Loss of TNIP1 leads to an increase in inflammatory proteins. (A) Loss of TNIP1 does not alter autophagy flux under basal and starvation conditions. TNIP1 knock out HeLa cells generated by CRISPR/Cas9 were used to study its effect on autophagy. Wild-type HeLa cells and the two TNIP1 knockout clones denoted KO1 and KO2 were kept in either fed or starved (HBSS) conditions and treated with either vehicle (DMSO) or BafA1 for 8 h. Blots were probed for several known SLRs as well as LC3. (B) Quantification of blots shown in A (n = 3). Error bars indicate SD. (C) Loss of TNIP1 leads to an increased transcription of inflammatory genes. Fold changes of RNA and protein intensities of TNIP1 KO and WT cells were compared. Shown are average values of two KO clones compared to WT cells (n = 3 per cell type for RNAseq; n = 5 per cell type for proteomics). Genes that were significantly regulated on RNA and protein level are highlighted in red (P < 0.01). Genes linked to immune effector processes and interferon-stimulated genes are annotated. (D) Protein-protein interactions of significantly regulated proteins. Proteins highlighted in red in C were analyzed on known interactions using STRING DB (Szklarczyk et al., 2019). Interactions between 17 proteins were identified, of which 13 are linked to stress response (marked in red). Thickness of edges indicate confidence of interaction. (E and F) Gene set enrichment analysis of significantly dysregulated mRNAs and proteins identifies an increased transcription and translation of genes involved in inflammation. NES denotes normalized enrichment score. (G–I) TNIP1 represses translation of pro-inflammatory gene products. Whereas knockout of TNIP1 led to an increased abundance of indicated inflammatory proteins (G), which is likely due to transcriptional changes (H, n = 3, error bars indicate SEM), re-expression of TNIP1^WT or TNIP1^mLIR1+2 blunted this phenotype (I). Source data are available for this figure: SourceData F5.