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Journal Articles
Cancer Res (2022) 82 (10_Supplement): B021.
Published: 15 May 2022
... resection of the bladder tumor (TURBT) and post-NAC radical cystectomy will be performed and incorporated into tissue microarrays. GeoMx Digital Spatial Profiler Cancer Transcriptome Atlas panel (Nanostring Technologies) will be applied for high-plex compartment-specific expression of genes covering...
Journal Articles
Cancer Res (2022) 82 (10_Supplement): B024.
Published: 15 May 2022
...-mortem interval (PMI) was 44 hours. Multiple tissue cores from formalin-fixed paraffin-embedded tumor tissue from the surgical resection and different tumor sites from the autopsy were assembled into a single tissue microarray (TMA) block. DNA was extracted from adjacent tissue cores obtained in parallel...
Images
Factors secreted by MITF<sup>low</sup> AXL<sup>high</sup> dedifferentiated ...
Published: 03 May 2022
Figure 3. Factors secreted by MITFlow AXLhigh dedifferentiated melanoma cells inhibit actomyosin cytoskeleton contraction of LN-F. A, Fluorescence staining of F-actin fibers, MLC2 phosphorylation (P-MLC2), and cell nuclei (Hoechst) in LN-F grown for 7 days in control medium or with CM from the dedifferentiated 1205Lu cell line or the melanocytic 501Mel cell line. Scale bar, 100 µm. A zoom on a single cell is shown for each condition. Scale bar, 20 µm. B, Quantification of mean fluorescence intensities (MFI) of active pS19 MLC2 (P-MLC2), F-actin fibers, and the cell shape index (n = 45 cells; median ± quartiles). C, Microarray-based gene expression profiling in control and 1205Lu CM-treated LN-F. D, The 1,110 most downregulated genes in 1205Lu-reprogrammed LN-F (with logFC ≤ -0.5) are surrounded and submitted to GSEA. E, GSEA plot comparing the gene expression of control- and 1205Lu-educated LN-F with signatures from inflammatory CAFs and myofibroblastic CAFs. *, P < 0.05; ***, P < 0.001; ****, P < 0.0001. NES, normalized enrichment scale. Figure 3. Factors secreted by MITFlow AXLhigh dedifferentiated melanoma cells inhibit actomyosin cytoskeleton contraction of LN-F. A, Fluorescence staining of F-actin fibers, MLC2 phosphorylation (P-MLC2), and cell nuclei (Hoechst) in LN-F grown for 7 days in control medium or with CM from the dedifferentiated 1205Lu cell line or the melanocytic 501Mel cell line (scale bar = 100 µmol/L). A zoom on a single cell is shown for each condition (scale bar = 20 µmol/L). B, Quantification of mean fluorescence intensities (MFI) of active pS19 MLC2 (P-MLC2), F-actin fibers, and the cell shape index (n = 45 cells; median ± quartiles; P* < 0.05, *** < 0.001, **** < 0.0001). C, Microarray-based gene expression profiling in control and 1205Lu CM-treated LN-F. The 1,110 most downregulated genes in 1205Lu-reprogrammed LN-F (with logFC ≤ -0.5) are surrounded and submitted to GSEA in (D). E, GSEA plot comparing the gene expression of control- and 1205Lu-educated LN-F with signatures from inflammatory CAFs and myofibroblastic CAFs. Ctrl, control; min, minimum; max, maximum; NES, normalized enrichment scale. More
Images
Expression of Wnt signaling pathway, c-Myc, CSC markers, and Tgfβ pathway w...
Published: 03 May 2022
Figure 3. Expression of Wnt signaling pathway, c-Myc, CSC markers, and Tgfβ pathway was increased in HKβ biliary spheroids. A, Schema of biliary spheroids established from EHBD and GB in H, HK, , and HKβ mice 4 weeks after the last tamoxifen administration (n = 3 mice/group). B, Microscopic images of H, HK, , and HKβ biliary spheroids on day 1 and day 5 after passage. Scale bars, 500 µm. C, Assay of the proliferation of H, HK, , and HKβ biliary spheroids on day 1, day 3, and day 5 after passage (n = 3/group). The assay of proliferation was performed using PrestoBlue. The values were calculated as described in Materials and Methods. Data are mean ± SEM. Analyzed by one-way ANOVA with Dunnett test (vs. HKβ spheroids; *, P < 0.05; **, P < 0.01). D, Top, commonly high fold change (>2 log, <−2 log) expression genes on microarray analysis in HKβ biliary spheroids. Bottom, upregulated gene sets on Hallmark gene set of GSEA in HKβ spheroids. FDR, q < 0.25 (vs. HKβ spheroids). E and F, qRT-PCR analysis of H, HK, , and HKβ biliary spheroids (n = 3/group). Data are shown as individual data points and the mean ± SEM for each experimental group. Analyzed by one-way ANOVA with Dunnett test (vs. HKβ spheroids; *, P < 0.05). G, Immunostaining for Dclk1 (top) and Aldh1a1 (bottom) in the EHBD and GB in H, HK, , and HKβ mice 4 weeks after the last tamoxifen administration. Aldh1a1 was expressed at a crypt-like location between BilIN in EHBD and the inner epithelial cells of ICPN in HKβ mice (arrowheads). Scale bars, 50 µm. Figure 3. Expression of Wnt signaling pathway, c-Myc, CSC markers, and Tgfβ pathway was increased in HKβ biliary spheroids. A, Schema of biliary spheroids established from EHBD and GB in H, HK, Hβ, and HKβ mice 4 weeks after the last tamoxifen administration (n = 3 mice/group). B, Microscopic images of H, HK, Hβ, and HKβ biliary spheroids on day 1 and day 5 after passage. Scale bars = 500 µmol/L. C, Assay of the proliferation of H, HK, Hβ, and HKβ biliary spheroids on day 1, day 3, and day 5 after passage (n = 3/group). The assay of proliferation was performed using PrestoBlue. The values were calculated as described in the Materials and Methods. Data are mean ± SEM. Analyzed by one-way ANOVA with Dunnett test (vs. HKβ spheroids; *, P < 0.05; **, P < 0.01). D, Commonly high fold-change (>2 log, <−2 log) expression genes on microarray analysis in HKβ biliary spheroids (top). Upregulated gene sets on Hallmark gene set of GSEA in HKβ spheroids (bottom). FDR q < 0.25 (vs. HKβ spheroids). E and F, qRT-PCR analysis of H, HK, Hβ, and HKβ biliary spheroids (n = 3/group). Data are shown as individual data points and the mean ± SEM for each experimental group. Analyzed by one-way ANOVA with Dunnett test (vs. HKβ spheroids; *, P < 0.05). G, Immunostaining for Dclk1 (top) and Aldh1a1 (bottom) in the EHBD and GB in H, HK, Hβ, and HKβ mice 4 weeks after the last tamoxifen administration. Aldh1a1 is expressed at a crypt-like location between BilIN in EHBD and the inner epithelial cells of ICPN in HKβ mice (arrowheads). Scale bars = 50 µmol/L. More
Images
PTDSS1 expression correlates with survival.  A–F,  Association of PS and et...
Published: 15 April 2022
Figure 7. PTDSS1 expression correlates with survival. A–F, Association of PS and ether lipid metabolizing enzymes with clinical parameters in publicly available breast cancer data sets. Correlation of PS and ether lipid metabolizing enzymes with survival ( A ), correlation of PTDSS1 with survival ( B ), PTDSS1 expression in breast cancer subtypes ( C ), and correlation of PTDSS1 expression with clinical parameters in the METABRIC cohort ( D ). Parameters used as binary categorical variables are in bold; continuous variables in light script. Correlation of PTDSS1 expression with survival ( E ) and metastasis ( F ) in the van de Vijver data set. G–J, PTDSS1 expression and clinical parameters in human breast cancer tissue microarrays. G, Representative microscopy images show CD163, pan-Cytokeratin (Pan-CK), and PTDSS1 expression in mammary carcinoma cores; nuclei stained with DAPI. Scale bars, 100 µm. Correlation of PTDSS1 expression with survival of all patients ( H ) and with survival of patients with estrogen receptor (ER), progesterone receptor (PR), HER2-expressing or triple-negative breast tumors (TNBC; I ). J, Correlation of PTDSS1 expression with clinical parameters. Parameters used as binary categorical variables are in bold; continuous variables in light script. K, Correlation of PTDSS1 expression with patient survival in the TCGA lung adenocarcinoma data set. L, Correlation of PTDSS1 and macrophage marker CD163 expression in breast cancer subtypes in the METABRIC dataset. M, PTDSS1 and CD163 expression in tissue microarrays. Representative microscopy images show cells expressing CD163 and PTDSS1; nuclei stained with DAPI. Scale bars, 100 µm. The graph shows PTDSS1 versus CD163 expression in breast cancer subtypes. A , B , E , H , I , and K, Log-rank test. D , J , L , and M, Spearman correlation coefficient when comparing continuous variables ( D , J , L , and M ) and point-biserial correlation coefficient when comparing continuous with binary categorical variables are shown ( D and J ). Significant correlations (P < 0.05) are in bold. F, Unpaired two-tailed Student t test; ***, P < 0.001. Figure 7. PTDSS1 expression correlates with survival. A–F, Association of PS and ether lipid metabolizing enzymes with clinical parameters in publicly available breast cancer data sets. A, Correlation of PS and ether lipid metabolizing enzymes with survival, (B) correlation of PTDSS1 with survival, and (C) PTDSS1 expression in breast cancer subtypes, and (D) correlation of PTDSS1 expression with clinical parameters in the METABRIC cohort. Parameters used as binary categorical variables are in bold, continuous variables in light script. E, Correlation of PTDSS1 expression with survival and (F) metastasis in the van de Vijver data set. G–J, PTDSS1 expression and clinical parameters in human breast cancer tissue microarrays. G, Representative microscopy images show CD163, pan-Cytokeratin (Pan-CK), and PTDSS1 expression in mammary carcinoma cores; nuclei stained with DAPI; bars 100 µmol/L. H, Correlation of PTDSS1 expression with survival of all patients, and (I) with survival of patients with estrogen receptor (ER), progesterone receptor (PR), HER2-expressing or triple-negative breast tumors (TNBC). J, Correlation of PTDSS1 expression with clinical parameters. Parameters used as binary categorical variables are in bold, continuous variables in light script. K, Correlation of PTDSS1 expression with patient survival in the TCGA lung adenocarcinoma data set. L, Correlation of PTDSS1 and macrophage marker CD163 expression in breast cancer subtypes in the METABRIC dataset. M, PTDSS1 and CD163 expression in tissue microarrays. Representative microscopy images show cells expressing CD163 and PTDSS1; nuclei stained with DAPI; bars 100 µmol/L. The graph shows PTDSS1 versus CD163 expression in breast cancer subtypes. A, B, E, H, I, K, Log-rank test. D, J, L, M, Spearman correlation coefficient when comparing continuous variables and (D, J) point-biserial correlation coefficient when comparing continuous with binary categorical variables are shown, significant correlations (P < 0.05) in bold (HF unpaired two-tailed Student t test; ***, P < 0.001). More
Journal Articles
Cancer Res canres.0410.2022.
Published: 18 May 2022
... 0.5 0 ** * G GFP GFP-FoxM1 GFP-FoxM1DD Averagee fold pull down 6 5 4 3 2 1 0 GFP-ChIP GFP GFP-FoxM1 GFP-FoxM1DD Pten Negative control ** Rb-ChIP I GFP GFP-FoxM1 GFP-FoxM1DD Pten Negative control mRNA expression (microarray): Pten FoxM1FOXM1 vs. PTENvs. Pten 12 11.5 11 Spearman:( = 6.00e-70) -0.39 10.5...
Includes: Supplementary data
Journal Articles
Cancer Res canres.CAN-21-2352-E.2021.
Published: 18 May 2022
... (Protocol 01-045) and Partners Healthcare (IRB 2006P000139). Briefly, formalin-fixed, paraffin-embedded (FFPE) prostate tissue from 345 patients (including 3 tumor cores and 2 matched normal cores per patient) were arrayed on seven panels. Tissue microarray (TMA) H&E sections were reviewed by a board...
Journal Articles
Cancer Res canres.3844.2021.
Published: 18 May 2022
... (both CD133+ve and CD133-ve). Additionally, substantially higher IC50s for FACS sorted CD133+ve cells were observed with combination and single MAPK signaling pathway inhibitors. Sensitivity to Dabrafenib and Trametinib was enhanced after siRNA-based knockdown of CD133. Furthermore, microarray results...
Journal Articles
Cancer Res (2022) 82 (9): 1803–1817.
Published: 03 May 2022
...; **, P < 0.01). D, Top, commonly high fold change (>2 log, <−2 log) expression genes on microarray analysis in HKβ biliary spheroids. Bottom, upregulated gene sets on Hallmark gene set of GSEA in HKβ spheroids. FDR, q < 0.25 (vs. HKβ spheroids). E...
Includes: Supplementary data
Journal Articles
Cancer Res (2022) 82 (10): 1872–1889.
Published: 16 May 2022
... assays were done in osteosarcoma cells fixed with 4% paraformaldehyde as described previously ( 27 ). IHC was carried out by the UTHSA Histology & Immunohistochemistry Core Laboratory using an anti-ALKBH5 (Sigma, HPA007196) antibody on tissue microarray cores from US Biomax, Inc. (osteosarcoma tissue...
Includes: Supplementary data
Journal Articles
Cancer Res (2022) 82 (9): 1774–1788.
Published: 03 May 2022
... shape index (n = 45 cells; median ± quartiles). C, Microarray-based gene expression profiling in control and 1205Lu CM-treated LN-F. D, The 1,110 most downregulated genes in 1205Lu-reprogrammed LN-F (with logFC ≤ -0.5) are surrounded and submitted to GSEA. E, GSEA plot...
Includes: Supplementary data
Journal Articles
Cancer Res canres.4152.2021.
Published: 18 May 2022
...:120295 doi 10.1101/120295. 25. Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 2015;43(7):e47 doi 10.1093/nar/gkv007. 26. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette...
Includes: Supplementary data
Journal Articles
Cancer Res (2022) 82 (9): 1832–1843.
Published: 03 May 2022
... GDCRNATools ( 25 ). The raw .CEL files of the four Affymetrix microarray datasets including CPC-Gene (GSE107299), Taylor (GSE21034), CancerMap (GSE94764), and CIT (E-MTAB-6128) were downloaded from GEO/ArrayExpress and normalized with the Robust Multichip Average (RMA) method implemented in the R package...
Includes: Supplementary data
Journal Articles
Cancer Res (2022) 82 (9): 1675–1681.
Published: 03 May 2022
... expression analysis by IHC of the ovarian tumors on the tissue microarray from chemo-naïve patients, showed both stromal and cellular staining ( 22 ). Besides published reports in other indications (e.g., sarcoma) where expression of LRRC15 on cancer and/or stromal fibroblasts was observed on treatment...
Journal Articles
Cancer Res canres.1825.2021.
Published: 17 May 2022
... of human cancer (18). To determine the relevance of KDM6A regulation by USP7 in prostate cancer patients. 17 We performed immunohistochemical staining of USP7 and KDM6A (Fig. 5H) on prostate cancer progression tissue microarrays. Of the 152 PCa tissue samples, 110 cases had strong USP7 expression and 42...
Journal Articles
Cancer Res (2022) 82 (10): 2031–2044.
Published: 16 May 2022
..., the average expression of all six collagen IV genes was quantified and compared with the patients’ age at diagnosis. For analysis of patient survival, we used kmplot.com, a meta-analysis tool that allows querying a large collection of breast cancer patient RNA microarray datasets. Either patients...
Includes: Supplementary data
Journal Articles
Cancer Res (2022) 82 (9): 1712–1723.
Published: 03 May 2022
...) analysis, 72 clustered IM glands and 24 clustered non-IM glands in the inflamed mucosa from 26 patients with IGC were obtained as described below; of these, 2 patients were included in the above-mentioned WES analysis. We also reanalyzed previously reported CN microarray data for 41 IGC samples from 19...
Includes: Supplementary data
Journal Articles
Cancer Res (2022) 82 (10): 1890–1908.
Published: 16 May 2022
... . Cell Reports Med 2020 ; 1 : 100143 . 49. Lee KC , Maturo C , Perera CN , Luddy J , Rodriguez R , Shorr R . Translational assessment of mitochondrial dysfunction of pancreatic cancer from in vitro gene microarray and animal efficacy studies, to early...
Includes: Multimedia, Supplementary data
Journal Articles
Cancer Res canres.0668.2022.
Published: 10 May 2022
... is: 304 tfa <- sciraEstRegAct(data,norm=c("zregnet.m=net.o$netTOI); 305 The esophageal-specific regulatory network was validated in two independent multi bulk 306 tissue expression datasets: one is an RNA-Seq dataset from the ProteinAtlas project (36) and 307 the other is an Affymetrix microarray set from...
Includes: Supplementary data
Images
TAK1L correlates with CAF activation, survival, and metastasis in patients ...
Published: 01 April 2022
Figure 8. TAK1L correlates with CAF activation, survival, and metastasis in patients with breast cancer. Human CDC breast cancer progression tissue microarrays were analyzed for correlation of TAK1L expression (encoded by MAP3K7CL) with CAF markers and clinical parameters. A, Representative microscopy images show cells expressing αSMA, VWF, SERPINH1, pp38, TAK1L, and KI67 in tumor cores. Nuclei were stained with DAPI. Scale bar, 100 μm. One example of TAK1L-high (left) and TAK1L-low cores (right) is shown. B, Relative abundance of tissue categories or cells in normal breast (n = 19), ductal carcinoma in situ (DCIS; n = 8), and invasive carcinoma (n = 129) is shown. C, Heatmap showing the correlation of tissue categories or cell subsets with clinical parameters. D and E, Kaplan–Meier plots indicate patient survival according to content of TAK1L+ SERPINH1+ CAF, or αSMA+ SERPINH1+ CAF. Nonparametric correlation analysis (Spearman) was performed, and P values for survival analyses were calculated using the log-rank test. Figure 8. TAK1L correlates with CAF activation, survival, and metastasis in patients with breast cancer. Human CDC breast cancer progression tissue microarrays were analyzed for correlation of TAK1L expression (encoded by MAP3K7CL) with CAF markers and clinical parameters. A, Representative microscopy images show cells expressing αSMA, VWF, SERPINH1, pp38, TAK1L, and KI67 in tumor cores. Nuclei were stained with DAPI. Scale bar, 100 μm. One example of TAK1L-high (left) and TAK1L-low cores (right) is shown. B, Relative abundance of tissue categories or cells in normal breast (n = 19), ductal carcinoma in situ (DCIS; n = 8), and invasive carcinoma (n = 129) is shown. C, Heatmap showing the correlation of tissue categories or cell subsets with clinical parameters. D and E, Kaplan–Meier plots indicate patient survival according to content of TAK1L+ SERPINH1+ CAF, or αSMA+ SERPINH1+ CAF. Nonparametric correlation analysis (Spearman) was performed, and P values for survival analyses were calculated using the log-rank test. More