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stage iv metastatic biopsies  (OriGene)


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    OriGene stage iv metastatic biopsies
    ( 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 <t>metastatic</t> 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.
    Stage Iv Metastatic Biopsies, supplied by OriGene, used in various techniques. Bioz Stars score: 94/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/tissuescan+breast+cancer+cdna+arrays/TissueScan%2C+Breast+Cancer+cDNA+Array+II/pmc12978252-415-31-35
    Average 94 stars, based on 39 article reviews
    stage iv metastatic biopsies - by Bioz Stars, 2026-10
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    Images

    1) Product Images from "Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer"

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

    Journal: Science Advances

    doi: 10.1126/sciadv.aea9061

    ( 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.
    Figure Legend 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.

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

    ( 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.
    Figure Legend 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.

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

    Related Articles

    Quantitative RT-PCR:

    Article Title: Targeting prooxidant MnSOD effect inhibits triple-negative breast cancer (TNBC) progression and M2 macrophage functions under the oncogenic stress
    Article Snippet: .. The SOD2 and NFE2L2 mRNA levels in normal breast and breast tumor specimens were quantified by qRT-PCR using TissueScan Breast Cancer cDNA Arrays I (BRCT101), III (BRCT103), and IV (BRCT104) (OriGene). ..

    Article Title: Targeting prooxidant MnSOD effect inhibits triple-negative breast cancer (TNBC) progression and M2 macrophage functions under the oncogenic stress.
    Article Snippet: .. The SOD2 and NFE2L2 mRNA levels in normal breast and breast tumor specimens were quantified by qRT-PCR using TissueScan Breast Cancer cDNA Arrays I (BRCT101), III (BRCT103), and IV (BRCT104) (OriGene). ..

    Article Title: IL-26, a non-canonical mediator of DNA inflammatory stimulation, promotes TNBC engraftment and progression in association with neutrophils.
    Article Snippet: RNA in situ hybridization (RNAscope): In situ detection of IL26 mRNA transcripts in was performed on formalin-fixed, paraffin-embedded Cancer Diagnosis Program (CDP) Breast Cancer Progression Tissue Microarray sets using the RNAscope Multiplex Fluorescent kit (323100; Advanced Cell Diagnostics, Newark, CA)( 28 ) following the manufacturer’s protocol. .. A more detailed description can be found in the Supplemental Methods . qRT-PCR Breast Cancer cDNA Arrays: Commercially available TissueScan Breast Cancer cDNA arrays were obtained from OriGene (Rockville, MD, United States). ..

    Expressing:

    Article Title: Non-redundant roles of the phosphoinositide phosphatases PTEN and PIPP in PI3K/AKT signaling in breast cancer
    Article Snippet: .. PTEN mRNA expression was measured in TissueScan Breast Cancer cDNA Arrays I, II, III and IV (OriGene, BCRT101, BCRT102, BCRT103, and BCRT104) which contained 176 breast cancers and 16 tumor-adjacent “normal” breast tissues. .. Relative transcript levels were determined using PTEN and B-ACTIN primers (OriGene) in an MX3000p qPCR system (Stratagene) according to the manufacturer’s instructions.



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    ( 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 <t>metastatic</t> 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.
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    A Normalized PTEN mRNA expression was determined by qPCR using TissueScan Breast Cancer <t>Arrays</t> <t>I-IV</t> 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.
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    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 <t>cDNA</t> sample (from OriGene <t>TissueScan</t> 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.
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    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 <t>cDNA</t> sample (from OriGene <t>TissueScan</t> 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.
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    Figure 2. RFC4 was highly expressed in breast cancer tissues and cell lines. (A) Expression levels of RFC4 in breast cancer tissues (n=1,097) and normal tissues (n=114) were analyzed using RNA‐seq data analysis from UALCAN. Box plot displays the expression levels of RFC4 in normal and cancer tissues based on sample types (left panel) and different subtypes of breast cancer (right panel) (***p<0.001, compared to normal tissues). (B) Expression levels of RFC4 in breast cancer were measured by breast cancer <t>TissueScan</t> qRT‐PCR array. Bar graphs represent the mRNA expression levels of RFC4 in each clinical status of breast cancer tissue samples. Scatter plot represent the mRNA expression levels of RFC4 in normal and breast cancer tissues (*p<0.05, compared to normal tissues). (C) RFC4 mRNA expression was analyzed using qRT‐PCR in breast cancer cell lines and normal fibroblast cell line, MCF10A. Graphs show the mean±SD from independent triplicate experiments (*p<0.05, **p<0.01, compared to MCF10A). (D) RFC4 protein expression was analyzed using western blot analysis in same cell lines. Cell lysates were immunoblotted with the RFC4 antibody and β‐actin was used as a loading control.
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    Figure 2. RFC4 was highly expressed in breast cancer tissues and cell lines. (A) Expression levels of RFC4 in breast cancer tissues (n=1,097) and normal tissues (n=114) were analyzed using RNA‐seq data analysis from UALCAN. Box plot displays the expression levels of RFC4 in normal and cancer tissues based on sample types (left panel) and different subtypes of breast cancer (right panel) (***p<0.001, compared to normal tissues). (B) Expression levels of RFC4 in breast cancer were measured by breast cancer <t>TissueScan</t> qRT‐PCR array. Bar graphs represent the mRNA expression levels of RFC4 in each clinical status of breast cancer tissue samples. Scatter plot represent the mRNA expression levels of RFC4 in normal and breast cancer tissues (*p<0.05, compared to normal tissues). (C) RFC4 mRNA expression was analyzed using qRT‐PCR in breast cancer cell lines and normal fibroblast cell line, MCF10A. Graphs show the mean±SD from independent triplicate experiments (*p<0.05, **p<0.01, compared to MCF10A). (D) RFC4 protein expression was analyzed using western blot analysis in same cell lines. Cell lysates were immunoblotted with the RFC4 antibody and β‐actin was used as a loading control.
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    ( 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.

    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

    ( 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.

    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

    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.

    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

    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.

    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: PTEN mRNA expression was measured in TissueScan Breast Cancer cDNA Arrays I, II, III and IV (OriGene, BCRT101, BCRT102, BCRT103, and BCRT104) which contained 176 breast cancers and 16 tumor-adjacent “normal” breast tissues.

    Techniques: Expressing, Mutagenesis, Gene Expression

    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.

    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

    Figure 2. RFC4 was highly expressed in breast cancer tissues and cell lines. (A) Expression levels of RFC4 in breast cancer tissues (n=1,097) and normal tissues (n=114) were analyzed using RNA‐seq data analysis from UALCAN. Box plot displays the expression levels of RFC4 in normal and cancer tissues based on sample types (left panel) and different subtypes of breast cancer (right panel) (***p<0.001, compared to normal tissues). (B) Expression levels of RFC4 in breast cancer were measured by breast cancer TissueScan qRT‐PCR array. Bar graphs represent the mRNA expression levels of RFC4 in each clinical status of breast cancer tissue samples. Scatter plot represent the mRNA expression levels of RFC4 in normal and breast cancer tissues (*p<0.05, compared to normal tissues). (C) RFC4 mRNA expression was analyzed using qRT‐PCR in breast cancer cell lines and normal fibroblast cell line, MCF10A. Graphs show the mean±SD from independent triplicate experiments (*p<0.05, **p<0.01, compared to MCF10A). (D) RFC4 protein expression was analyzed using western blot analysis in same cell lines. Cell lysates were immunoblotted with the RFC4 antibody and β‐actin was used as a loading control.

    Journal: Cancer genomics & proteomics

    Article Title: Replication Factor C Subunit 4 Plays a Role in Human Breast Cancer Cell Progression.

    doi: 10.21873/cgp.20515

    Figure Lengend Snippet: Figure 2. RFC4 was highly expressed in breast cancer tissues and cell lines. (A) Expression levels of RFC4 in breast cancer tissues (n=1,097) and normal tissues (n=114) were analyzed using RNA‐seq data analysis from UALCAN. Box plot displays the expression levels of RFC4 in normal and cancer tissues based on sample types (left panel) and different subtypes of breast cancer (right panel) (***p<0.001, compared to normal tissues). (B) Expression levels of RFC4 in breast cancer were measured by breast cancer TissueScan qRT‐PCR array. Bar graphs represent the mRNA expression levels of RFC4 in each clinical status of breast cancer tissue samples. Scatter plot represent the mRNA expression levels of RFC4 in normal and breast cancer tissues (*p<0.05, compared to normal tissues). (C) RFC4 mRNA expression was analyzed using qRT‐PCR in breast cancer cell lines and normal fibroblast cell line, MCF10A. Graphs show the mean±SD from independent triplicate experiments (*p<0.05, **p<0.01, compared to MCF10A). (D) RFC4 protein expression was analyzed using western blot analysis in same cell lines. Cell lysates were immunoblotted with the RFC4 antibody and β‐actin was used as a loading control.

    Article Snippet: To assess the mRNA expression of RFC4 in breast cancer tissues, the TissueScan Breast Cancer cDNA Array was purchased from OriGene (Origene Technologies, Rockville, MD, USA).

    Techniques: Expressing, RNA Sequencing, Quantitative RT-PCR, Western Blot, Control