Journal: Scientific Reports

Article Title: Molecular determinants of epithelial mesenchymal transition in mouse placenta and trophoblast stem cell

doi: 10.1038/s41598-023-37977-2

Figure Lengend Snippet: PCR array analysis profiling functional epithelial and mesenchymal transition (EMT) transcriptome and validation of EMT-associated transcripts in mouse implantation sites on E7.5 and E9.5. ( A ) Scatter plot of PCR array shows differential EMT gene expression of E7.5 and E9.5 mouse placental tissue. Genes represented by black dots (within black lines) are with similar expression patterns and close to the line of regression, whereas, up-regulated and down-regulated genes are represented by red dots (above black lines) and green dots (below black lines), respectively. The Scatter plot determines the log 10 of normalized gene expression levels in E7.5 (x axis) versus that in E9.5 (y axis). ( B ) Functional annotation of 14 differentially regulated EMT genes in all three experiments at the IS on E7.5 and E9.5 are shown in a flowchart. Quantitative real-time PCR analysis shows significant decrease in mRNA level of EMT-associated genes at IS of E9.5 when compared with E7.5. Real time data are grouped according to functional annotation. ( C ) Transcription factors: Snai2 , Zeb1 , Stat3 , FoxC2. ( D ) Extracellular matrix and Cell Adhesion genes: Bmp1 , Itga5 , Vcan , Col3A1. ( E ) Cell migration and motility genes: Vim , Msn , Fn1. ( F ) Genes associated with differentiation and development: Wnt5B , Jag1 , Notch1 . Gapdh was used as a reference gene for normalization. Error bars represents standard error of mean from three different biological replicates (n = 3, * p < 0.05, ** p < 0.01, and ***p < 0.005).

Article Snippet: 8 , COL3A1 , SCBT , sc-514601 , 1:200.

Techniques: Functional Assay, Biomarker Discovery, Gene Expression, Expressing, Real-time Polymerase Chain Reaction, Migration

Journal: Scientific Reports

Article Title: Molecular determinants of epithelial mesenchymal transition in mouse placenta and trophoblast stem cell

doi: 10.1038/s41598-023-37977-2

Figure Lengend Snippet: List of validated genes from the array.

Article Snippet: 8 , COL3A1 , SCBT , sc-514601 , 1:200.

Techniques: Binding Assay

Journal: Scientific Reports

Article Title: Molecular determinants of epithelial mesenchymal transition in mouse placenta and trophoblast stem cell

doi: 10.1038/s41598-023-37977-2

Figure Lengend Snippet: Decreased expression of EMT-associated proteins at implantation site on E9.5. Western Blot analysis of EMT-associated markers on E7.5–E9.5. Western Blots are grouped according to functional annotation. ( A ) Transcription factors: SNAI2, ZEB1, STAT3, FOXC2 . ( B ) Extracellular matrix and Cell Adhesion markers BMP1, ITGA5, VCAN, COL3A1 . ( C ) Proteins involved in cell migration and motility VIM, MSN, FN1 . ( D ) Proteins associated with differentiation and development WNT5B, JAG1, NOTCH1. GAPDH was used as loading control and densitometry analysis was done using ImageJ software. Error bars represents standard error of mean from three different biological replicates (n = 3, *p < 0.05, **p < 0.01, and ***p < 0.005).

Article Snippet: 8 , COL3A1 , SCBT , sc-514601 , 1:200.

Techniques: Expressing, Western Blot, Functional Assay, Migration, Control, Software

Journal: Scientific Reports

Article Title: Molecular determinants of epithelial mesenchymal transition in mouse placenta and trophoblast stem cell

doi: 10.1038/s41598-023-37977-2

Figure Lengend Snippet: List of primers used for real-time PCR analysis.

Article Snippet: 8 , COL3A1 , SCBT , sc-514601 , 1:200.

Techniques: Real-time Polymerase Chain Reaction, Sequencing

Journal: Scientific Reports

Article Title: Molecular determinants of epithelial mesenchymal transition in mouse placenta and trophoblast stem cell

doi: 10.1038/s41598-023-37977-2

Figure Lengend Snippet: List of antibodies used in western blot analysis.

Article Snippet: 8 , COL3A1 , SCBT , sc-514601 , 1:200.

Techniques: Western Blot

Journal: Cancer Immunology, Immunotherapy : CII

Article Title: Spatial transcriptomics reveals prognostically LYZ + fibroblasts and colocalization with FN1 + macrophages in diffuse large B-cell lymphoma

doi: 10.1007/s00262-025-03968-7

Figure Lengend Snippet: Prognostic value of LYZ and LILRB4 proteins in DLBCL receiving R-CHOP ( n = 37, 10X) and aNSCLC receiving ICIs ( n = 29, 2X and 10X). A Representative IHCs staining of LYZ in patient 1 (PFS = 1697 days) and patient 2 (PFS = 341 days), LILRB4 in patient 3 (PFS = 64 days) and patient 4 (PFS = 826 days). B Kaplan–Meier survival curves of PFS grouped by the LYZ and LILRB4 expression in DLBCL. C Representative mIF staining of LYZ, LILRB4, and pan Cytokeratin. D Kaplan–Meier survival curves of OS grouped by the LYZ and LILRB4 expression in aNSCLC. E Kaplan–Meier survival curves of PFS grouped by the COL3A1 expression and FN1 + macrophages in DLBCL. DLBCL: diffuse large B cell lymphoma; R-CHOP: rituximab, cyclophosphamide, doxorubicin: vincristine, and prednisone; aNSCLC: advanced non-small cell lung cancer; ICIs: immune checkpoint inhibitors; IHC: immunohistochemistry; PFS: progression-free survival; mIF: multiple immunofluorescence; and OS: overall survival

Article Snippet: Rabbit anti-human COL3A1 IgG antibody , #63034S , Cell Signaling Technology.

Techniques: Staining, Expressing, Immunohistochemistry, Immunofluorescence

Journal: Cancer Immunology, Immunotherapy : CII

Article Title: Spatial transcriptomics reveals prognostically LYZ + fibroblasts and colocalization with FN1 + macrophages in diffuse large B-cell lymphoma

doi: 10.1007/s00262-025-03968-7

Figure Lengend Snippet: Prognostic significance of autoantibodies against COL1A2, COL3A1, and FN1 in patients with DLBCL receiving R-CHOP ( n = 20 and 125) and NSCLC treated with ICIs ( n = 36). A Volcano plot, boxplot, and representative density plots of patients illustrating the distribution of COL1A2 autoantibodies in DLBCL. B Kaplan–Meier curve for PFS based on COL1A2 autoantibody levels in DLBCL. C Kaplan–Meier curves for OS and PFS in NSCLC patients receiving immunotherapy, stratified by COL1A2 and COL3A1 mRNA levels in GSE128989 and autoantibody presence, alongside representative density plots of COL1A2 and COL3A1 autoantibodies. D Comparison of FN1 autoantibody levels between healthy controls and DLBCL, with Kaplan–Meier analysis for PFS based on FN1 autoantibody levels. DLBCL: diffuse large B cell lymphoma; R-CHOP: rituximab, cyclophosphamide, doxorubicin: vincristine, and prednisone; NSCLC: non-small cell lung cancer; ICIs: immune checkpoint inhibitor; OS: overall survival; and PFS: progression-free survival

Article Snippet: Rabbit anti-human COL3A1 IgG antibody , #63034S , Cell Signaling Technology.

Techniques: Comparison

Journal: Cancer Immunology, Immunotherapy : CII

Article Title: Spatial transcriptomics reveals prognostically LYZ + fibroblasts and colocalization with FN1 + macrophages in diffuse large B-cell lymphoma

doi: 10.1007/s00262-025-03968-7

Figure Lengend Snippet: Reagents and tools table

Article Snippet: Rabbit anti-human COL3A1 IgG antibody , #63034S , Cell Signaling Technology.

Techniques: Formalin-fixed Paraffin-Embedded, Gene Expression, RNA Sequencing, Sequencing, Biomarker Discovery, Clinical Proteomics, Microarray, Control, Immunohistochemistry, Microscopy, Immunofluorescence, Software

Journal: International Journal of Nanomedicine

Article Title: Antioxidant Carbon Dots and Ursolic Acid Co-Encapsulated Liposomes Composite Hydrogel for Alleviating Adhesion Formation and Enhancing Tendon Healing in Tendon Injury

doi: 10.2147/ijn.s466312

Figure Lengend Snippet: Figure 4 RCDs/UA@Lipo alleviated H2O2-induced oxidative stress and TGF-β1 induced fibrosis-specific markers separately. (A) Immunofluorescence staining images of intracellular ROS and superoxide detected by DCFH-DA probe. (B) mitochondrial membrane potential (ΔΨm) detected by JC-1 probe. (C) tendon fibrosis markers (COL I, COL III, α-SMA) of NIH3T3. (D–H) Semiquantitative analysis of the relative fluorescent intensity of (A–C) (n = 3). (D and E) Model group is H2O2 group, (F–H) Model group is TGF-β1 group. Data are presented as mean ± SD; comparisons between the groups were performed one-way ANOVA. *P < 0.05; **P < 0.01; ***P < 0.001.

Article Snippet: Incubation proceeded with rabbit anti-mouse antibodies against COL I (1:500; Cat# 91144, CST, USA) and COL III (1:200; Cat#22734-1-AP, Proteintech, USA) and α-SMA (myofibroblast biomarker) (1:200; Cat #19245, CST, USA) at 4°C overnight.

Techniques: Immunofluorescence, Staining, Membrane

Journal: International Journal of Nanomedicine

Article Title: Antioxidant Carbon Dots and Ursolic Acid Co-Encapsulated Liposomes Composite Hydrogel for Alleviating Adhesion Formation and Enhancing Tendon Healing in Tendon Injury

doi: 10.2147/ijn.s466312

Figure Lengend Snippet: Figure 6 RCDs/UA@Lipo-HAMA reduced adhesion of injured tendons at macroscopic and histological levels at various time points post-injury. (A) Schematic diagram of surgical procedures of the ATI. (B) Gross view of ATI. (C)Representative images of immunofluorescence staining of tendon antioxidant (Nrf-2, HO-1) and anti-inflammatory markers (CD68, iNOS) at 2 weeks post-injury (n = 3). (D) Representative images of immunofluorescence staining of tendon antifibrosis (COL III, α-SMA) at 6 weeks post- injury (n = 3). (E) Representative images of immunohistochemical staining of tendon markers (Vimentin, MMP2, α-SMA) antifibrosis at 6 weeks post-injury (n = 4). (F–N) Semiquantitative analysis of expression level of tendon marker of (C–E), respectively. Data are presented as mean ± SD; comparisons between the groups were performed by one-way ANOVA. *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001.

Article Snippet: Incubation proceeded with rabbit anti-mouse antibodies against COL I (1:500; Cat# 91144, CST, USA) and COL III (1:200; Cat#22734-1-AP, Proteintech, USA) and α-SMA (myofibroblast biomarker) (1:200; Cat #19245, CST, USA) at 4°C overnight.

Techniques: Immunofluorescence, Staining, Immunohistochemical staining, Expressing, Marker

Journal: Breast Cancer Research : BCR

Article Title: BRCA1 mutation influences progesterone response in human benign mammary organoids

doi: 10.1186/s13058-019-1214-0

Figure Lengend Snippet: Confirmation and validation of ECM genes . a Confirmation of ECM genes was done by real-time PCR analysis of the samples used in the RNA-seq analysis. The data are fold changes of hormone treatment (dotted red line) and represent the mean ± SEM from three technical replicates (* p < 0.05, ** p < 0.01, *** p < 0.005, **** p < 0.001). b Validation of ECM genes was done by real-time PCR using new patient-derived individual BRCA1 mut and non-carrier organoids treated with E2+P4 and E2+P4+TPA. The data are fold changes of hormone treatment (dotted red line) and represent the mean ± SEM from three technical replicates (* p < 0.05, ** p < 0.01, *** p < 0.005, **** p < 0.001. c IHC staining of ECM proteins MMP10, COL1A1, COL3A1, and FN1 were performed in non-carrier and BRCA1 mut organoids. Scale bar, 100 μm

Article Snippet: The primary antibodies used were ER (1:200, Santa Cruz SC71064), PR (1:200, DAKO, M3568), pan cytokeratin (panCK; 1:200, Abcam, ab7753), Cytokeratin 18 (CK18; 1:200, Abcam, 93741), vimentin (Vim; 1:200, Abcam, 92547), α smooth muscle actin (αSMA; 1:200, Novus Biologicals, 600531), Cytokeratin 5/6 (CK5/6; 1:200, Agilent Technologies, M723729-2), COL3A1 (Atlas antibodies, 1:200, HPA007583), COL1A1 (LS Bio, 1:400, LS-C343921), MMP10 (LS Bio, 1:400, LS-C118518), MMP1(LS Bio, 1:400, LS-B8645), Ki67 (Dako, 1:200, GA62661-2), E-cadherin (BD Biosciences, 1:200, 610181), ITGB4 (LS Bio, 1:200, LS-B3778), and ALDH1A1 isoform (LSBio, 1:400, LS-B10149).

Techniques: Biomarker Discovery, Real-time Polymerase Chain Reaction, RNA Sequencing, Derivative Assay, Immunohistochemistry

Journal: Reproductive biomedicine online

Article Title: Transcriptomic analysis supports collective endometrial cell migration in the pathogenesis of adenomyosis

doi: 10.1016/j.rbmo.2022.05.007

Figure Lengend Snippet: Validation of potential target genes in top enriched biological processes in the eutopic endometrium of women with versus without adenomyosis. (A) mRNA levels of IL1B , IL18 and TNF in eutopic endometrium of adenomyosis patients ( n = 10) and controls ( n = 10) detected by quantitative reverse transcription polymerase chain reaction analysis (qRT-PCR). All endometrial samples were in the proliferative phase. β -ACTIN was used as reference gene for qRT-PCR analysis. P -values are 0.002, 0.041 and 0.022, respectively; (B) mRNA levels of MMP1 , MMP8 , MMP13 and TIMP1 in eutopic endometrium of adenomyosis patients ( n = 10) and controls ( n = 10) detected by qRT-PCR analysis. P -values are 0.002, 0.001, 0.008 and 0.0085, respectively; (C) mRNA levels of COL1A1 , COL1A2 and COL3A1 in eutopic endometrium of adenomyosis patients (n = 10) and controls (n = 10) detected by qRT-PCR analysis; (D) mRNA levels of HAS1 , HAS2 , HAS3 and CD44 in eutopic endometrium of adenomyosis patients ( n = 10) and controls ( n = 10) detected by qRT-PCR analysis. P -values are 0.016, 0.049, 0.015 and 0.484, respectively. Data are presented as means ± SEM. * P < 0.05, ** P < 0.01; (E) protein levels of COL1A1, COLIII, MMP1 and MMP13 in the endometrium of adenomyosis patients and controls. n = 6 for each group. GAPDH was used as reference control, and the ratio of band intensity of a target protein to that of the intensity of GAPDH was obtained at each target protein level . The P -value of the protein level of COL1A1, COLIII, MMP1 and MMP13 in adenomyosis versus controls are 0.009, 0.024, 0.018 and 0.031, respectively. * P < 0.05, ** P < 0.01; (F) Masson stain of eutopic endometrium in adenomyosis patients versus controls.

Article Snippet: Samples of protein (35 μg) were separated on 10% sodium dodecyl sulfate gels in 80–120 V for 1.5 h and then wet transferred to a nitrocellulose membrane at 200 mA for 1.5–2 h. After blocking in 5% bovine serum albumin for 1 h, the nitrocellulose membrane was incubated with primary antibody dilution buffer (Beyotime, Shanghai, China) diluted antibody against matrix metalloproteinase 1 (MMP1) (1:1000) (Proteintech, Wuhan, China), MMP13 (1:1000) (Proteintech, Wuhan, China), collagen III (COLIII) (1:1000) (Proteintech, Wuhan, China), and COL1A1 (1:1000) (Cell Signaling Technology, Danvers, MA, USA) at 4°C overnight.

Techniques: Biomarker Discovery, Reverse Transcription, Polymerase Chain Reaction, Quantitative RT-PCR, Control, Staining