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atcc sk hep1  (ATCC)
97
ATCC atcc sk hep1
Heterogeneity of response to 90 Y microsphere treatment across human liver cancer cell lines. A, Dose–response curves of cell viability after 10-day treatment to escalating 90 Y microsphere activities (0–20 MBq/mL) in each of 10 cell lines. Each point represents the mean surviving fraction relative to untreated baseline control across all independent experiments (error bars: SEM). B, For each experiment, the area under the dose–response curve was calculated and normalized to yield nAUC (0 = sensitive and 1 = resistant). Cell lines are ordered left to right by decreasing nAUC (increased sensitivity). Horizontal bar indicates mean nAUC for each cell line across experiments. Group differences were assessed by one-way ANOVA with a Tukey multiple comparisons test (*, P < 0.05; **, P < 0.01; ***, P < 0.001). C, Relationship between response to 90 Y and established HCC transcriptomic subtypes. Cell lines were assigned to select HCC transcriptomic subtypes by nearest template prediction. nAUC distributions differed by subtype, with Hoshida S1 and C1 (cholangiocarcinoma-like) subtypes associated with 90 Y resistance ( P < 0.05, Kruskal–Wallis rank-sum test). No correlation with the hepatoblastoma HB-16 signature was observed. D, PCA of RNA baseline expression profiles of all cell lines demonstrates clustering of the five most resistant cell lines by nAUC (red: <t>SK-Hep1,</t> SNU-449, SNU-475, SNU-387, and SNU-423) along PC2/PC3 (13.1%/8.2% variance), with clear separation of the three most 90 Y-sensitive cell lines (yellow: PLC/PRF/5, Hep3B, and HepG2) along PC2.
Atcc Sk Hep1, supplied by ATCC, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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sk hep1  (MedChemExpress)
93
MedChemExpress sk hep1
Heterogeneity of response to 90 Y microsphere treatment across human liver cancer cell lines. A, Dose–response curves of cell viability after 10-day treatment to escalating 90 Y microsphere activities (0–20 MBq/mL) in each of 10 cell lines. Each point represents the mean surviving fraction relative to untreated baseline control across all independent experiments (error bars: SEM). B, For each experiment, the area under the dose–response curve was calculated and normalized to yield nAUC (0 = sensitive and 1 = resistant). Cell lines are ordered left to right by decreasing nAUC (increased sensitivity). Horizontal bar indicates mean nAUC for each cell line across experiments. Group differences were assessed by one-way ANOVA with a Tukey multiple comparisons test (*, P < 0.05; **, P < 0.01; ***, P < 0.001). C, Relationship between response to 90 Y and established HCC transcriptomic subtypes. Cell lines were assigned to select HCC transcriptomic subtypes by nearest template prediction. nAUC distributions differed by subtype, with Hoshida S1 and C1 (cholangiocarcinoma-like) subtypes associated with 90 Y resistance ( P < 0.05, Kruskal–Wallis rank-sum test). No correlation with the hepatoblastoma HB-16 signature was observed. D, PCA of RNA baseline expression profiles of all cell lines demonstrates clustering of the five most resistant cell lines by nAUC (red: <t>SK-Hep1,</t> SNU-449, SNU-475, SNU-387, and SNU-423) along PC2/PC3 (13.1%/8.2% variance), with clear separation of the three most 90 Y-sensitive cell lines (yellow: PLC/PRF/5, Hep3B, and HepG2) along PC2.
Sk Hep1, supplied by MedChemExpress, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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human liver cancer cell lines sk hep1  (ATCC)
97
ATCC human liver cancer cell lines sk hep1
Heterogeneity of response to 90 Y microsphere treatment across human liver cancer cell lines. A, Dose–response curves of cell viability after 10-day treatment to escalating 90 Y microsphere activities (0–20 MBq/mL) in each of 10 cell lines. Each point represents the mean surviving fraction relative to untreated baseline control across all independent experiments (error bars: SEM). B, For each experiment, the area under the dose–response curve was calculated and normalized to yield nAUC (0 = sensitive and 1 = resistant). Cell lines are ordered left to right by decreasing nAUC (increased sensitivity). Horizontal bar indicates mean nAUC for each cell line across experiments. Group differences were assessed by one-way ANOVA with a Tukey multiple comparisons test (*, P < 0.05; **, P < 0.01; ***, P < 0.001). C, Relationship between response to 90 Y and established HCC transcriptomic subtypes. Cell lines were assigned to select HCC transcriptomic subtypes by nearest template prediction. nAUC distributions differed by subtype, with Hoshida S1 and C1 (cholangiocarcinoma-like) subtypes associated with 90 Y resistance ( P < 0.05, Kruskal–Wallis rank-sum test). No correlation with the hepatoblastoma HB-16 signature was observed. D, PCA of RNA baseline expression profiles of all cell lines demonstrates clustering of the five most resistant cell lines by nAUC (red: <t>SK-Hep1,</t> SNU-449, SNU-475, SNU-387, and SNU-423) along PC2/PC3 (13.1%/8.2% variance), with clear separation of the three most 90 Y-sensitive cell lines (yellow: PLC/PRF/5, Hep3B, and HepG2) along PC2.
Human Liver Cancer Cell Lines Sk Hep1, supplied by ATCC, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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sk hep1  (ATCC)
97
ATCC sk hep1
Heterogeneity of response to 90 Y microsphere treatment across human liver cancer cell lines. A, Dose–response curves of cell viability after 10-day treatment to escalating 90 Y microsphere activities (0–20 MBq/mL) in each of 10 cell lines. Each point represents the mean surviving fraction relative to untreated baseline control across all independent experiments (error bars: SEM). B, For each experiment, the area under the dose–response curve was calculated and normalized to yield nAUC (0 = sensitive and 1 = resistant). Cell lines are ordered left to right by decreasing nAUC (increased sensitivity). Horizontal bar indicates mean nAUC for each cell line across experiments. Group differences were assessed by one-way ANOVA with a Tukey multiple comparisons test (*, P < 0.05; **, P < 0.01; ***, P < 0.001). C, Relationship between response to 90 Y and established HCC transcriptomic subtypes. Cell lines were assigned to select HCC transcriptomic subtypes by nearest template prediction. nAUC distributions differed by subtype, with Hoshida S1 and C1 (cholangiocarcinoma-like) subtypes associated with 90 Y resistance ( P < 0.05, Kruskal–Wallis rank-sum test). No correlation with the hepatoblastoma HB-16 signature was observed. D, PCA of RNA baseline expression profiles of all cell lines demonstrates clustering of the five most resistant cell lines by nAUC (red: <t>SK-Hep1,</t> SNU-449, SNU-475, SNU-387, and SNU-423) along PC2/PC3 (13.1%/8.2% variance), with clear separation of the three most 90 Y-sensitive cell lines (yellow: PLC/PRF/5, Hep3B, and HepG2) along PC2.
Sk Hep1, supplied by ATCC, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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sk hep1 cells atcc htb  (ATCC)
97
ATCC sk hep1 cells atcc htb
Heterogeneity of response to 90 Y microsphere treatment across human liver cancer cell lines. A, Dose–response curves of cell viability after 10-day treatment to escalating 90 Y microsphere activities (0–20 MBq/mL) in each of 10 cell lines. Each point represents the mean surviving fraction relative to untreated baseline control across all independent experiments (error bars: SEM). B, For each experiment, the area under the dose–response curve was calculated and normalized to yield nAUC (0 = sensitive and 1 = resistant). Cell lines are ordered left to right by decreasing nAUC (increased sensitivity). Horizontal bar indicates mean nAUC for each cell line across experiments. Group differences were assessed by one-way ANOVA with a Tukey multiple comparisons test (*, P < 0.05; **, P < 0.01; ***, P < 0.001). C, Relationship between response to 90 Y and established HCC transcriptomic subtypes. Cell lines were assigned to select HCC transcriptomic subtypes by nearest template prediction. nAUC distributions differed by subtype, with Hoshida S1 and C1 (cholangiocarcinoma-like) subtypes associated with 90 Y resistance ( P < 0.05, Kruskal–Wallis rank-sum test). No correlation with the hepatoblastoma HB-16 signature was observed. D, PCA of RNA baseline expression profiles of all cell lines demonstrates clustering of the five most resistant cell lines by nAUC (red: <t>SK-Hep1,</t> SNU-449, SNU-475, SNU-387, and SNU-423) along PC2/PC3 (13.1%/8.2% variance), with clear separation of the three most 90 Y-sensitive cell lines (yellow: PLC/PRF/5, Hep3B, and HepG2) along PC2.
Sk Hep1 Cells Atcc Htb, supplied by ATCC, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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sk hep1 cells  (ATCC)
97
ATCC sk hep1 cells
Heterogeneity of response to 90 Y microsphere treatment across human liver cancer cell lines. A, Dose–response curves of cell viability after 10-day treatment to escalating 90 Y microsphere activities (0–20 MBq/mL) in each of 10 cell lines. Each point represents the mean surviving fraction relative to untreated baseline control across all independent experiments (error bars: SEM). B, For each experiment, the area under the dose–response curve was calculated and normalized to yield nAUC (0 = sensitive and 1 = resistant). Cell lines are ordered left to right by decreasing nAUC (increased sensitivity). Horizontal bar indicates mean nAUC for each cell line across experiments. Group differences were assessed by one-way ANOVA with a Tukey multiple comparisons test (*, P < 0.05; **, P < 0.01; ***, P < 0.001). C, Relationship between response to 90 Y and established HCC transcriptomic subtypes. Cell lines were assigned to select HCC transcriptomic subtypes by nearest template prediction. nAUC distributions differed by subtype, with Hoshida S1 and C1 (cholangiocarcinoma-like) subtypes associated with 90 Y resistance ( P < 0.05, Kruskal–Wallis rank-sum test). No correlation with the hepatoblastoma HB-16 signature was observed. D, PCA of RNA baseline expression profiles of all cell lines demonstrates clustering of the five most resistant cell lines by nAUC (red: <t>SK-Hep1,</t> SNU-449, SNU-475, SNU-387, and SNU-423) along PC2/PC3 (13.1%/8.2% variance), with clear separation of the three most 90 Y-sensitive cell lines (yellow: PLC/PRF/5, Hep3B, and HepG2) along PC2.
Sk Hep1 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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sk hep1 cell line  (ATCC)
97
ATCC sk hep1 cell line
Heterogeneity of response to 90 Y microsphere treatment across human liver cancer cell lines. A, Dose–response curves of cell viability after 10-day treatment to escalating 90 Y microsphere activities (0–20 MBq/mL) in each of 10 cell lines. Each point represents the mean surviving fraction relative to untreated baseline control across all independent experiments (error bars: SEM). B, For each experiment, the area under the dose–response curve was calculated and normalized to yield nAUC (0 = sensitive and 1 = resistant). Cell lines are ordered left to right by decreasing nAUC (increased sensitivity). Horizontal bar indicates mean nAUC for each cell line across experiments. Group differences were assessed by one-way ANOVA with a Tukey multiple comparisons test (*, P < 0.05; **, P < 0.01; ***, P < 0.001). C, Relationship between response to 90 Y and established HCC transcriptomic subtypes. Cell lines were assigned to select HCC transcriptomic subtypes by nearest template prediction. nAUC distributions differed by subtype, with Hoshida S1 and C1 (cholangiocarcinoma-like) subtypes associated with 90 Y resistance ( P < 0.05, Kruskal–Wallis rank-sum test). No correlation with the hepatoblastoma HB-16 signature was observed. D, PCA of RNA baseline expression profiles of all cell lines demonstrates clustering of the five most resistant cell lines by nAUC (red: <t>SK-Hep1,</t> SNU-449, SNU-475, SNU-387, and SNU-423) along PC2/PC3 (13.1%/8.2% variance), with clear separation of the three most 90 Y-sensitive cell lines (yellow: PLC/PRF/5, Hep3B, and HepG2) along PC2.
Sk Hep1 Cell Line, supplied by ATCC, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Heterogeneity of response to 90 Y microsphere treatment across human liver cancer cell lines. A, Dose–response curves of cell viability after 10-day treatment to escalating 90 Y microsphere activities (0–20 MBq/mL) in each of 10 cell lines. Each point represents the mean surviving fraction relative to untreated baseline control across all independent experiments (error bars: SEM). B, For each experiment, the area under the dose–response curve was calculated and normalized to yield nAUC (0 = sensitive and 1 = resistant). Cell lines are ordered left to right by decreasing nAUC (increased sensitivity). Horizontal bar indicates mean nAUC for each cell line across experiments. Group differences were assessed by one-way ANOVA with a Tukey multiple comparisons test (*, P < 0.05; **, P < 0.01; ***, P < 0.001). C, Relationship between response to 90 Y and established HCC transcriptomic subtypes. Cell lines were assigned to select HCC transcriptomic subtypes by nearest template prediction. nAUC distributions differed by subtype, with Hoshida S1 and C1 (cholangiocarcinoma-like) subtypes associated with 90 Y resistance ( P < 0.05, Kruskal–Wallis rank-sum test). No correlation with the hepatoblastoma HB-16 signature was observed. D, PCA of RNA baseline expression profiles of all cell lines demonstrates clustering of the five most resistant cell lines by nAUC (red: SK-Hep1, SNU-449, SNU-475, SNU-387, and SNU-423) along PC2/PC3 (13.1%/8.2% variance), with clear separation of the three most 90 Y-sensitive cell lines (yellow: PLC/PRF/5, Hep3B, and HepG2) along PC2.

Journal: Cancer Research Communications

Article Title: Epithelial–Mesenchymal Transition and Stress Adaptations Underlie Yttrium-90 Resistance in Liver Cancer Cell Lines

doi: 10.1158/2767-9764.CRC-25-0627

Figure Lengend Snippet: Heterogeneity of response to 90 Y microsphere treatment across human liver cancer cell lines. A, Dose–response curves of cell viability after 10-day treatment to escalating 90 Y microsphere activities (0–20 MBq/mL) in each of 10 cell lines. Each point represents the mean surviving fraction relative to untreated baseline control across all independent experiments (error bars: SEM). B, For each experiment, the area under the dose–response curve was calculated and normalized to yield nAUC (0 = sensitive and 1 = resistant). Cell lines are ordered left to right by decreasing nAUC (increased sensitivity). Horizontal bar indicates mean nAUC for each cell line across experiments. Group differences were assessed by one-way ANOVA with a Tukey multiple comparisons test (*, P < 0.05; **, P < 0.01; ***, P < 0.001). C, Relationship between response to 90 Y and established HCC transcriptomic subtypes. Cell lines were assigned to select HCC transcriptomic subtypes by nearest template prediction. nAUC distributions differed by subtype, with Hoshida S1 and C1 (cholangiocarcinoma-like) subtypes associated with 90 Y resistance ( P < 0.05, Kruskal–Wallis rank-sum test). No correlation with the hepatoblastoma HB-16 signature was observed. D, PCA of RNA baseline expression profiles of all cell lines demonstrates clustering of the five most resistant cell lines by nAUC (red: SK-Hep1, SNU-449, SNU-475, SNU-387, and SNU-423) along PC2/PC3 (13.1%/8.2% variance), with clear separation of the three most 90 Y-sensitive cell lines (yellow: PLC/PRF/5, Hep3B, and HepG2) along PC2.

Article Snippet: The following human liver cancer cell lines were obtained from the ATCC: SK-Hep1 (RRID: CVCL_0525), Hep-3B2 (RRID: CVCL_0326), HepG2/C3A (RRID: CVCL_1098), PLC/PRF/5 (RRID: CVCL_0485), SNU-387 (RRID: CVCL_0250), SNU-423 (RRID: CVCL_0366), SNU-449 (RRID: CVCL_0454), and SNU-475 (RRID: CVCL_0497).

Techniques: Control, Expressing

EMT and adhesion pathways associated with 90 Y resistance. A, EN regression analysis identified 18 protein-encoding genes with nonzero coefficients for which expression was correlated with 90 Y resistance across all cell lines at baseline (EN score >0.7). Among these, ITGA3 (EN = 0.911, R = 0.79) encodes the α subunit of the α3β1 integrin heterodimer, previously reported to influence HCC tumor progression and immune checkpoint expression. B, Differential expression analysis of RNA expression between 90 Y-resistant (SK-Hep1, SNU-449, SNU-475, SNU-387, and SNU-423) and -sensitive (PLC/PRF/5, Hep3B, and HepG2) cell lines. Groupings defined a priori by nAUC Z -scores and baseline PCA. Volcano plot of log 2 FC vs. −log 10 P value (FDR adjusted) of genes upregulated (red) and downregulated (blue) in 90 Y-resistant vs. -sensitive cell lines. Genes involved in the extracellular matrix ( ITGA3 ) and cancer stemness ( CD44 ) were significantly upregulated in 90 Y-resistant cell lines. C, GSEA of Hallmark pathways demonstrates strong upregulation of the EMT pathway in 90 Y-resistant cell lines (mean log FC 8.9), which contains CD44 and ITGB1 , the counterpart of ITGA3 in the a3b1 integrin heterodimer. Numbers next to each gene set bar represent FDR. D, Consistent with Hallmark EMT enrichment, KEGG and Reactome pathways associated with extracellular matrix and integrin cell surface interactions are enriched in resistant cell lines. E, qPCR (mean log 2 FC, error bars represent SEM, with n = 2 biological replicates) and Western blot validation of ITGA3/a3b1 and CD44 confirming elevated expression of these genes in the most 90 Y-resistant (SK-Hep1) vs. 90 Y-sensitive (PLC/PRF/5) and intermediate (SNU-398) cell lines, consistent with an EMT/adhesion phenotype associated with 90 Y resistance. F, qPCR of tumor vs. normal CD44 expression demonstrates a trend toward higher CD44 expression in those with IR or OFP ( n = 5) vs. SR ( n = 12), although not powered for statistical significance ( P = 0.43 Mann–Whitney). Color circle indicates treatment intent: blue, radiation segmentectomy; orange, multicompartment dosimetry (MCD) with TAD > 205 Gy. MIRD, medical internal radiation dose. Relative expression from qPCR data = 2 −(Cttarget − Cthousekeeping) , in which Ct is the detection crossing threshold.

Journal: Cancer Research Communications

Article Title: Epithelial–Mesenchymal Transition and Stress Adaptations Underlie Yttrium-90 Resistance in Liver Cancer Cell Lines

doi: 10.1158/2767-9764.CRC-25-0627

Figure Lengend Snippet: EMT and adhesion pathways associated with 90 Y resistance. A, EN regression analysis identified 18 protein-encoding genes with nonzero coefficients for which expression was correlated with 90 Y resistance across all cell lines at baseline (EN score >0.7). Among these, ITGA3 (EN = 0.911, R = 0.79) encodes the α subunit of the α3β1 integrin heterodimer, previously reported to influence HCC tumor progression and immune checkpoint expression. B, Differential expression analysis of RNA expression between 90 Y-resistant (SK-Hep1, SNU-449, SNU-475, SNU-387, and SNU-423) and -sensitive (PLC/PRF/5, Hep3B, and HepG2) cell lines. Groupings defined a priori by nAUC Z -scores and baseline PCA. Volcano plot of log 2 FC vs. −log 10 P value (FDR adjusted) of genes upregulated (red) and downregulated (blue) in 90 Y-resistant vs. -sensitive cell lines. Genes involved in the extracellular matrix ( ITGA3 ) and cancer stemness ( CD44 ) were significantly upregulated in 90 Y-resistant cell lines. C, GSEA of Hallmark pathways demonstrates strong upregulation of the EMT pathway in 90 Y-resistant cell lines (mean log FC 8.9), which contains CD44 and ITGB1 , the counterpart of ITGA3 in the a3b1 integrin heterodimer. Numbers next to each gene set bar represent FDR. D, Consistent with Hallmark EMT enrichment, KEGG and Reactome pathways associated with extracellular matrix and integrin cell surface interactions are enriched in resistant cell lines. E, qPCR (mean log 2 FC, error bars represent SEM, with n = 2 biological replicates) and Western blot validation of ITGA3/a3b1 and CD44 confirming elevated expression of these genes in the most 90 Y-resistant (SK-Hep1) vs. 90 Y-sensitive (PLC/PRF/5) and intermediate (SNU-398) cell lines, consistent with an EMT/adhesion phenotype associated with 90 Y resistance. F, qPCR of tumor vs. normal CD44 expression demonstrates a trend toward higher CD44 expression in those with IR or OFP ( n = 5) vs. SR ( n = 12), although not powered for statistical significance ( P = 0.43 Mann–Whitney). Color circle indicates treatment intent: blue, radiation segmentectomy; orange, multicompartment dosimetry (MCD) with TAD > 205 Gy. MIRD, medical internal radiation dose. Relative expression from qPCR data = 2 −(Cttarget − Cthousekeeping) , in which Ct is the detection crossing threshold.

Article Snippet: The following human liver cancer cell lines were obtained from the ATCC: SK-Hep1 (RRID: CVCL_0525), Hep-3B2 (RRID: CVCL_0326), HepG2/C3A (RRID: CVCL_1098), PLC/PRF/5 (RRID: CVCL_0485), SNU-387 (RRID: CVCL_0250), SNU-423 (RRID: CVCL_0366), SNU-449 (RRID: CVCL_0454), and SNU-475 (RRID: CVCL_0497).

Techniques: Expressing, Quantitative Proteomics, RNA Expression, Western Blot, Biomarker Discovery, MANN-WHITNEY

90 Y-resistant and -sensitive cell lines demonstrate distinct patterns of biological process enrichment after 90 Y microsphere treatment. A, Volcano plot of log 2 FC vs. −log 10 P value of genes upregulated (red) and downregulated (blue) after 90 Y microsphere treatment in select 90 Y-resistant cell lines (SK-Hep1, SNU-449, and SNU-387). B, GSEA of Hallmark pathways demonstrates upregulation of pathways involved with inflammation and immune response after treatment in the 90 Y-resistant group, such as IFNγ response (mean log 2 FC = 7.4), among others. C, Consistent with Hallmark IFNγ and IFNα enrichment, KEGG and Reactome pathways associated with cytokine signaling and antigen presentation were upregulated after treatment with 90 Y. D, Volcano plot of log 2 FC vs. −log 10 P value of genes upregulated (red) and downregulated (blue) after 90 Y microsphere treatment in select 90 Y-sensitive cell lines (PLC/PRF/5 and HepG2). E, GSEA of Hallmark pathways demonstrates downregulation of many of the inflammatory and immune response–related pathways that were upregulated in the resistant cell lines, including IFNγ response (mean log 2 FC = −4.3,) and IFNα response (mean log 2 FC = −4.7). No Hallmark pathways demonstrated significant upregulation after treatment in 90 Y-sensitive cells. F, KEGG and Reactome pathway analysis corroborates downregulation of interferon- and antigen presentation–associated pathways, along with those involved with growth signaling such as MAPK (mean log FC = −4.01) and TGFβ (mean log FC = −2.62). Numbers next to each gene set bar represent FDR. Significance set at FDR <0.05 and log 2 FC > 2. Heterogeneous activation of stress and survival pathways after 90 Y microsphere treatment across different liver cancer cell lines. Significant variation in Hallmark gene sets ( G ) IFNγ, ( H ) IFNα, ( I ) TNFα signaling, ( J ) hypoxia, ( K ) myogenesis, ( L ) p53 pathway, ( M ) oxidative phosphorylation, and ( N ) DNA repair, showing heterogeneity in stress and survival pathway activation across cell lines after 90 Y microsphere treatment.

Journal: Cancer Research Communications

Article Title: Epithelial–Mesenchymal Transition and Stress Adaptations Underlie Yttrium-90 Resistance in Liver Cancer Cell Lines

doi: 10.1158/2767-9764.CRC-25-0627

Figure Lengend Snippet: 90 Y-resistant and -sensitive cell lines demonstrate distinct patterns of biological process enrichment after 90 Y microsphere treatment. A, Volcano plot of log 2 FC vs. −log 10 P value of genes upregulated (red) and downregulated (blue) after 90 Y microsphere treatment in select 90 Y-resistant cell lines (SK-Hep1, SNU-449, and SNU-387). B, GSEA of Hallmark pathways demonstrates upregulation of pathways involved with inflammation and immune response after treatment in the 90 Y-resistant group, such as IFNγ response (mean log 2 FC = 7.4), among others. C, Consistent with Hallmark IFNγ and IFNα enrichment, KEGG and Reactome pathways associated with cytokine signaling and antigen presentation were upregulated after treatment with 90 Y. D, Volcano plot of log 2 FC vs. −log 10 P value of genes upregulated (red) and downregulated (blue) after 90 Y microsphere treatment in select 90 Y-sensitive cell lines (PLC/PRF/5 and HepG2). E, GSEA of Hallmark pathways demonstrates downregulation of many of the inflammatory and immune response–related pathways that were upregulated in the resistant cell lines, including IFNγ response (mean log 2 FC = −4.3,) and IFNα response (mean log 2 FC = −4.7). No Hallmark pathways demonstrated significant upregulation after treatment in 90 Y-sensitive cells. F, KEGG and Reactome pathway analysis corroborates downregulation of interferon- and antigen presentation–associated pathways, along with those involved with growth signaling such as MAPK (mean log FC = −4.01) and TGFβ (mean log FC = −2.62). Numbers next to each gene set bar represent FDR. Significance set at FDR <0.05 and log 2 FC > 2. Heterogeneous activation of stress and survival pathways after 90 Y microsphere treatment across different liver cancer cell lines. Significant variation in Hallmark gene sets ( G ) IFNγ, ( H ) IFNα, ( I ) TNFα signaling, ( J ) hypoxia, ( K ) myogenesis, ( L ) p53 pathway, ( M ) oxidative phosphorylation, and ( N ) DNA repair, showing heterogeneity in stress and survival pathway activation across cell lines after 90 Y microsphere treatment.

Article Snippet: The following human liver cancer cell lines were obtained from the ATCC: SK-Hep1 (RRID: CVCL_0525), Hep-3B2 (RRID: CVCL_0326), HepG2/C3A (RRID: CVCL_1098), PLC/PRF/5 (RRID: CVCL_0485), SNU-387 (RRID: CVCL_0250), SNU-423 (RRID: CVCL_0366), SNU-449 (RRID: CVCL_0454), and SNU-475 (RRID: CVCL_0497).

Techniques: Immunopeptidomics, Activation Assay, Phospho-proteomics

qRT-PCR validation of gene expression representing relevant biological pathways after 90 Y microsphere treatment in the most sensitive (PLC/PRF/5), resistant (SK-Hep1), and intermediate (SNU-398) cell lines. Select genes involved in ( A ) interferon stimulation and antigen presentation were mostly upregulated in both SNU-398 and SK-Hep1 after treatment, with the exception of GBP1 in SK-Hep1 and MX1 and IFI27 in SNU-398 which did not have reliable qPCR readouts. TXNIP was strongly upregulated in SK-Hep1 after treatment, consistent with increased oxidative stress signaling. ( B ) SNU-398 demonstrated very strong upregulation of inflammatory response genes, in particular CCL5 and TNFAIP2 . C, Distinct patterns of DNA damage and cell stress genes were seen across cell lines, with SK-Hep1 showing upregulation of BRCA1 and downregulation of BNIP3 . D, ECM genes CD44 and ITGA3 were strongly upregulated in SNU-398 after treatment, suggesting stress-induced EMT acquisition. Although there was slight downregulation of these genes in SK-Hep1, they remained at highest abundance in this line consistent with an EMT-associated expression profile. All experiments were performed in technical triplicate and error bars represent SEM when >1 biological replicate was performed. nd, no reliable qRT-PCR readout.

Journal: Cancer Research Communications

Article Title: Epithelial–Mesenchymal Transition and Stress Adaptations Underlie Yttrium-90 Resistance in Liver Cancer Cell Lines

doi: 10.1158/2767-9764.CRC-25-0627

Figure Lengend Snippet: qRT-PCR validation of gene expression representing relevant biological pathways after 90 Y microsphere treatment in the most sensitive (PLC/PRF/5), resistant (SK-Hep1), and intermediate (SNU-398) cell lines. Select genes involved in ( A ) interferon stimulation and antigen presentation were mostly upregulated in both SNU-398 and SK-Hep1 after treatment, with the exception of GBP1 in SK-Hep1 and MX1 and IFI27 in SNU-398 which did not have reliable qPCR readouts. TXNIP was strongly upregulated in SK-Hep1 after treatment, consistent with increased oxidative stress signaling. ( B ) SNU-398 demonstrated very strong upregulation of inflammatory response genes, in particular CCL5 and TNFAIP2 . C, Distinct patterns of DNA damage and cell stress genes were seen across cell lines, with SK-Hep1 showing upregulation of BRCA1 and downregulation of BNIP3 . D, ECM genes CD44 and ITGA3 were strongly upregulated in SNU-398 after treatment, suggesting stress-induced EMT acquisition. Although there was slight downregulation of these genes in SK-Hep1, they remained at highest abundance in this line consistent with an EMT-associated expression profile. All experiments were performed in technical triplicate and error bars represent SEM when >1 biological replicate was performed. nd, no reliable qRT-PCR readout.

Article Snippet: The following human liver cancer cell lines were obtained from the ATCC: SK-Hep1 (RRID: CVCL_0525), Hep-3B2 (RRID: CVCL_0326), HepG2/C3A (RRID: CVCL_1098), PLC/PRF/5 (RRID: CVCL_0485), SNU-387 (RRID: CVCL_0250), SNU-423 (RRID: CVCL_0366), SNU-449 (RRID: CVCL_0454), and SNU-475 (RRID: CVCL_0497).

Techniques: Quantitative RT-PCR, Biomarker Discovery, Gene Expression, Immunopeptidomics, Expressing