Objective:To analyze the expression of zinc homeostasis-related genes and related cells in the intestinal mucosa of inflammatory bowel disease (IBD) patients at the single-cell level and to evaluate their value in predicting the response to anti-tumor necrosis factor (TNF) therapy in IBD patients.Methods:Single-cell RNA sequencing data from 75 ileal or colorectal biopsy samples, including those from patients with Crohn's disease (CD), ulcerative colitis (UC), and normal controls (NC), were collected from four gene expression omnibus (GEO) databases. Unsupervised clustering analysis in R language was employed to classify IBD cells, zinc homeostasis-related gene scores were used to assess the zinc homeostasis status of different cell clusters, and the cell clusters closely related to zinc homeostasis-related genes, namely metallothionein-associated macrophages (MT Mph), were identified. Then the colon tissues from IBD patients and healthy individuals treated at the First Affiliated Hospital of Sun Yat-sen University were collected for immunofluorescence (IF) staining to compare the differences in MT Mph numbers between IBD and NC tissues. To further explore the function and origins of MT Mph, the characteristic genes of MT Mph and non- metallothionein-associated macrophages (non-MT Mph) from database were compared, the Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis was further used to enrich the characteristic genes, cell communication analysis was used to investigate the communication mechanisms between MT Mph and different cells, Quasi-time sequence was used to explore the origin of MT Mph and related signaling pathways, and the differences in transcription factors among monocytes, MT Mph and non-MT Mph were analyzed in R language. Single sample gene set enrichment analysis (ssGSEA) was used to evaluate the expression of MT Mph characteristic genes, and ssGSEA combined with the response to anti-TNF were used to construct the model in order to explore the predictive value of MT Mph characteristic genes for the response to anti-TNF therapy in IBD patients.Results:IBD cells were clustered and annotated into seven major cell clusters, namely T cells, B cells, plasma cells, myeloid cells, fibroblasts, endothelial cells, and epithelial cells. The results of zinc homeostasis-related gene scores showed that the scores of IBD myeloid cells were higher than those of the NC group. Myeloid cells could be divided into monocytes, macrophages, neutrophils, and dendritic cells. Based on the expression of zinc homeostasis genes, especially the high expression of metallothionein genes, the macrophages were divided into MT Mph and non-MT Mph, and the number of MT Mph in the IBD intestine was significantly increased compared to the NC group. IF validation showed that the number of CD68 +MT1G + cells (MT Mph) in both UC and CD were significantly higher than that in the NC group under per high-power field of view (UC vs. NC: 30.80 ± 7.29 vs. 9.80 ± 1.80, P < 0.001; CD vs. NC: 36.00 ± 9.30 vs. 9.80 ± 1.80, P < 0.001). KEGG pathway enrichment analysis revealed that the differential genes of MT Mph were enriched in key genes of inflammation-related pathways, especially the TNF signaling pathway. Cell communication analysis showed that the TNF signaling pathway between MT Mph and other cells in IBD was significantly enhanced compared to NC. Quasi-time sequence analysis results showed that monocytes could differentiate into MT Mph, and the expression of metallothionein genes ( MT2A, MT1X, MT1H and MT1G) was significantly upregulated during the differentiation process. Transcription factor analysis showed that the transcription factors SMARCB1 and ZMYND8 of MT Mph were significantly higher than those of monocytes, and the classical inflammatory transcription factors HIF1A, STAT3, and NFKB1 were significantly higher than those of non-MT Mph. Prediction models for CD and UC were constructed respectively based on ssGSEA and TNF treatment response [CD: area under the curve (AUC) = 0.966, P < 0.01; AUC = 0.793, P < 0.01]. Validation results showed that the model could not predict the response of CD and UC patients to vedolizumab therapy (both P > 0.05). Conclusions:There is a zinc homeostasis imbalance in IBD intestine, and MT Mph are a group of cells with high expression of zinc homeostasis-related genes, which are closely related to the TNF inflammatory pathway. The prediction model constructed based on the characteristic genes of MT Mph may be able to predict the response to anti-TNF therapy in IBD.

Objective:To analyze the expression of zinc homeostasis-related genes and related cells in the intestinal mucosa of inflammatory bowel disease (IBD) patients at the single-cell level and to evaluate their value in predicting the response to anti-tumor necrosis factor (TNF) therapy in IBD patients.Methods:Single-cell RNA sequencing data from 75 ileal or colorectal biopsy samples, including those from patients with Crohn's disease (CD), ulcerative colitis (UC), and normal controls (NC), were collected from four gene expression omnibus (GEO) databases. Unsupervised clustering analysis in R language was employed to classify IBD cells, zinc homeostasis-related gene scores were used to assess the zinc homeostasis status of different cell clusters, and the cell clusters closely related to zinc homeostasis-related genes, namely metallothionein-associated macrophages (MT Mph), were identified. Then the colon tissues from IBD patients and healthy individuals treated at the First Affiliated Hospital of Sun Yat-sen University were collected for immunofluorescence (IF) staining to compare the differences in MT Mph numbers between IBD and NC tissues. To further explore the function and origins of MT Mph, the characteristic genes of MT Mph and non- metallothionein-associated macrophages (non-MT Mph) from database were compared, the Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis was further used to enrich the characteristic genes, cell communication analysis was used to investigate the communication mechanisms between MT Mph and different cells, Quasi-time sequence was used to explore the origin of MT Mph and related signaling pathways, and the differences in transcription factors among monocytes, MT Mph and non-MT Mph were analyzed in R language. Single sample gene set enrichment analysis (ssGSEA) was used to evaluate the expression of MT Mph characteristic genes, and ssGSEA combined with the response to anti-TNF were used to construct the model in order to explore the predictive value of MT Mph characteristic genes for the response to anti-TNF therapy in IBD patients.Results:IBD cells were clustered and annotated into seven major cell clusters, namely T cells, B cells, plasma cells, myeloid cells, fibroblasts, endothelial cells, and epithelial cells. The results of zinc homeostasis-related gene scores showed that the scores of IBD myeloid cells were higher than those of the NC group. Myeloid cells could be divided into monocytes, macrophages, neutrophils, and dendritic cells. Based on the expression of zinc homeostasis genes, especially the high expression of metallothionein genes, the macrophages were divided into MT Mph and non-MT Mph, and the number of MT Mph in the IBD intestine was significantly increased compared to the NC group. IF validation showed that the number of CD68 +MT1G + cells (MT Mph) in both UC and CD were significantly higher than that in the NC group under per high-power field of view (UC vs. NC: 30.80 ± 7.29 vs. 9.80 ± 1.80, P < 0.001; CD vs. NC: 36.00 ± 9.30 vs. 9.80 ± 1.80, P < 0.001). KEGG pathway enrichment analysis revealed that the differential genes of MT Mph were enriched in key genes of inflammation-related pathways, especially the TNF signaling pathway. Cell communication analysis showed that the TNF signaling pathway between MT Mph and other cells in IBD was significantly enhanced compared to NC. Quasi-time sequence analysis results showed that monocytes could differentiate into MT Mph, and the expression of metallothionein genes ( MT2A, MT1X, MT1H and MT1G) was significantly upregulated during the differentiation process. Transcription factor analysis showed that the transcription factors SMARCB1 and ZMYND8 of MT Mph were significantly higher than those of monocytes, and the classical inflammatory transcription factors HIF1A, STAT3, and NFKB1 were significantly higher than those of non-MT Mph. Prediction models for CD and UC were constructed respectively based on ssGSEA and TNF treatment response [CD: area under the curve (AUC) = 0.966, P < 0.01; AUC = 0.793, P < 0.01]. Validation results showed that the model could not predict the response of CD and UC patients to vedolizumab therapy (both P > 0.05). Conclusions:There is a zinc homeostasis imbalance in IBD intestine, and MT Mph are a group of cells with high expression of zinc homeostasis-related genes, which are closely related to the TNF inflammatory pathway. The prediction model constructed based on the characteristic genes of MT Mph may be able to predict the response to anti-TNF therapy in IBD.