Somatic NAP1L1 p.D349E promotes cardiac hypertrophy through cGAS-STING-IFN signaling

Abstract

Hypertrophic cardiomyopathy (HCM) is the most common inherited heart disease, often caused by sarcomere gene mutations, though many sporadic cases remain genetically unexplained. Here we show that the somatic variant NAP1L1 p.D349E was involved in cardiac hypertrophy in sporadic HCM patients. Through next generation sequencing, we found that somatic variant NAP1L1 p.D349E was recurrent in the cardiomyocytes of gene-elusive sporadic HCM patients. Subsequent in vivo and in vitro functional analysis confirmed that NAP1L1 p.D349E contributes to HCM by triggering an innate immunity response. This mutation destabilizes nucleosome formation, causing DNA to leak into the cytoplasm. This leakage activates a key immune pathway, cGAS-STING, which leads to the release of inflammatory molecules and promotes heart muscle thickening. Our findings reveal a new mechanism driving HCM and suggest that somatic variants could be important in understanding and management of HCM.

Fig. 1. Characterization of the Somatic NAP1L1 p.D349E Variant and Its Clinical Associations.

A Variant allele frequency distribution of NAP1L1 p.D349E. Variant allele frequency distribution of NAP1L1 p.D349E. B Representative somatic variants identified by ddPCR in the discovery cohort (D60). X axis, fluorescence intensity detected in the HEX-channel (channel 2, wild type); Y axis, fluorescence intensity detected in the FAM-channel (channel 1, mutant type); gray dots, droplets with background fluorescence; green dots, droplets with fluorescence detected in the HEX-channel; orange dots, droplets with fluorescence detected in the FAM-channel; blue dots, droplets with signals in both channels. C Representative somatic mutations identified by ddPCR in the replication cohort (R31). D Representative plot of ddPCR-negative NAP1L1 p.D349E (H5 and H12). E Bar plot of the NYHA class in patients with and without somatic NAP1L1 p.D349E. Left, discovery cohort; F Dot-and-whisker plots show the association of the NAP1L1 p.D349E variant with NYHA class in gene-elusive sporadic patients, analyzed using linear regression (N = 20 for the discovery cohort, N = 59 for the replication cohort). Data are presented as mean values +/− SEM.

Fig. 2. Effects of Nap1l1 Knockdown on DNA Damage, Inflammatory Signaling, and Cellular Function in NRCMs and Cardiac Fibroblasts.

A Immunofluorescence staining showing the levels of γ-H2ax protein in NRCMs with siCon or siNap1l1; B Representative immunofluorescence staining showing the levels of DAPI, dsDNA and cGAS in NRCMs with siCon or siNap1l1; C qPCR analysis of Mito and B2m in NRCMs with siCon or siNap1l1. N = 6 for each group, and two-tailed unpaired Student’s t-test was applied; D, E Western blot and quantification showing the levels of Sting, Tbk1, Irf3, Ifna, Ifnb, and phosphorylation of Sting, Tbk1, and Irf3 in NRCMs with siCon or siNap1l1. N = 3 for each group, and two-tailed unpaired Student’s t-test was applied; F qPCR analysis of Ifna, Ifnb, Il-6, and Il-1b in NRCMs with siCon or siNap1l1. N = 6 for each group, and two-tailed unpaired Student’s t-test was applied; G Phalloidin staining and TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling) staining and quantification in NRCMs with siCon or siNap1l1. Relative cell surface: siCON, n = 15; siNap1l1, n = 10. TUNEL+ cell: N = 5 for each group, and two-tailed unpaired Student’s t-test was applied; H Measurement of heart rate and diastolic function over time after adding siRNA. N = 4 for each group and two-way ANOVA with Tukey tests were used for correction of multiple comparisons; I qPCR analysis of Ifit1, Ifit2, Ifi3, Zbp1, Isg15, Stat1, and Il6 in influenced cardiomyocytes and Ifit1, Ifit2, Ifi3, Isg15, Irf7, Il6 and Il1b in influenced cardiac fibroblasts. N = 6 for each group, and two-tailed unpaired Student’s t-test was applied; J Representative plot of KI67 staining and quantification. N = 5 for each group, and two-tailed unpaired Student’s t-test was applied; K qPCR analysis of Irf7, Il6, Stat1, Isg15, Ifit1, and Ifit2 in influenced cardiac fibroblasts. N = 6 for each group and a two-tailed unpaired Student’s t-test was applied. Data are presented as mean values +/− SEM.

Fig. 3. Nap1l1 p.D349E exacerbated cardiac hypertrophy via cGas-Sting signaling in mouse with Ang II treatment.

A Schematic diagram depicting the experimental strategy used in C57BL6/N mice. Created in BioRender. Lv, C. (2025) https://BioRender.com/w55g327. B, C Representative image of heart and wheat germ agglutinin (WGA) staining and quantification of the WT, MT, WT with Ang II and MT with Ang II groups. N = 19, 20, 12, and 10 for WT, MT, WT with Ang II and MT with Ang II groups, and one-way ANOVA with Tukey tests were used for correction of multiple comparisons; D Heart weight-to-body weight (HW/BW) ratios of the WT, MT, WT with Ang II and MT with Ang II groups. N = 8 for each group, and one-way ANOVA with Tukey tests was used for correction of multiple comparisons; E Heart weight-to-tibia length (HW/BW) ratio in the WT, MT, WT with Ang II and MT with Ang II groups. N = 8 for each group, and one-way ANOVA with Tukey tests was used for correction of multiple comparisons; F Representative hematoxylin and eosin (H&E) staining showing preserved heart size in the WT, MT, WT with Ang II and MT with Ang II groups. G Representative images of interstitial fibrosis stained by Masson’s trichrome staining showing preserved heart size in the WT, MT, WT with Ang II, and MT with Ang II groups. H Representative M-mode echocardiograms of the left ventricle in the WT, MT, WT with Ang II, and MT with Ang II groups. I Quantification of left ventricular end-diastolic anterior wall thickness (LVAW; d), left ventricular end-diastolic posterior wall thickness (LVPW; d), ejection fraction (EF), fractional shortening (FS) or left ventricular (LV) mass; J qPCR analysis of Anp, Bnp, and β-Mhc in the WT, MT, WT with Ang II and MT with Ang II groups. N = 5 for each group, and one-way ANOVA with Tukey tests was used for correction of multiple comparisons; K Relative concentration of second messenger cGAMP. N = 5 for each group, and one-way ANOVA with Tukey tests was used for correction of multiple comparisons; L qPCR analysis of Ifna and Ifnb in the WT, MT, WT with Ang II, and MT with Ang II groups. N = 5 for each group, and one-way ANOVA with Tukey tests were used for correction of multiple comparisons; M, N Western blot images and quantification showing cGAS, Sting, Tbk1, Ifna, and Ifnb expression and phosphorylation of Sting, Tbk1, and Irf3 in the WT with Ang II and MT with Ang II groups. MT: mutation type, NAP1L1 p.D349E. N = 5 for each group and one-way ANOVA with Tukey tests was used for the correction of multiple comparisons. Data are presented as mean values +/− SEM.

Fig. 4. Nap1l1 p.D349E activated cGas-Sting-IFN signaling via impaired histone oligomerization.

A, B Co-IP of the Nap1l1 p.D349E or wild type with H2a, H2a.x, H2a.z, and H2b; The antibodies used for pulling were IgG, HA, and Flag, and IgG is the isotype control group. N = 3 for each group, and two-tailed unpaired Student’s t-test was applied; C Agarose gel electrophoresis showing the nucleosome-bound DNA content, representing the number of nucleosomes in the WT and MT group. N = 4 for each group, and two-tailed unpaired Student’s t-test was applied; D, E, Western blot, qPCR analysis, and quantification of the levels of the γ-H2ax protein. N = 3 for each group, and two-tailed unpaired Student’s t-test was applied; F, G Representative immunofluorescence staining showing the levels of γ-H2ax, cGAS, and dsDNA; H, I Relative concentration of second messenger cGAMP. For H, n = 6 and for I, n = 4, and two-tailed unpaired Student’s t-test were applied; J Representative immunofluorescence staining showing the levels of phalloidin; K, L Representative Western blot images and quantification showing cGAS, Sting, Tbk1, Ifna, and Ifnb, and phosphorylation of Sting, Tbk1 and Irf3 expression in the wild-type and Nap1l1 p.D349E groups. N = 3 for each group, and two-tailed unpaired Student’s t-test was applied; M qPCR analysis of Ifna, Ifnb, Il-6, Il-1b. N = 6 for each group, and two-tailed unpaired Student’s t-test was applied; N qPCR analysis of Ifit1, Ifit2, Ifi3, Zbp1, Isg15, Stat1, and Il6 in influenced cardiomyocytes. N = 6 for each group, and two-tailed unpaired Student’s t-test was applied; O qPCR analysis of Ifit1, Ifit2, Ifi3, Isg15, Irf7, Il6, and Il1b in influenced cardiac fibroblasts. N = 6 for each group, and two-tailed unpaired Student’s t-test was applied; P, Q qPCR analysis of Irf7, Il6, Stat1, Isg15, Ifit1, and Ifit2 in influenced cardiomyocytes and cardiac fibroblasts. N = 6 for each group and a two-tailed unpaired Student’s t-test was applied. Data are presented as mean values +/− SEM.

Fig. 5. cGas-Sting-IFN blockade alleviated NAP1L1 p.D349E-induced cardiac hypertrophy.

A Schematic diagram depicting the experimental strategy used in C57BL6/N mice with antagonists and antibodies. C-176, a selective STING antagonist. Created in BioRender. Lv, C. (2025) https://BioRender.com/u41l117. B Representative image of heart and wheat germ agglutinin (WGA) staining and quantification of WT with AngII, MT with AngII, MT with AngII and C-176, and MT with AngII and anti-IFNAR groups; N = 10, 8, 9, 12 for WT with AngII, MT with AngII, MT with AngII and C-176, and MT with AngII and anti-IFNAR and one-way ANOVA with Tukey tests was used for correction of multiple comparisons; C Representative hematoxylin and eosin (H&E) staining and Masson’s trichrome staining showing heart size, cardiomyocyte size, and fibrosis in WT with AngII, MT with AngII, MT with AngII and C-176, and MT with AngII and anti-IFNAR groups; D Heart weight to body weight (HW/BW) ratio in WT with AngII, MT with AngII, MT with AngII and C-176, and MT with AngII and anti-IFNAR groups. N = 8 for each group, and one-way ANOVA with Tukey tests were used for correction of multiple comparisons; E Representative M-mode echocardiograms of the left ventricle in WT with AngII, MT with AngII, MT with AngII and C-176, and MT with AngII and anti-IFNAR groups; F Quantification left ventricular end-diastolic anterior wall thickness (LVAW;d), left ventricular end-diastolic posterior wall thickness (LVPW;d), Ejection fraction (EF), Fractional shortening (FS) or left ventricular (LV) mass. N = 8 for each group, and one-way ANOVA with Tukey tests were used for correction of multiple comparisons; G Western blot analysis showing the cGAS, Sting, Tbk1, Ifna, and Ifnb, and phosphorylation of Sting, Tbk1, and Irf3 expression in WT with AngII, MT with AngII, MT with AngII and C-176 groups; H Representative Western blot images and quantification showing the cGAS, Sting, Tbk1, Ifna, and Ifnb, and phosphorylation of Sting, Tbk1 and Irf3 expression in WT with AngII, MT with AngII, MT with AngII and C-176 groups. MT: mutation type, NAP1L1 p.D349E. N = 5 for each group, and one-way ANOVA with Tukey tests was used for correction of multiple comparisons; I Central Illustration of this study. Created in BioRender. Lv, C. (2025) https://BioRender.com/g82u862. Data are presented as mean values +/− SEM.