healthy brain tissue  (OriGene)

Journal: Communications Biology

Article Title: Non-redundant roles of the phosphoinositide phosphatases PTEN and PIPP in PI3K/AKT signaling in breast cancer

doi: 10.1038/s42003-025-09364-2

Figure Lengend Snippet: A Normalized PTEN mRNA expression was determined by qPCR using TissueScan Breast Cancer Arrays I-IV with PTEN and β-actin primers. The data are displayed as box and whiskers on a log scale. The center line indicates the median; the box extends from the 25th to 75th percentiles and the whiskers extend from the minimum to maximum values. PTEN mRNA expression was correlated with ER (140 cases), p values were determined using an unpaired t test. B PIPP mRNA expression was correlated with normal versus low PTEN mRNA expression in TissueScan Breast Cancer Arrays I-IV (Normal PTEN expression n = 82; low PTEN mRNA (2-fold reduction relative to normal breast tissue) n = 92). The data are displayed as box and whiskers on a log scale. The center line indicates the median; the box extends from the 25th to 75th percentiles, and the whiskers extend from the minimum to maximum values. C Breast cancer cases in TissueScan Breast Cancer Arrays I-IV were scored for normal ( PIPP + /PTEN + ) versus low ( PIPP-/PTEN- ) PIPP and PTEN mRNA expression in ER+ and ER– tumors (170 cases). Significance was determined using a two-sided Fisher’s exact test (p < 0.001). D Breast cancer cases in TissueScan Breast Cancer Arrays I-IV were scored for normal versus low PIPP and PTEN mRNA expression relative to breast cancer subtype (133 cases). E PIPP mRNA expression was correlated with PTEN alterations in the METABRIC dataset. PIPP expression was correlated with unaltered PTEN versus altered PTEN (mutated and/or low expression). The data are displayed as box and whiskers. The center line indicates the median; the box extends from the 25th to 75th percentiles, and the whiskers extend from the minimum to maximum values. p-values were determined using an unpaired t-test. F – J Breast cancer cases in the METABRIC dataset were scored for reduced PIPP expression and/or PTEN expression (Z-score threshold of <1.5 relative to all breast cancers in the cohort) and/or PTEN mutation and correlated with ER ( F ), PR ( G ), HER2 ( H ), breast cancer subtype ( I ) or tumor grade ( J ). K Overall survival analysis in breast cancer patients using the METABRIC dataset. Samples were dichotomized for high PIPP/PTEN gene expression (>40th percentile) versus low PIPP/PTEN gene expression (<40th percentile). Statistical significance for 10-year survival was determined using a log-rank test. L Disease-free survival analysis in breast cancer patients using the TCGA Pan Cancer dataset. Samples were dichotomized for high PIPP/PTEN gene expression (>40th percentile) versus low PIPP/PTEN gene expression (<40th percentile). Statistical significance was determined using a log-rank test.

Article Snippet: As reported, PIPP ( INPP5J ) mRNA expression was reduced in ER– relative to ER+ breast tumors based on analysis of 176 human cancers and 16 normal, adjacent breast tissues using Tissue Scan Breast Cancer cDNA array I-IV (OriGene) .

Techniques: Expressing, Mutagenesis, Gene Expression

Journal: RNA Biology

Article Title: E2-regulated transcriptome complexity revealed by long-read direct RNA sequencing: from isoform discovery to truncated proteins

doi: 10.1080/15476286.2025.2563860

Figure Lengend Snippet: A. Analysis of single-cell RNA sequencing data of GSE75688 verified the expression of IPA isoforms of TLE1 and GREB1 in breast cancer cells representing subtypes, B. GEO2R expression data for TLE1 -IPA (228284_at probe set) and FL isoforms (203221_at probe set) in NCI-60 cancer cell line data ( GSE32474 , GPL570 ). Red bars indicate breast cancer cell lines, C. Probe sets specific to IPA (228284_at) and FL (203221_at) in control cells compared with ER knockdown (KD) MCF7 cells ( GSE27473 ) (*** p < 0.001, students t-test), D. IPA/FL ratios were determined in breast cancer cell lines by RT-qPCR ( n = 3 technical replicates). IPA and FL expression levels were normalized to RPLP0. IPA/FL ratio was normalized to normal breast cDNA sample (from OriGene TissueScan cDNA tissue array) (*** p < 0.001, one-way ANOVA), E. TCGA breast cancer dataset showing a positive correlation between the levels of the FL and IPA isoforms of TLE1 , F. Kaplan-Meier relapse-free survival curves comparing high- and low-ratio of ENST00000376463.2/ENST00000376499.7 (IPA/FL) TLE1 in TCGA LumA breast cancers (BRCA). High-ratio patients (red) showed better relapse-free survival compared to low-ratio patients (black) (HR = 0.35, log-rank p = 0.042), G. Kaplan–Meier relapse-free survival analysis of LumA breast cancers, classified according to the St. Gallen criteria, was performed using microarray data from the KM-plotter database. Patients were stratified based on the expression ratio of the 228284_at probe set (IPA isoform) to the 203221_at probe set (FL isoform). High-ratio group (red) exhibited better relapse-free survival compared to the low-ratio group (black) (HR = 0.65, log-rank p = 0.0024). Patient numbers and at-risk counts are displayed on the plot.

Article Snippet: IPA/FL ratio was normalized to normal breast cDNA sample (from OriGene TissueScan cDNA tissue array) (*** p < 0.001, one-way ANOVA), E. TCGA breast cancer dataset showing a positive correlation between the levels of the FL and IPA isoforms of TLE1 , F. Kaplan-Meier relapse-free survival curves comparing high- and low-ratio of ENST00000376463.2/ENST00000376499.7 (IPA/FL) TLE1 in TCGA LumA breast cancers (BRCA).

Techniques: RNA Sequencing, Expressing, Control, Knockdown, Quantitative RT-PCR, Microarray

Journal: International Journal of Molecular Sciences

Article Title: The Study of Chromobox Protein Homolog 4 in 3D Organoid Models of Colon Cancer as a Potential Predictive Marker

doi: 10.3390/ijms26157385

Figure Lengend Snippet: CBX family genes expression in colon cancer. ( A ) CBX expression level by qRT-PCR in three colon cancer cell lines (CACO-2, SW480, and HCT 116) compared to a normal colon cell line (NMC 460D). ( B ) CBX gene expression level in a colon cancer cDNA RT-qPCR array consisting of tumor ( N = 40) and normal samples ( N = 8). ( C ) Expression analysis of CBX family genes of colon tumor in UALCAN dataset (Normal = 41, Primary Tumor = 286). The star symbol indicates statistical significance (**: p ≤ 0.01, ***: p ≤ 0.001, ****: p ≤ 0.0001).

Article Snippet: Human TissueScan Colon Cancer Tissue qPCR Panel IV (HCRT304), containing first-strand cDNA from 48 samples covering 8-normal, 5-Stage I, 8-IIA, 1-II, 1-IIIA, 6-IIIB, 3-IIIC, 6-III, and 10-IV patients, was purchased from Origene (Rockville, MD, USA).

Techniques: Expressing, Quantitative RT-PCR, Gene Expression

Journal: International Journal of Molecular Sciences

Article Title: The Study of Chromobox Protein Homolog 4 in 3D Organoid Models of Colon Cancer as a Potential Predictive Marker

doi: 10.3390/ijms26157385

Figure Lengend Snippet: Association between CBX4 expression levels and clinical stage and grade of CRC patients. ( A ) CBX4 expression analyses performed using the UALCAN dataset with relative statistical comparison among groups. ( B ) CBX4 expression analyses in a colon cancer cDNA RT-qPCR array consisting of tumor ( n = 40) and normal samples ( n = 8) stratifying patients according to stage and grade. The star symbol indicates statistical significance (**: p ≤ 0.01).

Article Snippet: Human TissueScan Colon Cancer Tissue qPCR Panel IV (HCRT304), containing first-strand cDNA from 48 samples covering 8-normal, 5-Stage I, 8-IIA, 1-II, 1-IIIA, 6-IIIB, 3-IIIC, 6-III, and 10-IV patients, was purchased from Origene (Rockville, MD, USA).

Techniques: Expressing, Comparison, Quantitative RT-PCR

Journal: International Journal of Molecular Sciences

Article Title: The Study of Chromobox Protein Homolog 4 in 3D Organoid Models of Colon Cancer as a Potential Predictive Marker

doi: 10.3390/ijms26157385

Figure Lengend Snippet: Characterization of CBX4 in CRC organoids. ( A ) Representative images of ex vivo PDO culture obtained from colorectal cancer biopsies are reported. Scale bar: 10 µm. ( B ) Real-time qPCR analysis of CBX4 in two groups of PDOs: the first one derived from healthy tissues (CNT) and the second one derived from tumor tissues (Tumor). Results were normalized to RPS18 mRNA and analyzed by 2 −ΔΔCt method. ( C ) Analysis of the knockdown efficiency of siCBX4 assessed by RT-PCR in PDOs after 72 h. ( D ) Effect of CBX4 silencing on PDO viability assessed by ATP Lite assay after 72 h. The star symbol indicates statistical significance (**: p ≤ 0.01).

Article Snippet: Human TissueScan Colon Cancer Tissue qPCR Panel IV (HCRT304), containing first-strand cDNA from 48 samples covering 8-normal, 5-Stage I, 8-IIA, 1-II, 1-IIIA, 6-IIIB, 3-IIIC, 6-III, and 10-IV patients, was purchased from Origene (Rockville, MD, USA).

Techniques: Ex Vivo, Derivative Assay, Knockdown, Reverse Transcription Polymerase Chain Reaction

Journal: International Journal of Molecular Sciences

Article Title: The Study of Chromobox Protein Homolog 4 in 3D Organoid Models of Colon Cancer as a Potential Predictive Marker

doi: 10.3390/ijms26157385

Figure Lengend Snippet: Role of CBX4 silencing in CRC organoids ( A , B ). Representative images of our target molecules through immunofluorescence analysis. Localization of NFkB in tumor ex vivo PDOs before (CNT) and after siCBX4. Maximal projection images of PDO incubated NFkB (green signal) and cell nuclei were stained with Hoechst 33342 (blue signal). Scale bar: 10 µm. ( C ) Real time qPCR analysis of NF-κB, c-myc, TNF-α, and IL-1 in tumor ex vivo PDOs before (CTR) and after CBX4 silencing. Results were normalized to RPS18 mRNA and analyzed by 2 −ΔΔCt method. The star symbol indicates statistical significance (*: p ≤ 0.05, **: p ≤ 0.01).

Article Snippet: Human TissueScan Colon Cancer Tissue qPCR Panel IV (HCRT304), containing first-strand cDNA from 48 samples covering 8-normal, 5-Stage I, 8-IIA, 1-II, 1-IIIA, 6-IIIB, 3-IIIC, 6-III, and 10-IV patients, was purchased from Origene (Rockville, MD, USA).

Techniques: Immunofluorescence, Ex Vivo, Incubation, Staining

Journal: Biomedicines

Article Title: Tazarotene-Induced Gene 3 (TIG3) Induces Apoptosis in Melanoma Cells Through the Modulation of Inhibitors of Apoptosis Proteins

doi: 10.3390/biomedicines13071749

Figure Lengend Snippet: Effects of TIG3 on cell viability and death in A2058 and A375 cells. TIG3 mRNA expression in malignant melanoma tissues was analyzed using a commercial melanoma cDNA tissue array (MERT301) via real-time PCR ( a ). A2058 or A375 cells were transfected with either an empty vector, the TIG3-myc-his expression vector, or the TIG3ΔC-myc-his expression vector, before being incubated for 24–48 h. Cell viability ( b ) and cell death ( c ) were assessed using WST-1 assays and LDH release assays, respectively ( n = 3). * p < 0.05 compared with the control group.

Article Snippet: A melanoma tissue cDNA array (MERT301) was obtained from OriGene Technologies (Rockville, MD, USA), comprising cDNAs from 3 normal skin tissues and 43 malignant melanoma samples at clinical stages III to IV.

Techniques: Expressing, Real-time Polymerase Chain Reaction, Transfection, Plasmid Preparation, Incubation, 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: (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