Journal: BBA Clinical

Article Title: Novel panel of protein biomarkers to predict response to bortezomib-containing induction regimens in multiple myeloma patients

doi: 10.1016/j.bbacli.2017.05.003

Figure Lengend Snippet: Label-free mass spectrometry data. List of statistically significant discovered proteins using LC-MS analysis. Proteins (in bold) were selected for further validation using ELISAs.

Article Snippet: Four commercially available kits for these four proteins; angiogenin (ANG) [Abcam, UK - ab99970], clusterin (CLU) [R&D system, UK - DCLU00], C-C Motif Chemokine 18 (CCL18) [Abcam, UK - ab100620], and Complement C1q [Abcam, UK - ab170246] were used.

Techniques: Mass Spectrometry, Biomarker Discovery, Variant Assay

Journal: BBA Clinical

Article Title: Novel panel of protein biomarkers to predict response to bortezomib-containing induction regimens in multiple myeloma patients

doi: 10.1016/j.bbacli.2017.05.003

Figure Lengend Snippet: ELISA Data. Mean, SD, Area under the curve (AUC) and p -value for each of the new and standard proteins found in the two groups of patients compared.

Article Snippet: Four commercially available kits for these four proteins; angiogenin (ANG) [Abcam, UK - ab99970], clusterin (CLU) [R&D system, UK - DCLU00], C-C Motif Chemokine 18 (CCL18) [Abcam, UK - ab100620], and Complement C1q [Abcam, UK - ab170246] were used.

Techniques: Enzyme-linked Immunosorbent Assay

Journal: BBA Clinical

Article Title: Novel panel of protein biomarkers to predict response to bortezomib-containing induction regimens in multiple myeloma patients

doi: 10.1016/j.bbacli.2017.05.003

Figure Lengend Snippet: Logistic regression analysis data. List of different protein combinations used to establish the best model that can be used as a predictive panel for response to induction therapy containing bortezomib regime.

Article Snippet: Four commercially available kits for these four proteins; angiogenin (ANG) [Abcam, UK - ab99970], clusterin (CLU) [R&D system, UK - DCLU00], C-C Motif Chemokine 18 (CCL18) [Abcam, UK - ab100620], and Complement C1q [Abcam, UK - ab170246] were used.

Techniques:

Journal: Proteomics

Article Title: Identification, prioritization and evaluation of glycoproteins for aggressive prostate cancer using quantitative glycoproteomics and antibody-based assays on tissue specimens

doi: 10.1002/pmic.201200541

Figure Lengend Snippet: Standard Curve of ELISA assays for protein quantification of cartilage oligomeric matrix protein (COMP), periostin, membrane primary amine oxidase (VAP-1) and cathepsin L. A), dose-response curves for COMP. B), dose-response curve for periostin. C), dose-response curve for VAP-1. D), dose-response curve for cathepsin L.

Article Snippet: Materials Hydrazide resin and sodium periodate were from Bio-Rad (Hercules, CA); sequencing-grade trypsin and TMB reagent were from Promega (Madison, WI); PNGase F was from New England Biolabs (Ipswich, MA); C18 columns were from Waters (Milford, MA); Recombinant protein, capture and detection antibody of human cartilage oligomeric matrix protein (COMP), periostin, cathepsin L, clusterin and galectin-3 binding protein, streptavidin-HRP conjugates, ELISA plates and human VAP-1 Quantikine ELISA Kit were from R&D systems (Minneapolis, MN); All other chemicals were from Sigma-Aldrich (St. Louis, MO).

Techniques: Enzyme-linked Immunosorbent Assay

Journal: PloS one

Article Title: Lineage-specific restraint of pituitary gonadotroph cell adenoma growth.

doi: 10.1371/journal.pone.0017924

Figure Lengend Snippet: Figure 3. Clusterin in human pituitary adenomas. Confocal image of A) human pituitary adenoma and non-tumorous pituitary tissue specimens showing clusterin (green) expressed exclusively in the cytoplasm; B) Co-localization of clusterin with GH, PRL and aGSU in respective human pituitary adenoma specimens (clusterin green, respective hormones red). doi:10.1371/journal.pone.0017924.g003

Article Snippet: Short hairpin RNA expressing vector targeting murine clusterin shClu-pGFP-V-RS (shClu) were purchased from OriGene( Rockvillle, MD).

Techniques:

Journal: PloS one

Article Title: Lineage-specific restraint of pituitary gonadotroph cell adenoma growth.

doi: 10.1371/journal.pone.0017924

Figure Lengend Snippet: Figure 4. Pituitary proliferation, DNA damage and senescence markers in the aGSU.PTTG pituitary gland. A) In vivo BrdU incorporation. Mice were injected with BrdU (50 mg/g BW), and pituitary sections stained for BrdU. One thousand cells/section, 3 sections/animal, n = 3 animals/ genotype were analyzed. *, p,0.05; Western blot analysis of B) proliferation markers; C) DNA damage, DNA repair and p53-dependent senescence markers, and D) oncogene-induced senescence markers; E) Confocal image showing immunofluorescent cytoplasmic clusterin, and intranuclear p15 and p16 expression (green) in WT and in pre-tumorous aGSU.PTTG pituitary glands, and in aGSU.PTTG pituitary adenomas; F) Pituitary SA-b- galactosidase enzymatic activity (blue) in WT and in pre-tumorous aGSU.PTTG pituitary gland. Three pituitary cryosections/animal were analyzed from 3 animals/genotype, and a representative image shown. Western blots here and elsewhere were repeated 3 times with similar results and representative blots shown. doi:10.1371/journal.pone.0017924.g004

Article Snippet: Short hairpin RNA expressing vector targeting murine clusterin shClu-pGFP-V-RS (shClu) were purchased from OriGene( Rockvillle, MD).

Techniques: In Vivo, BrdU Incorporation Assay, Injection, Staining, Western Blot, Expressing, Activity Assay

Journal: PloS one

Article Title: Lineage-specific restraint of pituitary gonadotroph cell adenoma growth.

doi: 10.1371/journal.pone.0017924

Figure Lengend Snippet: Figure 6. C/EBPs induce clusterin. A) C/EBPb is up-regulated in the aGSU.PTTG pituitary. Confocal image showing C/EBPb co-localization with aGSU-positive, GH-positive and PRL-positive cells in WT and pre-tumorous aGSU.PTTG pituitary glands. (Hormones-green, cytoplsmic, C/EBPb–red, intranuclear); B) Western blot analysis of C/EBPb and d isoforms induced in LbT2 cells stably transfected with mPttg; C) Effects of C/EBPs on the clusterin promoter in LbT2 and aT3 cells 24 h after transfection. Cells were co-transfected with 200 ng murine pGL3-luc-mClu reporter plasmid and 800 ng murine pCDNA3-C/EBPa, b or d. The ratio of luciferase to co-trasfected b-galactosidase control reporter vector was normalized to pCDNA3- null expression vector. SEM was calculated from triplicate assays, and experiments repeated three times with similar results. Results of a representative experiment are shown.*, p,0.05, **,p,0.01; D) Western blot analysis of clusterin expression in gonadotroph-derived aT3 cells 24 hours after transfection with pCDNA3-C/EBPb or E) pCDNA3-C/EBPd; F) Western blot analysis of clusterin expression in LbT2 mPttg cells 48 hours after simultaneous transfection with siC/EBPb and siC/EBPd (3 nM each). Two different combinations of siRNAs were used. doi:10.1371/journal.pone.0017924.g006

Article Snippet: Short hairpin RNA expressing vector targeting murine clusterin shClu-pGFP-V-RS (shClu) were purchased from OriGene( Rockvillle, MD).

Techniques: Western Blot, Stable Transfection, Transfection, Plasmid Preparation, Luciferase, Control, Expressing, Derivative Assay

Journal: PloS one

Article Title: Lineage-specific restraint of pituitary gonadotroph cell adenoma growth.

doi: 10.1371/journal.pone.0017924

Figure Lengend Snippet: Figure 7. Clusterin restrains pituitary cell proliferation by inducing Cdk inhibitors. Western blot analysis of Cdk inhibitors and proliferation markers A) in LbT2 cells, B) in aT3 cells 48 h after transfection with mClu; C) Confocal images of immunofluoprescence of histone H3 methylation on lysine 9 (H3-K9M) (red) in vector and Clu-expressing aT3 cells 48 hours after transfection; D) Quantification of positive H3-K9M foci. Cells were fixed, stained with H3-K9M antibody, and one thousand cells/field counted in three randomly chosen visual fields; E) Percentage of BrdU positive cells 48 h after transfection with mClu. Triplicate samples were pulsed with BrdU for 30 min and analyzed by flow cytometry, *, p,0.05; F) aT3 cells stably overexpressing mClu or vector were synchronized in 0.1% fetal bovine serum for 18 hours, and then cultured in 10% fetal bovine serum. At the indicated times, duplicate samples were pulsed with BrdU for 30 min, analyzed by flow cytometry, and cells in S-phase identified by staining with BrdU antibodies. doi:10.1371/journal.pone.0017924.g007

Article Snippet: Short hairpin RNA expressing vector targeting murine clusterin shClu-pGFP-V-RS (shClu) were purchased from OriGene( Rockvillle, MD).

Techniques: Western Blot, Transfection, Methylation, Plasmid Preparation, Expressing, Staining, Flow Cytometry, Stable Transfection, Cell Culture

Journal: PloS one

Article Title: Lineage-specific restraint of pituitary gonadotroph cell adenoma growth.

doi: 10.1371/journal.pone.0017924

Figure Lengend Snippet: Figure 8. Clusterin attenuation promotes proliferation. Western blot analysis of Cdk inhibitors and proliferation markers A) in LbT2 cells, B) in aT3 cells; C) Percentage of BrdU positive cells 48 h after transfection with siClu. D) Upper panel, Western blot confirms p15 down-regulation, Lower panel, Percentage of BrdU positive LbT2 cells 48 h after transfection with sip15. E) Upper panel, Western blot confirms p16 down-regulation, Lower panel, Percentage of BrdU positive LbT2 cells 48 h after transfection with sip16. For BrdU detection, cells were fixed, stained with BrdU antibody and one thousand cells/field in three randomly chosen fields counted. *, p,0.05. doi:10.1371/journal.pone.0017924.g008

Article Snippet: Short hairpin RNA expressing vector targeting murine clusterin shClu-pGFP-V-RS (shClu) were purchased from OriGene( Rockvillle, MD).

Techniques: Western Blot, Transfection, Staining

Journal: PloS one

Article Title: Lineage-specific restraint of pituitary gonadotroph cell adenoma growth.

doi: 10.1371/journal.pone.0017924

Figure Lengend Snippet: Figure 9. FOXL2 stimulates the clusterin promoter. A) Effects of FOXL2 on the clusterin promoter in aT3 cells 24 h after transfection. Cells were co-transfected with 200 ng murine pGL3-luc-mClu reporter plasmid and indicated amounts of pcDNA3-His-mFoxl2. The ratio of luciferase to co- trasfected b-galactosidase control reporter vector was normalized to pCDNA3-null expression vector. SEM was calculated from triplicate assays, and experiments repeated three times with similar results. Results of a representative experiment are shown; **,p,0.01; B) Western blot analysis of clusterin expression in aT3 cells 24 hours after transfection with pcDNA3-His-mFoxl2; C) ChiP assay was performed in nuclear fractions derived from aT3 cell lysates. Top, schematic of the approximate location of primers used in the PCR reactions. Enrichment of specific clusterin promoter sequences was obtained with primer Set 2. FOXL2, specific antibody, IgG, nonspecific antibody, PCP, positive control primers. The experiment was repeated twice, and results of a representative assay shown. doi:10.1371/journal.pone.0017924.g009

Article Snippet: Short hairpin RNA expressing vector targeting murine clusterin shClu-pGFP-V-RS (shClu) were purchased from OriGene( Rockvillle, MD).

Techniques: Transfection, Plasmid Preparation, Luciferase, Control, Expressing, Western Blot, Derivative Assay, Positive Control

Journal: PloS one

Article Title: Lineage-specific restraint of pituitary gonadotroph cell adenoma growth.

doi: 10.1371/journal.pone.0017924

Figure Lengend Snippet: Figure 10. Proliferation restricting pathways in the pituitary gonadotroph cell lineage. FOXL2 directly activates the clusterin promoter, while Pttg overexpression results in proliferation, DNA damage and stimulation of C/EBPb and d; C/EBPs activate the clusterin promoter. High levels of secretory clusterin trigger expression of Cdk inhibitors p15, p16 and p27, and C/EBPb also cooperates to induce p15. Up-regulated tumor suppressor proteins likely underlie proliferation restraint preventing uncontrolled growth of benign pituitary adenomas of gonadotroph cell origin. doi:10.1371/journal.pone.0017924.g010

Article Snippet: Short hairpin RNA expressing vector targeting murine clusterin shClu-pGFP-V-RS (shClu) were purchased from OriGene( Rockvillle, MD).

Techniques: Over Expression, Expressing

Journal: Human reproduction (Oxford, England)

Article Title: CDC42 deficiency leads to endometrial stromal cell senescence in recurrent implantation failure.

doi: 10.1093/humrep/deae246

Figure Lengend Snippet: Figure 1. Cellular senescence in the stroma of recurrent implantation (RIF) failure endometrium. (A) Gene ontology (GO) biological process enrichment of the differentially expressed genes (DEGs) between fertile control (CTR) patients and patients with RIF in SRP224538. (B) FPKM level of TP53 in CTR patients and RIF patients in SRP224538. (C) FPKM level of IL6 in CTR patients and RIF patients in SRP224538. (D–F) Levels of IL6, CLU, and sST2 secretion in primary endometrial stromal cell supernatant from CTR and RIF patients before and after 72 h of 8Br-cAMPþMPA treatment. (G and H) Representative images of immunohistochemical (IHC) staining of P16 in mid-secretory endometrium of CTR patients (n ¼ 22) versus RIF patients (n ¼ 22). Black arrows indicate typical P16þ cells. Quantitative analysis by number of P16þ cells per 200× field for P16 staining. (I and J) Representative images of IHC staining of P21 in mid-secretory endometrium of CTR patients (n ¼ 22) versus RIF patients (n ¼ 22). Black arrows indicate typical P21þ

Article Snippet: Commercially available ELISA kits were utilized to measure the level of secreted protein (PRL: Elabscience, No. E-EL-H0141; IGFBP1: Elabscience, No. E-EL-H0442; IL6: Elabscience, No. E-EL-H6156; IL8: MULTI SCIENCES, No. EK10896; CLU: Elabscience, No. E-EL-H0038; sST2: Elabscience, No. E-EL-H6082) in collected supernatants according to the manufacturer’s instructions.

Techniques: Control, Immunohistochemical staining, Immunohistochemistry, Staining

Journal: Human reproduction (Oxford, England)

Article Title: CDC42 deficiency leads to endometrial stromal cell senescence in recurrent implantation failure.

doi: 10.1093/humrep/deae246

Figure Lengend Snippet: Figure 2. CDC42 knockdown accelerates senescence of differentiated endometrial stromal cells (EnSCs). (A–C) Expression of CDC42, CDKN2A, and CDKN1A mRNA levels in primary EnSCs after 72 h of adenovirus treatment. (D) Expression of CDC42, P21, P53, and p-γ-H2AX protein levels in primary EnSCs after 72 h of adenovirus treatment. (E) Expressions of collagen I, collagen III, collagen IV, and MMP2 protein levels in primary EnSC after 72 h of adenovirus treatment. (F–H) Expressions of CDC42, CDKN2A, and CDKN1A mRNA levels in primary EnSC transfected with Ad-GFP or Ad-shCDC42-GFP following with 72 h of 8Br-cAMPþMPA treatment. (I–K) Level of IL6, CLU, and sST2 secretion in primary EnSCs transfected with Ad-GFP or Ad-shCDC42- GFP following with 72 h of 8Br-cAMPþMPA treatment. (L) Expression of CDC42, P21, and P53 protein levels in primary EnSCs transfected with Ad-GFP or Ad-shCDC42-GFP following with 72 h of 8Br-cAMPþMPA treatment. (M and N) Representative images of P16 and P21 immunofluorescence staining in primary EnSCs transfected with Ad-GFP or Ad-shCDC42-GFP following with 72 h of 8Br-cAMPþMPA treatment. (O and P) SA-β-gal staining of primary EnSCs after 48 h of Ad-GFP or Ad-shCDC42-GFP adenovirus treatment and then different days of 8Br-cAMPþMPA treatment. Quantitative analysis of integrated optical density for SA-β-gal staining, with value of the Ad-GFP group at 0 h set as 1. Mean ± SEM. P < 0.05, P < 0.01, P<0.001. ANOVA with Tukey’s multiple comparisons test. Two-way ANOVA with the Bonferroni multiple comparisons test in (P).

Article Snippet: Commercially available ELISA kits were utilized to measure the level of secreted protein (PRL: Elabscience, No. E-EL-H0141; IGFBP1: Elabscience, No. E-EL-H0442; IL6: Elabscience, No. E-EL-H6156; IL8: MULTI SCIENCES, No. EK10896; CLU: Elabscience, No. E-EL-H0038; sST2: Elabscience, No. E-EL-H6082) in collected supernatants according to the manufacturer’s instructions.

Techniques: Knockdown, Expressing, Transfection, Immunofluorescence, Staining

Journal: Proteome Science

Article Title: Potential plasma biomarkers for progression of knee osteoarthritis using glycoproteomic analysis coupled with a 2D-LC-MALDI system

doi: 10.1186/1477-5956-10-36

Figure Lengend Snippet: Biomarker candidates identified by proteomic analysis

Article Snippet: The membrane was then incubated with anti-human clusterin monoclonal antibody (1:1000, R&D Systems) or anti-human hemopexin polyclonal antibody (1:2500; Lifespan Biosciences, Seattle, WA) in TBST (0.05% Tween 20 in TBS) containing 5% skimmed milk overnight at 4°C.

Techniques: Biomarker Discovery

Journal: Proteome Science

Article Title: Potential plasma biomarkers for progression of knee osteoarthritis using glycoproteomic analysis coupled with a 2D-LC-MALDI system

doi: 10.1186/1477-5956-10-36

Figure Lengend Snippet: Comparison of MS peak intensities of potential biomarkers between progressors and non-progressors. Results are shown for clusterin ( A ), MSP ( B ), hemopexin ( C ), and AGP-2 ( D ). P and NP represent progressors and non-progressors, respectively. P -values were determined by Mann–Whitney U test.

Article Snippet: The membrane was then incubated with anti-human clusterin monoclonal antibody (1:1000, R&D Systems) or anti-human hemopexin polyclonal antibody (1:2500; Lifespan Biosciences, Seattle, WA) in TBST (0.05% Tween 20 in TBS) containing 5% skimmed milk overnight at 4°C.

Techniques: Comparison, MANN-WHITNEY

Journal: Proteome Science

Article Title: Potential plasma biomarkers for progression of knee osteoarthritis using glycoproteomic analysis coupled with a 2D-LC-MALDI system

doi: 10.1186/1477-5956-10-36

Figure Lengend Snippet: Concentrations of clusterin and hemopexin in serum samples

Article Snippet: The membrane was then incubated with anti-human clusterin monoclonal antibody (1:1000, R&D Systems) or anti-human hemopexin polyclonal antibody (1:2500; Lifespan Biosciences, Seattle, WA) in TBST (0.05% Tween 20 in TBS) containing 5% skimmed milk overnight at 4°C.

Techniques: Concentration Assay

Journal: Proteome Science

Article Title: Potential plasma biomarkers for progression of knee osteoarthritis using glycoproteomic analysis coupled with a 2D-LC-MALDI system

doi: 10.1186/1477-5956-10-36

Figure Lengend Snippet: Expression of candidate biomarkers in synovial tissues collected from OA knee joints. ( A ) Results of in situ hybridization for clusterin, hemopexin, MSP, and AGP-2 mRNA in OA synovial tissue. Clusterin, hemopexin, and MSP expression were observed primarily in synovial lining cells (thick arrows), while the expression of AGP-2 was mostly observed in endothelial cells (arrowheads). Expression of hemopexin was also observed in endothelial cells (arrowheads) and fibroblast-like cells (thin arrows). Bars, 50 μm. ( B ) Results of western blotting analysis of synovial tissue lysates. Clusterin and hemopexin were confirmed in all samples. Numbers above the lanes indicate numbers of synovium samples. PC: positive control.

Article Snippet: The membrane was then incubated with anti-human clusterin monoclonal antibody (1:1000, R&D Systems) or anti-human hemopexin polyclonal antibody (1:2500; Lifespan Biosciences, Seattle, WA) in TBST (0.05% Tween 20 in TBS) containing 5% skimmed milk overnight at 4°C.

Techniques: Expressing, In Situ Hybridization, Western Blot, Positive Control