Following undergraduate research in chemical biology with Stuart Schreiber at Harvard, I did my graduate work at UCSF under the mentorship of Jonathan Weissman. At UCSF, I developed new technologies for quantitative, systematic genetic approaches in budding yeast. I then used functional genomics and biochemical approaches to define the role of Orm family proteins in a novel feedback pathway that matches cellular production of sphingolipids to metabolic demand.

My current focus as a post-doctoral fellow with Maxence Nachury is to understand the functions of the mammalian primary cilium. I first established an in vitro system for analysis of cilia in semi-permeabilized cells, using this approach to characterize a diffusion barrier that partitions the cilium from the cell body. More recently, I have developed and applied functional genomics approaches to dissect cilium-dependent signal transduction in the Hedgehog pathway. In particular, I have developed a CRISPR-based genome-scale screening platform for identification and functionally characterization of cellular factors needed cilium function and Hedgehog signaling.

Honors & Awards

  • Graduate Fellowship, The Hertz Foundation (2005-2010)
  • Graduate Research Fellowship, National Science Foundation (2005)
  • Connie & Bob Lurie Post-doctoral fellow, Damon Runyon Cancer Research Foundation (2011-2014)
  • Dale F. Frey Award for Breakthrough Scientists, Damon Runyon Cancer Research Foundation (2014-2016)
  • K99 Pathway to Independence Award, NIH (2014)

Professional Education

  • A.B, Harvard University, Biochemical Sciences (2004)

All Publications

  • Analysis of soluble protein entry into primary cilia using semipermeabilized cells. Methods in cell biology Breslow, D. K., Nachury, M. V. 2015; 127: 203-221


    The primary cilium is a protrusion from the cell surface that serves as a specialized compartment for signal transduction. Many signaling factors are known to be dynamically concentrated within cilia and to require cilia for their function. Yet protein entry into primary cilia remains poorly understood. To enable a mechanistic analysis of soluble protein entry into cilia, we developed a method for semipermeabilization of mammalian cells in which the plasma membrane is permeabilized while the ciliary membrane remains intact. Using semipermeabilized cells as the basis for an in vitro diffusion-to-capture assay, we uncovered a size-dependent diffusion barrier that restricts soluble protein exchange between the cytosol and the cilium. The manipulability of this in vitro system enabled an extensive characterization of the ciliary diffusion barrier and led us to show that the barrier is mechanistically distinct from those at the axon initial segment and the nuclear pore complex. Because semipermeabilized cells enable a range of experimental perturbations that would not be easily feasible in intact cells, we believe this methodology will provide a unique resource for investigating primary cilium function in development and disease.

    View details for DOI 10.1016/bs.mcb.2014.12.006

    View details for PubMedID 25837393

  • An in vitro assay for entry into cilia reveals unique properties of the soluble diffusion barrier JOURNAL OF CELL BIOLOGY Breslow, D. K., Koslover, E. F., Seydel, F., Spakowitz, A. J., Nachury, M. V. 2013; 203 (1): 129-147


    Specific proteins are concentrated within primary cilia, whereas others remain excluded. To understand the mechanistic basis of entry into cilia, we developed an in vitro assay using cells in which the plasma membrane was permeabilized, but the ciliary membrane was left intact. Using a diffusion-to-capture system and quantitative analysis, we find that proteins >9 nm in diameter (∼100 kD) are restricted from entering cilia, and we confirm these findings in vivo. Interference with the nuclear pore complex (NPC) or the actin cytoskeleton in permeabilized cells demonstrated that the ciliary diffusion barrier is mechanistically distinct from those of the NPC or the axon initial segment. Moreover, applying a mass transport model to this system revealed diffusion coefficients for soluble and membrane proteins within cilia that are compatible with rapid exploration of the ciliary space in the absence of active transport. Our results indicate that large proteins require active transport for entry into cilia but not necessarily for movement inside cilia.

    View details for DOI 10.1083/jcb.201212024

    View details for Web of Science ID 000325742200013

    View details for PubMedID 24100294

  • Single molecule imaging reveals a major role for diffusion in the exploration of ciliary space by signaling receptors. eLife Ye, F., Breslow, D. K., Koslover, E. F., Spakowitz, A. J., Nelson, W. J., Nachury, M. V. 2013; 2


    The dynamic organization of signaling cascades inside primary cilia is key to signal propagation. Yet little is known about the dynamics of ciliary membrane proteins besides a possible role for motor-driven Intraflagellar Transport (IFT). To characterize these dynamics, we imaged single molecules of Somatostatin Receptor 3 (SSTR3, a GPCR) and Smoothened (Smo, a Hedgehog signal transducer) in the ciliary membrane. While IFT trains moved processively from one end of the cilium to the other, single SSTR3 and Smo underwent mostly diffusive behavior interspersed with short periods of directional movements. Statistical subtraction of instant velocities revealed that SSTR3 and Smo spent less than a third of their time undergoing active transport. Finally, SSTR3 and IFT movements could be uncoupled by perturbing either membrane protein diffusion or active transport. Thus ciliary membrane proteins move predominantly by diffusion, and attachment to IFT trains is transient and stochastic rather than processive or spatially determined. DOI:

    View details for DOI 10.7554/eLife.00654

    View details for PubMedID 23930224

  • Orm family proteins mediate sphingolipid homeostasis NATURE Breslow, D. K., Collins, S. R., Bodenmiller, B., Aebersold, R., Simons, K., Shevchenko, A., Ejsing, C. S., Weissman, J. S. 2010; 463 (7284): 1048-U65


    Despite the essential roles of sphingolipids both as structural components of membranes and critical signalling molecules, we have a limited understanding of how cells sense and regulate their levels. Here we reveal the function in sphingolipid metabolism of the ORM genes (known as ORMDL genes in humans)-a conserved gene family that includes ORMDL3, which has recently been identified as a potential risk factor for childhood asthma. Starting from an unbiased functional genomic approach in Saccharomyces cerevisiae, we identify Orm proteins as negative regulators of sphingolipid synthesis that form a conserved complex with serine palmitoyltransferase, the first and rate-limiting enzyme in sphingolipid production. We also define a regulatory pathway in which phosphorylation of Orm proteins relieves their inhibitory activity when sphingolipid production is disrupted. Changes in ORM gene expression or mutations to their phosphorylation sites cause dysregulation of sphingolipid metabolism. Our work identifies the Orm proteins as critical mediators of sphingolipid homeostasis and raises the possibility that sphingolipid misregulation contributes to the development of childhood asthma.

    View details for DOI 10.1038/nature08787

    View details for Web of Science ID 000275108400029

    View details for PubMedID 20182505

  • A comprehensive strategy enabling high-resolution functional analysis of the yeast genome NATURE METHODS Breslow, D. K., Cameron, D. M., Collins, S. R., Schuldiner, M., Stewart-Ornstein, J., Newman, H. W., Braun, S., Madhani, H. D., Krogan, N. J., Weissman, J. S. 2008; 5 (8): 711-718


    Functional genomic studies in Saccharomyces cerevisiae have contributed enormously to our understanding of cellular processes. Their full potential, however, has been hampered by the limited availability of reagents to systematically study essential genes and the inability to quantify the small effects of most gene deletions on growth. Here we describe the construction of a library of hypomorphic alleles of essential genes and a high-throughput growth competition assay to measure fitness with unprecedented sensitivity. These tools dramatically increase the breadth and precision with which quantitative genetic analysis can be performed in yeast. We illustrate the value of these approaches by using genetic interactions to reveal new relationships between chromatin-modifying factors and to create a functional map of the proteasome. Finally, by measuring the fitness of strains in the yeast deletion library, we addressed an enigma regarding the apparent prevalence of gene dispensability and found that most genes do contribute to growth.

    View details for DOI 10.1038/nmeth.1234

    View details for Web of Science ID 000258077400015

    View details for PubMedID 18622397

  • The intraflagellar transport protein IFT27 promotes BBSome exit from cilia through the GTPase ARL6/BBS3. Developmental cell Liew, G. M., Ye, F., Nager, A. R., Murphy, J. P., Lee, J. S., Aguiar, M., Breslow, D. K., Gygi, S. P., Nachury, M. V. 2014; 31 (3): 265-278


    The sorting of signaling receptors into and out of cilia relies on the BBSome, a complex of Bardet-Biedl syndrome (BBS) proteins, and on the intraflagellar transport (IFT) machinery. GTP loading onto the Arf-like GTPase ARL6/BBS3 drives assembly of a membrane-apposed BBSome coat that promotes cargo entry into cilia, yet how and where ARL6 is activated remains elusive. Here, we show that the Rab-like GTPase IFT27/RABL4, a known component of IFT complex B, promotes the exit of BBSome and associated cargoes from cilia. Unbiased proteomics and biochemical reconstitution assays show that, upon disengagement from the rest of IFT-B, IFT27 directly interacts with the nucleotide-free form of ARL6. Furthermore, IFT27 prevents aggregation of nucleotide-free ARL6 in solution. Thus, we propose that IFT27 separates from IFT-B inside cilia to promote ARL6 activation, BBSome coat assembly, and subsequent ciliary exit, mirroring the process by which BBSome mediates cargo entry into cilia.

    View details for DOI 10.1016/j.devcel.2014.09.004

    View details for PubMedID 25443296

  • Sphingolipid Homeostasis in the Endoplasmic Reticulum and Beyond COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY Breslow, D. K. 2013; 5 (4)


    Sphingolipids are a diverse group of lipids that have essential cellular roles as structural components of membranes and as potent signaling molecules. In recent years, a detailed picture has emerged of the basic biochemistry of sphingolipids-from their initial synthesis in the endoplasmic reticulum (ER), to their elaboration into complex glycosphingolipids, to their turnover and degradation. However, our understanding of how sphingolipid metabolism is regulated in response to metabolic demand and physiologic cues remains incomplete. Here I discuss new insights into the mechanisms that ensure sphingolipid homeostasis, with an emphasis on the ER as a critical regulatory site in sphingolipid metabolism. In particular, Orm family proteins have recently emerged as key ER-localized mediators of sphingolipid homeostasis. A detailed understanding of how cells sense and control sphingolipid production promises to provide key insights into membrane function in health and disease.

    View details for DOI 10.1101/cshperspect.a013326

    View details for Web of Science ID 000317175200004

    View details for PubMedID 23545423

  • Protein kinase Ypk1 phosphorylates regulatory proteins Orm1 and Orm2 to control sphingolipid homeostasis in Saccharomyces cerevisiae PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Roelants, F. M., Breslow, D. K., Muir, A., Weissman, J. S., Thorner, J. 2011; 108 (48): 19222-19227


    The Orm family proteins are conserved integral membrane proteins of the endoplasmic reticulum that are key homeostatic regulators of sphingolipid biosynthesis. Orm proteins bind to and inhibit serine:palmitoyl-coenzyme A transferase, the first enzyme in sphingolipid biosynthesis. In Saccharomyces cerevisiae, Orm1 and Orm2 are inactivated by phosphorylation in response to compromised sphingolipid synthesis (e.g., upon addition of inhibitor myriocin), thereby restoring sphingolipid production. We show here that protein kinase Ypk1, one of an essential pair of protein kinases, is responsible for this regulatory modification. Myriocin-induced hyperphosphorylation of Orm1 and Orm2 does not occur in ypk1 cells, and immunopurified Ypk1 phosphorylates Orm1 and Orm2 robustly in vitro exclusively on three residues that are known myriocin-induced sites. Furthermore, the temperature-sensitive growth of ypk1(ts) ypk2 cells is substantially ameliorated by deletion of ORM genes, confirming that a primary physiological role of Ypk1-mediated phosphorylation is to negatively regulate Orm function. Ypk1 immunoprecipitated from myriocin-treated cells displays a higher specific activity for Orm phosphorylation than Ypk1 from untreated cells. To identify the mechanism underlying Ypk1 activation, we systematically tested several candidate factors and found that the target of rapamycin complex 2 (TORC2) kinase plays a key role. In agreement with prior evidence that a TORC2-dependent site in Ypk1(T662) is necessary for cells to exhibit a wild-type level of myriocin resistance, a Ypk1(T662A) mutant displays only weak Orm phosphorylation in vivo and only weak activation in vitro in response to sphingolipid depletion. Additionally, sphingolipid depletion increases phosphorylation of Ypk1 at T662. Thus, Ypk1 is both a sensor and effector of sphingolipid level, and reduction in sphingolipids stimulates Ypk1, at least in part, via TORC2-dependent phosphorylation.

    View details for DOI 10.1073/pnas.1116948108

    View details for Web of Science ID 000297463100031

    View details for PubMedID 22080611

  • A Novel Protein LZTFL1 Regulates Ciliary Trafficking of the BBSome and Smoothened PLOS GENETICS Seo, S., Zhang, Q., Bugge, K., Breslow, D. K., Searby, C. C., Nachury, M. V., Sheffield, V. C. 2011; 7 (11)


    Many signaling proteins including G protein-coupled receptors localize to primary cilia, regulating cellular processes including differentiation, proliferation, organogenesis, and tumorigenesis. Bardet-Biedl Syndrome (BBS) proteins are involved in maintaining ciliary function by mediating protein trafficking to the cilia. However, the mechanisms governing ciliary trafficking by BBS proteins are not well understood. Here, we show that a novel protein, Leucine-zipper transcription factor-like 1 (LZTFL1), interacts with a BBS protein complex known as the BBSome and regulates ciliary trafficking of this complex. We also show that all BBSome subunits and BBS3 (also known as ARL6) are required for BBSome ciliary entry and that reduction of LZTFL1 restores BBSome trafficking to cilia in BBS3 and BBS5 depleted cells. Finally, we found that BBS proteins and LZTFL1 regulate ciliary trafficking of hedgehog signal transducer, Smoothened. Our findings suggest that LZTFL1 is an important regulator of BBSome ciliary trafficking and hedgehog signaling.

    View details for DOI 10.1371/journal.pgen.1002358

    View details for Web of Science ID 000297264500013

    View details for PubMedID 22072986

  • Primary Cilia: How to Keep the Riff-Raff in the Plasma Membrane CURRENT BIOLOGY Breslow, D. K., Nachury, M. V. 2011; 21 (11): R434-R436


    A recent report suggests that plasma membrane proteins are excluded from primary cilia via anchoring to the cortical actin cytoskeleton. These findings challenge the existence of a diffusion barrier at the base of the cilium.

    View details for DOI 10.1016/j.cub.2011.04.039

    View details for Web of Science ID 000291668100011

    View details for PubMedID 21640903

  • Membranes in Balance: Mechanisms of Sphingolipid Homeostasis MOLECULAR CELL Breslow, D. K., Weissman, J. S. 2010; 40 (2): 267-279


    Sphingolipids and their metabolites play key cellular roles both as structural components of membranes and as signaling molecules that mediate responses to physiologic cues and stresses. Despite progress during the last two decades in defining the enzymatic machinery responsible for synthesizing and degrading sphingolipids, comparatively little is known about how these enzymes are regulated to ensure sphingolipid homeostasis. Here, we review new insights into how cells sense and control sphingolipid biosynthesis and transport. We also discuss emerging evidence that sphingolipid metabolism is closely coordinated with that of sterols and glycerolipids and with other processes that occur in the secretory pathway. An improved understanding of sphingolipid homeostasis promises to shed light on basic processes in cell biology and disease, including how cells establish and maintain the complex membrane composition and architecture that is a defining feature of eukaryotic cell biology.

    View details for DOI 10.1016/j.molcel.2010.10.005

    View details for Web of Science ID 000284028100009

    View details for PubMedID 20965421

  • Single-cell proteomic analysis of S-cerevisiae reveals the architecture of biological noise NATURE Newman, J. R., Ghaemmaghami, S., Ihmels, J., Breslow, D. K., Noble, M., DeRisi, J. L., Weissman, J. S. 2006; 441 (7095): 840-846


    A major goal of biology is to provide a quantitative description of cellular behaviour. This task, however, has been hampered by the difficulty in measuring protein abundances and their variation. Here we present a strategy that pairs high-throughput flow cytometry and a library of GFP-tagged yeast strains to monitor rapidly and precisely protein levels at single-cell resolution. Bulk protein abundance measurements of >2,500 proteins in rich and minimal media provide a detailed view of the cellular response to these conditions, and capture many changes not observed by DNA microarray analyses. Our single-cell data argue that noise in protein expression is dominated by the stochastic production/destruction of messenger RNAs. Beyond this global trend, there are dramatic protein-specific differences in noise that are strongly correlated with a protein's mode of transcription and its function. For example, proteins that respond to environmental changes are noisy whereas those involved in protein synthesis are quiet. Thus, these studies reveal a remarkable structure to biological noise and suggest that protein noise levels have been selected to reflect the costs and potential benefits of this variation.

    View details for DOI 10.1038/nature04785

    View details for Web of Science ID 000238254100035

    View details for PubMedID 16699522