Suh, K.-S. | bioRxiv Science

bioRxiv2024

Identification of genes conferring individual-level variation responsible for metabolic dysfunction-associated steatohepatitis using single-cell eQTL analysis

Metabolic dysfunction-associated steatotic liver disease (MASLD) is increasingly recognized for its medical and socioeconomic impacts, driven by diverse genetic and environmental factors. To address the urgent need for individually tailored therapies, we performed single-cell expression quantitative trait loci (sc-eQTL) analysis on liver biopsies from 25 MASLD patients and 23 controls. This approach identified over 3,500 sc-eQTLs across major liver cell types and cell state-interacting eQTLs (ieQTLs) with significant enrichment for disease heritability (for MASLD trait, ieQTL enrichment odds ratio = 10.27). We integrated transcription factors (TFs) as upstream regulators of ieQTLs, revealing 601 functional units ("quartets") composed of TFs, cell states, ieSNPs, and ieGenes. From these results, we pinpoint the loss of an eQTL in EFHD1 during hepatocyte maladaptation associated with genotype-specific regulation by FOXO1, further contributing to the risk of MASLD. Our approach underscores the role of eQTL analysis in capturing crucial genetic variations that influence gene expression and clinical outcomes in complex diseases.

genetics↗

bioRxiv2023

The intrinsically disordered transcriptional activation domain of CIITA is functionally tuneable by single substitutions: An exception or a new rule?

During protein evolution, some amino acid substitutions modulate protein function ("tuneability"). In most proteins, the tuneable range is wide and can be sampled by a set of protein variants that each contains multiple amino acid substitutions. In other proteins, the full tuneable range can be accessed by a set of variants that each contains a single substitution. Indeed, in some globular proteins, the full tuneable range can be accessed by the set of site-saturating substitutions at an individual "rheostat" position. However, in proteins with intrinsically disordered regions (IDRs), most functional studies - which would also detect tuneability - used multiple substitutions or small deletions. In disordered transcriptional activation domains (ADs), studies with multiple substitutions led to the "acidic exposure" model, which does not anticipate the existence of rheostat positions. In the few studies that did assess effects of single substitutions on AD function, results were mixed: The ADs of two full-length transcription factors did not show tuneability, whereas a fragment of a third AD was tuneable by single substitutions. Here, we tested tuneability in the AD of full-length human class II transactivator (CIITA). Sequence analyses and experiments showed that CIITAs AD is an IDR. Functional assays of singly-substituted AD variants showed that CIITAs function was highly tuneable, with outcomes not predicted by the acidic exposure model. Four tested positions showed rheostat behaviour for transcriptional activation. Thus, tuneability of different IDRs can vary widely. Future studies are needed to illuminate the biophysical features that govern whether an IDR is tuneable by single substitutions.

biochemistry↗