In fall 2016, ASCB awarded ASCB-Gibco Emerging Leader Prizes to three cell biology researchers. ASCB introduced the prizes to honor not-yet-tenured independent investigators with outstanding scientific accomplishments and strong publication track records. The prizes were underwritten by Gibco, a brand of Thermo Fisher Scientific.
Peter Walter, 2016 ASCB President, invited each of the prize winners and each of the seven additional finalists to contribute an essay to the ASCB Newsletter. The writers were encouraged to provide a personal statement that articulates who they are, their science, and how they got into it; to describe their major scientific accomplishments; and to discuss their “dream results” and where they see themselves in the next five years.
This issue of the Newsletter features the essays of finalists Simon Alberti and Anthony Leung.
I am a research group leader at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden, Germany. My work focuses on elucidating the molecular logic of biological phase separation to understand stress adaptation and disease. I am a biologist by training and did my postdoctoral work with Susan Lindquist at the Whitehead Institute for Biomedical Research (Cambridge, USA). During my postdoc, I became fascinated with prions, proteins that adopt heritable amyloid-like conformations. I performed a proteome-wide screen in budding yeast and identified several new prions that generate heritable phenotypic diversity. Moreover, I found that the information for prion behavior is encoded in so-called prion domains, which are unusual low-complexity sequences composed of mostly polar amino acids.
In 2010 I joined the MPI-CBG to initiate my career as an independent scientist and continue my work on prion-like proteins. The goal of my lab is to understand how cells use prion-like proteins to adapt to stress and environmental perturbations. Stressed cells undergo changes on multiple levels to alter their physiology, metabolism, and architecture. Our work shows that many of these changes involve a reorganization of the cytoplasm mediated by prion-like proteins. One of our key discoveries was that prion-like proteins not only adopt heritable conformations, but can also assemble into structures with different physical properties such as liquids, gels, or glasses. We found that assembly into these different states of matter is mediated by a physical process known as demixing phase separation. Importantly, protein-mediated phase separation endows cells with spatiotemporal control over biochemical processes and the ability to form membrane-less compartments. This challenges an established paradigm in cell biology, which posits that compartmentalization requires membranes.
Together with Tony Hyman my lab and I recently made the important discovery that the initially beneficial ability to form membrane-less compartments through phase separation can lead to the formation of aberrant structures that are associated with pathology in age-related neurodegenerative disorders. Thus we propose a new model for age-related neurodegenerative diseases, such as amyotrophic lateral sclerosis, where the physiological function of prion-like proteins as compartment formers is linked to their role in disease. In the future, my lab will continue to study the link between membrane-less compartments and aging and disease. Most importantly, we aim to identify drugs that modulate the phase behavior of disease-causing proteins, which could be used as potential therapeutics to treat several devastating age-related diseases.
In another line of future research, we aim to understand how organisms use phase separation to adapt to stress. We recently discovered that stress induces an adaptive acidification of the budding yeast cytosol and widespread pH-driven macromolecular assembly by phase separation. Prion-like proteins are the key players in this process that sense changes in pH and then assemble into fibrillar structures, gels, or glasses. Importantly, assembly formation inhibits the activity of these proteins, and the assembled proteins can be reactivated when the cells resume growth, thus ensuring swift recovery from stress. Our primary goal in the next five years will be to elucidate the molecular logic and biology of stress-driven phase separation. Ultimately, we hope to be able to reconstruct the evolutionary history of biological phase separation by studying the sequence diversity of phase-separating proteins and their interactions with different stressful environments.
Anthony K. L. Leung
“You are a visual person,” remarked Phil Sharp, my postdoc mentor at the Massachusetts Institute of Technology (MIT), during one of our one-to-one meetings. Yes—to me, seeing is believing! Oftentimes, data open my eyes to scientific worlds that I never expected to see.
I have been fascinated by the polynucleotide RNA since my college years at Oxford and I always wanted to see how the RNA world works. My interest has led me to one RNA granule after another—nucleolus, splicing speckles, paraspeckles, Cajal bodies, P-bodies, and stress granules.
During my PhD training with Angus Lamond at the University of Dundee, I was part of the team uncovering the proteome of the nucleolus by mass spectrometry. Through characterizing novel components of the nucleolus, I discovered a nucleolar targeting pathway transiting via splicing speckles. With the guidance of Jan Ellenberg during two summers at EMBL Heidelberg, I tracked down how subcompartments of the nucleolus break down and reassemble during mitosis. When I got to Phil’s lab, I asked a fundamental question in the then-nascent field of microRNAs: Where do they function? At first sight, microRNAs and their binding proteins are found in RNA granules called P-bodies, but when I quantitated the signals I realized that only 1% is localized there while the majority is diffusively distributed in the cytoplasm. Intriguingly, when I stress the cells, at least 5% of the cytoplasmic signals redistribute to other structures called stress granules.
As I immerse myself more and more in the world of RNA granules, a fundamental question lingers in my heart: How do these various structures hold together without enveloping membranes?
One possible answer came at a scientific retreat in fall 2007 when I heard a talk by Paul Chang, who was starting his lab at MIT. After Paul described how mitotic spindle formation is regulated by poly(ADP-ribose) (PAR), I wondered whether this understudied polynucleotide could be a structural element for RNA granules. Therefore I wrote him an email to initiate a chat and got some antibodies against PAR to test. To my pleasant surprise, PAR is enriched in stress granules!
This serendipitous finding started my adventure to investigate this enigmatic polynucleotide, which is also known to be a post-translational modification on proteins (ADP-ribosylation). I discovered that PAR regulates microRNA activities and stress granule formation in the cytoplasm. This finding opens a new direction in the PAR field, which had been focused mainly on DNA metabolism in the nucleus since the discovery of PAR in 1963. Yet in all these cases it has been challenging to answer mechanistic questions about PAR partly due to the lack of techniques to identify ADP-ribosylation sites. This unmet need has serious clinical implications, especially when we consider that drugs for treating cancer patients have already been developed to inhibit the enzyme that adds ADP-ribosylation (PARP inhibitors). I therefore took on the challenge of solving this long-standing problem when I started my lab at Johns Hopkins in 2011.
With my mass spectrometry collaborator Shao-En Ong at the University of Washington (with whom I have worked since our PhD years), I developed multiple proteomics methods that can identify ADP-ribosylation sites on any amino acids in cells. In addition, by curating the ADP-ribosylation literature, my team created a database called ADPriboDB that includes over 12,300 entries for 2,311 ADP-ribosylated substrates. Our goals are to provide a one-stop resource for the PAR field and generate interest in the broader community. Intriguingly, informatics analyses on ADPriboDB reveal that ADP-ribosylated substrates are statistically enriched for proteins with low-complexity regions, which aid self-assembly in non-membranous structures including stress granules and nucleoli (p < 10-20). I therefore proposed a theoretical framework in which PAR directs the organization of cellular architecture.
For the next few years, I will use proteomics and informatics tools to reveal the signaling world of ADP-ribosylation. I want to uncover how PAR regulates the formation of RNA granules. My lab research is currently a mix of RNA and PAR biology. This hybrid strategy is, perhaps, rooted in the way I was raised in Hong Kong—a city intertwined with British and Chinese heritage. Different perspectives, I believe, allow better decisions and innovations. My best moments in lab meetings are to see my team bouncing ideas back-and-forth between the PAR and RNA worlds. Though therapeutically important, PAR has long been difficult to study due to the lack of tools. Using our RNA knowledge, we want to develop novel tools to investigate PAR. My vision is to make the scientific world of PAR as accessible as that of RNA.