Study subjects
We retrospectively investigated the mucosa of the middle portion of the greater curvature of the gastric corpus, approximately 8 cm from the gastric cardia, in patients who underwent upper gastrointestinal endoscopy with biopsy at Oita University Hospital, Japan, between January 2001 and December 2018. The biopsy site “B2”, which is recommended by the Updated Sydney System, is assumed to be best suited for evaluating the histological status of the fundic glands [19]. H. pylori infection was determined by culture, histology, and rapid urease test. In H. pylori-negative patients, we additionally confirmed the lack of endoscopic atrophy and histologic gastritis.
Histological analysis
Specimens were collected endoscopically from the greater curvature of the gastric middle bodies. Biopsy specimens were immediately fixed in 10% neutral buffered formalin for 24 h and embedded in paraffin wax blocks. Fixed samples were sliced into 3-μm-thick sections and stained with hematoxylin and eosin. Degrees of inflammation, activity, atrophy, and intestinal metaplasia were scored according to the Updated Sydney System (0, none; 1, weak; 2, moderate; 3, marked) [19].
Immunofluorescent staining
Anti-MUC5AC (1:50, Leica Biosystems), H+/K+ATPase (1:100; Medical & Biological Laboratories), MUC6 (1:200; BioRad), and PG1 (1:200; Abnova) antibodies were used for immunostaining to differentiate between cell types in the fundic glands. We performed immunohistochemistry using anti-dimethyl-eEF1AK55me2 antibody (1:400; ABclonal Technology), Nanog (1:10000; Cell Signaling Technology), and Oct4 (1:100; Santa Cruz Biotechnology, Santa Cruz, CA, USA). All biopsy materials were fixed in 10% buffered formalin for 24 h and then embedded in paraffin. After deparaffinization and subsequent rehydration to remove xylene, endogenous peroxidases were inactivated with 3% hydrogen peroxide solution (Wako, Osaka, Japan). Antigen retrieval was performed at pH 6.0. Next, the sections were incubated overnight with monoclonal anti-MUC5AC, MUC6, H+/K+ATPase, PG1, and dimethyl-eEF1A primary antibodies, followed by incubation with secondary antibodies (1:1000; Alexa Fluor R488 and 594) at room temperature for 2 h. After washing, images were captured with a Keyence BZ-9000 microscope (Keyence, Osaka, Japan).
Evaluation of dimethyl eEF1A level
Dimethylation levels of eEF1A were evaluated on surface, middle, and basal areas of gastric glands, which were identified by morphological appearance or immunostaining with antibodies for specific markers MUC5AC, H+/K+ ATPase, and PG1, respectively. After immunofluorescence staining with anti-dimethyl-eEF1A antibody, the mean fluorescent intensities of these areas were quantified using the region of interest (ROI) tool in ImageJ software. Multiple ROIs were set for each area based on marker immunofluorescence in one image, and several images at 4× magnification were used for each patient. Then, the dimethylation level of eEF1A for each area in each patient was expressed as an average of multiple mean fluorescent intensities from the ROIs.
Statistical analysis
We investigated the relationship between the clinical factors and dimethyl-eEF1A level of atrophic gastritis mucosa using univariate and multivariate analysis. All variables are expressed as means ± standard deviation for continuous data (Table 2). Prior to analysis, continuous data were divided into two groups using average values. Levels of eEF1A dimethylation were compared between groups using analysis of variance or analysis of covariance (for age-adjusted data), followed by the Tukey test. Univariate analyses were performed using the Student t-test or the Tukey test for continuous variables and chi-squared test for categorical variables. The results of the multivariate logistic regression analysis are expressed as adjusted odds ratios (aOR) with 95% confidence intervals (CI). A p-value <0.05 was considered to indicate statistical significance. All statistical analyses were performed using with JMP® 11 (SAS Institute Inc, Cary, NC, USA).
Cell culture and CRISPR/Cas9
TMK-1 was provided by Dr. H. Ito (Tottori Prefectural Kousei Hospital, Tottori, Japan) with permission from an original provider, Dr. A. Ochiai (National Cancer Center, Kashiwa, Japan). Cells were cultured in RPMI1640 (Sigma) with 10% fetal bovine serum. We established Mettl13-knockout TMK-1 cells using the CRISPR-Cas9 genome editing system and generated stable Mkettl13 knockdown TMK-1 cells. Briefly, a single guide (sgRNA) targeting Mettl13 (5′-AAGAAAGCTTTCGAGTGGTATGG -3′) was cloned into a Cas9-expressing plasmid (pSpCas9(BB)-2A-Puro(PX450); Addgene plasmid #62988), and the plasmid was transfected into TMK-1 cells, which was subsequently cloned after a 2-day treatment with 2 µg/mL puromycine. Knockout of Mettl13 was confirmed by Western blotting.
Western blotting
Western blotting was performed as described previously [20]. Cells were lysed on ice for 20 min in SDS-modified RIPA buffer containing protease and phosphatase inhibitor cocktails (cOmplete Mini; Roche Diagnostics, Mannheim, Germany) (PhosSTOP EASYpack; Roche Diagnostics) and then centrifuged at 4℃ at 15,000 rpm for 20 min. The resulting cell lysates (20 µg each) were boiled with Laemmli sample buffer and subjected to SDS-PAGE. The samples were transferred to a polyvinylidene difluoride membrane (Merk Millipore, Darmstadt, Germany), which was blocked for 1 h in Block Ace (DS Pharma, Osaka, Japan) at room temperature and then incubated overnight at 4℃ with primary antibodies against METTL13 (1:1000; Bethyl Laboratories), dimethyl-eEF1A (1:1000; ABclonal Technology), eEF1A(1:1000; ABclonal Technology), Nanog (1:1000; Abcam), Oct4 (1:1000, Abcam), and GAPDH (1:1000, Santa Cruz Biotechnology). After washing with TBS containing 0.1% Tween 20, the membranes were incubated for 1 h at room temperature with appropriate secondary antibodies, followed by rewashing [20]. Finally, the signals were detected using an ECL Western blotting analysis system (GE Healthcare, Piscataway, NJ, USA) in accordance with the manufacturer’s instructions.