Journal: BMC Cancer

Article Title: MAFb protein confers intrinsic resistance to proteasome inhibitors in multiple myeloma

doi: 10.1186/s12885-018-4602-4

Figure Lengend Snippet: Expression of MAFb gene and protein in primary plasma cells and HMCLs. Affymetrix expression of MAFb mRNA was high in the GEP MF subgroup ( a ). Gene expression of 803 newly diagnosed MM patients was measured by U133 plus2.0 Affymetrix oligonucleotide microarray probe set 218559_s_at. The box plots indicate the middle of GEP signaling and dot lines with bars in black indicate quartiles. The cells were cultured in the growth mediate for 48 h and harvested for isolated RNA and MAFb mRNA in 27 HMCLs by qRT-PCR analysis as described in Material and methods ( b ). The cells were cultured in the growth mediate for 48 h and MAFb protein was measured in HMCLs by immunoblotting analysis described in Materials and Methods ( c ). MAFb protein in nuclei and cytoplasm of HMCLs ( d ) and MM PC from 4 patients ( e ) was determined with immunofluorescence staining with DAPI counterstaining. Images were taken with a fluorescence microscope with digital camera as described in supplemental data

Article Snippet: The primers /probe sets including MAFb (Hs00271378_s1), ITGB7 (Hs01565750-m1) and CCR1 (Hs00174288-m1) were purchased from Life Technologies.

Techniques: Expressing, Microarray, Cell Culture, Isolation, Quantitative RT-PCR, Western Blot, Immunofluorescence, Staining, Fluorescence, Microscopy

Journal: BMC Cancer

Article Title: MAFb protein confers intrinsic resistance to proteasome inhibitors in multiple myeloma

doi: 10.1186/s12885-018-4602-4

Figure Lengend Snippet: High MAFb expression is associated with resistance to PIs. SACHI ( a ), H929 ( b ), EJM ( c ), XG2 ( d ), L363 ( e ), and OPM-2 ( f ) cells were seeded at 2 × 10^4 per well in 96-well plates in the presence of indicated concentrations of Bzb or CFZ for 48 h. Cell survival was measured by MTT Assay. Results are presented as mean ± SE ( n = 4). Data are representative of 3 separate experiments. HMCLs were treated with serial concentrations of Bzb (G) and CFZ (H) for 48 h and cell viability was measured by MTT assay. The IC50 of Bzb (G) and CFZ (H) were classified based on MAFb protein (+) or (−)

Article Snippet: The primers /probe sets including MAFb (Hs00271378_s1), ITGB7 (Hs01565750-m1) and CCR1 (Hs00174288-m1) were purchased from Life Technologies.

Techniques: Expressing, MTT Assay

Journal: BMC Cancer

Article Title: MAFb protein confers intrinsic resistance to proteasome inhibitors in multiple myeloma

doi: 10.1186/s12885-018-4602-4

Figure Lengend Snippet: Inhibition of GSK3 activity by SB216763 stabilized MAFb protein. HMCLs were treated with 5 μg/ml of CHX for serial indicated time points to inhibit de novo protein synthesis. The MAFb protein was determined by immunoblotting analysis using anti-MAFb. The membranes were striped and reblotted with Anti-β-actin ( a ). The half-life of MAFb protein was determined by autoradiographs analysis using Adobe Photoshop software and NIH image software ( b - f ). HMCLs were treated with or without a specific GSK3 inhibitor, SB216763, at a concentration of 5 μg/ml for indicated times. MAFb protein was determined by immunoblotting analysis using anti-MAFb antibody. The membranes were striped and reblotted with Anti-β-actin to indicate protein loading ( a ). The protein decay curve is as described in Fig. 3b (b-f)

Article Snippet: The primers /probe sets including MAFb (Hs00271378_s1), ITGB7 (Hs01565750-m1) and CCR1 (Hs00174288-m1) were purchased from Life Technologies.

Techniques: Inhibition, Activity Assay, Western Blot, Software, Concentration Assay

Journal: BMC Cancer

Article Title: MAFb protein confers intrinsic resistance to proteasome inhibitors in multiple myeloma

doi: 10.1186/s12885-018-4602-4

Figure Lengend Snippet: Proteasome Inhibitors stabilize MAFb protein. The SACHI ( a ) and XG2 ( b ) cells were treated with indicated concentrations of Bzb or CFZ at the presence of 10 μg/ml of CHX for 6 h. MAFb protein lysate was analyzed as described in Fig. . SACHI ( c ) were treated with 20-nM of Bzb or CFZ for 12 h; XG-2, and EJM cells ( d ) were treated with indicated serial concentrations of Bzb and CFZ for 12 h, MAFb protein in nuclei and cytoplasm of the cells was determined by analysis of immunofluorescence staining with DAPI counterstaining to indicate the nucleus. Images were taken with a fluorescence microscope with digital camera as described in

Article Snippet: The primers /probe sets including MAFb (Hs00271378_s1), ITGB7 (Hs01565750-m1) and CCR1 (Hs00174288-m1) were purchased from Life Technologies.

Techniques: Immunofluorescence, Staining, Fluorescence, Microscopy

Journal: BMC Cancer

Article Title: MAFb protein confers intrinsic resistance to proteasome inhibitors in multiple myeloma

doi: 10.1186/s12885-018-4602-4

Figure Lengend Snippet: Knockdown of MAFb restores sensitivity of myeloma to PIs. SACHI cells were infected with lentiviral expression system containing shRNA specific to MAFb gene (sh MAFb ) or shRNA containing scramble sequences (shCon) for 48 h. MAFb mRNA was measured by RT-qPCR analysis ( a ), MAFb protein in whole lysis buffer was analyzed by immunoblotting analysis ( b ) and in both cytoplasmic and in nucleus by immunofluorescent staining analysis ( c ) as described in Fig. 5d. MAFb target genes in sh MAFb and shCon cells were analyzed by qRT-PCR analysis ( d ). The cells were treated with indicated concentrations of Bzb ( e ) or CFZ ( f ) for 48 h and cell survival was measured by MTT assay. Results are presented as mean ± SE ( n = 4). Data are representative of 3 separate experiments. * P < 0 .01 versus control. ** P < 0 .001 versus control

Article Snippet: The primers /probe sets including MAFb (Hs00271378_s1), ITGB7 (Hs01565750-m1) and CCR1 (Hs00174288-m1) were purchased from Life Technologies.

Techniques: Infection, Expressing, shRNA, Quantitative RT-PCR, Lysis, Western Blot, Staining, MTT Assay

Journal: BMC Cancer

Article Title: MAFb protein confers intrinsic resistance to proteasome inhibitors in multiple myeloma

doi: 10.1186/s12885-018-4602-4

Figure Lengend Snippet: Silencing MAFb enhanced PIs-induced apoptosis and activation of caspases. SACHI/sh MAFb or SACHI/shCon cells were treated with serial concentrations of Bzb ( a ) or CFZ ( b and c ) with ( c ) or without HBMSC ( a and b ) for 14 h and apoptotic cell numbers determined by Annexin V staining and flow cytometry analysis as described in supplemental data. Results are presented as mean ± SE ( n = 3). * P < 0 .01 versus control. ** P < 0 .001 versus control. SACHI/sh MAFb and SACHI/shCon cells were treated with indicated concentrations of Bzb (A) or CFZ ( b ) for14 hours. Protein was resolved in SDS-PAGE. The full-length (FL) and cleavage fragments (CFs) of each indicated protein were determined by immunoblotting analysis using antibodies specifically recognizing of caspases-3, − 7, − 8 and − 9, PARP and lamin A/C

Article Snippet: The primers /probe sets including MAFb (Hs00271378_s1), ITGB7 (Hs01565750-m1) and CCR1 (Hs00174288-m1) were purchased from Life Technologies.

Techniques: Activation Assay, Staining, Flow Cytometry, SDS Page, Western Blot

Journal: PLoS ONE

Article Title: Repeated Small Perturbation Approach Reveals Transcriptomic Steady States

doi: 10.1371/journal.pone.0029241

Figure Lengend Snippet: A and B ) Seven genes were chosen randomly from the set of genes with steady-state characteristics for this comparison. egfl5, cnn3, and bcar3 ( A ) exhibit immediate down-regulated responses, while pmaip1, jun, id2, and gadd45a ( B ) exhibit immediate up-regulated responses followed by relaxation. Solid and dash lines represent real-time PCR data and microarray data, respectively. The error bar of the microarray data indicates standard deviation estimated by the log linear model. The error bar of real-time PCR data is the standard deviation derived from three sets of CTs. C ) Scatter plot of real-time PCR results versus microarray data. The correlation coefficient, R is 0.93. The red line is a linear fit through all points. These results clearly demonstrate that even at the small fold change data points, these two sets of data agree very well. It also demonstrates the high reliability and resolution of our cDNA microarray system, which makes this kind of small perturbation study possible.

Article Snippet: The assay ID of corresponding probe sets and primers in the ABI's database are Hs00182488_m1, Hs00156565_m1, Hs00323519_m1, Hs00169255_m1, Hs00747379_m1, Hs01103582_s1, and Hs00382168_m1, respectively.

Techniques: Real-time Polymerase Chain Reaction, Microarray, Standard Deviation, Derivative Assay

Journal: Heliyon

Article Title: Wound healing protects against chemotherapy-induced alopecia in young rats via up-regulating interleukin-1β-mediated signaling

doi: 10.1016/j.heliyon.2017.e00309

Figure Lengend Snippet: Strongly induced cytokine and chemokine gene expression in wounded skin 36 h post wounding. (A) Gene expression signature in wounded rat skin differed from the control unwounded skin, as indicated by hierarchical cluster analysis of microarray data. (B) A set of genes that were up-regulated (red) or down-regulated (green) by more than two folds in wounded skin compared with unwounded skin. (C) Quantitative real-time qPCR analysis confirmed increased expression of Cxcl2 , Osteopontin , and IL-1β , and decreased expression of Ccl24 , in wounded skin compared with unwounded skin, normalized to Gapdh expression. Bars = SD. (D) IL-1β was highly expressed 24 h post wounding in both anagen (n = 7) and telogen mouse skin (n = 9) ( p = 0.11). Bars = SEM.

Article Snippet: Real-time qPCR for mouse IL-1β and Gapdh was performed in triplicates using the Taqman probe sets Mm99999915_g1 for Gapdh and MM00434228_m1 for IL1 β (ThermoFisher Scientific).

Techniques: Gene Expression, Control, Microarray, Expressing

Journal: The Journal of Biological Chemistry

Article Title: Sphingosine 1-Phosphate Lyase Deficiency Disrupts Lipid Homeostasis in Liver *

doi: 10.1074/jbc.M109.081489

Figure Lengend Snippet: Gene trap disruption of the Sgpl1 gene causes S1P lyase deficiency. A, sphingolipid metabolic pathway and linkage to triacylglycerol and phosphatidylethanolamine synthesis. B, appearance and life span of Sgpl1−/−, Sgpl1+/−, and Sgpl1+/+ mice. C, RT-qPCR of Sgpl1 mRNA using RNA of various tissues from Sgpl1−/− (gray bars) and Sgpl1+/+ (open bars) mice. Gapdh was used as a reference gene for normalization. SI, small intestine. Data represent mean values ± S.E. D, top panel: Western blot of S1P lyase protein in various tissues from Sgpl1−/− and Sgpl1+/+ mice. Bottom panel, same blot probed with antibody to β-actin as a loading control. E, S1P lyase enzyme activity in extracts of various tissues from Sgpl1−/− (gray bars) and Sgpl1+/+ (open bars) mice. Data represent mean values ± S.E. of representative results from three independent experiments.

Article Snippet: Taqman primer-probe sets for Sgpl1 (mm00486079_m1), Pparg (mm00440945_ m1), Ppara (mm00440939_m1), Sptlc1 (mm00447343_m1), Sptlc2 (mm00448871_m1), Sphk1 (mm00448841_g1), Sphk2 (mm00445020_m1), Sgpp1 (mm00473016_m1), Sgpp2 (mm01158866_m1, and Gapdh (mm99999915_g1; reference gene) were purchased from Applied Biosystems.

Techniques: Disruption, Quantitative RT-PCR, Western Blot, Control, Activity Assay

Journal: The Journal of Biological Chemistry

Article Title: Sphingosine 1-Phosphate Lyase Deficiency Disrupts Lipid Homeostasis in Liver *

doi: 10.1074/jbc.M109.081489

Figure Lengend Snippet: Sphingolipid levels are elevated in serum of Sgpl1−/− mice. Sphingolipid levels were determined in serum of Sgpl1−/− (gray bars) and Sgpl1+/+ (open bars) mice by LC-MS. A, total ceramide (Cer), sphingosine (Sph). B, total sphingomyelin (SM). C, individual ceramide fatty acid chain species. D, individual sphingomyelin fatty acid chain species. Data represent mean values ± S.E. n = 3. *, p < 0.05; **, p < 0.01; ***, p < 0.005, paired Student's t test.

Article Snippet: Taqman primer-probe sets for Sgpl1 (mm00486079_m1), Pparg (mm00440945_ m1), Ppara (mm00440939_m1), Sptlc1 (mm00447343_m1), Sptlc2 (mm00448871_m1), Sphk1 (mm00448841_g1), Sphk2 (mm00445020_m1), Sgpp1 (mm00473016_m1), Sgpp2 (mm01158866_m1, and Gapdh (mm99999915_g1; reference gene) were purchased from Applied Biosystems.

Techniques: Liquid Chromatography with Mass Spectroscopy

Journal: The Journal of Biological Chemistry

Article Title: Sphingosine 1-Phosphate Lyase Deficiency Disrupts Lipid Homeostasis in Liver *

doi: 10.1074/jbc.M109.081489

Figure Lengend Snippet: Sgpl1−/− mice are hyperlipidemic. A, triacylglycerol (TAG), phospholipids, total cholesterol (TC), free cholesterol (FC), and cholesterol esters (CE) were determined in the serum of Sgpl1−/− (gray bars) and Sgpl1+/+ (open bars) mice. Data represent mean values ± S.E. n = 7. **, p < 0.01; ***, p < 0.005, paired Student's t test. B, pooled serum samples from Sgpl1−/− (closed circles) and Sgpl1+/+ (open circles) mice (n = 3 each genotype) were fractionated by FPLC to separate VLDL, LDL, and HDL.

Article Snippet: Taqman primer-probe sets for Sgpl1 (mm00486079_m1), Pparg (mm00440945_ m1), Ppara (mm00440939_m1), Sptlc1 (mm00447343_m1), Sptlc2 (mm00448871_m1), Sphk1 (mm00448841_g1), Sphk2 (mm00445020_m1), Sgpp1 (mm00473016_m1), Sgpp2 (mm01158866_m1, and Gapdh (mm99999915_g1; reference gene) were purchased from Applied Biosystems.

Techniques:

Journal: The Journal of Biological Chemistry

Article Title: Sphingosine 1-Phosphate Lyase Deficiency Disrupts Lipid Homeostasis in Liver *

doi: 10.1074/jbc.M109.081489

Figure Lengend Snippet: Sphingolipids are elevated in the liver of Sgpl1−/− mice. Sphingolipid levels were determined in the liver of Sgpl1−/− (gray bars) and Sgpl1+/+ (open bars) mice by LC-MS. A, total ceramide (Cer), sphingosine (Sph). B, total sphingomyelin (SM). C, individual ceramide fatty acid chain species. D, individual sphingomyelin fatty acid chain species. Data represent mean values ± S.E. n = 3. *, p < 0.05; **, p < 0.01; ***, p < 0.005; paired Student's t test.

Article Snippet: Taqman primer-probe sets for Sgpl1 (mm00486079_m1), Pparg (mm00440945_ m1), Ppara (mm00440939_m1), Sptlc1 (mm00447343_m1), Sptlc2 (mm00448871_m1), Sphk1 (mm00448841_g1), Sphk2 (mm00445020_m1), Sgpp1 (mm00473016_m1), Sgpp2 (mm01158866_m1, and Gapdh (mm99999915_g1; reference gene) were purchased from Applied Biosystems.

Techniques: Liquid Chromatography with Mass Spectroscopy

Journal: The Journal of Biological Chemistry

Article Title: Sphingosine 1-Phosphate Lyase Deficiency Disrupts Lipid Homeostasis in Liver *

doi: 10.1074/jbc.M109.081489

Figure Lengend Snippet: Lipid profile is altered in the liver of Sgpl1−/− mice. Lipid levels were determined in the liver of Sgpl1−/− (gray bars) and Sgpl1+/+ (open bars) mice as described under “Experimental Procedures.” PE, phosphatidylethanolamine; PC, phosphatidylcholine; PS, phosphatidylserine; LYPC, lysophosphatidylcholine; CL, cardiolipin; FA, fatty acids; DAG, diacylglycerol; TAG, triacylglycerol; CE, cholesterol esters; FC, free cholesterol. Data represent mean values ± S.E. n = 3. *, p < 0.05; **, p < 0.01; ***, p < 0.005; paired Student's t test.

Article Snippet: Taqman primer-probe sets for Sgpl1 (mm00486079_m1), Pparg (mm00440945_ m1), Ppara (mm00440939_m1), Sptlc1 (mm00447343_m1), Sptlc2 (mm00448871_m1), Sphk1 (mm00448841_g1), Sphk2 (mm00445020_m1), Sgpp1 (mm00473016_m1), Sgpp2 (mm01158866_m1, and Gapdh (mm99999915_g1; reference gene) were purchased from Applied Biosystems.

Techniques:

Journal: The Journal of Biological Chemistry

Article Title: Sphingosine 1-Phosphate Lyase Deficiency Disrupts Lipid Homeostasis in Liver *

doi: 10.1074/jbc.M109.081489

Figure Lengend Snippet: Excess lipids are stored in the liver of Sgpl1−/− mice. Paraffin-embedded liver sections from (A) Sgpl1+/+ or (B) Sgpl1−/− mice were stained with H&E (×10 magnification). Frozen sections of liver from (C) Sgpl1+/+ or (D) Sgpl1−/− mice were stained with Oil red O (×40 magnification). Arrows indicate lipid deposits. Liver samples from (E) Sgpl1+/+ or (F) Sgpl1−/− mice were analyzed by electron microscopy (×6000 magnification). Arrowheads indicate examples of lipid droplets. Liver sections from (G) Sgpl1+/+ or (H) Sgpl1−/− mice immunostained with LAMP-2 antibody (brown reaction product) and counterstained with hematoxylin (×100 magnification).

Article Snippet: Taqman primer-probe sets for Sgpl1 (mm00486079_m1), Pparg (mm00440945_ m1), Ppara (mm00440939_m1), Sptlc1 (mm00447343_m1), Sptlc2 (mm00448871_m1), Sphk1 (mm00448841_g1), Sphk2 (mm00445020_m1), Sgpp1 (mm00473016_m1), Sgpp2 (mm01158866_m1, and Gapdh (mm99999915_g1; reference gene) were purchased from Applied Biosystems.

Techniques: Staining, Electron Microscopy

Journal: The Journal of Biological Chemistry

Article Title: Sphingosine 1-Phosphate Lyase Deficiency Disrupts Lipid Homeostasis in Liver *

doi: 10.1074/jbc.M109.081489

Figure Lengend Snippet: Adiposity is reduced in Sgpl1−/− mice. A, weights of the mice were taken at about 18 days after birth. ***, p < 0.005. Sgpl1−/− (gray bars) and Sgpl1+/+ (open bars) mice were subjected to quantitative magnetic resonance body composition analysis to determine their fat (B) and lean mass (C) content. The fat mass as a percent of body weight is presented in (D). Data represent mean values ± S.E. n = 3. ***, p < 0.005, paired Student's t test.

Article Snippet: Taqman primer-probe sets for Sgpl1 (mm00486079_m1), Pparg (mm00440945_ m1), Ppara (mm00440939_m1), Sptlc1 (mm00447343_m1), Sptlc2 (mm00448871_m1), Sphk1 (mm00448841_g1), Sphk2 (mm00445020_m1), Sgpp1 (mm00473016_m1), Sgpp2 (mm01158866_m1, and Gapdh (mm99999915_g1; reference gene) were purchased from Applied Biosystems.

Techniques:

Journal: The Journal of Biological Chemistry

Article Title: Sphingosine 1-Phosphate Lyase Deficiency Disrupts Lipid Homeostasis in Liver *

doi: 10.1074/jbc.M109.081489

Figure Lengend Snippet: Lipid metabolism gene expression profile in the liver of Sgpl1−/− mice exhibits widespread alteration. A, Affymetrix microarray gene expression analysis was performed with liver RNA from three Sgpl1+/+ and three Sgpl1−/− mice. The raw signal values of the genes from the GO category lipid metabolic process were clustered to produce a heat map as described under “Experimental Procedures.” Blue corresponds to reduced expression relative to red, which corresponds to relatively increased expression. RT-qPCR analysis of (B) Ppara and Pparg, (C) Sptlc1, and Sptlc2, (D) Sphk1 and Sphk2, and (E) Sgpp1 and Sgpp2 in liver mRNA from Sgpl1−/− (gray bars) and Sgpl1+/+ (open bars) mice. Data represent mean values ± S.E. n = 3. *, p < 0.05; ***, p < 0.005, paired Student's t test.

Article Snippet: Taqman primer-probe sets for Sgpl1 (mm00486079_m1), Pparg (mm00440945_ m1), Ppara (mm00440939_m1), Sptlc1 (mm00447343_m1), Sptlc2 (mm00448871_m1), Sphk1 (mm00448841_g1), Sphk2 (mm00445020_m1), Sgpp1 (mm00473016_m1), Sgpp2 (mm01158866_m1, and Gapdh (mm99999915_g1; reference gene) were purchased from Applied Biosystems.

Techniques: Gene Expression, Microarray, Expressing, Quantitative RT-PCR

Journal: PLoS ONE

Article Title: Seasonal Changes in Bacterial and Archaeal Gene Expression Patterns across Salinity Gradients in the Columbia River Coastal Margin

doi: 10.1371/journal.pone.0013312

Figure Lengend Snippet: Phylogenetic composition of the 2226 microarray probe set.

Article Snippet: Several published studies describe evaluation of the sensitivity and specificity of various CombiMatrix microarray probe sets , , , – .

Techniques: Microarray

Journal: PLoS ONE

Article Title: Seasonal Changes in Bacterial and Archaeal Gene Expression Patterns across Salinity Gradients in the Columbia River Coastal Margin

doi: 10.1371/journal.pone.0013312

Figure Lengend Snippet: Cross-hybridizing sequence hits resulting from bioinformatic evaluation of 2226 microarray probes against the CAMERA repository.

Article Snippet: Several published studies describe evaluation of the sensitivity and specificity of various CombiMatrix microarray probe sets , , , – .

Techniques: Sequencing, Microarray, Environmental Sampling

Journal: PLoS ONE

Article Title: Seasonal Changes in Bacterial and Archaeal Gene Expression Patterns across Salinity Gradients in the Columbia River Coastal Margin

doi: 10.1371/journal.pone.0013312

Figure Lengend Snippet: Distribution of microarray probe hits within CAMERA's Non-Identical Nucleotide Sequence and All Prokaryotic Genomes databases.

Article Snippet: Several published studies describe evaluation of the sensitivity and specificity of various CombiMatrix microarray probe sets , , , – .

Techniques: Microarray, Sequencing