Lyndsay Murrow

Autophagy as a Stress-Response and Quality-Control Mechanism: Implications for Cell Injury and Human Disease

Autophagy, a vital catabolic process that degrades cytoplasmic components within the lysosome, is an essential cytoprotective response to pathologic stresses that occur during diseases such as cancer, ischemia, and infection. In addition to its role as a stress-response pathway, autophagy plays an essential quality-control function in the cell by promoting basal turnover of long-lived proteins and organelles, as well as by selectively degrading damaged cellular components. This homeostatic function protects against a wide variety of diseases, including neurodegeneration, myopathy, liver disease, and diabetes. This review discusses our current understanding of these two principal functions of autophagy and describes in detail how alterations in autophagy promote human disease.

ATG12 conjugation to ATG3 regulates mitochondrial homeostasis and cell death.

ATG12, an ubiquitin-like modifier required for macroautophagy, has a single known conjugation target, another autophagy regulator called ATG5. Here, we identify ATG3 as a substrate for ATG12 conjugation. ATG3 is the E2-like enzyme necessary for ATG8/LC3 lipidation during autophagy. ATG12-ATG3 complex formation requires ATG7 as the E1 enzyme and ATG3 autocatalytic activity as the E2, resulting in the covalent linkage of ATG12 onto a single lysine on ATG3. Surprisingly, disrupting ATG12 conjugation to ATG3 does not affect starvation-induced autophagy. Rather, the lack of ATG12-ATG3 complex formation produces an expansion in mitochondrial mass and inhibits cell death mediated by mitochondrial pathways. Overall, these results unveil a role for ATG12-ATG3 in mitochondrial homeostasis and implicate the ATG12 conjugation system in cellular functions distinct from the early steps of autophagosome formation.

Imaging intracellular protein dynamics by spinning disk confocal microscopy.

The palette of fluorescent proteins (FPs) has grown exponentially over the past decade, and as a result, live imaging of cells expressing fluorescently tagged proteins is becoming more and more mainstream. Spinning disk confocal (SDC) microscopy is a high-speed optical sectioning technique and a method of choice to observe and analyze intracellular FP dynamics at high spatial and temporal resolution. In an SDC system, a rapidly rotating pinhole disk generates thousands of points of light that scan the specimen simultaneously, which allows direct capture of the confocal image with low-noise scientific grade-cooled charge-coupled device cameras, and can achieve frame rates of up to 1000 frames per second. In this chapter, we describe important components of a state-of-the-art spinning disk system optimized for live cell microscopy and provide a rationale for specific design choices. We also give guidelines of how other imaging techniques such as total internal reflection microscopy or spatially controlled photoactivation can be coupled with SDC imaging and provide a short protocol on how to generate cell lines stably expressing fluorescently tagged proteins by lentivirus-mediated transduction.

Dissecting the stem cell niche with organoid models: an engineering-based approach

ABSTRACT For many tissues, single resident stem cells grown in vitro under appropriate three-dimensional conditions can produce outgrowths known as organoids. These tissues recapitulate much of the cell composition and architecture of the in vivo organ from which they derive, including the formation of a stem cell niche. This has facilitated the systematic experimental manipulation and single-cell, high-throughput imaging of stem cells within their respective niches. Furthermore, emerging technologies now make it possible to engineer organoids from purified cellular and extracellular components to directly model and test stem cell-niche interactions. In this Review, we discuss how organoids have been used to identify and characterize stem cell-niche interactions and uncover new niche components, focusing on three adult-derived organoid systems. We also describe new approaches to reconstitute organoids from purified cellular components, and discuss how this technology can help to address fundamental questions about the adult stem cell niche. Summary: This Review article discusses how organoids have been used to model and characterize stem cell-niche interactions and how new engineering approaches enable systematic study of the stem cell niche.

ATG12–ATG3 connects basal autophagy and late endosome function

In addition to supporting cell survival in response to starvation or stress, autophagy promotes basal protein and organelle turnover. Compared to our understanding of stress-induced autophagy, little is known about how basal autophagy is regulated and how its activity is coordinated with other cellular processes. We recently identified a novel interaction between the ATG12–ATG3 conjugate and the ESCRT-associated protein PDCD6IP/Alix that promotes basal autophagy and endolysosomal trafficking. Moreover, ATG12–ATG3 is required for diverse PDCD6IP-mediated functions including late endosome distribution, exosome secretion, and viral budding. Our results highlight the importance of late endosomes for basal autophagic flux and reveal distinct roles for the core autophagy proteins ATG12 and ATG3 in controlling late endosome function.

MULTI-seq: Scalable sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

We describe MULTI-seq: A rapid, modular, and universal scRNA-seq sample multiplexing strategy using lipid-tagged indices. MULTI-seq reagents can barcode any cell type from any species with an accessible plasma membrane. The method is compatible with enzymatic tissue dissociation, and also preserves viability and endogenous gene expression patterns. We leverage these features to multiplex the analysis of multiple solid tissues comprising human and mouse cells isolated from patient-derived xenograft mouse models. We also utilize MULTI-seq’s modular design to perform a 96-plex perturbation experiment with human mammary epithelial cells. MULTI-seq also enables robust doublet identification, which improves data quality and increases scRNA-seq cell throughput by minimizing the negative effects of Poisson loading. We anticipate that the sample throughput and reagent savings enabled by MULTI-seq will expand the purview of scRNA-seq and democratize the application of these technologies within the scientific community.

Mapping the complex paracrine response to hormones in the human breast at single-cell resolution

The human breast undergoes lifelong remodeling in response to estrogen and progesterone, but hormone exposure also increases breast cancer risk. Here, we use single-cell analysis to identify distinct mechanisms through which breast composition and cell state affect hormone signaling. We show that prior pregnancy reduces the transcriptional response of hormone-responsive (HR+) epithelial cells, whereas high body mass index (BMI) reduces overall HR+ cell proportions. These distinct changes both impact neighboring cells by effectively reducing the magnitude of paracrine signals originating from HR+ cells. Because pregnancy and high BMI are known to protect against hormone-dependent breast cancer in premenopausal women, our findings directly link breast cancer risk with person-to-person heterogeneity in hormone responsiveness. More broadly, our findings illustrate how cell proportions and cell state can collectively impact cell communities through the action of cell-to-cell signaling networks.Summary Reproductive history and body weight are two important breast cancer risk factors. Prior pregnancy (parity) reduces lifetime risk by up to 50%, and obesity reduces premenopausal risk by up to 45%. Here, we use single-cell RNA sequencing to directly link these risk factors with tumor-protective changes in epithelial cell proportions and hormone signaling in the premenopausal breast. We show that parity reduces the proportion of transformation-susceptible luminal cells and increases the proportion of tumor-suppressive myoepithelial cells in the epithelium. Additionally, we identify two distinct mechanisms by which parity and obesity contribute to reduced hormone signaling. First, parity reduces the per-cell transcriptional response to ovarian hormones in hormone-responsive cells. Second, parity and obesity reduce the overall proportion of hormone-responsive cells. Both mechanisms lead to a decreased paracrine signaling response in myoepithelial cells. Together these findings provide mechanistic insight into how BMI and parity affect the mammary epithelial microenvironment to modify breast cancer susceptibility.

DoubletFinder: Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors

Single-cell RNA sequencing (scRNA-seq) using droplet microfluidics occasionally produces transcriptome data representing more than one cell. These technical artifacts are caused by cell doublets formed during cell capture and occur at a frequency proportional to the total number of sequenced cells. The presence of doublets can lead to spurious biological conclusions, which justifies the practice of sequencing fewer cells to limit doublet formation rates. Here, we present a computational doublet detection tool – DoubletFinder – that identifies doublets based solely on gene expression features. DoubletFinder infers the putative gene expression profile of real doublets by generating artificial doublets from existing scRNA-seq data. Neighborhood detection in gene expression space then identifies sequenced cells with increased probability of being doublets based on their proximity to artificial doublets. DoubletFinder robustly identifies doublets across scRNA-seq datasets with variable numbers of cells and sequencing depth, and predicts false-negative and false-positive doublets defined using conventional barcoding approaches. We anticipate that DoubletFinder will aid in scRNA-seq data analysis and will increase the throughput and accuracy of scRNA-seq experiments.

Atg12–Atg3 coordinates basal autophagy, endolysosomal trafficking and exosome release

ABSTRACT We recently identified an interaction between Atg12–Atg3, a complex between 2 core autophagy regulators, and the ESCRT-associated protein Pdcd6ip (programmed cell death 6 interacting protein, commonly known as Alix), which coordinately regulates basal autophagy, late endosome-to-lysosome trafficking, and exosome release. Because these processes all serve fundamental roles in cancer progression and therapy, Atg12-Atg3 may be an attractive anticancer target.