Susan Lindquist

Whitehead Institute for Biomedical Research · Department of Biology

In neurodegenerative proteinopathies, intracellular inclusions are histopathologically and ultrastructurally heterogeneous but the significance of this heterogeneity is unclear. Patient- derived iPSC models, while promising for disease modeling, do not form analogous inclusions in a reasonable timeframe and suffer from limited tractability and scal...

Alpha-synuclein (αS) is a conformationally plastic protein that reversibly binds to cellular membranes. It aggregates and is genetically linked to Parkinson's disease (PD). Here, we show that αS directly modulates processing bodies (P-bodies), membraneless organelles that function in mRNA turnover and storage. The N terminus of αS, but not other sy...

Heat shock factor 1 (HSF1) is well known for its role in the heat shock response (HSR), where it drives a transcriptional program comprising heat shock protein (HSP) genes, and in tumorigenesis, where it drives a program comprising HSPs and many noncanonical target genes that support malignancy. Here, we find that HSF2, an HSF1 paralog with no subs...

Eukaryotic initiation factor 4A (eIF4A), the enzymatic core of the eIF4F complex essential for translation initiation, plays a key role in the oncogenic reprogramming of protein synthesis, and thus is a putative therapeutic target in cancer. As important component of its anticancer activity, inhibition of translation initiation can alleviate oncoge...

The E4 allele of the apolipoprotein E gene ( APOE ) has been established as a genetic risk factor for many diseases including cardiovascular diseases and Alzheimer’s disease (AD), yet its mechanism of action remains poorly understood. APOE is a lipid transport protein, and the dysregulation of lipids has recently emerged as a key feature of several...

The ε4 allele of apolipoprotein E (APOE4) is a genetic risk factor for many diseases, including late-onset Alzheimer's disease (AD). We investigate the cellular consequences of APOE4 in human iPSC-derived astrocytes, observing an endocytic defect in APOE4 astrocytes compared with their isogenic APOE3 counterparts. Given the evolutionarily conserved...

The heat shock protein 90 (Hsp90) chaperone functions as a protein-folding buffer and plays a role promoting the evolution of new heritable traits. To better understand how Hsp90 can affect mRNA translation, we screen more than 1,600 factors involved in mRNA regulation for physical interactions with Hsp90 in human cells. The mRNA binding protein CP...

The mechanisms by which cells adapt to proteotoxic stress are largely unknown, but are key to understanding how tumor cells, particularly in vivo, are largely resistant to proteasome inhibitors. Analysis of cancer cell lines, mouse xenografts and patient-derived tumor samples all showed an association between mitochondrial metabolism and proteasome...

An amendment to this paper has been published and can be accessed via a link at the top of the paper

Purpose: Despite the accumulation of extensive genomic alterations, many cancers fail to be recognized as “foreign” and escape destruction by the host immune system. Immunotherapies designed to address this problem by directly stimulating immune effector cells have led to some remarkable clinical outcomes, but unfortunately, most cancers fail to re...

New strategies are needed to counter the escalating threat posed by drug-resistant fungi. The molecular chaperone Hsp90 affords a promising target because it supports survival, virulence and drug-resistance across diverse pathogens. Inhibitors of human Hsp90 under development as anticancer therapeutics, however, exert host toxicities that preclude...

In Parkinson's disease (PD), α-synuclein (αS) pathologically impacts the brain, a highly lipid-rich organ. We investigated how alterations in αS or lipid/fatty acid homeostasis affect each other. Lipidomic profiling of human αS-expressing yeast revealed increases in oleic acid (OA, 18:1), diglycerides, and triglycerides. These findings were recapit...

The heat shock protein 90 (Hsp90) chaperone functions as a protein-folding buffer and plays a unique role promoting the evolution of new heritable traits. To investigate the role of Hsp90 in modulating protein synthesis, we screened more than 1600 proteins involved in mRNA regulation for physical interactions with Hsp90 in human cells. Among the to...

The mechanisms used by cancer cells to resist the severe disruption in protein homeostasis caused by proteasome inhibitors remain obscure. Here, we show this resistance correlates with a metabolic shift from glycolysis to oxidative phosphorylation (OXPHOS). Employing small molecule screens, we identified a striking overlap between compounds that pr...

Tyrosine phosphorylation is a key biochemical signal that controls growth and differentiation in multicellular organisms. Saccharomyces cerevisiae and nearly all other unicellular eukaryotes lack intact phosphotyrosine signaling pathways. However, many of these organisms have primitive phosphotyrosine-binding proteins and tyrosine phosphatases, lea...

Aggregates of human islet amyloid polypeptide (IAPP) in the pancreas of patients with type 2 diabetes (T2D) are thought to contribute to β cell dysfunction and death. To understand how IAPP harms cells and how this might be overcome, we created a yeast model of IAPP toxicity. Ste24, an evolutionarily conserved protease that was recently reported to...

The development of effective antifungal therapeutics remains a formidable challenge because of the close evolutionary relationship between humans and fungi. Mitochondrial function may present an exploitable vulnerability because of its differential utilization in fungi and its pivotal roles in fungal morphogenesis, virulence, and drug resistance al...

Significance Calcineurin is an essential Ca ²⁺ -dependent phosphatase in all eukaryotes. Whether calcineurin can be endogenously regulated by factors other than Ca ²⁺ and calmodulin is not known. Using a model of Parkinson's Disease (PD) as a surrogate for high pathophysiological calcineurin activity and employing a shotgun proteomic approach, we s...

Author summary Microbial species do not have control over their environment. In order to survive changes (for example, in temperature, pressure, humidity, or nutrient levels), microbes must either migrate to more habitable locations or adapt to better tolerate the changing environment. Such adaptation is typically thought to come about through chan...

FLO8-dependent migratory benefits of [SWI+] cells. (A) Comparison of migration of [SWI+] and [swi−] cells lacking a functional FLO8 gene, which is required for the expression of Flo1 and Flo11 [12]. (B) Fraction of the total liquid culture (notched bars) or supernatant only (plain bars) that is [SWI+] after 16 hours of growth in YPD or YPD + 5% eth...

[SWI+] pioneers are less fit than [swi−] settler cells. (A) Growth comparison of [swi−] cells (blue) and [SWI+] cells (red) in standard growth media supplemented with glucose, or B) raffinose. Cell density was measured by absorbance at 600 nm every 15 minutes. Numerical data is available from the Dryad Digital Repository: http://dx.doi.org/10.5061/...

Yeast strains used in this study. Each yeast strain used in the study is listed along with its Swi1 prion status, transformed plasmids, and genotype. (XLSX)

Experimental procedure for out-cross ratio measurement. [SWI+] and [swi−] diploid strains were sporulated. Each had the genotype HO+/ho−, where the ho locus was marked with a cassette expressing the green fluorescent protein NeonGreen. A large pool of these spores was diluted into mixed culture with a ho−, selectable, haploid tester strain. After a...

Protein aggregation is a hallmark of many diseases but also underlies a wide range of positive cellular functions. This phenomenon has been difficult to study because of a lack of quantitative and high-throughput cellular tools. Here, we develop a synthetic genetic tool to sense and control protein aggregation. We apply the technology to yeast prio...

α-Synuclein (αS) forms round cytoplasmic inclusions in Parkinson's disease (PD) and dementia with Lewy bodies (DLB). Evidence suggests a physiological function of αS in vesicle trafficking and release. In contrast to earlier tenets, recent work indicates that αS normally exists in cells in a dynamic equilibrium between monomers and tetramers/multim...

The lack of therapies for neurodegenerative diseases arises from our incomplete understanding of their underlying cellular toxicities and the limited number of predictive model systems. It is critical that we develop approaches to identify novel targets and lead compounds. Here, a phenotypic screen of yeast proteinopathy models identified dihydropy...

Significance Self-propagating changes in the conformation of amyloidogenic proteins play vital roles in normal biology and disease. Despite intense research, the architecture of amyloid fibers remains poorly understood. In this work, we used both segmental and specific isotopic labeling schemes in combination with dynamic nuclear polarization (DNP)...

HSP90 acts as a protein-folding buffer that shapes the manifestations of genetic variation in model organisms. Whether HSP90 influences the consequences of mutations in humans, potentially modifying the clinical course of genetic diseases, remains unknown. By mining data for >1,500 disease-causing mutants, we found a strong correlation between redu...

Numerous genes and molecular pathways are implicated in neurodegenerative proteinopathies, but their inter-relationships are poorly understood. We systematically mapped molecular pathways underlying the toxicity of alpha-synuclein (α-syn), a protein central to Parkinson’s disease. Genome-wide screens in yeast identified 332 genes that impact α-syn...

Synucleinopathies, including Parkinson’s disease (PD), are associated with the misfolding and mistrafficking of alpha-synuclein (α-syn). Here, using an ascorbate peroxidase (APEX)-based labeling method combined with mass spectrometry, we defined a network of proteins in the immediate vicinity of α-syn in living neurons to shed light on α-syn functi...

The proteasome is a central regulator of protein homeostasis in all eukaryotes. Targeted pharmaceutical inhibition of the proteasome complex has been implemented as a successful therapeutic strategy to treat several cancers including multiple myeloma. Unfortunately, many of the cancers show intrinsic resistance to proteasome inhibitors, and those t...

Significance In previous work, we used genome-wide screening to uncover a counterintuitive mechanism by which cells can acquire resistance to inhibitors of the proteasome’s catalytic core through experimentally induced imbalances in the composition of its regulatory particle. However, in many cases, mechanisms uncovered in vitro for acquired resist...

Prions are a paradigm-shifting mechanism of inheritance in which phenotypes are encoded by self-templating protein conformations rather than nucleic acids. Here, we examine the breadth of protein-based inheritance across the yeast proteome by assessing the ability of nearly every open reading frame (ORF; ∼5,300 ORFs) to induce heritable traits. Tra...

To cause disease, a microbial pathogen must adapt to the challenges of its host environment. The leading fungal pathogen Candida albicans colonizes nutrient-poor bodily niches, withstands attack from the immune system, and tolerates treatment with azole antifungals, often evolving resistance. To discover agents that block these adaptive strategies,...

Significance Prion proteins provide the best-understood mode for protein-based molecular memory. Since their discovery in mammals, prions have been identified in diverse organisms including fungi, Aplysia , and Drosophila , but not in the plant kingdom. Applying methods we used to uncover yeast prions, we identified nearly 500 Arabidopsis proteins...

In cellular systems, biophysical interactions between macromolecules underlie a complex web of functional interactions. How biophysical and functional networks are coordinated, whether all biophysical interactions correspond to functional interactions, and how such biophysical-versus-functional network coordination is shaped by evolutionary forces...

Heat shock factor 1 (HSF1) is best known as a key sensor of proteotoxic stress, but accumulating evidence also supports a major role for this transcriptional regulator in cancer biology. In a variety of human solid tumor cells, downregulation of HSF1 inhibits growth, induces cell death and limits metastatic potential. In breast cancers, nuclear acc...

Biological processes occur in complex environments containing a myriad of potential interactors. Unfortunately, limitations on the sensitivity of biophysical techniques normally restrict structural investigations to purified systems, at concentrations that are orders of magnitude above endogenous levels. Dynamic nuclear polarization (DNP) can drama...

KBM7 screening hits for MG132 and bortezomib, insertions and p-values. DOI: http://dx.doi.org/10.7554/eLife.08467.016

RNA-seq analysis. DOI: http://dx.doi.org/10.7554/eLife.08467.018

Validation reagents: lentivirus clones, selected shRNAs, antibodies. DOI: http://dx.doi.org/10.7554/eLife.08467.017

Genomics of drug sensitivity in cancer analysis. DOI: http://dx.doi.org/10.7554/eLife.08467.019

The delivery of diagnostic and therapeutic agents to solid tumors is limited by physical transport barriers within tumors, and such restrictions directly contribute to decreased therapeutic efficacy and the emergence of drug resistance. Nanomaterials designed to perturb the local tumor environment with precise spatiotemporal control have demonstrat...

Drugs that act more promiscuously provide fewer routes for the emergence of resistant mutants. This benefit, however, often comes at the cost of serious off-target and dose-limiting toxicities. The classic example is the antifungal amphotericin B (AmB), which has evaded resistance for more than half a century. We report markedly less toxic amphoter...

The emergence of drug resistance is a major limitation of current antimalarials. The discovery of new druggable targets and pathways including those that are critical for multiple life cycle stages of the malaria parasite is a major goal for developing next-generation antimalarial drugs. Using an integrated chemogenomics approach that combined drug...

In the absence of a single preventive or disease-modifying strategy, neurodegenerative diseases are becoming increasingly prevalent in our ageing population. The mechanisms underlying neurodegeneration are poorly understood, making the target-based drug screening strategies that are employed by the pharmaceutical industry fraught with difficulty. H...

Disclosed are genes that, when overexpressed in cells expressing alpha-synuclein, either suppress or enhance alpha-synuclein mediated cellular toxicity. Compounds that modulate expression of these genes or activity of the encoded proteins can be used to inhibit alpha-synuclein mediated toxicity and used to treat or prevent synucleinopathies such as...

How disease-associated mutations impair protein activities in the context of biological networks remains mostly undetermined. Although a few renowned alleles are well characterized, functional information is missing for over 100,000 disease-associated variants. Here we functionally profile several thousand missense mutations across a spectrum of Me...

The ribosome is centrally situated to sense metabolic states, but whether its activity, in turn, coherently rewires transcriptional responses is unknown. Here, through integrated chemical-genetic analyses, we found that a dominant transcriptional effect of blocking protein translation in cancer cells was inactivation of heat shock factor 1 (HSF1),...

Steadily increasing antifungal drug resistance and persistent high rates of fungal-associated mortality highlight the dire need for the development of novel antifungals. Characterization of inhibitors of one enzyme in the GPI anchor pathway, Gwt1, has generated interest in the exploration of targets in this pathway for further study. Utilizing a ch...

Significance Although hormonal therapies for estrogen receptor-positive (ER+) breast cancer make up the earliest, and arguably most effective, “molecularly targeted” anticancer drugs, continued progress in controlling metastatic disease has been slow. Heterogeneity and the complexity of signaling in advanced cancers have frustrated efforts to preve...

Significance Amyloids, which are protein fiber aggregates, are often associated with neurodegenerative diseases such as Alzheimer’s, but they can also be beneficial, as in yeasts, where they help cells adapt to environmental changes. Intriguingly, the same protein has the ability to aggregate into different fiber forms, known as strains, that gener...

The disheartening results of recent clinical trials for neurodegenerative disease (ND) therapeutics underscore the need for a more comprehensive understanding of the underlying disease biology before effective therapies can be devised. One hallmark of many NDs is a disruption in protein homeostasis. Therefore, investigating the role of protein home...

No disease-modifying therapies are available for synucleinopathies, including Parkinson's disease (PD), dementia with Lewy bodies (DLB), and multiple systems atrophy (MSA). The lack of therapies has been impeded by a paucity of validated drug targets and problematic cell-based model systems. New approaches are therefore needed to identify genes and...

Jarosz and Lancaster are co-first authors [ GAR ⁺] is a protein-based element of inheritance that allows yeast ( Saccharomyces cerevisiae ) to circumvent a hallmark of their biology: extreme metabolic specialization for glucose fermentation. When glucose is present, yeast will not use other carbon sources. [ GAR ⁺] allows cel...

In experimental science, organisms are usually studied in isolation, but in the wild, they compete and cooperate in complex communities. We report a system for cross-kingdom communication by which bacteria heritably transform yeast metabolism. An ancient biological circuit blocks yeast from using other carbon sources in the presence of glucose. [ G...

Significance Ca ²⁺ homeostasis is indispensable for the well being of all living organisms. Ca ²⁺ homeostasis is disrupted by α-synuclein (α-syn), whose misfolding plays a major role in neurodegenerative diseases termed synucleinopathies, such as Parkinson disease. We report that α-syn can induce sustained and highly elevated levels of cytoplasmic...

Significance Expansion of polyglutamine tracts in at least nine proteins causes neurodegeneration. Although the pathology caused by each protein is different, there must be common features of the polyglutamine expansion that contribute to toxicity. We modeled polyglutamine toxicity in yeast by expressing a 103-glutamine expanded fragment of hunting...

Stromal cells within the tumor microenvironment are essential for tumor progression and metastasis. Surprisingly little is known about the factors that drive the transcriptional reprogramming of stromal cells within tumors. We report that the transcriptional regulator heat shock factor 1 (HSF1) is frequently activated in cancer-associated fibroblas...

Chaperones are abundant cellular proteins that promote the folding and function of their substrate proteins (clients). In vivo, chaperones also associate with a large and diverse set of cofactors (cochaperones) that regulate their specificity and function. However, how these cochaperones regulate protein folding and whether they have chaperone-inde...

During heat shock and other proteotoxic stresses, cells regulate multiple steps in gene expression in order to globally repress protein synthesis and selectively upregulate stress response proteins. Splicing of several mRNAs is known to be inhibited during heat stress, often meditated by SRp38, but the extent and specificity of this effect have rem...

Prions are self-templating protein aggregates that stably perpetuate distinct biological states and are of keen interest to researchers in both evolutionary and biomedical science. The best understood prions are from yeast and have a prion-forming domain with strongly biased amino acid composition, most notably enriched for Q or N. PLAAC is a web a...

Cell signaling, one of key processes in both normal cellular function and disease, is coordinated by numerous interactions between membrane proteins that change in response to stimuli. We present a split ubiquitin-based method for detection of integral membrane protein-protein interactions (PPIs) in human cells, termed mammalian-membrane two-hybrid...

To understand the relationship of structure to the remarkably diverse bioactivities reported for withanolides, we obtained withaferin A (WA; 1) and 36 analogues (2-37), and compared their cytotoxicity to cytoprotective heat shock-inducing activity (HSA). Analyzing structure-activity relationships for the series, we found that the ring A enone is es...

Significance Identifying disease-modifying therapies for Alzheimer’s disease (AD) has been an insurmountable challenge. To provide a new discovery tool for high-throughput compound screening, we used a simple yeast model that makes toxic amounts of β-amyloid (Aβ), a peptide central to AD pathology. Previous genetic analysis established that Aβ comp...

Significance The small, lipid-binding protein, α-synuclein (α-syn), is associated with neurodegenerative diseases. α-Syn exists in various splice isoforms, and isoform expression varies with disease, but how these isoforms affect protein function is unknown. Using a yeast model expressing α-syn splice variants, we show that inhibition of sterol syn...

Yeast prions are self-templating protein-based mechanisms of inheritance whose conformational changes lead to the acquisition of diverse new phenotypes. The best studied of these is the prion domain (NM) of Sup35, which forms an amyloid that can adopt several distinct conformations (strains) that produce distinct phenotypes. Using magic-angle spinn...

For a protein to function appropriately, it must first achieve its proper conformation and location within the crowded environment inside the cell. Multiple chaperone systems are required to fold proteins correctly. In addition, degradation pathways participate by destroying improperly folded proteins. The intricacy of this multisystem process prov...