The prognostic impact of hypermethylation for a panel of tumor suppressor genes and cell of origin subtype on diffuse large B-cell lymphoma

Shawky, Samir A.; El-Borai, M.H.; Khaled, Hussein; Guda, Iman; Mohanad, Marwa; Abdellateif, Mona S.; Zekri, Abdel‐Rahman N.; Bahanasy, Abeer A.

doi:10.1007/s11033-019-04856-x

Cited by 8 publications

(3 citation statements)

References 38 publications

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“…The high expression of DAPK1 in cholangiocarcinoma can reduce autophagy induced by cholangiocarcinoma cells and promote apoptosis of cholangiocarcinoma cells [ 34 ]. In diffuse large B-cell lymphoma, DAPK1 is a promising prognostic and/or predictive marker of non-germinal central B-cell–like subtype, significantly reducing DFS and OS [ 35 ]. Jiang L. et al reported that in gastric cancer, SERPINA1 can regulate TGF-β signaling pathway to accelerate the growth and progression of tumor, indicating that SERPINA1 may be a novel candidate therapeutic target [ 36 ].…”

Section: Discussionmentioning

confidence: 99%

Development and validation of prognostic model based on the analysis of autophagy-related genes in colon cancer

Wang

Lin

et al. 2021

Aging

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Background: Autophagy, a process of self-digestion, is closely related to multiple biological processes of colon cancer. This study aimed to construct and evaluate prognostic signature of autophagy-related genes (ARGs) to predict overall survival (OS) in colon cancer patients. Materials and Methods: First, a total of 234 ARGs were downloaded via The Cancer Genome Atlas (TCGA) database. Based on the TCGA dataset, differentially expressed ARGs were identified in colon cancer. The univariate and multivariate Cox regression analysis was performed to screen prognostic ARGs to construct the prognostic model. The feasibility of the prognostic model was evaluated using receiver operating characteristic curves and Kaplan-Meier curves. A prognostic model integrating the gene signature with clinical parameters was established with a nomogram. Results: We developed an autophagy risk signature based on the 6 ARGs ( ULK3, ATG101, MAP1LC3C, TSC1, DAPK1, and SERPINA1 ). The risk score was positively correlated with poor outcome and could independently predict prognosis. Furthermore, the autophagy-related signature could effectively reflect the levels of immune cell type fractions and indicate an immunosuppressive microenvironment. Conclusion: We innovatively identified and validated 6 autophagy-related gene signature that can independently predict prognosis and reflect overall immune response intensity in the colon cancer microenvironment.

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Section: Discussionmentioning

confidence: 99%

Development and validation of prognostic model based on the analysis of autophagy-related genes in colon cancer

Wang

Lin

et al. 2021

Aging

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“…Specifically, Table 3 shows the peptide sharing between the immunoreactive EBV epitopes and human proteins that—when mutated, modified, improperly functioning or deficient—are implicated in lymphomagenesis/leukemogenesis. 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 It can be seen that the extent of the peptide sharing is very high and comes to the fore with glaring evidence when focusing on histone-lysine N -methyltransferase 2D (KMT2D), the disruption of which perturbs germinal center B cell development and promotes lymphomagenesis. 77 78 KMT2D alterations are involved in follicular lymphoma and diffuse large B-cell lymphoma, 92 cutaneous T-cell lymphoma and Sézary syndrome, 93 ocular adnexal MALT-type marginal zone lymphomas, 79 and chronic myeloid leukemia.…”

Section: Resultsmentioning

confidence: 99%

From Anti-EBV Immune Responses to the EBV Diseasome via Cross-reactivity

Kanduc

Shoenfeld

2020

Global Medical Genetics

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Sequence analyses highlight a massive peptide sharing between immunoreactive Epstein-Barr virus (EBV) epitopes and human proteins that—when mutated, deficient or improperly functioning—associate with tumorigenesis, diabetes, lupus, multiple sclerosis, rheumatoid arthritis, and immunodeficiencies, among others. Peptide commonality appears to be the molecular platform capable of linking EBV infection to the vast EBV-associated diseasome via cross-reactivity and questions the hypothesis of the “negative selection” of self-reactive lymphocytes. Of utmost importance, this study warns that using entire antigens in anti-EBV immunotherapies can associate with autoimmune manifestations and further supports the concept of peptide uniqueness for designing safe and effective anti-EBV immunotherapies.

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“…The CHD1 gene is known to be an invasion and tumor suppressor gene and its decreased expression due to hypermethylation could promote tumor cell invasion and metastasis. [38][39][40] Jiang L demonstrated that calcium-binding protein 39 (CAB39) promoted the carcinogenesis and development of HCC when CAB39 activated the ERK signaling pathway, suggesting that CAB39 may be useful as a biomarker for the prediction of prognosis as well as the potential of being a novel therapeutic target in clinical practice. 41 The hypomethylated DMGs were enriched in the GO categories including "protein binding", "extracellular ligand-gated ion channel activity", "regulation of signal transduction", "cytoskeletal protein binding".…”

Section: Dovepressmentioning

confidence: 99%

<p>Exploring DNA Methylation Profiles Altered in Cryptogenic Hepatocellular Carcinomas by High-Throughput Targeted DNA Methylation Sequencing: A Preliminary Study for Cryptogenic Hepatocellular Carcinoma</p>

Wang

Cheng

Liu

et al. 2020

OTT

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Background: Hepatocellular carcinoma (HCC) includes cryptogenic hepatocellular carcinomas (CR-HCC) that lack a defined cause. Specific DNA methylation patterns and comparisons of the aberrant alterations in DNA methylation between CR-HCC and adjacent peritumor tissues (APTs) have not yet been reported. Methods: The SureSelectXT Methyl-Seq Target Enrichment System was used to sequence targeted DNA methylation in three paired CR-HCC tissues and APTs. Gene Ontology (GO) enrichment and KEGG pathway analysis were performed to investigate the DNA methylation mechanism of CR-HCC. The mRNA expression levels of HOXB-AS3, HOXB6, HOXB3, USP18, MAP3K6, TIRAP, TNNI2, SHC3, CTTN, and TFAP2A, selected from the identified signaling pathways, were evaluated by quantitative real-time PCR (qPCR). Results: A total of 1728 differentially methylated regions (DMRs) were identified in tumor tissues compared with non-tumor tissues, of which 868 DMRs were hypermethylated and 860 were hypomethylated. The DMRs were mapped within 2091 DMR-associated genes (DMGs). The mRNA expression of HOXB-AS3, HOXB3, and MAP3K6 was downregulated in CR-HCC tissues compared to the APTs. However, the mRNA expression of TIRAP, SHC3, and CTTN was upregulated in the CR-HCC tissues. Differences between the mRNA expression of HOXB6, USP18, TNNI2, and TFAP2A in the CR-HCC and APTS tissues were not statistically significant. GO analysis showed that the molecular functions of "binding", "protein binding", and "cytoskeletal protein binding" were the main categories for the hypermethylated DMGs. The hypomethylated DMGs were mostly enriched in the molecular functions "binding", "protein binding", "calcium ion binding", among others. KEGG pathway analysis showed that the hypermethylated DMGs were enriched in several pathways such as "estrogen signaling pathway", while hypomethylated DMGs were enriched in several pathways such as "proteoglycans in cancer", suggesting that epigenetic modifications play important roles in the cryptogenic hepatocarcinogenesis. Conclusion: These results provide useful information for future work to characterize the functions of epigenetic mechanisms on CR-HCC.

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The prognostic impact of hypermethylation for a panel of tumor suppressor genes and cell of origin subtype on diffuse large B-cell lymphoma

Cited by 8 publications

References 38 publications

Development and validation of prognostic model based on the analysis of autophagy-related genes in colon cancer

Development and validation of prognostic model based on the analysis of autophagy-related genes in colon cancer

From Anti-EBV Immune Responses to the EBV Diseasome via Cross-reactivity

<p>Exploring DNA Methylation Profiles Altered in Cryptogenic Hepatocellular Carcinomas by High-Throughput Targeted DNA Methylation Sequencing: A Preliminary Study for Cryptogenic Hepatocellular Carcinoma</p>

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