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: Cancer Biology & Therapy

Article Title: Sulfatase 2 inhibition sensitizes triple-negative breast cancer cells to paclitaxel through augmentation of extracellular ATP

doi: 10.1080/15384047.2025.2483989

Figure Lengend Snippet: ELISA analysis of sulfatases and SULF2 immunohistochemistry. ELISAs were performed to examine the basal levels of (a) SULF1 and (b) SULF2 in adjusted cell supernatants inversely proportionate to the protein concentration in the corresponding cell lysate of MCF-10A cell line, TNBC MDA-MB 231, Hs 578t and MDA-MB 468 cell lines and ER+/PR+ T47D, MCF-7 and ZR-75-1 cell lines. MCF-10A expressed more SULF1 in comparison to the TNBCs but similar expression levels were observed in ER+/PR+ T47D and MCF-7 cells. However, the ER+/PR+ ZR-75-1 cell line expressed the most SULF1. Meanwhile, TNBCs and ER+/PR+ T47D and ZR-75-1 cells expressed more SULF2 in comparison to MCF-10A cells. Standard deviation was calculated from three independent experiments performed in triplicate. The student’s t-test was performed to determine significance with *representing p < 0.05 and **representing p < 0.01 comparing the protein expression MCF-10A to the protein expressions of TNBC cell lines. (b) The AMSBIO BR1202B breast cancer tissue array (120 cores with 82 TNBC cores, 20 ER+/PR+ cores, 14 HER2+ cores, and 4 necrotic cores; key can be found in supplemental Figure S6C) was stained with SULF2.

Article Snippet: The student’s t-test was performed to determine significance with *representing p < 0.05 and **representing p < 0.01 comparing the protein expression MCF-10A to the protein expressions of TNBC cell lines. (b) The AMSBIO BR1202B breast cancer tissue array (120 cores with 82 TNBC cores, 20 ER+/PR+ cores, 14 HER2+ cores, and 4 necrotic cores; key can be found in supplemental Figure S6C) was stained with SULF2.

Techniques: Enzyme-linked Immunosorbent Assay, Immunohistochemistry, Protein Concentration, Comparison, Expressing, Standard Deviation, Staining

Journal: Cancer Biology & Therapy

Article Title: Sulfatase 2 inhibition sensitizes triple-negative breast cancer cells to paclitaxel through augmentation of extracellular ATP

doi: 10.1080/15384047.2025.2483989

Figure Lengend Snippet: Statistical analysis for SULF2 immunohistochemistry. For the breast cancer tissue array and slides stained for heparanase: TNBC ( n =75), ER+/PR+ ( n =18), HER2+ ( n =14), (a) images were taken of SULF2-stained AMSBIO BR1202B breast cancer tissue array on an evos FL auto 2 microscope (40×). (b) Pairwise comparisons using Dunn’s test indicated that there was a significant difference in H-score between breast cancer sub-types TNBC and ER+/PR+ ( p = 0.0392). There was no significant different between TNBC and HER2+. (c) The Kruskal-Wallis test indicated that there was no significant difference in the average percentages of cells that stained positively for SULF2 in tissue sections of TNBC, ER+/PR+ breast cancer, and HER2+ breast cancer. (d) Pairwise comparisons using Dunn’s test indicated that there was a significant difference between breast cancer sub-types TNBC and ER+/PR+ ( p = 0.009), and TNBC and HER2+ ( p = 0.0338), in the percentages of cells that stained moderately or strongly positive for SULF2. (e) The same Dunn’s test from (d) also indicated that there was a significant difference between cancer sub-types TNBC and ER+/PR+ ( p = 0.0094), and TNBC and HER2+( p = 0.0338), in the percentages of cells that stained negative or weakly positive for SULF2. (f) Pairwise comparisons using Dunn’s test showed that there was a significant difference between TNBC breast cancer stages 2A and 2B ( p = 0.0007) in the percentages of cells that stained positively for SULF2. No other differences among different TNBC stages were significant. Standard error of the mean was calculated. For statistical analysis, *representing p < 0.05, **representing p < 0.01 and ***representing p < 0.001.

Article Snippet: The student’s t-test was performed to determine significance with *representing p < 0.05 and **representing p < 0.01 comparing the protein expression MCF-10A to the protein expressions of TNBC cell lines. (b) The AMSBIO BR1202B breast cancer tissue array (120 cores with 82 TNBC cores, 20 ER+/PR+ cores, 14 HER2+ cores, and 4 necrotic cores; key can be found in supplemental Figure S6C) was stained with SULF2.

Techniques: Immunohistochemistry, Staining, Microscopy

Journal: Cancer Biology & Therapy

Article Title: Sulfatase 2 inhibition sensitizes triple-negative breast cancer cells to paclitaxel through augmentation of extracellular ATP

doi: 10.1080/15384047.2025.2483989

Figure Lengend Snippet: ELISA analysis of sulfatases and SULF2 immunohistochemistry. ELISAs were performed to examine the basal levels of (a) SULF1 and (b) SULF2 in adjusted cell supernatants inversely proportionate to the protein concentration in the corresponding cell lysate of MCF-10A cell line, TNBC MDA-MB 231, Hs 578t and MDA-MB 468 cell lines and ER+/PR+ T47D, MCF-7 and ZR-75-1 cell lines. MCF-10A expressed more SULF1 in comparison to the TNBCs but similar expression levels were observed in ER+/PR+ T47D and MCF-7 cells. However, the ER+/PR+ ZR-75-1 cell line expressed the most SULF1. Meanwhile, TNBCs and ER+/PR+ T47D and ZR-75-1 cells expressed more SULF2 in comparison to MCF-10A cells. Standard deviation was calculated from three independent experiments performed in triplicate. The student’s t-test was performed to determine significance with *representing p < 0.05 and **representing p < 0.01 comparing the protein expression MCF-10A to the protein expressions of TNBC cell lines. (b) The AMSBIO BR1202B breast cancer tissue array (120 cores with 82 TNBC cores, 20 ER+/PR+ cores, 14 HER2+ cores, and 4 necrotic cores; key can be found in supplemental Figure S6C) was stained with SULF2.

Article Snippet: For the breast cancer tissue array and slides stained for heparanase: TNBC ( n =75), ER+/PR+ ( n =18), HER2+ ( n =14), (a) images were taken of SULF2-stained AMSBIO BR1202B breast cancer tissue array on an evos FL auto 2 microscope (40×). (b) Pairwise comparisons using Dunn’s test indicated that there was a significant difference in H-score between breast cancer sub-types TNBC and ER+/PR+ ( p = 0.0392).

Techniques: Enzyme-linked Immunosorbent Assay, Immunohistochemistry, Protein Concentration, Comparison, Expressing, Standard Deviation, Staining

Journal: Cancer Biology & Therapy

Article Title: Sulfatase 2 inhibition sensitizes triple-negative breast cancer cells to paclitaxel through augmentation of extracellular ATP

doi: 10.1080/15384047.2025.2483989

Figure Lengend Snippet: Statistical analysis for SULF2 immunohistochemistry. For the breast cancer tissue array and slides stained for heparanase: TNBC ( n =75), ER+/PR+ ( n =18), HER2+ ( n =14), (a) images were taken of SULF2-stained AMSBIO BR1202B breast cancer tissue array on an evos FL auto 2 microscope (40×). (b) Pairwise comparisons using Dunn’s test indicated that there was a significant difference in H-score between breast cancer sub-types TNBC and ER+/PR+ ( p = 0.0392). There was no significant different between TNBC and HER2+. (c) The Kruskal-Wallis test indicated that there was no significant difference in the average percentages of cells that stained positively for SULF2 in tissue sections of TNBC, ER+/PR+ breast cancer, and HER2+ breast cancer. (d) Pairwise comparisons using Dunn’s test indicated that there was a significant difference between breast cancer sub-types TNBC and ER+/PR+ ( p = 0.009), and TNBC and HER2+ ( p = 0.0338), in the percentages of cells that stained moderately or strongly positive for SULF2. (e) The same Dunn’s test from (d) also indicated that there was a significant difference between cancer sub-types TNBC and ER+/PR+ ( p = 0.0094), and TNBC and HER2+( p = 0.0338), in the percentages of cells that stained negative or weakly positive for SULF2. (f) Pairwise comparisons using Dunn’s test showed that there was a significant difference between TNBC breast cancer stages 2A and 2B ( p = 0.0007) in the percentages of cells that stained positively for SULF2. No other differences among different TNBC stages were significant. Standard error of the mean was calculated. For statistical analysis, *representing p < 0.05, **representing p < 0.01 and ***representing p < 0.001.

Article Snippet: For the breast cancer tissue array and slides stained for heparanase: TNBC ( n =75), ER+/PR+ ( n =18), HER2+ ( n =14), (a) images were taken of SULF2-stained AMSBIO BR1202B breast cancer tissue array on an evos FL auto 2 microscope (40×). (b) Pairwise comparisons using Dunn’s test indicated that there was a significant difference in H-score between breast cancer sub-types TNBC and ER+/PR+ ( p = 0.0392).

Techniques: Immunohistochemistry, Staining, Microscopy