Background: Retinal neovascularization, which is characterized by the increased proliferation, migration, and tube formation of retinal microvascular endothelial cells (RMECs), contributes to the progression of diabetic retinopathy (DR). MiR-409-5p has been reported to be upregulated in peripheral blood of DR patients and in vascular endothelial growth factor (VEGF)-induced RMECs. However, the role of miR-409-5p in retinal neovascularization of DR remains unelucidated. Method: The expression of miR-409-5p was measured in retinal tissues of streptozocin-induced and db/db...

Accumulating evidence indicates that N6-methyladenosine (m6A) and long noncoding RNAs (lncRNAs) play crucial roles in cancer development. However, the biological roles of m6A and lncRNAs in lung cancer tumorigenesis are largely unknown. In this study, SVIL antisense RNA 1 (SVIL-AS1) was downregulated in lung adenocarcinoma (LUAD) tissues and was associated with a favorable prognosis in patients with LUAD. SVIL-AS1 overexpression suppressed LUAD cell proliferation and blocked cell cycle arrest. Mechanistically, METTL3 increased the m6A modification...

TableS1. Clinical data of ovarian cancer patients from TCGA and ICGC.
TableS2.Identified DNA driver methylation (DNAme) in TCGA, ICGC and GSE146556.
TableS3. The correlation between DNAme and corresponding mRNA expression in TCGA, ICGC and GSE146556. TableS4.Analysis of pathway enrichment (KEGG) and Gene Ontology (GO) of DNAme-associated mRNA in TCGA.
TableS5. Univariate Cox regression analysis of DNAme-associated mRNA. (P < 0.05)
TableS6. Analysis of pathway enrichment (KEGG) and Gene Ontology (GO) of...

Additional file 2: Figure S2. CISD2 expression endows the cellular resistance to ferroptosis inducer. (A–D) Analysis of the CISD2 expression by western blot in HT-1080 (A, C) or HL60 (B, D) cells, GAPDH was used as loading control; (E, F) Cell survival analysis in CISD2-modified HT-1080 cells after the treatment of Erastin (0–10 µM); (G, H) Cell survival analysis in CISD2-modified HL60 cells after the treatment of Erastin (0–15 µM); Cell survival in control cells...

Additional file 2: Figure S2. CISD2 expression endows the cellular resistance to ferroptosis inducer. (A–D) Analysis of the CISD2 expression by western blot in HT-1080 (A, C) or HL60 (B, D) cells, GAPDH was used as loading control; (E, F) Cell survival analysis in CISD2-modified HT-1080 cells after the treatment of Erastin (0–10 µM); (G, H) Cell survival analysis in CISD2-modified HL60 cells after the treatment of Erastin (0–15 µM); Cell survival in control cells...

Additional file 11: Figure S7. Integrative analysis of the prognostic value of IRCGS in HCC patients and validation of its co-expressed correlation with five survival-related members of the STING pathway. K-M curve was performed to screen out three key IRCGS significantly associated with OS and DSS in the HCC cohort from TCGA database (A-D). The HCC dataset from ICGC database was used to validate the reliability of the co-expressed correlation of key IRCGS, namely VAV1...

Additional file 11: Figure S7. Integrative analysis of the prognostic value of IRCGS in HCC patients and validation of its co-expressed correlation with five survival-related members of the STING pathway. K-M curve was performed to screen out three key IRCGS significantly associated with OS and DSS in the HCC cohort from TCGA database (A-D). The HCC dataset from ICGC database was used to validate the reliability of the co-expressed correlation of key IRCGS, namely VAV1...

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

Additional file 4: Figure S1. The calibration curves at 1-year, 3-year, and 5-year time points were drawn in TCGA-all (A-C) and ICGC (D, E) HCC datasets. The 5-year follow-up data for the ICGC dataset currently is deficient.

Additional file 6: Figure S3. X-title software was utilized to determine the cut-off value of risk score to stratify HCC patients from TCGA-training cohort into low- and high-risk groups. The risk score calculated by gene signature of NRLC3, STING1, TBK1, TRIM21, and XRCC6, was associated with survival probability.

Additional file 2: Figure S2. CEF3 amino acid sequence alignment of WT and cef3 mutant

Additional file 3: Figure S3. Complementary assay. The phenotype (A) and the plant height (B) show the rescued properties in the complemented plants. Scale bars: 10 cm.

Additional file 2: Fig S2. Construct of intermediate cloning vectors for preparing Donor DNA. (A) Fragment A cloned from BW25113-T7 was concatenated to pACYCD-Blank to assemble pACYCD-gene. (B) Reverse-PCR to constructed pACYCD-Donor. (C) The map of Donor DNA, which contains HRL and HRR.

Supplementary Figure 1. Principal component analysis of the plaque bacteriome from HC, OPL, and OSCC individuals. Supplementary Figure 2. Principal component analysis of the saliva bacteriome from HC, OPL, and OSCC individuals. Supplementary Figure 3. Principal component analysis of the plaque mycobiome from HC, OPL, and OSCC individuals. Supplementary Figure 4. Principal component analysis of the saliva mycobiome from HC, OPL, and OSCC individuals. Supplementary Figure 5. Bubble plot of the plaque bacteriome and mycobiome...

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 2. Summary of the LC mutation information and the 10 DEMGs mutation information as well as CNV analysis of m6A-related genes in LC (GSCALite).

Additional file 9. Heatmap of DNA methylation expression levels of DEMGs in LUAD and LUSC by MethSurv platform.

Ulcerative colitis (UC) is the most prevalent form of chronic inflammatory bowel disease, the etiology of which is poorly understood. This study investigated the role of miR-151-5p on UC and explored the role of brain-derived neurotrophic factor (BDNF) in a UC mouse model and cell model. A UC mouse model was engineered by dextran sulfate sodium (DSS) induction. Primary mouse intestinal epithelial cells (IECs) were isolated. Colitis mice were intraperitoneally injected with miR-151-5p antagomir and...

Additional file 7: Figure S4. Yields of saturated mutants of three amino acid residues of Cv-ωTA converting cinnamaldehyde to cinnamylamine. (A) The production of cinnamylamine in saturated mutants of at the Phe22 site after adding cinnamaldehyde. (B) The production of cinnamylamine in saturated mutants of at the Tyr168 site after adding cinnamaldehyde. (C) The production of cinnamylamine in saturated mutants of at the Ala231 site after adding cinnamaldehyde. The mutant with the highest cinnamylamine production...

Additional file 7: Figure S4. Yields of saturated mutants of three amino acid residues of Cv-ωTA converting cinnamaldehyde to cinnamylamine. (A) The production of cinnamylamine in saturated mutants of at the Phe22 site after adding cinnamaldehyde. (B) The production of cinnamylamine in saturated mutants of at the Tyr168 site after adding cinnamaldehyde. (C) The production of cinnamylamine in saturated mutants of at the Ala231 site after adding cinnamaldehyde. The mutant with the highest cinnamylamine production...

Additional file 1: Figure S1. The downregulation of EMCN expression is related to metastasis and recurrence in breast cancer patients. (A) Heatmap of differentially expressed genes in breast cancer from TCGA datasets. (B) Volcano plot of differentially expressed mRNAs. Red dots represent upregulated mRNAs, and blue dots represent downregulated mRNAs. (C) EMCN expression in adjacent tissues and tumor tissues was analyzed (Wilcox tests, ****p < 0.0001, **p < 0.01, **p < 0.05). (D) EMCN gene...

Additional file 3: Figure S3. Knockdown efficiency of EMCN in HUVECs and the effect of EMCN on proliferation and metastasis. (A) qRT-PCR for the detection of EMCN mRNA in HUVECs infected with shRNA lentivirus that targets EMCN compared with HUVECs infected with a control shRNA. (B) Proliferation assays at 24, 48, 72 h and 96 h after plating. HUVECs with reduced EMCN expression display significantly less proliferative potential than control cells. (C) EMCN protein expression...

Additional file 4: Figure S4. The combination of anti-TGF-β antibody with DAPT synergistically suppresses tumor growth and metastasis. (A) and (B) Grayscale values of NICD and EMCN were quantified by ImageJ. (C) Representative Ki67 staining images of tumor sections from each group are shown from WT mice by IHC. (D) Representative photographs were obtained from the lungs of LLC-injected WT mice treated with vehicle, DAPT alone, anti-TGF-β antibody alone, or a combination of anti-TGF-β antibody...

Additional file 5: Figure S5. Toxicity of combined therapy and survival time of mice. (A) HE staining of liver, kidney and intestine from the vehicle and the combination of DAPT and anti-TGF-β antibody groups. (B) Body weight changes of LLC tumor-bearing mice treated with vehicle or the combination of DAPT and anti-TGF-β antibody. (C) The weight of subcutaneous tumors (B16-F10) in mice was measured (Left, *p < 0.05). (D) The number of B16-F10 lung metastasis...

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...