Journal: Cancer cell

Article Title: ATRX in-frame fusion neuroblastoma is sensitive to EZH2 inhibition via modulation of neuronal gene signatures

doi: 10.1016/j.ccell.2019.09.002

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Human: G401 , ATCC , CRL-1441.

Techniques: Virus, Microarray, Recombinant, Magnetic Beads, Bicinchoninic Acid Protein Assay, Cell Culture, DNA Library Preparation, Extraction, Expressing, Sequencing, Software

Journal: The Journal of Biological Chemistry

Article Title: Essential Role of the Zinc Finger Transcription Factor Casz1 for Mammalian Cardiac Morphogenesis and Development *

doi: 10.1074/jbc.M114.570416

Figure Lengend Snippet: Casz1 expression pattern during mouse embryogenesis. A, cartoon of the Casz1 gene trap that inserted with a βgeo reporter after Casz1 exon 9 resulting in a truncated Casz1. B, genotyping of Casz1-trapped mice by RT-PCR. C, whole mount X-gal staining (blue) of E9.5 Casz1+/βgeo embryos shows that Casz1 was expressed in the hindbrain, neural tube, and heart, which are further demonstrated by dissected embryo sagittal sections 1, 2, and 3 (100× magnification). Sagittal section 3b (200× magnification) shows that Casz1 was expressed in the cardiomyocytes. D and E, whole mount X-gal staining of E12.5 Casz1+/+, Casz1+/βgeo, and Casz1βgeo/βgeo embryos showed that Casz1 is expressed in the eye, dorsomedial telencephalon, cranial ganglia, nasal placode, somite, neural tube, and heart. F, real time PCR to detect wild type Casz1 allele and Gata4 mRNA levels in E12.5 hearts. G, the protein levels of Casz1a/Casz1b and GAPDH were visualized by immunoblotting E14.5 whole heart lysate with anti-Casz1 antibody and anti-GAPDH antibody. H, whole mount anti-β-galactosidase staining (red) of E14.5 Casz1+/+, Casz1+/βgeo, and Casz1βgeo/βgeo hearts.

Article Snippet: Rabbit anti-GAPDH (Santa Cruz, 1:4000) and rabbit anti-Casz1 (Rockland, 1:1000) were used to detect GAPDH and Casz1 protein level in heart.

Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Staining, Real-time Polymerase Chain Reaction, Western Blot

Journal: The Journal of Biological Chemistry

Article Title: Essential Role of the Zinc Finger Transcription Factor Casz1 for Mammalian Cardiac Morphogenesis and Development *

doi: 10.1074/jbc.M114.570416

Figure Lengend Snippet: Hypoplasia in the myocardium of Casz1βgeo/βgeo heart. A, phenotype of Casz1+/+, Casz1+/βgeo and Casz1βgeo/βgeo E 15.5 embryos. The edema was seen at the neck region on the back of Casz1βgeo/βgeo embryos but not other embryos (green arrow). B–D, column 1, H&E staining of transverse sections of E15.5 Casz1+/+ (B1), Casz1+/βgeo (C1), and Casz1βgeo/βgeo (D1) embryos. Column 2, right ventricle (RV) magnification of the respective green squares from column 1. Column 3, septum (SP) magnification of respective yellow squares from column 1. Column 4, left ventricle (LV) magnification of respective blue squares from column 1. E, representative photomicrographs indicate accumulation of blood cells in the liver of the Casz1βgeo/βgeo embryo (right panel) but not in the Casz1+/+ (left panel) or Casz1+/βgeo (middle panel) embryo.

Article Snippet: Rabbit anti-GAPDH (Santa Cruz, 1:4000) and rabbit anti-Casz1 (Rockland, 1:1000) were used to detect GAPDH and Casz1 protein level in heart.

Techniques: Staining

Journal: The Journal of Biological Chemistry

Article Title: Essential Role of the Zinc Finger Transcription Factor Casz1 for Mammalian Cardiac Morphogenesis and Development *

doi: 10.1074/jbc.M114.570416

Figure Lengend Snippet: Decreased proliferation in Casz1βgeo/βgeo heart. A, the E14.5 Casz1βgeo/βgeo hearts were morphologically different compared with the Casz1+/βgeo or wild type heart (compare the green arrow targeted region). B, lower magnification of H&E staining of transverse sections from E14.5 embryos (upper panels). The lower panels represent a magnification of the regions that are depicted in the blue squares in the upper panel. The green arrow denotes the septal defect apparent in the serial sectioning of the Casz1βgeo/βgeo heart compared with the Casz1+/+ heart. C, paraffin sections from E14.5 hearts from Casz1+/+ and Casz1βgeo/βgeo hearts were immunostained with antibodies for MF20 (red) and the mitosis marker phosphohistone H3 (pH3, green). The nuclei were stained with DAPI (blue; left top panels, original overview; left bottom panels, high magnification). In the high magnification images, arrows indicate pH3+ cells. The graph (right panel) represents the relative percentage of pH3 positive cells compared with the total number of DAPI positive Casz1βgeo/βgeo or Casz1+/+ cardiomyocytes from at least five sections from each embryo. The Casz1βgeo/βgeo cardiomyocytes proliferate significantly slower than Casz1+/+ cardiomyocytes (p < 0.00001). D, tunnel staining (green) was performed using E14.5 heart paraffin sections (upper panels), and nuclei were stained with DAPI (blue). The lower panels represent magnified areas delineated in the red squares in the upper panels. There was no significant difference in the number of apoptotic cells observed in Casz1βgeo/βgeo cardiomyocytes compared with Casz1+/+ cardiomyocytes.

Article Snippet: Rabbit anti-GAPDH (Santa Cruz, 1:4000) and rabbit anti-Casz1 (Rockland, 1:1000) were used to detect GAPDH and Casz1 protein level in heart.

Techniques: Staining, Marker

Journal: The Journal of Biological Chemistry

Article Title: Essential Role of the Zinc Finger Transcription Factor Casz1 for Mammalian Cardiac Morphogenesis and Development *

doi: 10.1074/jbc.M114.570416

Figure Lengend Snippet: Disorganized fiber orientation in Casz1βgeo/βgeo heart. To visualize thin filaments, Casz1+/+ and Casz1βgeo/βgeo E14.5 hearts were stained with phalloidin-488 (green) to detect F-Actin and co-stained with TOPRO3 to show cell nuclei. The left panels show the co-staining results of the left ventricles of the hearts. The right panels represent magnified areas delineated in the red squares in the left panels. Enlarged images showed complete disruption of the fiber orientation/cell alignment in the left ventricle (LV) of Casz1βgeo/βgeo heart.

Article Snippet: Rabbit anti-GAPDH (Santa Cruz, 1:4000) and rabbit anti-Casz1 (Rockland, 1:1000) were used to detect GAPDH and Casz1 protein level in heart.

Techniques: Staining

Journal: The Journal of Biological Chemistry

Article Title: Essential Role of the Zinc Finger Transcription Factor Casz1 for Mammalian Cardiac Morphogenesis and Development *

doi: 10.1074/jbc.M114.570416

Figure Lengend Snippet: Abnormal gene expression in Casz1βgeo/βgeo heart. A, microarray analysis of RNA from three E12.5 Casz1+/+ hearts and three E12.5 Casz1βgeo/βgeo hearts. The heat map was generated using Partek software. Two-thirds of these genes are aberrantly up-regulated, and one-third are aberrantly down regulated in Casz1βgeo/βgeo hearts. B, Partek gene ontology oncology analysis showed that the top two categories of enriched genes are “signaling” and the process of biological adhesion. Biological adhesion genes in Casz1βgeo/βgeo hearts that are up-regulated (red) or down-regulated (blue) are listed below. C, IPA assays showed gene enrichment in the categories of physiological system development and function (panel 1) with a key subcategory being skeletal and muscular system development and function genes that are up-regulated (red) or down-regulated (blue) in Casz1βgeo/βgeo hearts listed below and molecular and cellular function (panel 2) with a key subcategory of genes in molecular transport and the ion transport genes that are up-regulated (red) or down-regulated (blue) listed below. D, verification of microarray results. The mRNA levels of representative genes encoding cell adhesion molecules, muscle contraction, and muscular development proteins and ion channels were evaluated by real time PCR and normalized to GAPDH gene. The mRNA levels of these genes in Casz1βgeo/βgeo hearts were significantly different compared with their levels in Casz1+/+ hearts. The bar graph represents means ± S.D. (all p < 0.005).

Article Snippet: Rabbit anti-GAPDH (Santa Cruz, 1:4000) and rabbit anti-Casz1 (Rockland, 1:1000) were used to detect GAPDH and Casz1 protein level in heart.

Techniques: Expressing, Microarray, Generated, Software, Cell Function Assay, Real-time Polymerase Chain Reaction

Journal: The Journal of Biological Chemistry

Article Title: Essential Role of the Zinc Finger Transcription Factor Casz1 for Mammalian Cardiac Morphogenesis and Development *

doi: 10.1074/jbc.M114.570416

Figure Lengend Snippet: Abnormal expression of genes involved in cell cycle and regulation of cell proliferation in Casz1βgeo/βgeo heart. A, IPA assays showed gene enrichment in the categories of cell cycle and cellular growth and proliferation. The genes that are up-regulated (red) or down-regulated (blue) in Casz1βgeo/βgeo hearts were listed below. B, verification of microarray results. The mRNA levels of representative genes were evaluated by real time PCR and normalized to GAPDH gene. The mRNA levels of these genes in Casz1βgeo/βgeo hearts were significantly different compared with their levels in Casz1+/+ hearts. The bar graph represents means ± S.D. (all p < 0.05).

Article Snippet: Rabbit anti-GAPDH (Santa Cruz, 1:4000) and rabbit anti-Casz1 (Rockland, 1:1000) were used to detect GAPDH and Casz1 protein level in heart.

Techniques: Expressing, Microarray, Real-time Polymerase Chain Reaction

Journal: The Journal of Biological Chemistry

Article Title: Essential Role of the Zinc Finger Transcription Factor Casz1 for Mammalian Cardiac Morphogenesis and Development *

doi: 10.1074/jbc.M114.570416

Figure Lengend Snippet: Validation of Casz1 target genes in cellular models. A, human cardiac fibroblasts were transfected with empty vector (EMV) or CASZ1b vector and cultured for 5 days. Panel a, relative CASZ1b mRNA level was evaluated by real time PCR using human CASZ1 primer. The bar graph represents means ± S.E.(#, p < 0.05). Panel b, Western blot to show the overexpression of Casz1b in CASZ1b overexpressed cells. Panel c, after overexpression of CASZ1b, relative mRNA levels of representative genes were evaluated by real time PCR. The bar graph represents means ± S.E. (#, p < 0.05). B, knockdown or overexpression of Casz1 in HL-1 cells. Panel a, HL-1 cells were transfected with nontargeting control (con) siRNA or Casz1 siRNA, and after a 2-day culture, the relative mRNA levels of representative genes were evaluated by real time. The bar graph represents means ± S.D. (*, p < 0.005). Panel b, HL-1 cells were transfected with EMV or CASZ1b vector, and after a 2-day culture, the relative CASZ1b mRNA levels were evaluated by real time PCR using human CASZ1 primers. The graph represents mean ± S.D. (*, p < 0.005). Panel c, after transfection with CASZ1b and a two-dimensional culture, the relative mRNA levels of representative genes were evaluated by real time PCR. The bar graph represents means ± S.D. (#, p < 0.05; ns represents no statistic significant difference).

Article Snippet: Rabbit anti-GAPDH (Santa Cruz, 1:4000) and rabbit anti-Casz1 (Rockland, 1:1000) were used to detect GAPDH and Casz1 protein level in heart.

Techniques: Transfection, Plasmid Preparation, Cell Culture, Real-time Polymerase Chain Reaction, Western Blot, Over Expression

Journal: The Journal of Biological Chemistry

Article Title: Essential Role of the Zinc Finger Transcription Factor Casz1 for Mammalian Cardiac Morphogenesis and Development *

doi: 10.1074/jbc.M114.570416

Figure Lengend Snippet: Sarcomeric organization in Casz1βgeo/βgeo heart. A, GSEA assay indicated the negative enrichment of genes encoding contractile fiber proteins (panels a and b), as well as genes encoding contractile fiber part proteins (panel c). NES, normalized enrichment score; Nom, nominal; FDR, false discovery rate. B, sections containing the trabecular regions of E14.5 hearts were labeled for desmin (red), and nuclei were stained with DAPI (blue). There is a striated pattern for desmin labeling in both wild type and Casz1-deficient hearts, but the striated patterns are not as uniform or apparent in the Casz1-deficient heart.

Article Snippet: Rabbit anti-GAPDH (Santa Cruz, 1:4000) and rabbit anti-Casz1 (Rockland, 1:1000) were used to detect GAPDH and Casz1 protein level in heart.

Techniques: Labeling, Staining

Journal: The Journal of Biological Chemistry

Article Title: Essential Role of the Zinc Finger Transcription Factor Casz1 for Mammalian Cardiac Morphogenesis and Development *

doi: 10.1074/jbc.M114.570416

Figure Lengend Snippet: Abnormal Z line organization in E14.5 Casz1βgeo/βgeo heart. A, cardiomyocytes isolated from Casz1+/+ and Casz1βgeo/βgeo E14.5 embryo hearts were cultured in vitro for 2 days and immunostained for α-actinin (red) and F-actin (green), whereas the nuclei were stained with DAPI (blue). Representative images show that clear Z lines were presented in the wild type cardiomyocytes, but not in the Casz1βgeo/βgeo cardiomyocytes. B, the CHITEST histogram shows the percentage of Casz1+/+ or Casz1βgeo/βgeo cardiomyocytes with clear Z lines (Z line+) or abnormal Z lines (Z line−) (p < 0.00001). The data are from two independent experiments (>100 Casz1+/+ or Casz1βgeo/βgeo cardiomyocytes were counted in each experiment). C, more representative images show that clear Z lines are present in the Casz1+/+ cardiomyocytes. There are no clear Z lines in these Casz1βgeo/βgeo cardiomyocytes, and the α-actinin staining pattern is distinct compared with the Casz1+/+ cardiomyocytes.

Article Snippet: Rabbit anti-GAPDH (Santa Cruz, 1:4000) and rabbit anti-Casz1 (Rockland, 1:1000) were used to detect GAPDH and Casz1 protein level in heart.

Techniques: Isolation, Cell Culture, In Vitro, Staining

Journal: Cancer cell

Article Title: Hedgehog pathway drives fusion-negative rhabdomyosarcoma initiated from non-myogenic endothelial progenitors

doi: 10.1016/j.ccell.2017.12.001

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Rabbit polyclonal anti-RFP , Rockland , Cat #600-401-379; RRID:AB_2209751.

Techniques: Affinity Purification, Recombinant, Plasmid Preparation, SYBR Green Assay, Microarray, Expressing, Real-time Polymerase Chain Reaction, Software