Journal: Frontiers in Oncology

Article Title: Exploring the relationship between abnormally high expression of NUP205 and the clinicopathological characteristics, immune microenvironment, and prognostic value of lower-grade glioma

doi: 10.3389/fonc.2023.1007198

Figure Lengend Snippet: The mRNA and protein expression of NUP205 was increased in LGG. The results of (A) GEPIA, (B) GSE12657, (C) GSE21354, and (D) GSE70231 database showed that the mRNA expression of NUP205 increased in LGG tumor tissues. (E) The results of RT-qPCR showed that the mRNA expression of NUP205 was increased in LGG tissue. (F) The results of RT-qPCR showed that the mRNA expression of NUP205 was increased in glioma cells. (G) The results of IHC staining showed that the protein expression of NUP205 was increased in LGG tissue. ns, no statistically significant; *: p <0.05, **: p <0.01, ***: p <0.001. p <0.05 was considered statistically significant.

Article Snippet: To demonstrate whether NUP205 mRNA expression in glioma cells is regulated by DNA methylation, we added 100 μM ademetionine disulfate tosylate (SAM) (Topscience, China) and treated them with SHG44, T98, and LN229 for 10 h. After culturing with SAM, glioma cells were used to identify changes in NUP205 expression after DNA hypermethylation.

Techniques: Expressing, Quantitative RT-PCR, Immunohistochemistry

Journal: Frontiers in Oncology

Article Title: Exploring the relationship between abnormally high expression of NUP205 and the clinicopathological characteristics, immune microenvironment, and prognostic value of lower-grade glioma

doi: 10.3389/fonc.2023.1007198

Figure Lengend Snippet: The relationship between the expression of NUP205 and clinical features in LGG. (A) WHO grade, (B) Western blot results showed that the protein expression of NUP205 was significantly higher in WHO grade III than in WHO grade II. (C) Chemotherapy status, (D) Histology, (E) Radiotherapy status, (F) IDH-mutation status, (G) 1p19q codeletion status. * p <0.05. p <0.05 was considered statistically significant.

Article Snippet: To demonstrate whether NUP205 mRNA expression in glioma cells is regulated by DNA methylation, we added 100 μM ademetionine disulfate tosylate (SAM) (Topscience, China) and treated them with SHG44, T98, and LN229 for 10 h. After culturing with SAM, glioma cells were used to identify changes in NUP205 expression after DNA hypermethylation.

Techniques: Expressing, Western Blot, Mutagenesis

Journal: Frontiers in Oncology

Article Title: Exploring the relationship between abnormally high expression of NUP205 and the clinicopathological characteristics, immune microenvironment, and prognostic value of lower-grade glioma

doi: 10.3389/fonc.2023.1007198

Figure Lengend Snippet: The results based on TCGA RNA-seq database showed that the high expression of NUP205 leads to poor prognosis of LGG patients. The result of (A) Kaplan-Meier analysis for LGG patients of WHO Grade II & III, (B) Kaplan-Meier analysis for LGG patients of WHO Grade II, (C) Kaplan-Meier analysis for LGG patients of WHO Grade III, (D) ROC curve, (E) Univariate analysis, (F) Multivariate analysis. (G) Meta analysis. p <0.05 was considered statistically significant.

Article Snippet: To demonstrate whether NUP205 mRNA expression in glioma cells is regulated by DNA methylation, we added 100 μM ademetionine disulfate tosylate (SAM) (Topscience, China) and treated them with SHG44, T98, and LN229 for 10 h. After culturing with SAM, glioma cells were used to identify changes in NUP205 expression after DNA hypermethylation.

Techniques: RNA Sequencing, Expressing

Journal: Frontiers in Oncology

Article Title: Exploring the relationship between abnormally high expression of NUP205 and the clinicopathological characteristics, immune microenvironment, and prognostic value of lower-grade glioma

doi: 10.3389/fonc.2023.1007198

Figure Lengend Snippet: The relationship between the mRNA expression of NUP205 and its DNA methylation in LGG. (A) DNA methylation sites of NUP205 . (B) The result of Kaplan-Meier analysis showed that hypermethylation of cg25119219 led to reduce the overall survival of LGG patients. (C) The result of RT-qPCR showed that the expression of NUP205 was decreased in glioma cells treated with SAM. ns, no statistically significant; ****: p <0.0001. p <0.05 was considered statistically significant.

Article Snippet: To demonstrate whether NUP205 mRNA expression in glioma cells is regulated by DNA methylation, we added 100 μM ademetionine disulfate tosylate (SAM) (Topscience, China) and treated them with SHG44, T98, and LN229 for 10 h. After culturing with SAM, glioma cells were used to identify changes in NUP205 expression after DNA hypermethylation.

Techniques: Expressing, DNA Methylation Assay, Quantitative RT-PCR

Journal: Frontiers in Oncology

Article Title: Exploring the relationship between abnormally high expression of NUP205 and the clinicopathological characteristics, immune microenvironment, and prognostic value of lower-grade glioma

doi: 10.3389/fonc.2023.1007198

Figure Lengend Snippet: (A, B) The 5 most positive and negative genes related to NUP205 in LGG. The results of GSEA analysis suggested that NUP205 participated in the pathological process of LGG via (C) cell cycle, (D) notch signaling pathway, (E) aminoacyl-tRNA biosynthesis. p <0.05 was considered statistically significant.

Article Snippet: To demonstrate whether NUP205 mRNA expression in glioma cells is regulated by DNA methylation, we added 100 μM ademetionine disulfate tosylate (SAM) (Topscience, China) and treated them with SHG44, T98, and LN229 for 10 h. After culturing with SAM, glioma cells were used to identify changes in NUP205 expression after DNA hypermethylation.

Techniques:

Journal: Frontiers in Oncology

Article Title: Exploring the relationship between abnormally high expression of NUP205 and the clinicopathological characteristics, immune microenvironment, and prognostic value of lower-grade glioma

doi: 10.3389/fonc.2023.1007198

Figure Lengend Snippet: (A) The results of TIMER database showed that NUP205 expression was positively correlated with six immune infiltrations (B cell, CD4 + T cell, CD8 + T cell, neutrophil, macrophage, and dendritic cell). (B) The results of Kaplan-Meier analysis showed that the high level of six immune infiltration and high expression of NUP205 lead to poor prognosis of LGG patients. (C) The results of “CIBERSTART” analysis. (D) The results of Pearson analysis showed that NUP205 was positively correlated with the markers of M2 macrophages ( CD163 , VSIG4 , MS4A4A ). (E) The IHC staining of CD163 showed that the protein expression of CD163 in LGG tumor tissue was higher than that in control brain tissue. (F) The IHC staining of PD-L1 showed that the protein expression of PD-L1 in LGG tumor tissue was higher than that in control brain tissue. ns, no statistically significant; *: p <0.05, ****: p <0.0001. p <0.05 was considered statistically significant.

Article Snippet: To demonstrate whether NUP205 mRNA expression in glioma cells is regulated by DNA methylation, we added 100 μM ademetionine disulfate tosylate (SAM) (Topscience, China) and treated them with SHG44, T98, and LN229 for 10 h. After culturing with SAM, glioma cells were used to identify changes in NUP205 expression after DNA hypermethylation.

Techniques: Expressing, Immunohistochemistry, Control

Journal: Frontiers in Oncology

Article Title: Exploring the relationship between abnormally high expression of NUP205 and the clinicopathological characteristics, immune microenvironment, and prognostic value of lower-grade glioma

doi: 10.3389/fonc.2023.1007198

Figure Lengend Snippet: Results of correlation analysis between NUP205 and multiple immune-cell markers based on TCGA database.

Article Snippet: To demonstrate whether NUP205 mRNA expression in glioma cells is regulated by DNA methylation, we added 100 μM ademetionine disulfate tosylate (SAM) (Topscience, China) and treated them with SHG44, T98, and LN229 for 10 h. After culturing with SAM, glioma cells were used to identify changes in NUP205 expression after DNA hypermethylation.

Techniques: Marker

Journal: Frontiers in Oncology

Article Title: Exploring the relationship between abnormally high expression of NUP205 and the clinicopathological characteristics, immune microenvironment, and prognostic value of lower-grade glioma

doi: 10.3389/fonc.2023.1007198

Figure Lengend Snippet: Results of correlation between NUP205 and multiple immune-checkpoints based on TCGA database.

Article Snippet: To demonstrate whether NUP205 mRNA expression in glioma cells is regulated by DNA methylation, we added 100 μM ademetionine disulfate tosylate (SAM) (Topscience, China) and treated them with SHG44, T98, and LN229 for 10 h. After culturing with SAM, glioma cells were used to identify changes in NUP205 expression after DNA hypermethylation.

Techniques:

Journal: Oncotarget

Article Title: A k-mer based transcriptomics approach for antisense drug discovery targeting the Ewing’s family of tumors

doi: 10.18632/oncotarget.25736

Figure Lengend Snippet: For any given tumor, a cancer-specific transcriptome exists that only partially overlaps with the normal, healthy transcriptome. Within this cancer-specific pool of mRNA transcripts exists a subset of oncogenic transcripts that convey pro-survival cues via both protein expression and the activity of non-coding RNA. Antisense therapeutics (e.g. morpholinos) that can specifically degrade or modify this subset of RNA transcripts hold unique therapeutic potential as precision-cancer medicines with limited off-target effects in healthy tissues. We annotated a normal, healthy human mRNA transcriptome from a panel of 26 human tissues using 25-mer counts, and compared it to a composite transcriptome profile for Ewing’s Sarcoma (EWS), taken from 3 representative cell lines (TC-32, A673, and TTC-466). Exceptional mRNA transcripts, expressed at approximately 10,000-fold higher levels in EWS cells than in any normal human tissue, were selected for further analysis as potential chemotherapeutic targets using the gene-targeted therapeutic approach highlighted in Table and Figure .

Article Snippet: To accomplish this goal we developed a k-mer based counting strategy for cataloging all mRNA transcripts identified in 3 prototype EFT cell lines (A-673, TC-32 & TTC-446) and 26 healthy human tissues taken from the Human Protein Atlas [ ].

Techniques: Expressing, Activity Assay

Journal: Oncotarget

Article Title: A k-mer based transcriptomics approach for antisense drug discovery targeting the Ewing’s family of tumors

doi: 10.18632/oncotarget.25736

Figure Lengend Snippet: ( A ) RNA-Seq produces short sequencing reads (∼ 100 bp) from total or poly-A RNA and we can rapidly count all instances of any given ribonucleotide string (length = k) within that dataset. Here we demonstrate the total counts of all, individual 25-mer RNA strand sequences present in an RNA-Seq database for EWS cells, normalized to the total number of sequencing reads for the experiment. 25-mers found to be highly-abundant in EWS cells, with tumor (T) to normal (N) ratios (T:N) greater than 500 were assigned to individual protein coding or non-coding RNA transcripts found in the human genome (GRCh37; hg19). Next, the top 400 transcripts were plotted in a heat map visualizing, for each tissue/transcript combination, the abundance ratio for the selected k-mer across 26 tissues. EWS-specific gene transcripts with k-mer over-abundance levels exceeding 1000-fold over normal cells are colored blue, while those with levels 10,000-fold to 100,000-fold above normal tissues are colored from green to red, respectively. ( B ) Exceptional transcripts identified as having the maximum k-mer over-abundance across the maximum number of tissues were down-selected as high priority leads for antisense inhibition studies. We identified 12 EWS-specific gene targets from regions of the heat map where the T:N ratio approached or exceeded 10,000:1 across all 26 tissues. EFT-specific genes identified include: PHGDH, CCND1, IGFBP-2, XAGE1B/E, CYP4F22, RBM11, FBL, UGT3A2, ORAOV1, MDK, SSX5 and NKX2-2. 6 of the most exceptional genes with unique cellular functions (listed in Table ) were selected for further analysis using our reverse genetics approach.

Article Snippet: To accomplish this goal we developed a k-mer based counting strategy for cataloging all mRNA transcripts identified in 3 prototype EFT cell lines (A-673, TC-32 & TTC-446) and 26 healthy human tissues taken from the Human Protein Atlas [ ].

Techniques: RNA Sequencing, Sequencing, Inhibition