Fig. 5: The activation of autophagy in constitutive trisomic cells depends on cGAS.

a Quantification of TFEB nuclear localization upon cGAS siRNA treatment. The nuclear TFEB was quantified from delta MFI similarly as in Fig. 1f and plotted relative to CTRL siRNA for every cell line. In total, 3–14 independent experiments were performed in each cell line. b qRT-PCR data of selected TFEB target genes after cGAS depletion with siRNA. Relative LC3, SQSTM1, and LAMP2 levels were calculated using endogenous controls RPL27 and SPIKE. The data were plotted after normalization to the corresponding control siRNA sample for each cell line. In total, 3–6 independent experiments were performed for each cell line. c, e, g Examples of immunofluorescence images of TFEB localization upon cGAS or STING knockout with CRISPR/Cas9 nickase. Yellow arrow marks the cells efficiently transfected with the CRISPR–CAS9–GFP RNP that lack either nuclear TFEB (c, e) or IRF3 (g). White arrow marks the untransfected cells with normal nuclear expression of cGAS, IRF3, and TFEB. Scale bar 10 µm. d, f, h Quantification of the MFI of TFEB (d, f) and IRF3 (h) signals in cGAS or STING knockout cells transfected with CRISPR–CAS9–GFP. The data are presented in comparison with cells transfected with control CRISPR–CAS9–GFP. Both HCT116 and RPE1 diploid and all aneuploid cell lines were grouped together. About 4–11 measurements were performed in each sample group. Mann–Whitney test was applied for the statistical analysis of the graphs a and b, unpaired t-test was used for the graphs d, f, h. Individual measurements, mean values, p value, and standard deviations are shown in the plots, statistical evaluation is summarized in Supplementary table 4; source data is available in Supplementary Data 5.