Journal: Nutrients

Article Title: Effects of Lingonberry ( Vaccinium vitis-idaea L.) Supplementation on Hepatic Gene Expression in High-Fat Diet Fed Mice

doi: 10.3390/nu13113693

Figure Lengend Snippet: The twenty genes with the largest negative fold change (FC) in the lingonberry supplemented high-fat diet (HF + LGB) group relative to the high-fat diet (HF) group. Mean expression levels are given as DESeq2-normalized counts. p -values are adjusted by false discovery rate (FDR).

Article Snippet: For PCR validation, RNA was transcribed to cDNA (Maxima First Strand cDNA Synthesis Kit, Thermo Fisher Scientific) and subjected to quantitative PCR with TaqMan Universal Master Mix (Thermo Fisher Scientific) and ABI Prism 7500 sequence detection system (Applied Biosystems, Foster City, CA, USA) using the following TaqMan Gene Expression assays (Thermo Fisher Scientific); Mm00432403_m1 ( Cd36 ), Mm03047343_m1 ( Cd68 ), Mm00617672_m1 ( Cidec ), Mm00444699_m1 ( Cxcl14 ), Mm00725580_s1 ( Cyp2c29 ), Mm00472168_m1 ( Cyp2c55 ), Mm00731567_m1 ( Cyp3a11 ), Mm01607174_mH ( Cyp3a59 ), Mm00487306_m1 ( Cyp46a1 ), Mm00492632_m1 ( Igfbp2 ), Mm00434228_m1 ( IL1b ), Mm00440181_m1 ( Lepr ), Mm00503358_m1 ( Mogat1 ), Mm01184322_m1 ( Pparg ), Mm04208126_mH ( Saa2 ), Mm00446229_m1 ( Slc2a2 ), Mm00443260_g1 ( Tnfa ).

Techniques: Expressing, Activity Assay, Antioxidant Activity Assay, Migration, Binding Assay, Sequencing

Journal: Nutrients

Article Title: Effects of Lingonberry ( Vaccinium vitis-idaea L.) Supplementation on Hepatic Gene Expression in High-Fat Diet Fed Mice

doi: 10.3390/nu13113693

Figure Lengend Snippet: The 21 genes upregulated by the high-fat (HF) diet (FC > 1.5), and whose expression was significantly lower in the lingonberry-supplemented high-fat diet group (HF + LGB) (FC < −1.5), and the 2 genes (last two rows) downregulated by the high-fat (HF) diet (FC < −1.5), and whose expression was maintained at higher expression level in the lingonberry-supplemented high-fat diet group (HF + LGB) (FC > 1.5). Mean expression levels are given as DESeq2-normalized counts. p -values are adjusted by false discovery rate (FDR). * Mean of normalizations performed in comparisons HF vs. LF and HF + LGB vs. HF. LF = low-fat diet.

Article Snippet: For PCR validation, RNA was transcribed to cDNA (Maxima First Strand cDNA Synthesis Kit, Thermo Fisher Scientific) and subjected to quantitative PCR with TaqMan Universal Master Mix (Thermo Fisher Scientific) and ABI Prism 7500 sequence detection system (Applied Biosystems, Foster City, CA, USA) using the following TaqMan Gene Expression assays (Thermo Fisher Scientific); Mm00432403_m1 ( Cd36 ), Mm03047343_m1 ( Cd68 ), Mm00617672_m1 ( Cidec ), Mm00444699_m1 ( Cxcl14 ), Mm00725580_s1 ( Cyp2c29 ), Mm00472168_m1 ( Cyp2c55 ), Mm00731567_m1 ( Cyp3a11 ), Mm01607174_mH ( Cyp3a59 ), Mm00487306_m1 ( Cyp46a1 ), Mm00492632_m1 ( Igfbp2 ), Mm00434228_m1 ( IL1b ), Mm00440181_m1 ( Lepr ), Mm00503358_m1 ( Mogat1 ), Mm01184322_m1 ( Pparg ), Mm04208126_mH ( Saa2 ), Mm00446229_m1 ( Slc2a2 ), Mm00443260_g1 ( Tnfa ).

Techniques: Expressing, Migration, Activity Assay, Binding Assay, Protein Binding

Journal: International journal of oncology

Article Title: C-reactive protein is a biomarker of AFP-negative HBV-related hepatocellular carcinoma.

doi: 10.3892/ijo.2015.3042

Figure Lengend Snippet: Figure 3. Elisa verification and immunohistochemistry of CRP, C9 and SAA. (A) ELISA verification of iTRAQ results. Samples tested were the same as those used in the iTRAQ experiments. (B) Cohort verification with ELISA. Plasma concentrations of CRP, C9 and SAA were determined in 284 plasma samples. (C) Human tissue microarray and immunohistochemical analysis of CRP, C9 and SAA proteins in cirrhotic and HCC tissues. Scale bar, 100 µm. Data are shown as mean ± SD, *p<0.05.

Article Snippet: The human SAA ELISA kit (ELH-SAA-001) was purchased from Ray Biotech (Norcross, GA, USA).

Techniques: Enzyme-linked Immunosorbent Assay, Immunohistochemistry, Multiplex sample analysis, Clinical Proteomics, Microarray, Immunohistochemical staining

Journal: Frontiers in Pharmacology

Article Title: Unveiling novel serum biomarkers in intrahepatic cholangiocarcinoma: a pilot proteomic exploration

doi: 10.3389/fphar.2024.1440985

Figure Lengend Snippet: Serum proteins that could aid iCCA vs. HCC discrimination.

Article Snippet: These measurements were made from individual samples of the validation cohort and were performed in duplicate, following the instructions provided with the kits. (SAA1: ABclonal, WoburnMA, USA, catalogue number RK04228, detection range = 0.156–10 ng/mL sensitivity = 0.071 ng/mL, intra-assay precision coefficient of variation (CV) < 10%, inter-assay precision CV < 15%; SAA4: Elabscience Wuhan, China, catalogue number E-EL-H5638, detection range = 78.13–5,000 pg/mL sensitivity = 46.88 pg/mL, intra-assay precision coefficient of variation (CV) < 5%, inter-assay precision CV < 5%; VCAM1: ABclonal, WoburnMA, USA, catalogue number RK00026, detection range = 15.6–1,000 pg/mL sensitivity = 3.85 pg/mL, intra-assay precision coefficient of variation (CV) ≤10%, inter-assay precision CV ≤ 15%; LRG1: ABclonal, WoburnMA, USA, catalogue number RK01800, detection range = 31.2–2000 pg/mL, sensitivity = 15.6 pg/mL, intra-assay precision coefficient of variation (CV) ≤10%, inter-assay precision CV ≤ 15%).

Techniques:

Journal: Frontiers in Pharmacology

Article Title: Unveiling novel serum biomarkers in intrahepatic cholangiocarcinoma: a pilot proteomic exploration

doi: 10.3389/fphar.2024.1440985

Figure Lengend Snippet: Proposed biomarker panels for distinguishing the different liver diseases. AUC = area under the receiver operating characteristic (ROC) curve; CI = confidence interval; iCCA = intrahepatic cholangiocarcinoma; HCC = hepatocellular carcinoma; CIR = liver cirrhosis; PSC = primary sclerosing cholangitis; SAA1 = Serum amyloid-1; SAA4 = Serum amyloid-4; VCAM1 = Vascular cell adhesion protein 1; LRG1 = HP = Haptoglobin, PRKACB = cAMP-dependent protein kinase catalytic subunit beta; ANXA9 = Annexin A9; LVRN = Leucine-rich alpha-2-glycoprotein.

Article Snippet: These measurements were made from individual samples of the validation cohort and were performed in duplicate, following the instructions provided with the kits. (SAA1: ABclonal, WoburnMA, USA, catalogue number RK04228, detection range = 0.156–10 ng/mL sensitivity = 0.071 ng/mL, intra-assay precision coefficient of variation (CV) < 10%, inter-assay precision CV < 15%; SAA4: Elabscience Wuhan, China, catalogue number E-EL-H5638, detection range = 78.13–5,000 pg/mL sensitivity = 46.88 pg/mL, intra-assay precision coefficient of variation (CV) < 5%, inter-assay precision CV < 5%; VCAM1: ABclonal, WoburnMA, USA, catalogue number RK00026, detection range = 15.6–1,000 pg/mL sensitivity = 3.85 pg/mL, intra-assay precision coefficient of variation (CV) ≤10%, inter-assay precision CV ≤ 15%; LRG1: ABclonal, WoburnMA, USA, catalogue number RK01800, detection range = 31.2–2000 pg/mL, sensitivity = 15.6 pg/mL, intra-assay precision coefficient of variation (CV) ≤10%, inter-assay precision CV ≤ 15%).

Techniques: Biomarker Discovery

Journal: Frontiers in Pharmacology

Article Title: Unveiling novel serum biomarkers in intrahepatic cholangiocarcinoma: a pilot proteomic exploration

doi: 10.3389/fphar.2024.1440985

Figure Lengend Snippet: Serum levels of SAA1, SAA4, VCAM1, and LRG1 by ELISA.

Article Snippet: These measurements were made from individual samples of the validation cohort and were performed in duplicate, following the instructions provided with the kits. (SAA1: ABclonal, WoburnMA, USA, catalogue number RK04228, detection range = 0.156–10 ng/mL sensitivity = 0.071 ng/mL, intra-assay precision coefficient of variation (CV) < 10%, inter-assay precision CV < 15%; SAA4: Elabscience Wuhan, China, catalogue number E-EL-H5638, detection range = 78.13–5,000 pg/mL sensitivity = 46.88 pg/mL, intra-assay precision coefficient of variation (CV) < 5%, inter-assay precision CV < 5%; VCAM1: ABclonal, WoburnMA, USA, catalogue number RK00026, detection range = 15.6–1,000 pg/mL sensitivity = 3.85 pg/mL, intra-assay precision coefficient of variation (CV) ≤10%, inter-assay precision CV ≤ 15%; LRG1: ABclonal, WoburnMA, USA, catalogue number RK01800, detection range = 31.2–2000 pg/mL, sensitivity = 15.6 pg/mL, intra-assay precision coefficient of variation (CV) ≤10%, inter-assay precision CV ≤ 15%).

Techniques: Enzyme-linked Immunosorbent Assay

Journal: Frontiers in Pharmacology

Article Title: Unveiling novel serum biomarkers in intrahepatic cholangiocarcinoma: a pilot proteomic exploration

doi: 10.3389/fphar.2024.1440985

Figure Lengend Snippet: Validation of mass spectrometry-based results by ELISA HC = healthy controls; iCCA = intrahepatic cholangiocarcinoma; HCC = hepatocellular carcinoma; PSC = primary sclerosing cholangitis; SAA1 = Serum amyloid-1; SAA4 = Serum amyloid-4; VCAM1 = Vascular cell adhesion protein 1; LRG1 = Leucine-rich alpha-2-glycoprotein; * = statistically significant ( p < 0.05); MS = mass spectrometry; ELISA = enzyme-linked immunosorbent assay.

Article Snippet: These measurements were made from individual samples of the validation cohort and were performed in duplicate, following the instructions provided with the kits. (SAA1: ABclonal, WoburnMA, USA, catalogue number RK04228, detection range = 0.156–10 ng/mL sensitivity = 0.071 ng/mL, intra-assay precision coefficient of variation (CV) < 10%, inter-assay precision CV < 15%; SAA4: Elabscience Wuhan, China, catalogue number E-EL-H5638, detection range = 78.13–5,000 pg/mL sensitivity = 46.88 pg/mL, intra-assay precision coefficient of variation (CV) < 5%, inter-assay precision CV < 5%; VCAM1: ABclonal, WoburnMA, USA, catalogue number RK00026, detection range = 15.6–1,000 pg/mL sensitivity = 3.85 pg/mL, intra-assay precision coefficient of variation (CV) ≤10%, inter-assay precision CV ≤ 15%; LRG1: ABclonal, WoburnMA, USA, catalogue number RK01800, detection range = 31.2–2000 pg/mL, sensitivity = 15.6 pg/mL, intra-assay precision coefficient of variation (CV) ≤10%, inter-assay precision CV ≤ 15%).

Techniques: Biomarker Discovery, Mass Spectrometry, Enzyme-linked Immunosorbent Assay

Journal: The Journal of Clinical Investigation

Article Title: SAA1/FPR2 signaling between keratinocytes and neutrophils sustains chronic inflammation in Sweet syndrome

doi: 10.1172/JCI193566

Figure Lengend Snippet: ( A ) Ligand-receptor analysis reveals keratinocyte- and neutrophil-specific interactions. Keratinocytes expressed SAA1 transcripts and neutrophils expressed the FPR2 receptor (red dot, right-most column). ( B ) Dot plot demonstrating predominantly cell-specific expression of SAA1 and FPR2 transcripts. The dot size reflects the percentage of cells expressing the gene, and the color illustrates the level of gene expression. ( C ) Representative immunofluorescence staining images and quantification from 5 diseased and 5 control samples, confirming the expression of SAA1 and FPR2 in keratinocytes and neutrophils, respectively. Scale bars: 100 μm. ( D ) Dot plot comparing keratinocyte SAA1 and the control gene DEFB1 in different inflammatory skin conditions. The dot size reflects the percentage of cells expressing the gene, and the color illustrates the level of gene expression. ( E ) SAA1 secretion measured by ELISA in healthy neutrophils or healthy neutrophils exposed to keratinocytes. ( F ) Antibodies blocking SAA1 and FPR2 restored long-lived neutrophil lifespan to WT neutrophil levels. ( G ) Recombinant human SAA1 increased neutrophil survival at 72 hours ( n = 3 independent donors). Data indicate the mean ± SEM. * P < 0.05, ** P < 0.01, and *** P < 0.001, by 2-tailed, unpaired Student’s t test ( E and G ) and 1-way ANOVA with individual comparisons ( F ).

Article Snippet: For immunofluorescence microscopy, the following antibodies were used: CD3 (MCA1477, Bio-Rad), CD8 (170306S, Cell Signaling Technology), CD20 (14-0202-82, Thermo Fisher Scientific), CD68 (14-0688-82, Thermo Fisher Scientific), FCN1 (PA5-51552, Thermo Fisher Scientific), S100A8 (33254S, Cell Signaling Technology), S100A9 (34425S, Cell Signaling Technology), MHC-II (68258S, Cell Signaling Technology), IgG (66362S, Cell Signaling Technology), NE (AB68672, Abcam), ELANE (LS-B4244, LS-Bio), FPR2 (NLS1878, Novus), SAA1 (16721-1-AP, Proteintech), and MPO (sc-52707, Santa Cruz Biotechnology).

Techniques: Expressing, Gene Expression, Immunofluorescence, Staining, Control, Enzyme-linked Immunosorbent Assay, Blocking Assay, Recombinant

Journal: Frontiers in Immunology

Article Title: Balancing inflammation: the specific roles of serum amyloid A proteins in sterile and infectious diseases

doi: 10.3389/fimmu.2025.1544085

Figure Lengend Snippet: NF-κB activation in RAW cells overexpressing SAA proteins was assessed in response to stimulation with various immune ligands, or treatment with purified SAA proteins, compared to the response to LPS in control RAW cells. RAW-Blue™ cells (RAW 264.7) overexpressing SAA proteins were treated with a single dose of LPS, IL-6, TNFα, FSL-1, Pam3CSK4, FLAP2, R-848, Poly(I), ODN2395, C12-iE-DAP, MDP, Poly dT, LTA-SA, Zymosan, and Peptidoglycan overnight to activate NF-κB. Non-stimulated cells served as negative controls. (A) Heatmap showing NF-κB activity in RAW cells overexpressing SAA proteins (SAA1, SAA2, SAA3, SAA4) normalized against control RAW cells, with log2-transformed absorbance values (@600nm) displayed. (B) Representative bar graph of NF-κB activity in response to LPS stimulation in RAW cells overexpressing DDK-tagged SAA proteins (SAA1-DDK to SAA4-DDK) compared to unmodified RAW cells (n = 3). (C) NF-κB activity in RAW cells treated with purified SAA proteins (SAA1-100ng/ml, SAA2-10ng/ml, SAA3-10ng/ml, SAA4-100ng/ml) in the absence or presence of LPS (n = 3). Data represent mean ± SEM. Statistical significance is denoted as *(p < 0.05), **(p < 0.01), ***(p < 0.001), and ****(p < 0.0001). (ns = non-significant).

Article Snippet: The expression plasmids with Myc-DDK tags for SAA1 (MR200611, Saa1 (NM_009117) Mouse Tagged ORF Clone), SAA2 (MR219150, Saa2 (NM_011314) Mouse Tagged ORF Clone), SAA3 (MR200605, Saa3 (NM_011315) Mouse Tagged ORF Clone), and SAA4 (MR200725, Saa4 (NM_011316) Mouse Tagged ORF Clone) were purchased from Origene Technologies.

Techniques: Activation Assay, Purification, Control, Activity Assay, Transformation Assay

Journal: Frontiers in Immunology

Article Title: Balancing inflammation: the specific roles of serum amyloid A proteins in sterile and infectious diseases

doi: 10.3389/fimmu.2025.1544085

Figure Lengend Snippet: Concentrations of SAA proteins in response to LPS and P. aeruginosa infection. Concentrations of SAA1, SAA2, SAA3, and SAA4 were measured in samples from Healthy, LPS-treated, and P. aeruginosa -infected conditions (Healthy n = 6; LPS n=8; and P. aeruginosa n=10). Data represent mean ± SEM. Statistical significance is indicated by * (p < 0.05), ** (p < 0.01), *** (p < 0.001), and **** (p < 0.0001). (ns = non-significant).

Article Snippet: The expression plasmids with Myc-DDK tags for SAA1 (MR200611, Saa1 (NM_009117) Mouse Tagged ORF Clone), SAA2 (MR219150, Saa2 (NM_011314) Mouse Tagged ORF Clone), SAA3 (MR200605, Saa3 (NM_011315) Mouse Tagged ORF Clone), and SAA4 (MR200725, Saa4 (NM_011316) Mouse Tagged ORF Clone) were purchased from Origene Technologies.

Techniques: Infection

Journal: Frontiers in Immunology

Article Title: Balancing inflammation: the specific roles of serum amyloid A proteins in sterile and infectious diseases

doi: 10.3389/fimmu.2025.1544085

Figure Lengend Snippet: NF-κB activation in RAW cells overexpressing SAA proteins was assessed in response to stimulation with various immune ligands, or treatment with purified SAA proteins, compared to the response to LPS in control RAW cells. RAW-Blue™ cells (RAW 264.7) overexpressing SAA proteins were treated with a single dose of LPS, IL-6, TNFα, FSL-1, Pam3CSK4, FLAP2, R-848, Poly(I), ODN2395, C12-iE-DAP, MDP, Poly dT, LTA-SA, Zymosan, and Peptidoglycan overnight to activate NF-κB. Non-stimulated cells served as negative controls. (A) Heatmap showing NF-κB activity in RAW cells overexpressing SAA proteins (SAA1, SAA2, SAA3, SAA4) normalized against control RAW cells, with log2-transformed absorbance values (@600nm) displayed. (B) Representative bar graph of NF-κB activity in response to LPS stimulation in RAW cells overexpressing DDK-tagged SAA proteins (SAA1-DDK to SAA4-DDK) compared to unmodified RAW cells (n = 3). (C) NF-κB activity in RAW cells treated with purified SAA proteins (SAA1-100ng/ml, SAA2-10ng/ml, SAA3-10ng/ml, SAA4-100ng/ml) in the absence or presence of LPS (n = 3). Data represent mean ± SEM. Statistical significance is denoted as *(p < 0.05), **(p < 0.01), ***(p < 0.001), and ****(p < 0.0001). (ns = non-significant).

Article Snippet: The expression plasmids with Myc-DDK tags for SAA1 (MR200611, Saa1 (NM_009117) Mouse Tagged ORF Clone), SAA2 (MR219150, Saa2 (NM_011314) Mouse Tagged ORF Clone), SAA3 (MR200605, Saa3 (NM_011315) Mouse Tagged ORF Clone), and SAA4 (MR200725, Saa4 (NM_011316) Mouse Tagged ORF Clone) were purchased from Origene Technologies.

Techniques: Activation Assay, Purification, Control, Activity Assay, Transformation Assay

Journal: Frontiers in Immunology

Article Title: Balancing inflammation: the specific roles of serum amyloid A proteins in sterile and infectious diseases

doi: 10.3389/fimmu.2025.1544085

Figure Lengend Snippet: Concentrations of SAA proteins in response to LPS and P. aeruginosa infection. Concentrations of SAA1, SAA2, SAA3, and SAA4 were measured in samples from Healthy, LPS-treated, and P. aeruginosa -infected conditions (Healthy n = 6; LPS n=8; and P. aeruginosa n=10). Data represent mean ± SEM. Statistical significance is indicated by * (p < 0.05), ** (p < 0.01), *** (p < 0.001), and **** (p < 0.0001). (ns = non-significant).

Article Snippet: The expression plasmids with Myc-DDK tags for SAA1 (MR200611, Saa1 (NM_009117) Mouse Tagged ORF Clone), SAA2 (MR219150, Saa2 (NM_011314) Mouse Tagged ORF Clone), SAA3 (MR200605, Saa3 (NM_011315) Mouse Tagged ORF Clone), and SAA4 (MR200725, Saa4 (NM_011316) Mouse Tagged ORF Clone) were purchased from Origene Technologies.

Techniques: Infection

Journal: Cancer Immunology, Immunotherapy : CII

Article Title: Neutrophil-activating secretome characterizes palbociclib-induced senescence of breast cancer cells

doi: 10.1007/s00262-024-03695-5

Figure Lengend Snippet: Senescent cells express recruiting and activating factors for neutrophils. A Quantitative real-time PCR of SAA1 and SAA2 genes from total RNA extracted from control proliferating and senescent MCF7 and MDA-MB-231 cells. Data are reported as fold increase by using the 2 −ΔΔCt method and the average of control samples for the ΔΔ calculation. Bars show mean ± SEM from at least three independent experiments. Statistical analysis was performed using multiple t-test (one for each gene of interest). * P < 0.05. B Quantification by ELISA of SAA1 secreted by control proliferating and senescent MCF7 and MDA-MB-231 cells in 24 h-conditioned media. Bars show mean ± SEM and statistical significance was determined by unpaired two-tailed Student’s t-test. *** P < 0.001, **** P < 0.0001. C Quantification by ELISA of IL-8 and SAA1 secreted by proliferating, quiescent, and senescent human foreskin fibroblasts in 24 h-conditioned media. Bars show mean ± SEM and statistical significance was determined by one-way ANOVA followed by Tukey’s multiple-comparisons test. * P < 0.05, # P = 0.091

Article Snippet: For the targets CXCL1 (Hs00236937_m1), CXCL8 (Hs00174103_m1), SAA1 (Hs07291672_g1), and SAA2 (Hs01667582_m1), qPCR assays were performed using TaqMan Universal PCR Master Mix (#4369016) and gene expression assays from Applied Biosystems.

Techniques: Real-time Polymerase Chain Reaction, Control, Enzyme-linked Immunosorbent Assay, Two Tailed Test