Journal: Frontiers in Oncology

Article Title: Identifying key transcription factors and immune infiltration in non-small-cell lung cancer using weighted correlation network and Cox regression analyses

doi: 10.3389/fonc.2023.1112020

Figure Lengend Snippet: The primers of select genes.

Article Snippet: Antibodies used in this study included Vimentin (#5741), SLUG (#9585), β-catenin (#8480), and Anti-rabbit Alexa Fluor ® 594 Conjugate (#8889) from Cell Signaling Technology and MMP9 (10375-2-AP), SNAI1 (13099-1-AP), SNAI3 (21350-1-AP), and SETDB2 (14428-1-AP) from Proteintech.

Techniques:

Journal: Frontiers in Oncology

Article Title: Identifying key transcription factors and immune infiltration in non-small-cell lung cancer using weighted correlation network and Cox regression analyses

doi: 10.3389/fonc.2023.1112020

Figure Lengend Snippet: Expression profile and survival analysis of 5 transcription factors (TFs) in NSCLC. (A) Expression profile of 5 TFs (SETDB2, SNAI3, SCML4, ZNF540, and ETV1) in LUAD. (B) Expression profile of 5 TFs (SETDB2, SNAI3, SCML4, ZNF540, and ETV1) in LUSC. (C) Kaplan–Meier analysis of 5 TFs (SETDB2, SNAI3, SCML4, ZNF540, and ETV1) using Affymetrix microarray data. (D) Kaplan–Meier analysis of 5 TFs (SETDB2, SNAI3, SCML4, ZNF540, and ETV1) using RNA-seq data. (E) Analysis of the 5-TFs protein interaction network.

Article Snippet: Antibodies used in this study included Vimentin (#5741), SLUG (#9585), β-catenin (#8480), and Anti-rabbit Alexa Fluor ® 594 Conjugate (#8889) from Cell Signaling Technology and MMP9 (10375-2-AP), SNAI1 (13099-1-AP), SNAI3 (21350-1-AP), and SETDB2 (14428-1-AP) from Proteintech.

Techniques: Expressing, Microarray, RNA Sequencing

Journal: Frontiers in Oncology

Article Title: Identifying key transcription factors and immune infiltration in non-small-cell lung cancer using weighted correlation network and Cox regression analyses

doi: 10.3389/fonc.2023.1112020

Figure Lengend Snippet: Validating the TFs phenotypes, functions, and expression in lung cancer. (A) SETDB2, SNAI3, SCML4, ZNF540, and ETV1 mRNA expression levels in the normal human bronchial epithelial cell line (BEAS-2B), lung adenocarcinoma cell lines (A549, HCC827, H1299, and H1975), and lung squamous cell lines (EPLC-272H, H226, H157, and H2170) using RT-qPCR. Blue box: normal human bronchial epithelial cell line (BEAS-2B). Red box: lung cancer cell lines. (B) The mRNA expression levels of SETDB2 and SNAI3 in the normal human bronchial epithelial cell line (BEAS-2B), lung adenocarcinoma cell lines (A549, HCC827, H1299, and H1975), and lung squamous cell lines (EPLC-272H, H226, H157, and H2170) using RT-qPCR. (C) EdU assays were performed in A549 cells infected with siCtrl, siSETDB2, and siSNAI3. siCtrl, siControl; siSE2, siSETDB2; siSN3, siSNAI3. (D) Wound healing experiments were performed in A549, HCC827, and H1299 transfected with siCtrl, siSETDB2, and siSNAI3. siCtrl, siControl; siSE2, siSETDB2; siSN3, siSNAI3. (E) Transwell invasion assays were performed on lung cancer cells (A549, HCC827, and H1299) infected with siCtrl, siSETDB2, and siSNAI3. siCtrl, siControl; siSE2, siSETDB2; siSN3, siSNAI3. (F) Immunofluorescence staining including MMP9, Vimentin, β-catenin, SNAI1 and SLUG was performed in A549 cells transfected with siCtrl, siSETDB2 and siSNAI3. Blue fluorescence of DAPI labeled cell nucleus, red fluorescence of labeled corresponding protein. siCtrl, siControl; siSE2, siSETDB2; siSN3, siSNAI3. MFI, mean fluorescence intensity. (G) The mRNA expression levels of metastatic markers (MMP9, Vimentin, β-catenin, SNAI1, and SLUG) as well as SNAI3 and SETDB2 were detected by RT-qPCR in A549 cells transfected with siCtrl, siSETDB2, and siSNAI3. siCtrl, siControl. (H) The protein levels of metastatic markers (MMP9, Vimentin, β-catenin, SNAI1, and SLUG) as well as SNAI3 and SETDB2 were detected by western blotting in A549 cells transfected with siCtrl, siSETDB2, and siSNAI3. siCtrl, siControl; siSE2, siSETDB2; siSN3, siSNAI3. (I) The mRNA expression levels of stem cell markers (SOX2, OCT4, and NANOG) in A549 cells transfected with siCtrl, siSETDB2, and siSNAI3 using RT-qPCR. siCtrl, siControl. (B-E, G, I) Error bar represents mean ± SD of three independent experiments. * p < 0.05, ** p < 0.01. Student’s t-test.

Article Snippet: Antibodies used in this study included Vimentin (#5741), SLUG (#9585), β-catenin (#8480), and Anti-rabbit Alexa Fluor ® 594 Conjugate (#8889) from Cell Signaling Technology and MMP9 (10375-2-AP), SNAI1 (13099-1-AP), SNAI3 (21350-1-AP), and SETDB2 (14428-1-AP) from Proteintech.

Techniques: Expressing, Quantitative RT-PCR, Infection, Transfection, Immunofluorescence, Staining, Fluorescence, Labeling, Western Blot

Journal: bioRxiv

Article Title: Distinct Roles for SETα and SETβ in Early Cell Fate Decisions

doi: 10.1101/2024.09.21.614244

Figure Lengend Snippet: A) Western blot using anti-SET antibodies showing addback of SETα or SETβ in SET-KO background compared to SET-WT. α-tubulin (top band) was used as loading control. B) Venn diagrams comparing MAnorm-enriched IDR filtered MACS2-called peaks for SETα and SETβ. C) GREAT analysis of SETα-enriched regions for “GO Biological Processes” D) Same as (C) for SETβ. E) GREAT analysis of SETα-enriched regions for “Mouse Phenotype Single KO”. F) Same as (E) for SETβ.

Article Snippet: The following antibodies were used in this study: SET (A302-261A, Bethyl), α-TUBULIN (ab4074, Abcam) and HA (ab9110, Abcam).

Techniques: Western Blot, Control

Journal: Scientific Reports

Article Title: The prognostic significance of VISTA and CD33-positive myeloid cells in cutaneous melanoma and their relationship with PD-1 expression

doi: 10.1038/s41598-020-71216-2

Figure Lengend Snippet: Clinico-histopathological characteristics of the 136 cutaneous melanomas according to CD33, VISTA and PD-1 expression.

Article Snippet: Paraffin-embedded sections were immunostained with anti-VISTA (1:200, ProSci Incorporation, CA, USA), anti-CD33 (1:100, Leica Biosystems, Newcastle, UK), or anti-PD-1 (1:100, Ventana, Tucson, AZ, USA) antibodies.

Techniques: Expressing

Journal: Scientific Reports

Article Title: The prognostic significance of VISTA and CD33-positive myeloid cells in cutaneous melanoma and their relationship with PD-1 expression

doi: 10.1038/s41598-020-71216-2

Figure Lengend Snippet: Correlations among CD33, VISTA, and PD-1 expression.

Article Snippet: Paraffin-embedded sections were immunostained with anti-VISTA (1:200, ProSci Incorporation, CA, USA), anti-CD33 (1:100, Leica Biosystems, Newcastle, UK), or anti-PD-1 (1:100, Ventana, Tucson, AZ, USA) antibodies.

Techniques: Expressing

Journal: Scientific Reports

Article Title: The prognostic significance of VISTA and CD33-positive myeloid cells in cutaneous melanoma and their relationship with PD-1 expression

doi: 10.1038/s41598-020-71216-2

Figure Lengend Snippet: Expression of CD33 and VISTA in cutaneous melanoma. ( A ) High intratumoral expression (immunohistochemical score of 3, red color, cytoplasmic) of CD33 in acral melanoma (× 100). ( B ) High intratumoral expression (score 3, red color, cytoplasmic) of VISTA in nodular melanoma (× 100). ( C ) High peritumoral expression (score 3, red color, cytoplasmic) of CD33 in acral melanoma (× 100). ( D ) High peritumoral expression (score 3, red color, cytoplasmic) of VISTA in nodular melanoma (× 200). ( E ) Dual immunofluorescence staining of ( A ) CD33 and VISTA (CD33, red, cytoplasmic; VISTA, green, cytoplasmic) and ( F ) PD-1 and VISTA (PD-1, red, cytoplasmic; VISTA, green, cytoplasmic). Double-positive cells are shown in yellow (white arrow). VISTA, V-domain Ig suppressor of T-cell activation; PD-1, programmed cell death protein-1.

Article Snippet: Paraffin-embedded sections were immunostained with anti-VISTA (1:200, ProSci Incorporation, CA, USA), anti-CD33 (1:100, Leica Biosystems, Newcastle, UK), or anti-PD-1 (1:100, Ventana, Tucson, AZ, USA) antibodies.

Techniques: Expressing, Immunohistochemical staining, Immunofluorescence, Staining, Activation Assay

Journal: Scientific Reports

Article Title: The prognostic significance of VISTA and CD33-positive myeloid cells in cutaneous melanoma and their relationship with PD-1 expression

doi: 10.1038/s41598-020-71216-2

Figure Lengend Snippet: Patient survival according to CD33 and VISTA expression. ( A ) OS according to CD33 expression. ( B ) OS according to VISTA expression. ( C ) Worse OS in patients with high expression of both CD33 and VISTA. ( D ) OS according to the degree of CD33 and VISTA expression ( E ) Worse OS in cases with dual expression of VISTA and PD-1 among patients with high expression of PD-1. VISTA, V-domain Ig suppressor of T-cell activation; PD-1, programmed cell death protein-1.

Article Snippet: Paraffin-embedded sections were immunostained with anti-VISTA (1:200, ProSci Incorporation, CA, USA), anti-CD33 (1:100, Leica Biosystems, Newcastle, UK), or anti-PD-1 (1:100, Ventana, Tucson, AZ, USA) antibodies.

Techniques: Expressing, Activation Assay

Journal: Scientific Reports

Article Title: The prognostic significance of VISTA and CD33-positive myeloid cells in cutaneous melanoma and their relationship with PD-1 expression

doi: 10.1038/s41598-020-71216-2

Figure Lengend Snippet: Univariate and multivariate analyses of OS and PFS.

Article Snippet: Paraffin-embedded sections were immunostained with anti-VISTA (1:200, ProSci Incorporation, CA, USA), anti-CD33 (1:100, Leica Biosystems, Newcastle, UK), or anti-PD-1 (1:100, Ventana, Tucson, AZ, USA) antibodies.

Techniques: Expressing