Journal: Experimental and Therapeutic Medicine

Article Title: CDX2-UPK1B-PIK3IP1-PI3K/AKT signaling axis regulates gastric cancer cell invasion and migration and influences patient prognosis

doi: 10.3892/etm.2026.13179

Figure Lengend Snippet: Metastasis-related 12-gene signature, and identification of UPK1B and CGB5 as independent prognostic markers associated with advanced metastatic GC. (A) Venn diagram showing the intersection of genes upregulated in N1-3 stage and M1 stage GC tissues. (B) LASSO Cox regression analysis based on TCGA-STAD data identified a metastasis-associated prognostic risk signature. LASSO coefficient profiles of the signature genes in the merged dataset are shown (top) and the coefficient profile plot is generated against the log(λ) sequence (bottom). (C) The high-risk group of patients with GC exhibited a poor prognosis (overall survival). High expression of (D) CGB5 and (E) UPK1B was associated with poor overall survival in patients with GC based on data from the TCGA-STAD cohort. (F) Elevated UPK1B expression predicted poor prognosis (overall survival) of patients with GC in the Kaplan-Meier plotter database. UPK1B expression was increased in (G) M1 compared with M0 and in (H) N2 metastatic stage GC tissues compared with N0 stage. UPK1B, uroplakin 1B; CGB5, chorionic gonadotropin subunit β-5; GC, gastric cancer; LASSO, Least Absolute Shrinkage and Selection Operator; TCGA-STAD, The Cancer Genome Atlas Stomach Adenocarcinoma; HR, hazard ratio; TPM, transcripts per million.

Article Snippet: For gene knockdown experiments, cells were transfected with a GV493 short hairpin RNA (sh) plasmid targeting UPK1B ( ) or a negative control scrambled plasmid (sh-NC), both obtained from GeneChem, Inc.

Techniques: Generated, Sequencing, Expressing, Selection

Journal: Experimental and Therapeutic Medicine

Article Title: CDX2-UPK1B-PIK3IP1-PI3K/AKT signaling axis regulates gastric cancer cell invasion and migration and influences patient prognosis

doi: 10.3892/etm.2026.13179

Figure Lengend Snippet: UPK1B drives GC cell invasion and migration in a PI3K/AKT-dependent manner. (A) Gene set enrichment analysis indicated that genes upregulated in the UPK1B-high group were enriched in the PI3K/AKT pathway. (B) Protein levels of UPK1B in GC cell lines. (C) Knockdown of UPK1B reduced PI3K/AKT activation in MKN45 cells. Silencing UPK1B suppressed the (D) migration/invasion capacity and (E) wound closure rate of MKN45 cells. (F) Overexpression of UPK1B enhanced PI3K/AKT pathway activation in AGS cells, which was attenuated by the PI3K inhibitor LY294002. Inhibition of PI3K/AKT signaling reversed UPK1B-induced (G) migration/invasion capacity and (H) wound closure rate of AGS cells. UPK1B, uroplakin 1B; GC, gastric cancer; p-, phosphorylated; sh, short hairpin RNA; NC, negative control; OE, overexpression.

Article Snippet: For gene knockdown experiments, cells were transfected with a GV493 short hairpin RNA (sh) plasmid targeting UPK1B ( ) or a negative control scrambled plasmid (sh-NC), both obtained from GeneChem, Inc.

Techniques: Migration, Knockdown, Activation Assay, Over Expression, Inhibition, shRNA, Negative Control

Journal: Experimental and Therapeutic Medicine

Article Title: CDX2-UPK1B-PIK3IP1-PI3K/AKT signaling axis regulates gastric cancer cell invasion and migration and influences patient prognosis

doi: 10.3892/etm.2026.13179

Figure Lengend Snippet: CDX2 acts as a transcriptional repressor of UPK1B and its high expression is associated with favorable prognosis of patients with GC. (A) Venn diagram showing overlapping predicted transcriptional regulators of UPK1B from ChEA and ChEA3 databases. (B) Knockdown of CDX2 in AGS cells resulted in increased UPK1B (C) mRNA and (D) protein expression. (E) Overexpression of CDX2 in MKN45 cells reduced UPK1B protein levels. Data from (F) The Cancer Genome Atlas Stomach Adenocarcinoma cohort and (G) the Kaplan-Meier plotter database indicated that high CDX2 expression was associated with improved prognosis of patients with GC. UPK1B, uroplakin 1B; GC, gastric cancer; si, small interfering RNA; NC, negative control; OE, overexpression; HR, hazard ratio; CDX2, caudal-related homeobox transcription factor 2; ChEA, ChIP-X Enrichment Analysis.

Article Snippet: For gene knockdown experiments, cells were transfected with a GV493 short hairpin RNA (sh) plasmid targeting UPK1B ( ) or a negative control scrambled plasmid (sh-NC), both obtained from GeneChem, Inc.

Techniques: Expressing, Knockdown, Over Expression, Small Interfering RNA, Negative Control

Journal: Experimental and Therapeutic Medicine

Article Title: CDX2-UPK1B-PIK3IP1-PI3K/AKT signaling axis regulates gastric cancer cell invasion and migration and influences patient prognosis

doi: 10.3892/etm.2026.13179

Figure Lengend Snippet: UPK1B activates PI3K/AKT signaling by antagonizing the inhibitory regulator PIK3IP1 in gastric cancer cells. (A) Venn diagram showing that PIK3IP1 was identified as a putative UPK1B-interacting partner based on BioGRID and HIPPIE protein-protein interaction databases. (B) UPK1B and PIK3IP1 co-localized in the cytoplasm and plasma membrane of MKN45 cells. (C) Interaction between UPK1B and PIK3IP1 in MKN45 cells. (D) Knockdown of PIK3IP1 in MKN45 cells. (E) Silencing PIK3IP1 in UPK1B-knockdown MKN45 cells restored PI3K/AKT pathway activation. Knockdown of PIK3IP1 reversed the decrease in (F) migration/invasion and (G) wound-healing capacity in UPK1B-silenced MKN45 cells. UPK1B, uroplakin 1B; p-, phosphorylated; si, small interfering RNA; sh, short hairpin RNA; NC, negative control; PIK3IP1, PI3K inhibitor interacting protein 1; HIPPIE, Human Integrated Protein-Protein Interaction Reference; IP, immunoprecipitation.

Article Snippet: For gene knockdown experiments, cells were transfected with a GV493 short hairpin RNA (sh) plasmid targeting UPK1B ( ) or a negative control scrambled plasmid (sh-NC), both obtained from GeneChem, Inc.

Techniques: Clinical Proteomics, Membrane, Knockdown, Activation Assay, Migration, Small Interfering RNA, shRNA, Negative Control, Immunoprecipitation

Journal: Molecular Therapy Oncology

Article Title: CBX6 and CA9 as predictive indicators and therapeutic targets in GBM

doi: 10.1016/j.omton.2026.201159

Figure Lengend Snippet: CBX6 expression is downregulated in multiple cancer types (A) Statistical analysis of The Cancer Genome Atlas (TCGA) Pan-Cancer RNA sequencing (RNA-seq) database shows CBX6 expression is downregulated in various cancer types. (B) CBX6 expression is significantly suppressed in brain cancer, breast cancer, lung adenocarcinoma (abbreviated as LUAD), and prostate cancer, based on analysis of TCGA tumor microarray data using the BRowse All Variants Online (BRAVO) database method. (C and D) Comparison of CBX6 expression in patient-derived GBM tissues and primary tumor cells relative to respective normal controls using qRT-PCR. GAPDH was used as a loading control. (D) Reduced CBX6 expression is significantly associated with poor prognosis in patients with glioma, as shown in Kaplan-Meier survival curves derived from a public patient-derived microarray database, p = 1.94∗ e−7. PBT, primary brain tumor; RBT, recurrent brain tumor.

Article Snippet: A pCMV6-entry plasmid containing Myc-DDK (same as Flag)-tagged human CBX6 cDNA (Cat#: RC204166) and a CBX6 Human shRNA Plasmid Kit (Cat#: TF314170) were purchased from OriGene.

Techniques: Expressing, RNA Sequencing, Microarray, Comparison, Derivative Assay, Quantitative RT-PCR, Control

Journal: Molecular Therapy Oncology

Article Title: CBX6 and CA9 as predictive indicators and therapeutic targets in GBM

doi: 10.1016/j.omton.2026.201159

Figure Lengend Snippet: CBX6 modulation affects tumor cell morphology and proliferation (A) CBX6 modulation affects the morphology of U-251 MG cells in two-dimensional culture. (B) Downregulation of CBX6 increases growth and invasion of U-251 MG cells in 3D culture. (C) Overexpression of CBX6 significantly suppresses U-251 MG proliferation on days 3 and 5 post-plating, as measured by MTT assay. (D) MTT assay of KLuc cells stably overexpressing human CBX6 or transfected with control plasmid on days 3 and 5 post-plating. (E) Silencing CBX6 increases U-251 MG proliferation compared to shRNA controls. Images were captured randomly from different fields under 20× magnification. VC, vector control; OE, CBX6 overexpression; KD, CBX6 knockdown. “∗” indicated p < 0.05.

Article Snippet: A pCMV6-entry plasmid containing Myc-DDK (same as Flag)-tagged human CBX6 cDNA (Cat#: RC204166) and a CBX6 Human shRNA Plasmid Kit (Cat#: TF314170) were purchased from OriGene.

Techniques: Over Expression, MTT Assay, Stable Transfection, Transfection, Control, Plasmid Preparation, shRNA, Knockdown

Journal: Molecular Therapy Oncology

Article Title: CBX6 and CA9 as predictive indicators and therapeutic targets in GBM

doi: 10.1016/j.omton.2026.201159

Figure Lengend Snippet: Effects of CBX6 modulation on invasion and migration of U-251 MG cells (A and B) Representative images and cell quantification from transwell migration assays of U-251 MG cells with modulated CBX6 expression compared to corresponding controls. (C and D) Representative images and cell quantification from transwell invasion assays of U-251 MG cells with modulated CBX6 expression compared to respective controls. VC, vector control; OE, CBX6 overexpression; KD, CBX6 knockdown. “∗” Indicates p < 0.05.

Article Snippet: A pCMV6-entry plasmid containing Myc-DDK (same as Flag)-tagged human CBX6 cDNA (Cat#: RC204166) and a CBX6 Human shRNA Plasmid Kit (Cat#: TF314170) were purchased from OriGene.

Techniques: Migration, Expressing, Plasmid Preparation, Control, Over Expression, Knockdown

Journal: Molecular Therapy Oncology

Article Title: CBX6 and CA9 as predictive indicators and therapeutic targets in GBM

doi: 10.1016/j.omton.2026.201159

Figure Lengend Snippet: Effect of human CBX6 overexpression on glioma tumor growth (A and B) Bioluminescent imaging of NSG mice (A) and quantification of bioluminescence signal intensity as fold change (B) on days 4 and 8 ( n = 5). (C) Bioluminescent imaging at week 2 showing reduced Kluc tumor size in mice with human CBX6 overexpression compared to controls ( n = 10). (D and E) Kaplan-Meier survival analysis demonstrating that overexpression of human CBX6 in U-251 MG cells (D) ( n = 5) and Kluc cells (E) ( n = 10) improved mouse survival. (F) Histological analysis of tumor invasion and microsatellite metastasis in CBX6-overexpressing tumors. “∗” Indicates p < 0.05.

Article Snippet: A pCMV6-entry plasmid containing Myc-DDK (same as Flag)-tagged human CBX6 cDNA (Cat#: RC204166) and a CBX6 Human shRNA Plasmid Kit (Cat#: TF314170) were purchased from OriGene.

Techniques: Over Expression, Imaging

Journal: Molecular Therapy Oncology

Article Title: CBX6 and CA9 as predictive indicators and therapeutic targets in GBM

doi: 10.1016/j.omton.2026.201159

Figure Lengend Snippet: CBX6 binds to the CA9 promoter (A) Genes related to tumor cell invasion, proliferation, or migration were selected based on RNA sequencing data from U-251 MG cells with CBX6 knockdown compared to negative controls. (B) qRT-PCR results show that CA9 expression is affected by CBX6 dysregulation in U-251 MG cells, with overexpression or shRNA-mediated knockdown of CBX6, using GAPDH as a reference gene. (C) Gene expression correlation analysis from CGGA reveals an inverse relationship between CBX6 and CA9 expression patterns ( http://www.cgga.org.cn ). (D) Western blot and qRT-PCR data demonstrate changes in CBX6 and CA9 expression in U-251 MG and PBT030 cells under normoxic (N) and hypoxic (H) conditions for 24 and 48 h, using 28S as a reference gene. (E) ChIP assay results from CBX6-overexpressing U-251 MG cells show detection of the CA9 promoter sequence using two primer sets in CBX6/Flag pull-down products compared to a negative IgG control via qRT-PCR. VC, vector control; OE, CBX6 overexpression; KD, CBX6 knockdown. “∗” Indicates p < 0.05.

Article Snippet: A pCMV6-entry plasmid containing Myc-DDK (same as Flag)-tagged human CBX6 cDNA (Cat#: RC204166) and a CBX6 Human shRNA Plasmid Kit (Cat#: TF314170) were purchased from OriGene.

Techniques: Migration, RNA Sequencing, Knockdown, Quantitative RT-PCR, Expressing, Over Expression, shRNA, Gene Expression, Western Blot, Sequencing, Control, Plasmid Preparation

Journal: eBioMedicine

Article Title: Mechanistic analysis of an IRF7-dependent pathway in virus-induced fibrosis in chronic lung allograft dysfunction

doi: 10.1016/j.ebiom.2026.106285

Figure Lengend Snippet: IRF7 and pIRF7 are increased in human CLAD (BOS). (A) Representative Western blot images showing IRF7 and pIRF7 in CLAD (BOS) and Stable LTx whole lung lysates. Densitometric analyses of the above blots (fold change relative to Stable LTx) showing protein expression of (B) IRF7 and (C) pIRF7 in CLAD (BOS) and Stable LTx whole lung tissue (Stable LTx n = 3, CLAD (BOS) n = 4). Error bars represent mean ± SEM. ∗∗p < 0.01, unpaired t-test. (D) Representative immunofluorescence images showing H&E, Trichrome, DAPI (blue), IRF7 (magenta), and merged DAPI/IRF7 channels in Stable LTx and CLAD (BOS) lung tissue sections, demonstrating airway-centric distribution and increased IRF7 expression in CLAD (BOS). (E) Corresponding Integrated Intensity/cell of IRF7 in human CLAD (BOS) and Stable LTx specimens. Each data point represents the mean integrated IRF7 intensity/cell averaged across 3–4 image fields per patient (Stable LTx n = 3, CLAD (BOS) n = 4); group data presented as mean ± SEM; ∗p = 0.017, unpaired t-test.

Article Snippet: IRF7 shRNA plasmid complete kit (Origene, cat. TR315487) was used to suppress IRF7 expression in PCLS and were transfected with either IRF7-specific or control shRNA plasmid in the absence of antibiotics in the culture media.

Techniques: Western Blot, Expressing, Immunofluorescence

Journal: eBioMedicine

Article Title: Mechanistic analysis of an IRF7-dependent pathway in virus-induced fibrosis in chronic lung allograft dysfunction

doi: 10.1016/j.ebiom.2026.106285

Figure Lengend Snippet: Virus exposure induces IRF7 and airway fibrogenesis in the air-liquid-interface PBEC model, and IRF7 silencing attenuates it. (A) Representative Western blots showing protein expression of IRF7, α-SMA, and SMAD2/3 in stably expressing control (Ctr) shRNA and IRF7 shRNA primary bronchial epithelial cell (PBEC) cell line air-liquid-interface (ALI) cultures in the presence and absence of Influenza A virus (IAV). Densitometric analyses of the above blots showing protein expression of (B) IRF7, (C) α-SMA, and (D) SMAD2/3 in Ctr shRNA and IRF7 shRNA PBEC cell line ALI cultures (n = 6 each). Error bars represent mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, Mann–Whitney test for 2 samples, one way Anova with Tukeys multiple comparison test for >3 groups (E) Sircol assay showing fold change soluble collagen content in the ALI culture supernatants from the above experiments (n = 3 each). Error bars represent mean ± SEM. ∗∗p < 0.01, Mann–Whitney test. (F) Representative immunofluorescence images showing DAPI (blue) and MUC5AC (red) of stably expressing control shRNA and IRF7 shRNA cell line ALI cultures exposed to IAV, demonstrating attenuation of airway mucogenesis with IRF7 silencing.

Article Snippet: IRF7 shRNA plasmid complete kit (Origene, cat. TR315487) was used to suppress IRF7 expression in PCLS and were transfected with either IRF7-specific or control shRNA plasmid in the absence of antibiotics in the culture media.

Techniques: Virus, Western Blot, Expressing, Stable Transfection, Control, shRNA, MANN-WHITNEY, Comparison, Immunofluorescence

Journal: eBioMedicine

Article Title: Mechanistic analysis of an IRF7-dependent pathway in virus-induced fibrosis in chronic lung allograft dysfunction

doi: 10.1016/j.ebiom.2026.106285

Figure Lengend Snippet: Virus exposure induces fibrogenesis and IRF7 blockade attenuates it in the human precision-cut lung slice ex vivo model. (A) Representative immunofluorescence images showing IRF7 (red), α-SMA (green), DAPI (blue), and merged channels in a human precision-cut lung slice (PCLS) model in non-treated (NT) and Influenza A virus (IAV)-exposed conditions. (B) Corresponding fold change fluorescence intensity of IRF7 and α-SMA in the above experiment (n = 5–6 each). Error bars represent mean ± SEM. ∗∗p < 0.01, Mann–Whitney test. (C) Representative immunofluorescence images showing IRF7 (red), DAPI (blue), and merged channels, alongside trichrome staining showing collagen deposition, in IAV-exposed stably expressing control shRNA and IRF7 shRNA PCLS slices. (D) % Area of slices positive for trichrome stain in IAV-exposed stably expressing control shRNA and IRF7 shRNA PCLS slices (n = 5–6 each). Error bars represent mean ± SEM. ∗p < 0.05, Mann–Whitney test.

Article Snippet: IRF7 shRNA plasmid complete kit (Origene, cat. TR315487) was used to suppress IRF7 expression in PCLS and were transfected with either IRF7-specific or control shRNA plasmid in the absence of antibiotics in the culture media.

Techniques: Virus, Ex Vivo, Immunofluorescence, Fluorescence, MANN-WHITNEY, Staining, Stable Transfection, Expressing, Control, shRNA

Journal: eBioMedicine

Article Title: Mechanistic analysis of an IRF7-dependent pathway in virus-induced fibrosis in chronic lung allograft dysfunction

doi: 10.1016/j.ebiom.2026.106285

Figure Lengend Snippet: Virus induces IL-33 via IRF7 and IL-33 blockade attenuates virus-induced fibrogenesis. (A) Representative Western blots showing protein expression of IRF7 and IL-33 in stably expressing control shRNA and IRF7 shRNA primary bronchial epithelial cell (PBEC) cell line air-liquid-interface (ALI) cultures in the presence and absence of Influenza A virus (IAV). (B) Densitometry fold change protein expression of IL-33 in control shRNA and IRF7 shRNA PBEC cell line ALI cultures in the presence and absence of IAV (n = 4 each). Error bars represent mean ± SEM. ∗p < 0.05, 1-way ANOVA with Tukey’s multiple comparison post-test. (C) Representative Western blots showing protein expression of IRF7 and α-SMA in stably expressing control shRNA and IRF7 shRNA PBEC cell line ALI cultures in the presence and absence of IAV and IL-33 blockade. (D) Densitometry fold change of α-SMA protein expression in stably expressing control shRNA and IRF7 shRNA PBEC cell line ALI cultures in the presence and absence of IAV and IL-33 blockade (n = 4 each). Error bars represent mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ns = not significant, 1-way ANOVA with Tukey’s multiple comparison post-test.

Article Snippet: IRF7 shRNA plasmid complete kit (Origene, cat. TR315487) was used to suppress IRF7 expression in PCLS and were transfected with either IRF7-specific or control shRNA plasmid in the absence of antibiotics in the culture media.

Techniques: Virus, Western Blot, Expressing, Stable Transfection, Control, shRNA, Comparison

Journal: eBioMedicine

Article Title: Mechanistic analysis of an IRF7-dependent pathway in virus-induced fibrosis in chronic lung allograft dysfunction

doi: 10.1016/j.ebiom.2026.106285

Figure Lengend Snippet: MMP-9 blockade attenuates virus-mediated fibrogenesis. (A) Fold change mRNA expression of MMP-9 in stably expressing control shRNA and IRF7 shRNA primary bronchial epithelial cell (PBEC) cell line air-liquid-interface (ALI) cultures in the presence and absence of Influenza A virus (IAV) (n = 3 each). Error bars represent mean ± SEM. ∗∗p < 0.01, Mann–Whitney test. (B) MMP-9 (ng/ml of supernatant) concentrations by ELISA in the lower compartment of control shRNA and IRF7 shRNA PBEC cell line ALI culture medium in the presence and absence of IAV (n = 4 each). Error bars represent mean ± SEM. ∗∗∗∗p < 0.0001, 1-way ANOVA with Tukey’s multiple comparison post-test. (C) MMP-9 (ng/ml of supernatant) concentrations by ELISA in the lower compartment of IAV-exposed PBEC cell line ALI model with and without IL-33 blockade (n = 4 each). Error bars represent mean ± SEM. ∗∗∗∗p < 0.0001, ∗∗p < 0.01, ∗p < 0.05, 1-way ANOVA with Tukey’s multiple comparison post-test. (D) MMP-9 (ng/ml of supernatant) concentrations by ELISA in the lower compartment of IAV-exposed stably expressing IRF7 shRNA PBEC ALI model with and without IL-33 blockade (n = 4 each). Error bars represent mean ± SEM. ∗p < 0.05, ns = not significant, 1-way ANOVA with Tukey’s multiple comparison post-test. (E) Representative Western blots showing protein expression of α-SMA in virus-exposed ALI PBEC model with and without MMP-9 blockade. (F) Densitometry fold change protein expression of α-SMA in IAV-exposed ALI PBEC model with and without MMP-9 blockade (n = 5 each). ∗∗∗∗p < 0.0001, ∗∗p < 0.01, ns = not significant, 1-way ANOVA with Tukey’s multiple comparison post-test.

Article Snippet: IRF7 shRNA plasmid complete kit (Origene, cat. TR315487) was used to suppress IRF7 expression in PCLS and were transfected with either IRF7-specific or control shRNA plasmid in the absence of antibiotics in the culture media.

Techniques: Virus, Expressing, Stable Transfection, Control, shRNA, MANN-WHITNEY, Enzyme-linked Immunosorbent Assay, Comparison, Western Blot

Journal: eBioMedicine

Article Title: Mechanistic analysis of an IRF7-dependent pathway in virus-induced fibrosis in chronic lung allograft dysfunction

doi: 10.1016/j.ebiom.2026.106285

Figure Lengend Snippet: Schematic representation of the pathway involved in virus-induced airway fibrogenesis. (1 and 2) Influenza virus activates IRF7 via the RIG-1/MAVS/TBK1 axis, and activated IRF7 enters the nucleus and induces expression of IL-33. (3 and 4) IL-33 is secreted from the epithelial cells into the interstitial matrix, where it acts upon neighbouring epithelial cells, resident fibroblasts, and other cell types (paracrine), as well as the same cell (autocrine manner). (5) IL-33 induces MMP-9 expression, and MMP-9 is secreted into the interstitial matrix. (6) MMP-9 cleaves latent TGF-β to its active form. (7 and 8) Activated TGF-β induces SMAD2/3 signalling, driving expression of collagens and α-SMA and culminating in fibrogenesis and extracellular matrix remodelling.

Article Snippet: IRF7 shRNA plasmid complete kit (Origene, cat. TR315487) was used to suppress IRF7 expression in PCLS and were transfected with either IRF7-specific or control shRNA plasmid in the absence of antibiotics in the culture media.

Techniques: Virus, Expressing