Journal: Plant Physiology

Article Title: Long-distance translocation of CLAVATA3/ESR-related 2 peptide and its positive effect on roots sucrose status

doi: 10.1093/plphys/kiac227

Figure Lengend Snippet: Detection of the CLE2 peptide from Arabidopsis xylem exudate. A, Arabidopsis xylem exudate was collected from cut surfaces of hypocotyls. B, Base peak chromatogram of purified Arabidopsis xylem exudate. C, The MS/MS spectrum of m/z 863.4 eluted at 9.0 min in (B) showed a fragmentation pattern identical to that of arabinosylated CLE2 peptides. B and C, One typical experiment of two replicates is shown. D, Relative mRNA level of the CLE2 gene. Plants grown on sucrose-free or 1% sucrose-containing media were treated with 50-µM DCMU or incubated in darkness for 24 h. The expression levels of each CLE2 gene in the treated samples were normalized to control roots. The dots represent individual measurements. Each result is the mean ± standard error of the mean ( sem ) of measurements obtained from three independent experiments.

Article Snippet: Based on the Arabidopsis RNA-seq database ( http://ipf.sustech.edu.cn/pub/athrna/ ), the fragments per kilobase of transcript per million mapped reads values of the CLE1 and CLE4 – 7 genes appear to be comparable to those of the CLE2 and CLE3 genes .

Techniques: Purification, Tandem Mass Spectroscopy, Incubation, Expressing, Control

Journal: The Journal of Biological Chemistry

Article Title: Novel markers of MCL1 inhibitor sensitivity in triple-negative breast cancer cells

doi: 10.1016/j.jbc.2024.107375

Figure Lengend Snippet: Identification of commonly upregulated genes in S63845 resistant TNBC cell lines. A , volcano plot analysis of genes differentially expressed in resistant vs. sensitive cell lines identified the top 100 commonly upregulated genes in resistant cell lines (gene list seen in Table S1 ). B , 4 genes of interest whose levels (RPKM) are commonly significantly ( p < 0.05) upregulated in resistant cell lines. Note that MCL1 levels are not different. C , lysates of the indicated 8 cell lines were immunoblotted for the indicated proteins with relative signal indicated. Representative results of three independent experiments. Original images are presented in Fig. S2 .

Article Snippet: Briefly, the CCLE RNAseq gene expression (RPKM) database ( ) for 1019 cell lines (CCLE RNAseq genes rpkm 20180929.gct.gz) was downloaded from the Broad Institute CCLE database.

Techniques:

Journal: The Journal of Biological Chemistry

Article Title: Novel markers of MCL1 inhibitor sensitivity in triple-negative breast cancer cells

doi: 10.1016/j.jbc.2024.107375

Figure Lengend Snippet: A 4 gene signature (GS) correlates with AZD5991 sensitivity and MCL-1 dependency in TNBC cell lines. A , analysis of gene expression correlation with TIMER software in 139 TNBC tumors (TCGA) showed that the 4 genes positively correlate with each other. B , 18 TNBC cell lines from GDSC are divided into AZD5991 resistant ( green ) and sensitive ( yellow ) groups. mRNA levels (RPKM) of AXL, ETS1, IL6, and EFEMP1 in all cell lines were extracted from CCLE RNAseq database. The median level of each gene is calculated and listed on top. Gene levels above the median is marked in red and scored 1 and below median is scored 0. The sum of the 4 gene scores is listed on right . C , correlation of GS scores with AZD5991 sensitivity was analyzed with ROC curve with sensitive cells defined as event 1. The results showed a significant correlation ( p = 0.002) with an ROC area 0.95 (ROC area 1.0 indicates perfect correlation). D, 13 TNBC cell lines with MCL-1 CRISPR (DepMap public 23Q2) are divided into MCL-1 dependent ( green ) and independent ( yellow ) groups based on their Chromos scores. Gene scores are calculated as described in B. Correlation of GS scores with MCL-1 dependency was analyzed with ROC curve ( E ). The results showed a significant correlation ( p = 0.04) with a ROC area 0.79).

Article Snippet: Briefly, the CCLE RNAseq gene expression (RPKM) database ( ) for 1019 cell lines (CCLE RNAseq genes rpkm 20180929.gct.gz) was downloaded from the Broad Institute CCLE database.

Techniques: Gene Expression, Software, CRISPR

Journal: Oncotarget

Article Title: Krüppel-like factor 4 promotes survival and expansion in acute myeloid leukemia cells

doi: 10.18632/oncotarget.27878

Figure Lengend Snippet: ( A ) Analysis of KLF4 gene methylation from the Cancer Cell Line Encyclopedia (CCLE) in a panel of hematologic malignancy cell lines. ( B ) Correlation of KLF4 transcript levels and DNA methylation in AML and non-AML cell lines. Linear regression analysis was conducted with 95% confidence interval.

Article Snippet: KLF4 mRNA expression (RNASeq) and DNA methylation (RRBS) were downloaded for cell lines from the publicly accessible cancer cell line encyclopedia database from Broad Institute.

Techniques: Methylation, DNA Methylation Assay

Journal: Oncotarget

Article Title: Krüppel-like factor 4 promotes survival and expansion in acute myeloid leukemia cells

doi: 10.18632/oncotarget.27878

Figure Lengend Snippet: ( A ) Relative KLF4 expression was measured by qPCR in AML, CML, and LCL cell lines cultured in the presence of 250 and 500 nM 5-Aza for 96 hours to induce DNA demethylation. Data represents relative mRNA expression (DDC T ) expressed as mean ± s.d. ( n = 3). ( B ) Immunoblot analysis of KLF4 expression after treatment with 5-Aza for 96 hours. Actin was used as a loading control. ( C ) Immunoblot analysis of KLF4 and MYC expression in cell lines treated with 10 μM of MG-132 for 4 hours. Actin and GAPDH were used as loading control. Data shown are representative of two independent experiments. * p < 0.05, ** p < 0.01, *** p < 0.001, two-tailed Student’s t -test.

Article Snippet: KLF4 mRNA expression (RNASeq) and DNA methylation (RRBS) were downloaded for cell lines from the publicly accessible cancer cell line encyclopedia database from Broad Institute.

Techniques: Expressing, Cell Culture, Western Blot, Control, Two Tailed Test

Journal: Oncotarget

Article Title: Krüppel-like factor 4 promotes survival and expansion in acute myeloid leukemia cells

doi: 10.18632/oncotarget.27878

Figure Lengend Snippet: ( A ) Multiplex sgRNA targeting strategy to induce KLF4 gene deletion via CRISPR/CAS9 technology and comparison of sequencing tracks of parental and edited leukemic cells. ( B ) Cell growth of NB4 KO and MM6 KO cells compared to parental cell lines ( n = 3); inset shows loss of KLF4 expression in edited cell lines. ( C ) Flow cytometric detection of Annexin V and 7AAD in NB4 and NB4 KO cells. Representative plots are included on the left and statistical analysis on the right ( n = 3). ( D ) Cell cycle analysis of NB4 and NB4 KO by flow cytometric detection of propidium iodine staining of nuclei ( n = 3). ( E and F ) Apoptosis and cell cycle analysis for MM6 and MM6 KO cells. Data represent mean ± s.d. ( n = 3). * p < 0.05, *** p < 0.001, two-tailed Student’s t -test.

Article Snippet: KLF4 mRNA expression (RNASeq) and DNA methylation (RRBS) were downloaded for cell lines from the publicly accessible cancer cell line encyclopedia database from Broad Institute.

Techniques: Multiplex Assay, CRISPR, Comparison, Sequencing, Expressing, Cell Cycle Assay, Staining, Two Tailed Test

Journal: Oncotarget

Article Title: Krüppel-like factor 4 promotes survival and expansion in acute myeloid leukemia cells

doi: 10.18632/oncotarget.27878

Figure Lengend Snippet: Cytotoxicity was determined using Cell-Titer Glo cytotoxicity assay after 48 h treatment with either daunorubicin or ara-C. ( A ) Cytotoxicity of NB4 and NB4 KO cells to daunorubicin ( n = 3). ( B ) Cytotoxicity of NB4 and NB4 KO cells to ara-C ( n = 3). ( C ) Cytotoxicity of MM6 and MM6 KO cells to daunorubicin ( n = 3). ( D ) Cytotoxicity of MM6 and MM6 KO cells to ara-C ( n = 3). Expression of KLF4 protein in parental cells in response to treatment at IC 50 dose is shown in figure insets. Data represent mean ± s.d.

Article Snippet: KLF4 mRNA expression (RNASeq) and DNA methylation (RRBS) were downloaded for cell lines from the publicly accessible cancer cell line encyclopedia database from Broad Institute.

Techniques: Cytotoxicity Assay, Expressing

Journal: Oncotarget

Article Title: Krüppel-like factor 4 promotes survival and expansion in acute myeloid leukemia cells

doi: 10.18632/oncotarget.27878

Figure Lengend Snippet:

Article Snippet: KLF4 mRNA expression (RNASeq) and DNA methylation (RRBS) were downloaded for cell lines from the publicly accessible cancer cell line encyclopedia database from Broad Institute.

Techniques:

Journal: Cancer research

Article Title: HPV16 E5 Mediates Resistance to PD-L1 Blockade and can be targeted with Rimantadine in Head and Neck Cancer

doi: 10.1158/0008-5472.CAN-19-1771

Figure Lengend Snippet: Patients with high expression of HPV16 E5 have decreased HLA expression associated with worse disease-free survival. A, B) mRNA expression analyzed by RNAseq in HNSCC from normal, E245 high, and E67 high patients in Johns Hopkins University (JHU) cohort. (Normal; n = 25, E245 high: n = 26, E67 high: n = 10) (A) Correlation analysis of HPV16 E5 expression and HLA-subtype or TAP expression (n = 36, Spearman’s correlation coefficient) (B) Patients were assigned to 3 groups based on the mRNA expression level of HLA (low, average, and high). Patients with low and high expression of HLA are shown. (Chi-square test and residual analysis) C) Disease-free survival and overall survival of patients in JHU cohort. Patients were assigned to groups based on E5 and HLA expression level.

Article Snippet: In order to evaluate whether HPV E5 has an effect on HLA expression in human tumors, we analyzed a prospectively collected RNAseq database of 35 HNSCC patient tumors and 25 healthy volunteers [Johns Hopkins University (JHU) cohort] ( Supp Table 1 ).

Techniques: Expressing