve showed that the area under the curve of MECOM was 0.804 for LUAD and, of note, could reach 0.889 for advanced LUAD; specificity was up to 90%. Conclusion: MECOM may contribute to independently identifying LUAD patients, particularly in advanced stages.
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Affiliation(s)
- Anqi Li
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Meng Li
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jing Wang
- Department of Pulmonary & Critical Care Medicine, Shaanxi Provincial Second People's Hospital, Xi'an, 710005, China
| | - Jiejun Zhou
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Tian Yang
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Meng Fan
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Kun Zhang
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Hengxing Gao
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Hui Ren
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Mingwei Chen
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
- Department of Pulmonary & Critical Care Medicine, Shaanxi Provincial Second People's Hospital, Xi'an, 710005, China
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4
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Tan J, Mao W, Long S, Zhang T. Metastasis-related long non-coding RNAs AL359220.1, SH3BP5-AS1 and ZF-AS1 are significant for prognostic assessment of lung adenocarcinoma. Aging (Albany NY) 2023; 15:7551-7564. [PMID: 37566767 PMCID: PMC10457074 DOI: 10.18632/aging.204923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/19/2023] [Indexed: 08/13/2023]
Abstract
BACKGROUND Metastasis of lung adenocarcinoma (LUAD) severely worsens prognosis. Genetic alteration in the tumor microenvironment (TME) is closely associated with metastasis and other malignant biological properties of LUAD. In this study, we establish a metastasis-related risk model to accurately predict LUAD prognosis. METHODS RNA-sequencing profiles and clinical data of LUAD patients including 503 tumor tissues and 54 adjacent normal tissues were collected in TCGA database. Additionally, the paired specimens from 156 LUAD patients were obtained in a single center. The metastatic relevance and clinical significance of metastasis-related long non-coding RNA (MRLNRs) was validated by series of in vitro experiments including western blotting, qPCR and transwell assays. RESULTS Six MRLNRs were significantly correlated to prognoses of LUAD patients, of which AL359220.1, SH3BP5-AS1 and ZF-AS1 were further used to establish a metastasis-related risk scoring model (MRRS) due to the close associations with overall survival of LUAD patients. According to the MRRS, patients with higher scores in the high-risk group obtained poorer prognoses and survival outcomes. ZFAS1 expressed highly in tumor tissues and showed the inverse results compared to SH3BP5-AS1 and AL359220.1. In addition, the high expression of ZFAS1 was prominently correlated to the more advanced T-stage and distant metastasis. The reduction of ZFAS1 induced by siRNAs dramatically diminished the migration and invasion abilities of LUAD cells. CONCLUSIONS In the present research, we elucidate the metastatic relevance and clinical significance of AL359220.1, SH3BP5-AS1 and ZF-AS1 in LUAD. Moreover, MRRS provide a promising assessing model for clinical decision making and prognosis of LUAD.
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Affiliation(s)
- Jianjun Tan
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Department of Oncology, Three Gorges Hospital of Chongqing University, Chongqing 404000, China
| | - Weilin Mao
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Shuzi Long
- Department of Oncology, Three Gorges Hospital of Chongqing University, Chongqing 404000, China
| | - Tao Zhang
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
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5
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Han Y, Fu Y, Shi Q, Liu H, Sun H, Niu C, Fu L. The ALDH2, IGSF9, and PRDM16 Proteins as Predictive Biomarkers for Prognosis in Breast Cancer. Clin Breast Cancer 2023; 23:e140-e150. [PMID: 36639264 DOI: 10.1016/j.clbc.2022.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 12/04/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
INTRODUCTION ALDH2, IGSF9, and PRDM16 play crucial roles in regulating diverse cellular pathophysiologic functions. The current study was to evaluate the effect of the 3 proteins on clinicopathologic features and prognosis of patients with breast cancer. MATERIALS AND METHODS The formalin-fixed and paraffin-embedded tissue specimens were collected from breast cancer patients by immunohistochemistry (IHC) were analyzed. RESULTS Of the 216 patients enrolled, ALDH2 high expression was significantly correlated with the age (p = .040), larger tumor size (p = .001), LVI (p < .001), LNM (p < .001), advanced TNM staging (p < .001), PR (p = .027), HER2 status (p = .002), and molecular subtype (p = .003). IGSF9 low expression was significantly correlated with the LV1 (p = .024), LNM (p = .024), advanced TNM staging (p = .001). The low expression of PRDM16 was significantly correlated with age (p = .023), and LNM (p = .014). The A+I-P- expression (13.4%) were markedly correlated with lymphatic vessel invasion (LVI) (p < .001), lymph node metastasis (LNM) (p < .001), advanced TNM staging (p < .001). Furthermore, patients with A+I-P- expression had significantly advanced-stage breast cancer [stage III (72.4%) vs. (23.0%)]. Univariate and multivariate analysis identified variables (ie, larger tumor size, lymph node involvement, and A+I-P- expression) as independent prognostic factors for survival. CONCLUSION Our results reveal ALDH2 high expression, IGSF9 and PRDM16 low expression, A+I-P- expression was associated with advanced clinicopathological characteristics, and shorter OS and DFS in breast cancer patients. The 3 proteins may be potential prognosis markers and therapeutic targets for breast cancer patients.
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Affiliation(s)
- Yunwei Han
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; National Clinical Research Center of Cancer, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Tianjin, China; Ministry of Education, Breast Cancer Innovation Team of the Ministry of Education, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, State Key Laboratory of Breast Cancer Research, Tianjin, China
| | - Yiru Fu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; National Clinical Research Center of Cancer, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Tianjin, China; Ministry of Education, Breast Cancer Innovation Team of the Ministry of Education, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, State Key Laboratory of Breast Cancer Research, Tianjin, China
| | - Qianqian Shi
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; National Clinical Research Center of Cancer, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Tianjin, China; Ministry of Education, Breast Cancer Innovation Team of the Ministry of Education, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, State Key Laboratory of Breast Cancer Research, Tianjin, China; Department of Laboratory Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Hanjiao Liu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; National Clinical Research Center of Cancer, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Tianjin, China; Ministry of Education, Breast Cancer Innovation Team of the Ministry of Education, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, State Key Laboratory of Breast Cancer Research, Tianjin, China
| | - Hui Sun
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; National Clinical Research Center of Cancer, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Tianjin, China; Ministry of Education, Breast Cancer Innovation Team of the Ministry of Education, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, State Key Laboratory of Breast Cancer Research, Tianjin, China
| | - Chen Niu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; National Clinical Research Center of Cancer, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Tianjin, China; Ministry of Education, Breast Cancer Innovation Team of the Ministry of Education, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, State Key Laboratory of Breast Cancer Research, Tianjin, China
| | - Li Fu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; National Clinical Research Center of Cancer, Tianjin, China; Tianjin's Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Tianjin, China; Ministry of Education, Breast Cancer Innovation Team of the Ministry of Education, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, State Key Laboratory of Breast Cancer Research, Tianjin, China.
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PRDM16, Negatively Regulated by miR-372-3p, Suppresses Cell Proliferation and Invasion in Prostate Cancer. Andrologia 2023. [DOI: 10.1155/2023/9821829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent malignant tumors. The alternation of microRNA (miRNA) expression is associated with prostate cancer progression, whereas its way to influence progression of prostate cancer remains elusive. The expression levels of PRDM16 mRNA and miR-372-3p in PCa cell lines were analyzed using qRT-PCR. The protein expression of PRDM16 in PCa cell lines was also analyzed using western blot. CCK-8, wound healing, and Transwell assays were applied to examine cell proliferation, migration, and invasion in prostate cancer cells, respectively. Dual-luciferase reporter assay was utilized to validate the interaction between miR-372-3p and PRDM16. In the present study, markedly decreased PRDM16 mRNA and protein expression levels were observed in prostate cancer cells. PRDM16 overexpression hampered cellular proliferation, migration, and invasion, while silencing PRDM16 had the opposite effect. Moreover, miR-372-3p could target the regulation expression of PRDM16. Rescue experiments demonstrated that upregulating miR-372-3p conspicuously restored the inhibitory effect of increased PRDM16 on cell proliferation, migration, and invasion in PCa. Overall, our study clarifies the biological role of miR-372-3p/PRDM16 axis in prostate cancer progression, which may be effective biomarkers for clinical treatment of prostate cancer.
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Zhang Y, Zhang Q, Zhang Y, Han J. The Role of Histone Modification in DNA Replication-Coupled Nucleosome Assembly and Cancer. Int J Mol Sci 2023; 24:ijms24054939. [PMID: 36902370 PMCID: PMC10003558 DOI: 10.3390/ijms24054939] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 03/08/2023] Open
Abstract
Histone modification regulates replication-coupled nucleosome assembly, DNA damage repair, and gene transcription. Changes or mutations in factors involved in nucleosome assembly are closely related to the development and pathogenesis of cancer and other human diseases and are essential for maintaining genomic stability and epigenetic information transmission. In this review, we discuss the role of different types of histone posttranslational modifications in DNA replication-coupled nucleosome assembly and disease. In recent years, histone modification has been found to affect the deposition of newly synthesized histones and the repair of DNA damage, further affecting the assembly process of DNA replication-coupled nucleosomes. We summarize the role of histone modification in the nucleosome assembly process. At the same time, we review the mechanism of histone modification in cancer development and briefly describe the application of histone modification small molecule inhibitors in cancer therapy.
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Yan C, Wang P, Zhao C, Yin G, Meng X, Li L, Cai S, Meng B. Long Noncoding RNA MAGI2-AS3 Represses Cell Progression in Clear Cell Renal Cell Carcinoma by Modulating the miR-629-5p/PRDM16 Axis. Crit Rev Eukaryot Gene Expr 2023; 33:43-56. [PMID: 37602452 DOI: 10.1615/critreveukaryotgeneexpr.2023048338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
The objective of this study was to determine the regulatory mechanism of MAGI2-AS3 in clear cell renal cell carcinoma (ccRCC), thereby supplying a new insight for ccRCC treatment. Expression data in TCGA-KIRC were obtained. Target gene lncRNA for research was determined using expression analysis and clinical analysis. lncRNA's downstream regulatory miRNA and mRNA were predicted by bioinformatics databases. ccRCC cell malignant phenotypes were detected via CCK-8, colony formation, Transwell migration, and invasion assays. The targeting relationship between genes was assessed through dual-luciferase reporter gene analysis. Kaplan-Meier (K-M) analysis was carried out to verify the effect of MAGI2-AS3, miR-629-5p, and PRDM16 on the survival rate of ccRCC patients. MAGI2-AS3 expression in ccRCC tissue and cells was shown to be markedly decreased and its expression to continuously decline with tumor progression. MAGI2-AS3 suppresses ccRCC proliferation and migration. Dual-luciferase assay showed that MAGI2-AS3 binds miR-629-5p and that miR-629-5p binds PRDM16. In addition, functional experiments showed that MAGI2-AS3 facilitates PRDM16 expression by repressing miR-629-5p expression, thereby suppressing ccRCC cell aggression. K-M analysis showed that upregulation of either MAGI2-AS3 or PRDM16 significantly improves ccRCC patient survival, while upregulation of miR-629-5p has no significant impact. MAGI2-AS3 sponges miR-629-5p to modulate PRDM16 to mediate ccRCC development. Meanwhile, the MAGI2-AS3/miR-629-5p/PRDM16 axis, as a regulatory pathway of ccRCC progression, may be a possible therapeutic target and prognostic indicator of ccRCC.
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Affiliation(s)
- Chengquan Yan
- Department of Urology, Area 3, Tangshan Gongren Hospital, Tangshan City, Hebei Province, 063000, China
| | - Pengfei Wang
- Department of Urology, Area 3, Tangshan Gongren Hospital, Tangshan City, Hebei Province, 063000, China
| | - Chaofei Zhao
- Department of Urology, Area 3, Tangshan Gongren Hospital, Tangshan City, Hebei Province, 063000, China
| | - Guangwei Yin
- Department of Urology, Area 3, Tangshan Gongren Hospital, Tangshan City, Hebei Province, 063000, China
| | - Xin Meng
- Department of Urology, Area 3, Tangshan Gongren Hospital, Tangshan City, Hebei Province, 063000, China
| | - Lin Li
- Department of Urology, Area 3, Tangshan Gongren Hospital, Tangshan City, Hebei Province, 063000, China
| | - Shengyong Cai
- Department of Urology, Area 3, Tangshan Gongren Hospital, Tangshan City, Hebei Province, 063000, China
| | - Bin Meng
- Department of Urology, Area 3, Tangshan Gongren Hospital, Tangshan City, Hebei Province, 063000, China
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Yuan G, Hu B, Ma J, Zhang C, Xie H, Wei T, Yang Y, Ni B. Histone lysine methyltransferase
SETDB2
suppresses
NRF2
to restrict tumor progression and modulates chemotherapy sensitivity in lung adenocarcinoma. Cancer Med 2022; 12:7258-7272. [PMID: 36504353 PMCID: PMC10067124 DOI: 10.1002/cam4.5451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Aberrant epigenetic remodeling represents a molecular hallmark in lung adenocarcinoma (LUAD). We aim to investigate the biological roles of SETDB2 and its underlying associations with oxidative stress, providing therapeutic targets for individualized treatment of LUAD. METHODS Differential analysis was conducted via Limma package, and Kaplan-Meier analysis was performed with survival package. CCK-8, cell proliferation assay, transwell assay, and in vivo assays were conducted to assess the function of SETDB2. Western blot assay, RT-qPCR, and immunohistochemistry (IHC) were conducted to assess the expression levels of SETDB2/NRF2. Chromatin immunoprecipitation (ChIP) assay and ChIP-qPCR were conducted to assess the epigenetic roles of SETDB2. RESULTS We found that SETDB2 expression is decreased in tumor samples versus normal tissues in TCGA-LUAD cohort, LUAD-EAS cohort, GSE72094 dataset, and independent Soochow-LUAD dataset. Patients with low SETDB2 levels had a worse prognosis relative to those with high SETDB2. SETDB2 inhibition could significantly promote cell growth, migration ability, and stemness maintenance. Gene set enrichment analysis (GSEA) suggested that SETDB2 correlated with oxidative stress crosstalk and regulated NRF2 mRNA levels. ChIP assay suggested that SETDB2 mainly recruited the H3K9me3 enrichment at the NRF2 promoter region to suppress the mRNA levels of NRF2. Downregulated SETDB2 could activate NRF2 transcription and expression, thereby promoting its downstream targets, like NQO1, FTH1, and ME1. Functional experiments demonstrated that low SETDB2 allowed NRF2 to drive malignant processes of LUAD. SETDB2 overexpression attenuated the ability of NRF2 signaling to neutralize cellular reactive oxygen species (ROS) levels, leading to enhanced cell apoptosis. Overexpressed SETDB2 could inhibit tumor progression in vivo and further render LUAD cells sensitive to chemotherapy. CONCLUSIONS In conclusion, these findings uncovered the suppressive role of SETDB2 in LUAD. SETDB2 negatively regulates NRF2 signaling to modulate tumor progression, which creates a therapeutic vulnerability in LUAD.
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Affiliation(s)
- Guangda Yuan
- Department of Thoracic Surgery The First Affiliated Hospital of Soochow University Suzhou China
| | - Bowen Hu
- Department of Thoracic Surgery The First Affiliated Hospital of Soochow University Suzhou China
- Department of Thoracic Surgery The Affiliated Suzhou Hospital of Nanjing Medical University Suzhou China
| | - Jun Ma
- Department of Thoracic Surgery The Affiliated Suzhou Hospital of Nanjing Medical University Suzhou China
| | - Chuanyu Zhang
- Department of Thoracic Surgery The Affiliated Suzhou Hospital of Nanjing Medical University Suzhou China
| | - Hongya Xie
- Department of Thoracic Surgery The Affiliated Suzhou Hospital of Nanjing Medical University Suzhou China
| | - Tengteng Wei
- Department of Thoracic Surgery The Affiliated Suzhou Hospital of Nanjing Medical University Suzhou China
| | - Yong Yang
- Department of Thoracic Surgery The Affiliated Suzhou Hospital of Nanjing Medical University Suzhou China
| | - Bin Ni
- Department of Thoracic Surgery The First Affiliated Hospital of Soochow University Suzhou China
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10
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Li Q, Zhang L, You W, Xu J, Dai J, Hua D, Zhang R, Yao F, Zhou S, Huang W, Dai Y, Zhang Y, Baheti T, Qian X, Pu L, Xu J, Xia Y, Zhang C, Tang J, Wang X. PRDM1/BLIMP1 induces cancer immune evasion by modulating the USP22-SPI1-PD-L1 axis in hepatocellular carcinoma cells. Nat Commun 2022; 13:7677. [PMID: 36509766 PMCID: PMC9744896 DOI: 10.1038/s41467-022-35469-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Programmed death receptor-1 (PD-1) blockade have achieved some efficacy but only in a fraction of patients with hepatocellular carcinoma (HCC). Programmed cell death 1 ligand 1 (PD-L1) binds to its receptor PD1 on T cells to dampen antigen-tumor immune responses. However, the mechanisms underlying PD-L1 regulation are not fully elucidated. Herein, we identify that tumoral Prdm1 overexpression inhibits cell growth in immune-deficient mouse models. Further, tumoral Prdm1 overexpression upregulates PD-L1 levels, dampening anti-tumor immunity in vivo, and neutralizes the anti-tumor efficacy of Prdm1 overexpression in immune-competent mouse models. Mechanistically, PRDM1 enhances USP22 transcription, thus reducing SPI1 protein degradation through deubiquitination, which enhances PD-L1 transcription. Functionally, PD-1 mAb treatment reinforces the efficacy of Prdm1-overexpressing HCC immune-competent mouse models. Collectively, we demonstrate that the PRDM1-USP22-SPI1 axis regulates PD-L1 levels, resulting in infiltrated CD8+ T cell exhaustion. Furthermore, PRDM1 overexpression combined with PD-(L)1 mAb treatment provides a therapeutic strategy for HCC treatment.
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Affiliation(s)
- Qing Li
- grid.89957.3a0000 0000 9255 8984Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province China
| | - Liren Zhang
- grid.89957.3a0000 0000 9255 8984Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province China
| | - Wenhua You
- grid.263826.b0000 0004 1761 0489School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu Province China ,grid.89957.3a0000 0000 9255 8984Department of Immunology, Key Laboratory of Immune Microenvironment and Disease, Nanjing Medical University, Nanjing, Jiangsu Province China
| | - Jiali Xu
- grid.412676.00000 0004 1799 0784Department of Anesthesiology and Perioperative Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province China
| | - Jingjing Dai
- grid.412676.00000 0004 1799 0784Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province China
| | - Dongxu Hua
- grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Ruizhi Zhang
- grid.89957.3a0000 0000 9255 8984Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province China
| | - Feifan Yao
- grid.89957.3a0000 0000 9255 8984Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province China
| | - Suiqing Zhou
- grid.89957.3a0000 0000 9255 8984Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province China
| | - Wei Huang
- grid.411610.30000 0004 1764 2878Department of General Surgery, The Friendship Hospital of Ili Kazakh Autonomous Prefecture, Ili & Jiangsu Joint Institute of Health, Ili, China
| | - Yongjiu Dai
- grid.89957.3a0000 0000 9255 8984Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province China
| | - Yu Zhang
- grid.411610.30000 0004 1764 2878Department of General Surgery, The Friendship Hospital of Ili Kazakh Autonomous Prefecture, Ili & Jiangsu Joint Institute of Health, Ili, China
| | - Tasiken Baheti
- grid.411610.30000 0004 1764 2878Department of General Surgery, The Friendship Hospital of Ili Kazakh Autonomous Prefecture, Ili & Jiangsu Joint Institute of Health, Ili, China
| | - Xiaofeng Qian
- grid.89957.3a0000 0000 9255 8984Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province China
| | - Liyong Pu
- grid.89957.3a0000 0000 9255 8984Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province China
| | - Jing Xu
- grid.412676.00000 0004 1799 0784Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province China
| | - Yongxiang Xia
- grid.89957.3a0000 0000 9255 8984Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province China
| | - Chuanyong Zhang
- grid.89957.3a0000 0000 9255 8984Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province China
| | - Jinhai Tang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province China
| | - Xuehao Wang
- grid.89957.3a0000 0000 9255 8984Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), Nanjing, Jiangsu Province China
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LINC00589-dominated ceRNA networks regulate multiple chemoresistance and cancer stem cell-like properties in HER2 + breast cancer. NPJ Breast Cancer 2022; 8:115. [PMID: 36309503 PMCID: PMC9617889 DOI: 10.1038/s41523-022-00484-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 10/12/2022] [Indexed: 11/29/2022] Open
Abstract
Resistance to human epidermal growth factor receptor 2 (HER2)-targeted therapy (trastuzumab), cancer stem cell (CSC)-like properties and multiple chemoresistance often concur and intersect in breast cancer, but molecular links that may serve as effective therapeutic targets remain largely unknown. Here, we identified the long noncoding RNA, LINC00589 as a key regulatory node for concurrent intervention of these processes in breast cancer cells in vitro and in vivo. We demonstrated that the expression of LINC00589 is clinically valuable as an independent prognostic factor for discriminating trastuzumab responders. Mechanistically, LINC00589 serves as a ceRNA platform that simultaneously sponges miR-100 and miR-452 and relieves their repression of tumor suppressors, including discs large homolog 5 (DLG5) and PR/SET domain 16 (PRDM16, a transcription suppressor of mucin4), thereby exerting multiple cancer inhibitory functions and counteracting drug resistance. Collectively, our results disclose two LINC00589-initiated ceRNA networks, the LINC00589-miR-100-DLG5 and LINC00589-miR-452-PRDM16- mucin4 axes, which regulate trastuzumab resistance, CSC-like properties and multiple chemoresistance of breast cancer, thus providing potential diagnostic and prognostic markers and therapeutic targets for HER2-positive breast cancer.
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12
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Ye Y, Li L, Dai Q, Liu Y, Shen L. Comprehensive analysis of histone methylation modification regulators for predicting prognosis and drug sensitivity in lung adenocarcinoma. Front Cell Dev Biol 2022; 10:991980. [PMID: 36263018 PMCID: PMC9574078 DOI: 10.3389/fcell.2022.991980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/14/2022] [Indexed: 11/21/2022] Open
Abstract
Histone methylation is an epigenetic modification regulated by histone methyltransferases, histone demethylases, and histone methylation reader proteins that play important roles in the pathogenic mechanism of cancers. However, the prognostic value of histone methylation in lung adenocarcinoma (LUAD) remains unknown. Here, we found that LUAD cases could be divided into 2 subtypes by the 144 histone methylation modification regulators (HMMRs), with a significant difference in OS time. Ninety-five of the HMMRs were identified as differentially expressed genes (DEGs) between normal and tumor samples, and 13 of them were further discovered to be survival-related genes (SRGs). By applying the least absolute shrinkage and selector operator (LASSO) Cox regression, we constructed an 8-gene-based risk signature according to the TCGA (training) cohort, and the risk score calculated by the signature was proven to be an independent factor in both the training and validation cohorts. We then discovered that the immune functions were generally impaired in the high-risk groups defined by the HMMR signature (especially for the DCs and immune check-point pathway). Functional analyses showed that the DEGs between the low- and high-risk groups were related to the cell cycle. The drug sensitivity analysis indicated that our risk model could predict the sensitivity of commonly used drugs. Moreover, according to the DEGs between the low- and high-risk groups, we discovered several new compounds that showed potential therapeutic value for high-risk LUAD patients. In conclusion, our study demonstrated that HMMRs were promising predictors for the prognoses and drug therapeutic effects for LUAD patients.
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Affiliation(s)
- Ying Ye
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li Li
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qinjin Dai
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yan Liu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lin Shen
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Lin Shen,
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13
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Shahrear S, Zinnia MA, Ahmed T, Islam ABMMK. Deciphering the role of predicted miRNAs of polyomaviruses in carcinogenesis. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166537. [PMID: 36089125 DOI: 10.1016/j.bbadis.2022.166537] [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: 01/31/2022] [Revised: 08/13/2022] [Accepted: 09/01/2022] [Indexed: 11/20/2022]
Abstract
Human polyomaviruses are relatively common in the general population. Polyomaviruses maintain a persistent infection after initial infection in childhood, acting as an opportunistic pathogen in immunocompromised populations and their association has been linked to carcinogenesis. A comprehensive understanding of the underlying molecular mechanisms of carcinogenesis in consequence of polyomavirus infection remains elusive. However, the critical role of viral miRNAs and their potential targets in modifying the transcriptome profile of the host remains largely unknown. Polyomavirus-derived miRNAs have the potential to play a substantial role in carcinogenesis. Employing computational approaches, putative viral miRNAs along with their target genes have been predicted and possible roles of the targeted genes in many significant biological processes have been obtained. Polyomaviruses have been observed to target intracellular signal transduction pathways through miRNA-mediated epigenetic regulation, which may contribute to cancer development. In addition, BKPyV-infected human renal cell microarray data was coupled with predicted target genes and analysis of the downregulated genes indicated that viruses target multiple signaling pathways (e.g. MAPK signaling pathway, PI3K-Akt signaling pathway, PPAR signaling pathway) in the host as well as turning off several tumor suppression genes (e.g. FGGY, EPHX2, CACNA2D3, CDH16) through miRNA-induced mechanisms, assuring cell transformation. This study provides a conceptual framework for the underlying molecular mechanisms involved in the course of carcinogenesis upon polyomavirus infection.
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Affiliation(s)
- Sazzad Shahrear
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | | | - Tasnim Ahmed
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
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14
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MiR-96-5p Facilitates Lung Adenocarcinoma Cell Phenotypes by Inhibiting FHL1. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:7891222. [PMID: 36017148 PMCID: PMC9398840 DOI: 10.1155/2022/7891222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 12/09/2022]
Abstract
Objective FHL1 is understood as a tumor repressor gene in various cancers and a possible target for cancer treatment. We investigated the influences of FHL1 on cell functions as well as its molecular mechanisms in lung adenocarcinoma (LUAD) cells. Methods The miRNA-mRNA modulatory axis was predicted by bioinformatics. The expression levels of FHL1 mRNA and protein in LUAD cells were, respectively, analyzed by qRT-PCR and western blot. Dual luciferase analysis was introduced to verify the interaction between miR-96-5p and FHL1. CCK-8, cell colony formation, and Transwell assays were utilized to analyze proliferation, colony formation, migration, and invasion of A549 cells. Results Expression of FHL1 mRNA and protein in LUAD tissue and cells was downregulated, which was linked with poor prognoses of patients. In addition, FHL1 overexpression could hamper colony formation, proliferation, invasion, and migration of LUAD cells. In addition, dual-luciferase analysis verified miR-96-5p as an upstream regulator of FHL1. Overexpression of miR-96-5p suppressed FHL1 expression in LUAD cells and promoted proliferation, invasion, and migration of LUAD cells, while overexpression of FHL1 could simultaneously restore the above-mentioned promoting effect. Conclusion MiR-96-5p fostered cell malignant behaviors by targeting FHL1. This research uncovered the regulatory mechanism of FHL1 in LUAD and offered optional therapeutic targets for LUAD patients.
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15
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Yin G, Yan C, Hao J, Zhang C, Wang P, Zhao C, Cai S, Meng B, Zhang A, Li L. PRDM16, negatively regulated by miR-372-3p, suppresses cell proliferation and invasion in prostate cancer. Andrologia 2022:e14529. [PMID: 35858224 DOI: 10.1111/and.14529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/27/2022] [Accepted: 06/26/2022] [Indexed: 11/26/2022] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent malignant tumours. The alternation of microRNAs (miRNAs) expression is associated with prostate cancer progression, whereas its way to influence progression of prostate cancer remains elusive. The expression levels of PRDM16 mRNA and miR-372-3p in PCa cell lines were analysed using qRT-PCR. The protein expression of PRDM16 in PCa cell lines was also analysed using Western blot. CCK-8, wound healing and Transwell assays were applied to examine cell proliferation, migration, and invasion in prostate cancer cells, respectively. Dual-luciferase reporter assay was utilised to validate the interaction between miR-372-3p and PRDM16. In the present study, markedly decreased PRDM16 mRNA and protein expression levels were observed in prostate cancer cells. PRDM16 overexpression hampered cellular proliferation, migration, and invasion, while silencing PRDM16 had the opposite effect. Moreover, miR-372-3p could target the regulation expression of PRDM16. Rescue experiments demonstrated that upregulating miR-372-3p conspicuously restored the inhibitory effect of increased PRDM16 on cell proliferation, migration, and invasion in PCa. Overall, our study clarifies the biological role of miR-372-3p/PRDM16 axis in prostate cancer progression, which may be effective biomarkers for clinical treatment of prostate cancer.
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Affiliation(s)
- Guangwei Yin
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Chengquan Yan
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Jing Hao
- Office of Academic Affairs, North China University of Science and Technology, Tangshan, Hebei Province, China
| | - Chunying Zhang
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Pengfei Wang
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Chaofei Zhao
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Shengyong Cai
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Bin Meng
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Aili Zhang
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Lin Li
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
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16
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Petrovic D, Bodinier B, Dagnino S, Whitaker M, Karimi M, Campanella G, Haugdahl Nøst T, Polidoro S, Palli D, Krogh V, Tumino R, Sacerdote C, Panico S, Lund E, Dugué PA, Giles GG, Severi G, Southey M, Vineis P, Stringhini S, Bochud M, Sandanger TM, Vermeulen RCH, Guida F, Chadeau-Hyam M. Epigenetic mechanisms of lung carcinogenesis involve differentially methylated CpG sites beyond those associated with smoking. Eur J Epidemiol 2022; 37:629-640. [PMID: 35595947 PMCID: PMC9288379 DOI: 10.1007/s10654-022-00877-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/25/2022] [Indexed: 12/24/2022]
Abstract
Smoking-related epigenetic changes have been linked to lung cancer, but the contribution of epigenetic alterations unrelated to smoking remains unclear. We sought for a sparse set of CpG sites predicting lung cancer and explored the role of smoking in these associations. We analysed CpGs in relation to lung cancer in participants from two nested case-control studies, using (LASSO)-penalised regression. We accounted for the effects of smoking using known smoking-related CpGs, and through conditional-independence network. We identified 29 CpGs (8 smoking-related, 21 smoking-unrelated) associated with lung cancer. Models additionally adjusted for Comprehensive Smoking Index-(CSI) selected 1 smoking-related and 49 smoking-unrelated CpGs. Selected CpGs yielded excellent discriminatory performances, outperforming information provided by CSI only. Of the 8 selected smoking-related CpGs, two captured lung cancer-relevant effects of smoking that were missed by CSI. Further, the 50 CpGs identified in the CSI-adjusted model complementarily explained lung cancer risk. These markers may provide further insight into lung cancer carcinogenesis and help improving early identification of high-risk patients.
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Affiliation(s)
- Dusan Petrovic
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
- Department of Epidemiology and Health Systems (DESS), University Centre for General Medicine and Public Health (UNISANTE), Lausanne, Switzerland
- Department and Division of Primary Care Medicine, University Hospital of Geneva, Geneva, Switzerland
| | - Barbara Bodinier
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Sonia Dagnino
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Matthew Whitaker
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Maryam Karimi
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
- Bureau de Biostatistique et d'Épidémiologie, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Oncostat U1018, Inserm, Équipe Labellisée Ligue Contre Le Cancer, Université Paris-Saclay, Villejuif, France
| | - Gianluca Campanella
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Therese Haugdahl Nøst
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | | | - Domenico Palli
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute-ISPO, Florence, Italy
| | - Vittorio Krogh
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Rosario Tumino
- Hyblean Association for Epidemiological Research, AIRE- ONLUS, Ragusa, Italy
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology Città Della Salute e della Scienza University-Hospital, Via Santena 7, 10126, Turin, Italy
| | - Salvatore Panico
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy
| | - Eiliv Lund
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- The Norwegian Cancer Registry, Oslo, Norway
| | - Pierre-Antoine Dugué
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Gianluca Severi
- Centre for Research in Epidemiology and Population Health, Inserm (Institut National de La Sante Et de a Recherche Medicale), Villejuif, France
| | - Melissa Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, Australia
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Silvia Stringhini
- Department of Epidemiology and Health Systems (DESS), University Centre for General Medicine and Public Health (UNISANTE), Lausanne, Switzerland
- Department and Division of Primary Care Medicine, University Hospital of Geneva, Geneva, Switzerland
| | - Murielle Bochud
- Department of Epidemiology and Health Systems (DESS), University Centre for General Medicine and Public Health (UNISANTE), Lausanne, Switzerland
| | - Torkjel M Sandanger
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Roel C H Vermeulen
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
- Julius Centre for Health Sciences and Primary Care, University Medical Centre, Utrecht, Utrecht, The Netherlands
| | - Florence Guida
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
- Group of Genetic Epidemiology, International Agency for Research on Cancer (IARC) - World Health Organization (WHO), Lyon, France
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK.
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands.
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Jiang N, Yang M, Han Y, Zhao H, Sun L. PRDM16 Regulating Adipocyte Transformation and Thermogenesis: A Promising Therapeutic Target for Obesity and Diabetes. Front Pharmacol 2022; 13:870250. [PMID: 35462933 PMCID: PMC9024053 DOI: 10.3389/fphar.2022.870250] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Given that obesity and diabetes have been major public health concerns and that disease morbidities have been rising continuously, effective treatment for these diseases is urgently needed. Because adipose tissue metabolism is involved in the progression of obesity and diabetes, it might be efficient to target adipocyte metabolic pathways. Positive regulatory domain zinc finger region protein 16 (PRDM16), a transcription factor that is highly expressed in adipocytes, plays a key role in adipose tissue metabolism, such as the browning and thermogenesis of adipocytes, the beigeing of adipocytes, the adipogenic differentiation of myoblasts, and the conversion of visceral adipocytes to subcutaneous adipocytes. Furthermore, clinical and basic studies have shown that the expression of PRDM16 is associated with obesity and diabetes and that PRDM16 signaling participates in the treatment of the two diseases. For example, metformin promotes thermogenesis and alleviates obesity by activating the AMPK/αKG/PRDM16 signaling pathway; rosiglitazone alleviates obesity under the synergistic effect of PRDM16; resveratrol plays an antiobesity role by inducing the expression of PRDM16; liraglupeptide improves insulin resistance by inducing the expression of PRDM16; and mulberry leaves play an anti-inflammatory and antidiabetes role by activating the expression of brown fat cell marker genes (including PRDM16). In this review, we summarize the evidence of PRDM16 involvement in the progression of obesity and diabetes and that PRDM16 may be a promising therapy for obesity and diabetes.
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18
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Li M, Ren H, Zhang Y, Liu N, Fan M, Wang K, Yang T, Chen M, Shi P. MECOM/PRDM3 and PRDM16 Serve as Prognostic-Related Biomarkers and Are Correlated With Immune Cell Infiltration in Lung Adenocarcinoma. Front Oncol 2022; 12:772686. [PMID: 35174083 PMCID: PMC8841357 DOI: 10.3389/fonc.2022.772686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/03/2022] [Indexed: 12/24/2022] Open
Abstract
Background The MDS1 and EVI1 complex locus (MECOM, also called PRDM3) and PR domain containing 16 (PRDM16) are two highly related zinc finger transcription factors associated with many malignancies. However, the mechanisms of MECOM and PRDM16 in prognosis and tumor immune infiltration in lung adenocarcinoma (LUAD) remain uncertain. Methods The Cancer Genome Atlas (TCGA), Oncomine, UALCAN, GEPIA, and TIMER databases were searched to determine the relationship between the expression of MECOM and PRDM16, clinicopathological features, immune infiltration, and prognosis in LUAD. Coexpressed genes of the two genes were investigated by CBioPortal, and the potential mechanism of MECOM- and PRDM16-related genes was elucidated by GO and KEGG analyses. STRING database was utilized to further construct the protein-protein interaction network of the coexpressed genes, and the hub genes were identified by Cytoscape. Finally, qRT-PCR was performed to identify the mRNA levels of the target genes in LUAD. Results mRNA levels of MECOM and PRDM16 were downregulated in LUAD (p < 0.05), and the low expression of the two genes was associated with the age, gender, smoking duration, tissue subtype, poor stage, nodal metastasis status, TP53 mutation, and prognosis in LUAD (p < 0.05). MECOM and PRDM16 were also found to be correlated with the expression of a variety of immune cell subsets and their markers. KEGG analysis showed that both of them were mainly enriched in the cell cycle, cellular senescence, DNA replication, and p53 signaling pathway. Importantly, the mRNA levels of the two genes were also found to be decreased in the clinical samples of LUAD by qRT-PCR. Conclusion MECOM and PRDM16 may serve as potential prognostic biomarkers which govern immune cell recruitment to LUAD.
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Affiliation(s)
- Meng Li
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Talent Highland, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Hui Ren
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Talent Highland, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yanpeng Zhang
- Department of Talent Highland, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Thoracic Surgery, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Center for Translational Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Na Liu
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Meng Fan
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Ke Wang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Tian Yang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Mingwei Chen
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Puyu Shi, ; ; Mingwei Chen, ;
| | - Puyu Shi
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Puyu Shi, ; ; Mingwei Chen, ;
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19
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Shi Q, Shao K, Jia H, Cao B, Li W, Dong S, Liu J, Wu K, Liu M, Liu F, Zhou H, Lv J, Gu F, Li L, Zhu S, Li S, Li G, Fu L. Genomic alterations and evolution of cell clusters in metastatic invasive micropapillary carcinoma of the breast. Nat Commun 2022; 13:111. [PMID: 35013309 PMCID: PMC8748639 DOI: 10.1038/s41467-021-27794-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 10/25/2021] [Indexed: 11/09/2022] Open
Abstract
Invasive micropapillary carcinoma (IMPC) has very high rates of lymphovascular invasion and lymph node metastasis and has been reported in several organs. However, the genomic mechanisms underlying its metastasis are unclear. Here, we perform whole-genome sequencing of tumor cell clusters from primary IMPC and paired axillary lymph node metastases. Cell clusters in multiple lymph node foci arise from a single subclone of the primary tumor. We find evidence that the monoclonal metastatic ancestor in primary IMPC shares high frequency copy-number loss of PRDM16 and IGSF9 and the copy number gain of ALDH2. Immunohistochemistry analysis further shows that low expression of IGSF9 and PRDM16 and high expression of ALDH2 are associated with lymph node metastasis and poor survival of patients with IMPC. We expect these genomic and evolutionary profiles to contribute to the accurate diagnosis of IMPC.
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Affiliation(s)
- Qianqian Shi
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China
| | - Kang Shao
- BGI-Shenzhen, 518120, Shenzhen, China.,BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, 450000, Zhengzhou, China
| | - Hongqin Jia
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China.,National Clinical Research Center for Cancer, 300060, Tianjin, China
| | - Boyang Cao
- BGI-Shenzhen, 518120, Shenzhen, China.,BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, 450000, Zhengzhou, China
| | - Weidong Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China.,National Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, 300060, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, 300060, Tianjin, China
| | - Shichen Dong
- BGI-Shenzhen, 518120, Shenzhen, China.,BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, 450000, Zhengzhou, China
| | - Jian Liu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China.,National Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, 300060, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, 300060, Tianjin, China
| | - Kailiang Wu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China.,National Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, 300060, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, 300060, Tianjin, China
| | - Meng Liu
- BGI-Shenzhen, 518120, Shenzhen, China.,BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, 450000, Zhengzhou, China
| | - Fangfang Liu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China.,National Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, 300060, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, 300060, Tianjin, China
| | - Hanlin Zhou
- BGI-Shenzhen, 518120, Shenzhen, China.,BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, 450000, Zhengzhou, China
| | - Jianke Lv
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China.,National Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, 300060, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, 300060, Tianjin, China
| | - Feng Gu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China.,National Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, 300060, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, 300060, Tianjin, China
| | - Luyuan Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, 300071, Tianjin, China
| | - Shida Zhu
- BGI-Shenzhen, 518120, Shenzhen, China.,BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, 450000, Zhengzhou, China
| | - Shuai Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China. .,National Clinical Research Center for Cancer, 300060, Tianjin, China. .,Key Laboratory of Cancer Prevention and Therapy, 300060, Tianjin, China. .,Tianjin's Clinical Research Center for Cancer, 300060, Tianjin, China. .,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, 300060, Tianjin, China.
| | - Guibo Li
- BGI-Shenzhen, 518120, Shenzhen, China. .,BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, 450000, Zhengzhou, China. .,Shenzhen Key Laboratory of Single-Cell Omics, 518120, Shenzhen, China.
| | - Li Fu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China. .,National Clinical Research Center for Cancer, 300060, Tianjin, China. .,Key Laboratory of Cancer Prevention and Therapy, 300060, Tianjin, China. .,Tianjin's Clinical Research Center for Cancer, 300060, Tianjin, China. .,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, 300060, Tianjin, China.
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20
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Cui Y, Luo C, Luo L, Yu Z. High-Dimensional Mediation Analysis Based on Additive Hazards Model for Survival Data. Front Genet 2021; 12:771932. [PMID: 35003213 PMCID: PMC8734376 DOI: 10.3389/fgene.2021.771932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
Mediation analysis has been extensively used to identify potential pathways between exposure and outcome. However, the analytical methods of high-dimensional mediation analysis for survival data are still yet to be promoted, especially for non-Cox model approaches. We propose a procedure including "two-step" variable selection and indirect effect estimation for the additive hazards model with high-dimensional mediators. We first apply sure independence screening and smoothly clipped absolute deviation regularization to select mediators. Then we use the Sobel test and the BH method for indirect effect hypothesis testing. Simulation results demonstrate its good performance with a higher true-positive rate and accuracy, as well as a lower false-positive rate. We apply the proposed procedure to analyze DNA methylation markers mediating smoking and survival time of lung cancer patients in a TCGA (The Cancer Genome Atlas) cohort study. The real data application identifies four mediate CpGs, three of which are newly found.
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Affiliation(s)
- Yidan Cui
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Chengwen Luo
- Public Laboratory, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, China
| | - Linghao Luo
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Zhangsheng Yu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
- Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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21
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Lan C, Liu CC, Nie XC, Lei L, Xiao ZX, Li MX, Tang XN, Jia MY, Xu HT. FAM83A Promotes the Proliferative and Invasive Abilities of Cervical Cancer Cells via Epithelial-Mesenchymal Transition and the Wnt Signaling Pathway. J Cancer 2021; 12:6320-6329. [PMID: 34659522 PMCID: PMC8489145 DOI: 10.7150/jca.62563] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/19/2021] [Indexed: 12/15/2022] Open
Abstract
The family with sequence similarity 83, member A (FAM83A) gene is associated with the occurrence and development of many malignant tumors. Our aim was to explore the role of FAM83A in cervical cancer. FAM83A was overexpressed or knocked down in cervical cancer cells, and the expressions of FAM83A, key proteins involved in the epithelial-mesenchymal transition (EMT), and Wnt signaling pathway-related proteins were detected by western blot analysis. Cell proliferative and invasive abilities were also examined using cell proliferation, colony formation, and Matrigel invasion assays. Cells were treated with the Wnt pathway inhibitor XAV-939 to determine whether Wnt signaling was necessary for the effect of FAM83A on cervical cancer cells. FAM83A was highly expressed in cervical cancer tissues and was associated with differentiation, TNM stage, lymph node metastasis, and poor prognosis in patients with cervical cancer. Knockdown of FAM83A inhibited the proliferation, colony formation, and invasion of cervical cancer cells. The opposite results were observed in FAM83A-overexpressing cells, and FAM83A overexpression also promoted EMT and Wnt signaling. XAV-939 reversed the activation of Wnt signaling and EMT induced by FAM83A. In conclusion, FAM83A expression was increased in cervical cancers and correlated with poor prognosis of patients. FAM83A overexpression can activate the Wnt signaling pathway, facilitate EMT, and promote the proliferative and invasive abilities of cervical cancer cells.
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Affiliation(s)
- Chong Lan
- Department of Gynecology, Shenyang Women and Children's Hospital, Shenyang, China
| | - Chen-Chen Liu
- Department of Pathology, the First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, 110001, China
| | - Xiao-Cui Nie
- Department of Gynecology, Shenyang Women and Children's Hospital, Shenyang, China
| | - Lei Lei
- Department of Pathology, the First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, 110001, China
| | - Zhang-Xian Xiao
- Department of Pathology, the First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, 110001, China
| | - Ming-Xi Li
- Department of Pathology, the First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, 110001, China
| | - Xue-Nan Tang
- Department of Gynecology, Shenyang Women and Children's Hospital, Shenyang, China
| | - Ming-Yu Jia
- Department of Gynecology, Shenyang Women and Children's Hospital, Shenyang, China
| | - Hong-Tao Xu
- Department of Pathology, the First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, 110001, China
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22
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Lei L, Wang Y, Li ZH, Fei LR, Huang WJ, Zheng YW, Liu CC, Yang MQ, Wang Z, Zou ZF, Xu HT. PHLDA3 promotes lung adenocarcinoma cell proliferation and invasion via activation of the Wnt signaling pathway. J Transl Med 2021; 101:1130-1141. [PMID: 34006890 DOI: 10.1038/s41374-021-00608-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 01/05/2023] Open
Abstract
The PHLDA3 gene encodes a small 127 amino acid protein with a pleckstrin homology (PH)-only domain. The expression and significance of PHLDA3 in lung cancer remain unclear. Here, we investigated the role of PHLDA3 in tumor proliferation and invasion in lung adenocarcinoma. Immunohistochemistry and immunoblotting analyses were used to assess PHLDA3 expression in lung cancer tissues, and its correlation with clinicopathological factors in lung cancer. Plasmids encoding PHLDA3 and small interfering RNA against PHLDA3 were used to regulate the expression of PHLDA3 in lung cancer cells. Furthermore, the effects of PHLDA3 on lung cancer cell proliferation and invasion were investigated using the MTS, colony formation, Matrigel invasion, and wound healing assays. Co-immunoprecipitation analysis and inhibitors of both the Wnt signaling pathway and GSK3β were used to explore the regulatory mechanisms underlying the role of PHLDA3 in lung cancer cells. PHLDA3 was found to be overexpressed in lung cancer tissues, and its expression was correlated with poor outcomes in lung adenocarcinoma patients. PHLDA3 expression promoted the proliferation, invasion, and migration of lung cancer cells. Overexpression of PHLDA3 activated the Wnt signaling pathway and facilitated epithelial-mesenchymal transition. Inhibition of Wnt signaling pathway activity, using XAV-939, reversed the effects of PHLDA3 overexpression in lung cancer cells; moreover, PHLDA3 could bind to GSK3β. Inhibition of GSK3β activity, using CHIR-99021, restored the proliferative and invasive abilities of PHLDA3 knockdown cells. Our findings demonstrate that PHLDA3 is highly expressed in lung adenocarcinomas and is correlated with poor outcomes. Furthermore, it promotes the proliferation and invasion of lung cancer cells by activating the Wnt signaling pathway.
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Affiliation(s)
- Lei Lei
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Yuan Wang
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
- Department of Pathology, Jinzhou Medical University, Jinzhou, China
| | - Zhi-Han Li
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Liang-Ru Fei
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Wen-Jing Huang
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
- Department of Pathology, The Fourth People's Hospital of Shenyang, Shenyang, China
| | - Yi-Wen Zheng
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Chen-Chen Liu
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Mai-Qing Yang
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
- Department of Pathology, Changyi People's Hospital, Changyi, China
| | - Zhao Wang
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China
- Department of Pathology, General Hospital of Heilongjiang Land Reclamation Bureau, Harbin, China
| | - Zi-Fang Zou
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Hong-Tao Xu
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China.
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23
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Pratama R, Hwang JJ, Lee JH, Song G, Park HR. Authentication of differential gene expression in oral squamous cell carcinoma using machine learning applications. BMC Oral Health 2021; 21:281. [PMID: 34051764 PMCID: PMC8164276 DOI: 10.1186/s12903-021-01642-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/22/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recently, the possibility of tumour classification based on genetic data has been investigated. However, genetic datasets are difficult to handle because of their massive size and complexity of manipulation. In the present study, we examined the diagnostic performance of machine learning applications using imaging-based classifications of oral squamous cell carcinoma (OSCC) gene sets. METHODS RNA sequencing data from SCC tissues from various sites, including oral, non-oral head and neck, oesophageal, and cervical regions, were downloaded from The Cancer Genome Atlas (TCGA). The feature genes were extracted through a convolutional neural network (CNN) and machine learning, and the performance of each analysis was compared. RESULTS The ability of the machine learning analysis to classify OSCC tumours was excellent. However, the tool exhibited poorer performance in discriminating histopathologically dissimilar cancers derived from the same type of tissue than in differentiating cancers of the same histopathologic type with different tissue origins, revealing that the differential gene expression pattern is a more important factor than the histopathologic features for differentiating cancer types. CONCLUSION The CNN-based diagnostic model and the visualisation methods using RNA sequencing data were useful for correctly categorising OSCC. The analysis showed differentially expressed genes in multiwise comparisons of various types of SCCs, such as KCNA10, FOSL2, and PRDM16, and extracted leader genes from pairwise comparisons were FGF20, DLC1, and ZNF705D.
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Affiliation(s)
- Rian Pratama
- School of Computer Science and Engineering, Pusan National University, 63 Busandaehak-Ro, Busan, 46241, Republic of Korea
| | - Jae Joon Hwang
- Department of Oral and Maxillofacial Radiology, School of Dentistry, Pusan National University, Dental Research Institute, Yangsan, 50610, Republic of Korea
| | - Ji Hye Lee
- Department of Oral Pathology, School of Dentistry, Pusan National University, 49 Busandaehak-Ro, Yangsan, 50612, Republic of Korea.,Periodontal Disease Signaling Network Research Center, School of Dentistry, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Giltae Song
- School of Computer Science and Engineering, Pusan National University, 63 Busandaehak-Ro, Busan, 46241, Republic of Korea.
| | - Hae Ryoun Park
- Department of Oral Pathology, School of Dentistry, Pusan National University, 49 Busandaehak-Ro, Yangsan, 50612, Republic of Korea. .,Periodontal Disease Signaling Network Research Center, School of Dentistry, Pusan National University, Yangsan, 50612, Republic of Korea.
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24
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Fuemmeler BF, Dozmorov MG, Do EK, Zhang J(J, Grenier C, Huang Z, Maguire RL, Kollins SH, Hoyo C, Murphy SK. DNA Methylation in Babies Born to Nonsmoking Mothers Exposed to Secondhand Smoke during Pregnancy: An Epigenome-Wide Association Study. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:57010. [PMID: 34009014 PMCID: PMC8132610 DOI: 10.1289/ehp8099] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 02/09/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Maternal smoking during pregnancy is related to altered DNA methylation in infant umbilical cord blood. The extent to which low levels of smoke exposure among nonsmoking pregnant women relates to offspring DNA methylation is unknown. OBJECTIVE This study sought to evaluate relationships between maternal prenatal plasma cotinine levels and DNA methylation in umbilical cord blood in newborns using the Infinium HumanMethylation 450K BeadChip. METHODS Participants from the Newborn Epigenetics Study cohort who reported not smoking during pregnancy had verified low levels of cotinine from maternal prenatal plasma (0 ng / mL to < 4 ng / mL ), and offspring epigenetic data from umbilical cord blood were included in this study (n = 79 ). Multivariable linear regression models were fit to the data, controlling for cell proportions, age, race, education, and parity. Estimates represent changes in response to any 1 -ng / mL unit increase in exposure. RESULTS Multivariable linear regression models yielded 29,049 CpGs that were differentially methylated in relation to increases in cotinine at a 5% false discovery rate. Top CpGs were within or near genes involved in neuronal functioning (PRKG1, DLGAP2, BSG), carcinogenesis (FHIT, HSPC157) and inflammation (AGER). Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggest cotinine was related to methylation of gene pathways controlling neuronal signaling, metabolic regulation, cell signaling and regulation, and cancer. Further, enhancers associated with transcription start sites were enriched in altered CpGs. Using an independent sample from the same study population (n = 115 ), bisulfite pyrosequencing was performed with infant cord blood DNA for two genes within our top 20 hits (AGER and PRKG1). Results from pyrosequencing replicated epigenome results for PRKG1 (cg17079497, estimate = - 1.09 , standard error ( SE ) = 0.45 , p = 0.018 ) but not for AGER (cg09199225; estimate = - 0.16 , SE = 0.21 , p = 0.44 ). DISCUSSION Secondhand smoke exposure among nonsmoking women may alter DNA methylation in regions involved in development, carcinogenesis, and neuronal functioning. These novel findings suggest that even low levels of smoke exposure during pregnancy may be sufficient to alter DNA methylation in distinct sites of mixed umbilical cord blood leukocytes in pathways that are known to be altered in cord blood from pregnant active smokers. https://doi.org/10.1289/EHP8099.
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Affiliation(s)
- Bernard F. Fuemmeler
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, Virginia, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Elizabeth K. Do
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, Virginia, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Junfeng (Jim) Zhang
- Nicholas School of the Environment and Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Carole Grenier
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Zhiqing Huang
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Rachel L. Maguire
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Biological Sciences, Center for Human Health and the Environment North Carolina State University, Raleigh, North Carolina, USA
| | - Scott H. Kollins
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, North Carolina, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, Center for Human Health and the Environment North Carolina State University, Raleigh, North Carolina, USA
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
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25
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El Khoury LY, Fu S, Hlady RA, Wagner RT, Wang L, Eckel-Passow JE, Castle EP, Stanton ML, Thompson RH, Parker AS, Ho TH, Robertson KD. Identification of DNA methylation signatures associated with poor outcome in lower-risk Stage, Size, Grade and Necrosis (SSIGN) score clear cell renal cell cancer. Clin Epigenetics 2021; 13:12. [PMID: 33461589 PMCID: PMC7814746 DOI: 10.1186/s13148-020-00998-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/21/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Despite using prognostic algorithms and standard surveillance guidelines, 17% of patients initially diagnosed with low risk clear cell renal cell carcinoma (ccRCC) ultimately relapse and die of recurrent disease, indicating additional molecular parameters are needed for improved prognosis. RESULTS To address the gap in ccRCC prognostication in the lower risk population, we performed a genome-wide analysis for methylation signatures capable of distinguishing recurrent and non-recurrent ccRCCs within the subgroup classified as 'low risk' by the Mayo Clinic Stage, Size, Grade, and Necrosis score (SSIGN 0-3). This approach revealed that recurrent patients have globally hypermethylated tumors and differ in methylation significantly at 5929 CpGs. Differentially methylated CpGs (DMCpGs) were enriched in regulatory regions and genes modulating cell growth and invasion. A subset of DMCpGs stratified low SSIGN groups into high and low risk of recurrence in independent data sets, indicating that DNA methylation enhances the prognostic power of the SSIGN score. CONCLUSIONS This study reports a global DNA hypermethylation in tumors of recurrent ccRCC patients. Furthermore, DMCpGs were capable of discriminating between aggressive and less aggressive tumors, in addition to SSIGN score. Therefore, DNA methylation presents itself as a potentially strong biomarker to further improve prognostic power in patients with low risk SSIGN score (0-3).
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Affiliation(s)
- Louis Y El Khoury
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Epigenomics Program, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Shuang Fu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Epigenomics Program, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.,Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ryan A Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Epigenomics Program, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Ryan T Wagner
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Epigenomics Program, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Jeanette E Eckel-Passow
- Division of Biomedical Statistics and Informatics, Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Erik P Castle
- Department of Urology, Mayo Clinic, Phoenix, AZ, USA
| | - Melissa L Stanton
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, AZ, USA
| | | | - Alexander S Parker
- Office of Research Affairs, University of Florida, Jacksonville, FL, USA
| | - Thai H Ho
- Division of Hematology and Medical Oncology, Mayo Clinic, 13400 E. Shea Blvd, Scottsdale, AZ, 85259, USA.
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA. .,Center for Individualized Medicine, Epigenomics Program, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
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26
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Emerging Roles of PRDM Factors in Stem Cells and Neuronal System: Cofactor Dependent Regulation of PRDM3/16 and FOG1/2 (Novel PRDM Factors). Cells 2020; 9:cells9122603. [PMID: 33291744 PMCID: PMC7761934 DOI: 10.3390/cells9122603] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/13/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022] Open
Abstract
PRDI-BF1 (positive regulatory domain I-binding factor 1) and RIZ1 (retinoblastoma protein-interacting zinc finger gene 1) (PR) homologous domain containing (PRDM) transcription factors are expressed in neuronal and stem cell systems, and they exert multiple functions in a spatiotemporal manner. Therefore, it is believed that PRDM factors cooperate with a number of protein partners to regulate a critical set of genes required for maintenance of stem cell self-renewal and differentiation through genetic and epigenetic mechanisms. In this review, we summarize recent findings about the expression of PRDM factors and function in stem cell and neuronal systems with a focus on cofactor-dependent regulation of PRDM3/16 and FOG1/2. We put special attention on summarizing the effects of the PRDM proteins interaction with chromatin modulators (NuRD complex and CtBPs) on the stem cell characteristic and neuronal differentiation. Although PRDM factors are known to possess intrinsic enzyme activity, our literature analysis suggests that cofactor-dependent regulation of PRDM3/16 and FOG1/2 is also one of the important mechanisms to orchestrate bidirectional target gene regulation. Therefore, determining stem cell and neuronal-specific cofactors will help better understanding of PRDM3/16 and FOG1/2-controlled stem cell maintenance and neuronal differentiation. Finally, we discuss the clinical aspect of these PRDM factors in different diseases including cancer. Overall, this review will help further sharpen our knowledge of the function of the PRDM3/16 and FOG1/2 with hopes to open new research fields related to these factors in stem cell biology and neuroscience.
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Ning Y, Zheng H, Zhan Y, Liu S, Yang Y, Zang H, Luo J, Wen Q, Fan S. Comprehensive analysis of the mechanism and treatment significance of Mucins in lung cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:162. [PMID: 32807223 PMCID: PMC7433199 DOI: 10.1186/s13046-020-01662-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/03/2020] [Indexed: 12/19/2022]
Abstract
Aberrant expression of mucin proteins has played a complex and essential role in cancer development and metastasis. Members of the mucin family have been intimately implicated in lung cancer progression, metastasis, survival and chemo-resistance. During the progression of lung cancer, mucin proteins have involved all of the procession of lung cancer, which is interacted with many receptor tyrosine kinases signal pathways and mediated cell signals for tumor cell growth and survival. Mucins thus have been considerable as the indicator of negative prognosis and desirable therapeutic targets of lung cancers. In this review, we comprehensively analyzed the role of each member of the mucin family in lung cancer by combining open-accessed database analysis and assembling cutting-edge information about these molecules.
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Affiliation(s)
- Yue Ning
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Hongmei Zheng
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Yuting Zhan
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Sile Liu
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Yang Yang
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Hongjing Zang
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Jiadi Luo
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Qiuyuan Wen
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Songqing Fan
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
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Batista-Gomes JA, Mello FAR, de Oliveira EHC, de Souza MPC, Wanderley AV, da Costa Pantoja L, dos Santos NPC, Khayat BCM, Khayat AS. Identifying novel genetic alterations in pediatric acute lymphoblastic leukemia based on copy number analysis. Mol Cytogenet 2020; 13:25. [PMID: 32607130 PMCID: PMC7320540 DOI: 10.1186/s13039-020-00491-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/08/2020] [Indexed: 11/12/2022] Open
Abstract
Copy number variations (CNVs) analysis may reveal molecular biomarkers and provide information on the pathogenesis of acute lymphoblastic leukemia (ALL). We investigated the gene copy number in childhood ALL by microarray and select three new recurrent CNVs to evaluate by real-time PCR assay: DMBT1, KIAA0125 and PRDM16 were selected due to high frequency of CNVs in ALL samples and based on their potential biological functions in carcinogenesis described in the literature. DBMT1 deletion was associated with patients with chromosomal translocations and is a potential tumor suppressor; KIAA0125 and PRDM16 may act as an oncogene despite having a paradoxical behavior in carcinogenesis. This study reinforces that microarrays/aCGH is it is a powerful tool for detection of genomic aberrations, which may be used in the risk stratification.
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Casamassimi A, Rienzo M, Di Zazzo E, Sorrentino A, Fiore D, Proto MC, Moncharmont B, Gazzerro P, Bifulco M, Abbondanza C. Multifaceted Role of PRDM Proteins in Human Cancer. Int J Mol Sci 2020; 21:ijms21072648. [PMID: 32290321 PMCID: PMC7177584 DOI: 10.3390/ijms21072648] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/29/2020] [Accepted: 04/08/2020] [Indexed: 12/15/2022] Open
Abstract
The PR/SET domain family (PRDM) comprise a family of genes whose protein products share a conserved N-terminal PR [PRDI-BF1 (positive regulatory domain I-binding factor 1) and RIZ1 (retinoblastoma protein-interacting zinc finger gene 1)] homologous domain structurally and functionally similar to the catalytic SET [Su(var)3-9, enhancer-of-zeste and trithorax] domain of histone methyltransferases (HMTs). These genes are involved in epigenetic regulation of gene expression through their intrinsic HMTase activity or via interactions with other chromatin modifying enzymes. In this way they control a broad spectrum of biological processes, including proliferation and differentiation control, cell cycle progression, and maintenance of immune cell homeostasis. In cancer, tumor-specific dysfunctions of PRDM genes alter their expression by genetic and/or epigenetic modifications. A common characteristic of most PRDM genes is to encode for two main molecular variants with or without the PR domain. They are generated by either alternative splicing or alternative use of different promoters and play opposite roles, particularly in cancer where their imbalance can be often observed. In this scenario, PRDM proteins are involved in cancer onset, invasion, and metastasis and their altered expression is related to poor prognosis and clinical outcome. These functions strongly suggest their potential use in cancer management as diagnostic or prognostic tools and as new targets of therapeutic intervention.
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Affiliation(s)
- Amelia Casamassimi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Correspondence: (A.C.); (C.A.); Tel.: +39-081-566-7579 (A.C.); +39-081-566-7568 (C.A.)
| | - Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
| | - Erika Di Zazzo
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy;
| | - Anna Sorrentino
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
| | - Donatella Fiore
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Maria Chiara Proto
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Bruno Moncharmont
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy;
| | - Patrizia Gazzerro
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, 80131 Naples, Italy;
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Correspondence: (A.C.); (C.A.); Tel.: +39-081-566-7579 (A.C.); +39-081-566-7568 (C.A.)
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