Journal: Frontiers in Molecular Biosciences

Article Title: Comprehensive Analysis of the Potential Immune-Related Biomarker Transporter Associated With Antigen Processing 1 That Inhibits Metastasis and Invasion of Ovarian Cancer Cells

doi: 10.3389/fmolb.2021.763958

Figure Lengend Snippet: The expression of transporter associated with antigen processing 1 (TAP1) in pan-cancer. (A) TAP1 expression of 31 kinds of normal tissues downloaded from genotype-tissue expression (GTEx) database. (B) TAP1 expression in 21 kinds of cancer cell lines derived from the cancer cell line encyclopedia (CCLE). (C) TAP1 expression in tumor samples and the adjacent normal samples of 20 cancers derived from the TCGA. (D) TAP1 expression in tumor samples and normal samples of 27 cancers derived from the cancer genome atlas (TCGA) and GTEx database. * p < 0.05. ** p < 0.01. *** p < 0.001.

Article Snippet: The membrane was incubated with the following primary antibodies TAP1 (1:3,000), MEF2A (1:2000, #12382-1-AP, Proteintech, United States), LEF1 (1:1000, #14972-1-AP, Proteintech), E-cadherin (1:10000, #20874-1-AP, Proteintech), vimentin (1:2000, #10366-1-AP, Proteintech), and beta actin (1:1000, # 20536-1-AP, Proteintech).

Techniques: Expressing, Derivative Assay

Journal: Frontiers in Molecular Biosciences

Article Title: Comprehensive Analysis of the Potential Immune-Related Biomarker Transporter Associated With Antigen Processing 1 That Inhibits Metastasis and Invasion of Ovarian Cancer Cells

doi: 10.3389/fmolb.2021.763958

Figure Lengend Snippet: The prediction ability of transporter associated with antigen processing 1 (TAP1) in pan-cancer prognosis. (A–C) The top three cancers correlated with TAP1 in disease-free survival (DFS). (D–F) The top three cancers correlated with TAP1 in disease-specific survival (DSS). (G–I) The top three cancers correlated with TAP1 in progression-free survival (PFS). (J–L) The top three cancers correlated with TAP1 in Overall survival (OS).

Article Snippet: The membrane was incubated with the following primary antibodies TAP1 (1:3,000), MEF2A (1:2000, #12382-1-AP, Proteintech, United States), LEF1 (1:1000, #14972-1-AP, Proteintech), E-cadherin (1:10000, #20874-1-AP, Proteintech), vimentin (1:2000, #10366-1-AP, Proteintech), and beta actin (1:1000, # 20536-1-AP, Proteintech).

Techniques:

Journal: Frontiers in Molecular Biosciences

Article Title: Comprehensive Analysis of the Potential Immune-Related Biomarker Transporter Associated With Antigen Processing 1 That Inhibits Metastasis and Invasion of Ovarian Cancer Cells

doi: 10.3389/fmolb.2021.763958

Figure Lengend Snippet: The correlation of transporter associated with antigen processing 1 (TAP1) with immune infiltration in multiple cancers. The top three cancers with the strongest correlation with 6 immune infiltration cells which included B cells, CD4+T cells, CD8+T cells, neutrophils, macrophages, and dendritic cells. The cancers were colon adenocarcinoma (COAD), kidney renal clear cell carcinoma (KIRC), and breast invasive carcinoma (BRCA), respectively.

Article Snippet: The membrane was incubated with the following primary antibodies TAP1 (1:3,000), MEF2A (1:2000, #12382-1-AP, Proteintech, United States), LEF1 (1:1000, #14972-1-AP, Proteintech), E-cadherin (1:10000, #20874-1-AP, Proteintech), vimentin (1:2000, #10366-1-AP, Proteintech), and beta actin (1:1000, # 20536-1-AP, Proteintech).

Techniques:

Journal: Frontiers in Molecular Biosciences

Article Title: Comprehensive Analysis of the Potential Immune-Related Biomarker Transporter Associated With Antigen Processing 1 That Inhibits Metastasis and Invasion of Ovarian Cancer Cells

doi: 10.3389/fmolb.2021.763958

Figure Lengend Snippet: The relationship between TAP1 and ESTIMATE score in multiple cancers. The ESTIMATE score was used to determine the correlation of TAP1 with immune cells and stromal cells in 33 tumors. TAP1 was positively correlated with ESTIMATE scores in cervical squamous cell carcinoma (CESC), ovarian cancer (OC), uveal melanoma (UVM), testicular germ cell tumors (TGCT), and thyroid carcinoma (THCA) ( p < 0.05).

Article Snippet: The membrane was incubated with the following primary antibodies TAP1 (1:3,000), MEF2A (1:2000, #12382-1-AP, Proteintech, United States), LEF1 (1:1000, #14972-1-AP, Proteintech), E-cadherin (1:10000, #20874-1-AP, Proteintech), vimentin (1:2000, #10366-1-AP, Proteintech), and beta actin (1:1000, # 20536-1-AP, Proteintech).

Techniques:

Journal: Frontiers in Molecular Biosciences

Article Title: Comprehensive Analysis of the Potential Immune-Related Biomarker Transporter Associated With Antigen Processing 1 That Inhibits Metastasis and Invasion of Ovarian Cancer Cells

doi: 10.3389/fmolb.2021.763958

Figure Lengend Snippet: The relationship between transporter associated with antigen processing 1 (TAP1) and immune checkpoint therapy in multiple cancers. (A) The relationship between TAP1 and 47 immune checkpoint genes. Color green represented negative correlation with TAP1 and color red represented positive correlation with TAP1. (B) The correlation of TAP1 with tumor mutation burden (TMB). (C) The correlation of TAP1 with microsatellite instability (MSI). * p < 0.05. ** p < 0.01. *** p < 0.001.

Article Snippet: The membrane was incubated with the following primary antibodies TAP1 (1:3,000), MEF2A (1:2000, #12382-1-AP, Proteintech, United States), LEF1 (1:1000, #14972-1-AP, Proteintech), E-cadherin (1:10000, #20874-1-AP, Proteintech), vimentin (1:2000, #10366-1-AP, Proteintech), and beta actin (1:1000, # 20536-1-AP, Proteintech).

Techniques: Mutagenesis

Journal: Frontiers in Molecular Biosciences

Article Title: Comprehensive Analysis of the Potential Immune-Related Biomarker Transporter Associated With Antigen Processing 1 That Inhibits Metastasis and Invasion of Ovarian Cancer Cells

doi: 10.3389/fmolb.2021.763958

Figure Lengend Snippet: The relationship between transporter associated with antigen processing 1 (TAP1) and neoantigen in various cancers. TAP1 was positively related to neoantigens in ovarian cancer (OC), cervical squamous cell carcinoma (CESC), lung adenocarcinoma (LUAD), breast invasive carcinoma (BRCA), skin cutaneous melanoma (SKCM), and brain lower grade glioma (LGG) ( p < 0.05), whereas it was negatively correlated in colon adenocarcinoma (COAD) and rectum adenocarcinoma (READ).

Article Snippet: The membrane was incubated with the following primary antibodies TAP1 (1:3,000), MEF2A (1:2000, #12382-1-AP, Proteintech, United States), LEF1 (1:1000, #14972-1-AP, Proteintech), E-cadherin (1:10000, #20874-1-AP, Proteintech), vimentin (1:2000, #10366-1-AP, Proteintech), and beta actin (1:1000, # 20536-1-AP, Proteintech).

Techniques: Immunopeptidomics

Journal: Frontiers in Molecular Biosciences

Article Title: Comprehensive Analysis of the Potential Immune-Related Biomarker Transporter Associated With Antigen Processing 1 That Inhibits Metastasis and Invasion of Ovarian Cancer Cells

doi: 10.3389/fmolb.2021.763958

Figure Lengend Snippet: Correlation of transporter associated with antigen processing 1 (TAP1) expression with the prognosis of ovarian cancer (OC) and cervical cancer (CC). (A) Immunohistochemical (IHC) analysis of transporter associated with antigen processing 1 (TAP1) protein expression in OC tissues. Original magnifications:×200 and ×400. i represents strong positive staining, ii represents moderately positive staining, and iii represents weakly positive staining. (B) IHC analysis of TAP1 protein expression in CC tissues. Original magnifications:×200 and ×400. i represents strong positive staining, ii represents moderately positive staining, and iii represents weakly positive staining. Scale bars 200 μm. (C) 5-Year Kaplan–Meier analysis of overall survival in OC patients on the basis of TAP1 protein expression. (D) 5-Year Kaplan–Meier analysis of overall survival in CC patients on the basis of the TAP1 protein expression. (E) The protein-protein interaction (PPI) network of TAP1 and top 26 correlated transcription factors (TFs) were identified using STRING ( https://string-db.org/cgi/input.pl ). Color blue represented TFs negatively correlated with TAP1, color red represented TFs positively correlated with TAP1, and color white represented TFs significantly correlated with the top 26 TFs in enrichment analysis. (F) Gene set enrichment analysis of transporter associated with antigen processing 1 (TAP1) and pivotal TFs in OC. (G) TAP1, MEF2A, LEF1, and β-actin protein expression in normal cell lines and cancer cell lines. Error bars represent the SD of triplicate measurements. * p < 0.05; ** p < 0.01; *** p < 0.001.

Article Snippet: The membrane was incubated with the following primary antibodies TAP1 (1:3,000), MEF2A (1:2000, #12382-1-AP, Proteintech, United States), LEF1 (1:1000, #14972-1-AP, Proteintech), E-cadherin (1:10000, #20874-1-AP, Proteintech), vimentin (1:2000, #10366-1-AP, Proteintech), and beta actin (1:1000, # 20536-1-AP, Proteintech).

Techniques: Expressing, Immunohistochemical staining, Staining

Journal: Frontiers in Molecular Biosciences

Article Title: Comprehensive Analysis of the Potential Immune-Related Biomarker Transporter Associated With Antigen Processing 1 That Inhibits Metastasis and Invasion of Ovarian Cancer Cells

doi: 10.3389/fmolb.2021.763958

Figure Lengend Snippet: Downregulation of transporter associated with antigen processing 1 (TAP1) reduces the invasion and migration in ovarian cancer cells. (A) The volcano map of TAP1-related pathways by gene set variation analysis. (B) Enriching pathway analysis in ovarian cancer of TAP1. (C) The migration abilities of OVCAR3 and SKOV3 were photographed (i, ii) and measured (iii) by examining the wound closure after TAP1 knockdown using wound healing assays. Original magnifications, ×100. Scale bars 150 μm. (D) Transwell assays were photographed (i) and measured (ii) to detect the migration abilities after TAP1 knockdown in SKOV3 and OVCAR3 cells. Original magnifications, ×200. Scale bars 100 μm. (E) Colony formation assays were photographed (i) and measured (ii) to detect the proliferation abilities after TAP1 knockdown in SKOV3 and OVCAR3 cells. (F) Effects of TAP1 knockdown on migration-associated protein (E-cadherin and vimentin) and transcription factor (MEF2A and LEF1) were analyzed by western blotting in SKOV3 and OVCAR3 cells (i). Error bars of histogram (ii) represented the SD of triplicate measurements. * p < 0.05; ** p < 0.01; *** p < 0.001.

Article Snippet: The membrane was incubated with the following primary antibodies TAP1 (1:3,000), MEF2A (1:2000, #12382-1-AP, Proteintech, United States), LEF1 (1:1000, #14972-1-AP, Proteintech), E-cadherin (1:10000, #20874-1-AP, Proteintech), vimentin (1:2000, #10366-1-AP, Proteintech), and beta actin (1:1000, # 20536-1-AP, Proteintech).

Techniques: Migration, Knockdown, Western Blot

Journal: Frontiers in Molecular Biosciences

Article Title: Comprehensive Analysis of the Potential Immune-Related Biomarker Transporter Associated With Antigen Processing 1 That Inhibits Metastasis and Invasion of Ovarian Cancer Cells

doi: 10.3389/fmolb.2021.763958

Figure Lengend Snippet: To establish the model of tumor metastasis, SKOV3 cells were injected into nude mice by the i.p. route and randomly treated with si-TAP1_01 or si-NC ( n = 4/group). (A) Representative images of metastatic tumors in the peritoneal cavity. Yellow arrows and rectangles highlighted visible tumor nodes and liver metastasis. (B,C) Number of metastasis and total weight of all metastases were shown (mean ± SEM). (D) Body weight growth of all mice were shown (mean ± SEM). (E) The protein expression of migration-associated protein (E-cadherin and vimentin) and transcription factor (MEF2A and LEF1) in the tumor of si-TAP1_01 group and si-NC group (i). Error bars of histogram (ii) represented the SD of quadruplicate measurements. * p < 0.05; ** p < 0.01; *** p < 0.001.

Article Snippet: The membrane was incubated with the following primary antibodies TAP1 (1:3,000), MEF2A (1:2000, #12382-1-AP, Proteintech, United States), LEF1 (1:1000, #14972-1-AP, Proteintech), E-cadherin (1:10000, #20874-1-AP, Proteintech), vimentin (1:2000, #10366-1-AP, Proteintech), and beta actin (1:1000, # 20536-1-AP, Proteintech).

Techniques: Injection, Expressing, Migration

Journal: Microbiology (Reading, England)

Article Title: Quantification of type VI secretion system activity in macrophages infected with Burkholderia cenocepacia.

doi: 10.1099/mic.0.000174

Figure Lengend Snippet: Fig. 4. Investigation of the B. cenocepacia VgrGs. (a) Measurement of T6SS activity. The infections were performed at an m.o.i. of 50 : 1 for 4 h with B. cenocepacia K56-2 DatsR and derivative vgrG mutants. The proportion of dark ‘beads on a string-like’ structures around macrophages was measured as described in Methods and in the legend of Fig. 1.The dotted line indicates the 0.2 relative unit threshold indicative of no ‘beads on a string-like’ structures. Values are means¡SD for at least 21 fields of view and are representative of three independent experiments. All the single vgrG deletion strains induced ‘beads on a string-like’ structures at a similar level to DatsR (no statistically significant differences) and significantly different levels (P,0.001) from uninfected cells. (b, c) Western blot analysis of total cell lysates (Pellet) and concentrated culture supernatants recovered from B. cenocepacia K56-2 DatsR, DatsRDhcp, vgrG mutants and the vgrG-less strain K56-2 DatsR D10vgrGs using anti-RNAP a subunit (cytosolic protein, cell lysis control) and anti-Hcp antibodies.

Article Snippet: After blocking (Roche), the membranes were incubated with the following primary antibodies as required: 4RA2 monoclonal antibody (Neoclone), which cross-reacts with the B. cenocepacia and B. multivorans RNA polymerase subunit alpha (cytosolic/cell lysis control; dilution 1 : 25 000); anti-Hcp polyclonal antiserum (dilution 1 : 1 000; ProSci) and FLAG M2 monoclonal antibody (dilution 1 : 50 000; Sigma).

Techniques: Activity Assay, Western Blot, Lysis, Control

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Ectopic germinal centers are rare in Sjogren's syndrome salivary glands and do not exclude autoreactive B cells.

doi: 10.4049/jimmunol.0803588

Figure Lengend Snippet: FIGURE 2. Microdissection of GC-like struc- tures from salivary glands and tonsils before quan- titative-RT-PCR analysis. A, Sections were stained with HistoGene to locate infiltrates, and with FITC-anti-CD19 to recognize B cells. FDCs were found in real GCs, as well as in aggregates, through their staining with CD21 and CD35. B, The levels of mRNAs for activation-induced cytidine deami- nase (AICDA) were determined by quantitative RT-PCR and normalized relative to GAPDH. All of the four real GC-containing structures expressed AID, compared with none of the seven aggregate- containing structures.

Article Snippet: In parallel, anti-CD19 mAb was combined with rabbit anti-BR3, anti-Bcl-6 (both from ProSci), or anti-IRF-4 (Abcam) Abs.

Techniques: Laser Capture Microdissection, Reverse Transcription Polymerase Chain Reaction, Staining, Activation Assay, Quantitative RT-PCR

Journal: The EMBO Journal

Article Title: A G1‐like state allows HIV ‐1 to bypass SAMHD 1 restriction in macrophages

doi: 10.15252/embj.201696025

Figure Lengend Snippet: A, B Stimulated or unstimulated MDM were stained for classical macrophage markers (CD68, CD14) and M1 and M2 macrophage markers (CD163, CD80, CD86 and CD40) and analysed by FACS.

Article Snippet: Antibodies used were as follows: anti‐cdc2 (Cell Signaling Technology, Beverly, MA, USA); anti‐CDK2 (H‐298, Santa Cruz Biotechnology); anti‐pCDK2(Thr160) (Bioss Inc., MA, USA); anti‐CDK4 (DCS156, Cell Signaling Technology); anti‐CDK6 (B‐10, Santa Cruz Biotechnology); anti‐SAMHD1 (ab67820, Abcam, UK), beta‐actin (ab6276, abcam, UK); mouse anti‐MCM2 (BM‐28, BD Biosciences, UK); and rabbit anti‐MCM2 (SP85) from Sigma; pSAMHD1 (a kind gift from M. Benkirane) and ProSci (Poway, CA, USA); anti‐Geminin (NCL‐L‐Geminin, Leica); anti‐mouse F4/80 and CD11b (kind gift from S. Yona, UCL); anti‐human CD68, CD14, CD163, CD80, CD86, CD40 (kind gift from M. Noursadeghi).

Techniques: Staining

Journal: bioRxiv

Article Title: Targeting Langerhans cells using a modular mannosylated nucleic acid-based vaccine platform

doi: 10.1101/2025.06.04.657560

Figure Lengend Snippet: Delivery of gp100 on mannosylated HJ scaffolds into moLCs for antigen presentation. A ) Reaction scheme for gp100-functionalization of Q2 and Q4 with NHS-DBCO ( 1 ), followed by SPAAC reaction to azide-modified ( pink ) Val-Cit-PAB-linked ( yellow) gp100 ( red ) ( 2 ). B ) Schematic representation of gp100-conjugated HJs employed for antigen presentation. C ) Visual representation of the antigen-presentation assay using moLCs incubated with gp100-conjugated HJs to facilitate receptor-mediated endocytosis ( I ), followed by release of gp100 in the lysosomes ( II ) and presentation of gp100 on HLA-A2 ( III ). Subsequently, moLCs were co-cultured with wildtype- or gp100 Jurkat cells to verify antigen presentation by T cell activation. D ) IL-2 concentration (pg/mL) in the co-culture media by ELISA. Results shown from four independent human donors were expressed by the mean ± SD. Statistical analysis was conducted by a one-way ANOVA followed by a Tukey’s post hoc test. E ) Antigen-presentation assay comparing HJ-3xTriMan-1xgp100 assembled with either a cleavable linker ( Val-Cit ) or a non-cleavable linker. Results shown from three independent human donors were expressed by the mean ± SD. Statistical analysis was conducted by a two-way t test. p-value * = <0.05, ** = <0.01, *** = <0.001, ****= <0.0001.

Article Snippet: Antigenic peptide gp100 154-162 (sequence: KTWGQYWQV, specificity: HLA-A*02:01, GENAXXON bioscience) was conjugated to the oligonucleotide strands in a 2-step one-pot reaction.

Techniques: Immunopeptidomics, Modification, Incubation, Cell Culture, Activation Assay, Concentration Assay, Co-Culture Assay, Enzyme-linked Immunosorbent Assay