Journal: eLife

Article Title: Reprogramming of bone marrow myeloid progenitor cells in patients with severe coronary artery disease

doi: 10.7554/eLife.60939

Figure Lengend Snippet:

Article Snippet: Circulating IL-1β, IL-1Ra, IL-6, and IL-18 concentrations were measured with the SimplePlex cartridge on the Ella platform (ProteinSimple, San Jose, CA).

Techniques: Isolation, Staining, Enzyme-linked Immunosorbent Assay, Sequencing, Recombinant, Software, Flow Cytometry, Gene Expression, Positron Emission Tomography-Computed Tomography

Journal: medRxiv

Article Title: Physiological and molecular characterization of individuals carrying a diabetogenic mtDNA mutation establishes a mitochondrial basis for insulin resistance in humans

doi: 10.64898/2025.12.17.25342274

Figure Lengend Snippet: (A-D) Time course of venous and arterial plasma GDF15 levels during the hyperinsulinemic-euglycemic (HE) clamp. (B) GDF15 levels in venous plasma samples obtained before (Basal) and during the steady-state period of HE clamp (Insulin). (C) Time course of the venous-arterial difference in plasma GDF15 levels during the HE clamp. (D) Venous-arterial difference in plasma GDF15 before (Basal) and during the steady-state period of the HE clamp (Insulin). (E) Time course of venous and arterial plasma FGF21 levels during the HE clamp. n = 29 (15 in m.3243A>G, 14 in Controls). (F) FGF21 levels in venous plasma samples obtained before (Basal) and during the steady-state period of the HE clamp (Insulin). n = 29 (15 in m.3243A>G, 14 in Controls). (G) Time course of the venous-arterial difference in plasma FGF21 levels during the HE clamp. n = 29 (15 in m.3243A>G, 14 in Controls). (H) Venous-arterial difference in plasma FGF21 before (Basal) and during the steady-state period of the HE clamp (Insulin). n = 29 (15 in m.3243A>G, 14 in Controls). Linear mixed models were used to estimate within– and between-group differences [(B), (D), (F), and (H)]. Data are presented as observed individual values (with lines connecting individually matched participants) and estimated means ± 95% confidence limits, unless otherwise stated. For m.3243A>G carriers, individual datapoints are color-shaded to indicate muscle mtDNA heteroplasmy (light red = low, dark red = high). *Different from Basal ( P < 0.05). † Different from zero ( P < 0.05). n = 30 unless otherwise stated.

Article Snippet: Arterial and venous plasma samples were also analyzed for GDF15 and FGF21 using the automated immunoassay platform Ella (ProteinSimple, San Jose, California, USA) with Simple Plex assays for human GDF15 and FGF21 detection, according to the manufacturer’s instructions.

Techniques: Clinical Proteomics

Journal: bioRxiv

Article Title: BMP9 regulates the endothelial secretome to drive pulmonary hypertension

doi: 10.1101/2025.08.29.673113

Figure Lengend Snippet: (A) Uniform manifold approximation and projection (UMAP) plot showing identified endothelial cell types in lungs from 3 IPAH patients and 6 donor controls (GSE169471). (B) Venn diagram showing the overlap of upregulated genes in SU-Hx rat lung (SU-Hx–Isotype control vs. Nx), downregulated genes in Ab93-treated SU-Hx rat lung (SU-Hx–Ab93 vs. SU-Hx–Isotype), and upregulated genes in IPAH pulmonary general capillary endothelial cells (gCap) (IPAH vs. Control, GSE169471). (C) Venn diagram showing the overlap of upregulated genes in BMP9-treated HPMVEC (BMP9-1.5h vs. control) and upregulated genes in IPAH pulmonary gCap ECs (IPAH vs. Control, GSE169471). (D-G) Volcano plots showing changes and significance of candidate driver genes across different datasets, including (D) upregulation of ID1 , BMPR2 , CXCL12, EDN1, COL18A1 , and IGFBP4 in IPAH vs. control lungs; (E) upregulation of ID1, BMPR2 , EDN1, IGFBP4, VEGFA, PDGFA, PDGFB, VWA1 , and SOX18 in BMP9-treated PMVEC; (F) upregulation of Edn1, Cald1, Vwa1, Col18a1 , and Igfbp4 in Su-Hx treated rats vs. normoxia; and (G) downregulation of Cxcl12, Igfbp4, Col18a1, Vwa1 , and Cald1 in Ab93-treated vs. isotype control treated SU-Hx rats. (H-L) Violin plots showing increased expression of CXCL12 , IGFBP4 , EDN1 , ENG , and BMPR2 in various subsets of endothelial cells from IPAH patients (GSE169471). (M) BMP9 (40 pM) increased CXLC12 mRNA expression in HPMVEC in a time-dependent manner. (N-R) BMP9 (40 pM) increased secretion of CXCL12, IGFBP4, ET-1, PDGF-BB and CCL2 in cultured HPMVEC supernatants. ( n = 3 per group, means ± SD. *P<0.05 as compared to 0 h or all the other groups, Dunnett’s test) (S-U) BMP9 (40 pM) treatment of HPMVEC increased mRNA expression of CXCL12 , which was diminished when BMPR2 , ACVRL1 or ENG were knocked down. ( n = 3 per group, mean ± SD, * P <0.05, ** P <0.01, *** P <0.001, **** P <0.0001 by one-way ANOVA with Sidak’s test).

Article Snippet: To test the concentration of CXCL12, ET1, PDGF-BB, and CCL2 in PMVECs culture medium, the Ella Simple Plex system and the cartridges (Human CXCL12, SPCKB-PS-000299; Human Endothelial-1, SPCKC-PS-000265; HumanCCL2 and PDGF-BB, SPCKC-PS-006510; Protein Simple) were used according to the manufacturer’s instructions.

Techniques: Control, Expressing, Cell Culture

Journal: bioRxiv

Article Title: BMP9 regulates the endothelial secretome to drive pulmonary hypertension

doi: 10.1101/2025.08.29.673113

Figure Lengend Snippet: ( A ) Dot plot highlighting log 10 average expression of selected marker genes used to identify endothelial clusters. The dot size corresponds to the percentage of cells expressing a gene in a given cluster. ( B ) Venn diagram showing the overlap of upregulated genes in SU-Hx rat lung (SU-Hx– Isotype control vs Nx), downregulated genes in Ab93-treated SU-Hx rat lungs (SU-Hx–Ab93 vs SU-Hx–Isotype), and upregulated genes in IPAH pulmonary artery endothelial cells (AEC, IPAH vs Control, GSE169471). ( C ) Venn diagram showing the overlap of upregulated genes in BMP9-treated HPMVEC (BMP9-1.5h vs control) and upregulated genes in IPAH pulmonary AECs (IPAH vs Control, GSE169471). ( D ) Volcano plot showing potential candidate genes upregulated in IPAH pulmonary AEC (IPAH vs Control, GSE169471). BMP9 (40 pM) increased CXLC12 mRNA ( E ) and ( F ) protein expression in HPAEC at varying intervals up to 24h. Stimulation of cultured HPAEC with BMP9 (40 pM) increased ( G ) IGFBP4 mRNA and ( H ) protein expression, as well as protein expression of ( I ) Endothelin-1, ( J ) PDGF-BB, and ( K ) CCL2 protein in supernatants at varying intervals over 24h. ( n = 3 per group, mean ± SD, *P<0.05 as compared to 0 h, one-way ANOVA with Dunnett’s multiple comparisons test).

Article Snippet: To test the concentration of CXCL12, ET1, PDGF-BB, and CCL2 in PMVECs culture medium, the Ella Simple Plex system and the cartridges (Human CXCL12, SPCKB-PS-000299; Human Endothelial-1, SPCKC-PS-000265; HumanCCL2 and PDGF-BB, SPCKC-PS-006510; Protein Simple) were used according to the manufacturer’s instructions.

Techniques: Expressing, Marker, Control, Cell Culture

Journal: BMC neurology

Article Title: Intrathecal interleukin-6 levels are associated with progressive disease and clinical severity in multiple sclerosis.

doi: 10.1186/s12883-025-04145-0

Figure Lengend Snippet: Fig. 2 Ella vs. Planar Array. IL-6 levels in CSF were determined using the Ella® microfluidics assay, which correlates with the SiMOA® Planar Array results

Article Snippet: IL-6 was further quantified using Simple Plex Human NfL Cartridge with an Ella® automated immunoassay system (Catalog # SPCKB-PS-003028, Protein Simple, San Jose, CA, USA, Table 1).

Techniques:

Journal: BMC neurology

Article Title: Intrathecal interleukin-6 levels are associated with progressive disease and clinical severity in multiple sclerosis.

doi: 10.1186/s12883-025-04145-0

Figure Lengend Snippet: Fig. 3 Intrathecal IL-6 is increased in PPMS. IL-6 levels in CSF of HCs vs. RRMS and PPMS measured with Ella®. (A) IL-6 levels were significantly higher in PPMS vs. HCs (p = 0.0428). Statistical significance was determined using the Mann-Whitney test. * p < 0.5. (B) Receiver operating characteristic (ROC) analysis demonstrated the capacity of IL-6 levels to distinguish between RRMS and PPMS with an area under the curve (AUC) of 0.7060, and statistical significance (p = 0.0139)

Article Snippet: IL-6 was further quantified using Simple Plex Human NfL Cartridge with an Ella® automated immunoassay system (Catalog # SPCKB-PS-003028, Protein Simple, San Jose, CA, USA, Table 1).

Techniques: MANN-WHITNEY

Journal: Nature genetics

Article Title: Functional characterization of Alzheimer’s disease genetic variants in microglia

doi: 10.1038/s41588-023-01506-8

Figure Lengend Snippet: a, Overview of CRISPRi perturbation and single cell gene expression analysis of fine-mapped AD risk loci in iPSC-derived microglia. dCas9-KRAB-WTC11 were differentiated into microglia and transfected with lentivirus library to perturb fine-mapped AD risk loci. CRISPRi effect were evaluated by HyPR-seq after 1 week. b, Cumulative frequency distribution (CFD) of the number of cells with each gRNA used in analysis. c, Volcano plot of the gRNA-to-gene pairs tested in cis. 14 genes were significantly affected by AD risk loci perturbation (FDR < 0.05, log2(fold change) < −0.1) for 10 AD risk variants in 5 cCREs. Genes from the same AD risk locus are labeled with the same color. Triangles mark transcriptional changes of genes in cells with TSS gRNA-gene pairs, and circles mark changes with distal cCRE gRNA-gene pairs. d, A risk cCRE (orange) interacting with the INPP5D promoter. e, The risk cCRE overlaps five prioritized AD variants (red dots) which were not significant (−log10(P value) < 8) in AD summary statistics. f, Quantitative effects of AD risk cCRE on the expression of INPP5D in cis and three other neighboring genes, including ATG16L1, GIGYF2, and EIF4E2. P values calculated using two-sided two-sample t-test and adjusted by Benjamini-Hochberg FDR multiple testing correction. The median, upper and lower quantiles are indicated by circle and bar. Each dot represents one single cell. N are indicated in Supplementary Table 7d. g, Genome browser snapshot of the TREM2 locus. h, CRIPSRi perturbation targeting TREM2 cCREs followed by RT-qPCR analysis in WTC11-derived microglia-like cells. i, Quantification of TREM2 expression in WTC11- and H1-derived microglia-like cells infected with gRNAs for non-human targeting controls (black), TREM2 TSS (dark blue), TSS and cCRE1 (light blue), TSS and cCRE2 (green), cCRE1 (orange), cCRE2 (brown) under control and IFNß stimulated conditions. P values calculated using two-sided two-sample t-test for (h) and (i). Three independent replicates per condition and two sgRNAs per replicate were used for each experiment. Boxplots indicate the median and interquartile range. Whiskers mark the 5th and 95th percentiles.

Article Snippet: Assay for soluble TREM2 (sTREM2) We used the Human TREM2 assay (biotechne/ProteinSimple SPCKB-PS-001847) on the Ella system according to manufacturer’s protocol.

Techniques: Gene Expression, Derivative Assay, Transfection, Labeling, Expressing, Quantitative RT-PCR, Infection, Control

Journal: Nature genetics

Article Title: Functional characterization of Alzheimer’s disease genetic variants in microglia

doi: 10.1038/s41588-023-01506-8

Figure Lengend Snippet: a, CRIPSRi validation on cCREs at INPP5D, BIN1, RIN3 and TREM2 loci in WTC11 microglia-like cells treated with IFNβ. P values calculated using two-sided two-sample t-test. Three independent replicates per condition and two sgRNAs per replicate were used for each experiment. Boxplots indicate the median and interquartile range. Whiskers mark the 5th and 95th percentiles. b, Scatter plot showing the fold change of cCRE perturbation in control or IFNβ treated condition. The Pearson correlation coefficient and its P value are reported. Linear regression line (black) with 95% confident interval (gray shade) are plotted. c, Genome browser snapshot showing the INPP5D locus containing a cCRE with prioritized AD variants and gRNAs for perturbation in single cell analysis. Genes expressed in microglia at this locus (red labels) are analyzed. Green boxes highlight the cCRE and promoters of neighboring genes. d, Down-regulation of INPP5D, GIGYF2, ATG16L1, and EIF4E2 by perturbing the cCRE region are confirmed by bulk CRISPRi followed by RT-qPCRs. P values are calculated with two-sided two sample t-test. Three independent replicates per condition and two sgRNAs per replicate were used for each experiment. Boxplots indicate the median and interquartile range. Whiskers mark the 5th and 95th percentiles.

Article Snippet: Assay for soluble TREM2 (sTREM2) We used the Human TREM2 assay (biotechne/ProteinSimple SPCKB-PS-001847) on the Ella system according to manufacturer’s protocol.

Techniques: Functional Assay, Biomarker Discovery, Control, Single-cell Analysis

Journal: Nature genetics

Article Title: Functional characterization of Alzheimer’s disease genetic variants in microglia

doi: 10.1038/s41588-023-01506-8

Figure Lengend Snippet: a-d, In all examples, tested cCREs are highlighted with orange or brown boxes. gRNAs targeting cCREs with AD variants are shown as red vertical lines. Genes expressed in microglia and exhibiting expression changes upon perturbation are shown with red labels. Distributions of relative gene expression levels are shown in violin plots where circles mark the median, and the black bars mark the upper and lower quantiles. Each dot represents one single cell. Number of cells are indicated in Supplementary Table 7d. P values are calculated by comparing gene expression between cells infected with control gRNAs and cells infected with gRNAc targeting cCREs using two-sided two-sample t-test and adjusted by Benjamini-Hochberg FDR multiple testing correction. Adjusted P values (FDR) are labeled. (a) TREM2 locus, (b) RIN3 locus, (c) BIN1 locus, and (d) PICALM locus. Notably at the TREM2 locus, microglia receiving both TSS gRNA2 and cCRE1 showed enhanced downregulation of TREM2 compared to cells with TSS gRNA2 alone. e, Gene expression levels after CRIPSRi targeting cCREs at BIN1 and RIN3 loci with 2 gRNAs in WTC11-derived microglia-like cells. P values calculated using two-sided two-sample t-test (n = 3). Boxplots indicate the median and interquartile range. Whiskers mark the 5th and 95th percentiles.

Article Snippet: Assay for soluble TREM2 (sTREM2) We used the Human TREM2 assay (biotechne/ProteinSimple SPCKB-PS-001847) on the Ella system according to manufacturer’s protocol.

Techniques: Expressing, Gene Expression, Infection, Control, Labeling, Derivative Assay

Journal: Nature genetics

Article Title: Functional characterization of Alzheimer’s disease genetic variants in microglia

doi: 10.1038/s41588-023-01506-8

Figure Lengend Snippet: a, FACS analysis of proliferation for WTC11- and H1-derived microglia-like cells perturbed with synergistic inhibition of TREM2 enhancer and promoter in both control and IFNβ stimulated conditions. b, Representative contour plots of Ki-67 FITC FACS gating strategy. Cells were separated from debris based on the forward scatter area and side scatter area. Two singlet gates were applied using the width and height metrics of the side scatter and forward scatter. Ki-67 FITC signals are shown for all singlets. c, Negative control population using microglia not stained with Ki-67 antibody. d, FACS analysis of phagocytosis capacity for WTC11- and H1-derived microglia-like cells perturbed with synergistic inhibition of TREM2 enhancer and promoter in both control and IFNβ stimulated conditions. e, Representative contour plots of Latex beads-FITC FACS gating strategy. Cells were separated from debris based on the forward scatter area and side scatter area. Two singlet gates were applied using the width and height metrics of the side scatter and forward scatter. Latex beads-FITC signals are shown for all singlets. f, Negative control population using microglia not incubated with Latex beads.

Article Snippet: Assay for soluble TREM2 (sTREM2) We used the Human TREM2 assay (biotechne/ProteinSimple SPCKB-PS-001847) on the Ella system according to manufacturer’s protocol.

Techniques: Derivative Assay, Inhibition, Control, Negative Control, Staining, Incubation

Journal: Nature genetics

Article Title: Functional characterization of Alzheimer’s disease genetic variants in microglia

doi: 10.1038/s41588-023-01506-8

Figure Lengend Snippet: a, Two prioritized AD variants located in a cCRE (highlighted in orange) physically interacting with TSPAN14 promoter. b, hESC H1 genome is heterozygous for the two AD variants. The P1 allele has the risk alleles: rs7922621 (A) and rs7910643 (A), while the P2 allele has the non-risk alleles: rs7922621 (C) and rs7910643 (G). c, Allelic analysis of ATAC-seq data in H1 derived microglia reveals decreased chromatin accessibility of the P1 allele compared to the P2 allele (two-sided binomial test, n = 4). d, Allelic analysis using haplotype-resolved SNPs in the TSPAN14 gene body shows reduced TSPAN14 expression from the P1 allele compared to the P2 allele in microglia (two-sided binomial test, n = 5). e, Illustration of the prime editing strategy to convert rs7922621 (A) and rs7910643 (A) on the P1 allele to rs7922621 (C) and rs7910643 (G), respectively. Representative results from sanger sequencing display wildtype clones and KI clones. f, Allelic imbalance of TSPAN14 gene expression in the wild type clones (A/C) is partially reduced by prime-editing of rs7922621 (A/C to C/C) but not rs7910643. P values calculated using two-sided two-sample t-test (n = 5). g, Microglia with rs7922621 (C/C) genotype have elevated cell surface ADAM10 than wildtype microglia by immunostaining and FACS analysis. P values calculated using one-sided (edited > WT) two-sample Wilcoxon test (n = 5). h, rs7922621 (C/C) prime-edited microglia, but not rs7910643 (G/G) edited microglia, shed significantly more sTREM2 than wildtype microglia. P values calculated using two-sided paired (dash line) t-test between wildtype and prime-edited microglia from the same differentiation batch (n = 3). Boxplot indicates the median and interquartile range and whiskers mark the 5th and 95th percentiles for (c), (d), (f), (h). I, Proposed model of linking AD risk variant rs7922621 to function. rs7922621 risk allele A disrupts cis-regulatory function and down-regulate TSPAN14 expression, which leads to impaired ADAM10 trafficking and maturation to cell surface. The reduced ADAM10 level at the cell surface reduces TREM2 cleavage and sTREM2 shedding.

Article Snippet: Assay for soluble TREM2 (sTREM2) We used the Human TREM2 assay (biotechne/ProteinSimple SPCKB-PS-001847) on the Ella system according to manufacturer’s protocol.

Techniques: Derivative Assay, Expressing, Sequencing, Clone Assay, Gene Expression, Immunostaining, Variant Assay

Journal: Cell Reports Medicine

Article Title: A genetically modified minipig model for Alzheimer’s disease with SORL1 haploinsufficiency

doi: 10.1016/j.xcrm.2022.100740

Figure Lengend Snippet:

Article Snippet: Simple Plex Human NF-L Cartridge , Protein Simple , Cat# SPCKB-PS-002448.

Techniques: Recombinant, Plasmid Preparation, Software, CRISPR