Journal: Bioengineering

Article Title: COVID-19 Diagnostic Strategies Part II: Protein-Based Technologies

doi: 10.3390/bioengineering8050054

Figure Lengend Snippet: The developed protein microarray-based tests for COVID-19 detection.

Article Snippet: PEPperPRINT GmbH [ ] , PEPperCHIP ® Pan-Corona Spike Protein Microarray , Antibodies against S antigen , S proteins derived from seven coronaviruses translated into overlapping peptides , (No info) , (No info) , One array with 4564 peptides in duplicate , RUO , For Serum antibody fingerprint analysis, Immune monitoring and Epitope studies.

Techniques: Microarray, Peptide Microarray, Bioprocessing, Derivative Assay, High Throughput Screening Assay, Enzyme-linked Immunosorbent Assay, Western Blot, Virus, Clinical Proteomics

Journal: Nutrition & Diabetes

Article Title: Human mediastinal adipose tissue displays certain characteristics of brown fat

doi: 10.1038/nutd.2013.6

Figure Lengend Snippet: Comparison of gene expression in human subcutaneous and mediastinal adipose tissue. Real-time PCR validation of genes selected from the microarray analysis. Each dot represents one individual ( n =23). Box plots represent median (thick black lines), first and third quartiles (outlined boxes), the lowest data point still within 1.5 times the interquartile range from the first quartile (lower whiskers) and the highest data point still within 1.5 times the interquartile range from the third quartile (upper whiskers) of the expression levels of UCP1 , PPARGC1A , CIDEA , PRDM16 , S HOX2 and HOXC8 in subcutaneous and mediastinal adipose tissue. Gene expression was normalized to reference gene PPIA . P -values were calculated according to Wilcoxon paired-sample test.

Article Snippet: RNA samples from a separate group of 23 patients (see description in ) were used for complementary DNA synthesis with SuperScript III (Invitrogen) and analysed with TaqMan gene expression assays ( PPIA : Hs99999904_m1, TBP : Hs00427620_m1, UCP1 : Hs00222453_m1, PRDM16 : Hs00223161_m1, COBL: Hs00391205_m1, CIDEA : Hs00154455_m1, PPARGC1A : Hs00222453_m1, SHOX2 : Hs00243203_m1 and HOXC8 : Hs00224073_m1; Applied Biosystems, Foster City, CA, USA).

Techniques: Comparison, Gene Expression, Real-time Polymerase Chain Reaction, Biomarker Discovery, Microarray, Expressing

Journal: Cancer Cell

Article Title: Hoxa9 and Meis1 Cooperatively Induce Addiction to Syk Signaling by Suppressing miR-146a in Acute Myeloid Leukemia

doi: 10.1016/j.ccell.2017.03.001

Figure Lengend Snippet: Meis1 Increases Syk Protein Levels in Hoxa9-Driven Leukemia (A) Kaplan-Meier survival curves of mice transplanted with either H- or H/M-transformed myeloid progenitor cells (n = 11). The p value is from a Mantel-Cox test. (B) Volcano plot relating q values for differential protein expression to average normalized SILAC ratios from six biological replicates. Blue (higher expression in H cells) and orange (higher expression in H/M cells) dots indicate significantly regulated proteins (q < 0.01). (C) Heatmap of SILAC ratios for significantly differentially expressed proteins in H and H/M cells across the six biological replicates. (D) Syk protein expression in H and H/M cells by immunoblotting. Actin was used as loading control for relative protein quantification. (E) Relative Syk mRNA expression as measured by qPCR, normalized to GAPDH expression (mean ± SD, n = 3); ns, not significant (two-sided unpaired t test). (F and G) Immunohistochemical staining of HOXA9, MEIS1, and SYK in bone marrow biopsies from patients with AML. SYK expression levels were analyzed in 21 AML cases with high HOXA9 expression (F) and 28 cases with high HOXA9/MEIS1 expression (G). Proportions of SYK expression levels as determined by two independent pathologists using a three-stage staining score are shown. See also Figure S1 , , and .

Article Snippet: TaqMan® MicroRNA Assay Gapdh , Thermo Fisher Scientific , Cat# 4331182 Assay ID: Mm99999915_g1.

Techniques: Transformation Assay, Expressing, Multiplex sample analysis, Western Blot, Control, Immunohistochemical staining, Staining

Journal: Cancer Cell

Article Title: Hoxa9 and Meis1 Cooperatively Induce Addiction to Syk Signaling by Suppressing miR-146a in Acute Myeloid Leukemia

doi: 10.1016/j.ccell.2017.03.001

Figure Lengend Snippet: Syk Is a Direct Target of miR-146a (A) Schematic workflow of the miRNA expression analysis in H- and H/M-transformed myeloid progenitors. (B) Volcano plot relating q values for differential miRNA expression between H and H/M cells to average miRNA expression fold-changes from three biological replicates. Blue (higher expression in H cells) and orange (higher expression in H/M cells) dots indicate significantly regulated miRNAs (q < 0.01). (C and D) Relative mmu-miR-146a expression (C) and pri-miR-146a expression (D) in H/M versus H cells, measured by qPCR and normalized to sno202 and GAPDH expression, respectively (mean ± SD, n = 3). The p values are from a two-sided unpaired t test. (E) Luciferase assay validating binding of miR-146a to the predicted target sites within the 3′ UTR of Syk (mean ± SD, n = 4); WT, predicted miR-146a target sequence; MUT, mutated version thereof. The p values are from a two-sided unpaired t test. ns, not significant. (F) Luciferase assay validating binding of miR-146a to the full-length Syk 3′ UTR (mean ± SD, n = 4). The p value is from a two-sided unpaired t test. (G) Left, secondary structure of mmu-miR-146 as predicted by RNAfold ( Lorenz et al., 2011 ). The CRISPR/Cas9 cleavage site is indicated. Right, relative expression of miR-146a, measured by qPCR and normalized to sno202 expression, in H cells transduced with either a lentiviral non-specific (nsp) control CRISPR or a CRISPR targeting miR-146 (ΔmiR-146) (mean ± SD, n = 3). The p value is from a two-sided unpaired t test. (H) Corresponding Syk protein expression by immunoblotting. Actin was used as loading control for relative protein quantification. (I) Cell-proliferation curves for H cells transduced with either a lentiviral non-specific (nsp) control CRISPR or a CRISPR targeting miR-146 (ΔmiR-146) (mean ± SD, n = 3). (J) Kaplan-Meier survival curves of mice transplanted with H or H/M cells transduced with a lentiviral non-specific (nsp) control CRISPR, or with H cells transduced with a CRISPR targeting miR-146 (ΔmiR-146) (n = 7). The p value is from a Mantel-Cox test. See also Figure S3 .

Article Snippet: TaqMan® MicroRNA Assay Gapdh , Thermo Fisher Scientific , Cat# 4331182 Assay ID: Mm99999915_g1.

Techniques: Expressing, Transformation Assay, Luciferase, Binding Assay, Sequencing, CRISPR, Transduction, Control, Western Blot

Journal: Cancer Cell

Article Title: Hoxa9 and Meis1 Cooperatively Induce Addiction to Syk Signaling by Suppressing miR-146a in Acute Myeloid Leukemia

doi: 10.1016/j.ccell.2017.03.001

Figure Lengend Snippet: Meis1 Downregulates miR-146a through PU.1 (A) Fold enrichment of PU.1 binding over IgG control as measured by ChIP-qPCR in H and H/M cells (mean ± SD, n = 3). The miR-146a −10 kb region spans the transcription start site of the miR-146a host gene; ns, not significant. (B) PU.1 protein expression in H and H/M cells by immunoblotting. Histone H3 was used as loading control for relative protein quantification. (C) Relative PU.1 mRNA expression in H versus H/M cells measured by qPCR and normalized to GAPDH expression (mean ± SD, n = 3). (D and E) Immunohistochemical staining of PU.1 in bone marrow biopsies from patients with AML. PU.1 expression levels were analyzed in 21 AML cases with high HOXA9 expression (D) and 28 cases with high HOXA9/MEIS1 expression (E). Proportions of PU.1 expression levels as determined by two independent pathologists using a three-stage staining score are shown. (F) PU.1 and SYK protein expression by immunoblotting in H cells transfected with either a control shRNA (nsp) or an shRNA targeting PU.1 (KD). Tubulin was used as loading control for relative protein quantification. (G) mmu-miR-146a and pri-miR-146a expression as measured by qPCR after PU.1 knockdown (KD) relative to control shRNA (nsp) (mean ± SD, n = 4). The p values are from a two-sided unpaired t test. See also Figure S4 and .

Article Snippet: TaqMan® MicroRNA Assay Gapdh , Thermo Fisher Scientific , Cat# 4331182 Assay ID: Mm99999915_g1.

Techniques: Binding Assay, Control, ChIP-qPCR, Expressing, Western Blot, Immunohistochemical staining, Staining, Transfection, shRNA, Knockdown

Journal: Cancer Cell

Article Title: Hoxa9 and Meis1 Cooperatively Induce Addiction to Syk Signaling by Suppressing miR-146a in Acute Myeloid Leukemia

doi: 10.1016/j.ccell.2017.03.001

Figure Lengend Snippet: Meis1 Sensitizes Hoxa9-Driven Leukemia to Syk Inhibition (A) Syk protein expression in H/M cells transfected with either a control shRNA (GL2) or two shRNAs targeting Syk. Actin was used as loading control for relative protein quantification. (B) Percentage of BFP-positive shRNA-expressing cells relative to BFP-negative shRNA-negative cells at the times indicated (mean ± SD, normalized to day 0, n = 3). (C) Same as (A), before and after 5 days of doxycycline (dox) treatment in vivo. (D) Kaplan-Meier survival curves of mice transplanted with H/M cells and treated with doxycycline for 43 days to express non-specific control and Syk-specific shRNA (n = 8). The p value is from a Mantel-Cox test. (E) Percentage of YFP-positive cells from peripheral blood of mice transplanted with H (left) or H/M (right) cells after treating for 7 days with R788 or placebo. Measurements were taken at the indicated time points. The black line connects median values. (F) Kaplan-Meier survival curves of mice transplanted with either H or H/M cells and treated for 20 days with R788 or placebo (n = 11). The p value is from a Mantel-Cox test. (G) Relative HOXA9 and MEIS1 mRNA expression in MV4-11 and KG1 cell lines, and in patient-derived AML cells as measured by qPCR, normalized to GAPDH expression (mean ± SD, n = 3). (H) (p)SYK expression in the patient-derived AML cells in (G). Actin was used as loading control for relative protein quantification. avg, average. (I) Half maximal inhibitory concentration (IC 50 ) for R406 (left) and PRT062607 (right) in patient-derived AML cells as determined by an Annexin V/7-AAD apoptosis assay. Cells were treated for 24 hr and DMSO was used as a control (n = 3). Representative dose-response curves for AML no. 1 (HOXA9 high, MEIS1 low) and AML no. 5 (HOXA9 high, MEIS1 high) are shown at the top. Ticks correspond to estimated IC 50 values. (J) Relative viability of CD34 + bone marrow cells from healthy donors. Cells were treated with either R406 or PRT062607. Blue lines indicate the IC 50 for both SYK inhibitors in H cells. (K) Kaplan-Meier survival curves of NSG mice transplanted with patient-derived AML cells indicated in (G) and treated for 14 days with R788 or vehicle (n = 6 for AML no. 1 and 5; n = 5 for AML no. 2 and 6). The p values are from a Mantel-Cox test. See also Figure S6 .

Article Snippet: TaqMan® MicroRNA Assay Gapdh , Thermo Fisher Scientific , Cat# 4331182 Assay ID: Mm99999915_g1.

Techniques: Inhibition, Expressing, Transfection, Control, shRNA, In Vivo, Derivative Assay, Concentration Assay, Apoptosis Assay

Journal: Cancer Cell

Article Title: Hoxa9 and Meis1 Cooperatively Induce Addiction to Syk Signaling by Suppressing miR-146a in Acute Myeloid Leukemia

doi: 10.1016/j.ccell.2017.03.001

Figure Lengend Snippet:

Article Snippet: TaqMan® MicroRNA Assay Gapdh , Thermo Fisher Scientific , Cat# 4331182 Assay ID: Mm99999915_g1.

Techniques: Recombinant, Blocking Assay, Lysis, SYBR Green Assay, Reporter Assay, Extraction, Bicinchoninic Acid Protein Assay, cDNA Synthesis, Reverse Transcription, TaqMan microRNA Assay, Mass Spectrometry, Microarray, Gene Expression, Retroviral, Negative Control, Plasmid Preparation, Software, Multiplex sample analysis

Journal: Oncotarget

Article Title: Dual inhibition of HDAC and EGFR signaling with CUDC-101 induces potent suppression of tumor growth and metastasis in anaplastic thyroid cancer.

doi: 10.18632/oncotarget.3268

Figure Lengend Snippet: Figure 3: CUDC-101 inhibits ATC cell proliferation, and induces cell cycle arrest and apoptosis. (A) Basal expression of HDAC1, HDAC2 and EGFR in ATC cell lines. (B) Cell proliferation assay. Error bars are mean ± SD. (C) Cell cycle analysis after 24 hours of treatment. (D) The Caspase-Glo 3/7 assay after 48 hours of treatment with CUDC-101. *p < 0.05, **p < 0.01, ***p < 0.001. NS, no significant difference.

Article Snippet: Phospho-kinase and apoptosis protein arrays Human phospho-kinase (Catalog # ARY003B) array (detecting site-specific phosphorylation of 43 kinases and 2 related total proteins, and apoptosis array (Catalog # ARY009 detecting the expression level of 35 apoptosisrelated proteins) were purchased from R&D Systems (Minneapolis, MN).

Techniques: Expressing, Proliferation Assay, Cell Cycle Assay, Caspase-Glo Assay

Journal: Oncotarget

Article Title: Dual inhibition of HDAC and EGFR signaling with CUDC-101 induces potent suppression of tumor growth and metastasis in anaplastic thyroid cancer.

doi: 10.18632/oncotarget.3268

Figure Lengend Snippet: Figure 5: Protein targets of CUDC-101 in ATC cells. (A) CUDC-101 inhibits HDACs and MAPK in ATC cells. (B) Targets of CUDC-101 identified by phospho-kinase array. Phospho-kinase arrays were performed using cell lysates treated with and without CUDC-101. Shown are those proteins that were altered with CUDC-101 treatment in both ATC cell lines with > 1.5-fold difference. (C) Differentially expressed apoptotic proteins with and without CUDC-101 treatment. Apoptosis arrays were performed. Shown are those proteins that were altered with CUDC-101 treatment in both ATC cell lines with > 1.5-fold difference. For A–C, ATC cells were treated with the vehicle or CUDC-101 at 1.1 μM for 24 hours. (D) CUDC-101 reduces the expression of survivin, XIAP, and β-catenin. Cells were treated with the vehicle or CUDC-101 for 24 hours.

Article Snippet: Phospho-kinase and apoptosis protein arrays Human phospho-kinase (Catalog # ARY003B) array (detecting site-specific phosphorylation of 43 kinases and 2 related total proteins, and apoptosis array (Catalog # ARY009 detecting the expression level of 35 apoptosisrelated proteins) were purchased from R&D Systems (Minneapolis, MN).

Techniques: Expressing