easysep immunomagnetic cd19 positive selection kit  (STEMCELL Technologies Inc)

Journal: bioRxiv

Article Title: IFI16/AIM2 inflammasomes control Gal-9 and PVR in myeloid cells from PWH and their targeting improves immunotherapy against HIV-1

doi: 10.64898/2026.01.26.701473

Figure Lengend Snippet: (A): ELISA analysis of plasma concentration of IL-1β, comparing PWH with normal CD4/CD8 T cell ratio (defined as ≥1) and low CD4/CD8 T cell ratio (defined as < 0.8). Statistical significance was calculated using two-tailed Wilcoxon test. (B): Spearman correlation between plasma concentrations of soluble CD14 (ssCD14) and IL-1β. P and R values are shown (C): Expression of Gal-9 (Gal9; higher plot) or PVRhi (lower plot) in activated CD40hi in Mo from HIV- 1-negative controls, and PWH with low CD4/CD8 T cell ratio or normal CD4/CD8 T cell ratio after 16-hour stimulation with PAMPs mimicking bacterial translocation (LPS, red; Flagellin, Flag, purple) or viral replication (CL097, ssRNA, orange; Poly I:C, dsRNA, blue). Statistical significance was calculated using Kruskal-Wallis test for comparison of stimulation with the same PAMP between groups (*p<0.05; **p<0.01), and One-Way ANOVA Friedman test with Dunn’s multiple comparison test for comparison within the same group (*p<0.05; **p<0.01; ***p<0.001; ****p<0.0001).

Article Snippet: Mo were isolated from PBMC from our study cohort by the human CD14 MicroBeads kit positive immunomagnetic selection using MS Columns (Miltenyi Biotec).

Techniques: Enzyme-linked Immunosorbent Assay, Clinical Proteomics, Concentration Assay, Two Tailed Test, Expressing, Translocation Assay, Comparison

Journal: bioRxiv

Article Title: IFI16/AIM2 inflammasomes control Gal-9 and PVR in myeloid cells from PWH and their targeting improves immunotherapy against HIV-1

doi: 10.64898/2026.01.26.701473

Figure Lengend Snippet: (A-B): Histological analysis of IFI-16 (A) or AIM2 (B) (green) and Caspase-1 (red) expression and DAPI (blue) in the spleen from a viremic HIV-1 infected humanized BLT mouse. Quantifications of cells positive cells for each inflammasome sensor alone (top plots), co-expressing Caspase 1 (CASP1) (middle plots) or both Caspase 1 and CD14 (bottom plots) are shown on the right. (C): Histological analysis of Gal-9 (Gal9; green), CD14 (white) and Caspase-1 (Casp1, red) expression and DAPI (blue) in the spleen from a viremic HIV-1 infected humanized BLT mouse. Zoomed area demonstrating co-expression between Gal9, CD14 and Caspase-1 are shown on the right. Arrows highlight cells co-expressing the mentioned markers

Article Snippet: Mo were isolated from PBMC from our study cohort by the human CD14 MicroBeads kit positive immunomagnetic selection using MS Columns (Miltenyi Biotec).

Techniques: Expressing, Infection

Journal: bioRxiv

Article Title: Tumor-infiltrating CD27 - IgD - regulatory B cells suppress cytotoxic CD8 + T cell responses in renal cell carcinoma

doi: 10.1101/2025.07.08.663720

Figure Lengend Snippet: (A) Representative contour plots and cumulative data showing the frequencies of CD19 + CD27 - IgD - (double negative (DN)), CD19 + CD27 + IgD - , CD19 + CD27 + IgD + (unswitched memory (USM)) and CD19 + CD27 - IgD + (naive) B cells ex vivo in paired BK and matching tumor tissue; ** p <0.01, *** p <0.001. n= 32 biologically independent samples. DN, USM, and naive B cells analyzed by paired two-tailed Student’s t -test, CD19 + CD27 + IgD - B cells analyzed by paired two-tailed Wilcoxon test. Error bars represented as mean±SEM. (B) Representative contour plots and cumulative data showing the frequencies of CD19 + CD24 lo/- CD38 hi (plasma cells (PCs)) and BLIMP-1 + B cells ex vivo in paired BK and matching tumor tissue. BLIMP-1 expression overlaid onto the B cell contour plot; ** p <0.01, **** p <0.0001. For plasma cells n =31 and for BLIMP-1 + B cells n =15 biologically independent samples. Paired two-tailed Wilcoxon test. Error bars represented as mean±SEM. (C) Representative contour plots and cumulative data showing the frequencies of CD19 + CD27 + IgD - CD24 + CD38 - IgM + (IgM + memory) and CD19 + CD27 + IgD - CD24 + CD38 - IgM - (class-switched memory (CSM)) B cells ex vivo in paired BK and tumor; *** p <0.001. n= 32 biologically independent samples. CSM analyzed by paired two-tailed Student’s t -test, IgM + memory analyzed by paired two-tailed Wilcoxon test. Error bars represented as mean±SEM. (D) Representative contour plots and cumulative data showing the frequencies of CD19 + CD27 - IgD + CD24 int CD38 int (mature) and CD19 + CD27 - IgD + CD24 hi CD38 hi transitional B cells ex vivo in paired BK and tumor. n= 32 biologically independent samples. Paired two-tailed Wilcoxon test. Error bars represented as mean±SEM. (E) Representative contour plots and cumulative data showing the frequencies of CD19 + CD27 - IgD - CD21 + CD11c - (DN1), CD19 + CD27 - IgD - CD21 - CD11c + (DN2), CD19 + CD27 - IgD - CD21 - CD11c - (DN3), and CD19 + CD27 - IgD - CD21 + CD11c + (DN4) B cells ex vivo in BK and tumor; ** p <0.01. n= 18 biologically independent samples. Paired two-tailed Student’s t -test. Error bars represented as mean±SEM. (F) Cumulative data showing the frequencies of CD19 + CD27 - IgD + (naive), CD19 + CD27 + IgD - , CD19 + CD27 - IgD - CD21 + CD11c - (DN1), CD19 + CD27 - IgD - CD21 - CD11c - (DN3) B cells, and CD19 + CD24 lo/- CD38 hi (plasma cells (PCs)) stratified according to intermediate (3-5) or high (>6) Leibovich scores; * p <0.05, ** p <0.01. For naive, CD27 + IgD - , and plasma cells n= 26, for DN1 and DN3 n= 13 biologically independent samples. Naive, DN1, DN3, and PC analyzed by unpaired two-tailed Student’s t -test, CD27 + IgD - analyzed by unpaired Mann-Whitney U test. Error bars represented as mean±SEM.

Article Snippet: Tissue-resident B cells were isolated using the EasySep immunomagnetic CD19 positive selection kit (STEMCELL, cat. no. 17854).

Techniques: Ex Vivo, Two Tailed Test, Clinical Proteomics, Expressing, MANN-WHITNEY

Journal: bioRxiv

Article Title: Tumor-infiltrating CD27 - IgD - regulatory B cells suppress cytotoxic CD8 + T cell responses in renal cell carcinoma

doi: 10.1101/2025.07.08.663720

Figure Lengend Snippet: (A) Density UMAPs showing the distribution of IL10 hi , TGFB hi , TXN hi , AHR hi , HAVCR2 hi , TIGIT hi , CD274 hi and PDCD1 hi RCC-resident B cells. (B) Dotplot showing the proportion of cells expressing a Breg score comprising IL10, CD274, AHR, TXN, LAG3, TIGIT, CTLA4, CD86, TGFB1, and GZMB (dot size), and their average expression levels (color intensity) in the tumor, tumor margin, BK, and blood. (C) Spatial analysis of segmented CD20 + Bregs in a representative TLS. Staining of DAPI (dark blue) overlaid with cell segmentation (gating strategy shown in Figure S5A) of CD20 + IL-10 + Bregs (red), CD20 + TGFβ + Bregs (green), and CD20 + IL-10 + TGFβ + Bregs (orange). Scale bar = 100µm. (D) Cumulative data showing the frequencies of CD20 + IL-10 + Bregs, CD20 + TGFβ + Bregs, CD20 + IL-10 + TGFβ + within ROIs; * p <0.05, ** p <0.01. 13 ROIs across n =3 biologically independent samples. One-way ANOVA with Tukey’s test for multiple comparisons. Error bars represented as mean±SEM. (E) Spatial analysis of segmented CD138 + Bregs in a representative TLS. Staining of DAPI (dark blue) overlaid with cell segmentation (gating strategy shown in Figure S5A) of CD138 + IL-10 + Bregs (pink), CD138 + TGFβ + Bregs (dark green), and CD138 + IL-10 + TGFβ + Bregs (yellow) within TLSs. (F) Cumulative data showing the frequencies of CD138 + IL-10 + Bregs, CD20 + CD138 + TGFβ + Bregs, CD138 + IL-10 + TGFβ + Bregs within ROIs; * p <0.05, ** p <0.01. 13 ROIs across n =3 biologically independent samples. One-way ANOVA with Tukey’s test for multiple comparisons. Error bars represented as mean±SEM. (G) Cumulative data showing the frequencies of CD20 + CD27 - IgD + (naive), CD20 + CD27 + IgD + (unswitched memory (USM)), CD20 + CD27 + IgD - B cells, CD20 + CD27 - IgD - CD21 + CD11c - (DN1), CD20 + CD27 - IgD - CD21 - CD11c + (DN2), CD20 + CD27 - IgD - CD21 - CD11c - (DN3), and CD20 + CD27 - IgD - CD21 + CD11c + (DN4) within CD20 + IL-10 + Bregs; * p <0.05, ** p <0.01, *** p <0.001, **** p <0.0001. 13 ROIs across n =3 biologically independent samples. Fridman test with Dunn’s test for multiple comparisons. Error bars represented as mean±SEM. (H) Cumulative data showing the frequencies of CD20 + CD27 - IgD + (naive), CD20 + CD27 + IgD + (unswitched memory (USM)), CD20 + CD27 - IgD - (double negative (DN)), CD20 + CD27 + IgD - B cells, CD20 + CD27 - IgD - CD21 + CD11c - (DN1), CD20 + CD27 - IgD - CD21 - CD11c + (DN2), CD20 + CD27 - IgD - CD21 - CD11c - (DN3), and CD20 + CD27 - IgD - CD21 + CD11c + (DN4) B cells within CD20 + TGFβ + Bregs; * p <0.05, ** p <0.01. 13 ROIs across n =3 biologically independent samples. Fridman test with Dunn’s test for multiple comparisons. Error bars represented as mean±SEM. (I) Prognostic association of high versus low CD19, IL-10, TGFB1 signature with survival in RCC using The Cancer Genome Atlas (TCGA) data. p values were derived by Cox proportional hazard model adjusting for signature group, age, sex, and American Joint Committee on Cancer (AJCC) stage.

Article Snippet: Tissue-resident B cells were isolated using the EasySep immunomagnetic CD19 positive selection kit (STEMCELL, cat. no. 17854).

Techniques: Expressing, Staining, Derivative Assay

Journal: bioRxiv

Article Title: Tumor-infiltrating CD27 - IgD - regulatory B cells suppress cytotoxic CD8 + T cell responses in renal cell carcinoma

doi: 10.1101/2025.07.08.663720

Figure Lengend Snippet: (A) Radar plot showing the Human Molecular Signatures Database and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched in each tumor-infiltrating B cell (TIB) cluster. (B) Density UMAPs showing the distribution of TLR7 hi , TLR9 hi , MYD88 hi , IRAK1 hi , IRAK4 hi , TRAF6 hi , MAP3K7 hi , and NFKB1 hi RCC-resident B cells. (C) Representative contour plots and cumulative data showing IL-10 expression by tumor-infiltrating CD19 + B cells ex vivo (white) and following 72h stimulation with R848 (light grey) or CpGC (dark grey); ** p <0.01, *** p <0.001. For ex vivo n =16, R848 and CpGC n =22 biologically independent samples. Mixed-effects one-way ANOVA with Dunnett’s test for multiple comparisons. Error bars represented as mean±SEM. (D) Representative contour plots and cumulative data showing TGFβ expression by tumor-infiltrating CD19 + B cells ex vivo (white) and following 72h stimulation with R848 (light grey) or CpGC (dark grey); * p <0.05, ** p <0.01. For ex vivo n =13, R848 and CpGC n =10 biologically independent samples. One-way Fridman test with Dunn’s test for multiple comparisons. Error bars represented as mean±SEM. (E) Representative contour plots and cumulative data showing the frequencies of CD19 + CD27 - IgD + (naive), CD19 + CD27 + IgD + (unswitched memory (USM)), CD19 + CD27 + IgD - , and CD19 + CD27 - IgD - (double negative (DN)) B cells within tumor-infiltrating CD19 + IL-10 + B cells, ex vivo and following 72h stimulation with R848 or CpGC; * p <0.05, ** p <0.01, **** p <0.0001. n =24 biologically independent samples. Two-way ANOVA with Tukey’s test for multiple comparisons. Error bars represented as mean±SEM. (F) Representative contour plots and cumulative data showing the frequencies of CD19 + CD27 - IgD - CD21 + CD11c - (DN1), CD19 + CD27 - IgD - CD21 - CD11c + (DN2), CD19 + CD27 - IgD - CD21 - CD11c - (DN3) and CD19 + CD27 - IgD - CD21 + CD11c + (DN4) B cells within tumor-infiltrating CD19 + IL-10 + B cells, ex vivo and following 72h stimulation with R848 or CpGC; * p <0.05, *** p <0.001, **** p <0.0001. n =18 biologically independent samples. Two-way ANOVA with Tukey’s test for multiple comparisons. Error bars represented as mean±SEM. (G) Representative contour plots and cumulative data showing the frequencies of CD19 + CD27 - IgD + (naive), CD19 + CD27 + IgD + (unswitched memory (USM)), CD19 + CD27 + IgD - , and CD19 + CD27 - IgD - (double negative (DN)) B cells within tumor-infiltrating CD19 + TGFβ + B cells, ex vivo and following 72h stimulation with R848 or CpGC; ** p <0.01, **** p <0.0001. n =12 biologically independent samples. Two-way ANOVA with Tukey’s test for multiple comparisons. Error bars represented as mean±SEM. (H) Representative contour plots and cumulative data showing the frequencies of CD19 + CD27 - IgD - CD21 + CD11c - (DN1), CD19 + CD27 - IgD - CD21 - CD11c + (DN2), CD19 + CD27 - IgD - CD21 - CD11c - (DN3) and CD19 + CD27 - IgD - CD21 + CD11c + (DN4) B cells within tumor-infiltrating CD19 + TGFβ + B cells, ex vivo and following 72h stimulation with R848 or CpGC; *** p <0.001, **** p <0.0001. n =11 biologically independent samples. Two-way ANOVA with Tukey’s test for multiple comparisons. Error bars represented as mean±SEM.

Article Snippet: Tissue-resident B cells were isolated using the EasySep immunomagnetic CD19 positive selection kit (STEMCELL, cat. no. 17854).

Techniques: Expressing, Ex Vivo

Journal: bioRxiv

Article Title: Human memory CD4 + T-cells recognize Mycobacterium tuberculosis -infected macrophages amid broader pathogen-specific responses

doi: 10.1101/2025.02.23.639515

Figure Lengend Snippet: (A) Schematic of experimental workflow to co-culture infected macrophages with autologous memory CD4 + T cells for flow cytometry or sorting. Created in BioRender. Carpenter, S. (2025). (B) Representative flow plots comparing activation marker co-expression of CD69 with CD40L (top row) or IFNγ (bottom row), gated on CD45RA Lo CD4 + T cells after 16-18 h co-culture with Mtb infected macrophages ± treatment with MTB300 or lysate, and (C) in the presence of α-MHC-II blocking antibodies. Data are representative of 10 (CD69 vs CD40L) and 6 (CD69 vs IFNγ) experiments and participants. (D) Summary bar graphs compare mean (± SEM) co-expression of CD69 and CD40L, and (E) the difference in activation when MTB300 is added to infected macrophages (10 LTBI and 7 non-LTBI). (F) Summary bar graphs compare mean (± SEM) CD69 and IFNγ co-expression, and (G) change in activation when MTB300 is added (6 LTBI and 3 non-LTBI). Each symbol represents the mean of 1-3 replicates from independent experiments. Statistical significance was determined by Wilcoxon matched pairs signed rank test. * p < 0.05, ** p < 0.01. See also Supplemental Figure 1.

Article Snippet: Following stimulation, CD4 positive immunomagnetic selection was performed according to manufacturer’s instructions using human anti-CD4 microbeads (Miltenyi Biotec), followed by flow sorting of the activated CD4 + T cells for downstream scTCRseq.

Techniques: Co-Culture Assay, Infection, Flow Cytometry, Activation Assay, Marker, Expressing, Blocking Assay

Journal: bioRxiv

Article Title: Human memory CD4 + T-cells recognize Mycobacterium tuberculosis -infected macrophages amid broader pathogen-specific responses

doi: 10.1101/2025.02.23.639515

Figure Lengend Snippet: (A) Bar graphs of the top 50 TCR clonotypes and their frequencies from representatives of 8 LTBI and (B) 6 non-LTBI participants. Clonotypes are displayed as CDR3α_CDR3β sequences; some TCRs contained two CDR3α or β chains. Blue font highlights a CDR3β motif previously annotated as specific for EspA 301-315 . (C) Summary box plots of the average Shannon and (D) Inverse Simpson diversity index scores of 8 LTBI and 6 non-LTBI participants. Each symbol represents individual participant TCR repertoires. (E) Summary box plots of %TCR clonotypes present in ≥ 2, 3, or 4 copies with fold-differences listed above each graph. Statistical significance was determined by unpaired t test with Welch’s correction. (F) Pie charts combining TCRs from 7-8 participants, each, showing percent (and number) of unique TCRβ sequences linked to memory CD4 + T cell activation in response to infected macrophages (green) or after adding MTB300 (blue), or (G) lysate (yellow). Plots include all unique TCR clonotypes that meet each expansion threshold (≥2, 3, or 4 copies). (H) Pie charts for percent (and number) of total TCRs for each are also plotted. * p < 0.05. See also Supplemental Figure 2.

Article Snippet: Following stimulation, CD4 positive immunomagnetic selection was performed according to manufacturer’s instructions using human anti-CD4 microbeads (Miltenyi Biotec), followed by flow sorting of the activated CD4 + T cells for downstream scTCRseq.

Techniques: Activation Assay, Infection

Journal: bioRxiv

Article Title: Human memory CD4 + T-cells recognize Mycobacterium tuberculosis -infected macrophages amid broader pathogen-specific responses

doi: 10.1101/2025.02.23.639515

Figure Lengend Snippet: (A) Venn diagram indicating the number of GLIPH2 groups containing TCRs linked to responses to infected macrophages (green, stars), MTB300 (blue, squares), Control peptide megapools (red), or lysate (yellow, triangle). Data were generated from a combined list of TCRs from all experimental conditions (10 experiments; 10 LTBI and 6 non-LTBI participants). (B) Pie charts of percent (and number) of remaining GLIPH2 groups that respond to infected macrophages (green; sum of star groups from A) or MTB300 only (blue; sum of square groups from A). (C) Pie charts of GLIPH2 groups (left) and corresponding unique TCRβs (right) after removing GLIPH2 groups containing TCRs linked to viral antigen responses. (D) Bar graph of GLIPH2 groups (x-axis) estimated to be Mtb-specific, rank-ordered by sum of highest number of TCR copies per condition (y-axis). Responses to infected macrophages (green), MTB300 only (blue), or both (blue stripes) are indicated. (E) Pie charts comparing responses to infected macrophages (green) or MTB300 peptides only (blue) for GLIPH2 groups (left) containing unique TCRβs (right) from at least 2 participants. (F) Bar graphs of CD69 expression of ‘TKYN’ TCR-transduced SKW-3 cells by flow cytometry (gated on CD4 + TCRβ + Live-Dead Lo ) 18 h after co-culture with APCs loaded with MTB300 megapool, 15 subpools (20 peptides each), or (G) individual peptides from subpool #3 from 2 independent experiments. (H) Representative flow plots of CD69 and TCRβ expression gated on total CD4 + SKW-3 cells after TCR transduction in response to cognate peptide (top left), irrelevant peptide (top right) and controls. See also Supplemental Figure 3.

Article Snippet: Following stimulation, CD4 positive immunomagnetic selection was performed according to manufacturer’s instructions using human anti-CD4 microbeads (Miltenyi Biotec), followed by flow sorting of the activated CD4 + T cells for downstream scTCRseq.

Techniques: Infection, Control, Generated, Expressing, Flow Cytometry, Co-Culture Assay, Transduction

Journal: bioRxiv

Article Title: Human memory CD4 + T-cells recognize Mycobacterium tuberculosis -infected macrophages amid broader pathogen-specific responses

doi: 10.1101/2025.02.23.639515

Figure Lengend Snippet: (A) Pie charts comparing percent (and number) of GLIPH2 groups or (B) unique TCRβs (right) linked to a response to Mtb-infected macrophages (green), MTB300 only (blue), or lysate only (yellow) from ≥ 3 participants in the combined TCR dataset. (C) Bar graph of GLIPH2 groups estimated to be Mtb-specific (x-axis) from ≥ 3 participants, rank-ordered by sum of highest number of TCR copies per condition (y-axis). Responses to infected macrophages (green), MTB300 only (blue), both (blue stripes), or lysate only (yellow) are indicated. GLIPH2 groups containing TCRs annotated as Mtb antigen-specific in IEDB, or from our peptide screen, are in red and blue font, respectively. (D) Pie charts comparing total or (E) percent of total circulating TCRβs for CD4 + T cells from 10×10 6 unstimulated PBMCs after cross-referencing CDR3β sequences from Cleveland participants from GLIPH2 groups. Each dot represents TCRβ count from a separate participant. (F) Bar graph of mean circulating frequency of Cleveland participants’ TCRβ clonotypes (symbols) for each GLIPH2 group after cross-referencing with unstimulated PBMCs. (G) Bar graphs of mean CDR3β (top) and CDR3α (bottom) lengths of TCRs from Cleveland participants within GLIPH2 groups from the combined dataset. (H) Sequence logo plots show the probability of each amino acid for CDR3β (top) and CDR3α (bottom) motifs of six GLIPH2 groups common in the initial and combined analyses, created using WebLogo3. The number of CDR3 sequences used for each plot is indicated (top-right). See also Supplemental Figure 3.

Article Snippet: Following stimulation, CD4 positive immunomagnetic selection was performed according to manufacturer’s instructions using human anti-CD4 microbeads (Miltenyi Biotec), followed by flow sorting of the activated CD4 + T cells for downstream scTCRseq.

Techniques: Infection, Sequencing

Journal: bioRxiv

Article Title: Human memory CD4 + T-cells recognize Mycobacterium tuberculosis -infected macrophages amid broader pathogen-specific responses

doi: 10.1101/2025.02.23.639515

Figure Lengend Snippet: (A) UMAP visualization plot including Louvain clustering of 157,462 cells, flow-sorted based on expression of CD4 and AIMs, from 7 LTBI participants (12 samples, including memory CD4 + T cells in co-culture with Mtb-infected macrophages ± lysate) and 6 non-LTBI participants (6 samples, memory CD4 + T cells in co-culture with Mtb-infected macrophages) after integration and QC. (B) Kernel density estimation of gene transcripts for T helper subset genes projected onto UMAP plot. Density metrics values were reduced to max/min scale. (C) Heatmap with hierarchical clustering showing top 5 DEGs (left) for each cluster (top and bottom), conserved across treatment groups. (D) Split UMAP plots for experimental groups showing mapping of all TCRs. Expanded (≥2 copies) and non-expanded (single) TCR clonotypes are shown in red and blue, respectively. (E) Representative stacked bar plots showing percent clonally expanded versus non-expanded TCRs in LTBI participant samples, normalized to each cluster’s total cell number and (F) total number of TCRs. (G) UMAP plot showing joint density estimation for plot for CCR7 and SELL transcripts in the integrated dataset. (H) UMAP plot illustrating the single-cell trajectory and pseudotime analysis of CD4+ populations within the integrated dataset. Cell fates (gray circles), transition states (black circles), proximity to (purple), and remoteness from (yellow) the root are indicated. See also Supplemental Figure 4.

Article Snippet: Following stimulation, CD4 positive immunomagnetic selection was performed according to manufacturer’s instructions using human anti-CD4 microbeads (Miltenyi Biotec), followed by flow sorting of the activated CD4 + T cells for downstream scTCRseq.

Techniques: Expressing, Co-Culture Assay, Infection

Journal: Cell Reports Medicine

Article Title: Single-cell analysis of neoplastic plasma cells identifies myeloma pathobiology mediators and potential targets

doi: 10.1016/j.xcrm.2024.101925

Figure Lengend Snippet: Inter-patient heterogeneity (A) UMAPs representing scRNA-seq data from enriched PCs from all patients with color codes representing unique samples (left), mPC and pPC populations (middle), and mPCs and pPCs by diagnosis (right). (B) Number of genes detected as dysregulated with a log2 FC of ≥ 0.5 or ≤ −0.5 when the analysis was conducted using all CD138 + PCs, or CD138 + mPCs from each sample identified by scBCR-seq, using “ FindAllMarkers ” in Seurat. Horizontal lines indicate little to no difference in the number of DEGs, while upward lines indicate more DEGs found when the analysis focused only on the mPCs. ∗ indicates p ≤ 0.05; ∗∗ p ≤ 0.01; ∗∗∗ p ≤ 0.001; ∗∗∗∗ p ≤ 0.0001; and n.s. non-significant differences, as determined by the Wilcoxon test. (C) UMAP based on the single-cell transcriptome of a downsampled Seurat object with a color code of CytoTRACE score (left), and a superplot of the mean CytoTRACE score per sample group by diagnosis (right). Statistical testing was performed as in (B). (D) Boxplot of normalized UMIs detected in each sample, color coded by diagnosis, including myeloma-related markers, and commonly up- and down-regulated markers. (E) Heatmap of the fraction of PCs with myeloma IGH translocations detected by FISH (top), and boxplots of normalized UMIs of associated oncogene expression levels (next three rows). (F) Circos plots of three t(11;14) + myelomas evaluated by Lumpy using WGS data from germline and tumor-matched samples. (G) Heatmap of the fraction of cells with inferred large chromosomal gains (red) or losses (blue) in each PC population organized by diagnosis. Total number of PCs isolated and the fraction of mPCs in each sample are represented at the top. These plots include a dataset of pPC samples ( n = 4), and mPCs from patients with MGUS ( n = 11), SMM ( n = 22), NDMM ( n = 17), RRMM ( n = 15), and PCL ( n = 2).

Article Snippet: Bone marrow (BM) aspirates and one blood sample (one PCL sample, 82) were collected, and PCs were immediately enriched using CD138 + immunomagnetic positive selection (StemCell Technologies).

Techniques: Biomarker Discovery, Expressing, Isolation

Journal: Cell Reports Medicine

Article Title: Single-cell analysis of neoplastic plasma cells identifies myeloma pathobiology mediators and potential targets

doi: 10.1016/j.xcrm.2024.101925

Figure Lengend Snippet:

Article Snippet: Bone marrow (BM) aspirates and one blood sample (one PCL sample, 82) were collected, and PCs were immediately enriched using CD138 + immunomagnetic positive selection (StemCell Technologies).

Techniques: Recombinant, Selection, Cell Isolation, Proliferation Assay, Staining, Enzyme-linked Immunosorbent Assay, Detection Assay, Reporter Assay, RNA Sequencing, Transgenic Assay, Software