Supplementary Materials

The PDF file includes:

  • Materials and Methods
  • Fig. S1. PCA plot analysis using RNA-seq data from the discovery cohort.
  • Fig. S2. Effect of genotype on mRNA expression within the NAFLD discovery cohort.
  • Fig. S3. Unsupervised clustering of NALD RNA-seq cohort.
  • Fig. S4. Supervised clustering of NALD RNA-seq cohort.
  • Fig. S5. Pathview enrichment and candidate gene analysis in the NAFLD-control comparison.
  • Fig. S6. GO annotation pairwise analysis using the NAFLD discovery cohort.
  • Fig. S7. Nanostring analysis using the replication cohort.
  • Fig. S8. Integrated scRNA-seq analysis.
  • Fig. S9. Expression of 25-gene signature in scRNA-seq cell clusters.
  • Fig. S10. Immunohistochemistry for AKR1B10, GDF15, and STMN2.
  • Fig. S11. Enzymatic activity of HSD17B14 and HSD17B13 against estradiol and retinol.
  • Table S2. Clinicopathological features unsupervised clustering B1 and B2.
  • Table S10. Demographics of discovery, replication, and biomarker cohorts.
  • Table S14. Previous reports on the relevance of 25-gene signature members to NAFLD.
  • Table S15. Annotation clusters scRNA-seq data.
  • Reference (53).

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Top 250 DEGs comparing unsupervised cluster A with cluster B.
  • Table S3 (Microsoft Excel format). DEGs comparing NASH F2 to baseline NAFL using discovery cohort RNA-seq data.
  • Table S4 (Microsoft Excel format). DEGs comparing NASH F3 to baseline NAFL using discovery cohort RNA-seq data.
  • Table S5 (Microsoft Excel format). DEGs comparing NASH F4 to baseline NAFL using discovery cohort RNA-seq data.
  • Table S6 (Microsoft Excel format). DEGs comparing NASH F3 to baseline NASH F0/F1 using discovery cohort RNA-seq data.
  • Table S7 (Microsoft Excel format). DEGs comparing NASH F4 to baseline NASH F0/F1 using discovery cohort RNA-seq data.
  • Table S8 (Microsoft Excel format). DEGs associated with NAS ≥4 based on RNA-seq data.
  • Table S9 (Microsoft Excel format). DEGs associated with SAF activity ≥2 based on RNA-seq data.
  • Table S11 (Microsoft Excel format). Correlation of the 25-gene signature with discovery cohort histological features.
  • Table S12 (Microsoft Excel format). Logistical univariate analyses of the 25-gene signature.
  • Table S13 (Microsoft Excel format). Logistical multivariate analyses of the 25-gene signature.
  • Table S16 (Microsoft Excel format). Proteomics analysis of NAFLD serum samples.
  • Data file S1 (Microsoft Excel format). Individual-level data from figures.