University of WashingtonSponsor: David Baker
Despite the tremendous efforts spent towards genetically reprogramming T cells for therapeutic purposes, the complex ex vivo procedures and costs involved in producing genetically modified lymphocytes remain major obstacles for implementing them as a standard of care in the treatment of cancer. As a JCC fellow, my goal has been to bypass these obstacles by developing a technology that combines designed protein logic with engineered viruses to target and genetically engineer specific cell populations in vivo. To achieve targeted cellular engineering in vivo, I adapted a co-localization dependent protein switch, named Co-LOCKR, that classifies cells based on their receptor expression. Upon locating cells with the correct receptor combination, Co-LOCKR presents a target peptide that guides engineered viruses to genetically modify tagged cells.
Rockefeller UniversitySponsor: Elaine Fuchs
Profound alterations in gene expression profiles occur as stem cells from normal tissue transform into cancer stem cells (or tumor-initiating cells) that are able to initiate tumor growth and propagate tumor masses. However, how the gene expression program is rewired during tumorigenesis remains elusive. My research project centers on exploring and identifying key factors that are responsible for driving the divergence of their gene expression profiles. Using in vivo mouse models and genomics and imaging approaches, I am investigating how spatiotemporal genome organization plays a role in oncogenic transcriptional reprogramming during skin squamous cell carcinoma (SCC) development. Skin SCC has emerged as a public health issue due to its increasing incidence and potential for metastasis and recurrence, particularly for the patients placed on immunosuppressive drugs. If successful, my work would further our understanding of the mechanisms underlying oncogenic transcriptional reprogramming and provide new avenues for developing new cancer therapeutics.
St. Jude Children's HospitalSponsor: Jeffrey Klco
University of Minnesota Twin CitiesSponsor: Andrew Venteicher
Human chordoma is a locally aggressive and invasive type of cancer that occurs in the bones of the skull base and spine, and it is part of a group of malignant bone and soft tissue tumors called sarcomas. It is characterized by high recurrence rates and a lack of chemotherapy response. Although studies using exome sequencing identified a few genetic alterations, the vast majority of chordomas do not appear to have a causal genetic mutation, given that the overall somatic mutation burden in chordoma is modest. Recently, the Chordoma Genome Project provided essential clues about novel genes implicated in chordoma tumorigenesis. DNA sequencing revealed that mutations in the gene encoding the lysosomal trafficking regulator protein (LYST) have a role in chordoma biology, as recurrent truncating mutations were found in 10% of tumors. Our lab has preliminary data suggesting that epigenetic regulation of LYST leads to a clinically aggressive chordoma variant, marked by reduced survival and a high rate of metastasis. Herein, this research focuses on elucidating the mechanisms of epigenetic regulation of chordoma-related genes, like LYST, by applying chromosome conformation capture and protein-DNA interaction techniques. Initial findings have shown differences in chromatin accessibility and conformation between tumor subtypes, suggesting an association with the patient’s prognosis.
Boston UniversitySponsor: Dr, Elliott Hagedorn, Dr. Christopher Chen, and Boston University
The vascular system transports blood and immune cells throughout the body. Yet, how these cells selectively cross the endothelium and enter the appropriate cellular tissues is unclear. Dr. Gwendolyn Beacham will explore the fundamental mechanisms underlying this endothelial transmigration in Dr. Elliott Hagedorn’s and Dr. Christopher Chen’s labs at Boston University. Beacham predicts that endocytosis is important for this process and has identified candidate proteins by investigating blood stem cells. She will use zebrafish as a model system to validate her preliminary findings. Then, Beacham will use this understanding to engineer blood vessels with controllable endothelial transmigration in zebrafish and in human cell culture. This research may help improve the efficiencies of cancer therapies that rely on endothelial transmigration, such as bone marrow transplants and engineered CAR T-cells.
As a Ph.D. student in Dr. Gunther Hollopeter’s lab at Cornell University, Beacham investigated clathrin-mediated endocytosis. In particular, she discovered that endocytosis is inactivated via phosphorylation of the clathrin Adaptor Protein 2. These findings revealed a novel regulatory mechanism for endocytosis and set up Dr. Beacham to explore how endocytosis contributes to endothelial transmigration.
Whitehead Institute for Biomedical ResearchRead more
Whitehead Institute for Biomedical ResearchSponsor: Jonathan Weissman
Chemical modifications to DNA and histones are implicated in the establishment of heritable cell type-specific transcriptional networks. The emergence of molecular epigenetic editors creates new opportunities to mechanistically probe these relationships and understand the functional repercussions of epigenetic dysregulation in cancer and aging. The CRISPRoff editor was developed in a collaboration between the Weissman and Gilbert labs as a single fusion protein containing the catalytically inactive dCas9, a repressive KRAB domain, and DNA methyltransferase domains. Transient expression of RNA-guided CRISPRoff achieves robust and heritable gene silencing in human cells, likely as a product of the synergistic spatiotemporal relationship between the coupled domains. Using a CRISPR-based screening approach, I plan to uncover and mechanistically characterize additional cooperative protein interactions which facilitate the establishment and maintenance of long-term transcriptional memory.
University of Texas Southwestern Medical CenterRead more
University of Texas Southwestern Medical CenterSponsor: Michael K Rosen
Biomolecular Condensates are defined foci found in cells that have selectively concentrated biomolecules. The formation of biomolecular condensates via liquid-liquid phase separation, involving multivalent interactions among biomolecules, has emerged as an important principle for the organization of cellular structure and biochemistry. The molecular underpinnings governing the macroscopic behavior of multi-component condensates, formed by modular protein domains, remain poorly understood. There is limited understanding of how inter-domain binding affinities affect condensate energetics and dynamics, and whether the energetic behaviors can be inferred from known evolutionary relationships between the molecules. Studying these requires quantitative mapping of a phase diagram, which is a two-dimensional array of points for a two-component system and extends to being n-dimensional for n-components. The traditional methods used for mapping phase diagrams require substantial amounts of reagents and are labor-intensive. Hence, I have developed a high-throughput microfluidics-based platform in which hundreds of thousands of pL volume droplets can be made and analyzed as individual reaction chambers in a single experiment, enabling dense sampling of even high-dimensional phase spaces. With this method, I will be mapping phase diagrams and condensate dynamics for systems of increasing complexity. The characterization of the energetics of phase separation with a dataset of unprecedented scale will help in understanding (and eventually predicting) the behaviors of condensates from knowledge of the interactions and co-evolution of individual molecules.
University of California, BerkeleySponsor: Susan Marqusee
The majority of functions we associate with living thing are made possible thanks to the molecular functions of proteins. Proteins, just like cars and other macroscopic machines, require a specific 3D structure in order to be able to perform their functions and improper protein folding is linked to diseases cut as Alzheimer’s, Parkinson’s, and various cancers. Yet despite decades of research, we still do not understand how proteins fold up into these structures, and what determines whether folding ultimately proceeds correctly—these questions are not addressed by structure-prediction algorithms such as DeepMind’s AlphaFold. It is crucial that we make progress on these issues if we are to rationally design treatments for misfolding diseases, and to predict evolution of organisms, which is often mediated by changes to protein folding and function.
All proteins are made up of one or more chains of amino acids. For some proteins, the physical and chemical interactions between these amino acids are entirely sufficient to drive protein folding into correct native structure. But growing evidence suggests that, for many other proteins, these interactions instead cause the amino acid chain to misfold into non-functional molecular structures. A major goal of my research is to understand how this conundrum is resolved in the complex cellular environment.
One possible resolution to this issue may lie in the fact that, in addition to folding, a protein molecule needs to be synthesized one amino acid at a time by the ribosome. It turns out that many proteins can start folding as they are being synthesized, a process known as co-translational folding which has been shown to significantly increase the odds that certain proteins fold correctly. Indeed, many proteins contain evolutionarily conserved slowdowns in their rate of synthesis at chain lengths corresponding to putative co-translational folding intermediates, indicating it is broadly useful to modulate synthesis rates to give time for co-translational folding. This is akin to how dance (analogous to a chain’s folding) is closely linked to musical rhythm (how quickly amino acids are added)—I may have taken this analogy a bit too far and written a musical piece inspired by it (The Dance of the Nascent Chain).
My research aims to develop a detailed molecular picture of this process, and why it is beneficial to fold co-translationally for many proteins, by combining in vitro and in vivo experimental techniques, physics theory and atomistic simulations. In the future, this interdisciplinary pipeline can also be applied to investigate additional complex processes in the cell including mechanisms of misfolding in disease.
New York UniversitySponsor: Satija Rahul
Protein phosphorylation is a fundamental, dynamic process that can have drastic effects on cellular physiology. Mutations in kinases, the enzymes that phosphorylate other proteins, are often implicated in neurological disease. Understanding the context and consequences of protein phosphorylation in different cell types throughout neurodevelopment is imperative to developing new treatments as well as our basic understanding of cell biology. Recent technological developments permit the simultaneous quantification of protein levels, chromatin accessibility and gene expression from single cells (DOGMA-Seq). I am extending this technology to quantify both phosphorylated proteins and total proteins as well as chromatin accessibility and gene expression. I am applying this assay at discrete timepoints throughout in vitro neurodevelopment to reveal previously uncharacterized cell-type specific signaling patterns affecting gene expression and ultimately, cell fate decisions.
Harvard University Medical SchoolSponsor: Galit Lahav
In response to DNA damage, the tumor suppressor protein p53 induces expression of stress-responsive genes to inhibit proliferation of cells with damaged DNA. Changes in p53 protein levels over time (p53 dynamics) impact cellular outcomes: p53 oscillations facilitate repair of DNA-damaged cells, whereas sustained levels of p53 promote senescence and cell death. While it is now established that p53 dynamics contribute to these competing cell-autonomous processes, how p53 dynamics regulate genes involved in non-cell-autonomous events, such as those involved in immune signaling, is not known. I propose to develop new tools and approaches to study the role of p53 in regulating immune gene expression in cancer cells and in mediating the killing of cancer cells by immune cells. This research will provide fundamental insights into the mechanisms that govern of cancer cell-immune cell interactions and pave the way for developing effective combination therapies to treat cancer
University of California, San FranciscoSponsor: Orion Weiner
Infertility represents a significant societal burden, as nearly 60% of human pregnancies fail before the embryo implants into the uterus. These miscarriages become more prevalent as women age above 35 years. But implantation remains a black box within development because it occurs within the mother’s body, so progress revealing its physical mechanisms is lagging. Early in preimplantation sages, primitive placental lineages must be specified for faithful implantation. Driving these lineage commitments are subcellular mechanical forces that transduce expression of downstream fate determinants for specification and ultimate invasion of placental tissues. However, in mammalian embryos of aged mothers, embryos display poor developmental health with decreased placental structures owing to impaired implantation. We hypothesize that these pathologies may stem from either early defects in tissue specification or later mechanical uterine invasion, both of which could give rise to age-related spontaneous abortions. This proposal therefore seeks to understand how the early cell biological and biophysical mechanisms are altered in the embryo with advanced maternal age, and how these mechanisms can be tuned to rejuvenate “aged” embryos to rescue developmental potential. Working in embryos of aged mice, we will combine approaches from cell and developmental biology, biophysics, and synthetic biology to ask: (1) Does maternal aging decouple the embryo’s upstream mechanics from downstream signal transduction during placental fate acquisition? (2) Is the logic of signal transduction for placental fate determinants altered via maternal aging? and (3) Do these age-related mechanisms together promote defective mechanical invasion during uterine implantation? Bridging these disparate scientific spheres will be critical in understanding infertility and improving female reproductive longevity.
Harvard UniversitySponsor: Mansi Srivistava
How animal brains evolved the capacity for sophisticated computation is not well understood. One major facet of this problem is the evolution of chemosensation. Chemosensation is the primary sense of most animals, and involves complex neural computations. We do not know how this sense evolved, or how most animals – which are aquatic invertebrates – perform chemosensation. I am studying chemosensation in an acoel worm, an aquatic invertebrate that by virtue of its phylogenetic position as the likely outgroup to all other animals with central nervous systems, retains some primitive features of early central nervous systems. Acoels nonetheless perform sophisticated behavior that requires complex chemosensory processing, but how their brains and chemosensors work is unknown. Using a combination of automated behavioral tracking, transgenics, and neural activity imaging, I aim to understand the logic of chemosensory processing in a tractable acoel worm. Through comparisons with known chemosensory mechanisms of other animals, this will shed light on how complex chemosensory systems evolved. This project will also establish experimental approaches for the future study of neural computations and behavior in acoel worms and other aquatic invertebrates.
New York University, Grossman School of MedicineSponsor: Damian Eikiert - Co-Sponsor Darwin Hern
Mycobacterium tuberculosis, the causative agent of tuberculosis, is one of the leading causes of death due to infectious disease. Mtb establishes a replicative niche within the phagosomal compartment of host macrophages where it siphons nutrients from the host cell for its survival. To thrive within this hostile environment, Mtb has evolved a complex, protective cell envelope along with an ensemble of active transporters to import nutrients across this nearly impermeable barrier. The Mammalian Cell Entry (MCE) proteins have been implicated in nutrient transport as well as outer membrane maintenance and are important virulence factors in Mtb. However, the molecular bases for these functions are not known and the MCE proteins could play additional roles in the cell that have yet to be characterized. Therefore, I am currently determining the first structures of the mycobacterial MCE proteins and their associated factors using a combination of endogenous purification strategies and cryo-electron microscopy (cryo-EM), and developing in vivo assays to monitor MCE substrate binding and transport. This work will provide structural and mechanistic insights into these important virulence factors, which are potential targets for drug development.
University of California, San DiegoSponsor: Dr. Elizabeth Villa
Mutations in LRRK2, a multi-domain kinase and GTPase, is the most frequent cause of familial Parkinson’s disease. However, we currently lack the detailed understanding of LRRK2 function that could lead to therapeutics for Parkinson’s. Dr. Siyu Chen will use cryo-EM and cryo-ET to study LRRK2 and its mutants in biochemical reconstitutions and in cells. Dr. Chen will conduct these experiments in Dr. Elizabeth Villa’s lab at the University of California, San Diego. These experiments will directly visualize the molecular mechanisms of LRRK2 and interacting partners’ function in the cell, and how pathogenic mutations disrupt these processes. Therefore, Dr. Chen’s research may inform on novel therapies for Parkinson’s disease.
As a graduate student in Dr. Yuan He’s lab at Northwestern University, Chen studied DNA double-strand break repair. Specifically, Dr. Chen used Cryo-EM to solve two key intermediate states in the non-homologous end-joining pathway (NHEJ). These structures revealed novel interaction surfaces between NHEJ proteins and allowed Dr. Chen to propose a near complete reaction cycle for NHEJ. Dr. Chen will now apply his cryo-EM expertise to LRRK2 and will use cryo-ET to visualize LRRK2 in cells.
University of WashingtonSponsor: Michael Bruchas
Internal brain states greatly influence our sensations and perception of the external world. Incidents such as stress, hunger, thirst, and pregnancy have all been described as inducing different ‘brain states’ within individuals, altering basic neural properties such as sensory perception, memory, interception, and attention. However, we do not understand how our brains dynamically shape our perceptions and behaviors during state shifts. Here we aimed to create stable brain state models by exposing animals to either chronic social isolation or exercise, two opposing types of behavioral intervention to represent positive and negative experiences. By measuring multi-domain behavioral profiles across the brain during long-term social isolation or exercise, we tested if these biological fingerprints can predict animals’ brain states. To further dissect the neuromodulation changes during brain state shifts, we focused first on the locus coeruleus (LC). LC both receives and sends broad projections throughout the brain. LC cells could then mediate brain-wide changes through its noradrenergic population to control arousal, attention, and sensory perceptions. When simultaneously imaging LCDBH cell body and terminal activities across multiple brain regions, we observed different activity patterns when mice were presented with a diverse array of stimuli. We have also observed dynamic single-cell activities toward different sensory cues, which further confirms the heterogeneity within the LCDBH population. By combing in vivo imaging, circuitry mapping, and biochemical detection, we aim to examine the neuromodulatory signaling dynamics in and out of LC during brain state shifts induced by long-term exercise and social isolation.
University of UtahSponsor: Dr. Nels Elde
A wide range of organisms – such as nematodes, sea anemones, and bacteria – possess immune defenses to protect themselves against infectious microbes and viruses. Yet studying the interactions between hosts and infectious microbes remains limited to a handful of species. Dr. Katherine Deets will expand this list by examining the interactions between Tetrahymena thermophila and viruses in Dr. Nels Elde’s lab at the University of Utah. Dr. Deets is currently identifying novel viruses that infect Tetrahymena, and working to understand how Tetrahymena defend themselves against these viruses. This research will unlock a new experimental platform with powerful genetic tools for diversifying studies of the evolution of host-virus interactions.
As a graduate student, Deets investigated host-microbe interactions in the context of the mouse small intestine in Dr. Russell Vance’s lab at the University of California, Berkeley. Dr. Deets discovered a novel mode of antigen presentation that only occurs following inflammasome activation. This finding revealed a new connection between innate and adaptive immunity in the intestine. Dr. Deets will use her experience in host-microbe interactions to expand our understanding of immune defense in diverse.
University of MichiganSponsor: Kevin Wood
Cells and organisms such as bacteria or cancer cells live in communities and have complex population-level dynamics and emergent behaviors. These behaviors can significantly change their collective properties, including resistance to drugs and other environmental selective pressures. Predicting how cellular communities, rather than individuals, respond to drug exposure could help delay or prevent drug resistance during treatment.
Spatial structure and heterogeneity are important features of such communities – from the cell to the ecosystem scale. In my research, I aim to understand the essential, but poorly understood, relationship between spatial structure and population-level dynamics in bacterial biofilm communities responding to antibiotic selection via theoretical and experimental approaches.
Duke UniversitySponsor: Dr. Stefano Di Talia, Dr. Kenneth Poss, and Duke University
Many animals, including zebrafish, have the ability to regenerate limbs, tails, or fins following amputation. The regeneration process is thought to faithfully reconstruct the appendage, yet it is unknown how spatial and temporal dynamics in gene expression and cell-signaling pathways control regrowth. Dr. Rocky Diegmiller will use quantitative imaging approaches to investigate morphological and patterning dynamics in regrowth of the paired zebrafish pectoral fin. Diegmiller will conduct these studies in Dr. Stefano Di Talia’s and Dr. Kenneth Poss’ labs at Duke University. Diegmiller will explore how gene expression patterns are re-formed following amputation, and throughout regeneration. These studies will reveal insights into the dynamics and robustness of regeneration, and will dissect how multiple signaling pathways are integrated to ensure faithful regeneration. Furthermore, these studies will generate quantitative tools for studying regeneration that can be applied to other systems.
As a graduate student, Diegmiller used mathematical models and imaging to investigate developmental biology in Dr. Stanislav Shvartsman’s lab at Princeton University. Specifically, Dr. Diegmiller used the Drosophila germline cyst as a model system to investigate cell polarity and the emergence of symmetry breaking mechanisms in cell clusters. With his multidisciplinary background in developmental biology, Dr. Diegmiller hopes his research will also yield important connections and distinctions between developmental and regenerative pathways.
Johns Hopkins UniversitySponsor: Laboratories of Rachel Green and Bin Wu
Protein synthesis is metabolically costly; it is therefore critical that cells regulate translation based on nutrient availability. Translation regulation must be flexible to enable cells to adapt to persistent nutrient deprivation, but still recover when nutrients are replenished. Signaling through the kinases GCN2 and mTORC1 can suppress both translation initiation and elongation in response to nutrient depletion, but how each mechanism contributes to global translational control is unclear. Here we investigate translation dynamics upon acute and long-term nutrient depletion, as well as during recovery from nutrient stress. In the immediate response to starvation, GCN2 robustly inhibits initiation to prevent ribosome loading onto transcripts. However, over longer periods of starvation, increased initiation causes translating ribosomes to collide with ribosomes stalled on transcripts. To explore these different temporal regimes, we employ a mass spectrometry-based approach to identify factors that modulate ribosome activity in response to nutrient stress through differential ribosome binding. This work will provide a more integrated understanding of how cells regulate translation and ribosome homeostasis across nutrient environments.
University of California, San FranciscoSponsor: Diana Laird
Mammals with ovaries are born with a non-renewing supply of differentiated oocytes ranging from the thousands in mice to the millions in humans. While these high numbers imply a large stockpile, only a comparatively small number of the oocytes present at birth will ever be successfully ovulated and fertilized. To achieve this maturation, an oocyte must first be activated from its quiescent state and then undergo a period of extensive growth in order to accumulate large quantities of biosynthetic materials that are necessary to support the embryo prior to zygotic genome activation. We are currently limited in our understanding of factors that determine whether an oocyte will complete this growth or be fated for elimination/atresia. My research focuses on how both the intrinsic characteristics of oocytes and the extrinsic support provided by the surrounding somatic tissue determine whether an oocyte present at birth will ever be successfully ovulated. My goal is to apply this knowledge to future therapeutics for infertility.
Vanderbilt University Medical CenterSponsor: Dr. Eric Skaar
Clostridioides difficile infection (CDI) is the leading cause of hospital-acquired and antibiotic-associated intestinal infections. However, we do not currently have a clear understanding of CDI pathogenesis, which impedes the development of additional therapeutic strategies. Dr. Martin Douglass will investigate how CDI overcomes the human microbiota and immune system in Dr. Eric Skaar’s lab at Vanderbilt University Medical Center. Dr. Douglass will examine how CDI competes for nutrients with the microbiota and immune system. Furthermore, Dr. Douglass will identify which CD genes are required for host colonization and persistence. These studies may provide insight into novel therapeutic targets for treating CDI.
As a graduate student in Dr. M. Stephen Trent’s lab at the University of Georgia, Douglass examined the outer membrane of Gram-negative bacteria. Dr. Douglass discovered novel proteins that are required for the transport of lipids to the outer membrane. These studies provide potential therapeutic targets for novel antibiotics and provide Douglass with a solid foundation for interrogating new targets in CDI.
Johns Hopkins University School of MedicineSponsor: Dr. Seth Blackshaw
Sleep disorders are common and negatively impact our quality of life and biological health. Yet, how the brain encodes the need for restorative sleep is poorly understood. Dr. Leah Elias will investigate the cellular circuits and molecular signals that encode sleep pressure in Dr. Seth Blackshaw’s lab at Johns Hopkins University School of Medicine. Using single nucleus RNA sequencing, Dr. Elias has identified a cluster of neurons that are activated by sleep deprivation. Furthermore, she has identified candidate genes that are differentially regulated in response to sleep deprivation. She will leverage these findings to mechanistically dissect sleep signals in the brain at the cellular and molecular levels. Dr. Elias’ research has important implications for the basic biology of sleep and may reveal novel therapeutic targets for sleep and metabolic disorders.
As a PhD student in Dr. Ishmail Abdus-Saboor‘s lab at the University of Pennsylvania, Dr. Elias studied the neural circuitry controlling social touch. Specifically, she identified a new pathway that connects social touch in the skin to reward circuits in the brain. With this background in neural circuitry, Dr. Elias will now investigate how the need for sleep is encoded in the brain.
Brandeis UniversitySponsor: Amy Lee
Stanford UniversitySponsor: Dr. Eric Kool
c-Myc is a transcription factor and an attractive therapeutic target as it drives the majority of human cancers. However, inhibiting c-Myc at the protein level is difficult, in part due to its intrinsically disordered structure. Dr. Sheng Feng aims to circumvent this problem by inhibiting c-Myc mRNA with small molecules. Dr Feng will use a fragment-based approach using an RNA-biased library that is functionalized to improve affinity for RNA. Dr. Feng will tether fragments that bind to adjacent RNA sites to improve binding affinity and selectivity. These experiments will be conducted in Dr. Eric Kool’s lab at Stanford University. Dr. Feng’s research will explore a new route for inhibiting an important target in oncology and represents a general method for inhibiting other difficult protein targets.
As a graduate student in Dr. Stephen Buchwald’s lab at the Massachusetts Institute of Technology, Feng developed copper hydride-catalyzed bond forming reactions that are highly regio- and stereoselective. Such reactions produce important substructures for pharmaceuticals, agrochemicals, and natural products. Dr. Feng’s background in organic chemistry has prepared her to design and prepare small molecule ligand libraries for targeting c-Myc mRNA.
California Institute of TechnologySponsor: Dianne Newman
While cells are often studied in suspension or monolayers, more structured forms like tissues and biofilms dominate natural environments. In such settings, the concentrations of critical nutrients like sugars and O2 vary in space and time because cells produce and consume them locally, leading to measurable differences in physiology and gene expression between nearby cells. Spatially structured environments therefore represent many-body systems interacting on multiple timescales through a rich collection of chemical and physical processes. My overriding goal is to determine whether metabolism in mixed biofilms can be predicted quantitatively from simple models with intelligible and measurable parameters. I am currently developing Pseudomonas aeruginosa, a model bacterium that grows in suspension and as a biofilm, as a model for studying metabolic heterogeneity in spatially structured environments. It is commonly assumed that variation in the local O2 concentration is a primary determinant of metabolic heterogeneity in biofilms. As such, I am developing optical approaches to measure local O2 concentrations in real time to test whether a mathematical model can explain O2 dynamics, cell growth, and metabolic rates in biofilms.
Massachusetts General HospitalSponsor: Dr. Luke Chao
Mitochondria generate energy needed to power cells and multicellular organisms. Wrinkles in the inner mitochondrial membrane, known as cristae, concentrate molecular motors for energy production. However, it is unclear how the wrinkly cristae are formed. Dr. Michelle Fry will use a clever approach to investigate cristae formation in cells. She will introduce candidate protein/protein complexes into parasitic protist mitochondria. These mitochondria are smooth, making them amenable for testing with proteins are sufficient to generate cristae. Dr. Fry will use advanced electron microscopy techniques to image changes in mitochondrial morphology. Fry will conduct these studies in Dr. Luke Chao’s lab at Massachusetts General Hospital. These experiments will provide fundamental insights into mitochondrial biology and may provide clues for mitochondrial pathological dysfunction.
As a graduate student in Dr. Bil Clemons lab at the California Institute of Technology, Fry used structural biology to study the targeting of membrane proteins to the endoplasmic reticulum. Specifically, Dr. Fry captured several structural conformations of a protein chaperone, Get3. Fry demonstrated how conformational flexibility is important for Get3 to integrate multiple regulatory signals (binding partners, client proteins, nucleotide binding and hydrolysis). Dr Fry is now excited to use cryo-electron tomography to capture the conformational landscape of proteins that regulate mitochondrial cristae formation in cells.
National Cancer Institute / NIHSponsor: Daniel Larson
Enhancers are distal cis-regulatory elements that control precise execution of transcriptional programs during development and in response to external stimuli. How enhancers find and activate their target genes, and what molecular activities are required for enhancer function remains a central outstanding question in the field. Recent advances in nascent RNA-sequencing uncovered widespread transcription from enhancers, which has become widely recognized as a robust signature of enhancer activity. However, mechanistic understanding of enhancer transcription, its regulation and, most importantly, functional role in gene activation is currently missing.
In my work, I aim to address these fundamental questions by using single-molecule and live-cell imaging approaches to characterize the intrinsic dynamics of enhancer transcription in single cells. To generalize my conclusions from individual enhancers to a genome scale, my ultimate goal is to develop high-throughput single-molecule approaches for systematic characterization of enhancer transcription. Using these new tools, I will investigate how transcription at enhancers and their target gene promoters is coordinated at the single-cell level to discover if these processes are functionally linked. Together, this work will be an essential step towards a deeper mechanistic understanding of enhancer function in gene activation and how enhancer perturbations can lead to severe developmental disorders and cancer.
University of California, San FranciscoSponsor: Massimo Scanziani
Primary visual cortex (V1) receives visual information ascending from the eyes as well as
descending from higher order visual areas. As such, V1 is the first cortical stage of visual processing at the intersection between two major pathways, the bottom-up, feedforward and the top-down, feedback streams of visual information. Despite current advances in understanding the integration of information from feedforward and feedback pathways in V1, our knowledge relative to how single neurons in V1 combine information from different origins to form their responses to visual stimuli remains rudimentary. To investigate this question, we apply advanced volumetric imaging technique to measure populations of excitatory synaptic inputs impinging onto single neurons in V1. Using this approach, we characterize the visual response properties of excitatory synaptic inputs to visual stimuli as well as the spatial organization of synaptic inputs along the dendritic tree of single V1 neurons. The results from this project will provide insights into the input – output relationship of a neuron to visual stimuli, namely how the visual response properties of synaptic inputs impinging onto a given neuron combine to give rise to the response of that neuron to visual stimuli.
University of California, BerkeleySponsor: HHMI Fellow
Aging is a complex physiological process coordinated across tissues within an organism. Loss of protein homeostasis is a hallmark of aging, yet it is not understood why dysregulation in protein synthesis occurs, and if this dysregulation drives aging pathologies. Dr. Naomi Genuth will investigate these questions in Dr. Andrew Dillin’s lab at the University of California, Berkeley. Dr. Genuth will use C. elegans to visualize protein synthesis patterns in vivo in different tissues during the aging process. Ultimately, Genuth aims to define the molecules that contribute to dysregulation of protein synthesis and see whether manipulation of these molecules can delay and/or prevent the aging process. Dr. Genuth’s research will improve our understanding of changes in protein synthesis during aging at the molecular, cellular, and organismal levels, and may reveal new therapeutic strategies for aging pathologies.
As a Ph.D. student in Dr. Maria Barna’s lab at Stanford University, Genuth investigated the role of translational regulation in gene expression. Specifically, she developed a quantitative roadmap of how ribosome composition changes during human embryonic stem cell differentiation. Dr. Genuth will now investigate protein synthesis during aging in Dr. Dillin‘s lab.
MRC Laboratory of Molecular BiologySponsor: Kelly Nguyen
Telomeres are repetitive nucleoprotein structures that protect the ends of linear eukaryotic chromosomes. Despite their importance, telomeres shorten at each round of cellular division due to an inherently incomplete replication process at DNA ends. This poses a threat to genome stability. The telomerase complex extends the telomeric repeats by processively copying from an internal template sequence, thereby counterbalancing telomere shortening. The action of telomerase at the telomeres is highly regulated in the cell. The current evidence indicates that a protein complex called shelterin orchestrates telomerase recruitment and activity at the telomeres. In mammals, shelterin is a six-subunit complex that binds telomeric DNA repeats and recruits telomerase through its TPP1 subunit, which assembles as a heterodimer with POT1. TPP1-POT1 not only recruit telomerase, but also stimulates its processivity. Stimulation and recruitment by shelterin are essential for telomerase function in vivo, yet the structural basis of telomerase-shelterin interactions and shelterin-mediated telomerase processivity remains elusive. We determined the cryo-EM structures of telomeric DNA-bound telomerase in complex with TPP1 and with TPP1-POT1 at 3.2 Å and 3.9 Å resolution, respectively. These structures define the molecular interactions between telomerase and TPP1-POT1 required for telomerase recruitment to telomeres. The interaction with TPP1-POT1 stabilizes the DNA, revealing an unexpected path exiting the active site and a conserved DNA anchor site on telomerase, which is important for telomerase processivity. Overall, our findings provide important insights into telomerase recruitment to telomeres and set a framework for future studies on telomerase regulation by shelterin.
Brigham and Women's HospitalSponsor: Stephen J Elledge
Viruses are obligate intracellular pathogens that shape host cell physiology to promote replication and spread. Viral infection is counterbalanced by the host immune response which attempts to detect and eliminate virally infected cells. To reproduce and evade immune detection, viruses modulate expression and post-translational modification of host proteins. The ubiquitin-proteasome system (UPS) mediates targeted degradation of proteins and consists of E1, E2, and E3 enzymes. The modular nature of the ubiquitin ligase pathway has led to co-option by pathogens which alter host protein stability in order to enhance replication and evade immune detection. Understanding how viruses manipulate the host cell proteome to promote infection and how these changes are detected by the immune system is central to the development of anti-viral therapies and vaccines. My postdoctoral research uses genetic and biochemical techniques to discover and dissect host-pathogen interactions with a focus on post translational modifications and their impact on cell signaling.
Massachusetts Institute of TechnologySponsor: Dr. Fan Wang
Medication for chronic pain often leads to addiction. Dr. Nitsan Goldstein thinks this may be because around one third of people experiencing chronic pain also suffer from anxiety. Additionally, anxiety is a strong predictor of chronic pain development. Dr. Goldstein predicts that targeting pain and pain-induced anxiety together may reduce chronic pain symptoms. She has identified neurons that are anxiolytic and will test their functional relationship with pain-induced anxiety and a chronic pain-like state. Goldstein will conduct her experiments in Dr. Fan Wang’s lab at the Massachusetts Institute of Technology. Dr. Goldstein hopes that investigating both the central and peripheral causes of chronic pain and anxiety will open avenues for more effective pain treatments.
As a graduate student in Dr. J. Nicholas Betley’s lab at the University of Pennsylvania, Goldstein investigated how the brain regulates food intake. Specifically, Dr. Goldstein discovered that the activation of hunger circuits enhances dopamine release, which is critical for motivating humans to seek rewards like food. These studies helped reveal new relationships between neural programs and have prepared Dr. Goldstein to investigate the relationship between chronic pain and anxiety.
Harvard University Medical SchoolSponsor: Dr. L. Stirling Churchman
mRNA degradation is an important step in gene expression that is traditionally thought to occur in the cytoplasm. However, a recent genome-wide study uncovered a class of genes whose transcripts are predicted to be primarily degraded in the nucleus. Yet, it is unclear how and why these mRNAs undergo nuclear degradation. Dr. Chantal Guegler will use both candidate- and screening-based approaches to determine which pathways are important for nuclear mRNA degradation, and how this process influences cellular physiology. Dr. Guegler will conduct this research in Dr. Stirling Churchman’s lab at Harvard Medical School. This work will reveal the key determinants of nuclear mRNA degradation and how this process contributes to gene expression regulation.
As a graduate student, Guegler studied bacterial toxin-antitoxin (TA) systems and their role in protecting against bacteriophage infection in Dr. Michael Laub’s lab at the Massachusetts Institute of Technology. There, Dr. Guegler demonstrated that the RNase toxin ToxN cleaves phage mRNAs to disrupt the translation and assembly of viral particles. Interestingly, Guegler also demonstrated that T4 phage can combat ToxN using the phage-encoded antitoxin TifA that sequesters RNA-bound ToxN to prevent it from degrading additional phage mRNAs. With her background in RNA degradation in bacterial TA systems, Dr. Guegler will now investigate nuclear mRNA degradation in eukaryotic cells.
Harvard UniversitySponsor: Catherine Dulac
Animals rely on instinctive behaviors and homeostatic responses, such as parenting, feeding, mating, and sleeping, to ensure individual and species survival. Maximizing survival requires meeting the most pressing needs at the right time, forcing animals to establish behavioral priorities based on a hierarchy of needs. Neurons controlling many of these behaviors are located within the highly interconnected medial preoptic area of the hypothalamus (MPA), making this structure a likely control hub underlying behavioral hierarchy. However, the neural logic of intra-MPA connectivity and how this directs behavioral priorities across physiological states is unknown.
Using the mouse MPA as a model system, I am studying the cell type-specific structural and functional connectivity underlying key competing behavioral and physiological responses. Further, I am determining how animal states, such as virgin or parent, alter neuron function to induce new behavioral priorities. This work will provide the first depiction of a neural basis of the hierarchy of needs and open new avenues for understanding the neural basis of behavior.
Fred Hutchinson Cancer CenterSponsor: Dr. Sue Biggins
Aneuploidy is a hallmark of cancer development and occurs due to defects in chromosome segregation. The kinetochore, a complex consisting of over 100 different types of proteins, is required for the proper segregation of chromosomes. However, we lack an in depth understanding of the step-by-step assembly process resulting in a functional kinetochore due to the extreme molecular and temporal complexity of this complex. Dr. Changkun Hu will reconstitute kinetochore assembly in vitro and use TIRF microscopy to measure individual kinetochore protein recruitment times in Dr. Sue Biggins’ lab at the Fred Hutch. This approach will allow Dr. Hu to determine rate-limiting steps and key regulating mechanisms in kinetochore assembly and will serve as a blueprint for future studies examining the assembly of other large complexes. Furthermore, this work may reveal novel trouble points in chromosome segregation that lead to aneuploidy in cancer.
As a PhD student in Dr. Nicholas Wallace’s lab at Kansas State University, Dr. Hu’s research focused on the repair of DNA double-strand breaks (DSBs). Dr. Hu demonstrated that beta human papillomavirus type 8 protein E6 (8E6), long known to impair traditional DNA-repair pathways, also promotes DNA repair via a mutagenic DSB repair pathway termed alternative end joining. In this way, 8E6 promotes cancer development by increasing genomic instability. Dr. Hu will now pivot to study genome stability at the chromosome level in Dr. Biggins’ lab.
Harvard UniversitySponsor: Adam Cohen
Cancer metastasis and immune cell migration require motile movement, meaning the cell membrane must slip relative to the cytoskeleton. Thus, membrane-cytoskeleton attachments in motile cells likely rearrange, allowing tension to propagate across the membrane. In the current literature, there are ~106-fold discrepancies in reported timescales of membrane tension propagation. I hypothesize these discrepancies reflect variability between cell types, arising from differences in membrane microstructure. I specifically hypothesize that in motile cells, transmembrane proteins are arranged to allow membrane flow, enabling rapid tension equilibration, while non-motile cell membranes are structured to impede tension propagation.
I will directly measure tension propagation timescales in motile and non-motile cells and simultaneously characterize the arrangement of cytoskeleton-anchored transmembrane proteins. I will use optical tweezers to stretch membrane tethers, perturbing and measuring tension. I will visualize immobile transmembrane proteins with targeted photochemical labeling and high-resolution fluorescence imaging, revealing how transmembrane protein arrangement regulates membrane fluidity, and how cancer cells might exploit this to metastasize
Harvard UniversitySponsor: Dr. Mansi Srivastava
Many animals are capable of whole-body regeneration, enabling the regrowth of missing structures to their original size and shape after major amputation. Most studies investigating this phenomenon have focused on the transcriptional control of differentiation from adult pluripotent stem cells. However, Dr. Allison Kann predicts that an important, yet underappreciated, aspect of regeneration is the role of cell adhesion. Regeneration from stem cells requires free progenitor cells to unite and integrate into multicellular tissues and organs. Dr. Kann will use Hofstenia miamia, a genetically tractable invertebrate model system to investigate the disassembly, formation, and remodeling of cellular junctions during regeneration. Kann will conduct these studies in Dr. Mansi Srivastava’s lab at Harvard University. These studies will reveal new principles of regeneration and identify mechanisms that cells use to converge into multicellular structures.
As a graduate student in Dr. Robert Krauss’ lab at Icahn School of Medicine at Mount Sinai, Kann investigated the activation of muscle stem cells. She identified that cytoskeletal regulation is a key driver of muscle stem cell fate decisions and demonstrated how stem cells transduce injury signals into activation. With her background in adult stem cell biology, Dr. Kann is now ready to investigate how cellular interactions between progenitor cells regulate organismal regeneration.
Massachusetts General HospitalSponsor: Vamsi Mootha
Description: Mitochondria are present in nearly all human cells where they play key roles in energy metabolism, biosynthesis, signaling, and cell death. Mitochondrial homeostasis depends on the proper maintenance and expression of the mitochondrial genome (mtDNA). Germline mtDNA mutations can lead to severe, maternally inherited disorders with limited treatment possibilities. Moreover, somatic mtDNA mutations accumulate in neurodegeneration, cancer and aging. mtDNA is a high copy number genome and a mixture of wild-type and mutant mtDNA molecules can co-exist within one cell resulting in “heteroplasmy”. Heteroplasmy dynamics are governed by a complex mix of random drift and selection, but the underlying molecular mechanisms remain unknown. The aim of my post-doctoral research is to uncover the molecular mechanisms that govern mtDNA heteroplasmy. Mechanistic studies of heteroplasmy dynamics will shed the light on the mitochondrial contribution to human health and disease and possibly inspire novel therapeutic approaches to mtDNA disease.
Boston Children's HospitalSponsor: Christopher Walsh
While somatic mutations have been heavily studied in tumors, their prevalence and significance to disease risk in healthy individuals is much less well-understood. The Walsh lab and others revealed that somatic mutation is a widespread phenomenon. Human neurons each contain 100 or more clonal somatic single nucleotide variants (sSNV) at birth, acquired during prenatal development, and gain 15-20 additional sSNVs arising per year. Most somatic variants, including those associated with cancer risk, occur in noncoding regions such as enhancers. Despite being the main source of genetic diversity between cells within an individual, the mechanisms by which noncoding somatic mutations form as well as their functional impact are not well understood. My research will focus on developing new strategies to detect rare noncoding somatic variants as well as dissect their epigenomic impact across different cell types in the human brain. This will help illuminate how much this source of variation contributes to cancer risk and brain disease.
University of Colorado, BoulderSponsor: Aaron Whiteley
Antagonistic interactions are ubiquitous across life. From the conflict between a lion and its prey to the molecular battle between a virus and its host, life is filled with the competition to survive. This has led to the evolution of intricate mechanisms to mediate predatory prey interactions. At the cellular level this has led to the development of immune systems devoted to counteracting attacks and virulence factors dedicated to overcoming these defenses. Over the last several years it has become increasingly clear that bacteria, like humans, possess intricate immune systems to counteract the viruses that invade them, bacteriophages (phage). However, within nature, bacteria face a much wider range of threats than phage and predatory DNA elements. These include neighboring bacteria invading their niche, amoeba seeking out a meal, extracellular toxins, and predatory bacteria. This led us to hypothesize that the bacterial innate immune system has multiple branches capable of defending against this array of threats. But how do you identify a new immune pathway? At this conference, I will present my work developing a technique termed Exploring the Pangenome for Novel Defense (ExPND) which allowed me to uncover and characterize the first genetically encoded mechanism by which Escherichia coli can defend itself against predatory bacteria.
Through the work of numerous groups, it is now clear that the majority of phage defense
systems, the bacterial innate immune components we best understand, are encoded within mobile genetic elements. Therefore, to begin to survey for novel immune systems we obtained a collection of wild E. coli strains collected from natural sources across the globe and, importantly for my work, encodes a wide array of mobile genetic elements. To begin testing our hypothesis I focused on the predatory bacteria Bdellovibrio bacteriovorus. Predatory bacteria, such as Bdellovibrio, robustly and non-selectively prey on Gram-negative bacteria by invading into the periplasm of prey cells and catabolizing cellular components. To date, there are no known genetically encoded resistance mechanism against Bdellovibrio. However, most of the studies investigating this question were performed with lab adapted strains which notoriously lack defense systems. By challenging our E. coli collection with B. bacteriovorus I uncovered
numerous E. coli strains that are highly resistant to predation. Follow-up studies utilizing
transposon mutagenesis have allowed me to identify two mechanisms by which bacteria can
protect themselves including an elaborate extracellular structure that robustly blocks Bdellovibrio predation. By utilizing ExPND, my work sets the foundation for understanding the threats sensed by the bacterial innate immune system and provides a platform for uncovering novel mechanisms at the interface of predator-prey interactions.
Dana-Farber Cancer InstituteSponsor: David Pellman
Common fragile sites (CFSs) are hotspots for genomic rearrangements in cancers, but why and how these rearrangements occur is poorly understood. CFSs are characteristically difficult to replicate and often persist as under-replicated DNA into mitosis. Previous work from my host laboratories showed that stalled DNA replication forks are disassembled upon exposure to the mitotic kinase Cyclin B-CDK1. Unloading of the replisome leads to the formation of DNA breaks at the stalled forks followed by break-end ligation events. Coordinated DNA repair events at converging stalled forks in mitosis could lead to the formation of deletions and sister chromatid exchanges, both of which are signatures of CFS expression.
Recent studies have shown that CIP2A is a mitosis-specific repair factor that localizes to sites of DNA damage and replication stress. My aim is to investigate the role of CIP2A in cellular responses to unreplicated DNA in mitosis and how these processes contribute to genomic instability at CFSs. I will use the Xenopus egg extract system to uncover the biochemical mechanism of CIP2A function and conduct cell-based studies to observe the effects of CIP2A on genome stability.
University of California, BerkeleySponsor: Christopher Chang
It has long been a focus for the identification of protein drivers and for the development of corresponding cancer therapeutics. Traditionally, drug discovery efforts mainly rely on “druggable” proteins, which possess easily identifiable binding pockets or catalytic active sites. However, over 85% of the proteome is still considered “undruggable”, posing additional challenges for further development. Recently, Activity-Based Protein Profiling, has arisen to spotlight the undruggable proteome via covalent linkage of reactivity-based chemical probes and “ligandable hotspots” in the proteome. In the proposed research, I aim to develop new chemoproteomic platforms based on inexpensive and biocompatible main-group molecules for chemoselective methionine and methionine sulfoxide bioconjugation, to further promote cancer drug discovery. This contribution will be significant because it can develop a ligandability map against undruggable proteome, serve as efficient tools in cancer cell early-stage diagnosis, and further provide a handle to decipher and drug methionine redox regulation in cancer cells, thus yielding novel therapeutics.
Pennsylvania State UniversitySponsor: Joseph Bollinger
Protein-based radicals participate in biological processes and natural product biosynthesis that link to life and death in organisms. One remarkable example is class I ribonucleotide reductases (RNRs), which catalyze DNA synthesis with tyrosyl radical relays. To compete for available resources, particularly in pathogens that live in the context of a host, RNRs have evolved distinct cofactors, assembly strategies, and radical translocation mechanisms. Understanding these distinctions from human counterparts is a key step in developing successful anticancer, antimicrobial, and antiviral drugs that inhibit RNRs. However, tyrosines are abundant and form highly cooperative networks, presenting difficulties in isolating their contribution to vectorial redox. I aim to dissect these tyrosines in the newly discovered class I RNRs to probe the free energy landscape of their one-electron oxidation and determine the active state structures. To further advance the field of redox enzyme design for difficult chemical reactions, I will elucidate the crucial protein environmental factors that modulate productive tyrosyl radical relays and prevent detrimental side reactions.
Stanford UniversitySponsor: Chen Xiaoke
Chronic pain affects approximately 20% of the adult population in the United States (~50M people), incurring an annual economic impact exceeding 3% US GDP (~$600Bn). This critical public health issue lacks effective treatments beyond classic opiate-based therapies, which itself is a major underlying contributor to the development of the opiate addiction epidemic. Our laboratory has previously found a population of neurons, which are marked by the expression of an opiate receptor and which project from the brainstem to the spinal cord, that are required to facilitate the development chronic pain. We are currently seeking to gain insights into the molecular mechanisms of how these neurons facilitate chronic mechanical hypersensitivity after nerve injury.
More specifically, we have carried out transcriptional profiling of these neurons and found that they selectively upregulate a handful of neuropeptides in the chronic pain state. Currently, we are using RNA-interference to characterize the contribution(s) of individual neuropeptides to the development of chronic pain. With this data in hand, we next aim to identify the cells and corresponding neuropeptide receptor(s) in the spinal cord that are innervated by these neurons. In this way, we will define the peptide-based circuit from brainstem to spinal cord that acts as a gate for the development of chronic pain. Success of this aim will describe a new signaling pathway and therapeutic target(s) that underly the development of this devastating condition.
Yale UniversitySponsor: Dr. Sidi Chen
Dr. Xinyu Ling aims to improve cellular immunotherapies targeting solid tumors in Dr. Sidi Chen’s lab at Yale University. To date, cellular immunotherapies have shown unsatisfactory results in treating solid tumors due to the immunosuppressive tumor microenvironment. Furthermore, CRISPR screening is a powerful tool for the identification of new cancer immunotherapy targets. However, existing approaches are limited in which types of cells can be targeted and in understanding the spatial arrangement of those cells. Dr. Ling will develop a versatile CRISPR screening method that will allow for simple “plug-and-play” targeting of many different cell types. The resulting platform will expand the use of CRISPR screening tools for cancer immunotherapies and may lead to the discovery of novel immunotherapy targets.
As a PhD student in Dr. Tao Liu‘s lab at Peking University, Ling used unnatural amino acid technology to improve the genome-editing and cost efficiencies of CRISPR Cas9/Cas12a genome editors. This prior experience in optimizing genome engineering strategies will assist Dr. Ling in developing an agile cellular targeting platform to identify novel cancer immunotherapy targets.
Harvard University Medical SchoolSponsor: Jun R Huh
The human gastrointestinal tract harbors trillions of microbes that have been coevolving with humans for a long time. Growing evidence suggested that the gut microbiota produces a myriad of metabolites, and some of these small molecules possess bioactivity that can shape host development and fitness, such as modulating gut immune cells and promoting brain development. G protein-coupled receptors (GPCRs) represent the largest class of membrane receptors that relay extracellular cues into a cellular response. Many of these GPCRs including orphan GPCRs may evolutionally be designed for communicating with microbes through microbial metabolites. My research seeks to develop a genetic tool and platform that can characterize ligand-activated GPCRs in vivo and uncover GPCRs that sense microbial metabolites. This work potentially sheds light to understand the underlying mechanisms of host-microbiota interaction.
Broad InstituteSponsor: Stuart Schreiber
There is an urgent need for cancer therapeutics with improved target specificity and novel mechanisms of action. Molecular glues combine the demonstrated capabilities of small molecules as potent drugs with the power of chemically induced proximity. In enabling new protein-protein associations, molecular glues can address many shortcomings of current small molecule cancer therapeutics, which are often limited to protein targets presenting a clear binding pocket. Furthermore, since protein-protein interactions are widely known to facilitate a range of fundamental cellular activities, chemical compounds which intercede on these pathways can provide access to novel mechanisms of action and enhanced target specificity. The wide-ranging therapeutic potential of molecular glue has already been recognized; however, to date the discovery of these compounds has been limited to serendipity or the synthesis of bifunctional molecules. The systematic and generalizable path to molecular glue discovery has not yet been established. In my research, I will leverage the recording and reporting power of DNA encoded libraries to deliver a new path to molecular glue discovery
Fred Hutchinson Cancer CenterSponsor: Sue Biggins
Each time a cell divides, it must ensure equal segregation of chromosomes. Error in this process causes either loss or gain of chromosomes, resulting in aneuploidy, a hallmark of cancer and other diseases. Chromosome segregation is mediated by a megadalton protein complex called kinetochore that assembles at the centromere of each chromosome and serves as the physical linker between chromosomes and the microtubules. Early in mitosis, microtubule-kinetochore attachments are stabilized by tension that distinguishes proper attachment from the improper ones. However, during anaphase, kinetochore-microtubule attachments become vulnerable as tension drops when the chromosomes separate, and the microtubules start shortening. It is major question how kinetochores remain attached to microtubules under low tension. There are two competitive pathways that recruit the major microtubule binding protein, Ndc80c to the kinetochore- Mis12c and CENP-TCnn1 pathway. The CENP-TCnn1 pathway gets enriched at the kinetochore during anaphase, making it a potential pathway that could stabilize low tension attachments. I hypothesize that the CENP-TCnn1 pathway is key to understanding how kinetochores adapt to low tension during anaphase. My goals are to uncover the underlying regulatory mechanism facilitating upregulation of this pathway at the kinetochore during anaphase and how it contributes to kinetochore-microtubule attachments under low tension.
Rockefeller UniversitySponsor: Roderick MacKinnon
Many transmembrane proteins reside in functionally important clusters on cell membranes. Fluorescence microscopy of membrane proteins in cells has revealed ‘hot spots’ of co-localized proteins such as a2A-adreneregic G-protein coupled receptors and G proteins participating in signaling complexes. Yet the functional significance of these signaling clusters in cells is not well established. Developing tools to induce controlled clustering of membrane proteins in the lab would thus provide valuable insight into the function of these signaling complexes in cells.
My project proposes three complementary strategies to induce controlled protein clustering in lipid bilayers. The approaches span raft-forming lipid mixtures, tetraspanin and MARVEL domain 4-TM proteins, and membrane-anchored scaffolding proteins with multiple PDZ domains. These tools will be applied to a signaling pathway comprised of G protein-gated K+ channels (GIRK) and their activator, the βγ complex of G proteins (Gβγ). The extent of protein clustering and the subsequent effect on activity will be assessed using fluorescence microscopy and electrophysiology
University of WashingtonSponsor: Jane Coffin Childs Fellow
CRISPR systems are the adaptive immune systems of bacteria that are crucial for defense against bacteriophage infection. Immune memory is stored as short DNA sequences in the CRISPR array, called “spacers”, and upon transcription and processing these associate with Cas nucleases to search for matching viral targets and initiate nucleic acid cleavage. Type VI CRISPR systems are unique in that they recognize RNA, and target recognition leads the nuclease Cas13 to indiscriminately cleave cellular RNA. While the targeting steps of this CRISPR type are well-understood, it is still unknown how new spacers are acquired, especially since most type VI CRISPR operons lack the known acquisition machinery. Here, we probe the mechanisms of type VI CRISPR immune memory generation using Listeria seeligeri, a genetically tractable host that endogenously encodes type VI CRISPRs. We show that type VI CRISPR can use the adaptation genes from other CRISPR systems in the genome to integrate new memories into the type VI array, both in vivo and in vitro. In addition, we find no clear bias for acquisition of functional, RNA targeting spacers during growth or infection; however, we do observe some bias for acquisition from highly transcribed regions. In the future, we aim to identify additional factors required for acquisition of new spacers in the type VI CRISPR locus and determine the origin of newly acquired spacers.
Dana-Farber Cancer InstituteSponsor: Kathleen Burns
Long interspersed element-1 (LINE-1) is the only active, protein-coding transposon in humans. LINE-1 overexpression and LINE-1 retrotransposition are hallmarks of human cancers, although the impact of LINE-1 activity on cancer genomes and cancer cell growth remains poorly understood. My research focuses on addressing the hypothesis that LINE-1 retrotransposition causes substantial gross genome instability in cancers. Supporting this hypothesis, a recent pan-cancer analysis demonstrated associations between somatically-acquired LINE-1 insertions and segmental copy-number changes. Moreover, our lab recently identified that the Fanconi anemia/ BRCA pathway is required for growth of LINE-1(+) cells, suggesting that this DNA repair pathway might limit genotoxic effects of LINE-1. I am developing several approaches to assess the impact of LINE-1 on genome integrity, and I am evaluating the contribution of the FA/ BRCA pathway to LINE-1-associated DNA damage. These studies will be the first to evaluate the scope of LINE-1-mediated genome instability and should inform efforts to exploit LINE-1 genotoxicity as a cancer therapeutic strategy.