tumor samples  (OriGene)

Journal: Science Advances

Article Title: Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer

doi: 10.1126/sciadv.aea9061

Figure Lengend Snippet: ( A to C ) Lung colonization assay for control and either RBMS3 knockdown or RBMS3 overexpression. Luciferase-labeled cells were injected via tail vein, and their metastatic growth in the lungs was measured over time. The magnitude of the signal, shown here as a heatmap for a representative mouse from each cohort, reflects the metastatic burden. Bars on time-course plots show means ± SEM, and ANOVA was performed (left). Also included are area under the curve (AUC) of log-normalized signal in the lungs of mice over 25 days. Summary overlay shows means ± SEM and Mann-Whitney U test used to determine statistical significance (middle). Also, hematoxylin and eosin–stained lung sections for exemplary mice (right). (A) Lung colonization assays of control ( N = 4 biological replicates) and RBMS3 knockdown MDA-MB-231 cells ( N = 4 biological replicates). (B) Lung colonization assays for control ( N = 5 biological replicates) and RBMS3 overexpression MDA-LM2 cells ( N = 5 biological replicates). (C) Lung colonization assays for control ( N = 5 biological replicates) and RBMS3 knockdown HCC1806 cells ( N = 5 biological replicates). ( D ) Invasion assays for control and RBMS3 knockdown MDA-MB-231 cells. Images are representative (i.e., median) in each group. In processed images, black is empty space and white is cells. The graph shows fraction that is white (i.e., % area covered), and the Mann-Whitney U test was used for statistical comparison. * P < 0.05; *** P < 0.001.

Article Snippet: We measured TXNIP expression using qPCR in 96 clinical samples across all stages of breast cancer, namely 5 normal epithelial, 23 stage I, 30 stage II, 29 stage III, and 9 stage IV metastatic biopsies (Origene, BCRT102, BCRT103), from which 90 samples yielded sufficient amount of cDNA.

Techniques: Control, Knockdown, Over Expression, Luciferase, Labeling, Injection, MANN-WHITNEY, Staining, Comparison

Journal: Science Advances

Article Title: Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer

doi: 10.1126/sciadv.aea9061

Figure Lengend Snippet: ( A ) Schematic of the dual-guide CRISPR interference (CRISPRi) screen. ( B ) Analysis of CRISPRi screen comparing the abundance of cells expressing each guide between in vivo– and in vitro–grown cells with DESeq2. TXNIP was observed to be present at high levels in vivo and low levels in vitro indicating high metastasis but low proliferation. ( C ) Comparative analysis of TXNIP to RBMS3 expression in the METABRIC cohort . Shown is Pearson correlation with t statistic for nonzero correlation. ( D ) Analysis of disease-free survival in the METABRIC cohort relative to TXNIP expression. ( E ) Meta-analysis of relapse-free survival in smaller published cohorts relative to TXNIP expression. (D and E) The Mantel-Cox test was used to measure significance. Low TXNIP expression is indicative of poor prognosis for disease-free survival in patients with breast cancer. ( F ) The expression levels of TXNIP in 90 tumor samples at different stages of breast cancer was measured by qPCR; bars show means and SEM. ANOVA was performed. ( G ) The expression levels of TXNIP in RBMS3 knockdown MDA-MB-231 cells and control cells was measured by qPCR and compared using Mann-Whitney U test. ( H ) Lung colonization assays of control ( N = 5 mice), TXNIP knockdown ( N = 5 mice), and RBMS3-TXNIP double knockdown ( N = 5 mice) in MDA-MB-231 cells. Luciferase-labeled cells were injected via tail vein, and their metastatic growth in the lungs was measured over time. ANOVA was performed; bars indicate means and SEM. ( I ) Molecular mechanism of RBMS3 metastasis suppression through posttranscriptional regulatory action.

Article Snippet: We measured TXNIP expression using qPCR in 96 clinical samples across all stages of breast cancer, namely 5 normal epithelial, 23 stage I, 30 stage II, 29 stage III, and 9 stage IV metastatic biopsies (Origene, BCRT102, BCRT103), from which 90 samples yielded sufficient amount of cDNA.

Techniques: CRISPR, Expressing, In Vivo, In Vitro, Knockdown, Control, MANN-WHITNEY, Luciferase, Labeling, Injection

Journal: bioRxiv

Article Title: Stress-Survival Pathway Profiling Reveals MCM10 as a Candidate Biomarker of Hispanic Colorectal Cancer Disparities

doi: 10.64898/2026.01.06.698057

Figure Lengend Snippet: A. Expression of targeted SSP genes were quantified using qRT-PCR in six CRC cell lines compared to normal colon cells CCD841. The quantitative analysis demonstrated significant upregulation of 12 SSP genes including BCL2L1, BCL2L12, CCNB1, CDK1, CDK4, CHEK1, CSE1L, FOXM1, MCM10, NUDT1, PDCD2L, and PRDX4 in six CRC cell lines, SW116, SW480, SW620, SW48, Caco-2, and WiDr, compared to normal colon cell, CCD841. B. The stage-specific expression of SSP genes were evaluated in both early (Stage I and II) and late stages (Stage III and IV) CRC tissues compared to the adjacent normal tissues. The significant over expressions of BCL2L1, CCNB1, CDK1, CDK4, CHEK1, CSE1L, FOXM1, MCM10, PDCD2L, and PRDX4 were determined in human CRC tissues across early and late stages using cDNA array. Each bar represents relative gene expression, calculated from at least three biological replicates of this study. (* P<0.05, ** P< 0.01, ***P<0.001 ).

Article Snippet: We further explored the transcript-level expression of these 12 SSP genes at different stages of CRC by using commercially available Colon Cancer cDNA Array IV from OriGene Technologies Inc., (Rockville, MD, USA).

Techniques: Expressing, Quantitative RT-PCR, Gene Expression

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