Journal: bioRxiv

Article Title: Oral exposure to Perfluorooctanoic acid disrupts the microbiota-gut-liver axis and enhances the severity of chemically induced colitis in mice

doi: 10.64898/2026.05.26.727994

Figure Lengend Snippet: Histological scoring of the colon and liver following PFOA exposure (1mg/kg, 8 weeks). Crypt depth was quantified ( A ). Representative immunofluorescence images of colon sections stained for Ki67 [green], CDH1/E-cadherin [red] nuclei DAPI [blue], with quantification of Ki67+ IEC per crypt ( B ). Representative periodic acid–Schiff (PAS) staining and quantification of total goblet cell-associated mucins (magenta) ( C ). Representative hematoxylin and eosin (H&E) staining and nuclei counts of hepatocytes in the liver ( D ) Liver-to-body weight ratio following 8 weeks of PFOA exposure ( E ). Data are presented as mean ± SEM; n=7-12; *p<0.05, **p < 0.01, ***p<0.001 by two-way ANOVA with Bonferroni correction, (Scale bar = 100 μm).

Article Snippet: Images were acquired on a Leica SP8 confocal microscope (40x objective, 0.7 μm step size), and overlapping tiles were stitched and Huygens deconvolved as needed, followed by quantification of Ki67 + CDH1 + cells/crypt in Imaris 8.2 software.

Techniques: Immunofluorescence, Staining

Journal: Molecular & Cellular Proteomics : MCP

Article Title: O -Mannose Glycosylations Influence E-Cadherin Functional Interactions

doi: 10.1016/j.mcpro.2026.101559

Figure Lengend Snippet: Mapping the O -Man dependent E-cadherin interactome using IP screening. A , Schematic diagrams and structural model of CDH1 EC domains : ( left ) CDH1 is a transmembrane protein with five EC domains that form cis- and trans interactions; ( middle ) TMTC2 mediates O -Man on CDH1 EC B-strands, while TMTC3 mediates glycosylations on G-strands ( O -Man structures were grafted onto an AlphaFold model of EC4 using the GlycoShape tool – the mannoses are depicted as green sticks and translucent surfaces on recipient serine and threonine residues ); ( right ) schematic of the β-strand arrangement of an EC domain, highlighting O -Man sites ( green dots ) on the B- ( red ) and G- ( blue ) strands of EC2-4. B , Schematic diagram of the IP-MS-based interactome screen applied to CDH1 : Cryomilled cells are distributed to a 96-well plate and combined with different extractants; CDH1-associated complexes are affinity enriched from each extract using an antibody coupled magnetic medium and then analyzed by protein MS; the compositions of the enriched macromolecular assemblies will vary according to the stabilizing/destabilizing responses of the protein constituents and a putative interactome is constituted by the combined results. C , Results of the IP screen using 32 extraction conditions : ( upper ) silver-stained SDS-PAGE gel showing CDH1 capture by IP screening; ( lower ) hierarchical clustering of MS data, with log 2 -transformed protein abundance values from Proteome Discoverer displayed by color. Grey shading in the heatmap indicates proteins not detected (ND). Six extractants, highlighted in red, were selected for further quantitative analysis. Selected reagents present in extraction solutions are labeled with colored dots.

Article Snippet: Anti-CDH3 (MAB861, R&D systems 1:500 in 10% (v/v) FBS in PBS) and Anti-CDH1 primary antibodies (AF648 R&D systems 1:200 in 10% (v/v) FBS in PBS) were added to the cells and incubated for 1 h. The cells were washed 3 times with 100 μl of 10% (v/v) FBS in PBS and incubated with secondary antibody conjugated to fluorophore (Goat anti-Mouse IgG (H; + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 or Donkey anti-Goat IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 at 1ug/ml in 10% (v/v) FBS in PBS).

Techniques: Protein-Protein interactions, Extraction, Staining, SDS Page, Transformation Assay, Quantitative Proteomics, Labeling

Journal: Molecular & Cellular Proteomics : MCP

Article Title: O -Mannose Glycosylations Influence E-Cadherin Functional Interactions

doi: 10.1016/j.mcpro.2026.101559

Figure Lengend Snippet: I-DIRT screen for CDH1. A , Depiction of the approach : BG1 WT cells and BG1 CDH1::HA cells were cultured in both light and heavy isotope-labeling media for label-swapped I-DIRT experiments. The resulting cell powders were combined in 1:1 (w:w) ratios for IP-MS analyses. Specific CDH1 interactors are enriched in one isotope-labeled channel in MS, while non-specific interactors are quantified comparably in both the heavy and light channels. BG1 CDH1::HA cells cultured in heavy-isotope media were designated ‘I-DIRT,’ while BG1 CDH1::HA cells cultured in light-isotope media were designated ‘I-DIRT swap.’ B , Specific interactors identified across six I-DIRT experimental conditions : The interactors are grouped based on how many times they were identified as specific interactors in six extractants. Orange lines represent interactions identified in this study, while gray lines indicate interactions retrieved from the STRING database . C , overlap of the I-DIRT interactor list with two previously published datasets ( , ): the panel on the right lists the 27 common interactors. Proteins are colored by their identification frequency, as in ( B ).

Article Snippet: Anti-CDH3 (MAB861, R&D systems 1:500 in 10% (v/v) FBS in PBS) and Anti-CDH1 primary antibodies (AF648 R&D systems 1:200 in 10% (v/v) FBS in PBS) were added to the cells and incubated for 1 h. The cells were washed 3 times with 100 μl of 10% (v/v) FBS in PBS and incubated with secondary antibody conjugated to fluorophore (Goat anti-Mouse IgG (H; + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 or Donkey anti-Goat IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 at 1ug/ml in 10% (v/v) FBS in PBS).

Techniques: Cell Culture, Quantitative Proteomics, Protein-Protein interactions, Labeling

Journal: Molecular & Cellular Proteomics : MCP

Article Title: O -Mannose Glycosylations Influence E-Cadherin Functional Interactions

doi: 10.1016/j.mcpro.2026.101559

Figure Lengend Snippet: Bioinformatic analyses of CDH1 interactors. Gene Ontologies (GO) ( A – C ) and Reactome pathways ( D ) enriched among the specific CDH1 interactors. A , enrichment of GO Cellular Components (CC) associated with CDH1 interactors. B , enrichment of GO Biological Processes (BP) associated with CDH1 interactors. C , enrichment of GO Molecular Functions (MF) associated with CDH1 interactors. D , the enriched Reactome pathways is shown on the left . The specific interactors involved in each pathway are detailed on the right . E , Localizations of select CDH1 interactors : proteins with annotated localizations at the cell surface or extracellular matrix are listed. The X-axis of panels ( A – C ) represents the proportion of proteins enriched in each GO pathway.

Article Snippet: Anti-CDH3 (MAB861, R&D systems 1:500 in 10% (v/v) FBS in PBS) and Anti-CDH1 primary antibodies (AF648 R&D systems 1:200 in 10% (v/v) FBS in PBS) were added to the cells and incubated for 1 h. The cells were washed 3 times with 100 μl of 10% (v/v) FBS in PBS and incubated with secondary antibody conjugated to fluorophore (Goat anti-Mouse IgG (H; + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 or Donkey anti-Goat IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 at 1ug/ml in 10% (v/v) FBS in PBS).

Techniques:

Journal: Molecular & Cellular Proteomics : MCP

Article Title: O -Mannose Glycosylations Influence E-Cadherin Functional Interactions

doi: 10.1016/j.mcpro.2026.101559

Figure Lengend Snippet: O -Man-dependent CDH1 interactome. A , Average log 2 fold change values for CDH1 interactors in TMTC deficient cell lines: colors represent the average log 2 FC values across the six IP conditions, with red indicating increased interaction with CDH1 and blue indicating decreased interaction with CDH1. The circle size indicates the number of IP conditions where the interactor was significantly changed in different TMTC KO cell lines (log 2 FC ≥ 1 or ≤ −1, and p-adj. value ≤ 0.05). B , Selected interactors across different co-enrichment groups, for distinct IP conditions. Symbols indicate statistical significance, with “∗” representing log 2 FC ≥ 1 or ≤ −1 and p-adj. value ≤ 0.05. C , Interactions dependent on O-mannosylation position :: ( upper - panel ) example interactions affected by O -Man on EC domain G-strands; ( middle - panel ) example interactions affected by O -Man on EC domain B- and G-strands together; ( lower - panel ) ANXA1 exhibits increased co-enrichment when O -Man is depleted from EC domain B-strands (see conditions 16 and 20, KO: TMTC2 ). D , cell adhesion ability in cell lines expressing CDH1 with varying O- Man modification statuses. Data are presented as mean ± SEM ( n = 6). Statistical significance is denoted as follows: ∗∗∗ p ≤ 0.001; ∗∗∗∗ p ≤ 0.0001.

Article Snippet: Anti-CDH3 (MAB861, R&D systems 1:500 in 10% (v/v) FBS in PBS) and Anti-CDH1 primary antibodies (AF648 R&D systems 1:200 in 10% (v/v) FBS in PBS) were added to the cells and incubated for 1 h. The cells were washed 3 times with 100 μl of 10% (v/v) FBS in PBS and incubated with secondary antibody conjugated to fluorophore (Goat anti-Mouse IgG (H; + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 or Donkey anti-Goat IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 at 1ug/ml in 10% (v/v) FBS in PBS).

Techniques: Expressing, Modification

Journal: Molecular & Cellular Proteomics : MCP

Article Title: O -Mannose Glycosylations Influence E-Cadherin Functional Interactions

doi: 10.1016/j.mcpro.2026.101559

Figure Lengend Snippet: Effects of TMTC knock - out on CDH1 and CDH3 abundance and localization. A , Western blot analysis of endogenous CDH3 abundance in BG1 cells with different TMTC KO statuses. B , Flow cytometry analysis of cell surface CDH1 and CDH3 : ( left ) representative histograms comparing fluorescence intensities in BG1 CDH1::HA cells ( green ), BG1 CDH1::HA/KO:TMTC1-4 cells ( pink ), and BG1 KO:CDH1 negative control cells ( grey ); signals normalized to mode; ( right ) Quantification of fold-change in median fluorescence intensity for surface CDH1 and CDH3 in BG1 CDH1::HA cells relative to BG1 CDH1::HA/KO:TMTC1-4 cells (n = 3). C , representative immunofluorescence images showing cellular localization of CDH1 ( green ) and CDH3 ( red ) in control BG1 CDH1::HA cells ( top panels ) and BG1 CDH1::HA/ KO :TMTC1-4 cells ( bottom panels ). Nuclei were counter-stained with DAPI ( blue ). Scale bar = 10 μm. D , Schematic model of the O-Man-dependent CDH1 interactome : some CDH1 interactors are modulated by O- Man, leading to their decreased or increased co-enrichment, based on changes e.g., in their affinity, localization, and/or abundance.

Article Snippet: Anti-CDH3 (MAB861, R&D systems 1:500 in 10% (v/v) FBS in PBS) and Anti-CDH1 primary antibodies (AF648 R&D systems 1:200 in 10% (v/v) FBS in PBS) were added to the cells and incubated for 1 h. The cells were washed 3 times with 100 μl of 10% (v/v) FBS in PBS and incubated with secondary antibody conjugated to fluorophore (Goat anti-Mouse IgG (H; + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 or Donkey anti-Goat IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 at 1ug/ml in 10% (v/v) FBS in PBS).

Techniques: Knock-Out, Western Blot, Flow Cytometry, Fluorescence, Negative Control, Immunofluorescence, Control, Staining

Journal: Journal of Cellular and Molecular Medicine

Article Title: YTHDF3 Mediates the Occurrence and Development of Breast Cancer by Regulating Glycolysis Through the mTOR – HIF1α – LHDA Axis

doi: 10.1111/jcmm.71105

Figure Lengend Snippet: Silence of YTHDF3 restrain cell proliferation and migration of breast cancer cells and arrested the cell cycle. (A) Relative expression of YTHDF3 mRNA and protein after transfection of shNC and shYTHDF3 in MDA‐MB‐231 and MCF‐7 cells; (B) the growth ability of MDA‐MB‐231 and MCF‐7 cells transfected with shNC and shYTHDF3 was detected by CCK‐8 assay; (C) colony formation assay was used to detect the proliferation ability of MDA‐MB‐231 and MCF‐7 cells in shNC and shYTHDF3 groups; (D) the cell cycle distribution of MDA‐MB‐231 and MCF‐7 cells in shNC and shYTHDF3 groups was detected by flow cytometry; (E) expression of cyclin D1 and CDK4 in shNC and shYTHDF3 in MDA‐MB‐231 and MCF‐7 cells; (F, G) transwell invasion assay was used to detect the migration ability of breast cancer cells in the shNC group and the shYTHDF3 group in MCF‐7 and MDA‐MB‐231 cells; (H) the expression of vimentin, MMP9, E‐cadherin, N‐cadherin and snail in shNC and shYTHDF3 in MDA‐MB‐231 and MCF‐7 cells.

Article Snippet: Primary antibodies used in the present study were listed as follows: GAPDH (ab313650, Abcam), HIF1 alpha (ab1, Abcam), mTOR (BM4182, Boster), p‐mTOR (BM4840, Boster), RICTOR (A03195‐1, Boster), RAPTOR (BM4438, Boster), AKT (BM4390, Boster), p‐AKT (BM4744, Boster), S6K (BM4240, Boster), p‐S6K (BM4141, Boster), LDHA (A1146, ABclonal), YTHDF3 (A8395, ABclonal), cyclin D1 (A11022, ABclonal), CDK4 (A23522, ABclonal), vimentin ( PAB48967 , Bioswamp), MMP9 (FNab05247, FineTest), LDHB (A5131, ABclonal), PKM1/2 (A27199PM, ABclonal), PFKL (A23687, ABclonal), snail (13099–1‐AP, Proteintech), E‐cadherin (PB9561, Boster), N‐cadherin (A01577‐3, Boster).

Techniques: Migration, Expressing, Transfection, CCK-8 Assay, Colony Assay, Flow Cytometry, Transwell Invasion Assay

Journal: Cancer Medicine

Article Title: Role of Ca 2+ ‐Dependent Epithelial‐Mesenchymal Transition in Malignant Progression of Colorectal Cancer: Special Focus on REG Iα/ EDNRB

doi: 10.1002/cam4.71754

Figure Lengend Snippet: REG Iα promotes cell migration, invasion, and EMT via EDNRB. (A) Cell migration was assessed by Transwell assay. (B) Matrigel‐coated Transwell assay assessed cell invasion. (C) Western blot analysis of EMT‐related markers, including the epithelial marker E‐Cadherin and mesenchymal markers N‐Cadherin and Vimentin. β‐actin was used as the loading control. Data are presented as mean ± SD. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

Article Snippet: CHOP (Abcam, ab317378), Cleaved‐Caspase 3 (Abcam, ab32042), Cleaved‐PARP (Cell Signaling Technology, 9541), E‐Cadherin (BOSTER, PB9561), N‐Cadherin (BOSTER, A01577‐3), and Vimentin (BOSTER, BM4029).

Techniques: Migration, Transwell Assay, Western Blot, Marker, Control

Journal: Cancer Medicine

Article Title: Role of Ca 2+ ‐Dependent Epithelial‐Mesenchymal Transition in Malignant Progression of Colorectal Cancer: Special Focus on REG Iα/ EDNRB

doi: 10.1002/cam4.71754

Figure Lengend Snippet: The REG Iα‐EDNRB axis promotes cell migration, invasion, and EMT via the Ca 2+ signaling pathway. (A) Transwell assay assessed cell migration. (B) Cell invasion was assessed by Matrigel‐coated Transwell assay. (C) EMT‐related protein levels (E‐Cadherin, N‐Cadherin, Vimentin) were detected by Western blot. β‐actin served as the loading control. Data are presented as mean ± SD. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

Article Snippet: CHOP (Abcam, ab317378), Cleaved‐Caspase 3 (Abcam, ab32042), Cleaved‐PARP (Cell Signaling Technology, 9541), E‐Cadherin (BOSTER, PB9561), N‐Cadherin (BOSTER, A01577‐3), and Vimentin (BOSTER, BM4029).

Techniques: Migration, Transwell Assay, Western Blot, Control

Journal: Cancer Medicine

Article Title: Role of Ca 2+ ‐Dependent Epithelial‐Mesenchymal Transition in Malignant Progression of Colorectal Cancer: Special Focus on REG Iα/ EDNRB

doi: 10.1002/cam4.71754

Figure Lengend Snippet: The REG Iα‐EDNRB‐Ca 2+ axis promotes tumor growth and EMT in vivo. (A) Representative images of the xenograft tumors and excised tumor tissues from the indicated groups. (B) Statistical analysis of the final tumor weights. (C) Tumor growth curves measuring tumor volume over time. (D) H&E staining showed pathological changes in tumor tissues. (E) TUNEL assay detected cell apoptosis in tumor tissues. (F) Cell proliferation in tumor tissues was shown by Ki67 IHC staining. (G) Expression of REG Iα (Immunofluorescence, upper row) and EDNRB (IHC, lower row) in tumor tissues. (H) Western blot analysis of REG Iα, EDNRB, and p‐CaMKII protein levels in tumor tissues. β‐actin was used as the loading control. (I) Western blot analysis of EMT‐related proteins (E‐Cadherin, N‐Cadherin, Vimentin) in tumor tissues. β‐actin was used as the loading control. Data are presented as mean ± SD. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

Article Snippet: CHOP (Abcam, ab317378), Cleaved‐Caspase 3 (Abcam, ab32042), Cleaved‐PARP (Cell Signaling Technology, 9541), E‐Cadherin (BOSTER, PB9561), N‐Cadherin (BOSTER, A01577‐3), and Vimentin (BOSTER, BM4029).

Techniques: In Vivo, Staining, TUNEL Assay, Immunohistochemistry, Expressing, Immunofluorescence, Western Blot, Control