Journal: Nature cardiovascular research

Article Title: A single-cell comparison of adult and fetal human epicardium defines the age-associated changes in epicardial activity.

doi: 10.1038/s44161-022-00183-w

Figure Lengend Snippet: Fig. 6 | EPDCs were found in sub-epicardium and myocardium. a, Spatial validation of this cluster as EPDCs was carried out using a pseudostain targeting strategy from UMAP of scRNA-seq data, with gene expression displayed in RGB color space and a constant blue channel value of 0.2 for heuristic DAPI simulation. b, Staining of fetal hearts using double stains for TM4SF1 and POSTN (bi), PRG4

Article Snippet: The primary antibodies used in this study for immunofluorescent imaging included: UPK3B, PA552696 (Themo Fisher Scientific); MSLN, sc33672 (Santa Cruz Biotechnology); KRT19, sc6278 (Santa Cruz Biotechnology); POSTN, MAB3548 (R&D Systems); DCN, AF143 (R&D Systems); PRG4, MABT400 (Sigma-Aldrich); and TM4SF1, MAB8164 (R&D Systems).

Techniques: Biomarker Discovery, Gene Expression, Staining

Journal: Journal of Gastrointestinal Oncology

Article Title: Analyzing the role of TM4SF1 expression in pancreatic adenocarcinoma: understanding prognostic implications and therapeutic opportunities

doi: 10.21037/jgo-24-564

Figure Lengend Snippet: Differential gene expression and functional enrichment analysis of PAAD. (A) Volcano plot highlighting DEGs between PAAD and normal tissues. The most significant upregulated gene in the tumor tissues was TM4SF1 . Red dots signify genes that are highly expressed in the tumor group. Blue dots indicate genes with low expression in the tumor group. Gray dots, labeled as ‘not’, represent genes deemed non-differentially expressed due to not meeting the screening threshold. (B) Bubble plot depicting the GO and KEGG functional enrichment of the up- and downregulated DEGs. (C) GSEA analysis results illustrating the signaling pathways significantly enriched with DEGs. BP, biological process; CC, cellular component; MF, molecular function; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; NES, normalized enrichment score; PAAD, pancreatic adenocarcinoma; DEGs, differentially expressed genes.

Article Snippet: Primary antibodies against β-actin (#AF0003, Beyotime) and TM4SF1 (#NBP1-76549, NOVUS, Colorado, USA) were incubated on the membranes overnight at 4 °C.

Techniques: Gene Expression, Functional Assay, Expressing, Labeling, Protein-Protein interactions

Journal: Journal of Gastrointestinal Oncology

Article Title: Analyzing the role of TM4SF1 expression in pancreatic adenocarcinoma: understanding prognostic implications and therapeutic opportunities

doi: 10.21037/jgo-24-564

Figure Lengend Snippet: Immune cell infiltration analysis between high- and low-TM4SF1 expression groups. (A) Scatter plot correlating TM4SF1 expression with levels of immune cell infiltration. (B) Correlation analysis reinforcing the findings in (A). (C) Differential immune cell infiltration based on ssGSEA analysis between the high- and low-TM4SF1 expression groups. (D) High- and low-risk immune features. *, P<0.05; **, P<0.01; ***, P<0.001. MDSC, myeloid-derived suppressor cell; ssGSEA, single-sample gene set enrichment analysis; L, low; H, high.

Article Snippet: Primary antibodies against β-actin (#AF0003, Beyotime) and TM4SF1 (#NBP1-76549, NOVUS, Colorado, USA) were incubated on the membranes overnight at 4 °C.

Techniques: Expressing, Derivative Assay

Journal: Journal of Gastrointestinal Oncology

Article Title: Analyzing the role of TM4SF1 expression in pancreatic adenocarcinoma: understanding prognostic implications and therapeutic opportunities

doi: 10.21037/jgo-24-564

Figure Lengend Snippet: Gene mutation analysis of the five key prognostic genes. (A) Chromosomal positions of the five key genes. (B) Forest plot illustrating the hazard ratios of the five genes concerning PAAD prognosis. (C) Correlation heatmap of the five key genes. (D) Distribution of the mutation frequencies across patients. (E) Waterfall plot of the genes ranked by mutation count. (F) Tissue samples from 10 patients were obtained to examine the mRNA expression differences of TM4SF1, BPIFB4, CPTP, DVL1, PLEKHN1 , and DDR1 between cancer and normal tissues. **, P<0.01. SNP, single nucleotide polymorphism; INS, insertion; DEL, deletion; SNV, single-nucleotide variant; PAAD, pancreatic adenocarcinoma; mRNA, messenger RNA; HR, hazard ratio.

Article Snippet: Primary antibodies against β-actin (#AF0003, Beyotime) and TM4SF1 (#NBP1-76549, NOVUS, Colorado, USA) were incubated on the membranes overnight at 4 °C.

Techniques: Mutagenesis, Expressing, Variant Assay

Journal: Journal of Gastrointestinal Oncology

Article Title: Analyzing the role of TM4SF1 expression in pancreatic adenocarcinoma: understanding prognostic implications and therapeutic opportunities

doi: 10.21037/jgo-24-564

Figure Lengend Snippet: TM4SF1 expression and its functional effects on pancreatic cancer cell behavior. (A) Box plot depicting the relative expression of TM4SF1 mRNA in pancreatic tumor tissues compared to normal tissues, demonstrating a significant upregulation in tumors (*, P<0.05). (B) Kaplan-Meier survival curves stratifying patients into quartiles based on TM4SF1 expression levels, showing an inverse relationship between high TM4SF1 expression and overall survival. (C) Western blot analysis of TM4SF1 protein levels in normal (N1–N5) and tumor (T1–T5) pancreatic tissue samples, with tumors exhibiting higher expression levels. (D) Western blot comparison of the TM4SF1 protein across a panel of pancreatic cancer cell lines, identifying varying expression levels. (E) Bar graph quantifying TM4SF1 mRNA expression in various pancreatic cancer cell lines, with PANC-1 cells showing the highest expression. (F,G) Bar graph showing TM4SF1 mRNA levels in PANC-1 cells after treatment with NC or TM4SF1 -targeting siRNAs (si TM4SF1 #1, #2 and #3), indicating effective knockdown. Proliferation assay (H) and colony formation assay (1×) (stained with 0.1% crystal violet) (I) of PANC-1 cells following si TM4SF1 treatment, revealing reduced cell growth and colony number compared to NC. (J) Cell viability assay assessing the sensitivity of PANC-1 cells to Gemcitabine post-si TM4SF1 treatment, showing increased drug sensitivity. Transwell migration, invasion (10×) (stained with 0.1% crystal violet) (K) and cellular wound healing (5×) (L) assays in si TM4SF1 -treated PANC-1 cells demonstrated decreased migratory and invasive capacities. (M) Western blot confirming overexpression of TM4SF1 in CFPAC-1 cells transfected with oe TM4SF1 versus NC. Cell proliferation assay (N) and colony formation assay (1×) (stained with 0.1% crystal violet) (O) in CFPAC-1 cells with oe TM4SF1 showed enhanced growth and colony-forming ability. Transwell migration, invasion (10×) (stained with 0.1% crystal violet) (P) and cellular wound healing (5×) (Q) assays in oe TM4SF1 -expressing CFPAC-1 cells indicated increased migration and invasion potential. *, P<0.05; **, P<0.01; ***, P<0.001. TPM, transcripts per million; PAAD, pancreatic adenocarcinoma; HR, hazard ratio; NC, control; IC 50 , half-maximal inhibitory concentration; oeTM4SF1, overexpression of TM4SF1; mRNA, messenger RNA.

Article Snippet: Primary antibodies against β-actin (#AF0003, Beyotime) and TM4SF1 (#NBP1-76549, NOVUS, Colorado, USA) were incubated on the membranes overnight at 4 °C.

Techniques: Expressing, Functional Assay, Western Blot, Comparison, Knockdown, Proliferation Assay, Colony Assay, Staining, Viability Assay, Migration, Over Expression, Transfection, Control, Concentration Assay