Journal: Haematologica

Article Title: The process of somatic hypermutation increases polyreactivity for central nervous system antigens in primary central nervous system lymphoma

doi: 10.3324/haematol.2019.242701

Figure Lengend Snippet: Expression of SNRPC in primary lymphoma of the central nervous system (PCNSL). (A) Nearly all CD20+ (FITC) tumor cells of PCNSL show a nuclear expression of SNRPC (Cy3). (B) Intermingled with tumor cells of a PCNSL, single CD68+ (FITC) macrophages also express SNRPC (arrows, Cy3); additionally, there are also SNRPC-negative CD68+ macrophages (arrowheads). (C) Cortical NeuN+ (FITC) neurons express SNRPC (arrows, Cy3). (D) Strongly activated GFAP+ (FITC) reactive astrocytes express SNRPC (arrows, Cy3). (E) In the white matter, some Olig2+ (FITC) oligodendrocytes express SNRPC (arrows, Cy3). (F) CD34+ (FITC) endothelial cells of neocortical cerebral blood vessels do not express SNRPC (Cy3). (G) mRNA expression of SNRPC recognized on the ProtoArray in the normal central nervous system (CNS) and PCNSL. SNRPC is downregulated CNS and upregulated in PCNSL samples. The line represents the SNRPC tag on the U95Av2 microarray (Affymetrix) in individual samples of ten normal CNS tissues and 21 PCNSL published previously.15 SNRPC was significantly differentially expressed between CNS and PCNSL ( P <0.01, Student t -test). (A-F) Double immunofluorescence with rabbit anti-SNRPC (clone EPR16034, Abcam, Cy3) and mouse anti-CD20 (clone L26, DCS, FITC in A), mouse anti-CD68 (clone KP1, DCS, FITC in B), mouse anti-NeuN (clone A60, Millipore, FITC in C), mouse anti-GFAP (clone GA-5, Biogenex, FITC in D), mouse anti- Olig2 (clone Olig2/2400, Abcam, FITC in E), and mouse anti-CD34 (cloneQBend/10, Biogenex, FITC in F). Microphotographs were taken with an Axiophot (Zeiss, Jena, Germany) and Zen 2 software (Zeiss). Original magnification: x400 (objective: x40). Inserts: x750 (A-C), x1000 (D-F). Overlay of the microphotographs and adjustment for contrast and brightness were performed with Adobe Photoshop software version CC.

Article Snippet: Protein microarray slides (9374 human proteins, ProtoArray, Thermo Fisher Scientific) including internal controls were analyzed as described previously., ,

Techniques: Expressing, Microarray, Immunofluorescence, Software

Journal: Scientific Reports

Article Title: Identification of potential autoantigens in anti-CCP-positive and anti-CCP-negative rheumatoid arthritis using citrulline-specific protein arrays

doi: 10.1038/s41598-021-96675-z

Figure Lengend Snippet: Immunome slide design and protein categories on the protein microarray. ( A ) The Immunome protein microarray consists of four identical subarrays, each containing 1631 different proteins in addition to 11 control proteins (BCCP, BSA, Cy3BSA, IgA, IgG, IgM, and four different control probes for the BCCP tag acting as negative controls). The control proteins are located between the subarrays. ( B ) The proteins spotted on the microarray represent different protein groups, such as cancer-associated antigens, transcription factors, kinases, and signaling proteins. The number of proteins in each category is shown. BCCP biotin carboxyl carrier protein, BSA bovine serum albumin.

Article Snippet: Plasma from anti-CCP-positive or anti-CCP-negative RA patients was incubated with Immunome protein microarray slides containing native proteins or proteins citrullinated by PAD2 or PAD4.

Techniques: Microarray

Journal: eLife

Article Title: Mucosal effects of tenofovir 1% gel

doi: 10.7554/eLife.04525

Figure Lengend Snippet: ( A and B ) Quantification of mRNA copy numbers measured in 9 cm biopsies by reverse transcription (RT) droplet digital PCR (ddPCR) relative to the housekeeping gene hemoglobin beta (HBB) copy numbers in seven additional study participants. ( A ) Nine selected genes induced in the microarrays: CCL19, CCL21, CCL23, CXCL9, CCR7, CD7, CD19, matrix metallopeptidase 12 (MMP12), and serine peptidase inhibitor of the Kazal type 4 (SPINK4). Copy numbers at baseline (0), after a single tenofovir gel application (I) and after seven consecutive once-daily applications (VII) are shown. Line colors signify each of the seven study participants. ( B ) Six selected suppressed genes: p21-activated kinase (PAK2), nuclear factor of activated T cells 5 (NFAT5), desmoplakin (DSP), TGF-β receptor associated protein (TGFBRAP), interleukin 10 (IL-10), and tripartite motif-containing protein 5 (TRIM5). ( C ) Normalized fold changes of gene expression at Day VII over baseline in all 15 individuals treated with tenofovir 1% gel. Red dots depict fold changes measured by microarray, blue dots depict fold changes measured by RT-ddPCR. The boxes indicate median and 25th–75th percentiles and the whiskers indicate 10th–90th percentile. Asterisks indicate statistical significance level relative to baseline (one asterisk p < 0.05; two asterisks p < 0.01, by one-sided Wilcoxon tests, adjusted for multiple testing). ( D ) Immunostaining of formalin-fixed 9 cm rectal biopsies from 10 participants for the proteins CD7 (immunohistochemistry [IHC]), CD3 (immunofluorescence) and ubiquitin D (UBD; IHC), predicted to be induced by the microarrays, and for IL-10 (IHC), predicted to be suppressed. For CD7 and CD3, tissue sections were evaluated in their entirety and positive cells per mm 2 are shown at baseline (0) and after seven consecutive once-daily applications (VII). Representative images are shown in . For UBD and IL-10, only columnar epithelial cells were evaluated. For UBD, the average mean staining intensities (MSI) per cell are shown. Representative images are shown in . Colors signify each of the 10 study participants. The boxes indicate median and 25th–75th percentiles and the whiskers indicate the range. Paired Wilcoxon signed-rank test p values for differences between 0 and VII are listed. DOI: http://dx.doi.org/10.7554/eLife.04525.006

Article Snippet: For CD3 staining, the slides were incubated with anti-CD3 for 60 min at a dilution of 1:25, washed in Wash Buffer, incubated for 30 min with sheep-anti-rabbit Dylight 649 (611-643-122; Rockland Immunochemicals, Limerick, PA), washed, and incubated for 30 min with donkey-anti-sheep Dylight 649 (613-743-168; Rockland).

Techniques: Digital PCR, Expressing, Microarray, Immunostaining, Immunohistochemistry, Immunofluorescence, Staining

Journal: eLife

Article Title: Mucosal effects of tenofovir 1% gel

doi: 10.7554/eLife.04525

Figure Lengend Snippet: Individual study participants are designated by letters. Blue indicates nuclei, red indicates CD3 or CD7. DOI: http://dx.doi.org/10.7554/eLife.04525.007

Article Snippet: For CD3 staining, the slides were incubated with anti-CD3 for 60 min at a dilution of 1:25, washed in Wash Buffer, incubated for 30 min with sheep-anti-rabbit Dylight 649 (611-643-122; Rockland Immunochemicals, Limerick, PA), washed, and incubated for 30 min with donkey-anti-sheep Dylight 649 (613-743-168; Rockland).

Techniques:

Journal: Biomolecules

Article Title: Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays

doi: 10.3390/biom13040602

Figure Lengend Snippet: Different microarray printing strategies: ( A ) Fabrication of PDA patterned CYTOP (perfluoropolymer) glass slides via photolithography approach (reprinted with permission from ), ( B ) a representative of various steps involved in inkjet printing process (taken from https://gesim-bioinstruments-microfluidics.com/microarray-printer/ ; Accessed on 12 December 2022), and ( C ) GLAD method used to fabricate silver nanorods on glass slides (reprinted with permission from ).

Article Snippet: In various studies, commercially available microarrays, such as the Explorer Antibody Microarray (ASB6000, Full Moon Biosystems, Sunnyvale, CA, USA) with 656 antibodies [ ], VaxArray Coronavirus SeroAssay kit (#VXCV-5100, InDevR, Boulder, CO, USA) [ ], Human Cytokine Antibody Microarray slides (AAH-CYT-G4000 kit, RayBiotech, Peachtree Corners, GA, USA) [ ], Biotin-labeled Human antibody microarray (RayBio Biotech, Guangzhou, China) [ ], Protein Microarray Slides (Grace Bio-Labs, Bend, OR, USA) [ ], HuProt human proteome microarrays (CDI laboratories, Mayaguez, PR, USA) [ ], SBC Mouse ceRNA microarray V1.0 (Shanghai Biotechnology Corporation, Shanghai, China) [ ], and Agilent Whole Mouse 44 K ver.

Techniques: Microarray

Journal: Biomolecules

Article Title: Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays

doi: 10.3390/biom13040602

Figure Lengend Snippet: Detection methods: ( A ) FRET based approach to detect target DNA. In presence of target DNA only, the existing complex of fluorescence dye (Cy3) and quencher (BHQ2) is disrupted and generates fluorescence signal (). ( B ) CL based enzymatic approach. This approach involves multiple steps: immunoreaction, HCR amplification, enzyme conjugation, and enzyme-CL (luminol p-iodophenol) substrate reaction (). ( C ) Colorimetric detection (use of streptavidin-coated gold nanoparticles) of isothermal DNA amplification. Interaction of biotin and streptavidin was explored (). ( D ) OIRD, a label-free detection method to study protein/antibody interactions with target molecules on a protein microarray chip ().

Article Snippet: In various studies, commercially available microarrays, such as the Explorer Antibody Microarray (ASB6000, Full Moon Biosystems, Sunnyvale, CA, USA) with 656 antibodies [ ], VaxArray Coronavirus SeroAssay kit (#VXCV-5100, InDevR, Boulder, CO, USA) [ ], Human Cytokine Antibody Microarray slides (AAH-CYT-G4000 kit, RayBiotech, Peachtree Corners, GA, USA) [ ], Biotin-labeled Human antibody microarray (RayBio Biotech, Guangzhou, China) [ ], Protein Microarray Slides (Grace Bio-Labs, Bend, OR, USA) [ ], HuProt human proteome microarrays (CDI laboratories, Mayaguez, PR, USA) [ ], SBC Mouse ceRNA microarray V1.0 (Shanghai Biotechnology Corporation, Shanghai, China) [ ], and Agilent Whole Mouse 44 K ver.

Techniques: Fluorescence, Amplification, Conjugation Assay, Microarray

Journal: Biomolecules

Article Title: Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays

doi: 10.3390/biom13040602

Figure Lengend Snippet: ( A ) A pictorial workflow presentation of hybrid tetrahedral DNA structured probe in conjugation with hybridization chain reaction (DTSP-HCR) concept used to distinguish single-base mismatches in DNA () and ( B ) an overview of acute tuberculosis (ATB) biomarker identification using a two-phase strategy (discovery phase and validation phase) (). Venn diagram and microarray chip visual analysis revealed the potential of 5 protein biomarkers to distinguish ATB and LTBI/HC. LTBI represents latent tuberculosis infection, and HC represents healthy control.

Article Snippet: In various studies, commercially available microarrays, such as the Explorer Antibody Microarray (ASB6000, Full Moon Biosystems, Sunnyvale, CA, USA) with 656 antibodies [ ], VaxArray Coronavirus SeroAssay kit (#VXCV-5100, InDevR, Boulder, CO, USA) [ ], Human Cytokine Antibody Microarray slides (AAH-CYT-G4000 kit, RayBiotech, Peachtree Corners, GA, USA) [ ], Biotin-labeled Human antibody microarray (RayBio Biotech, Guangzhou, China) [ ], Protein Microarray Slides (Grace Bio-Labs, Bend, OR, USA) [ ], HuProt human proteome microarrays (CDI laboratories, Mayaguez, PR, USA) [ ], SBC Mouse ceRNA microarray V1.0 (Shanghai Biotechnology Corporation, Shanghai, China) [ ], and Agilent Whole Mouse 44 K ver.

Techniques: Conjugation Assay, Hybridization, Biomarker Assay, Microarray, Infection

Journal: Biomolecules

Article Title: Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays

doi: 10.3390/biom13040602

Figure Lengend Snippet: A generic workflow of the application of glycan microarray chip to efficiently profile enzyme activities and determine enzyme inhibitor IC 50 values ().

Article Snippet: In various studies, commercially available microarrays, such as the Explorer Antibody Microarray (ASB6000, Full Moon Biosystems, Sunnyvale, CA, USA) with 656 antibodies [ ], VaxArray Coronavirus SeroAssay kit (#VXCV-5100, InDevR, Boulder, CO, USA) [ ], Human Cytokine Antibody Microarray slides (AAH-CYT-G4000 kit, RayBiotech, Peachtree Corners, GA, USA) [ ], Biotin-labeled Human antibody microarray (RayBio Biotech, Guangzhou, China) [ ], Protein Microarray Slides (Grace Bio-Labs, Bend, OR, USA) [ ], HuProt human proteome microarrays (CDI laboratories, Mayaguez, PR, USA) [ ], SBC Mouse ceRNA microarray V1.0 (Shanghai Biotechnology Corporation, Shanghai, China) [ ], and Agilent Whole Mouse 44 K ver.

Techniques: Microarray

Journal: Cancers

Article Title: Understanding the Interplay between COX-2 and hTERT in Colorectal Cancer Using a Multi-Omics Analysis

doi: 10.3390/cancers11101536

Figure Lengend Snippet: Representative tissue microarray (TMA) slides with COX-1, COX-2, and TERT-staining. ( A ) Negative COX-1 staining was detected in 4/10 (40%) CRC samples; ( B ) Low COX-1 staining was detected in 5/10 (50%) CRC samples; ( C ) Medium intensity COX-1 staining was detected in 1/10 (10%) CRC samples; ( D ) Negative COX-2 staining was detected in 7/12 CRC samples (58.3%); ( E ) Low COX-2 staining was detected in 4/12 CRC samples (33%); ( F ) Medium COX-2 staining was detected in 1/12 (8.3%) CRC samples; TERT staining was negative in all CRC samples (11/11, 100%) ( G – I ). All slides were retrieved from the Human Protein Atlas (HPA). Magnification, ×100.

Article Snippet: The following are available online at https://www.mdpi.com/2072-6694/11/10/1536/s1 , Figure S1: PTGS1 or PTGS2 expression levels did not differ with regard to tumor staging ( p > 0.05), but PTGES3 expression was lower, and TERT expression was higher in high stage tumors (III and IV), compared to low-stage tumors (I and II); Figure S2: Heatmap depicting the PTGS1, PTGS2 and TERT expression levels (log2(TPM + 0.001)) in the TCGA-COAD and GTEx projects; Figure S3: Transcript analysis of PTGS1, PTGS2 and TERT in colorectal cancer (TCGA-Colon/Rectum Adenocarcinoma) vs. the normal colon (GTEx Colon); Table S1: Gene expression (RNAseq), promoter methylation, copy number aberration and somatic mutations (SNPs and small INDELs) in the COX-2 and TERT genes, across the TCGA-COAD dataset samples; Table S2: Summary table integrating all the generated data in the present study (mRNA expression data from TCGA and GTEx studies on Colon Adenocarcinoma (RSEM TPM), as well as immunohistochemistry (IHC) data from the tissue microarray (TMA) slides of the Human Protein Atlas (HPA).

Techniques: Microarray, Staining