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pbabe krasg12d plasmid  (Addgene inc)


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    Addgene inc pbabe krasg12d plasmid
    Pbabe Krasg12d Plasmid, supplied by Addgene inc, used in various techniques. Bioz Stars score: 93/100, based on 41 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/pbabe+kras+g12d/pBabe-Kras+G12D+(Plasmid+%2358902)/bio_rxiv__64898__2026__03__24__711280-204-3-11
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    pbabe krasg12d plasmid - by Bioz Stars, 2026-09
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    93
    Addgene inc pbabe krasg12d plasmid
    Pbabe Krasg12d Plasmid, supplied by Addgene inc, 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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    Addgene inc pbabe kras g12d puro
    Cholangiocyte-derived organoids harboring Trp53 deletion and Kras <t>G12D</t> mutation give rise to iCCA in a syngeneic orthotopic model. (A) Illustration of the syngeneic orthotopic CCA tumor model. Isolated wild-type chol-orgs were genetically engineered to harbor Trp53 deletion and Kras G12D mutation by CRISPR/Cas9 and implanted intrahepatically. (B) Bright-field microscopic images of wildtype (WT) chol-orgs and with Trp53 deletion (P) and Kras G12D mutation (PK). The CRISPR/Cas9-induced genetic modifications in Trp53 and Kras genes are indicated below. (C) Representative stains of WT and PK chol-orgs indicating positive biliary lineage marker expression (CK19) and upregulation of CD44 in chol-PK orgs. (D) Representative histopathology images of liver tumors obtained upon orthotopic implantation of chol-PK resembling CCA. Stains as indicated. Red dotted line demarcates the boundary between non-tumor liver (N) and tumor (T). All scale bars in (B) indicate 500 μm, and in (C) and (D) 100 μm.
    Pbabe Kras G12d Puro, supplied by Addgene inc, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/pbabe+kras+g12d/pBabe-Kras+G12D+(Plasmid+%2358902)/bio_rxiv__64898__2026__03__24__711280-204-8-11
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    Addgene inc pbabe kras g12d
    Cholangiocyte-derived organoids harboring Trp53 deletion and Kras <t>G12D</t> mutation give rise to iCCA in a syngeneic orthotopic model. (A) Illustration of the syngeneic orthotopic CCA tumor model. Isolated wild-type chol-orgs were genetically engineered to harbor Trp53 deletion and Kras G12D mutation by CRISPR/Cas9 and implanted intrahepatically. (B) Bright-field microscopic images of wildtype (WT) chol-orgs and with Trp53 deletion (P) and Kras G12D mutation (PK). The CRISPR/Cas9-induced genetic modifications in Trp53 and Kras genes are indicated below. (C) Representative stains of WT and PK chol-orgs indicating positive biliary lineage marker expression (CK19) and upregulation of CD44 in chol-PK orgs. (D) Representative histopathology images of liver tumors obtained upon orthotopic implantation of chol-PK resembling CCA. Stains as indicated. Red dotted line demarcates the boundary between non-tumor liver (N) and tumor (T). All scale bars in (B) indicate 500 μm, and in (C) and (D) 100 μm.
    Pbabe Kras G12d, supplied by Addgene inc, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/pbabe+kras+g12d/pBabe-Kras+G12D+(Plasmid+%2358902)/bio_rxiv__64898__2026__03__24__711280-206-4-11
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    Addgene inc pbabe puro kras g12d
    A The gene expression data were downloaded from TCGA database for GSEA analysis (KRAS WT -CRC patients ( n = 150) and KRAS G12/13* -CRC patients ( n = 150). B The association between KRAS status and CD8 + TILs in pre-neoCRT biopsies and post-neoCRT surgical tissues was analyzed in advanced CRC patients (Unpaired t test, n = 94, p = 0.0385). C HT29-KRAS WT (endogenous wild-type KRAS) and HT29-KRAS <t>G12D</t> cells were irradiated (5 Gy) and labeled with CFSE. These cells were individually co-cultured with immature dendritic cells (THP1-iDCs) for 24 hr and Jurkat T cells for 18 hr. The level of surface CD80 (THP1-iDC) and intracellular IFNγ (Jurkat) was evaluated by flow cytometry ( n = 3). One-way ANOVA t test. D CT26 shNC and CT26 shKRAS cells were generated by infecting with lentivirus carrying shNC and shKRAS. Cells were inoculated into right hind leg (2 × 10 5 cells) and left back (1 × 10 5 cells) by subcutaneous injection for 14 day. On days 14 and 18, local tumors in right hind leg were irradiated (5 Gy). The tumor volume was measured every 3 days ( n = 4–6). The resected tumors on Day 28 were weighted ( n = 4-6). One-way ANOVA and two-way ANOVA t test. * p < 0.05, ** p < 0.01 and *** p < 0.001. E The subset of tumor-infiltrating CD4 + cells within primary tumors was analyzed by flow cytometric analysis ( n = 3–4). One-way ANOVA t test. * p < 0.05. F The subset of tumor-infiltrating CD8 + cells within primary tumors was analyzed by flow cytometric analysis ( n = 3–4). One-way ANOVA t test. * p < 0.05. G The subset of tumor-infiltrating MDSCs (Gr1 + CD11b + ) within primary tumors was analyzed by flow cytometric analysis ( n = 3-4). One-way ANOVA t test. H. The subset of tumor-infiltrating regulatory T lymphocytes (CD4 + CD25 + Foxp3 + , T reg ) within primary tumors was analyzed by flow cytometric analysis ( n = 3–4). One-way ANOVA t test. * p < 0.05.
    Pbabe Puro Kras G12d, supplied by Addgene inc, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Addgene inc pbabe purokrasg12d
    A The gene expression data were downloaded from TCGA database for GSEA analysis (KRAS WT -CRC patients ( n = 150) and KRAS G12/13* -CRC patients ( n = 150). B The association between KRAS status and CD8 + TILs in pre-neoCRT biopsies and post-neoCRT surgical tissues was analyzed in advanced CRC patients (Unpaired t test, n = 94, p = 0.0385). C HT29-KRAS WT (endogenous wild-type KRAS) and HT29-KRAS <t>G12D</t> cells were irradiated (5 Gy) and labeled with CFSE. These cells were individually co-cultured with immature dendritic cells (THP1-iDCs) for 24 hr and Jurkat T cells for 18 hr. The level of surface CD80 (THP1-iDC) and intracellular IFNγ (Jurkat) was evaluated by flow cytometry ( n = 3). One-way ANOVA t test. D CT26 shNC and CT26 shKRAS cells were generated by infecting with lentivirus carrying shNC and shKRAS. Cells were inoculated into right hind leg (2 × 10 5 cells) and left back (1 × 10 5 cells) by subcutaneous injection for 14 day. On days 14 and 18, local tumors in right hind leg were irradiated (5 Gy). The tumor volume was measured every 3 days ( n = 4–6). The resected tumors on Day 28 were weighted ( n = 4-6). One-way ANOVA and two-way ANOVA t test. * p < 0.05, ** p < 0.01 and *** p < 0.001. E The subset of tumor-infiltrating CD4 + cells within primary tumors was analyzed by flow cytometric analysis ( n = 3–4). One-way ANOVA t test. * p < 0.05. F The subset of tumor-infiltrating CD8 + cells within primary tumors was analyzed by flow cytometric analysis ( n = 3–4). One-way ANOVA t test. * p < 0.05. G The subset of tumor-infiltrating MDSCs (Gr1 + CD11b + ) within primary tumors was analyzed by flow cytometric analysis ( n = 3-4). One-way ANOVA t test. H. The subset of tumor-infiltrating regulatory T lymphocytes (CD4 + CD25 + Foxp3 + , T reg ) within primary tumors was analyzed by flow cytometric analysis ( n = 3–4). One-way ANOVA t test. * p < 0.05.
    Pbabe Purokrasg12d, supplied by Addgene inc, 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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    A The gene expression data were downloaded from TCGA database for GSEA analysis (KRAS WT -CRC patients ( n = 150) and KRAS G12/13* -CRC patients ( n = 150). B The association between KRAS status and CD8 + TILs in pre-neoCRT biopsies and post-neoCRT surgical tissues was analyzed in advanced CRC patients (Unpaired t test, n = 94, p = 0.0385). C HT29-KRAS WT (endogenous wild-type KRAS) and HT29-KRAS <t>G12D</t> cells were irradiated (5 Gy) and labeled with CFSE. These cells were individually co-cultured with immature dendritic cells (THP1-iDCs) for 24 hr and Jurkat T cells for 18 hr. The level of surface CD80 (THP1-iDC) and intracellular IFNγ (Jurkat) was evaluated by flow cytometry ( n = 3). One-way ANOVA t test. D CT26 shNC and CT26 shKRAS cells were generated by infecting with lentivirus carrying shNC and shKRAS. Cells were inoculated into right hind leg (2 × 10 5 cells) and left back (1 × 10 5 cells) by subcutaneous injection for 14 day. On days 14 and 18, local tumors in right hind leg were irradiated (5 Gy). The tumor volume was measured every 3 days ( n = 4–6). The resected tumors on Day 28 were weighted ( n = 4-6). One-way ANOVA and two-way ANOVA t test. * p < 0.05, ** p < 0.01 and *** p < 0.001. E The subset of tumor-infiltrating CD4 + cells within primary tumors was analyzed by flow cytometric analysis ( n = 3–4). One-way ANOVA t test. * p < 0.05. F The subset of tumor-infiltrating CD8 + cells within primary tumors was analyzed by flow cytometric analysis ( n = 3–4). One-way ANOVA t test. * p < 0.05. G The subset of tumor-infiltrating MDSCs (Gr1 + CD11b + ) within primary tumors was analyzed by flow cytometric analysis ( n = 3-4). One-way ANOVA t test. H. The subset of tumor-infiltrating regulatory T lymphocytes (CD4 + CD25 + Foxp3 + , T reg ) within primary tumors was analyzed by flow cytometric analysis ( n = 3–4). One-way ANOVA t test. * p < 0.05.
    Pbabe Puro Krasg12d, supplied by Addgene inc, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/pbabe+kras+g12d/pBabe-Kras+G12D+(Plasmid+%2358902)/pm41241302-47-6-11
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    a Normal human bronchial epithelial cell (BEAS-2B), <t>KRAS</t> Mut cell lines (H358 and H460), KRAS WT and EGFR WT cell lines (HCC1666 and H522), and EGFR Mut cell lines (HCC827 and PC9) were collected with lysis buffer, and immunoblotted with anti-SIRT1 and β-actin antibody. b Immunohistochemical staining for SIRT1 with the lung from LSL-Kras <t>G12D</t> Tg mouse at 16 weeks after administration of adenovirus Cre recombinase induction. Representative images are shown. Scale bar, 100 μm. High-magnification images correspond to the areas marked by the black box. c SIRT1 mRNA expression was measured by RT–qPCR with the same cell lines as in a . RPL32 was used as internal control and for normalization. Student’s t -test, mean ± s.d.; n = 6, * P < 0.05. d The mRNA expression of Sirt1 was analyzed by RT–qPCR with the cancerous and adjacent noncancerous lung tissues of LSL- Kras G12D Tg mouse. Rpl32 was used as internal control and for normalization. Student’s t -test, mean ± s.e.m.; n = 6, *, P < 0.05. e H358 and H460 cells were transfected with the 2-μg plasmids of pcDNA , KRAS WT and KRAS G12D . The cells were collected with cell lysis buffer and subjected to western blotting with anti-KRAS, anti-SIRT1 and β-actin antibodies. f H358 and H460 cells were transfected with siCon and siKRAS (80 nM). The cells were collected with cell lysis buffer and subjected to western blotting with same antibodies in e . g H358 and H460 cell extracts were immunoprecipitated with anti-KRAS and anti-SIRT1, and immunoblotted with anti-KRAS, anti-SIRT1 and β-actin antibodies.
    Kras G12d, supplied by Addgene inc, 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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    a Normal human bronchial epithelial cell (BEAS-2B), <t>KRAS</t> Mut cell lines (H358 and H460), KRAS WT and EGFR WT cell lines (HCC1666 and H522), and EGFR Mut cell lines (HCC827 and PC9) were collected with lysis buffer, and immunoblotted with anti-SIRT1 and β-actin antibody. b Immunohistochemical staining for SIRT1 with the lung from LSL-Kras <t>G12D</t> Tg mouse at 16 weeks after administration of adenovirus Cre recombinase induction. Representative images are shown. Scale bar, 100 μm. High-magnification images correspond to the areas marked by the black box. c SIRT1 mRNA expression was measured by RT–qPCR with the same cell lines as in a . RPL32 was used as internal control and for normalization. Student’s t -test, mean ± s.d.; n = 6, * P < 0.05. d The mRNA expression of Sirt1 was analyzed by RT–qPCR with the cancerous and adjacent noncancerous lung tissues of LSL- Kras G12D Tg mouse. Rpl32 was used as internal control and for normalization. Student’s t -test, mean ± s.e.m.; n = 6, *, P < 0.05. e H358 and H460 cells were transfected with the 2-μg plasmids of pcDNA , KRAS WT and KRAS G12D . The cells were collected with cell lysis buffer and subjected to western blotting with anti-KRAS, anti-SIRT1 and β-actin antibodies. f H358 and H460 cells were transfected with siCon and siKRAS (80 nM). The cells were collected with cell lysis buffer and subjected to western blotting with same antibodies in e . g H358 and H460 cell extracts were immunoprecipitated with anti-KRAS and anti-SIRT1, and immunoblotted with anti-KRAS, anti-SIRT1 and β-actin antibodies.
    Krasg12d, supplied by Addgene inc, 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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    A The scheme for generating the HPNE-based in vitro stepwise transformation model system. B Diagram illustrating the retroviral vector that expresses Doxycycline (Dox)-inducible human PR55α. HPNE cells were transduced with Dox-inducible PR55α retroviral vector (pRevTRE-PR55α) or control empty vector and selected with 200 μg/ml Hygromycin for stably transduced cells. The PR55α-transduced cells were induced by 1 μg/ml Dox for 3 days and analyzed for the protein levels of PR55α and GAPDH by Western blotting. C HPNE/Control and HPNE/PR55α cells were transduced with a retroviral vector expressing V5-tagged human p53 R175H mutant or control vector. The stably transduced clones were selected for Blasticidin (4 μg/mL) and verified for the expression of ectopic V5-p53 R175H by Western blot analysis with an anti-V5 antibody. D The indicated HPNE isogenic cell lines were transduced with a retroviral vector expressing the KRAS <t>G12D</t> mutant, the most frequently detected KRAS mutant in human pancreatic cancer (PC), and selected by 800 μg/ml Zeocin for stably transduced cells. The expression of KRAS G12D in the resulting cells was validated by Western blot analysis using a specific antibody.
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    Addgene inc pbabe
    A The scheme for generating the HPNE-based in vitro stepwise transformation model system. B Diagram illustrating the retroviral vector that expresses Doxycycline (Dox)-inducible human PR55α. HPNE cells were transduced with Dox-inducible PR55α retroviral vector (pRevTRE-PR55α) or control empty vector and selected with 200 μg/ml Hygromycin for stably transduced cells. The PR55α-transduced cells were induced by 1 μg/ml Dox for 3 days and analyzed for the protein levels of PR55α and GAPDH by Western blotting. C HPNE/Control and HPNE/PR55α cells were transduced with a retroviral vector expressing V5-tagged human p53 R175H mutant or control vector. The stably transduced clones were selected for Blasticidin (4 μg/mL) and verified for the expression of ectopic V5-p53 R175H by Western blot analysis with an anti-V5 antibody. D The indicated HPNE isogenic cell lines were transduced with a retroviral vector expressing the KRAS <t>G12D</t> mutant, the most frequently detected KRAS mutant in human pancreatic cancer (PC), and selected by 800 μg/ml Zeocin for stably transduced cells. The expression of KRAS G12D in the resulting cells was validated by Western blot analysis using a specific antibody.
    Pbabe, supplied by Addgene inc, 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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    Image Search Results


    Cholangiocyte-derived organoids harboring Trp53 deletion and Kras G12D mutation give rise to iCCA in a syngeneic orthotopic model. (A) Illustration of the syngeneic orthotopic CCA tumor model. Isolated wild-type chol-orgs were genetically engineered to harbor Trp53 deletion and Kras G12D mutation by CRISPR/Cas9 and implanted intrahepatically. (B) Bright-field microscopic images of wildtype (WT) chol-orgs and with Trp53 deletion (P) and Kras G12D mutation (PK). The CRISPR/Cas9-induced genetic modifications in Trp53 and Kras genes are indicated below. (C) Representative stains of WT and PK chol-orgs indicating positive biliary lineage marker expression (CK19) and upregulation of CD44 in chol-PK orgs. (D) Representative histopathology images of liver tumors obtained upon orthotopic implantation of chol-PK resembling CCA. Stains as indicated. Red dotted line demarcates the boundary between non-tumor liver (N) and tumor (T). All scale bars in (B) indicate 500 μm, and in (C) and (D) 100 μm.

    Journal: bioRxiv

    Article Title: Cell-of-Origin, not Oncogenic Effect, Determines Desmoplastic Immune Exclusion in KRAS-Driven Liver Cancer

    doi: 10.64898/2026.03.24.711280

    Figure Lengend Snippet: Cholangiocyte-derived organoids harboring Trp53 deletion and Kras G12D mutation give rise to iCCA in a syngeneic orthotopic model. (A) Illustration of the syngeneic orthotopic CCA tumor model. Isolated wild-type chol-orgs were genetically engineered to harbor Trp53 deletion and Kras G12D mutation by CRISPR/Cas9 and implanted intrahepatically. (B) Bright-field microscopic images of wildtype (WT) chol-orgs and with Trp53 deletion (P) and Kras G12D mutation (PK). The CRISPR/Cas9-induced genetic modifications in Trp53 and Kras genes are indicated below. (C) Representative stains of WT and PK chol-orgs indicating positive biliary lineage marker expression (CK19) and upregulation of CD44 in chol-PK orgs. (D) Representative histopathology images of liver tumors obtained upon orthotopic implantation of chol-PK resembling CCA. Stains as indicated. Red dotted line demarcates the boundary between non-tumor liver (N) and tumor (T). All scale bars in (B) indicate 500 μm, and in (C) and (D) 100 μm.

    Article Snippet: [ ] The pBabe-KrasG12D plasmid was reconstructed from pBabe-Kras G12D -puro (Addgene #58902) by removing the puromycin resistance gene through digestion with HindIII-HF and BspDI, blunt-ended by Klenow and re-ligation to restore plasmid circularity.

    Techniques: Derivative Assay, Mutagenesis, Isolation, CRISPR, Marker, Expressing, Histopathology

    Hepatocyte-derived organoids harboring Trp53 deletion and Kras G12D overexpression give rise to HCC in a syngeneic orthotopic model. (A) Illustration of the syngeneic orthotopic HCC tumor model. Isolated wild-type hep-orgs were genetically engineered to harbor Trp53 deletion by CRISPR/Cas9 and Kras G12D via lentiviral transduction and implanted intrahepatically. (B) Bright-field microscopic images of wildtype (WT) hep-orgs and with Trp53 deletion (P) and Kras G12D overexpression (PK). The CRISPR/Cas9-induced genetic modifications in the Trp53 gene and the sequence of the overexpressing Kras G12D transgene are indicated below. (C) Representative stains of WT and PK hep-orgs indicating positive hepatocyte marker expression (HNF4α) and upregulation of CD44 in hep-PK orgs. (D) Bar plot of tumor penetrance of chol-PK and hep-PK organoids upon orthotopic tumor implantation. (E) Representative histopathology images of liver tumors obtained upon orthotopic implantation of hep-PK organoids resembling HCC. Stains as indicated. Red dotted line demarcates the boundary between non-tumor liver (N) and tumor (T). All scale bars in (B) indicate 500 μm, and in (C) and (E) 100 μm.

    Journal: bioRxiv

    Article Title: Cell-of-Origin, not Oncogenic Effect, Determines Desmoplastic Immune Exclusion in KRAS-Driven Liver Cancer

    doi: 10.64898/2026.03.24.711280

    Figure Lengend Snippet: Hepatocyte-derived organoids harboring Trp53 deletion and Kras G12D overexpression give rise to HCC in a syngeneic orthotopic model. (A) Illustration of the syngeneic orthotopic HCC tumor model. Isolated wild-type hep-orgs were genetically engineered to harbor Trp53 deletion by CRISPR/Cas9 and Kras G12D via lentiviral transduction and implanted intrahepatically. (B) Bright-field microscopic images of wildtype (WT) hep-orgs and with Trp53 deletion (P) and Kras G12D overexpression (PK). The CRISPR/Cas9-induced genetic modifications in the Trp53 gene and the sequence of the overexpressing Kras G12D transgene are indicated below. (C) Representative stains of WT and PK hep-orgs indicating positive hepatocyte marker expression (HNF4α) and upregulation of CD44 in hep-PK orgs. (D) Bar plot of tumor penetrance of chol-PK and hep-PK organoids upon orthotopic tumor implantation. (E) Representative histopathology images of liver tumors obtained upon orthotopic implantation of hep-PK organoids resembling HCC. Stains as indicated. Red dotted line demarcates the boundary between non-tumor liver (N) and tumor (T). All scale bars in (B) indicate 500 μm, and in (C) and (E) 100 μm.

    Article Snippet: [ ] The pBabe-KrasG12D plasmid was reconstructed from pBabe-Kras G12D -puro (Addgene #58902) by removing the puromycin resistance gene through digestion with HindIII-HF and BspDI, blunt-ended by Klenow and re-ligation to restore plasmid circularity.

    Techniques: Derivative Assay, Over Expression, Isolation, CRISPR, Transduction, Sequencing, Marker, Expressing, Tumor Implantation, Histopathology

    Cell-of-origin is the dominant determinant of transcriptional identity in Trp53-deleted , Kras G12D -mutant liver cancer organoids. (A) Messenger RNA expression of fibroblast activation markers in mHSCs treated for 24 hours with CCM from chol-or hep-derived organoids (WT or PK). (B) Schematic of multi-factorial transcriptome analysis in chol and hep organoids. Gene expression was modelled with lineage (chol vs hep), oncogenic effect (PK vs WT), and their interaction to identify lineage-specific PK effects. (C) Principal component analysis (PCA) plot of transcriptomes from indicated lines. Shown are PC1 (79.2% variance) versus PC3 (3.9%), which separate samples primarily by cell lineage and, to a lesser extent, oncogenic activation. (D) Distribution of variance in normalized expression of DEGs explained by lineage and oncogenic effect shown as violin plot with integrated box plot. For each gene, we fit a linear model on normalized counts with lineage, oncogenic effect, their interaction (lineage × oncogenic effect), and mouse strain as predictors. Residuals capture remaining variation. DEGs are the union across the four contrasts: chol-PK vs chol-WT, chol-PK vs hep-PK, chol-WT vs hep-WT, and hep-PK vs hep-WT. (E) Scatter plot showing upregulated DEGs in chol-PK organoids from multi-factorial analysis. Dot color indicates the significance of the interaction effect (adjusted p-value), and dot size reflects the significance of PK versus WT comparison in chol-orgs (adjusted p-value). (F) Gene Set Enrichment Analysis (GSEA) of Hallmark pathways specifically enriched in the lineage-dependent PK effect. The pathways selected for cancer-related cell cycle and oncogenic signaling, tumor-stroma crosstalk, and tumor-immune and inflammation with positive enrichment (i.e. PK effects stronger in chol-orgs) are shown.

    Journal: bioRxiv

    Article Title: Cell-of-Origin, not Oncogenic Effect, Determines Desmoplastic Immune Exclusion in KRAS-Driven Liver Cancer

    doi: 10.64898/2026.03.24.711280

    Figure Lengend Snippet: Cell-of-origin is the dominant determinant of transcriptional identity in Trp53-deleted , Kras G12D -mutant liver cancer organoids. (A) Messenger RNA expression of fibroblast activation markers in mHSCs treated for 24 hours with CCM from chol-or hep-derived organoids (WT or PK). (B) Schematic of multi-factorial transcriptome analysis in chol and hep organoids. Gene expression was modelled with lineage (chol vs hep), oncogenic effect (PK vs WT), and their interaction to identify lineage-specific PK effects. (C) Principal component analysis (PCA) plot of transcriptomes from indicated lines. Shown are PC1 (79.2% variance) versus PC3 (3.9%), which separate samples primarily by cell lineage and, to a lesser extent, oncogenic activation. (D) Distribution of variance in normalized expression of DEGs explained by lineage and oncogenic effect shown as violin plot with integrated box plot. For each gene, we fit a linear model on normalized counts with lineage, oncogenic effect, their interaction (lineage × oncogenic effect), and mouse strain as predictors. Residuals capture remaining variation. DEGs are the union across the four contrasts: chol-PK vs chol-WT, chol-PK vs hep-PK, chol-WT vs hep-WT, and hep-PK vs hep-WT. (E) Scatter plot showing upregulated DEGs in chol-PK organoids from multi-factorial analysis. Dot color indicates the significance of the interaction effect (adjusted p-value), and dot size reflects the significance of PK versus WT comparison in chol-orgs (adjusted p-value). (F) Gene Set Enrichment Analysis (GSEA) of Hallmark pathways specifically enriched in the lineage-dependent PK effect. The pathways selected for cancer-related cell cycle and oncogenic signaling, tumor-stroma crosstalk, and tumor-immune and inflammation with positive enrichment (i.e. PK effects stronger in chol-orgs) are shown.

    Article Snippet: [ ] The pBabe-KrasG12D plasmid was reconstructed from pBabe-Kras G12D -puro (Addgene #58902) by removing the puromycin resistance gene through digestion with HindIII-HF and BspDI, blunt-ended by Klenow and re-ligation to restore plasmid circularity.

    Techniques: Mutagenesis, RNA Expression, Activation Assay, Derivative Assay, Gene Expression, Expressing, Comparison

    Cholangiocyte-derived organoids harboring Trp53 deletion and Kras G12D mutation give rise to iCCA in a syngeneic orthotopic model. (A) Illustration of the syngeneic orthotopic CCA tumor model. Isolated wild-type chol-orgs were genetically engineered to harbor Trp53 deletion and Kras G12D mutation by CRISPR/Cas9 and implanted intrahepatically. (B) Bright-field microscopic images of wildtype (WT) chol-orgs and with Trp53 deletion (P) and Kras G12D mutation (PK). The CRISPR/Cas9-induced genetic modifications in Trp53 and Kras genes are indicated below. (C) Representative stains of WT and PK chol-orgs indicating positive biliary lineage marker expression (CK19) and upregulation of CD44 in chol-PK orgs. (D) Representative histopathology images of liver tumors obtained upon orthotopic implantation of chol-PK resembling CCA. Stains as indicated. Red dotted line demarcates the boundary between non-tumor liver (N) and tumor (T). All scale bars in (B) indicate 500 μm, and in (C) and (D) 100 μm.

    Journal: bioRxiv

    Article Title: Cell-of-Origin, not Oncogenic Effect, Determines Desmoplastic Immune Exclusion in KRAS-Driven Liver Cancer

    doi: 10.64898/2026.03.24.711280

    Figure Lengend Snippet: Cholangiocyte-derived organoids harboring Trp53 deletion and Kras G12D mutation give rise to iCCA in a syngeneic orthotopic model. (A) Illustration of the syngeneic orthotopic CCA tumor model. Isolated wild-type chol-orgs were genetically engineered to harbor Trp53 deletion and Kras G12D mutation by CRISPR/Cas9 and implanted intrahepatically. (B) Bright-field microscopic images of wildtype (WT) chol-orgs and with Trp53 deletion (P) and Kras G12D mutation (PK). The CRISPR/Cas9-induced genetic modifications in Trp53 and Kras genes are indicated below. (C) Representative stains of WT and PK chol-orgs indicating positive biliary lineage marker expression (CK19) and upregulation of CD44 in chol-PK orgs. (D) Representative histopathology images of liver tumors obtained upon orthotopic implantation of chol-PK resembling CCA. Stains as indicated. Red dotted line demarcates the boundary between non-tumor liver (N) and tumor (T). All scale bars in (B) indicate 500 μm, and in (C) and (D) 100 μm.

    Article Snippet: The Lenti-CRISPR-sgRNA( Trp53 ), pBabe- Kras G12D , or Lenti-luciferase-P2A-Neo plasmid (Addgene #105621) was co-transfected with packaging plasmid psPAX2 and pMD2.G (both from PlasmidFactory GmbH & Co. KG, Bielefeld, Germany) into HEK293T cells by TransIT LT1 transfection reagent according to the manufacturer’s instructions (Mirus Bio, Madison, WI, USA).

    Techniques: Derivative Assay, Mutagenesis, Isolation, CRISPR, Marker, Expressing, Histopathology

    Hepatocyte-derived organoids harboring Trp53 deletion and Kras G12D overexpression give rise to HCC in a syngeneic orthotopic model. (A) Illustration of the syngeneic orthotopic HCC tumor model. Isolated wild-type hep-orgs were genetically engineered to harbor Trp53 deletion by CRISPR/Cas9 and Kras G12D via lentiviral transduction and implanted intrahepatically. (B) Bright-field microscopic images of wildtype (WT) hep-orgs and with Trp53 deletion (P) and Kras G12D overexpression (PK). The CRISPR/Cas9-induced genetic modifications in the Trp53 gene and the sequence of the overexpressing Kras G12D transgene are indicated below. (C) Representative stains of WT and PK hep-orgs indicating positive hepatocyte marker expression (HNF4α) and upregulation of CD44 in hep-PK orgs. (D) Bar plot of tumor penetrance of chol-PK and hep-PK organoids upon orthotopic tumor implantation. (E) Representative histopathology images of liver tumors obtained upon orthotopic implantation of hep-PK organoids resembling HCC. Stains as indicated. Red dotted line demarcates the boundary between non-tumor liver (N) and tumor (T). All scale bars in (B) indicate 500 μm, and in (C) and (E) 100 μm.

    Journal: bioRxiv

    Article Title: Cell-of-Origin, not Oncogenic Effect, Determines Desmoplastic Immune Exclusion in KRAS-Driven Liver Cancer

    doi: 10.64898/2026.03.24.711280

    Figure Lengend Snippet: Hepatocyte-derived organoids harboring Trp53 deletion and Kras G12D overexpression give rise to HCC in a syngeneic orthotopic model. (A) Illustration of the syngeneic orthotopic HCC tumor model. Isolated wild-type hep-orgs were genetically engineered to harbor Trp53 deletion by CRISPR/Cas9 and Kras G12D via lentiviral transduction and implanted intrahepatically. (B) Bright-field microscopic images of wildtype (WT) hep-orgs and with Trp53 deletion (P) and Kras G12D overexpression (PK). The CRISPR/Cas9-induced genetic modifications in the Trp53 gene and the sequence of the overexpressing Kras G12D transgene are indicated below. (C) Representative stains of WT and PK hep-orgs indicating positive hepatocyte marker expression (HNF4α) and upregulation of CD44 in hep-PK orgs. (D) Bar plot of tumor penetrance of chol-PK and hep-PK organoids upon orthotopic tumor implantation. (E) Representative histopathology images of liver tumors obtained upon orthotopic implantation of hep-PK organoids resembling HCC. Stains as indicated. Red dotted line demarcates the boundary between non-tumor liver (N) and tumor (T). All scale bars in (B) indicate 500 μm, and in (C) and (E) 100 μm.

    Article Snippet: The Lenti-CRISPR-sgRNA( Trp53 ), pBabe- Kras G12D , or Lenti-luciferase-P2A-Neo plasmid (Addgene #105621) was co-transfected with packaging plasmid psPAX2 and pMD2.G (both from PlasmidFactory GmbH & Co. KG, Bielefeld, Germany) into HEK293T cells by TransIT LT1 transfection reagent according to the manufacturer’s instructions (Mirus Bio, Madison, WI, USA).

    Techniques: Derivative Assay, Over Expression, Isolation, CRISPR, Transduction, Sequencing, Marker, Expressing, Tumor Implantation, Histopathology

    Cell-of-origin is the dominant determinant of transcriptional identity in Trp53-deleted , Kras G12D -mutant liver cancer organoids. (A) Messenger RNA expression of fibroblast activation markers in mHSCs treated for 24 hours with CCM from chol-or hep-derived organoids (WT or PK). (B) Schematic of multi-factorial transcriptome analysis in chol and hep organoids. Gene expression was modelled with lineage (chol vs hep), oncogenic effect (PK vs WT), and their interaction to identify lineage-specific PK effects. (C) Principal component analysis (PCA) plot of transcriptomes from indicated lines. Shown are PC1 (79.2% variance) versus PC3 (3.9%), which separate samples primarily by cell lineage and, to a lesser extent, oncogenic activation. (D) Distribution of variance in normalized expression of DEGs explained by lineage and oncogenic effect shown as violin plot with integrated box plot. For each gene, we fit a linear model on normalized counts with lineage, oncogenic effect, their interaction (lineage × oncogenic effect), and mouse strain as predictors. Residuals capture remaining variation. DEGs are the union across the four contrasts: chol-PK vs chol-WT, chol-PK vs hep-PK, chol-WT vs hep-WT, and hep-PK vs hep-WT. (E) Scatter plot showing upregulated DEGs in chol-PK organoids from multi-factorial analysis. Dot color indicates the significance of the interaction effect (adjusted p-value), and dot size reflects the significance of PK versus WT comparison in chol-orgs (adjusted p-value). (F) Gene Set Enrichment Analysis (GSEA) of Hallmark pathways specifically enriched in the lineage-dependent PK effect. The pathways selected for cancer-related cell cycle and oncogenic signaling, tumor-stroma crosstalk, and tumor-immune and inflammation with positive enrichment (i.e. PK effects stronger in chol-orgs) are shown.

    Journal: bioRxiv

    Article Title: Cell-of-Origin, not Oncogenic Effect, Determines Desmoplastic Immune Exclusion in KRAS-Driven Liver Cancer

    doi: 10.64898/2026.03.24.711280

    Figure Lengend Snippet: Cell-of-origin is the dominant determinant of transcriptional identity in Trp53-deleted , Kras G12D -mutant liver cancer organoids. (A) Messenger RNA expression of fibroblast activation markers in mHSCs treated for 24 hours with CCM from chol-or hep-derived organoids (WT or PK). (B) Schematic of multi-factorial transcriptome analysis in chol and hep organoids. Gene expression was modelled with lineage (chol vs hep), oncogenic effect (PK vs WT), and their interaction to identify lineage-specific PK effects. (C) Principal component analysis (PCA) plot of transcriptomes from indicated lines. Shown are PC1 (79.2% variance) versus PC3 (3.9%), which separate samples primarily by cell lineage and, to a lesser extent, oncogenic activation. (D) Distribution of variance in normalized expression of DEGs explained by lineage and oncogenic effect shown as violin plot with integrated box plot. For each gene, we fit a linear model on normalized counts with lineage, oncogenic effect, their interaction (lineage × oncogenic effect), and mouse strain as predictors. Residuals capture remaining variation. DEGs are the union across the four contrasts: chol-PK vs chol-WT, chol-PK vs hep-PK, chol-WT vs hep-WT, and hep-PK vs hep-WT. (E) Scatter plot showing upregulated DEGs in chol-PK organoids from multi-factorial analysis. Dot color indicates the significance of the interaction effect (adjusted p-value), and dot size reflects the significance of PK versus WT comparison in chol-orgs (adjusted p-value). (F) Gene Set Enrichment Analysis (GSEA) of Hallmark pathways specifically enriched in the lineage-dependent PK effect. The pathways selected for cancer-related cell cycle and oncogenic signaling, tumor-stroma crosstalk, and tumor-immune and inflammation with positive enrichment (i.e. PK effects stronger in chol-orgs) are shown.

    Article Snippet: The Lenti-CRISPR-sgRNA( Trp53 ), pBabe- Kras G12D , or Lenti-luciferase-P2A-Neo plasmid (Addgene #105621) was co-transfected with packaging plasmid psPAX2 and pMD2.G (both from PlasmidFactory GmbH & Co. KG, Bielefeld, Germany) into HEK293T cells by TransIT LT1 transfection reagent according to the manufacturer’s instructions (Mirus Bio, Madison, WI, USA).

    Techniques: Mutagenesis, RNA Expression, Activation Assay, Derivative Assay, Gene Expression, Expressing, Comparison

    A The gene expression data were downloaded from TCGA database for GSEA analysis (KRAS WT -CRC patients ( n = 150) and KRAS G12/13* -CRC patients ( n = 150). B The association between KRAS status and CD8 + TILs in pre-neoCRT biopsies and post-neoCRT surgical tissues was analyzed in advanced CRC patients (Unpaired t test, n = 94, p = 0.0385). C HT29-KRAS WT (endogenous wild-type KRAS) and HT29-KRAS G12D cells were irradiated (5 Gy) and labeled with CFSE. These cells were individually co-cultured with immature dendritic cells (THP1-iDCs) for 24 hr and Jurkat T cells for 18 hr. The level of surface CD80 (THP1-iDC) and intracellular IFNγ (Jurkat) was evaluated by flow cytometry ( n = 3). One-way ANOVA t test. D CT26 shNC and CT26 shKRAS cells were generated by infecting with lentivirus carrying shNC and shKRAS. Cells were inoculated into right hind leg (2 × 10 5 cells) and left back (1 × 10 5 cells) by subcutaneous injection for 14 day. On days 14 and 18, local tumors in right hind leg were irradiated (5 Gy). The tumor volume was measured every 3 days ( n = 4–6). The resected tumors on Day 28 were weighted ( n = 4-6). One-way ANOVA and two-way ANOVA t test. * p < 0.05, ** p < 0.01 and *** p < 0.001. E The subset of tumor-infiltrating CD4 + cells within primary tumors was analyzed by flow cytometric analysis ( n = 3–4). One-way ANOVA t test. * p < 0.05. F The subset of tumor-infiltrating CD8 + cells within primary tumors was analyzed by flow cytometric analysis ( n = 3–4). One-way ANOVA t test. * p < 0.05. G The subset of tumor-infiltrating MDSCs (Gr1 + CD11b + ) within primary tumors was analyzed by flow cytometric analysis ( n = 3-4). One-way ANOVA t test. H. The subset of tumor-infiltrating regulatory T lymphocytes (CD4 + CD25 + Foxp3 + , T reg ) within primary tumors was analyzed by flow cytometric analysis ( n = 3–4). One-way ANOVA t test. * p < 0.05.

    Journal: NPJ Precision Oncology

    Article Title: Loss of MicroRNA-29b promotes DNMT3b-mediated STING downregulation to attenuate radiotherapy-induced antitumor immunity in KRAS-mutated colorectal cancer

    doi: 10.1038/s41698-026-01290-8

    Figure Lengend Snippet: A The gene expression data were downloaded from TCGA database for GSEA analysis (KRAS WT -CRC patients ( n = 150) and KRAS G12/13* -CRC patients ( n = 150). B The association between KRAS status and CD8 + TILs in pre-neoCRT biopsies and post-neoCRT surgical tissues was analyzed in advanced CRC patients (Unpaired t test, n = 94, p = 0.0385). C HT29-KRAS WT (endogenous wild-type KRAS) and HT29-KRAS G12D cells were irradiated (5 Gy) and labeled with CFSE. These cells were individually co-cultured with immature dendritic cells (THP1-iDCs) for 24 hr and Jurkat T cells for 18 hr. The level of surface CD80 (THP1-iDC) and intracellular IFNγ (Jurkat) was evaluated by flow cytometry ( n = 3). One-way ANOVA t test. D CT26 shNC and CT26 shKRAS cells were generated by infecting with lentivirus carrying shNC and shKRAS. Cells were inoculated into right hind leg (2 × 10 5 cells) and left back (1 × 10 5 cells) by subcutaneous injection for 14 day. On days 14 and 18, local tumors in right hind leg were irradiated (5 Gy). The tumor volume was measured every 3 days ( n = 4–6). The resected tumors on Day 28 were weighted ( n = 4-6). One-way ANOVA and two-way ANOVA t test. * p < 0.05, ** p < 0.01 and *** p < 0.001. E The subset of tumor-infiltrating CD4 + cells within primary tumors was analyzed by flow cytometric analysis ( n = 3–4). One-way ANOVA t test. * p < 0.05. F The subset of tumor-infiltrating CD8 + cells within primary tumors was analyzed by flow cytometric analysis ( n = 3–4). One-way ANOVA t test. * p < 0.05. G The subset of tumor-infiltrating MDSCs (Gr1 + CD11b + ) within primary tumors was analyzed by flow cytometric analysis ( n = 3-4). One-way ANOVA t test. H. The subset of tumor-infiltrating regulatory T lymphocytes (CD4 + CD25 + Foxp3 + , T reg ) within primary tumors was analyzed by flow cytometric analysis ( n = 3–4). One-way ANOVA t test. * p < 0.05.

    Article Snippet: The retroviral pBabe-puro vector (#1764) and pBabe-puro-KRAS G12D (#58902) were purchased from Addgene.

    Techniques: Gene Expression, Irradiation, Labeling, Cell Culture, Flow Cytometry, Generated, Injection

    A WiDr cells were infected with lentivirus carrying pBabe-puro-vector (Vec.) or pBabe-puro-KRAS G12D and selected for three days. WiDr-Vec. and WiDr-KRAS G12D cells were irradiated (5 Gy), and then harvested for qRT-PCR analysis after 24 hr ( n = 3). One-way ANOVA t test. * p < 0.05. B CoLo320 cells were infected with lentivirus carrying pBabe-puro-vector (Vec.) or pBabe-puro-KRAS G12D and selected for three days. CoLo320-Vec. and CoLo320-KRAS G12D cells were irradiated (5 Gy), and then harvested for qRT-PCR analysis after 24 hr ( n = 3). One-way ANOVA t test. * p < 0.05. C HCT116 cells were infected with lentivirus carrying pLKO-scramble shRNA (shNC) or pLKO-shKRAS (shKRAS) and selected for three days. HCT116 shNC and HCT116 shKRAS cells were irradiated (5 Gy), and then harvested for qRT-PCR analysis after 24 hr ( n = 3). One-way ANOVA t test. * p < 0.05 and ** p < 0.01. D SW620 shNC and SW620 shKRAS cells were irradiated (5 Gy), and then harvested for qRT-PCR analysis after 24 hr ( n = 3). One-way ANOVA t test. * p < 0.05 and ** p < 0.01. E WiDr and Colo320DM (endogenous wild-type KRAS) cells were individually infected with vector (Vec.) and KRAS G12D . Cells were selected by puromycin for three days. The level of DNMT1, DNMT3a and DNMT3b was evaluated by immunoblotting ( n = 3). One-way ANOVA t test. ** p < 0.01. F CT26, HCT116 and SW620 (endogenous mutant KRAS) cells individually infected with lentivirus carry shNC and shKRAS. Cells were selected by puromycin for three days. The level of DNMT1, DNMT3a and DNMT3b was evaluated by immunoblotting ( n = 3). One-way ANOVA t test. ** p < 0.01. G KRAS G12D -tranduced WiDr (endogenous wild-type KRAS) cells were treated with 2.5 μmol/L and 5.0 μmol/L AZA for two days. The level of STING was evaluated by immunoblotting ( n = 3). One-way ANOVA t test. * p < 0.05 and ** p < 0.01. H . KRAS G12D -tranduced CoLo320 (endogenous wild-type KRAS) cells were treated with 2.5 μmol/L and 5.0 μmol/L AZA for two days. The level of STING was evaluated by immunoblotting ( n = 3). One-way ANOVA t test. * p < 0.05 and ** p < 0.01. I HCT116 and SW620 (endogenous mutant KRAS) cells individually infected with lentivirus carry shDNMT1, shDNMT3a and shDNMT3b. Cells were selected by puromycin for three days. The mRNA level of STING was evaluated by qRT-PCR ( n = 3). One-way ANOVA t test. * p < 0.05. J The protein level of STING was evaluated by immunoblotting ( n = 3).

    Journal: NPJ Precision Oncology

    Article Title: Loss of MicroRNA-29b promotes DNMT3b-mediated STING downregulation to attenuate radiotherapy-induced antitumor immunity in KRAS-mutated colorectal cancer

    doi: 10.1038/s41698-026-01290-8

    Figure Lengend Snippet: A WiDr cells were infected with lentivirus carrying pBabe-puro-vector (Vec.) or pBabe-puro-KRAS G12D and selected for three days. WiDr-Vec. and WiDr-KRAS G12D cells were irradiated (5 Gy), and then harvested for qRT-PCR analysis after 24 hr ( n = 3). One-way ANOVA t test. * p < 0.05. B CoLo320 cells were infected with lentivirus carrying pBabe-puro-vector (Vec.) or pBabe-puro-KRAS G12D and selected for three days. CoLo320-Vec. and CoLo320-KRAS G12D cells were irradiated (5 Gy), and then harvested for qRT-PCR analysis after 24 hr ( n = 3). One-way ANOVA t test. * p < 0.05. C HCT116 cells were infected with lentivirus carrying pLKO-scramble shRNA (shNC) or pLKO-shKRAS (shKRAS) and selected for three days. HCT116 shNC and HCT116 shKRAS cells were irradiated (5 Gy), and then harvested for qRT-PCR analysis after 24 hr ( n = 3). One-way ANOVA t test. * p < 0.05 and ** p < 0.01. D SW620 shNC and SW620 shKRAS cells were irradiated (5 Gy), and then harvested for qRT-PCR analysis after 24 hr ( n = 3). One-way ANOVA t test. * p < 0.05 and ** p < 0.01. E WiDr and Colo320DM (endogenous wild-type KRAS) cells were individually infected with vector (Vec.) and KRAS G12D . Cells were selected by puromycin for three days. The level of DNMT1, DNMT3a and DNMT3b was evaluated by immunoblotting ( n = 3). One-way ANOVA t test. ** p < 0.01. F CT26, HCT116 and SW620 (endogenous mutant KRAS) cells individually infected with lentivirus carry shNC and shKRAS. Cells were selected by puromycin for three days. The level of DNMT1, DNMT3a and DNMT3b was evaluated by immunoblotting ( n = 3). One-way ANOVA t test. ** p < 0.01. G KRAS G12D -tranduced WiDr (endogenous wild-type KRAS) cells were treated with 2.5 μmol/L and 5.0 μmol/L AZA for two days. The level of STING was evaluated by immunoblotting ( n = 3). One-way ANOVA t test. * p < 0.05 and ** p < 0.01. H . KRAS G12D -tranduced CoLo320 (endogenous wild-type KRAS) cells were treated with 2.5 μmol/L and 5.0 μmol/L AZA for two days. The level of STING was evaluated by immunoblotting ( n = 3). One-way ANOVA t test. * p < 0.05 and ** p < 0.01. I HCT116 and SW620 (endogenous mutant KRAS) cells individually infected with lentivirus carry shDNMT1, shDNMT3a and shDNMT3b. Cells were selected by puromycin for three days. The mRNA level of STING was evaluated by qRT-PCR ( n = 3). One-way ANOVA t test. * p < 0.05. J The protein level of STING was evaluated by immunoblotting ( n = 3).

    Article Snippet: The retroviral pBabe-puro vector (#1764) and pBabe-puro-KRAS G12D (#58902) were purchased from Addgene.

    Techniques: Infection, Plasmid Preparation, Irradiation, Quantitative RT-PCR, shRNA, Western Blot, Mutagenesis

    A CoLo320-Vec. and CoLo320-KRAS G12D cells were harvested for miRNA-seq and identified miR-29b-3p as the potential candidate to regulate DNMT3b expression. B The level of miR-29b-3p was evaluated in KRAS-mutated cell lines in CCLE and TCGA-COAD database. One-way ANOVA t test. C The level of miR29b-3p was evaluated in HT29-KRAS G12D and CoLo320-KRAS G12D cells, compared to their parental KRAS WT cells. One-way ANOVA t test. * p < 0.05. D The level of miR-29b-3p was evaluated in SW620 shKRAS and HCT116 shKRAS cells, compared to their parental KRAS Mut cells. One-way ANOVA t test. * p < 0.05 and *** p < 0.001. E HT29-KRAS G12D cells were transfected with miR-29b mimetic (20 nM) for 24 hr and then irradiated (5 Gy). After 24 hr, cells were harvested for qRT-PCR ( n = 3). One-way ANOVA t test. * p < 0.05 and ** p < 0.01. F SW620 shKRAS cells were transfected with miR-29b-3p antagomir (20 nM) for 24 hr and then irradiated (5 Gy). After 24 hr, cells were harvested for qRT-PCR ( n = 3). One-way ANOVA t test. * p < 0.05 and ** p < 0.01. G HT29-KRAS G12D cells were transfected with miR-29b-3p mimetic (20 nM) for 24 hr and then irradiated (5 Gy). After 24 hr, cells were harvested for immunoblotting ( n = 3). One-way ANOVA t test. ** p < 0.01. H SW620 shKRAS cells were transfected with miR-29b-3p antagomir (20 nM) for 24 hr and then irradiated (5 Gy). After 24 hr, cells were harvested for immunoblotting ( n = 3). One-way ANOVA t test. ** p < 0.01.

    Journal: NPJ Precision Oncology

    Article Title: Loss of MicroRNA-29b promotes DNMT3b-mediated STING downregulation to attenuate radiotherapy-induced antitumor immunity in KRAS-mutated colorectal cancer

    doi: 10.1038/s41698-026-01290-8

    Figure Lengend Snippet: A CoLo320-Vec. and CoLo320-KRAS G12D cells were harvested for miRNA-seq and identified miR-29b-3p as the potential candidate to regulate DNMT3b expression. B The level of miR-29b-3p was evaluated in KRAS-mutated cell lines in CCLE and TCGA-COAD database. One-way ANOVA t test. C The level of miR29b-3p was evaluated in HT29-KRAS G12D and CoLo320-KRAS G12D cells, compared to their parental KRAS WT cells. One-way ANOVA t test. * p < 0.05. D The level of miR-29b-3p was evaluated in SW620 shKRAS and HCT116 shKRAS cells, compared to their parental KRAS Mut cells. One-way ANOVA t test. * p < 0.05 and *** p < 0.001. E HT29-KRAS G12D cells were transfected with miR-29b mimetic (20 nM) for 24 hr and then irradiated (5 Gy). After 24 hr, cells were harvested for qRT-PCR ( n = 3). One-way ANOVA t test. * p < 0.05 and ** p < 0.01. F SW620 shKRAS cells were transfected with miR-29b-3p antagomir (20 nM) for 24 hr and then irradiated (5 Gy). After 24 hr, cells were harvested for qRT-PCR ( n = 3). One-way ANOVA t test. * p < 0.05 and ** p < 0.01. G HT29-KRAS G12D cells were transfected with miR-29b-3p mimetic (20 nM) for 24 hr and then irradiated (5 Gy). After 24 hr, cells were harvested for immunoblotting ( n = 3). One-way ANOVA t test. ** p < 0.01. H SW620 shKRAS cells were transfected with miR-29b-3p antagomir (20 nM) for 24 hr and then irradiated (5 Gy). After 24 hr, cells were harvested for immunoblotting ( n = 3). One-way ANOVA t test. ** p < 0.01.

    Article Snippet: The retroviral pBabe-puro vector (#1764) and pBabe-puro-KRAS G12D (#58902) were purchased from Addgene.

    Techniques: Expressing, Transfection, Irradiation, Quantitative RT-PCR, Western Blot

    a Normal human bronchial epithelial cell (BEAS-2B), KRAS Mut cell lines (H358 and H460), KRAS WT and EGFR WT cell lines (HCC1666 and H522), and EGFR Mut cell lines (HCC827 and PC9) were collected with lysis buffer, and immunoblotted with anti-SIRT1 and β-actin antibody. b Immunohistochemical staining for SIRT1 with the lung from LSL-Kras G12D Tg mouse at 16 weeks after administration of adenovirus Cre recombinase induction. Representative images are shown. Scale bar, 100 μm. High-magnification images correspond to the areas marked by the black box. c SIRT1 mRNA expression was measured by RT–qPCR with the same cell lines as in a . RPL32 was used as internal control and for normalization. Student’s t -test, mean ± s.d.; n = 6, * P < 0.05. d The mRNA expression of Sirt1 was analyzed by RT–qPCR with the cancerous and adjacent noncancerous lung tissues of LSL- Kras G12D Tg mouse. Rpl32 was used as internal control and for normalization. Student’s t -test, mean ± s.e.m.; n = 6, *, P < 0.05. e H358 and H460 cells were transfected with the 2-μg plasmids of pcDNA , KRAS WT and KRAS G12D . The cells were collected with cell lysis buffer and subjected to western blotting with anti-KRAS, anti-SIRT1 and β-actin antibodies. f H358 and H460 cells were transfected with siCon and siKRAS (80 nM). The cells were collected with cell lysis buffer and subjected to western blotting with same antibodies in e . g H358 and H460 cell extracts were immunoprecipitated with anti-KRAS and anti-SIRT1, and immunoblotted with anti-KRAS, anti-SIRT1 and β-actin antibodies.

    Journal: Experimental & Molecular Medicine

    Article Title: Targeting TGF-β–Smad2/3–JNK1-mediated SIRT1 activity overcomes the chemoresistance of KRAS mutation lung cancer

    doi: 10.1038/s12276-025-01536-8

    Figure Lengend Snippet: a Normal human bronchial epithelial cell (BEAS-2B), KRAS Mut cell lines (H358 and H460), KRAS WT and EGFR WT cell lines (HCC1666 and H522), and EGFR Mut cell lines (HCC827 and PC9) were collected with lysis buffer, and immunoblotted with anti-SIRT1 and β-actin antibody. b Immunohistochemical staining for SIRT1 with the lung from LSL-Kras G12D Tg mouse at 16 weeks after administration of adenovirus Cre recombinase induction. Representative images are shown. Scale bar, 100 μm. High-magnification images correspond to the areas marked by the black box. c SIRT1 mRNA expression was measured by RT–qPCR with the same cell lines as in a . RPL32 was used as internal control and for normalization. Student’s t -test, mean ± s.d.; n = 6, * P < 0.05. d The mRNA expression of Sirt1 was analyzed by RT–qPCR with the cancerous and adjacent noncancerous lung tissues of LSL- Kras G12D Tg mouse. Rpl32 was used as internal control and for normalization. Student’s t -test, mean ± s.e.m.; n = 6, *, P < 0.05. e H358 and H460 cells were transfected with the 2-μg plasmids of pcDNA , KRAS WT and KRAS G12D . The cells were collected with cell lysis buffer and subjected to western blotting with anti-KRAS, anti-SIRT1 and β-actin antibodies. f H358 and H460 cells were transfected with siCon and siKRAS (80 nM). The cells were collected with cell lysis buffer and subjected to western blotting with same antibodies in e . g H358 and H460 cell extracts were immunoprecipitated with anti-KRAS and anti-SIRT1, and immunoblotted with anti-KRAS, anti-SIRT1 and β-actin antibodies.

    Article Snippet: KRAS WT (#75282), KRAS G12C (#58901), KRAS G12D (#58902), KRAS G12V (#46746) and JNK1-GFP (#86830) plasmids were purchased from Addgene.

    Techniques: Lysis, Immunohistochemical staining, Staining, Expressing, Quantitative RT-PCR, Control, Transfection, Western Blot, Immunoprecipitation

    a Normal human bronchial epithelial cell (BEAS-2B) and KRAS Mut cell lines (H358, A427 and H727) were collected with lysis buffer and subjected to western blotting with anti-pERK, ERK and β-actin antibodies. b A luciferase assay was performed to assess the AP-1-mediated transcriptional regulatory activity with cell lysates in Fig. 4a. Student’s t -test, mean ± s.d.; n = 6, * P < 0.05. c TGFB1 mRNA expression was measured by RT–qPCR with same cell lines as in a . RPL32 was used as internal control and for normalization. Student’s t -test, mean ± s.d.; n = 6, * P < 0.05. d The medium of four cell lines were changed by FBS-free medium before cell collection at 24 h. Conditioned medium was collected and concentrated using an Amicon Ultra-15 tube, and total TGF-β1 levels were measured by ELISA. e KRAS Mut cell lines (H358, A427 and H727) were transfected with pcDNA , KRAS G12C , G12D and G12V plasmids (2 μg). TGF-β1 levels were measured under the same method as in d . f H358, A427 and H727 cells were transplanted with pcDNA , KRAS G12C , G12D and G12V plasmids, siCon and siSmad2/3 (80 nM) for 48 h, and then the activity of Smad2/3, JNK1 and KRAS was measured. g The cell lysates of each different KRAS Mut cell lines (H358, A427 and H727) under KWN-C with indicated dosage for 24 h were transferred by immunoblotting assay with anti-pSmad2/3, anti-Smad2/3, pJNK1, JNK1, anti-pSIRT1 Ser27 , pSIRT1 Ser47 , SIRT1, KRAS–GTP-bound and β-actin antibodies. h , H358, A427 and H460 cells were treated with DMSO or KWN-C (10 μM), and cell extracts were then immunoprecipitated using immunoglobulin G, anti-KRAS, and RAF-1 agarose bead antibodies. Immunoblotting was performed using anti-acetyl, anti-KRAS–GTP-bound, anti-SIRT1, anti-KRAS and β-actin antibodies.

    Journal: Experimental & Molecular Medicine

    Article Title: Targeting TGF-β–Smad2/3–JNK1-mediated SIRT1 activity overcomes the chemoresistance of KRAS mutation lung cancer

    doi: 10.1038/s12276-025-01536-8

    Figure Lengend Snippet: a Normal human bronchial epithelial cell (BEAS-2B) and KRAS Mut cell lines (H358, A427 and H727) were collected with lysis buffer and subjected to western blotting with anti-pERK, ERK and β-actin antibodies. b A luciferase assay was performed to assess the AP-1-mediated transcriptional regulatory activity with cell lysates in Fig. 4a. Student’s t -test, mean ± s.d.; n = 6, * P < 0.05. c TGFB1 mRNA expression was measured by RT–qPCR with same cell lines as in a . RPL32 was used as internal control and for normalization. Student’s t -test, mean ± s.d.; n = 6, * P < 0.05. d The medium of four cell lines were changed by FBS-free medium before cell collection at 24 h. Conditioned medium was collected and concentrated using an Amicon Ultra-15 tube, and total TGF-β1 levels were measured by ELISA. e KRAS Mut cell lines (H358, A427 and H727) were transfected with pcDNA , KRAS G12C , G12D and G12V plasmids (2 μg). TGF-β1 levels were measured under the same method as in d . f H358, A427 and H727 cells were transplanted with pcDNA , KRAS G12C , G12D and G12V plasmids, siCon and siSmad2/3 (80 nM) for 48 h, and then the activity of Smad2/3, JNK1 and KRAS was measured. g The cell lysates of each different KRAS Mut cell lines (H358, A427 and H727) under KWN-C with indicated dosage for 24 h were transferred by immunoblotting assay with anti-pSmad2/3, anti-Smad2/3, pJNK1, JNK1, anti-pSIRT1 Ser27 , pSIRT1 Ser47 , SIRT1, KRAS–GTP-bound and β-actin antibodies. h , H358, A427 and H460 cells were treated with DMSO or KWN-C (10 μM), and cell extracts were then immunoprecipitated using immunoglobulin G, anti-KRAS, and RAF-1 agarose bead antibodies. Immunoblotting was performed using anti-acetyl, anti-KRAS–GTP-bound, anti-SIRT1, anti-KRAS and β-actin antibodies.

    Article Snippet: KRAS WT (#75282), KRAS G12C (#58901), KRAS G12D (#58902), KRAS G12V (#46746) and JNK1-GFP (#86830) plasmids were purchased from Addgene.

    Techniques: Lysis, Western Blot, Luciferase, Activity Assay, Expressing, Quantitative RT-PCR, Control, Enzyme-linked Immunosorbent Assay, Transfection, Immunoprecipitation

    a After administration of adenovirus Cre recombinase in KRAS G12D mice for 10 weeks, mice were treated using the same method as in Fig. . Representative H&E staining images and pJNK1, cleaved caspase-3, cleaved PARP, TUNEL and Ki-67 were analyzed by immunohistochemical staining in tumor tissues at the end of experiments. b Tumor tissue from each drug-treated group was collected with lysis buffer, and SIRT1 activity was measured with cell lysates. Student’s t -test, mean ± s.e.m.; n = 10, * P < 0.05. c Tumor area was quantified using ImageJ software. Student’s t -test, mean ± s.e.m.; n = 10, * P < 0.05. d Tumor numbers per lung area were counted under the microscope in specimens collected from mice treated with drugs. Student’s t -test, mean ± s.e.m.; n = 10, * P < 0.05 . e Survival rates of mice treated with drugs (log-rank test). f Median survival days and P values were calculated using the log-rank test and the Gehan–Breslow–Wilcoxon test, respectively, based on Student’s t -test. g A schematic overview of the mechanism of enhanced SIRT1 activity in KRAS Mut lung cancer and definition of a rational combination strategy between SIRT1 activity inhibitor and conventional chemotherapy.

    Journal: Experimental & Molecular Medicine

    Article Title: Targeting TGF-β–Smad2/3–JNK1-mediated SIRT1 activity overcomes the chemoresistance of KRAS mutation lung cancer

    doi: 10.1038/s12276-025-01536-8

    Figure Lengend Snippet: a After administration of adenovirus Cre recombinase in KRAS G12D mice for 10 weeks, mice were treated using the same method as in Fig. . Representative H&E staining images and pJNK1, cleaved caspase-3, cleaved PARP, TUNEL and Ki-67 were analyzed by immunohistochemical staining in tumor tissues at the end of experiments. b Tumor tissue from each drug-treated group was collected with lysis buffer, and SIRT1 activity was measured with cell lysates. Student’s t -test, mean ± s.e.m.; n = 10, * P < 0.05. c Tumor area was quantified using ImageJ software. Student’s t -test, mean ± s.e.m.; n = 10, * P < 0.05. d Tumor numbers per lung area were counted under the microscope in specimens collected from mice treated with drugs. Student’s t -test, mean ± s.e.m.; n = 10, * P < 0.05 . e Survival rates of mice treated with drugs (log-rank test). f Median survival days and P values were calculated using the log-rank test and the Gehan–Breslow–Wilcoxon test, respectively, based on Student’s t -test. g A schematic overview of the mechanism of enhanced SIRT1 activity in KRAS Mut lung cancer and definition of a rational combination strategy between SIRT1 activity inhibitor and conventional chemotherapy.

    Article Snippet: KRAS WT (#75282), KRAS G12C (#58901), KRAS G12D (#58902), KRAS G12V (#46746) and JNK1-GFP (#86830) plasmids were purchased from Addgene.

    Techniques: Staining, TUNEL Assay, Immunohistochemical staining, Lysis, Activity Assay, Software, Microscopy

    A The scheme for generating the HPNE-based in vitro stepwise transformation model system. B Diagram illustrating the retroviral vector that expresses Doxycycline (Dox)-inducible human PR55α. HPNE cells were transduced with Dox-inducible PR55α retroviral vector (pRevTRE-PR55α) or control empty vector and selected with 200 μg/ml Hygromycin for stably transduced cells. The PR55α-transduced cells were induced by 1 μg/ml Dox for 3 days and analyzed for the protein levels of PR55α and GAPDH by Western blotting. C HPNE/Control and HPNE/PR55α cells were transduced with a retroviral vector expressing V5-tagged human p53 R175H mutant or control vector. The stably transduced clones were selected for Blasticidin (4 μg/mL) and verified for the expression of ectopic V5-p53 R175H by Western blot analysis with an anti-V5 antibody. D The indicated HPNE isogenic cell lines were transduced with a retroviral vector expressing the KRAS G12D mutant, the most frequently detected KRAS mutant in human pancreatic cancer (PC), and selected by 800 μg/ml Zeocin for stably transduced cells. The expression of KRAS G12D in the resulting cells was validated by Western blot analysis using a specific antibody.

    Journal: Oncogene

    Article Title: PR55α subunit of protein phosphatase 2A supports KRAS G12D -driven tumorigenesis that requires YAP activation

    doi: 10.1038/s41388-025-03477-y

    Figure Lengend Snippet: A The scheme for generating the HPNE-based in vitro stepwise transformation model system. B Diagram illustrating the retroviral vector that expresses Doxycycline (Dox)-inducible human PR55α. HPNE cells were transduced with Dox-inducible PR55α retroviral vector (pRevTRE-PR55α) or control empty vector and selected with 200 μg/ml Hygromycin for stably transduced cells. The PR55α-transduced cells were induced by 1 μg/ml Dox for 3 days and analyzed for the protein levels of PR55α and GAPDH by Western blotting. C HPNE/Control and HPNE/PR55α cells were transduced with a retroviral vector expressing V5-tagged human p53 R175H mutant or control vector. The stably transduced clones were selected for Blasticidin (4 μg/mL) and verified for the expression of ectopic V5-p53 R175H by Western blot analysis with an anti-V5 antibody. D The indicated HPNE isogenic cell lines were transduced with a retroviral vector expressing the KRAS G12D mutant, the most frequently detected KRAS mutant in human pancreatic cancer (PC), and selected by 800 μg/ml Zeocin for stably transduced cells. The expression of KRAS G12D in the resulting cells was validated by Western blot analysis using a specific antibody.

    Article Snippet: The pBABE-zeo/KRAS G12D construct was generated by cloning human KRAS G12D cDNA into the pBABE-zeo retroviral vector (Addgene #1766).

    Techniques: Transformation Assay, In Vitro, Retroviral, Plasmid Preparation, Transduction, Control, Stable Transfection, Western Blot, Expressing, Mutagenesis, Clone Assay

    A The indicated HPNE isogenic cell lines were subcutaneously implanted into the flanks of athymic mice and monitored for tumor growth over a 10-week period. Tumor size was measured weekly using a digital caliper. For mice implanted with cells expressing Dox-inducible PR55α, Dox (1 mg/ml) was administered in the drinking water and refreshed every 48 h. As a positive control, CD18/HPAF pancreatic cancer cells were implanted into athymic nude mice and monitored for tumor growth in parallel. The table summarizes the tumor formation rates for each cell line. In a separate cohort, CA3 treatment (1 mg/kg) was initiated 10 days after implantation of HPNE/PR55α + KRAS G12D cells and administered via intraperitoneal injection three times per week for three weeks, as described previously [ 41 ]. Following treatment, mice remained in remission for an additional six weeks. B Representative images of tumor-bearing mice and excised tumor samples at the end of the experiment. C Line graph depicts the number of mice with tumors over time. Statistical significance ( p -value) was assessed using Student’s t-test with SigmaPlot software. D Line graph shows average tumor volume measured weekly for 8 weeks following implantation. E At the study endpoint, tumor xenografts from mice implanted with PK and BK cells were excised and weighed. F Tumor xenograft and adjacent normal tissues were analyzed by IHC analysis for expression of Ki67 (a proliferation biomarker), PR55α, and YAP, as described in Materials and Methods . Histological analysis was also performed using H&E staining. Scale bar = 50 μm.

    Journal: Oncogene

    Article Title: PR55α subunit of protein phosphatase 2A supports KRAS G12D -driven tumorigenesis that requires YAP activation

    doi: 10.1038/s41388-025-03477-y

    Figure Lengend Snippet: A The indicated HPNE isogenic cell lines were subcutaneously implanted into the flanks of athymic mice and monitored for tumor growth over a 10-week period. Tumor size was measured weekly using a digital caliper. For mice implanted with cells expressing Dox-inducible PR55α, Dox (1 mg/ml) was administered in the drinking water and refreshed every 48 h. As a positive control, CD18/HPAF pancreatic cancer cells were implanted into athymic nude mice and monitored for tumor growth in parallel. The table summarizes the tumor formation rates for each cell line. In a separate cohort, CA3 treatment (1 mg/kg) was initiated 10 days after implantation of HPNE/PR55α + KRAS G12D cells and administered via intraperitoneal injection three times per week for three weeks, as described previously [ 41 ]. Following treatment, mice remained in remission for an additional six weeks. B Representative images of tumor-bearing mice and excised tumor samples at the end of the experiment. C Line graph depicts the number of mice with tumors over time. Statistical significance ( p -value) was assessed using Student’s t-test with SigmaPlot software. D Line graph shows average tumor volume measured weekly for 8 weeks following implantation. E At the study endpoint, tumor xenografts from mice implanted with PK and BK cells were excised and weighed. F Tumor xenograft and adjacent normal tissues were analyzed by IHC analysis for expression of Ki67 (a proliferation biomarker), PR55α, and YAP, as described in Materials and Methods . Histological analysis was also performed using H&E staining. Scale bar = 50 μm.

    Article Snippet: The pBABE-zeo/KRAS G12D construct was generated by cloning human KRAS G12D cDNA into the pBABE-zeo retroviral vector (Addgene #1766).

    Techniques: Expressing, Positive Control, Injection, Software, Biomarker Discovery, Staining

    Oncogenic mutations in the KRAS oncogene cause KRAS activation, which is present in 90–95% of PC and serves as the driver of PC. The Raf/MEK/ERK oncogenic pathway is the major downstream effector of KRAS [ 45 ]. PR55α/PP2A was shown to facilitate the activation of the Raf/MEK/ERK signaling pathway by dephosphorylating the inhibitory sites in Raf and KSR1 [ 16 , 17 ]. Raf1 activation can block MST activity in activating LATS1/2. Conversely, the activation of LATS1/2 can suppress Raf1 [ 36 – 38 ]. YAP oncogene activation is required for KRAS-driven PC progression [ 26 – 28 ]. Our studies show that PR55α-associated PP2A promotes YAP activation by inhibiting the LATS/MOB1 auto-activation loop and dephosphorylating YAP, thus stabilizing YAP protein [ 19 ]. Our previous studies also identified a positive feedback regulation of the MST/LATS cascade by PR55α expression [ 19 ]. However, this PR55α-stimulated MST/LATS signaling was abolished by oncogenic KRAS G12D .

    Journal: Oncogene

    Article Title: PR55α subunit of protein phosphatase 2A supports KRAS G12D -driven tumorigenesis that requires YAP activation

    doi: 10.1038/s41388-025-03477-y

    Figure Lengend Snippet: Oncogenic mutations in the KRAS oncogene cause KRAS activation, which is present in 90–95% of PC and serves as the driver of PC. The Raf/MEK/ERK oncogenic pathway is the major downstream effector of KRAS [ 45 ]. PR55α/PP2A was shown to facilitate the activation of the Raf/MEK/ERK signaling pathway by dephosphorylating the inhibitory sites in Raf and KSR1 [ 16 , 17 ]. Raf1 activation can block MST activity in activating LATS1/2. Conversely, the activation of LATS1/2 can suppress Raf1 [ 36 – 38 ]. YAP oncogene activation is required for KRAS-driven PC progression [ 26 – 28 ]. Our studies show that PR55α-associated PP2A promotes YAP activation by inhibiting the LATS/MOB1 auto-activation loop and dephosphorylating YAP, thus stabilizing YAP protein [ 19 ]. Our previous studies also identified a positive feedback regulation of the MST/LATS cascade by PR55α expression [ 19 ]. However, this PR55α-stimulated MST/LATS signaling was abolished by oncogenic KRAS G12D .

    Article Snippet: The pBABE-zeo/KRAS G12D construct was generated by cloning human KRAS G12D cDNA into the pBABE-zeo retroviral vector (Addgene #1766).

    Techniques: Activation Assay, Blocking Assay, Activity Assay, Expressing