Triggering receptor expressed on myeloid cells 1 (TREM1) participates in the development of endometritis. This study aims at identifying the effects and interaction of TREM1 and upstream stimulatory factor 2 (USF2) in endometritis by using a model of lipopolysaccharide (LPS)-induced human endometrial epithelial cells (HEnEpCs). ELISA was performed to determine the levels of interleukin (IL)-6, IL-1β, and tumor necrosis factor (TNF-α) after LPS stimulation. TREM1 and USF2 expression was examined with RT-qPCR and Western blot....

The dysregulated circular RNAs (circRNAs) are linked to progression and chemoresistance in colorectal cancer (CRC). However, the role of circRNA protein tyrosine kinase 2 (circPTK2) in CRC progression and chemoresistance is uncertain. The circPTK2, microRNA (miR)-136-5p, m6A ‘reader’ protein YTH domain family protein 1 (YTHDF1), β-catenin and cyclin D1 abundances were examined via quantitative reverse transcription PCR or Western blotting. The progression was investigated by cell counting kit-8 (CCK-8), colony formation, transwell and xenograft analysis....

Additional file 1: Figure S1. The distribution comparison of Candida species isolated from mixed C/B-BSIs and mono-candidemia. Mono-candidemia, monomicrobial candidemia; Mixed C/B-BSIs, mixed Candida/bacterial bloodstream infections.

Additional file 2: Fig. S1. A Schematic diagram of the genomic locus of CEBPA-DT (www.ncbi.nlm.nih.gov/). B The protein-coding potential of CEBPA-DT predicted by Open reading frame (ORF) Finder software prediction ( https://www.ncbi.nlm.nih.gov/orffinder/ ). C The protein-coding potential of CEBPA-DT predicted by Coding-Potential Assessment Tool ( wlcb.oit.uci.edu/cpat/ ).

Additional file 5: Fig. S4. A Clustering heatmap of significant differentially expressed mRNAs in HCCLM9 cells transfected with negative control or CEBPA-DT siRNAs. B Significantly enriched pathways annotated by the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. C Significantly enriched pathways annotated by the Gene Ontology (GO) database. D Significantly enriched pathways annotated by the Molecular Signatures Database (MSigDB). E The binding sites of hnRNPC and 3’UTR of DDR2 were predicted by PRIdictor database...

Additional file 6: Fig. S5. A-B The expression levels of DDR2 were measured by western blot and RT-qPCR in indicated HCCLM9 and SNU-449 cells transfected with negative control siRNA or siRNAs targeting DDR2. C-D Cell migration capacity of indicated HCCLM9 and SNU-449 cells were measured by scratch wound-healing assays. Scale bar, 100μm. E-F Cell migration and invasion capacity of indicated HCCLM9 and SNU-449 cells were measured by transwell migration and matrigel invasion assays. Scale bar,...

Additional file 3: Fig S3. Gene map for targeted Cas9-mediated gene Knock-In. (A) The knock-out site of hemF in BW25113-T7. (B) map of hemF knock-out in ideal condition and the location of PCR product (899 bp) for sequencing.

Additional file 5: Fig S5. Detection of successful gene knock-outs of BW25113-T7.

Supplementary Material 11

Additional file 2: Figure S2. Quality assessment and publication bias. (A) Risk of bias graph for all studies included. (B) The comparison-adjusted funnel plots for R0 resection rate.

Additional file 2: Supplementary Fig. S1. TNFAIP2 expression in normal tissues and cancer cell lines. (a) TNFAIP2 expression in normal tissues, analyzed by GTEx portal; (b) TNFAIP2 expression in cancer cell lines analyzed by CCLE.

Additional file 3: Supplementary Fig. S2. Epigenetic alterations of TNFAIP2 in AML. (a) The exact location of CpG sites in gene body of TNFAIP2 from UCSC database. (b) Kaplan-Meier analysis of the prognostic value of TNFAIP2 methylation at gene body region on OS in AML patients, analyzed by MethSurv.

Additional file 4: Supplementary figure 4. Efficiency of miR-185-3p transfection and functional enrichment analyses of target genes of circ_0002078. (A) Efficiency verification of miR-185-3p overexpression in MEC-1 cells by qRT-PCR. (B) GO analysis results demonstrated that the target genes of circ_0002078 were enriched in positive regulation of gene expression, lymphocyte proliferation, and regulation of B cell apoptotic process. (C) KEGG pathway analysis showed that the target genes were primarily relevant to JAK-STAT signaling pathway and...

Additional file 4: Figure S4. Enrichment of differentially expressed genes in Serpine1-overexpressing MLE-12 cells. A, B GO and KEGG enrichment of the upregulated genes. C, D GO and KEGG enrichment of the downregulated genes. Q-value ≤ 0.05 and fold-change ≥ 2 were used as the thresholds for screening the differentially expressed genes.

Additional file 6: Figure S6. HDAC2 inhibition promoted the expression of Serpine1. A SDS-PAGE identification of the proteins pulled-down by DNA fragment of Serpine1 promoter. The gel was stained with Coomassie blue. The indicated differential bands were excised with a scalpel and identified by LC-MS. B Total ion chromatogram of proteins. C–E Serpine1 expression analysed using RT-qPCR and western blot in trichostatin A (TSA)-treated MLE-12 cells. Data show mean ± SEM; Data was analysed using...

Additional file 6: Figure S6. HDAC2 inhibition promoted the expression of Serpine1. A SDS-PAGE identification of the proteins pulled-down by DNA fragment of Serpine1 promoter. The gel was stained with Coomassie blue. The indicated differential bands were excised with a scalpel and identified by LC-MS. B Total ion chromatogram of proteins. C–E Serpine1 expression analysed using RT-qPCR and western blot in trichostatin A (TSA)-treated MLE-12 cells. Data show mean ± SEM; Data was analysed using...

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.

Supplementary Material 1

Additional file 10: Supplementary Figure 6. A Image of subcutaneous tumors of four groups implanted with LLC-circZNF451: WT + PBS, WT + PD1 blockade, ELF4 KO + PBS, and ELF4 KO + PD1 (n = 5 for each group) and the statistical analysis on the tumor growth of the four groups. The conditional knockout of ELF4 is accomplished with C57BL/6J-Lyz2CreERT2 and C57BL/6J-ELF4em1(flox)Smoc mice; KO, knockout. B TIM3 expression and GZMB secretion in CD8+ T cells...

Additional file 5: Supplementary Figure 1. A The enrichment of 4 most significantly changed circRNAs (FC > 4, P < 0.05) of the circRNA sequencing in the exosomes of 6 LUAD patients (3 PR and 3 PD) accepting the PD1 blockade was measured by qRT-PCR. B Correlation between exosomal circRNA-seq results of circZNF451 and the expression of circZNF451 in the tumor tissues of six LUAD patients was analyzed by Spearman correlation analysis. C The expression...

Additional file 6: Supplementary Figure 2. A Infiltration of CD4+T, CD8+T, Foxp3+Treg, CD56+NK and CD11C+dendritic cells and CD86+ and CD163+ macrophages in the circZNF451high and circZNF451low group was presented in the violin plot. B The transfection efficiency of circZNF451 in LLC was measured by qRT-PCR. C The construction of A549-shcircZNF451, H1299-shcircZNF451, H1395-circZNF451 and H1975-circZNF451 cell lines was confirmed by qRT-PCR. D IFN-γ and GZMB levels in the supernatant of CD8+ T cells were measured via...

Additional file 7: Supplementary Figure 3. A Silver staining of the complexes precipitated by the biotinylated circZNF451/NC probe. The red arrow marks the specific band of the circZNF451 probe. B The overlap of the mass spectrometry data, the predicted candidates for circZNF451 in circInteractome and the most detected binding motifs for circZNF451 in catRAPID database. C After coculturing with H1395/H1975-shcircZNF451 and GW4869 (20μM), FXR1 expression in macrophages was detected via western blotting. D and E...

Additional file 1: Figure S1.Expression, purification and immunoblot analysis of recombinant PvRAMA protein. A Expression and purification of recombinant PvRAMA (appox. 43 kDa). M, Marker; T, total translation mix; S, supernatant; P, precipitate; Ft, flow through; Ne, elution treated with non-reducing buffer; E, elution treated with reducing buffer. b-d Recombinant PvRAMA protein (appox. 43 kDa) under reducing conditions was probed with the anti-His tag antibody (b), rPvRAMA-immunized mouse serum (c) and PBS-immunized mouse serum (d).

Additional file 3: Figure S2.Comparison of PvRAMA amino acid sequences. The first line was the reference sequence: PvRAMA of the Sal-1 strain. The number of P. vivaxisolates with the same amino acid sequence is shown in parentheses.