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: Biotechnology Reports

Article Title: Integrative analysis of RAS signaling effectors reveals stage-dependent oncogenic patterns in colon adenocarcinoma

doi: 10.1016/j.btre.2025.e00902

Figure Lengend Snippet: Validation of the core RAS effector expression changes in COAD patient’s samples. The left panel (A) illustrates gene expression changes across stages using TCGA data, while the right panel (B) presents results from analysis of a tissue cDNA array via qPCR. (C) The available protein expression levels of core RAS effectors were examined using data from the UALCAN proteomics database.

Article Snippet: OriGene Tissue cDNA Arrays, such as the TissueScanTM Cancer and Normal Tissue cDNA Arrays, are commercially available kits for gene expression analysis using human tissue samples.

Techniques: Biomarker Discovery, Expressing, Gene Expression

Journal: Biotechnology Reports

Article Title: Integrative analysis of RAS signaling effectors reveals stage-dependent oncogenic patterns in colon adenocarcinoma

doi: 10.1016/j.btre.2025.e00902

Figure Lengend Snippet: Correlation analysis of the core RAS effectors based on qPCR results of COAD patient’s samples. Pearson’s correlation coefficients were calculated for the five selected RAS effectors to analyze co-expression patterns in normal (A), COAD tumor (B), and Stage I COAD (C) samples. Heatmaps were created using tissue cDNA array results. The correlation coefficients, ranging from −1 to 1, represent the strength and direction of the relationships. The size of the circles reflects the magnitude of the correlation, with red indicating positive correlation and blue representing negative correlation between gene pairs. (D-E) The early tumorigenic impact of core RAS effector gene expression dynamics at the normal-to-cancer transition.

Article Snippet: OriGene Tissue cDNA Arrays, such as the TissueScanTM Cancer and Normal Tissue cDNA Arrays, are commercially available kits for gene expression analysis using human tissue samples.

Techniques: Expressing, Gene Expression

Journal: Biotechnology Reports

Article Title: Integrative analysis of RAS signaling effectors reveals stage-dependent oncogenic patterns in colon adenocarcinoma

doi: 10.1016/j.btre.2025.e00902

Figure Lengend Snippet: (A) Linear discriminant analysis (LDA) was performed on the tissue cDNA array dataset, combining the expression levels of five core RAS effectors, then determined the separation efficiency between normal samples and the samples representing the four stages of COAD. (B) The LD1 axis projection of the LDA analysis. Confusion matrices were generated by integrating the expression profiles of the five core RAS effectors, applied to the TCGA dataset (C) and tissue cDNA array dataset (D).

Article Snippet: OriGene Tissue cDNA Arrays, such as the TissueScanTM Cancer and Normal Tissue cDNA Arrays, are commercially available kits for gene expression analysis using human tissue samples.

Techniques: Expressing, Generated

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