huc  (ATCC)

Journal: bioRxiv

Article Title: The RNA and protein landscapes of mouse brain organoids

doi: 10.64898/2026.03.13.711293

Figure Lengend Snippet: (A) Schematic timeline of brain organoids generation from mESCs. mESCs and brain organoids developed for 7, 14 and 21 days were profiled by transcriptomics and proteomics. Part of the figure was created with Biorender. (B) Immunostaining of mESCs-derived brain organoids. Cultures of mESCs were stained with NANOG (green), POU5F1/OCT4 (red), and nuclei with DAPI (blue). Scale bars: 10 µm. (C) Organoid cryosections were stained with NESTIN and PAX6 (at day 7), ELAVL3 and TBR1 (at day 14), and TUBB3 and GFAP (at day 21). Scale bars: 100 µm. (D) PCA showing the distribution of the transcriptomes of mESCs, brain organoids (at days 7, 14, and 21), and NBB samples. (E) Venn diagram showing the overlapping upregulated and downregulated genes between D21 organoids and NBB, both compared to mESCs. (F) Histograms of enriched GO terms in NBB vs ESCs and D21 organoids vs ESCs performed on upregulated genes (black and grey bars) and on downregulated genes (red and light red bars) determined using DAVID. For each term category (Cellular component, molecular function, and biological process), the five highest enriched terms in each gene list are shown.

Article Snippet: The primary antibodies were (species, provider; catalog number): anti-NESTIN –Rat-401- (mouse, Santa-Cruz, sc-33677); PAX6 (Rabbit, Covance, PRB-278P); NANOG (mouse, BD Pharmingen, 560259); POU5F1 (rabbit, Cell Signalling, 2840), ELAVL3 (mouse, Santa Cruz, sc-515624), TUBB3 (mouse, Covance, MMS-435P); TBR1 (rabbit, Cell Signalling, 49661), REELIN (mouse, Covance; MAB5364), GRM5 (rabbit, Millipore, AB5675), and GFAP (rabbit, Dako, Z0334).

Techniques: Transcriptomics, Immunostaining, Derivative Assay, Staining

Journal: PLOS One

Article Title: Integrated light and electron microscopy workflow for morphological, molecular and ultrastructural analysis of spheroids

doi: 10.1371/journal.pone.0342659

Figure Lengend Snippet: Representative haematoxylin–eosin (HE)-stained sections of SV-HUC-1 and T24 spheroids prepared by cryosectioning ( A-F ) and paraffin embedding (G-L) . A necrotic core (indicated by asterisks, A-B , D-E , G-H , J-K ) is visible in most cross sections, except those obtained from peripheral regions. Scale bars: 500 µm (A, D, G, J), 100 µm (B, E, H, K), 50 µm (C, F, I, L).

Article Snippet: Normal human urothelial SV-HUC-1 cells (CRL-9520) and muscle-invasive human bladder cancer urothelial T24 cells (HTB-4) were purchased from ATCC (Manassas, VA, United States) and cultured in a 1:1 mixture of A-DMEM medium (Gibco, Thermo Fisher Scientific, Waltham, MA, United States) and F12 (Sigma-Aldrich, St. Louis, MO, United States), supplemented with 5% fetal bovine serum (Invitrogen, Carlsbad, CA, United States) and 4 mM GlutaMAX (Gibco, Thermo Fisher Scientific, Waltham, MA, United States).

Techniques: Staining

Journal: PLOS One

Article Title: Integrated light and electron microscopy workflow for morphological, molecular and ultrastructural analysis of spheroids

doi: 10.1371/journal.pone.0342659

Figure Lengend Snippet: Representative images of paraffin sections show E-cadherin (green) in the plasma membrane in cells of SV-HUC-1 spheroids ( A-a3 ) and N-cadherin (red) in the plasma membrane of T24 spheroids ( B-b3 ). Some SV-HUC-1 cells are also positive for N-cadherin (arrows, a2 and a3 ). Yellow insets (in A and B) are magnified (a1-a3 and b1-b3) and display individual and merged channels of E-cadherin, N-cadherin, and DAPI-stained nuclei. Scale bars: 100 µm (A, B) , 20 µm (a1-a3, b1-b3).

Article Snippet: Normal human urothelial SV-HUC-1 cells (CRL-9520) and muscle-invasive human bladder cancer urothelial T24 cells (HTB-4) were purchased from ATCC (Manassas, VA, United States) and cultured in a 1:1 mixture of A-DMEM medium (Gibco, Thermo Fisher Scientific, Waltham, MA, United States) and F12 (Sigma-Aldrich, St. Louis, MO, United States), supplemented with 5% fetal bovine serum (Invitrogen, Carlsbad, CA, United States) and 4 mM GlutaMAX (Gibco, Thermo Fisher Scientific, Waltham, MA, United States).

Techniques: Clinical Proteomics, Membrane, Staining

Journal: PLOS One

Article Title: Integrated light and electron microscopy workflow for morphological, molecular and ultrastructural analysis of spheroids

doi: 10.1371/journal.pone.0342659

Figure Lengend Snippet: SV-HUC-1 (A) and T24 cells (C) form spheroids with a spherical morphology. (B) SV-HUC-1 cells are tightly attached to each other (arrows), and microvilli are seen on their surface. (D) T24 cells are loosely attached, displaying wider intercellular spaces (arrowheads) and have fewer microvilli. Scale bars: 100 µm (A, C) , 10 µm (B, D) .

Article Snippet: Normal human urothelial SV-HUC-1 cells (CRL-9520) and muscle-invasive human bladder cancer urothelial T24 cells (HTB-4) were purchased from ATCC (Manassas, VA, United States) and cultured in a 1:1 mixture of A-DMEM medium (Gibco, Thermo Fisher Scientific, Waltham, MA, United States) and F12 (Sigma-Aldrich, St. Louis, MO, United States), supplemented with 5% fetal bovine serum (Invitrogen, Carlsbad, CA, United States) and 4 mM GlutaMAX (Gibco, Thermo Fisher Scientific, Waltham, MA, United States).

Techniques:

Journal: PLOS One

Article Title: Integrated light and electron microscopy workflow for morphological, molecular and ultrastructural analysis of spheroids

doi: 10.1371/journal.pone.0342659

Figure Lengend Snippet: Outermost cells in SV-HUC-1 spheroids display cuboidal morphology (A) , whereas T24 cells are more elongated (B) . The presence of cell junctions in the outermost cell layer of SV-HUC-1 (C) and T24 spheroid (D) (boxed regions) indicates a tight cellular network of the outermost cell layer. The central necrotic zone (asterisks) is filled with necrotic cells in SV-HUC-1 and T24 spheroids (E, F) , as clearly demonstrated on semithin sections (G, H) , prepared before ultrathin sectioning. Scale bars: 100 µm (G-H) , 10 µm (A-B) , 5 µm (E-F) , 1 µm (C-D) .

Article Snippet: Normal human urothelial SV-HUC-1 cells (CRL-9520) and muscle-invasive human bladder cancer urothelial T24 cells (HTB-4) were purchased from ATCC (Manassas, VA, United States) and cultured in a 1:1 mixture of A-DMEM medium (Gibco, Thermo Fisher Scientific, Waltham, MA, United States) and F12 (Sigma-Aldrich, St. Louis, MO, United States), supplemented with 5% fetal bovine serum (Invitrogen, Carlsbad, CA, United States) and 4 mM GlutaMAX (Gibco, Thermo Fisher Scientific, Waltham, MA, United States).

Techniques:

Journal: Cancer Genomics & Proteomics

Article Title: Proteomic Signatures of Cellular Reprogramming in Bladder Cancer: Insights into the Acquisition of Cancer Stem-like States and Phenotypic Plasticity

doi: 10.21873/cgp.20578

Figure Lengend Snippet: Heatmap analysis of global and functional protein expression during bladder cancer cell reprogramming. (A) Whole proteome clustering reveals distinct segregation of reprogrammed bladder cancer cell passages and partial convergence toward SV-HUC-1. (B) Proteins associated with cell adhesion exhibit partial restoration of epithelial-like profile. (C) Proteins in cellular developmental process show progressive modulation in early cellular reprogramming. (D) Cell motility-related proteins exhibit reduced expression in later reprogramming passages, suggesting a shift away from a migratory phenotype. (E) Proteins related to epithelial cell differentiation in rep HTB-4 cells demonstrate increased similarity to SV-HUC-1, highlighting the re-establishment of epithelial characteristics. Color scale represents Z-score–normalized abundance values (green=low; red=high).

Article Snippet: HTB-4 (ATCC HTB-4; RRID: CVCL_0554) and SV-HUC-1 (ATCC CRL-9520; RRID: CVCL_3798) cell lines were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Functional Assay, Expressing, Cell Differentiation

Journal: Cancer Genomics & Proteomics

Article Title: Proteomic Signatures of Cellular Reprogramming in Bladder Cancer: Insights into the Acquisition of Cancer Stem-like States and Phenotypic Plasticity

doi: 10.21873/cgp.20578

Figure Lengend Snippet: Comparative proteomic analysis of reprogrammed bladder cancer cells and normal uroepithelial SV-HUC-1 cells. (A) Venn diagrams showing the total numbers of regulated, upregulated, and downregulated proteins shared or uniquely detected at passages p1, p4, and p7. (B) Protein-protein interaction (PPI) network of proteins commonly upregulated in all three passages (p1, p4, p7) in comparison to the normal uroepithelial cell line SVHUC- 1. Nodes represent proteins and edges show experimentally validated interactions. Enriched pathways are indicated in different colors. (C) PPI network of commonly downregulated proteins across rep HTB-4 p1, p4, p7. (D) Gene ontology (GO) analysis showed enrichment of commonly upregulated proteins in rep HTB-4 p1, p4, and p7 cells, involved in biological processes, molecular function, and cellular components [fold change >2 and false discovery rate (FDR)<0.01]. Significant overrepresentation of processes related to biosynthesis, peptide metabolic pathways, RNA binding, and cadherin binding was detected. (E) Gene ontology (GO) analysis showed enrichment of commonly downregulated proteins in rep HTB-4 p1, p4, and p7 cells, involved in biological processes, molecular function, and cellular components [fold change >2 and false discovery rate (FDR) <0.01]. Reductions in pathways linked to RNA processing, the catenin complex, and the ribonucleoprotein complex were detected.

Article Snippet: HTB-4 (ATCC HTB-4; RRID: CVCL_0554) and SV-HUC-1 (ATCC CRL-9520; RRID: CVCL_3798) cell lines were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Comparison, RNA Binding Assay, Binding Assay

Journal: BMC Cancer

Article Title: Conjoining cell reprogramming and mass spectrometry to identify the proteomic variations in the reprogrammed bladder cancer cells: finding cues of normalisation

doi: 10.1186/s12885-026-15634-x

Figure Lengend Snippet: Comparative proteomic analysis of bladder cancer cell line HTB-5, reprogrammed bladder cancer cell line HTB-5-PR and human normal bladder epithelial cell line SV-HUC-1. A In total, 3654 proteins were identified with high confidence (false discovery rate < 1%) with at least two or more unique peptide fragments. Data analysis was enhanced by filtering the identified proteins to 1969 proteins that contain at least 5 or more unique peptides. In the hierarchical clustering of proteins with 2-fold change in abundance (FC > 2 or < 0.5), HTB-5 PR cells exhibit a transition state between normal epithelial cells and grade 4 bladder cancer cells. B Heat maps representing the regulated proteins involved in pluripotency, stem cell differentiation and extracellular matrix in each sample. The dendrogram depicts a separation of HTB-5-PR from HTB-5 and SV-HUC-1 cells in terms of pluripotency-associated protein expression. The cluster analysis was performed using Pearson correlation for the distance measure, protein intensities are shown using a colour scale ranging from red (high) to blue (low). The dendrogram above the heatmap shows the degree of relationship between protein profiles in the three samples. Red colour corresponds to higher z-scores. A z-score equivalent to 0 represents the mean abundance value for that protein. C During the reprogramming process, the abundance ratios of HTB-5/SV-HUC-1 were analysed against the expression levels of proteins in the normal bladder epithelial cell line. In the transition phase from grade 4 bladder cancer cell line toward reprogrammed HTB-5 PR cells, a variety of biological processes were shown to be regulated by g: Profiler analysis. D Out of 348 proteins were upregulated and out of 281 proteins downregulated, the expression levels of 295 proteins, which comprise 47% of the regulated proteins, were normalised in HTB-5 cells upon reprogramming

Article Snippet: SV-HUC-1 cells were cultured with F-12 K Medium (ATCC 30-2004) supplemented with 10% FBS.

Techniques: Cell Differentiation, Expressing

Journal: BMC Cancer

Article Title: Conjoining cell reprogramming and mass spectrometry to identify the proteomic variations in the reprogrammed bladder cancer cells: finding cues of normalisation

doi: 10.1186/s12885-026-15634-x

Figure Lengend Snippet: STRING network analysis of upregulated and downregulated proteins indicate progress toward normalisation in parental HTB-5 cells. Results of annotated keywords (by UniProt) obtained using functional enrichment analysis in STRING 12.5 (FDR < 0.05), indicating enriched categories and number of proteins mapped. After reprogramming, 47% of total proteins in parental HTB-5 cells that approximate the expression levels to those of the normal bladder epithelial cell line SV-HUC-1 cells were considered to be normalised and analysed for protein-protein interaction. A Protein-protein interactions of upregulated 149 proteins and downregulated 148 proteins (upper panel) and the proteins involved in the GO annotations showing the most clustering are presented at the bottom of each protein-protein interaction network (lower panel). Nodes represent proteins, lines between nodes represent edges showing interactions with a minimum confidence score of 0.7. Each GO annotation is indicated with a different colour, and the nodes are coloured depending on their involvement in certain biological processes. B g: Profiler analysis of upregulated and downregulated proteins during the reprogramming process. The graphs show the enriched terms, most of which are also highlighted in the STRING analysis. The ten most highly upregulated terms (lower left panel) and downregulated terms (lower right panel) are ranked by decreasing protein number detected in each term

Article Snippet: SV-HUC-1 cells were cultured with F-12 K Medium (ATCC 30-2004) supplemented with 10% FBS.

Techniques: Functional Assay, Expressing, Protein-Protein interactions

Journal: BMC Cancer

Article Title: Conjoining cell reprogramming and mass spectrometry to identify the proteomic variations in the reprogrammed bladder cancer cells: finding cues of normalisation

doi: 10.1186/s12885-026-15634-x

Figure Lengend Snippet: Functional enrichment analysis of reprogrammed HTB-5 PR cells. A The STRING database was used to construct the protein-protein interaction (PPI) networks of upregulated 145 proteins (left panel) and downregulated 85 proteins (right panel) in HTB-5 PR cells. Nodes represent proteins, and the lines between them depict interactions with a minimum confidence score of 0.7. B g: Profiler analysis of upregulated and downregulated proteins in the reprogrammed HTB-5 PR cells. The graph represents the GO enrichment analysis of upregulated proteins (left panel in shaded red) in the biological process and downregulated proteins (right panel in shaded blue) in the biological process. Ten highly upregulated and downregulated GO terms are ranked by the number of proteins detected in each term, listed in decreasing order. Spontaneous differentiation upon reprogramming leads to an increase in nervous system development markers and to a decrease in epithelium development markers (marked in blue) as detected by both STRING and g: Profiler analysis. C The clustering of differentially expressed proteins involved in neural development and epithelial cell differentiation is displayed in heatmaps. The parental HTB-5 cells and normal epithelial cell line SV-HUC-1 are grouped based on similar protein expression profiles showing downregulation of neuronal markers and upregulation of epithelial markers, while the reprogrammed bladder cancer cell line HTB-5 PR exhibits an opposite expression profile. The data is consistent with the morphological evidence documented during the reprogramming process (from right to left), showing the parental HTB-5 cells transform into pluripotent-like colonies and gain neuron-like trajectories as a result of spontaneous differentiation in time. The protein intensities are shown using a colour scale ranging from red (high) to blue (low). Red colour corresponds to higher z-scores. A z-score equivalent to 0 represents the mean abundance value for that protein

Article Snippet: SV-HUC-1 cells were cultured with F-12 K Medium (ATCC 30-2004) supplemented with 10% FBS.

Techniques: Functional Assay, Construct, Cell Differentiation, Expressing