Smriti Parashar

In this Research Topic, we curated original and review articles that highlight the latest discoveries related to mechanisms of autophagy evasion by diverse pathogens, as well as the potential therapeutic targeting of autophagy pathways to enhance host defense and combat intracellular infections.Mycobacterium tuberculosis evades host autophagy to promote intracellular survival. They also highlight the potential of selective autophagy enhancers as hostdirected therapies to complement existing antimicrobial treatments. If successfully translated into clinical practice, these approaches could improve treatment outcomes, particularly for drugresistant tuberculosis.Zhang et al. combine bioinformatic and experimental approaches to show that Brucella melitensis infection upregulates core autophagy genes, including ATG14, through the downregulation of miR-1, a negative regulator of ATG14, in sheep Leydig cells. These findings provide a mechanistic insight into the early host-pathogen interactions elicited by B. melitensis. Future work can reveal whether this regulatory axis alters autophagic flux and bacterial survival and determine its relevance to infection in vivo.Melanson et al. develop a dual-cell air-liquid interface (ALI) airway model incorporating differentiated epithelial cells and human peripheral blood monocyte-derived macrophages to investigate host-pathogen interactions during Pseudomonas aeruginosa infection. Macrophage incorporation into this model altered IL-8 secretion and bacterial spatial distribution without significantly affecting the overall bacterial burden. These findings highlight the importance of incorporating immune cells into airway models to better capture infection dynamics.Sundaram et al. review how type VII secretion systems contribute to Mycobacterium tuberculosis pathogenesis and immune evasion, including interference with phagosome maturation and autophagy. Further understanding how these systems manipulate host anti-bacterial pathways may reveal new therapeutic targets to enhance host defense against tuberculosis.Mycobacterium tuberculosis disrupts host autophagy to evade immune clearance and persist within macrophages. They highlight the need for safer, more selective, hostdirected autophagy enhancers to complement current anti-bacterial therapies. They also emphasize the need to optimize the targeted delivery of autophagy activators and verify their efficacy and safety through systematic clinical studies.Li et al. review how poxviruses interact with host autophagy and the endo-lysosomal system, highlighting that these interactions vary across viral species and can either restrict or support infection. They also discuss how manipulating autophagy could help improve the effectiveness of oncolytic poxviruses for cancer therapy.Taken together, the contributions to this research topic highlight the complex and often opposing roles of autophagy in host defense and pathogen survival. From the manipulation of autophagic machinery by intracellular bacteria to the diverse interactions between viruses and host degradation pathways, these studies highlight the need to understand autophagy within the specific context of each infection. They also emphasize that successful therapeutic translation will require a clearer understanding of pathogen-specific mechanisms, cell-type-dependent responses, and the consequences of modulating autophagy in vivo. Ultimately, a deeper understanding of autophagy during infection may help bridge the gap between basic discoveries and the development of new treatments for infectious diseases.

Immune checkpoint inhibitor–induced inflammatory arthritis (ICI-IA) is an immune-related adverse event (irAE) following treatment with PD-1, PD-L1, or CTLA-4 inhibitors in patients with cancer. In this issue of the JCI , Ma and colleagues identified a subset of regulatory T cells (Tregs) that coexpress CD137 and IL-6 receptor (IL6R), termed atypical Tregs (AtpTregs), which are selectively enriched in patients with ICI-IA. Functionally, AtpTregs exhibited reduced suppressive capacity and a Th17-like proinflammatory phenotype. Notably, these cells were associated with more severe arthritis, yet improved cancer outcomes, suggesting a potential role in tumor control. The anti-IL6R therapy tocilizumab, administered as an off-label intervention for ICI-IA, reduced AtpTreg abundance and alleviated arthritis while maintaining antitumor immunity in a small cohort of patients with new-onset ICI-IA. Thus, anti-IL6R could be a targeted approach to manage ICI-IA and potentially other irAEs involving AtpTregs.

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.

Atherosclerosis underlies most coronary artery disease (CAD). It involves a significant autoimmune component against apolipoprotein B (APOB). In this study, we used short activation-induced marker (AIM) assays to characterize APOB-reactive CD4⁺ T cells in patients with angiographically verified CAD. APOB-reactive CD4⁺ T cells expressing CD25 and 4-1BB markers were the most abundant. Their frequency correlated positively with CAD severity. Transcriptomic analysis revealed that these cells were clonally expanded and significantly enriched in genes expressed in tissue-homing effector regulatory T (eT_reg) cells. They shared signatures with CD4⁺ T cells in mouse and human plaques, including expression of the plaque-homing chemokine receptor CXCR6. With increasing disease severity, the T_reg signature was progressively and significantly lost. Conversely, APOB-specific T_reg cells from patients with severe CAD gained glycolytic and interferon response signatures. We conclude that mild CAD is associated with a regulatory program in APOB-reactive CD4⁺ T cells, which is replaced by a pro-inflammatory program in patients with severe CAD.

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.

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.

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