Journal: iScience

Article Title: Single-cell transcriptomics reveals the role of antigen presentation in liver metastatic breast cancer

doi: 10.1016/j.isci.2024.108896

Figure Lengend Snippet: Overview of using scRNA technology to study cancer liver metastasis

Article Snippet: The sections were stained for three panels by using 4-color Novo-Light multiplex fluorescence immunohistochemistry: panel 1 including Rabbit anti-FCN3 (C-term) Polyclonal Antibody (abs101543, Absin), Rabbit anti-C1QC Polyclonal Antibody (A9227, Abclonal) and Mouse anti-HLA-E Monoclonal Antibody (abs154728, Absin); panel 2 including Rabbit anti-XCR1 (D2F8T) Monoclonal Antibody (44665S, CST), Mouse anti-HLA-E Monoclonal Antibody (abs154728, Absin), Rabbit anti-HLA-DQA1 Polyclonal Antibody (16918-1-AP, Proteintech) and Rabbit anti-HLA-DPA1 Polyclonal Antibody (16109-1-AP, Proteintech); panel 3 including Rabbit anti-LAMP3 Polyclonal Antibody (A2895, Abclonal) and Mouse anti-HLA-E Monoclonal Antibody (abs154728, Absin).

Techniques: Sequencing, RNA Sequencing, Migration

Journal: iScience

Article Title: Single-cell transcriptomics reveals the role of antigen presentation in liver metastatic breast cancer

doi: 10.1016/j.isci.2024.108896

Figure Lengend Snippet: Clinical verification of alteration and function of FCN3 + macrophage, cDC1 and LAMP3 + DC in LM (A) Ratio of FCN3 + C1QC + HLA-E + cells, XCR1 + HLA-E + cells, XCR1 + HLA-DQA1 + cells, XCR1 + HLA-DPA1 + cells and LAMP3 + HLA-E + cells in normal mammary ducts or lobules, primary tumor of invasive ductal breast carcinoma (above phase 3C, staged by AJCC 6 th Edition) and liver metastasis. (B) Representative immunofluorescence appearance of FCN3 + C1QC + HLA-E + cells, XCR1 + HLA-E + cells, XCR1 + HLA-DQA1 + cells, XCR1 + HLA-DPA1 + cells and LAMP3 + HLA-E + cells (above phase 3c, staged by AJCC 6 th Edition). Panel 1 (left): blue for DAPI, green for FCN3, purple for C1QC and red for HLA-E; panel 2 (middle): blue for DAPI, green for XCR1, red for HLA-E, purple for HLA-DQA1 and yellow for HLA-DPA1; panel 3 (right): blue for DAPI, green for LAMP3 and red for HLA-E. Scale bar: 20 μm. (C) Analysis of OS between patients with high and low levels of MHC signature score filtered by top and bottom 25% values of XCR1 and LAMP3 from the TCGA-BRCA cohort. (D) Analysis of OS between patients with high and low levels of MHC signature score filtered by top and bottom 25% values of LAMP3 from the TCGA-LIHC cohort. In bar plots, Student’s t test was performed. p < 0.05∗, p < 0.01∗∗, p < 0.001∗∗∗, p < 0.0001∗∗∗∗. In survival analysis, Log rank was used to calculate the p value, p < 0.05 was considered to be significant.

Article Snippet: The sections were stained for three panels by using 4-color Novo-Light multiplex fluorescence immunohistochemistry: panel 1 including Rabbit anti-FCN3 (C-term) Polyclonal Antibody (abs101543, Absin), Rabbit anti-C1QC Polyclonal Antibody (A9227, Abclonal) and Mouse anti-HLA-E Monoclonal Antibody (abs154728, Absin); panel 2 including Rabbit anti-XCR1 (D2F8T) Monoclonal Antibody (44665S, CST), Mouse anti-HLA-E Monoclonal Antibody (abs154728, Absin), Rabbit anti-HLA-DQA1 Polyclonal Antibody (16918-1-AP, Proteintech) and Rabbit anti-HLA-DPA1 Polyclonal Antibody (16109-1-AP, Proteintech); panel 3 including Rabbit anti-LAMP3 Polyclonal Antibody (A2895, Abclonal) and Mouse anti-HLA-E Monoclonal Antibody (abs154728, Absin).

Techniques: Immunofluorescence

Journal: iScience

Article Title: Single-cell transcriptomics reveals the role of antigen presentation in liver metastatic breast cancer

doi: 10.1016/j.isci.2024.108896

Figure Lengend Snippet:

Article Snippet: The sections were stained for three panels by using 4-color Novo-Light multiplex fluorescence immunohistochemistry: panel 1 including Rabbit anti-FCN3 (C-term) Polyclonal Antibody (abs101543, Absin), Rabbit anti-C1QC Polyclonal Antibody (A9227, Abclonal) and Mouse anti-HLA-E Monoclonal Antibody (abs154728, Absin); panel 2 including Rabbit anti-XCR1 (D2F8T) Monoclonal Antibody (44665S, CST), Mouse anti-HLA-E Monoclonal Antibody (abs154728, Absin), Rabbit anti-HLA-DQA1 Polyclonal Antibody (16918-1-AP, Proteintech) and Rabbit anti-HLA-DPA1 Polyclonal Antibody (16109-1-AP, Proteintech); panel 3 including Rabbit anti-LAMP3 Polyclonal Antibody (A2895, Abclonal) and Mouse anti-HLA-E Monoclonal Antibody (abs154728, Absin).

Techniques: Recombinant, Lysis, Staining, Software

Journal: Journal of the American Society of Nephrology

Article Title: Contribution of Prolonged Ischemia and Donor Age to Chronic Renal Allograft Dysfunction

doi: 10.1681/asn.v1171317

Figure Lengend Snippet: Figure 6. Cellular infiltrates (ED11 monocytes/macrophages, CD51 T cells and their subsets CD41 and CD81 T cells, and MHC II expression) were quantified as cells/field of view or on a 0 to 41 scale in allografts from 3- (ATx 3), 12- (ATx 12), and 18- (ATx 18) mo-old donor animals with ischemic times of 5, 60, and 120 min (ATx 3.5, x.60, and x.120, etc.). Cellular infiltrates increased in parallel with donor age and prolongation of ischemia; MHC II was expressed moderately in all experimental groups.

Article Snippet: Portions of representative kidneys in experimental and control grafts were examined at the end of the observation period, snap-frozen in liquid nitrogen, cut (4 mm), fixed in acetone for 10 min, air-dried, and stained with mouse monoclonal antibodies (mAb) to CD51 T cells (OX-19), CD41 T helper cells (W3/25), CD81 T cytotoxic/ suppressor cells (OX-8), monocytes/macrophages (ED1), and MHC class II (OX3; all mAb from Serotec, Wiesbaden, Germany).

Techniques: Expressing

Journal: PLoS Genetics

Article Title: Natural Polymorphisms in Tap2 Influence Negative Selection and CD4∶CD8 Lineage Commitment in the Rat

doi: 10.1371/journal.pgen.1004151

Figure Lengend Snippet: (A) Genome scans of the CD4∶CD8 ratio (green), and the surface expression of MHC class I (MHC-I, red) and MHC class II (MHC-II, blue). The vertical axis shows the negative log P value for the 20 autosomes. Note that the left and right axis show −log P values for different phenotypes. Q1–Q10 indicate significant QTLs. (B) Close-up for Q8–Q10 on chromosome 20 showing the approximate location of the MHC region. (C) Position (in megabases, Mb) of peak marker (Pos.), confidence intervals (CI) in Mb, and effect sizes (%) of the peak markers in the QTLs shown in (A). The RMIP value is a measure of the probability that the loci are correctly identified (max = 1.0).

Article Snippet: The following Alexa Fluor 488, FITC, PE, Pe-Cy5, PerCP-Cy5.5, APC, APC-Cy7, Pe-Cy7, Alexa Fluor 648 and biotin conjugated antibodies were used: CD4 (OX35), CD8a (OX8), CD8b (341), CD45RA (OX22), anti-granulcoytes (His48), RT1-B (OX6), RT1-D (OX17), MHC class I (OX18) were purchased from BD Pharmingen (CA, USA); CD45 (OX1), CD45RA (OX33), CD90 (OX7), CD4 (W3/25), CD11b/c (OX42), CD103 (OX62) and αβ-TCR (R73) were purchased from BioLegend (CA, USA); CD68 (ED1) and RT1-A (F16-4-4, conjugated in-house with Alexa Fluor 647 using the APEX labeling kit, Invitrogen) were obtained from AbD Serotec (Düsseldorf, Germany).

Techniques: Expressing, Marker

Journal: PLoS Genetics

Article Title: Natural Polymorphisms in Tap2 Influence Negative Selection and CD4∶CD8 Lineage Commitment in the Rat

doi: 10.1371/journal.pgen.1004151

Figure Lengend Snippet: CD4∶CD8 T cell ratio and extracellular MHC class I and II expression in spleens of congenic and recombinant strains.

Article Snippet: The following Alexa Fluor 488, FITC, PE, Pe-Cy5, PerCP-Cy5.5, APC, APC-Cy7, Pe-Cy7, Alexa Fluor 648 and biotin conjugated antibodies were used: CD4 (OX35), CD8a (OX8), CD8b (341), CD45RA (OX22), anti-granulcoytes (His48), RT1-B (OX6), RT1-D (OX17), MHC class I (OX18) were purchased from BD Pharmingen (CA, USA); CD45 (OX1), CD45RA (OX33), CD90 (OX7), CD4 (W3/25), CD11b/c (OX42), CD103 (OX62) and αβ-TCR (R73) were purchased from BioLegend (CA, USA); CD68 (ED1) and RT1-A (F16-4-4, conjugated in-house with Alexa Fluor 647 using the APEX labeling kit, Invitrogen) were obtained from AbD Serotec (Düsseldorf, Germany).

Techniques: Expressing, Recombinant

Journal: PLoS Genetics

Article Title: Natural Polymorphisms in Tap2 Influence Negative Selection and CD4∶CD8 Lineage Commitment in the Rat

doi: 10.1371/journal.pgen.1004151

Figure Lengend Snippet: The map was constructed according to the NCBI build 3.4 genome assembly. Genes (left) are depicted according to scale (positions in Mb), except for positions indicated with crotchets. The gross organization of MHC-Ia, II, III and Ib -regions are adopted from Hurt et al. . Recombinant congenic strains are shown as gray vertical bars with dashed lines representing congenic borders (intervals of unknown genotype). Markers, short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), are shown in italic numbers. Numbers with asterisks at the top and bottom of the figure represent the position of the closest negative (DA) marker. Genes in Tcs1 are red and in Tcs2 blue (see box for definitions). Inset shows the organization of the human (HLA) and rat (RT1) MHC regions. Non-recombinant congenic strains, which have fragments spanning the entire MHC region, are not shown. xMHC-II, extended MHC class II region; xMHC-I, extended MHC class I region.

Article Snippet: The following Alexa Fluor 488, FITC, PE, Pe-Cy5, PerCP-Cy5.5, APC, APC-Cy7, Pe-Cy7, Alexa Fluor 648 and biotin conjugated antibodies were used: CD4 (OX35), CD8a (OX8), CD8b (341), CD45RA (OX22), anti-granulcoytes (His48), RT1-B (OX6), RT1-D (OX17), MHC class I (OX18) were purchased from BD Pharmingen (CA, USA); CD45 (OX1), CD45RA (OX33), CD90 (OX7), CD4 (W3/25), CD11b/c (OX42), CD103 (OX62) and αβ-TCR (R73) were purchased from BioLegend (CA, USA); CD68 (ED1) and RT1-A (F16-4-4, conjugated in-house with Alexa Fluor 647 using the APEX labeling kit, Invitrogen) were obtained from AbD Serotec (Düsseldorf, Germany).

Techniques: Construct, Recombinant, Marker

Journal: PLoS Genetics

Article Title: Natural Polymorphisms in Tap2 Influence Negative Selection and CD4∶CD8 Lineage Commitment in the Rat

doi: 10.1371/journal.pgen.1004151

Figure Lengend Snippet: Nonsynonymous- and structural variants in Tcs2 were determined by Sanger sequencing of DA.1F (f), DA (a), DA.1I (i), DA.1U (u) and DA.1H (h) (see also ). Amino acid substitutions are indicated in standard single letter codes and insertions/deletions as DEL. Gene annotations are from UniProt; protein domains depicted in DOb are derived from the human homolog. Letters in boxes depict residues with background allele (DA) with numbers above indicating amino acid positions in the translated cds. On top is a schematic illustration of the genes in the region according to the 3.4 genome assembly (genes outside the QTL are shown in gray). Annotations used: TM, transmembrane domain; CD, cytoplasmic domain; CP, connecting peptide; β1, beta 1 domain; β2, beta 2 domain; α1, alpha 1 domain; α2, alpha 2 domain. *Residues associated with class-I modification (cim).

Article Snippet: The following Alexa Fluor 488, FITC, PE, Pe-Cy5, PerCP-Cy5.5, APC, APC-Cy7, Pe-Cy7, Alexa Fluor 648 and biotin conjugated antibodies were used: CD4 (OX35), CD8a (OX8), CD8b (341), CD45RA (OX22), anti-granulcoytes (His48), RT1-B (OX6), RT1-D (OX17), MHC class I (OX18) were purchased from BD Pharmingen (CA, USA); CD45 (OX1), CD45RA (OX33), CD90 (OX7), CD4 (W3/25), CD11b/c (OX42), CD103 (OX62) and αβ-TCR (R73) were purchased from BioLegend (CA, USA); CD68 (ED1) and RT1-A (F16-4-4, conjugated in-house with Alexa Fluor 647 using the APEX labeling kit, Invitrogen) were obtained from AbD Serotec (Düsseldorf, Germany).

Techniques: Sequencing, Derivative Assay, Modification

Journal: PLoS Genetics

Article Title: Natural Polymorphisms in Tap2 Influence Negative Selection and CD4∶CD8 Lineage Commitment in the Rat

doi: 10.1371/journal.pgen.1004151

Figure Lengend Snippet: MHC class I proteins expressed in splenocytes from DA and Tcs1 -congenic strains.

Article Snippet: The following Alexa Fluor 488, FITC, PE, Pe-Cy5, PerCP-Cy5.5, APC, APC-Cy7, Pe-Cy7, Alexa Fluor 648 and biotin conjugated antibodies were used: CD4 (OX35), CD8a (OX8), CD8b (341), CD45RA (OX22), anti-granulcoytes (His48), RT1-B (OX6), RT1-D (OX17), MHC class I (OX18) were purchased from BD Pharmingen (CA, USA); CD45 (OX1), CD45RA (OX33), CD90 (OX7), CD4 (W3/25), CD11b/c (OX42), CD103 (OX62) and αβ-TCR (R73) were purchased from BioLegend (CA, USA); CD68 (ED1) and RT1-A (F16-4-4, conjugated in-house with Alexa Fluor 647 using the APEX labeling kit, Invitrogen) were obtained from AbD Serotec (Düsseldorf, Germany).

Techniques:

Journal: PLoS Genetics

Article Title: Natural Polymorphisms in Tap2 Influence Negative Selection and CD4∶CD8 Lineage Commitment in the Rat

doi: 10.1371/journal.pgen.1004151

Figure Lengend Snippet: (A) CD68+ cells were stained on the cell surface with OX18 (anti-class Ia and Ib). Histograms show representative samples from DA, DA.1H and DA.1H derived strains with different alleles of RT1-A and Tap2 as stated on top. Data from all individuals are shown in scatterplot (far right); * significant compared to DA.1H (1H); ** significant compared to DA. (B) CD68+ cells stained with a class Ia specific antibody (F16-4-4). (C) T cells from animals shown in (A) stained intracellularly with OX18 (scatterplot) and F16-4-4 (histogram). (D–E) Subsets of leukocytes from DA and DA.1IR85 spleen stained extracellularly (D) and intracellularly (E) with OX18. Data are representative of 6 individuals per group. (F) Surface expression of MHC class I (OX18) on CD68+ cells from DA and DA.1U congenic strains. (G) CD68+ cells (same as in F) stained with F16-4-4. Vertical lines in scatterplots show mean values. Representative results of at least two independent experiments are shown.

Article Snippet: The following Alexa Fluor 488, FITC, PE, Pe-Cy5, PerCP-Cy5.5, APC, APC-Cy7, Pe-Cy7, Alexa Fluor 648 and biotin conjugated antibodies were used: CD4 (OX35), CD8a (OX8), CD8b (341), CD45RA (OX22), anti-granulcoytes (His48), RT1-B (OX6), RT1-D (OX17), MHC class I (OX18) were purchased from BD Pharmingen (CA, USA); CD45 (OX1), CD45RA (OX33), CD90 (OX7), CD4 (W3/25), CD11b/c (OX42), CD103 (OX62) and αβ-TCR (R73) were purchased from BioLegend (CA, USA); CD68 (ED1) and RT1-A (F16-4-4, conjugated in-house with Alexa Fluor 647 using the APEX labeling kit, Invitrogen) were obtained from AbD Serotec (Düsseldorf, Germany).

Techniques: Staining, Derivative Assay, Expressing

Journal: PLoS Genetics

Article Title: Natural Polymorphisms in Tap2 Influence Negative Selection and CD4∶CD8 Lineage Commitment in the Rat

doi: 10.1371/journal.pgen.1004151

Figure Lengend Snippet: (A) Thymic conventional DCs (CD103+, CD11b/c+) stained extracellularly for class I (OX18). Scatterplots show results from two different experiments with Tcs1 and Tcs2 -congenic strains. The variation between the strains is comparable to data shown in for CD68+ cells. (B–C) Splenic DCs (CD103+, CD68+, CD11b/c+) (B) and thymic DCs (C) stained extracellularly for RT1-D (OX17) and RT1-B (OX6). Histograms show representative samples from DA (solid lines) and DA.1HR10 (dashed lines).

Article Snippet: The following Alexa Fluor 488, FITC, PE, Pe-Cy5, PerCP-Cy5.5, APC, APC-Cy7, Pe-Cy7, Alexa Fluor 648 and biotin conjugated antibodies were used: CD4 (OX35), CD8a (OX8), CD8b (341), CD45RA (OX22), anti-granulcoytes (His48), RT1-B (OX6), RT1-D (OX17), MHC class I (OX18) were purchased from BD Pharmingen (CA, USA); CD45 (OX1), CD45RA (OX33), CD90 (OX7), CD4 (W3/25), CD11b/c (OX42), CD103 (OX62) and αβ-TCR (R73) were purchased from BioLegend (CA, USA); CD68 (ED1) and RT1-A (F16-4-4, conjugated in-house with Alexa Fluor 647 using the APEX labeling kit, Invitrogen) were obtained from AbD Serotec (Düsseldorf, Germany).

Techniques: Staining

Journal: PLoS Genetics

Article Title: Natural Polymorphisms in Tap2 Influence Negative Selection and CD4∶CD8 Lineage Commitment in the Rat

doi: 10.1371/journal.pgen.1004151

Figure Lengend Snippet: (A) The QTLs in Tcs1 and Tcs2 did not affect the total number of double negative cells (DN; CD4−, CD8b−). B cells (CD45RA+) were excluded from the DN gate. (B) DN cell maturation is defined by CD45RC and CD2 (see ). DN cells in DA.1FR9 showed a lower frequency of early thymic precursors (ETP) compared to DA. Counter plot shows gating strategy with numbers indicating percent (%) of parent population (stated above plot). (C) Counter plot shows CD45RC−, CD2 hi DN cells from DA.1UR83, and scatter plots the frequency of TCRβ− and TCRβ+ (DN4 in mouse) cells in DA and DA.1UR83. (D) Thymi from Tcs2 -congenic strains with TAP-B (HR10 and UR10) contained fewer double positive (DP) cells but more cells (in %) with high TCR expression. (E) TAP-B strains (HR10 and UR10) showed higher frequencies (histograms) and total numbers (scatter plots) of CD8 single positive (SP) cells with high TCR expression. Numbers (%) in histograms represent mean-values ±SD of cells with high TCR expression (gated, n = 5). (F) Frequencies (histograms; n = 5) and total numbers (scatter plot) of CD8SP cells with high TCR expression in DA.1H (RT1-A h , TAP-B) and in strains with low levels of surface MHC class I (HR83 [RT1-A h , TAP-A] and IR85 [RT1-A n , TAP-A]). (G) Virtually all CD4SP cells express high levels of TCR. Histogram shows expression of TCR on CD4SP thymocytes in DA ( n = 5). Scatterplot shows total number of CD4SP cells per thymus in Tcs2 -congenic strains.

Article Snippet: The following Alexa Fluor 488, FITC, PE, Pe-Cy5, PerCP-Cy5.5, APC, APC-Cy7, Pe-Cy7, Alexa Fluor 648 and biotin conjugated antibodies were used: CD4 (OX35), CD8a (OX8), CD8b (341), CD45RA (OX22), anti-granulcoytes (His48), RT1-B (OX6), RT1-D (OX17), MHC class I (OX18) were purchased from BD Pharmingen (CA, USA); CD45 (OX1), CD45RA (OX33), CD90 (OX7), CD4 (W3/25), CD11b/c (OX42), CD103 (OX62) and αβ-TCR (R73) were purchased from BioLegend (CA, USA); CD68 (ED1) and RT1-A (F16-4-4, conjugated in-house with Alexa Fluor 647 using the APEX labeling kit, Invitrogen) were obtained from AbD Serotec (Düsseldorf, Germany).

Techniques: Expressing