China
Africa
Explore chapters and articles related to this topic
Cancer Informatics
Published in Trevor F. Cox, Medical Statistics for Cancer Studies, 2022
Next we are going to consider a group of 30 known melanoma related genes, mentioned in the original paper: ALCAM, ANGPT1, B2M, BRAF, BRCA1, CASP8, CDH1, CDK2, CDKN1A, CDKN2A, CDKN2B, CIITA, EGF, FAS, ITGA4, KIT, MAGEA1, MAGEA4, MAGEA9B, MAGEB2, MAGEC2, MGMT, MMP15, MMP19, MYC, NRAS, PTEN, RBL2, TEP1 and TP53BP2. Figure 10.10 shows a heatmap for the 30 genes and 48 arrays. We have had to use a grey-scale, whereas normally a colour scale, e.g. red-blue, would be used. We cannot distinguish a large negative x-score from a large positive one. We could use the heatmap to select clusters of genes and arrays. Looking at the dendrograms, suggested clusters for genes and arrays might be, {MAGEA4, MAGEC2, B2M, MAGEA1, MAGEA9B, CIITA, MMP19, MMP15, ANGPT1, ITGA4, CASP8, EGF}{CDKN2A, CDKN2B, MYC, MGMT, BRAF, TEP1, PTEN, BRCA1, CDK2, NRAS, RBL2, TP53BP2 }{ALCAM, CDKN1A, FAS, MAGEB2, CDH1, KIT }{A/2a, A/3a, A/4, A/3b, A/2b, A/3c, A/1}{20, 9, D/2, D/1, G/1, 14, C/3 }{2, E/2, E/1, 10, E/3, 6, 5, 22, 3 }{7, 4, F/1, G/3, G/2, H/2, H/1 }{17, 13, 11, C/1, C/2, 19, 1 }{F/2, H/3, F/3, 21, 16, 12, 18, 8, 15, B/2, B/1 },
Transcription factor ETV1-induced lncRNA MAFG-AS1 promotes migration, invasion, and epithelial–mesenchymal transition of pancreatic cancer cells by recruiting IGF2BP2 to stabilize ETV1 expression
Published in Growth Factors, 2023
Hanqin Weng, Weijian Feng, Fengling Li, Dong Huang, Liangyi Lin, Zaiguo Wang
Long non-coding RNA (lncRNA) is a class of RNA with over 200 nt and no protein-coding ability (Lei et al. 2020). It can regulate an array of key tumor biological activities, such as EMT, proliferation, and drug resistance (Li et al. 2016; Tan et al. 2017; Yuan et al. 2014). LncRNA MAFG-AS1 is an antisense RNA of MAF BZIP transcription factor G (MAFG) located at chromosome 17q25.3, with a transcript size of 1895 bp, which is well-acknowledged as a carcinogenic lncRNA in various cancers (Chen, Huang, and Pan 2021; Dabbaghi et al. 2023; Fu et al. 2021). For example, overexpression of MAFG-AS1 in bladder urothelial carcinoma (BUC) is associated with aggressive characteristics and poor prognoses of BUC (Xiao et al. 2020). LncRNA MAFG-AS1 is upregulated in breast cancer cells and tissues and can decrease the expression of miR-339-5p, and in addition, matrix metalloproteinase 15 (MMP15) is a functional downstream gene of miR-339-5p, suggesting that MAFG-AS1 promotes breast cancer invasion by regulating the miR-339-5p/MMP15 (Li et al. 2019). Furthermore, MAFG-AS1 can promote the progress of hepatocellular carcinoma (HCC) by upregulating OTX1 expression via inhibition of miR-3196 (Hu et al. 2020). What is more, MAFG-AS1 promotes nuclear factor I X by spongingmiR-3196, thereby exacerbating the progression of PC (Heeg et al. 2016). Nevertheless, whether MAFG-AS1 is involved in the EMT regulation of PC has not been reported.
Exosomes derived from HeLa cells break down vascular integrity by triggering endoplasmic reticulum stress in endothelial cells
Published in Journal of Extracellular Vesicles, 2020
Yinuo Lin, Chi Zhang, Pingping Xiang, Jian Shen, Weijian Sun, Hong Yu
In addition, the protein components of ExoHeLa and triton-treated ExoHeLa were compared using LC-MS/MS analysis (See Online Supplemental data). Unique peptides that can only be detected in ExoHeLa at least two times were listed in Table S2, and grouped according to their functions (Figure S12), which include 60S ribosomal protein L28 isoform 5 (RPL28), syntaxin-7 isoform b (STX-7), charged multivesicular body protein 4b (CHMP4B). Since numerous MMPs have been reported to be presented in different cancer cell lines [27], MMPs were examined by both LC-MS/MS analysis and western blot. Although MMPs were detected in HeLa and Shiha cells, no MMPs were detectable in ExoHeLa (Figure S13, Table S2, Online Supplemental Excel data). MMP14 and MMP15, but not MMP2 and MMP9, were detected in ExoSiha.
Comprehensive analysis of matrix metalloproteinases and their inhibitors in head and neck squamous cell carcinoma
Published in Acta Oncologica, 2022
Mingyuan Zou, Chen Zhang, Yan Sun, Huina Wu, Feng Xiao, Wei Gao, Fengfeng Zhao, Xiaobo Fan, Guoqiu Wu
To understand the expression patterns of MMPs and TIMPs in HNSCC, we assessed the mRNA expression levels of MMPs and TIMPs in 500 HNSCC cancer tissues compared to those in 44 adjacent normal tissues. As shown in Figure 2(A) and Table S1, the heat map showed that the expression levels of MMP1, MMP3, MMP9, MMP10, MMP11, MMP12, and MMP13 in tumor tissues were significantly higher than those in normal tissues. The expression levels of MMP2, MMP14, and MMP28 were differentially expressed in both tumor and normal tissues. In contrast, the expression levels of MMP8, MMP16, MMP20, MMP21, MMP8, MMP16, MMP20, MMP21, MMP23A, MMP23B, and MMP26 were low or undetectable in both tumor and normal tissues. Regarding TIMPs, the heat map indicated that the expression levels of TIMP1 and TIMP2 were differentially expressed in both tumor and normal tissues, the expression level of TIMP3 was low in both tumor and normal tissues, and the expression level of TIMP4 appeared to be weaker in tumor tissue than in normal tissue. As shown in Table S1, when FDR ≤ 0.05 and log2FC ≥ 1 (upregulated) or log2FC≤ −1 (downregulated) were set as thresholds for DEGs, the expression levels of 17 of 24 MMPs, except MMP7, MMP15, MMP21, MMP23A, MMP24, MMP26, and MMP27, were upregulated in HNSCC cancer tissues compared to those in adjacent normal tissues. The expression levels of MMP27 were significantly downregulated in tumor tissues compared to those in normal tissues. However, none of the TIMPs were upregulated in HNSCC cancer tissues. In contrast, the expression levels of TIMP4 were downregulated in HNSCC cancer tissues compared to those in adjacent tissues. The above results suggested that most MMPs and TIMPs were highly expressed in HNSCC tissues compared to normal tissues.