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8 protocols using ab11197

1

Glutamine Assay and Inhibitor Evaluation

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Glutamine assay (Glutamine/Glutamate-Glo™; Cat# J8021) was purchased from Promega (Madison, WI, USA). SLC1A5 inhibitor GPNA (G6133), spermine, and spermidine were purchased from Sigma-Aldrich (St. Louis, MO, USA). Mouse monoclonal anti-MUC2 antibody (ab11197, Abcam; Cambridge, UK), Fluorescein-labeled BacTrace anti-EHEC antibody (KPL (LGC Seracare, Milford, MA, USA), secondary donkey anti-mouse AlexaFluor™ 568-labeled antibody, and 3 kDa Alexa Fluor™ 680-labeled dextran (Cat # 34681) were from Invitrogen (Waltham, MA, USA); Hoechst for DNA/nuclear staining (Thermo Fisher Scientific; Waltham, MA, USA).
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2

Immunofluorescence Imaging of MUC2 in Cells

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Cells were seeded on Chamber slide (C6932, Sigma-Aldrich) with the seeding density of 30 × 103 per well. The cells were allowed to attach to the wells overnight before transfecting with siRNA. After transfection with the siRNA for 72 h, slides were incubated with 4% paraformaldehyde (sc-281692, Santa Cruz, Heidelberg, Germany) 20 min at room temperature; PBS 5 min 3 times, 0.1% Triton X-100 (11332481001, Sigma-Aldrich, Saint Louis, MO, USA) 10 min at room temperature, PBS 5 min 3 times, 3% BSA block 1 h at 37 °C. After that, the slides were incubated with anti-MUC2 antibody (ab11197, Abcam, Cambridge, UK, 1:500) for 3 h at 37 °C, PBS 5 min 3 times, and with anti-mouse IgG (ab150113, Abcam, Cambridge, UK, 1:1000) for 1 h at 37 °C, PBS 5 min 3 times. The nucleus was dyed with 1 ug/mL DAPI (62248, Thermo Scientific) for 2 min at room temperature, PBS 2 min 3 times. The slides were mounted with Limonene Mounting Medium (ab104141, Abcam, Cambridge, UK,) and covered by coverslips (7695031, Th. Geyer, Renningen, Germany). Confocal microscopy was performed with Leica SP8, and images were saved as TIFF file formats. For each group in every experiment, we randomly selected three images with similar numbers of cells and uniform background.
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3

Immunoblotting and Immunofluorescence Assays

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In the present study, mouse monoclonal anti-MUC2 (ab11197, 1/500 WB and 1/100 IF, Abcam), rabbit monoclonal anti-TFF3 (ab108599, 1/1500 WB, Abcam), mouse monoclonal anti-SI ([53]; HSI-4/34 or Caco-3/73, 1/100 WB), rabbit monoclonal anti-DPPIV or CD26 [EPR20819] (ab215711, 1/2000 WB, Abcam), rabbit monoclonal anti-YAP/TAZ (D24E4, 1/1500 WB, Cell Signaling Technology, Danvers, MA, USA), rabbit monoclonal anti-YAP (D8H1X, 1/1000 WB, 1/150 IF, Cell Signaling Technology), mouse monoclonal anti-TAZ (M2-616, 1/300 IF, BD Biosciences, NJ, USA) mouse monoclonal anti-CDX2-CD88 (MU392A-UC, 1/700, BioGenex, Freemont, CA, USA), mouse monoclonal anti-HNF1α [F-7] (sc-393925, 1/300 WB, Santa Cruz Biotechnology, Dallas, TX, USA), goat polyclonal anti-HNF4α [C-19] (sc-6556, 1/600 WB, Santa Cruz Biotechnology) and anti-β-actin (MAB1501, 1/20,000, Millipore, Etobicoke, ON, Canada) were used as primary antibodies. In addition, AlexaFluor 488 or 594 goat anti-mouse (A11017, A11072, 1/400; Thermo Fisher Scientific, Ottawa, ON, Canada) and goat anti-rabbit (A11070, A11072, 1/400), ECL HRP-linked anti-mouse (NA931V, 1/4000, GE Healthcare, Mississauga, ON, Canada) and anti-rabbit (NA934V, 1/4000) and HRP-linked bovine anti-goat (sc-2350, 1/4000, Santa Cruz Biotechnology) were used as secondary antibodies.
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4

Immunofluorescence Staining of MUC2 and MUC5AC

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The slides were soaked in 1 × PBS for 3 min, 4% paraformaldehyde was used to fix the slides for 30 min, and soak the slides for 3 min each time with 1 × PBS. PBS was sucked dry using an absorbent paper, and the slides were sealed with normal goat serum at room temperature for 30 min. After blocking, the cells were incubated with the corresponding primary antibodies mouse monoclonal anti‐MUC2 (ab11197; Abcam) and rabbit monoclonal anti‐MUC5AC (61193S; Cell signaling Technology) overnight at 4 °C, followed by treatment with Goat anti‐Mouse IgG (H+L) Cross‐Adsorbed‐Alexa Fluor 488 Secondary Antibody and Goat anti‐Rabbit IgG (H+L) Cross‐Adsorbed‐Alexa Fluor 594 Secondary antibody, respectively, for 1 h at room temperature, after which the sections were washed with 1 × PBS thrice for 3 min each time. The nucleus was stained with 4′, 6‐diamidinophenyl‐indole (DAPI) (D9542; Sigma). The sealing was performed using the sealing liquid containing an anti‐fluorescence quenching agent, and the slides were finally observed under a confocal microscope (TCS‐SP5; Leica, Mannheim, Germany).
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5

Comprehensive Immunohistochemical Profiling of Intestinal Cells

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Rabbit anti-LYZ (1:200, ab108508; Abcam), mouse anti-MUC2 (1:200, ab11197; Abcam), rabbit anti-NUSAP1 (1:100, 12024–1-AP; Proteintech), mouse-anti Ki67 (1:300, 9449s; CST), mouse anti-E-Cad (1:1,000, 610182; BD Biosciences), rabbit anti-ITLN1 (1:50, 11770–1-AP; Proteintech), rabbit anti-TFF1 (1:50, 13734–1-AP; Proteintech), rabbit anti-APOB (1:50, 20578–1-AP; Proteintech), rabbit anti-APOA4 (1:100, 17996–1-AP; Proteintech), rabbit anti-SLC26A2 (1:200, 27759–1-AP; Proteintech), rabbit anti-SCNN1B (1:200, 14134–1-AP; Proteintech), rabbit anti-SLC35A1 (1:400, 16342–1-AP; Proteintech), rabbit anti-FABP6 (1:500, 13781–1-AP; Proteintech), rabbit anti-SLC38A1 (1:100, 12039–1-AP; Proteintech), and rabbit anti-SLC44A1 (1:100, 14687–1-AP; Proteintech).
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6

Characterization of Intestinal Epithelial Markers

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The primary antibodies used in this study include mouse monoclonal anti-MUC2 (Abcam, ab11197, 1/500 WB and 1/100 IF), rabbit monoclonal anti-TFF3 (ab108599, 1/1500 WB, Abcam, Toronto, ON, Canada), mouse monoclonal anti-SI ([53 (link)]; HSI-4/34 or Caco-3/73, 1/100 WB), rabbit polyclonal anti-DPPIV or CD26 (ab129060, 1/2000 WB, Abcam), mouse monoclonal anti-DPPIV (ab3154, 1/100 WB, Abcam), mouse monoclonal anti-DPPIV ([54 (link)] DAO 7/219, 1/100 IF, a gift from A. Quaroni), rabbit monoclonal anti-YAP/TAZ (D24E4, 1/1500 WB, 1/50 IF, Cell Signaling, Danvers, MA, USA), mouse monoclonal anti-CDX2-CD88 (MU392A-UC, 1/700, BioGenex, Freemont, CA, USA), mouse monoclonal anti-LGR5 (UMAB212, 1/100 WB and 1/100 IF, Origene, Rockville, MD, USA) and anti-β-actin (MAB1501, 1/20,000, Millipore, Etobicoke, ON, Canada). The secondary antibodies used in this study include AlexaFluor 488 or 594 goat anti-mouse (A11017, A11072, 1/400, and goat anti-rabbit (A11070, A11072, 1/400; Thermo Fisher Scientific, Ottawa, ON, Canada), ECL HRP-linked anti-mouse (NA931 V, 1/4000, GE Healthcare, Mississauga, ON, Canada) and anti-rabbit (NA934 V, 1/4000).
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7

Immunostaining of 3D Cell Scaffolds

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All samples were fixed in 4% PFA (Thermo Fisher Scientific) for 20 min at room temperature. After thorough washing with PBS, each scaffold was stored at 4°C until it is ready to use for optical analysis. Before immunostaining, cells were permeabilized in 0.1% (v/v) Triton X-100 (Fisher) for 15 min and then blocked for nonspecific binding with 1% (w/v) bovine serum albumin (Fisher) and 0.1% (v/v) Tween 20 (Fisher) in PBS for 1 hour at room temperature. To label the samples for actin filaments, tight junction protein ZO-1, MUC2, VE-cadherin, and nuclei, the following primary and secondary antibodies were used: Rb polyclonal anti–ZO-1 (617300, Thermo Fisher Scientific), Ms monoclonal anti-MUC2 (ab11197, Abcam), bisbenzimide H (Hoechst 33342; ab228511, Abcam), goat-anti-rabbit Alexa Fluor 488 (ab150077, Abcam), goat–anti-mouse Alexa Fluor 647 (ab150115, Abcam), Phalloidin-iFluor 594 Reagent (ab176757, Abcam), and Rb monoclonal VE-cadherin (D87F2, Cell Signaling Technology). Slices were then placed on microscopy plates and were maintained hydrated with PBS during imaging with the epifluorescence/confocal microscope Axio Observer Z1 LSM 800 (ZEISS).
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8

Immunohistochemical Characterization of Tumor Organoids

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On day 7, HGA and LGA tumor organoids were washed twice with DPBS and fixed with 4% paraformaldehyde for 1 h and then additionally washed twice with DPBS. Cultures were histologically processed, paraffin embedded, and sectioned at 5-μm thickness. Tissue sections on microscope slides were then stained with hemotoxylin and eosin (H&E).
IHC was used to visualize biomarkers mucin 2 (MUC2) and cytokeratin 20 (CK20). Blocking was performed by incubation under Dako Protein Block for 15 min. Primary antibodies MUC2 (ab11197, abcam, raised in mouse), CK20 (ab76126, abcam, raised in rabbit), or CD44 (ab157107, abcam, raised in rabbit) were applied to the sections on the slides at a 1:200 dilution in Dako Antibody Diluent and incubated at room temperature for 1 h. Next, secondary Alexa Fluor 488 or Alexa Fluor 594 antibodies (ThermoFisher) with appropriate species reactivity were applied to all samples at 1:200 in Dako Antibody Diluent and left at room temperature for 1 h (anti-mouse Alexa Fluor 488 and anti-rabbit Alexa Fluor 594, Life Technologies, Carlsbad, CA, A-11070). Sections were then incubated with Dapi for 5 min before coverslipping. Sections were imaged on a Leica upright fluorescent microscope.
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