Additional file 7: Figure S4. The correlation of risk score calculated by gene signature of NRLC3, STING1, TBK1, TRIM21, and XRCC6, and survival probability and disease progression respectively in patients from TCGA-all (A-C) and ICGC cohort (D-F). All *: P < 0.05, **: P < 0.01, ***: P < 0.001.

Additional file 1: Supplementary Figure 1. Skin lesions of patient 1 before (A) and after (B) the 12-week TNFi treatment. The severe acne characterized by cyst nodules and abscesses in the cheeks improved after the treatment. The area of the acne shrank.

Additional file 2: Supplementary Figure 2. Skin lesions of patient 2 before (A) and after (B) the 12-week TNFi treatment. The severe acne characterized by cyst nodules and abscesses in the forehead and nose improved after the treatment, left only some slight scar formation.

Additional file 2: Supplementary Figure 2. Skin lesions of patient 2 before (A) and after (B) the 12-week TNFi treatment. The severe acne characterized by cyst nodules and abscesses in the forehead and nose improved after the treatment, left only some slight scar formation.

Additional file 9: Figure S4. Cis-acting elements within the promoters of CsFLS2 and CsFLS3.

Additional file 1: Figure S1. Enrichment analysis of CISD2 related genes. (A) Protein-protein interaction network of CISD2 from STRING website ( https://www.string-db.org/ ) and Cytoscape 3.7.2 software; (B) The enrichment analysis of CISD2 related genes in GO terms, including BP (biological process), CC (cell component) and MF (molecular function), and KEGG pathway.

Additional file 3: Figure S3. Quantitative analysis of FTH expression in Fig. 3B.

Additional file 3: Figure S3. ShRNA Panx 1-AAV or Ctrl-AAV-labeled EGFP-positive cells have a sound co-localization with S100 β-labeled Schwann cells. Enlarged images in lower panel are from the inset boxes of upper panel. Upper panel, scale bar = 50 μm. Lower panel, scale bar = 25 μm. n = 3–4 mice/group.

Additional file 7: Figure S7. Cytokine array reveals Panx 1-dependent cytokines and chemokines in LPS-treated Schwann cells. A. Coordinates of the cytokine array containing 40 different cytokines and chemokines, including three positive control (PC) proteins. B. Array membranes of protein expression among Ctrl, Ctrl-siRNA, and Panx 1-siRNA groups in LPS-treated Schwann cells.

Additional file 9: Fig. S4. Whole-genome variation of two parental lines of QYSM. a, Density and chromosome distribution of polymorphic SNPs between Q9311B and WSSM. b, The principal component analysis. c, Phylogenetic positions of two parental lines (Q9311B and WSSM) in the neighbor-joining tree of 1,946 rice accessions from 3 K-RG, in which the known information on the clades of 3 K-RG is indicated.

Additional file 15: Figure S6. circPVT1 promotes the migration and invasion of NPC cells by regulating cell adhesion andcytoskeleton remodeling. The 231 differentially expressed proteins regulated by c-Myc from LC-MS/MS data using the Ingenuity Pathway Analysis (IPA) software.

Additional file 15: Figure S11. The raw results of western blotting for the indicated gene.

Additional file 5: Figure S2. The co-expressed correlation of gene signature of NRLC3, STING1, TBK1, TRIM21, and XRCC6 in HCC patients from TCGA-training (A), TCGA-all (B), and ICGC (C), respectively.

Additional file 12: Figure S5. Characterization of myeloid cells in the KUL3 cohort. A. UMAP plot of myeloid cells colored by cell cluster and sample origin. B. Heatmap of marker genes identified through Seurat. For each cell cluster, cells were down-sampled to 100. C. Heatmap plot of the top 5 ranked regulons in TAM1-TAM4 identified by pySCENIC. D. Dot plot of the correlation between the proportions of C4 cells in epithelial cells and macrophages (left),...

Additional file 12: Figure S5. Characterization of myeloid cells in the KUL3 cohort. A. UMAP plot of myeloid cells colored by cell cluster and sample origin. B. Heatmap of marker genes identified through Seurat. For each cell cluster, cells were down-sampled to 100. C. Heatmap plot of the top 5 ranked regulons in TAM1-TAM4 identified by pySCENIC. D. Dot plot of the correlation between the proportions of C4 cells in epithelial cells and macrophages (left),...

Additional file 15: Figure S8. Workflow of this study. Single-cell transcriptomes and bulk RNA-seq data were integrated to fully analyze the complicated relationship between colorectal epithelium and surrounding environment. C4 cells were featured with high invasive potential and related with TAMs and CAFs, and further validated in vitro using IHC and mIHC.

Additional file 13: Figure S6. Characterization of stromal cells in the SMC cohort. A. UMAP plot of stromal cells colored by cell cluster and sample origin. B. Heat map of marker genes identified through Seurat. For each cell cluster, cells were down-sampled to 100. C. Differentiation trajectories inferred by Monocle2. Dots represent stromal cells and are colored by identified cell cluster. D. Heat map of the top 5 ranked regulons in S5 and S6. E....

Additional file 8: Figure S1. Cellular landscape of CRC in the KUL3 cohort. A. UMAP plot of 26,268 cells colored by cell cluster, CMS and sample origin. Each dot represents a cell and cellular cluster is annotated with text. B. Proportions of the identified cell clusters distributed across tumor, border and adjacent normal tissues with the relative cell type proportions and total cell numbers. Upper: all cell clusters; lower: immune and stromal cell clusters. C....

Additional file 9: Figure S2. Functional heterogeneity of CRC epithelial cells in the SMC cohort. A. UMAP feature plot of the top 10 upregulated genes in the SMC cohort. B. Correlation heat map of 123 programs identified by cNMF. The Pearson correlation coefficient is indicated by the color. C. Heatmap of the relative mean signature score of cancer cell functional signatures across C1-C7. The signature score was calculated using the “AUCell” package. D. Heatmap of...

Additional file 13: Figure S9. The transcriptional expression of VAV1, RHOA, and ZC3HAV1 was positively correlated to the distribution of EMT scores in the HCC cohort from TCGA (A, D, and G) and ICGC (B, E, and H) database, and GSE14520 (C, F, and I) dataset. EMT: epithelial-mesenchymal transition. r: Pearson's correlation coefficient.

Additional file 14: Figure S10. The relationship between transcriptional expression of VAV1 (A), RHOA (B), and ZC3HAV1 (C) and the infiltration of immune cell subtypes in three independent single-cell sequencing HCC datasets from TISCH database. TISCH: Tumor Immune Single-cell Hub.

Additional file 2: Figure S2. Consensus clustering analysis of DEGs in GC. (A) The cumulative distribution function (CDF) curves in consensus cluster analysis for cluster numbers k = 2–9. (B) Relative change in the area under the CDF curve from k = 2 to k = 9. (C) The tracking plot for k = 2–9; The vertical axis shows consensus matrix k-value, the horizontal axis represents the GC samples. (D-L) Consensus matrix heat map when...

Additional file 2. The function of tucidinostat on tumor immunity. a Functional annotation clustering of genes regulated in tumor from CT26 tumor-bearing mice on day 10 post treatment with tucidinostat (25 mg/kg, gavage, daily, n=3) or DMSO as vehicle control (DMSO, n=3). b Representative cytograms (left) or summary histograms (right) for the cell surface PD-L1 expression in CT26 cells following different doses (2.5, 5, 7.5 μM) of vorinostat, tucidinostat, and TMP-195 treatment for 24h. c...

Additional file 3. Tucidinostat plus checkpoint blockade induces improved therapeutic efficacy. a Schema of the experiment. For bioluminescence imaging (BLI) in vivo, mouse 4T1-luc (5 × 105 cells) were engrafted into the flank of BALB/c mice. When established tumors were palpable 7 days after tumor cells inoculation, mice were treated with vehicle (DMSO, n=7), tucidinostat (25 mg/kg, gavage, daily, n=7), aPD-L1 (200 μg, i.p. injection, once every 3 days, n=7), or combination (n=7). Tumors volume...

Additional file 5. Tucidinostat plus checkpoint blockade induces CCL5 secretion. a Mouse CT26 cells (5 × 105 cells) were engrafted into the flank of BALB/c mice. When established tumors were palpable 7 days after tumor cells inoculation, mice were treated with different doses (12.5, 25, 75 mg/kg, gavage, daily, n=5) of tucidinostat. The expression of CCL5 in peripheral blood serum from CT26 tumor-bearing mice on day 10 post treatment initiation. Mouse CT26 cells (5 ×...