Medical Research

Grant Abstracts 2017

Salk Institute for Biological Studies

Inder Verma, Gerald Pao, Junko Ogawa, Nina Tonnu
La Jolla, CA
December 2017

The goal of this project is to harness the high refractive index of reflectin proteins to manipulate the optical properties of living cells and tissues.  Reflectins are found predominantly in the skin and eyes of cephalopods (squids, cuttlefishes, and octopi) and are essential for their unique camouflage and visual communication abilities.  By expressing reflectin genes in mammalian cells, investigators at Salk Institute aim to: (1) Generate transparent tissues in live mammals by matching the refractive index of the cellular cytoplasm and of the extracellular space to the higher refractive index of cell membranes; this would allow optical manipulation and microscopic observation of deep tissue areas.  (2) Create novel, optogenetic sensors for monitoring dynamic behavior within cellular compartments; these optical readouts would be dependent on optical refractive index changes resulting from the isotropic or anisotropic distribution of reflectins.  These technologies would collectively enable multiple types of imaging and achieve a completely novel modality of microscopy applications.

University of California, Irvine

Robert Spitale, John Chaput
Irvine, CA
December 2017

A grand challenge in the post-genomic era is to elucidate the complex layers of epigenetic control that regulate gene expression pathways in human cells.  Genome-wide association studies indicate that RNA modifications participate in all major post-transcriptional processes, including RNA stability, tagging, transport, and cellular localization.  However, the underlying mechanism by which these pathways operate remains largely unknown because current RNA biology tools do not distinguish the contributions of individual modifications.  This limitation poses a significant barrier to our understanding of the mechanism by which RNA markers influence cellular regulation.  Moving from a global understanding of the epi-transcriptome to a local understanding requires the development of new RNA biology tools that would make it possible, for the first time, to measure the contribution of specific modifications found on individual RNAs.  This project aims to determine whether cellular functions are regulated by individual post-transcriptional modifications or by ensembles of RNA modifications that function as a synergistic unit.  The approach of the two investigators at the University of California, Irvine involves creating a novel set of reagents (aptamers) and methods that can selectively disrupt and monitor specific RNA modifications at pre-defined sites in the human transcriptome.  Successful completion of this project would have a profound impact on our understanding of RNA biology and human disease.

University of California, Riverside

Sachiko Haga-Yamanaka, Naoki Yamanaka, Frances Sladek
Riverside, CA
December 2017

Steroid hormones regulate diverse biological processes, including immune response, energy homeostasis, sexual maturation and cancer progression.  In contrast to the extensive knowledge on their biosynthesis and downstream signaling, relatively little is known about the mechanisms that regulate steroid transport across cell membranes.  This is due to the widely accepted notion that lipophilic steroid hormones can freely enter and exit cells by simple diffusion across lipid bilayers.  However, the simple diffusion model of steroid hormone transport has not been critically tested in any in vivo model to date.  Work by three investigators at the University of California, Riverside, challenges this dogma by showing that a membrane transporter (named ecdysone importer) is required for cellular uptake of ecdysone, the primary insect steroid hormone, in the fruit fly model system.  Importantly, the same type of transporters exists in a wide variety of animals as well as humans.  The team therefore hypothesizes that mammalian steroid hormones also need transporters to enter target tissues.  Successful completion of this project would overturn the long-standing paradigm in endocrinology that steroid hormones enter cells by simple diffusion.  Moreover, the transporters are ideal targets for drug development to control steroid hormone function in vivo.

University of Notre Dame

Patricia Clark, Masaru Kuno
Notre Dame, IN
December 2017

Proteins are central to every cellular mechanism, and proper protein folding is a crucial prerequisite for proper cell function.  Yet established approaches to study protein folding have proven insufficient to develop a predictive understanding of the folding behavior of most proteins, including those implicated in human diseases.  This is due to both our inability to replicate the cellular environment in the test tube and the complexity of studying protein folding in the cell.  In the cell, every protein is synthesized vectorially (from one end to the other) and many proteins fold as they are being synthesized, i.e., vectorially as well.  There is strong – albeit anecdotal – evidence that vectorial folding can significantly alter folding mechanisms, including how likely a protein is to fold correctly rather than misfold and aggregate.  Currently, no method is available to recapitulate vectorial protein folding in the test tube.  As a result, there is no experimental platform available to study in detail its precise effects on folding mechanisms and outcomes.  To overcome these obstacles, two investigators at Notre Dame University will develop a first-of-its-kind approach to explicitly test, with unprecedented detail and on a proteome-wide scale, the impact of vectorial folding on folding mechanism and outcome.  They will use this strategy to study folding mechanisms of proteins that aggregate in typical folding assays.  This approach is expected to transform the current understanding of what leads to proper protein folding, versus aggregation.

Fred Hutchinson Cancer Research Center

Cyrus Ghajar, Peter Nelson, Patrick Paddison, Slobodan Beronja, Stephen Tapscott, Kirk Hansen
Seattle, WA
June 2017

The majority of cancer metastasis research is focused on uncovering why certain organs (or “soils”) are permissive to colonization by tumor cells.  But why other tissues only very rarely succumb to metastasis is almost completely ignored.  Using skeletal muscle (SkM) as a model of infertile soil, a team of investigators at the Fred Hutchinson Cancer Research Center and at the University of Colorado, Denver proposes a series of experiments at the biological and technological cutting edge to specify the molecular mechanisms by which SkM suppresses metastasis.  Their goal is to test whether ectopic expression of SkM-derived metastasis suppressors prevents colonization of susceptible sites.  The team plans to: (1) identify metastasis suppressors within SkM; (2) reverse engineer growth resistance using rare tumor cells that successfully colonize SkM; and, (3) express SkM-derived factors specifically within the lungs of mice to determine whether this converts the lung from a metastasis-prone site to a metastasis-suppressive one.  The innovation of this work is the application of sophisticated models and techniques – including some pioneered by the team – to address a long-standing biological mystery: how SkM suppresses metastatic outgrowth. Solving this mystery could hold the key to creating a new paradigm in metastasis research; one that is based on defining the molecular nature of tissue-driven tumor suppression, and applying this information to convert fertile tissues into resistant ones.

Mayo Clinic

Jan van Deursen, Darren Baker, Atta Behfar, Hu Li, Andre Terzic
Rochester, MN
June 2017

Humans and mice have the innate capacity to regenerate heart tissue, but the proliferative capacity of cardiomyocytes dramatically declines after birth, which is a key barrier to the use of regenerative medicine in the treatment of various heart diseases.  In contrast, lower vertebrates retain cardiac regenerative ability throughout life, which has spurred interest into the underlying molecular and cellular mechanisms with the intent to exploit the insights gained to reestablish cardiac homeostasis and repair in humans.  In zebrafish, the three layers that surround the myocardium, referred to as the pericardium, have been identified as a source of cells and signaling factors critical for cardiac regeneration.  A multidisciplinary team of Mayo Clinic investigators discovered that, in adult mice, senescent cells accumulate in the pericardium with aging and that the systemic elimination of senescent cells from midlife on attenuates fundamental aspects of cardiac aging, including cardiomyocyte hypertrophy, loss of stress tolerance and diastolic dysfunction, all of which are linked to heart failure.  These findings provide a rare, unexpected and promising entry point for closing the longstanding knowledge gap about the mechanisms that limit cardiac maintenance and repair as humans and mice age.  The investigators will exploit this opportunity by combining innovative mouse models and cell culture methods with advanced systems biology to identify pericardial signaling pathways that act to sustain myocardial architectural integrity and function.  They will also determine how bioactive factors secreted from pericardial senescent cells that accumulate with aging perturb these signaling networks.  Lastly, the team will evaluate the role of senescent cells in cardiac loss of function and regeneration in mice subjected to myocardial infarction.

Sanford Burnham Prebys Medical Discovery Institute

Duc Dong, Clyde Campbell, Joseph Lancman, Sean Zeng
La Jolla
June 2017

The prevailing strategy for regenerative medicine is to transplant into patients, replacement cells that have been derived outside the body (in vitro), from pluripotent stem cells. However low survival and functional integration of these cultured cells, as well as the inherent risks associated with the process of transplantation and the use of differentiated stem cells which may have acquired tumorigenic defects, remain formidable obstacles for this approach to be considered effective and safe.  To bypass these obstacles, Sanford Burnham Prebys investigators plan to generate replacement cells by directly converting any cell of choice, while they remain in the body (in vivo).  To do this, the investigators must push the boundaries of induced in vivo lineage conversion, challenging the dogma that cells are lineage restricted in their native microenvironment.  Leveraging zebrafish genetics, they have developed a novel in vivo vertebrate platform to rapidly identify and optimize transcription factors that can induce differentiated cells to change into lineages of interest.  Using this in vivo platform, the researchers have been able to directly induce several differentiated vertebrate cells, including skeletal muscle and skin epidermal cells, to directly convert into unrelated gut lineages, disputing the longstanding model that differentiated cells in vivo are lineage restricted.  In this project, the investigators plan to determine whether most cells in the body, at any age, have the potential to be directly converted into any other cell types, and to uncover and exploit the molecular mechanisms involved in this in vivo cell lineage conversion process.  These studies may pave the way towards a vast new in vivo supply of replacement cells/organs: shifting the paradigm of using an in vitro derivation, stem cell-dependent approach to using an in vivo lineage conversion, stem cell-independent approach to advancing regenerative medicine.

Stony Brook University

Lilianne R. Mujica-Parodi, Ken Dill, Steven Skiena, Steven Stufflebeam, Jacob Hooker
Stony Brook, NY
June 2017

In moving towards the goal of personalized medicine, investigators at Stony Brook University in collaboration with researchers at Massachusetts General Hospital/Harvard Medical School approach brain network connectivity, assessed by functional magnetic resonance imaging (fMRI) and associated cognitive function, as a dynamic emergent phenomenon.  They plan to integrate human neuroimaging data (7-Tesla fMRI and positron emission tomography, the latter to measure nutrient consumption by brain cells) with multi-scale biomimetic modeling, to test hypotheses with respect to how energy constraints (from diet to mitochondria) affect neural efficiency with age.  The interdisciplinary team of researchers will also experimentally investigate the use of exogenous ketones, a fuel source that is alternative to glucose, as a way to ameliorate age-related effects.  Based upon single subject-specific parameters, models will predict how networks self-organize in response to changes in energy supply and demand, then will be compared against human network trajectories.  Using an iterative approach, in which human data provide feedback, informing the models, which then make predictions that are tested against the next individual’s data, models will eventually converge in predicting human network trajectories based upon individually variable parameters.  In addition to generating fundamental understanding of how nutrition of brain neurons affects cognitive capacity and aging in humans, the project could provide a critical first step towards personalized neurology.  This would be accomplished by simulating—for a single individual—the potential consequences of different dietary interventions in protecting the aging brain.

University of Delaware

Jennifer Biddle, Adam Marsh, Thomas Hanson
Newark, DE
June 2017

It is well known that DNA alone does not determine the destiny of mammalian cells and organisms and that environments exert significant influence through epigenetic “above the genome” mechanisms.  What is not known is how the environment can shape the destiny of a microbe.  All organisms need to control which genes they express and send specific signals to coordinate metabolism and growth.  While humans and larger eukaryotes are known to have epigenetic components to this regulation, a new and exciting area of interdisciplinary research has emerged as researchers discovered that microbes may also use DNA methylation as an epigenetic control.  A team of investigators at the University of Delaware proposes to investigate the relationship between DNA methylation, gene regulation and energy stress in model and environmental microbial systems at genomic scales by building on their current platform development efforts.  Their hypothesis is that microbes do employ functional epigenetic signals, and that this mode of regulation is important under energy stress or in low-energy environments.  Through a better understanding of microbial gene control, the team expects to better understand how microbes impact the environment and human health.

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