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Targeting DNA Methylation in Leukemia, Myelodysplastic Syndrome, and Lymphoma: A Potential Diagnostic, Prognostic, and Therapeutic Tool. Int J Mol Sci 2022; 24:ijms24010633. [PMID: 36614080 PMCID: PMC9820560 DOI: 10.3390/ijms24010633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022] Open
Abstract
DNA methylation represents a crucial mechanism of epigenetic regulation in hematologic malignancies. The methylation process is controlled by specific DNA methyl transferases and other regulators, which are often affected by genetic alterations. Global hypomethylation and hypermethylation of tumor suppressor genes are associated with hematologic cancer development and progression. Several epi-drugs have been successfully implicated in the treatment of hematologic malignancies, including the hypomethylating agents (HMAs) decitabine and azacytidine. However, combinations with other treatment modalities and the discovery of new molecules are still the subject of research to increase sensitivity to anti-cancer therapies and improve patient outcomes. In this review, we summarized the main functions of DNA methylation regulators and genetic events leading to changes in methylation landscapes. We provide current knowledge about target genes with aberrant methylation levels in leukemias, myelodysplastic syndromes, and malignant lymphomas. Moreover, we provide an overview of the clinical trials, focused mainly on the combined therapy of HMAs with other treatments and its impact on adverse events, treatment efficacy, and survival rates among hematologic cancer patients. In the era of precision medicine, a transition from genes to their regulation opens up the possibility of an epigenetic-based approach as a diagnostic, prognostic, and therapeutic tool.
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Wu DL, Wang Y, Zhang TJ, Chu MQ, Xu ZJ, Yuan Q, Ma JC, Lin J, Qian J, Zhou JD. SLIT2 promoter hypermethylation predicts disease progression in chronic myeloid leukemia. Eur J Med Res 2022; 27:259. [PMID: 36411451 PMCID: PMC9677675 DOI: 10.1186/s40001-022-00899-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/13/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Aberrant DNA methylation plays a crucial role in the progression of myeloid neoplasms. Previously, our literature reported that slit guidance ligand 2 (SLIT2) promoter methylation was associated with disease progression and indicated a poor prognosis in patients with myelodysplastic syndrome. Herein, we further investigated the clinical implications and role of SLIT2 promoter methylation in patients with chronic myeloid leukemia (CML). METHODS The level of SLIT2 promoter methylation was determined in 104 CML patients, and its clinical significance was analyzed. Moreover, demethylation studies were performed in K562 cells to determine the epigenetic mechanism by which SLIT2 promoter methylation is regulated in CML. RESULTS The level of SLIT2 promoter methylation was similar between CML patients and controls. However, deeper analysis revealed that the SLIT2 promoter methylation level in the accelerated phase (AP) and blast crisis (BC) was markedly higher than that in the chronic phase (CP) and controls. Additionally, a marked difference was identified between the SLIT2 promoter hypermethylated and non-hypermethylated groups among CML patients grouped by clinical stage. The frequency of SLIT2 hypermethylation was markedly increased with the progression of clinical stage, that is, it was the lowest in CP samples (12/80, 15%), higher in AP samples (4/8, 50%) and the highest in BC samples (11/16, 69%). Importantly, the level/density of SLIT2 promoter methylation was significantly higher in the advanced stage than in the early stage among the 6 tested paired CML patients. Epigenetically, the expression of the SLIT2-embedded non-coding genes SLIT2-IT1 and miR-218 expression was decreased in patients with CML. SLIT2 promoter hypermethylated cases had a markedly lower SLIT2-IT1 expression level than SLIT2 promoter non-hypermethylated cases. Moreover, SLIT2-IT1 and miR-218 expression was remarkably upregulated in a dose-dependent manner after demethylation treatment of K562 cells. CONCLUSIONS Hypermethylation of the SLIT2 promoter is correlated with disease progression in CML. Furthermore, SLIT2 promoter methylation may function by regulating the expression of the SLIT2-embedded non-coding genes SLIT2-IT1 and miR-218 during CML progression.
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Affiliation(s)
- De-long Wu
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,Department of Oncology, Dongtai People’s Hospital, Dongtai, Jiangsu People’s Republic of China
| | - Yun Wang
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Ting-juan Zhang
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Department of Oncology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China
| | - Ming-qiang Chu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China
| | - Zi-jun Xu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China
| | - Qian Yuan
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China
| | - Ji-chun Ma
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China
| | - Jiang Lin
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China
| | - Jun Qian
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Jing-dong Zhou
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
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Zhang TJ, Xu ZJ, Wen XM, Gu Y, Ma JC, Yuan Q, Lin J, Zhou JD, Qian J. SLIT2 promoter hypermethylation-mediated SLIT2-IT1/miR-218 repression drives leukemogenesis and predicts adverse prognosis in myelodysplastic neoplasm. Leukemia 2022; 36:2488-2498. [PMID: 35906386 DOI: 10.1038/s41375-022-01659-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/13/2022] [Accepted: 07/19/2022] [Indexed: 01/09/2023]
Abstract
Epigenetic modifications have been found to play crucial roles in myelodysplastic neoplasm (MDS) progression. Previously, we investigated genome-wide DNA methylation alterations during MDS evolution to acute myeloid leukemia (AML) by next-generation sequencing (NGS). Herein, we further determined the role and clinical implications of an evident methylation change in CpG islands at the SLIT2 promoter identified by NGS. First, increased SLIT2 promoter methylation was validated in 11 paired MDS/AML patients during disease evolution. Additionally, SLIT2 promoter methylation was markedly increased in MDS/AML patients compared with controls and was correlated with poor clinical phenotype and outcome. Interestingly, SLIT2 expression was particularly upregulated in AML patients and was not correlated with SLIT2 promoter methylation. However, the SLIT2-embedded genes SLIT2-IT1 and miR-218 were downregulated in AML patients, which was negatively associated with SLIT2 promoter methylation and further validated by demethylation studies. Functionally, SLIT2-IT1/miR-218 overexpression exhibited antileukemic effects by affecting cell proliferation, apoptosis and colony formation in vitro and in vivo. Mechanistically, SLIT2-IT1 may function as a competing endogenous RNA by sponging miR-3156-3p to regulate BMF expression, whereas miR-218 may directly target HOXA1 in MDS progression. In summary, our findings demonstrate that SLIT2 promoter hypermethylation is associated with disease evolution in MDS and predicts poor prognoses in both MDS and AML. Epigenetic inactivation of SLIT2-IT1/miR-218 by SLIT2 promoter hypermethylation could be a promising therapeutic target in MDS.
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Affiliation(s)
- Ting-Juan Zhang
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Department of Oncology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Zi-Jun Xu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Xiang-Mei Wen
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Yu Gu
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Ji-Chun Ma
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Qian Yuan
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Jiang Lin
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China.
| | - Jing-Dong Zhou
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.
| | - Jun Qian
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.
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Aberrant Methylation of SLIT2 Gene in Plasma Cell-Free DNA of Non-Small Cell Lung Cancer Patients. Cancers (Basel) 2022; 14:cancers14020296. [PMID: 35053460 PMCID: PMC8773699 DOI: 10.3390/cancers14020296] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/02/2022] [Accepted: 01/04/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary Despite significant advances in the detection, prevention, and treatment of lung cancer, the prognosis of the patients is still very poor due in part to micrometastasis of cancer cells to surrounding tissues at the time of diagnosis. Therefore, identifying biomarkers for early detection of lung cancer is very important for prolonging the lifespan of patients with lung cancer. The methylation statuses of SLIT1, SLIT2, SLIT3 genes were analyzed in bronchial washing, bronchial biopsy, sputum, tumor and matched normal tissues, or plasma samples obtained from a total of 208 non-small cell lung cancer (NSCLC) patients and 121 cancer-free patients to understand the feasibility of the genes as biomarkers for early detection and survival prediction of NSCLC. The present study suggests that aberrant methylation of SLIT2 in plasma cell-free DNA might be a potential biomarker for the early detection and prognosis prediction of NSCLC patient. Abstract This study aimed to understand aberrant methylation of SLITs genes as a biomarker for the early detection and prognosis prediction of non-small cell lung cancer (NSCLC). Methylation levels of SLITs were determined using the Infinium HumanMethylation450 BeadChip or pyrosequencing. Five CpGs at the CpG island of SLIT1, SLIT2 or SLIT3 genes were significantly (Bonferroni corrected p < 0.05) hypermethylated in tumor tissues obtained from 42 NSCLC patients than in matched normal tissues. Methylation levels of these CpGs did not differ significantly between bronchial washings obtained from 76 NSCLC patients and 60 cancer-free patients. However, methylation levels of SLIT2 gene were significantly higher in plasma cell-free DNA of 72 NSCLC patients than in that of 61 cancer-free patients (p = 0.001, Wilcoxon rank sum test). Prediction of NSCLC using SLIT2 methylation was achieved with a sensitivity of 73.7% and a specificity of 61.9% in a plasma test dataset (N = 40). A Cox proportional hazards model showed that SLIT2 hypermethylation in plasma cell-free DNA was significantly associated with poor recurrence-free survival (hazards ratio = 2.19, 95% confidence interval = 1.21–4.36, p = 0.01). The present study suggests that aberrant methylation of SLIT2 in plasma cell-free DNA is a valuable biomarker for the early detection of NSCLC and prediction of recurrence-free survival. However, further research is needed with larger sample size to confirm results.
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Kaul K, Benej M, Mishra S, Ahirwar DK, Yadav M, Stanford KI, Jacob NK, Denko NC, Ganju RK. Slit2-Mediated Metabolic Reprogramming in Bone Marrow-Derived Macrophages Enhances Antitumor Immunity. Front Immunol 2021; 12:753477. [PMID: 34777365 PMCID: PMC8581492 DOI: 10.3389/fimmu.2021.753477] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/06/2021] [Indexed: 11/13/2022] Open
Abstract
Slit2 exerts antitumor effects in various cancers; however, the underlying mechanism, especially its role in regulating the immune, especially in the bone marrow niche, system is still unknown. Elucidating the behavior of macrophages in tumor progression can potentially improve immunotherapy. Using a spontaneous mammary tumor virus promoter-polyoma middle T antigen (PyMT) breast cancer mouse model, we observed that Slit2 increased the abundance of antitumor M1 macrophage in the bone marrow upon differentiation in vitro. Moreover, myeloablated PyMT mice injected with Slit2-treated bone marrow allografts showed a marked reduction in tumor growth, with enhanced recruitment of M1 macrophage in their tumor stroma. Mechanistic studies revealed that Slit2 significantly enhanced glycolysis and reduced fatty acid oxidation in bone marrow-derived macrophages (BMDMs). Slit2 treatment also altered mitochondrial respiration metabolites in macrophages isolated from healthy human blood that were treated with plasma from breast cancer patients. Overall, this study, for the first time, shows that Slit2 increases BMDM polarization toward antitumor phenotype by modulating immune-metabolism. Furthermore, this study provides evidence that soluble Slit2 could be developed as novel therapeutic strategy to enhance antitumor immune response.
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Affiliation(s)
- Kirti Kaul
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States.,Department of Pathology, The Ohio State University, Columbus, OH, United States
| | - Martin Benej
- Department of Radiation Oncology, The Ohio State University, Columbus, OH, United States
| | - Sanjay Mishra
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States.,Department of Pathology, The Ohio State University, Columbus, OH, United States
| | - Dinesh K Ahirwar
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States.,Department of Pathology, The Ohio State University, Columbus, OH, United States
| | - Marshleen Yadav
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States.,Department of Radiation Oncology, The Ohio State University, Columbus, OH, United States
| | - Kristin I Stanford
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Naduparambil K Jacob
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States.,Department of Radiation Oncology, The Ohio State University, Columbus, OH, United States
| | - Nicholas C Denko
- Department of Radiation Oncology, The Ohio State University, Columbus, OH, United States
| | - Ramesh K Ganju
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States.,Department of Pathology, The Ohio State University, Columbus, OH, United States
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Li P, Lin Z, Liu Q, Chen S, Gao X, Guo W, Gong F, Wei J, Lin H. Enhancer RNA SLIT2 Inhibits Bone Metastasis of Breast Cancer Through Regulating P38 MAPK/c-Fos Signaling Pathway. Front Oncol 2021; 11:743840. [PMID: 34722297 PMCID: PMC8554345 DOI: 10.3389/fonc.2021.743840] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/23/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Breast cancer (BRCA) is the most common cancer in women, while the bones are one of the most common sites of metastasis. Although new diagnostic methods or radiation or chemotherapies and targeted therapies have made huge advances, the occurrence of bone metastasis is also linked with poorer survival. Enhancer RNAs (eRNAs) have been demonstrated to participate in the progression of tumorigenesis and metastasis. However, the role of eRNAs in BRCA bone metastasis remains largely unclear. METHOD Gene expression profiling of 1,211 primary BRCA and 17 bone metastases samples were retrieved from The Cancer Genome Atlas (TCGA) database, and the significant prognostic eRNAs were identified by Cox regression and least absolute shrinkage and selection operator (LASSO) regression. The acceptable accuracy and discrimination of the nomogram were indicated by the receiver operating characteristic (ROC) and the calibration curves. Then target genes of eRNA, immune cell percentage by CIBERSORT analysis, immune genes by single-sample gene set enrichment analysis (ssGSEA), hallmark of cancer signaling pathway by gene set variation analysis (GSVA), and reverse phase protein array (RPPA) protein chip were used to build a co-expression regulation network and identified the key eRNAs in bone metastasis of BRCA. Finally, Cell Counting Kit-8 (CCK8) assay, cell cycle assay, and transwell assay were used to study changes in cell proliferation, migration, and invasiveness. Immunoprecipitation assay and Western blotting were used to test the interaction and the regulation signaling pathways. RESULTS The 27 hub eRNAs were selected, and a survival-related linear risk assessment model with a relatively high accuracy (area under curve (AUC): 0.726) was constructed. In addition, seven immune-related eRNAs (SLIT2, CLEC3B, LBPL1, FRY, RASGEF1B, DST, and ITIH5) as prognostic signatures for bone metastasis of BRCA were further confirmed by LASSO and multivariate Cox regression and CIBERSORT analysis. Finally, in vitro assay demonstrated that overexpression of SLIT2 reduced proliferation and metastasis in BRCA cells. Using high-throughput co-expression regulation network, we identified that SLIT2 may regulating P38 MAPK/c-Fos signaling pathway to promote the effects of metastasis. CONCLUSION Based on the co-expression network for bone metastasis of BRCA, we screened key eRNAs to explore a prognostic model in predicting the bone metastasis by bioinformatics analysis. Besides, we identified the potential regulatory signaling pathway of SLIT2 in BRCA bone metastasis, which provides a promising therapeutic strategy for metastasis of BRCA.
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Affiliation(s)
- Peng Li
- Stem Cell Research and Cellular Therapy Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Zhiping Lin
- Orthopedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- Orthopedic Center, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Qianzheng Liu
- Orthopedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Siyuan Chen
- Orthopedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Xiang Gao
- Stem Cell Research and Cellular Therapy Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Weixiong Guo
- Orthopedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Fan Gong
- Orthopedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jinsong Wei
- Orthopedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Hao Lin
- Orthopedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
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Kaulen LD, Erson-Omay EZ, Henegariu O, Karschnia P, Huttner A, Günel M, Baehring JM. Exome sequencing identifies SLIT2 variants in primary CNS lymphoma. Br J Haematol 2021; 193:375-379. [PMID: 33481259 DOI: 10.1111/bjh.17319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/14/2020] [Indexed: 12/21/2022]
Abstract
SLIT2 constitutes a known tumour suppressor gene, which has not yet been implicated in the pathogenesis of primary central nervous system lymphoma (PCNSL). Performing exome sequencing on paired blood and tumour DNA samples from six treatment-naïve PCNSL patients, we identified novel SLIT2 variants (p.N63S, p.T590M, p.T732S) that were associated with shorter progression-free survival in our cohort and shorter overall survival in a large validation cohort of lymphoid malignancies from the cBio Cancer Genomics Portal. WNT- and NF-κB-reporter luciferase assays suggest detected alterations are loss-of-function variants. Given the possible prognostic implications, the role of SLIT2 in PCNSL pathogenesis and progression warrants further investigation.
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Affiliation(s)
- Leon D Kaulen
- Department of Neurology, Yale School of Medicine, New Haven, USA.,Department of Neurology, Heidelberg University Hospital, Heidelberg, Germany.,Department of Neurosurgery, Yale School of Medicine, New Haven, USA
| | - E Zeynep Erson-Omay
- Department of Neurosurgery, Yale School of Medicine, New Haven, USA.,Department of Genetics, Yale School of Medicine, New Haven, USA
| | - Octavian Henegariu
- Department of Neurosurgery, Yale School of Medicine, New Haven, USA.,Department of Genetics, Yale School of Medicine, New Haven, USA
| | - Philipp Karschnia
- Department of Neurology, Yale School of Medicine, New Haven, USA.,Department of Neurosurgery, Ludwig Maximilians University School of Medicine, Munich, Germany
| | - Anita Huttner
- Department of Pathology, Yale School of Medicine, New Haven, USA
| | - Murat Günel
- Department of Neurosurgery, Yale School of Medicine, New Haven, USA.,Department of Genetics, Yale School of Medicine, New Haven, USA
| | - Joachim M Baehring
- Department of Neurology, Yale School of Medicine, New Haven, USA.,Department of Neurosurgery, Yale School of Medicine, New Haven, USA
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Dong H, Wang Q, Zhang G, Li N, Yang M, An Y, Xie L, Li H, Zhang L, Zhu W, Zhao S, Zhang H, Guo X. OSdlbcl: An online consensus survival analysis web server based on gene expression profiles of diffuse large B-cell lymphoma. Cancer Med 2020; 9:1790-1797. [PMID: 31918459 PMCID: PMC7050097 DOI: 10.1002/cam4.2829] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/11/2019] [Accepted: 12/26/2019] [Indexed: 12/12/2022] Open
Abstract
Diffuse large B‐cell lymphoma (DLBCL) is the most common subtype of non‐Hodgkin lymphoma (NHL) and is a clinical, pathological, and molecular heterogeneous disease with highly variable clinical outcomes. Currently, valid prognostic biomarkers in DLBCL are still lacking. To optimize targeted therapy and improve the prognosis of DLBCL, the performance of proposed biomarkers needs to be evaluated in multiple cohorts, and new biomarkers need to be investigated in large datasets. Here, we developed a consensus Online Survival analysis web server for Diffuse Large B‐Cell Lymphoma, abbreviated OSdlbcl, to assess the prognostic value of individual gene. To build OSdlbcl, we collected 1100 samples with gene expression profiles and clinical follow‐up information from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. In addition, DNA mutation data were also collected from the TCGA database. Overall survival (OS), progression‐free survival (PFS), disease‐specific survival (DSS), disease‐free interval (DFI), and progression‐free interval (PFI) are important endpoints to reflect the survival rate in OSdlbcl. Moreover, clinical features were integrated into OSdlbcl to allow data stratifications according to the user's special needs. By inputting an official gene symbol and selecting desired criteria, the survival analysis results can be graphically presented by the Kaplan‐Meier (KM) plot with hazard ratio (HR) and log‐rank p value. As a proof‐of‐concept demonstration, the prognostic value of 23 previously reported survival associated biomarkers, such as transcription factors FOXP1 and BCL2, was evaluated in OSdlbcl and found to be significantly associated with survival as reported (HR = 1.73, P < .01; HR = 1.47, P = .03, respectively). In conclusion, OSdlbcl is a new web server that integrates public gene expression, gene mutation data, and clinical follow‐up information to provide prognosis evaluations for biomarker development for DLBCL. The OSdlbcl web server is available at https://bioinfo.henu.edu.cn/DLBCL/DLBCLList.jsp.
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Affiliation(s)
- Huan Dong
- Department of Predictive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Qiang Wang
- Department of Predictive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Guosen Zhang
- Department of Predictive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Ning Li
- Department of Predictive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Mengsi Yang
- Department of Predictive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Yang An
- Department of Predictive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Longxiang Xie
- Department of Predictive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Huimin Li
- Department of Predictive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Lu Zhang
- Department of Predictive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Wan Zhu
- Department of Anesthesia, Stanford University School of Medicine, Stanford, CA, USA
| | - Shuchun Zhao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Haiyu Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Xiangqian Guo
- Department of Predictive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Software, School of Basic Medical Sciences, Henan University, Kaifeng, China
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