ER-phagy keeps cells healthy: In eukaryotic cells, about one-third of all proteins are targeted to the endoplasmic reticulum (ER), which serves as a hub for secretory protein traffic and quality control. Cui et al. studied a protein known as Lst1 in yeast and SEC24C in mammalian cells that is involved in loading secretory cargo into vesicles that are delivered to the Golgi complex. In response to stress caused by starvation or misfolded aggregate-prone secretory proteins, Lst1 acted to promote an additional function—ER-phagy. Together with autophagy receptors on the ER, Lst1 targeted ER domains for degradation to avert protein aggregation, thus preserving cellular health. Science , this issue p. 53

Significance: Vps13, a conserved phospholipid transporter, localizes to contact sites between the endoplasmic reticulum (ER) and different organelles. While budding yeast has oneVPS13gene, humans have four. The yeast Vps13 protein is most closely related to VPS13A and VPS13C. VPS13A localizes to ER–mitochondria contact sites, while VPS13C resides at ER–late endosome contact sites. Here we report that thevps13Δ mutant is defective in the selective autophagy of ER (ER-phagy). In the absence of Vps13, the ER accumulates at late endosomes and fails to be packaged into autophagosomes. These findings highlight the importance of Vps13 function at late endosomes in ER-phagy, and may have implications for understanding the role of VPS13C, which has been linked to early-onset Parkinson’s disease.

Here, we report that the RTN3L–SEC24C endoplasmic reticulum autophagy (ER-phagy) receptor complex, the CUL3KLHL12 E3 ligase that ubiquitinates RTN3L, and the FIP200 autophagy initiating protein, target mutant proinsulin (Akita) condensates for lysosomal delivery at ER tubule junctions. When delivery was blocked, Akita condensates accumulated in the ER. In exploring the role of tubulation in these events, we unexpectedly found that loss of the Parkinson’s disease protein, PINK1, reduced peripheral tubule junctions and blocked ER-phagy. Overexpression of the PINK1 kinase substrate, DRP1, increased junctions, reduced Akita condensate accumulation, and restored lysosomal delivery in PINK1-depleted cells. DRP1 is a dual-functioning protein that promotes ER tubulation and severs mitochondria at ER–mitochondria contact sites. DRP1-dependent ER tubulating activity was sufficient for suppression. Supporting these findings, we observed PINK1 associating with ER tubules. Our findings show that PINK1 shapes the ER to target misfolded proinsulin for RTN3L–SEC24C–mediated macro-ER-phagy at defined ER sites called peripheral junctions. These observations may have important implications for understanding Parkinson’s disease.

Under conditions of chronic unresolved inflammation characteristic of atherosclerosis, regulatory CD4 ⁺ T cells (Tregs) become unstable and convert to cytotoxic exTregs. The mechanism driving this conversion in humans is unclear. Here, we show unresolved endoplasmic reticulum (ER) stress as a key factor driving Treg instability. Human exTregs undergo ER stress and consequent mitochondrial dysfunction that remains unchecked due to defective mitophagy. Integrated stress response (ISR), a pathway that can trigger inflammatory signaling, is also upregulated in exTregs. exTregs are highly apoptotic and are more susceptible to stress-mediated cellular dysfunction due to their senescent state. In a phenotype reminiscent of exTregs, Tregs from coronary artery disease (CAD) patients show high ER stress and mitochondrial depolarization. This is further exacerbated in CD4 ⁺ T cells residing in atherosclerotic plaques. Pro-atherosclerotic stressors such as oxLDL and interferon-γ induce ER stress and mitochondrial dysfunction in Tregs in vitro. We conclude that the maladaptive inflammatory environment in atherosclerosis triggers ER stress and mitochondrial dysfunction, contributing to Treg instability in CAD.

HIV infection is known to increase the risk for cardiovascular disease (CVD). Although almost 400 single-nucleotide polymorphisms (SNPs) are significantly associated with CAD alone, a subtype of CVD, the functions of most of these risk loci are unclear. Here, we investigated the impact of genetic variants/SNPs on the expression of nearby genes as potential cis expression quantitative trait loci (cis-eQTLs). We investigated peripheral blood mononuclear cells (PBMCs) from 31 participants in the Women’s Interagency HIV Study (WIHS) using genotyping, single-cell (sc)RNA-seq, and CITE-seq. We found 187 statistically significant sc-eQTLs (single-cell eQTLs). In total, 160 were specific for just one immune cell type. We found a set of 3 sc-eQTLs impacting expression of IFNGR1 in CD4+ T cells at the mRNA and protein level as detected by flow cytometry. Two other sc-eQTLs representing one locus impact IFNG expression in CD8+ T cells, one of the primary sources of this cytokine. The sc-eQTLs impacting IFNG were associated with Th1 (T-helper1) gene expression patterns in CD4+ T cells in this cohort. These data suggest that some individuals are genetically predisposed to greater levels of Th1 polarization, which is known to be associated with atherosclerosis.