gene expression  (OriGene)

Journal: The Journal of Cell Biology

Article Title: Epigenetic deprogramming by disruption of CIZ1-RNA nuclear assemblies in early-stage breast cancers

doi: 10.1083/jcb.202409123

Figure Lengend Snippet: (Related to and ). CIZ1 domains, transcript levels , and domain expression in common solid tumors. (A) Protein domain map aligning human ( NP_001124488.1 ) and mouse ( NP_082688.1 ) CIZ1. Numbers correspond to amino acids encoded at exon boundaries. The domains highlighted are: Prion-like domains 1 and 2 (PLD1 and PLD2, purple) at positions 1–78 and 360–451, respectively (human), and positions 1–67 and 361–399, respectively (mouse), 10 three zinc fingers (ZnF_C2H2 SM00355, ZF_C2H2 sd00020, and ZF_C2H2 sd00020, blue) at positions 593–617, 656–676, and 687–709, respectively (human), and 537–561, 600–620, and 631–653, respectively (mouse), an acidic domain (red) containing a concentrated area of aspartates and glutamates at position 741–761 (human) and 689–709 (mouse), and a matrin-3 homology domain (ZnF_U1 smart0045, yellow) at position 796–831 (human) and 746–770 (mouse). Box shows % identity at the amino acid level across these domains. Human and mouse CIZ1 are 65% identical at the protein level, with identity concentrated in the conserved domains (up to 96%). (B) Bright-field images of breast-derived cell types ordered based on phenotype, with corresponding hormone and growth factor receptor status. The bar is 100 μm. (C) CIZ1 locus in Homo sapiens with corresponding exon numbers. Potential CIZ1 alternative transcription start sites (TSSs) in exons 10 and 11 predicted in the FANTOM5 project are indicated (red stars). The coding sequence would be expected to begin at a methionine in exon 11. The chromatin landscape in human mammary epithelial cells (HMEC), a cervical cancer cell line (HeLa) and a breast cancer cell line (MCF7) is shown below. Diagram generated using UCSC genome browser . (D) Total CIZ1 TPM derived from the indicated number of cancer (C) and normal (N) tissues in TCGA compared using GEPIA for the indicated disease types. No significant difference is detected (where log 2 FC was >1, and P value <0.05) when comparing all amalgamated transcripts that map to the CIZ1 gene (unresolved by exon). (E) Relative expression of exons 7 (red) and 16 (blue), normalized to the average of three unmatched control samples for each of six common solid tumor types in multi-tissue cDNA array CSRT101. Individual patient data plus the average of the controls calibrated to 1 (Av.C, left) and data aggregated by disease stage (0–IV, right) are shown. 0 represents histologically normal tissue. Individual sample information for all arrays is given in .

Article Snippet: TissueScan cancer and normal tissue cDNA arrays , Origene , https://www.origene.com/products/tissues/tissuescan.

Techniques: Expressing, Zinc-Fingers, Derivative Assay, Sequencing, Generated, Control

Journal: The Journal of Cell Biology

Article Title: Epigenetic deprogramming by disruption of CIZ1-RNA nuclear assemblies in early-stage breast cancers

doi: 10.1083/jcb.202409123

Figure Lengend Snippet: Resources

Article Snippet: TissueScan cancer and normal tissue cDNA arrays , Origene , https://www.origene.com/products/tissues/tissuescan.

Techniques: Virus, Recombinant, Transfection, Protease Inhibitor, Mutagenesis, Plasmid Preparation, Generated, Sequencing, Software, Gene Expression, Functional Assay, Inverted Microscopy

Journal: bioRxiv

Article Title: Dominant CIZ1 fragments drive epigenetic instability and are expressed in early stage cancers

doi: 10.1101/2023.09.22.558821

Figure Lengend Snippet: A) Exon structure of CIZ1 based on human reference sequence NM_012127.2 which encodes 898 amino acids, showing all 16 translated exons (2-17). Untranslated alternative exons 1’s are not shown. The boundaries of partially characterised alternatively-spliced exons are indicated in pink (Coverley et al., 2005; Dahmcke et al., 2008; Higgins et al., 2012; Rahman et al., 2007; Sofi et al., 2022; Swarts et al., 2018). The location of amplicons detected by human quantitative RT-PCR detection tools are also shown. These are four Taqman primer/probe sets; DT5 and DT7 which detect the 5’ end of CIZ1 transcripts, and DT14 and DT16 which detect the 3’ end . Right, comparison of outputs with the indicated pairs of detection tools applied to 46 human tissue-derived cDNAs in Origene cDNA array. Pearson’s correlation coefficients show strong agreement between exons 5 and 7, and between 14 and 16, but poor agreement between exons 7 and 16, or 5 and 14. This shows that the 5’ and 3’ ends of CIZ1 are typically imbalanced at the transcript level. B) Left, relative expression of exons 7 (red) and 16 (blue), normalized to the average of 3 unmatched control samples for each of six common solid tumour types in multi-tissue cDNA array CSRT101 (Origene), aggregated by disease stage (0-IV, where 0 represents histologically normal tissue). Middle, individual tissue data plus the average of the controls calibrated to 1 (Av.C). Right, plots show the ratio of exon 7 to exon 16 ordered by stage, with trendline (polynomial 2). Individual sample information for all array samples in given in Supplemental Dataset 1.

Article Snippet: To quantify relative expression of CIZ1 amplicons in primary tumours, TissueScan TM Tumour cDNA arrays from OriGene Technologies, Inc. (Rockville, MD) containing 2-3 ng of cDNA were analysed by qPCR.

Techniques: Sequencing, Quantitative RT-PCR, Comparison, Derivative Assay, Expressing, Control

Journal: The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology

Article Title: SIX1 Downregulation Suppresses Self-renewal Capacity and THY1 Expression in Hepatocellular Carcinoma and SIX1 Dominate the Survival in Liver Cancer.

doi: 10.5152/tjg.2023.22293

Figure Lengend Snippet: Figure 1. The SIX1 gene expression levels both in vivo and using bioinformatic analysis in different types of cancer. (A) Analysis of the expression levels of SIX1 in cancer cDNA arrays representing tissues from 3 non-malignant and 9 tumor samples from 8 different types of cancer. Compared with the control tissue, the expression levels of SIX1 in the liver, colon, breast, ovary, kidney, lung, and prostate tumor tissues were markedly upregulated, while they were slightly downregulated in thyroid cancer. mRNA expression levels were quantified using the 2−ΔΔCq method. (B) mRNA transcription levels of SIX1 in colon, liver, and breast cancers depending on the pathological stages using an Expression Project for Oncology (expO) dataset. SIX1 expression was significantly upregulated in pathological stage 3 compared to pathological stage 1 in the liver and colon cancer, and also SIX1 high expression was detected in stage 4 compared to stage 1 in all 3 types of cancer (*P < .05). (C) SIX1 expression levels in tumor tissues were compared with normal tissues in 3 different grades of hepatocellular carcinoma. SIX1 expression levels in grade 1 (n = 6) and grade 3 (n = 20) were significantly different in the tumor tissues compared with the normal tissues. In contrast, no significant differences were observed in grade 2 tissues (n = 12). NAT, non-associated tissue; SIX1, Sine oculis homeoprotein 1. *P < .05, unpaired Student’s t-test. Magnification, ×40; scale bar, 200 μm.

Article Snippet: The expression of SIX1 was assessed by RT-qPCR in commercial TissueScan qPCR Cancer Survey cDNA arrays I (Origene, #CSRT101).

Techniques: Gene Expression, In Vivo, Expressing, Control

Journal: The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology

Article Title: SIX1 Downregulation Suppresses Self-renewal Capacity and THY1 Expression in Hepatocellular Carcinoma and SIX1 Dominate the Survival in Liver Cancer.

doi: 10.5152/tjg.2023.22293

Figure Lengend Snippet: Figure 4. Determining the effect of SIX1 on sphere formation and self-renewal ability. (A) These cells were passaged 2 times to determine the effect of SIX1 on the self-renewal capacity following the sphere formation assay. It was subsequently observed that the shSIX1- SNU398 cells were unable to self-renew. (B) RT-qPCR was used to analyze the expression levels of SIX1, ZEB2, VIM, KLF4, and THY1 genes in sphere-forming cells. (C) CD90 cell population in shSIX1-SNU398 and control-SNU398 cells was analyzed using flow cytometry. The CD90+ subpopulation was decreased in shSIX1-SNU398 cells compared with the control-SNU398 cells. The differences between groups were analyzed using a Student’s t-test. SIX1, SIX1, Sine oculis homeoprotein 1. **P < .01, ***P < .0001. Magnification, ×5; scale bars, 200-μm.

Article Snippet: The expression of SIX1 was assessed by RT-qPCR in commercial TissueScan qPCR Cancer Survey cDNA arrays I (Origene, #CSRT101).

Techniques: Tube Formation Assay, Quantitative RT-PCR, Expressing, Control, Flow Cytometry