Harvard University

NSF Awards · FY 2024 · 2024-08

This award supports the conference "Advances in probability theory and interacting particle systems" that will be held from the 26th-28th of August, 2024, at Harvard University. The conference has 21 confirmed speakers in very active and fundamental areas at the intersection of probability, analysis, and mathematical physics. The main aim is the rigorous study of universal phenomena for particle systems; to explain how random microscopic systems display predictable and statistically universal collective macroscopic behaviors. Large deviations are often key to understanding such problems, especially in large dimensions. Many problems remain in explaining how initial conditions and the details of the microscopic models govern the pre-stationary behavior. Many different approaches in this area will be represented at the conference, including spin-glasses, stochastic PDEs, and random walks in random environments. It is expected that this gathering will lead to cross-fertilization between these approaches, and inspire and inform a new generation of researchers. Many of the complex systems which will be discussed in this conference aim to describe real world phenomena and results proved for the mathematical models provide predictions applicable to the real systems. A key aspect of the conference proposal is centered on general methods for hydrodynamic limits and fluctuations of particle systems, in fixed or diverging dimensions. In the past, recent progress and the inclusion of new methods has shed light on many of the important questions related to the above. These include the understanding of p-spin models, a proof of the cutoff phenomena for the statistical physics models, fine asymptotics of mixing and cover times for general models, universality in random matrix theory. However, many of the original questions and conjectures remain open. Besides physical applications, complex systems (e.g., spin glasses, growth processes and random matrices) have found many applications in computer science, machine learning, data science, bioinformatics, chemistry, and even areas like ecology and earth science. The website for this conference is: https://www.math.harvard.edu/event/math-conference-honoring-srinivasa-varadhan/ This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2025 · 2024-08

PROJECT SUMMARY/ABSTRACT: Since its emergence, the Human Immunodeficiency Virus (HIV) has infected 84 million people worldwide and led to the deaths of 40 million people1. Despite the development of over 20 different treatment options, there is still no cure available. As a result, many individuals infected with HIV experience long-term side effects from antiretroviral therapy and have more comorbidities earlier in their lives than those who are not infected2,3. Therefore, there is a need to further research alternative ways to reduce or prevent HIV infection. The two coreceptors for HIV infection, CCR5 and CXCR4, which play an essential role in HIV infecting CD4 cells, are promising opportunities to limit HIV. While elimination of CCR5 in hematopoietic cells is being pursued, it is clear that CCR5-null hematopoietic cells can still be infected by CXCR4-tropic forms of HIV. Therefore, I seek to develop HIV resistant hematopoietic stem cells by targeting both of the CCR5 and CXCR4 co-receptors with base editing to prevent HIV entry while not impairing central functions of these proteins in hematopoiesis. My first AIM will use a base editor screen to identify CCR5 mutants that knock out CCR5 expression but also decrease the cell surface expression of CXCR4, which has been seen with other CCR5 mutants. The results of the screen will be analyzed with fluorescence-activated cell sorting (FACS) and single cell DNA sequencing. My second AIM will also use a base editor screen to identify CXCR4 mutants that prevent the binding of the HIV surface proteins, but allow for the binding of the natural ligand. These CXCR4 mutants will be tested with HIV pseudoviruses to identify mutations that prevent viral infection of the cells and a transwell migration assay to identify mutants that maintain CXCR4 responsiveness. Single cell DNA sequencing will be run on the cells that pass both of these tests to identify mutation candidates that meet the goals of this AIM. The Sankaran lab has extensive expertise in base editor screens and hematopoiesis. To complement this skill set I have contacted other faculty in the area, such as Dr. Alajandro Balazs, to assist with any HIV related questions I have and assist with the production of HIV pseudoviruses to test the hits from my base editor screens. My training plan focuses on gaining further expertise in hematopoiesis, HIV biology, DNA sequencing, processing of sequencing data, written and oral scientific communication, and scientific mentoring. With access to the Broad Institute of MIT and Harvard, Boston Children’s Hospital, and Harvard University I have all the tools, resources, and access to expertise necessary to excel in my research.

NIH Research Projects · FY 2024 · 2024-08

PROJECT SUMMARY Genomic imprinting is an epigenetic phenomenon in which somatic genes are mono-allelically expressed depending on their parental origin. Imprinted genes play critical roles in prenatal and postnatal development, including growth, metabolism, and neurodevelopment. Thus, genomic imprinting is essential for organismal viability, and disrupted imprinting frequently results in human disease. Imprinted genes are abundantly expressed in the brain; however, investigation into their regulatory mechanisms and physiological significance in the brain has been limited. Emerging evidence suggests that chromatin structure at imprinted domains may differ between the two parental alleles, implying a mechanistical model where differential chromatin structures may confer allele-specific regulatory roles. Nevertheless, the exploration of the impact of allele-specific chromatin structure on imprinted gene regulation is still in its early stages. The Mest-Copg2 imprinted domain, located on mouse chromosome 6 and human chromosome 7, presents a neuron-specific imprinting pattern and is associated with developmental and postnatal growth defects and atypical maternal behavior. In preliminary data, striking differences in parental chromatin structures at the Mest-Copg2 domain were observed. Yet, the extent to which chromatin structures play a role in imprinted expression of Mest-Copg2 remains entirely uncharted. Thus, this proposed research delves into the regulatory mechanism and functional role of the Mest-Copg2 domain. The focus of Aim 1 will be elucidating how allelic chromatin structures are established in the Mest- Copg2 domain. Epigenetic perturbation tools will be used to establish what are the basis of allelic chromatin structures in this domain. Aim 2 will identify cis-regulatory elements modulating Mest-Copg2 imprinted expression. CRISPRi experiments will be conducted in hybrid primary neurons to validate the activities of cis- regulatory elements in mediating imprinted Mest-Copg2 expression. In Aim 3, the physiological implication of neuron specific Copg2 imprinting will be investigated to provide insights into the role of genomic imprinting in neurons. These results will provide a novel regulatory mechanism mediated by chromatin structure, as well as functional implication of genomic imprinting in the Mest-Copg2 domain. The Harvard University will provide a vibrant research atmosphere with ample opportunities for inter- and intradepartmental collaborations. This environment, coupled with the guidance of Dr. Whipple and Dr. Dulac, will provide valuable training opportunities to develop scientific and professional skills necessary for becoming an independent researcher.

NIH Research Projects · FY 2024 · 2024-08

PROJECT SUMMARY Human patients who lose limbs due to injury or disease are faced with profound challenges for the rest of their lives. Prostheses, while increasingly sophisticated, lack key functionalities, and amputees report dissatisfaction with current prosthetic options. A long-term goal of regenerative medicine is to develop therapeutic limb regeneration strategies. Yet, this goal remains in the distant future because of a fundamental lack of scientific understanding of how to stimulate and guide a patient’s own cells to create a new limb. Animal models are likely to be key in building this missing foundation in scientific understanding of how to regenerate a limb. While mice offer many advantages in genetic studies, they are extremely limited in their limb regeneration abilities—like humans, mice are only naturally capable of regenerating the extreme distal tip of their digits. Full, natural limb regeneration has not been reported in any mammal to date. Frogs can naturally regenerate full limbs but only as tadpoles before development is complete. In contrast, many (if not all) salamander species studied to date can regenerate full limbs following amputation throughout life. Salamander limbs are remarkably similar in tissue composition and anatomy to human limbs. Thus, salamanders are ideal models for elucidating the fundamental biological processes required to regenerate limbs. Among salamanders, axolotls have emerged as a premier model because many genetic and experimental tools have now been developed for axolotl. An important missing piece of the overall puzzle is how stem cells are specified to form during axolotl embryological development and how these relate to the axolotl’s ability to regenerate limbs later in life. Here, we propose to use modern molecular genetic tools to build a map of transcriptional control of axolotl embryogenesis with single-cell resolution. This resource will enable us to identify the origin and nature of stem cells in axolotl embryos, and it will enable other researchers to develop hypotheses about other cell types as well. We will identify stem cells as they arise during development, along with the key transcripts that distinguish these cells from other cells, which will be essential for future studies, including those directed at understanding how limb regeneration may use stem cells. In parallel, in a complementary strategy, we will interrogate the embryological origins of 8 putative fibroblast stem cell types we recently isolated from axolotl limbs and demonstrated become activated to proliferate by amputation. We will extend this analysis to developing limbs. This work is essential for understanding the contribution of stem cells to the diverse tissues of the regenerate limb. It will also pave the way to experimentally manipulate specific stem cell populations in future studies in order to rigorously define their activities and the factors they use to execute these functions.

NSF Awards · FY 2024 · 2024-08

This project seeks to develop our understanding of the biology and evolution of plasmids, small DNA molecules that can transfer traits like antibiotic resistance between distantly related bacteria. The research will develop novel experimental tools and techniques that will be shared broadly with the scientific community. The project will also create engaging educational videos to teach evolution concepts to students and the public and develop low-cost tools for fluorescence experiments suitable for research and teaching labs. These efforts aim to make cutting-edge science more accessible and understandable to a wide audience. The research will investigate how plasmids compete and evolve within bacterial cells, a process critical to understanding bacterial adaptation but previously difficult to study experimentally. Using synthetic biology approaches, the researchers will construct artificial plasmid systems that allow precise measurement of intracellular plasmid competition. They will examine tradeoffs between gene expression and plasmid fitness, probe the molecular mechanisms involved, and explore how selection acts on plasmids across different scales. The project combines experimental techniques like microfluidics, fluorescence imaging, and DNA sequencing with theoretical modeling to gain insights into the evolutionary dynamics of these important mobile genetic elements in bacteria. This work has the potential to transform our understanding of horizontal gene transfer and bacterial evolution, with implications for predicting and potentially manipulating the spread of traits like antibiotic resistance. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-08

The broader impact of this Partnerships for Innovation - Technology Translation (PFI-TT) project lies in transforming the field of medical implants by introducing a new catheter-based additive manufacturing platform. Current medical devices are mass-produced and often do not fit the unique anatomical features of individual patients, leading to increased risks, complications, and higher healthcare costs. This solution addresses the challenge of creating on-demand customized implants that fit the unique anatomical features of individual patients, as opposed to the current one-size-fits-all approach. By enabling the creation of customized 3D implants directly inside the human body, this technology aims to reduce medical complications, improve patient recovery times, and lower healthcare costs. If realized, this technology has the potential to disrupt the medical device market, leading to more effective treatments and broader access to personalized healthcare solutions. Additionally, this project will use new component designs and assembly methods for in-vivo manufacturing, combining the advantages of minimally-invasive procedures with the benefits of the 3D biofabrication toolkit, which could be broadly applied to a wide range of medical applications. The project focuses on addressing the critical unmet need for personalized biomedical implants that conform to the unique anatomical features of individual patients. The primary research objective is to develop a catheter-based additive manufacturing platform capable of creating customized medical implants directly inside the human body. This project involves designing, synthesizing, and optimizing granular hydrogels that can be delivered through catheters to form three-dimensional structures in-vivo. The research will encompass the development of delivery mechanisms, material characterization, and the long-distance formation and stabilization of 3D implants. Key activities include the data-driven synthesis and characterization of soft implant-grade biomaterials, the development of sophisticated catheter-based delivery systems, the definition of in-vivo personalized manufacturing strategies, and extensive benchtop testing. The anticipated technical results include the design, development, and demonstration of this technology in benchtop models, establishing the technology's potential for future clinical efficacy and safety. By advancing the in-situ biomanufacturing toolbox, this project aims to set new standards for personalized medical treatments, ultimately leading to more effective and less invasive device-based healthcare solutions. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2026 · 2024-07

Project Summary The midbrain dopamine system plays a crucial role in various brain functions such as learning, motivation, and movement, and its dysregulation has been linked to various disorders such as addiction, mood disorders and Parkinson’s disease. A significant amount of evidence suggests that the activity of dopamine neurons in the ventral tegmental area (VTA) resembles a temporal difference (TD) reward prediction error (RPE) signal, which is the discrepancy between predicted and actual rewards, particularly, in those dopamine neurons projecting to the ventral striatum (VS). However, how the activity of dopamine neurons, particularly the RPE-related activity, is generated remains not fully understood. By combining new molecular, genetic, and electrophysiological tools, this project aims to uncover how neural circuits compute RPE-like responses. Aim 1 will examine the roles of glutamate inputs to dopamine neurons in the generation of dopamine responses. The overall pattern of glutamate inputs to dopamine neurons will be assessed using genetically-encoded glutamate sensors. The hypotheses to be tested is that glutamate and GABA inputs to dopamine neurons act synergistically to produce dopamine RPE signals, but compete to shape dopamine responses to aversive events. Aim 2 will create anatomical and functional maps of cell type-specific presynaptic neurons to dopamine neurons. Input neurons for dopamine neurons are distributed across many brain regions throughout the brain. Understanding the specific information transmitted from each region is crucial to comprehend how dopamine responses are generated. A novel method using a modified rabies virus will be applied to perform cell type-specific labeling of input neurons to projection-specific dopamine neurons. Using these tools, an anatomical map of glutamate and GABA inputs to dopamine neurons projecting to the VS will be created. Then electrophysiology and fiber photometry will be used to characterize functional activities of these input neurons during behavior. Their roles in the regulation of dopamine activity will then be tested by manipulating the activity of the major inputs. Aim 3 aims to elucidate the mechanism of dopamine-dependent incremental development of dopamine cue responses. Optogenetically-induced local dopamine release will be paired with sensory cues to elucidate the mechanisms underlying the development of dopamine cue responses. The preliminary results have indicated that local dopamine release in the VS, but not in the dorsal striatum, causes the development of dopamine cue responses broadly across the striatum. The hypothesis to be tested is that dopamine responses as well as value-related activity in the striatum gradually shift in time between cue and optogenetic dopamine activation, as predicted by TD learning models. Further, how this learning modulates the activity of neurons in VS and other brain regions will be examined. This Aim will clarify the neural mechanism through which dopamine responses dynamically change by learning, and reveal not only the mechanisms modulating dopamine activity, but also the mechanism of TD learning itself.

NSF Awards · FY 2024 · 2024-07

The integrity of the genetic information, carried by large chain molecules called nucleic acids (DNA and RNA), is vital for all organisms on Earth. When exposed to ultraviolet (UV) sunlight, DNA and RNA can form structural defects, which damage their function, cause mutations, or in severe cases - lead to cell death. But sunlight can be also a healer. The PI’s lab recently discovered that some short RNA strands can self-repair in a manner very similar to DNA. The PI observed that short RNA strands do so by developing states under UV-sunlight, which last long enough to transfer an electron to the damaged site and heal it. This discovery of RNA self-repair opens the door for a number of experimental projects on RNA’s origins and non-enzymatic replication, on RNA sequence selectivity, on tRNA function, etc. From a practical perspective, these results also have implications for how cells handle RNA damage in modern organisms, so the PI pay close attention to potential biomedical applications. Therefore, this award promotes progress in fundamental science, as well as advances in national health issues, as the handling of RNA damage by cells and viruses has become a newly active area since the pandemic. While advancing discovery, this award will also contribute to the education and training of future scientists and engineers as well. The research-based education of undergraduate and graduate students in our lab, and the high representation of women in the PIs lab will broaden participation in achieving these goals. This award project plans to elucidate the mechanism of the self-repair process in RNA and to extend its generality by experimenting with an array of RNA sequences, as well as with non-canonical nucleotides like Inosine. Working with short two- and four-base sequences is just the necessary first step. In addition to longer length, the investigators will explore both the base selection and the sequence directionality. The latter turns out to make a difference, as the investigators recently showed with DNA sequences of GAT=T versus T=TAG, assigning this disparity to the importance of different stacking overlap between the G and A bases. This award is exciting and important because no existing RNA photolyase enzymes are known, and the results from this award may shed light on how cells handle damaged RNA with mechanisms that are very different from DNA repair activity as known to-date. Therefore, some results from this award may have implications to physiology and medicine. On the other hand, as there were no enzymes during the emergence of life, this award will contribute to understanding the prebiotic sequence selectivity in RNA’s early functions in prebiotic chemistry and/or as information carrier in translation or replication. The investigators will explore the long-lived charge-transfer states in tRNA-analogs and similar RNA oligos as potential functional switches in the early evolution of translation. The ability of RNA and cofactors, like NADH, to form UV-induced charge-separated states and to transfer charge in a selective manner is not only intriguing but could be of paramount importance to the emergence of primitive cell functions during the origins and early evolution of life. What is often viewed simply as damage (or lesion), could well be a life-saving functionality for a primitive cell surviving on low-fidelity non-enzymatic RNA replication. With this new approach to nucleic acid UV-induced damage, the investigators will pursue a number of experiments into the emergence of functionality at the origins of translation (e.g., aminoacylation of RNA) and non-enzymatic RNA replication. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-07

Regeneration is the process by which animals can restore fully functional tissues and organs that have been damaged or lost. To do so, an animal must know precisely which cells and tissues need to be replaced. This work will focus on the striking case of an animal that can restore an entire head including a new brain, or a tail, in the correct place every time it is challenged to regenerate, and will ask how the animal determines which tissues it must build. To ask how genes specific to head versus tail tissue are turned on in the right place, achieving polarity along the head-tail axis of the body, the project will examine (1) how the decision to make mRNA from these genes is made in the genomes of head- versus tail-regenerating wounds, and (2) how the actions of these genes’ mRNAs, once made, may be controlled specifically in head- versus tail-regenerating wounds. By studying two distinct levels of gene regulation, using state-of-the-art sequencing and genome editing technologies, the project’s unbiased approach will provide new insights into polarity establishment during regeneration. The researchers will broaden this work’s impact by helping the research community in using the three-banded panther worm (the research organism that this project focuses on), by training undergraduates and middle school students, and by engaging the public through an accessible video explaining the project. This project will use the acoel worm Hofstenia miamia, which regenerates robustly from small body fragments generated by amputation. During the regeneration of H. miamia, a key polarity-determining gene, wnt-3, is specifically expressed in the posterior-facing (tail-forming) wound site, but not the anterior-facing (head-forming) wound site. This asymmetric wnt-3 expression requires the wound response gene egr. However, egr is expressed at both head and tail wound sites, raising the question of how symmetric injury stimuli such as egr expression result in asymmetric outputs driving patterning. This project will first focus on cell signaling events launched upon injury that may activate early gene expression, measuring Erk and Wnt signaling levels at head and tail wounds and assessing whether perturbing these pathways affects polarity outcomes. Next, asymmetric gene expression, such as for wnt-3, will be investigated at the level of transcriptional regulation, using chromatin accessibility data to find transcriptional activators/repressors that influence gene expression. Finally, the hypothesis that the asymmetry of wnt-3 in head versus tail wounds results from differential post-transcriptional regulation mechanisms, for example by microRNAs, will be tested. This work will answer questions about a regeneration patterning phenomenon at three levels of regulation (cell signaling, transcriptional, and post-transcriptional), building an understanding of the mechanisms beneath the stunning feat of regeneration with correct polarity. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-07

This project aims to enhance our understanding of motile cilia and flagella, cellular structures responsible for the locomotion of many single-celled eukaryotes, including the swimming of sperm cells and the movement of fluids such as mucus and cerebrospinal fluid in multi-cellular organisms. Despite the highly conserved internal machineries of cilia and flagella, each exhibits a unique waveform and behavior, tailored for a specific function or environmental niche. The study of ciliary structures is essential to identify the proteins involved in this process and determine how they function together to generate a sustained beat. By comparing ciliary structures across different organisms, we can gain information about the evolution of cilia and their adaptation to different environments and functions. The knowledge gained from this study can be used to help develop sophisticated computational models of ciliary motility and improve predictions of the effect of genetic perturbations and evolutionary adaptations. This project focuses on the axoneme, the highly conserved functional unit of motile cilia. Despite its significance for how cells move and behave, our understanding of this molecular machine is incomplete. The investigators plan to bridge this gap by studying flagellated organisms from the trypanosomatid family, which are particularly suitable for structural investigations, genetic manipulation, and waveform analysis. The first goal is to use high-resolution electron cryomicroscopy to determine the structure of the axoneme from Leishmania tarentolae flagella. The high-resolution information will allow us to identify every protein within a motile flagellum and understand their interactions. The investigators will then systematically analyze the contribution of each identified protein to flagellar movement, using a gene knockout screen and video microscopy. Lastly, they will explore the mechanisms that regulate flagellar beating using targeted CRISPR-based gene editing, quantitative mass spectrometry and electron cryotomography. This comprehensive, integrated approach will enhance the understanding of axoneme structures and the molecular mechanisms regulating flagellar motility. This collaborative U.S.-Swiss project is supported by the U.S. National Science Foundation (NSF) and the Swiss National Science Foundation (SNSF), where NSF funds the U.S. investigator and SNSF funds the partners in Switzerland. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-07

Scientists who work with materials such as cell lines, roundworms, zebrafish, and mice are grappling with the question of how to consider sex as a biological variable in laboratory models. This project aims to improve rigor, reproducibility, and precision in the study of biological sex in laboratory models and to promote constructive dialogue across biological fields and other related disciplines. This project investigates the conceptual foundations of research paradigms for the study of biological sex in basic, preclinical, nonhuman biological research. The project uses a case study approach to analyze four research programs across the fields of drug metabolism, endocrinology, behavioral science, and genetics, and examines a range of models from gene expression assays to in vitro organ cultures to animal models. Through these case studies, the project will analyze scientific practices surrounding questions of how to study biological variables. Through the in-depth case studies, interviews, and conceptual analysis, the team will study laboratory research practices across a range of scientific fields. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2026 · 2024-07

Abstract This proposal aims to determine the mechanisms that lead to the generation of astrocytes in the developing human cortex. Astrocytes are the most abundant cell type in the adult human brain, mediating vital functions including myelination, axonal guidance, synaptogenesis, and maintenance of the blood-brain barrier. During development, control over the spatio-temporal patterns of the production and numbers of astrocytes is necessary for proper brain function. The developmental potential of neocortical progenitors exhibits evolutionary divergence across mammalian clades, leading to primate-specific cell types, such as interlaminar astrocytes. Progress in studying human astrocytic development is limited by the ethical and practical challenges in working with human fetal tissue and fundamental differences between mammalian models and humans. Consequently, how the developmental potential of progenitor cells of the cortex is restricted to generate astrocytes remains unknown. Addressing this question is essential for understanding human brain development and will lay the foundation for uncovering the causes and devising new treatment strategies for astrocyte-related human diseases In mouse, astrocytic progenitors arise only after cortical neurons from the six layers are generated. The common hypothesis was that, similarly, astrocytes arise from outer radial glia in humans in the second trimester of development after the layers of the cortex are already formed. Preliminary work obtained through the analysis of single-cell gene expression data from the developing human cortex, in vitro embryonic stem cell experiments, and in vitro to in vivo mapping shows that the astrocytic lineage in humans arises very early before the cortical layers are formed and likely from the neuroepithelium of the forebrain. Computational analysis of the fetal tissue single-cell expression data and preliminary experiments implicate cell-to-cell contact-dependent signaling through YAP and NOTCH pathways in determining the astrogliogenic fate of the progenitors. Further, preliminary computational analyses of human fetal data identify critical transcription factors involved in this fate decision. The proposal aims to determine the developmental potential and the lineage decisions of the newly identified astrogliogenic progenitors over 9 months. This will be accomplished by tracing the lineage decisions of progenitors in the validated in vitro system using viral bar-coded viral libraries and clonal analyses and mapping the results, through data analysis, onto in vivo human fetal data as well as through immunostaining of cryosectioned fetal tissue obtained at different time points. The proposal further aims to determine the role of YAP and NOTCH signaling and the computationally implicated transcription factors in generating these newly identified progenitors. This is accomplished through novel human embryonic stem cell lines and live imaging to monitor the dynamics of these signaling pathways, chemical, and genetic perturbations that allow modulation of pathway activity, and inducible CRISPRi to knock down specific genes while monitoring their effects on the generation and patterning of the progenitors.

NIH Research Projects · FY 2025 · 2024-07

The ability to regenerate complex, multi-lineage organs remains one of the key challenges in regenerative medicine. Many mammalian organs, including the heart, digit tip, and skin, retain some ability to regenerate after damage during neonatal or fetal development, but the ability to regenerate decreases dramatically as the animal develops. Elucidating the mechanistic basis of this differential regenerative capacity is key to understanding the principles of regenerative control and laying the foundation for therapeutic reactivation of regeneration after injury. To this end, we propose to determine the genetic and molecular basis of scarless, multi-lineage regeneration after fetal skin injury. Healing of full-thickness injuries to postnatal skin is accompanied by fibrosis (scar formation), but injuries to fetal skin heal without scar formation, a phenomenon that has fascinated biologists for decades, but the mechanisms behind these differences remain poorly understood. We have overcome three technical hurdles and are now uniquely positioned to take on this challenge: (1) We have developed a robust surgical procedure to conduct wounding in fetal mice in utero. (2) We have optimized a cell isolation protocol to collect sufficient cells for single-cell RNA and ATAC analyses from wounded tissues. (3) We have established a strategy for rapid, in vivo genetic manipulation directly in wild-type mice by delivering targeted genetic cargo with viral vectors. Together, these approaches will enable us to identify and assay a relatively large number of genes in vivo for their involvement in either regeneration or scar formation. Furthermore, we have substantial preliminary data suggesting that injuries in fetal skin (E16.5) are healed with regeneration of diverse cell types from multiple lineages—hair follicles, innervations, blood and lymphatic vessels, and diverse dermal cell types—resulting in skin that is morphologically similar to unwounded skin. By contrast, these cell types fail to regenerate properly upon postnatal injury. We have also already identified one candidate factor—CXCL12, a postnatal wound-specific secreted factor, that inhibits regeneration when overexpressed in fetal skin. Building on this foundation, we propose to create comprehensive cellular and molecular atlases of fetal vs. postnatal wound healing processes using a single-cell multiomic approach (combining single-cell RNAseq and single-cell ATACseq) to assess both transcriptome and chromatin changes in the same single-cell. We will then determine if the reduction of CXCL12 in postnatal wounds promotes regeneration. We will also systematically test additional secreted factors that are unique to either fetal or postnatal wounds in their ability to drive or inhibit multilineage regeneration in the skin. Collectively, this work will provide critical insights into how regeneration ability is blocked or lost as an organ develops, open new research directions for studying organ- level regeneration in mammals, and guide new therapeutic strategies that promote regenerative healing under challenging conditions including burns and chronic non-healing wounds.

NIH Research Projects · FY 2025 · 2024-07

Project Summary Mitogen activated protein kinase (MAPK) signaling regulates cell growth in normal cells and is frequently overactivated in cancer. Within this pathway, RAF kinases are core signaling nodes and are of particular interest as cancer drug targets. Despite extensive study, RAF kinase function and regulation remain incompletely understood. Intriguingly, several studies have shown that the expression of CRAF protein but not CRAF kinase activity is essential for the growth of KRAS mutant lung cancer. To date, only a handful of function modifying mutations have been used to study CRAF function in this context, and these are often utilized in vitro or in exogenous overexpression experiments where stoichiometry is non-physiological and native scaffolding factors are absent. Interpretation of these experimental results can also be complicated by the modular nature of RAF dimers, and it is seldom clear which RAF homo-/hetero-dimers are responsible for observed cellular phenotypes. A clearer understanding of CRAF’s oncogenic role, including homo-/hetero-dimer functions, would inform future efforts to target CRAF in KRAS-driven cancers via inhibition, targeted degradation, or other mechanisms. This proposal will utilize a combination of unbiased base editor scans and “bump-hole” methodologies to elucidate the role of CRAF in KRAS-driven cancer and understand the relative activity of various RAF dimers. Specifically, I will test the hypothesis that CRAF’s role in KRAS mutant lung cancer is to form less active RAF dimers, diminish downstream signaling, and prevent otherwise toxic levels of MAPK signaling. Confirming this hypothesis has direct implications for cancer therapeutic development and would suggest that CRAF degraders but not competitive active-site inhibitors would be effective in this tumor subtype. This project will also advance fundamental knowledge of RAF kinases and expand the methods used to study them. In confirming the central hypothesis of this proposal, I will validate the goldilocks premise of RAF signaling – that too little or too much signaling impedes cancer growth. In aim one, unbiased base editor scanning paired with rigorous follow-up characterizations will expand knowledge of CRAF’s multiple functions and interaction partners. In aim two, I will validate a co-mutational approach to reveal the relative contribution of each RAF dimer to cancer growth and MAPK signaling. This aim also has broad application in cell signaling research and could constitute a generalizable approach to studying protein homo-/hetero-dimers with conserved dimerization interfaces. While advancing knowledge of RAF biology, this fellowship will also provide a rich training environment across two cutting edge research institutions: Harvard’s department of Chemistry and Chemical Biology and the Dana Farber Cancer Institute. Training will include regular meetings with my mentors, seminars with relevant scientific experts, and opportunities to present my research internally and externally. Mentorship provided by Brian Liau and Andrew Aguirre will greatly facilitate my development as an independent cancer researcher.

NSF Awards · FY 2024 · 2024-07

The research program proposed by scientists from the Harvard University (HU) and École Polytechnique Fédérale de Lausanne (EPFL) is expected to provide completely new insights into the physics and feasibility of photonics-enabled communication systems from one single platform. The program will explore and leverage the rich physics of nonlinear dynamics of highly nonlinear and resonant systems, and will result in novel types of miniaturized detectors, receivers and systems. The individual blocks will have a significant impact in sensing since the system can be used equally well for broadband spectroscopy. This may find applications in quality control, e.g. in food and pharma, but also in security scanners or environmental monitoring. This interdisciplinary program that combines theory, computational electro-magnetism, material science, photonics, microwave, and THz technologies, has very strong technological components, and requires mastery of nanofabrication techniques. Therefore, it will provide a unique training ground for involved undergraduate, graduate, and post-graduate students alike, and help train a new generation of engineers and scientists who are better prepared to address interdisciplinary challenges that they will face in the future. Technical description: The proposed project aims to research thin film lithium niobate (TFLN) for terahertz wireless both at chip scale and at the system level to address the need for efficient communication networks operational in the so far little allocated terahertz frequency range. It is intended to analyze the efficiency, speed, and versatility of high-Q resonators to generate, shape, collect and detect terahertz radiation coherently. Using frequency mixing with carriers in the telecom range research teams will also develop strategies to modulate the generated terahertz carriers in phase and amplitude. Their work will largely leverage on this platform's unique ability to tolerate large optical powers, have negligible insertion losses and large nonlinearity, which no other platform provides as a package today. Researchers’ goal is to demonstrate attractive solutions for all building blocks of a wireless link in TFLN. They will study, by theory and experiment, the physics of nonlinear effects with the following objectives: 1. Demonstration of terahertz generators for continuous-wave carriers and strategies to modulate them in amplitude and phase. 2. Demonstration of large-area electro-optic receivers (up to 5~mm). 3. Proof-of-concept of all-TFLN terahertz transmitter-receiver system and testing at 3 m distance. Scientists will use numerical solvers of coupled modes in the resonant regime in tandem with simulation tools CST and Lumerical and analytical models to distill fundamental limits in crosstalk, efficiency, and speed of the proposed devices in the presence of competing effects. They will build specialized optical setups capable of operating at ultra-high speeds. The project, if successful, will provide efficient, ultrafast sources, detectors and signal processing units that will significantly impact related fields in computing, sensing, imaging, or spectroscopy, besides communications. The proposed interdisciplinary program that combines theory, electromagnetism, material science, nanofabrication, photonics, microwave, and THz technologies, will provide invaluable training for students at all levels. Although it takes a fundamental approach to the addressed questions, commercialization will be considered. The project is designed to leverage on combined expertise in nanophotonics, microwave and fabrication of Lončar group at HU and in terahertz spectroscopy and metrology of Benea-Chelmus group at EPFL. This collaborative U.S.-Swiss project is supported by the U.S. National Science Foundation (NSF) and the Swiss National Science Foundation (SNSF), where NSF funds the U.S. investigator and SNSF funds the partners in Switzerland. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-07

The focus of this award is the development of a plan for the coexistence at the South Pole of transmissions to and from large communications satellite constellations like Starlink with instruments in the Antarctic Dark Sector vulnerable to these transmissions. This builds on extensive and varied experience in understanding and mitigating interference in precision CMB instruments. The proposed work would also continue ongoing efforts in understanding harmful interference thresholds and developing reasonable and well-justified plans for the inevitable existence of RF transmissions at some level within the Dark Sector. Historically, these efforts have addressed situations as they arise, or after data is discovered to be contaminated. The emerging threat of interference from large satellite constellations is too complex and potentially devastating to scientific datasets to address in the same ad hoc way. The project consists of coordination with the SpaceX network (Starlink) on a plan of coexistence; development of a prototype Starlink terminal suitable for long-term installation, including a winterized remote user terminal; development of an improved RFI monitoring system capable of detecting Starlink transmissions, with visualization tools and integration into scientific data streams; analysis of current data sets from the Dark Sector to characterize and understand RFI issues, and development of standardized RFI susceptibility tests to determine vulnerability of future instruments. The primary focus for this project is instruments (such as CMB-S4) designed to measure the cosmic microwave background with very long integrations. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-07

This Pathways to Enable Open-Source Ecosystems (POSE) Phase II project aims to revolutionize machine learning (ML) for scientific discovery by establishing an open-source ecosystem (OSE) that focuses on identifying, developing, and applying foundation models for science. MLCommons, a non-profit consortium comprising over 60 corporations, universities, and government entities with more than 2000 members, will leverage its existing community and resources to create an OSE that facilitates access to, experimentation with, and modification of benchmarks, datasets, and models for machine learning research. The OSE will also offer courseware, training, and documentation, serving as a national beacon for linking industry, government, and academia to democratize artificial intelligence (AI) technologies. The project will enhance education and workforce opportunities by engaging a wide community of students, teachers, and underrepresented groups in AI creation. The OSE's foundation models will enable diverse users to construct custom AI systems without requiring high-level AI knowledge, meeting societal and national needs while driving scientific breakthroughs, improving public health outcomes, and contributing to the nation's economic growth and competitiveness. This Pathways to Enable Open-Source Ecosystems (POSE) Phase II project, MLCommons Research Open-source ecosystem (OSE), will advance the identification and development of foundation models for science, promoting scientific progress by facilitating the transfer of artificial intelligence (AI) models across scientific domains. The project will expand the community of scientific contributors through proactive outreach, enhancing intellectual access to applied AI technologies currently limited to large-scale private enterprises. To address the shortage of AI talent and the challenges of scaling AI across academic and industry verticals, the OSE will develop a new generation of open-source ML technologies, adhering to FAIR (Findability, Accessibility, Interoperability and Reusability) principles and identifying standard APIs (application programming interfaces) and ontologies needed to integrate multi-modal datasets into foundation models. The OSE materials will be searchable, and the expansion of MLCommons Research under this project result in more collaborators with broader skills across multiple industry verticals and academia, leading to a greater variety of data and model structures that will better challenge future AI systems and serve as a valuable resource for those developing AI models for new and emerging application domains. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY Multicellular nervous systems allow animals to sense and respond to their specific environments. Yet animals evolved from unicellular eukaryotes, in which a single cell must carry out signal transduction from sensation to behavior. Therefore, understanding how unicellular eukaryotes sense and transduce important environmental cues into specific behaviors can reveal foundational principles of cellular signaling upon which animal multicellular sensory systems are built. Choanoflagellates (choanos) are a diverse group of micro-eukaryotes that are the closest living relatives of animals. Choanos are bacterivorous, requiring them to sense and navigate changes in pH, oxygen, and metabolites within their environment to find bacterial prey. Choanos have diversified to occupy a range of aquatic habitats, providing an opportunity to understand how their sensory mechanisms evolve to meet the demands of diverse ecologies. Furthermore, while typically unicellular, some choanos also have simple multicellular forms. Here, I propose to investigate how unicellular organisms detect and respond to a range of environmental cues and how these sensory systems evolve in conjunction with diverse ecologies and the innovation of multicellularity. This project builds on my expertise in bioinformatics, microscopy, and choano genetics, while learning new skills in electrophysiology and the biochemistry of sensory systems in the lab of Dr. Nicholas Bellono (Harvard MCB), who has pioneered physiological studies of sensory systems in non-traditional model organisms such as sharks, octopuses, anemones, and more. I plan to uncover fundamental principles of sensory biology and signal transduction, as well as to help reconstruct the types of sensory systems found in the unicellular ancestors of animals. I will be aided by an interdisciplinary advisory team, including my co-sponsor Dr. Richard Losick (Harvard MCB), a rigorous molecular biologist who will push me towards a mechanistic understanding of my system. I will also collaborate with Dr. Agnese Seminara (Univeristy of Genoa), a biophysicist specializing in fluid dynamics and decision-making, as well as Dr. Ryan Nett (Harvard MCB), an expert on small molecule isolation and characterization. I will characterize choano behavior and physiology in response to pH, oxygen, and bacterial metabolites, using electrophysiology and genetically encoded Ca2+ indicator strains (Aim 1). I will identify the receptors mediating these sensory systems and use gene family evolution analyses to explore how these choano receptor families have diversified in response to divergent aquatic environments (Aim 2). Finally, I will explore how choanos integrate multiple simultaneous sensory cues (e.g. pH and oxygen) in both their unicellular and multicellular forms to understand how multicellular evolution drives the innovation and integration of sensory systems, essential for animal origins.

NIH Research Projects · FY 2025 · 2024-07

PROJECT SUMMARY/ABSTRACT The mammalian SWI/SNF (mSWI/SNF) complexes represent a diverse family of ATP-dependent chromatin remodeling complexes (CRCs) that play critical roles in the modulation of chromatin accessibility and gene expression. mSWI/SNF complexes are combinatorically assembled from 29 different gene products to generate three distinct 11-15-subunit classes termed BAF, pBAF, and ncBAF complexes. Importantly, mSWI/SNF genes are mutated in over 20% of human cancers and several neurodevelopmental disorders (NDDs), in several cases representing causative genomic abnormalities. While biochemical, structural, and genomics-based studies have begun to define subunit-specific contributions to overall mSWI/SNF complex function, the specific roles for DNA- binding and histone reader domains present on subunits remain largely unassigned. In particular, the functional contributions of sequence-non-specific DNA-binding domains, including the winged-helix (WH) domain of SMARCB1, the high-mobility group (HMG) domain of SMARCE1, and the ARID domain of ARID1A/B subunits, have not been identified and represent key ‘hubs’ of frequent single-residue mutations in human cancer and NDDs. I aim to define the role for these domains in mSWI/SNF complex function in vitro and in the human cell context via the assessment of disease-associated perturbations. During this F31 fellowship, I will determine the roles for sequence-non-specific DNA-binding domains in a) proper mSWI/SNF complex assembly and biochemical integrity; b) mSWISNF complex catalytic (ATPase) activity and nucleosome remodeling; and c) for genome-wide mSWI/SNF targeting and DNA accessibility generation in human cell line model systems. I will accomplish this by generating wild-type (WT) and DNA-binding-deficient disease-associated mutant variants of mSWI/SNF complexes and evaluating their biochemical assembly, stoichiometry, and catalytic and nucleosome remodeling functions. Further, I aim to determine the impact of DNA-binding domain perturbations on mSWI/SNF complex genomic targeting, DNA accessibility generation, and subsequent gene expression in human cell contexts. This research will elucidate key features of DNA-binding domain-mediated SWI/SNF complex assembly, integrity, activities, and chromatin localization, linking these functions to resulting DNA accessibility and gene expression programs in human cells in normal and disease states. The mechanisms governing chromatin remodeling complex activities during basic cellular processes and in human disease remain incompletely understood, and with the highly frequent mutations in these processes observed in human cancers and neurodevelopmental conditions, such studies are uniquely pertinent and represent a high-impact priority for the field at-large.

NSF Awards · FY 2024 · 2024-07

This proposal aims to address the challenges of achieving optimal nonlinear control for dynamical systems in stochastic environments considering applications such as robots, aircraft, and automated manufacturing processes. Traditional methods to control these systems either provide sub-optimal solutions, lack rigorous analysis, or require a large amount of computation that could result in intractable solutions. Our research introduces a novel approach called spectral dynamic embedding, which aims to create efficient and reliable control algorithms suitable for a wide range of nonlinear systems. These methods will be tested in both virtual simulation environments and real-world robotic labs. The practical algorithms developed through this research can be applied to various applications, enhancing technologies in robotics, aerospace, manufacturing, energy, and beyond. The team will collaborate with industry partners to broaden the impact on society. Additionally, the project will involve students at various levels in cutting-edge research and experimentation, and also develop K-12 educational materials to inspire the next generation of scientists and engineers. The key innovation of this research lies in the unified spectral dynamic embedding approach, which reformulates the system dynamics in stochastic nonlinear control linearly to a nonlinear spectral feature space, rather than linearizing the dynamic model. This novel perspective allows for tractable dynamic programming or linear programming to solve the optimal policy and enables rigorous analysis of control optimality for general stochastic nonlinear dynamics. It also facilitates a simple learning procedure and computationally tractable exploration to accelerate data collection, both grounded in solid theoretical foundations. The research will develop computationally efficient methods for stochastic nonlinear control with either known or unknown models and will ensure the robustness and safety of the system. This interdisciplinary effort combines expertise in online control, reinforcement learning, optimization, statistical learning, and reproducing kernel Hilbert space to tackle this longstanding problem, aiming for transformative impacts on both control theory and machine learning. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-06

This POSE Phase I project establishes a community-driven effort to provide essential access to the fundamental components of the field of soft robotics and empower all members of the community to create new applications of soft robotics in all areas of the economy with reduced difficulty. This is through a combination of community management, design activities, and curation of well-documented and accessible open-source technologies that lower the barrier to entry for those looking to contribute to and innovative in this field. The project has invested, diverse leadership and collects and disseminates domain knowledge and standardized approaches for the fabrication, design, characterization, modeling, and material selection for soft robotics. This project builds upon the foundation of existing efforts of the Soft Robotics Toolkit and explores the scope and needs of the soft robotics community, inclusive of all facets such as academia, industry, art, hobby, and other overlapping sectors. The project also explores how soft robotics can bring together materials science, engineering disciplines, and biology and thereby serve to further entice larger audiences to participate, in particular underrepresented minority groups commonly excluded in science, technology, engineering and mathematics disciplines. To assess the needs of the soft robotics community, this project seeks expert insights, performs key stakeholder interviews, and distributes broad surveys. This project engages and interviews many of the stakeholders for the field of soft robotics. Relevant groups include: academic units, faculty, students studying soft robotics, industries and companies involved in soft robots, members of the hobby and art community that experiment with soft robots, as well as professional organizations that contribute to open-source products in general. Additionally, the project uses digital surveys to determine the needs of the aforementioned groups, while being inclusive of a broader audience and assessing general trends. The project establishes an organizing body incite growth of the community. The goal is to create a comprehensive and distributed resource that provides essential access to the fundamental components of the field and empowers all members of the soft robotics community to create new applications of soft robotics. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2026 · 2024-06

PROJECT SUMMARY: In this project, we seek to test the hypothesis that age-related perturbation of interorgan communication signals emanating from the hematopoietic (blood-forming) system may be a common driver of age-associated dysfunction across the body’s major organ systems. This possibility is based on recent human studies, which document an unexpected increase in the likelihood of diseases affecting non-blood organs in individuals with clonally expanded, mutant blood cells. To test our hypothesis, we will apply a novel in vivo gene editing system to introduce into mouse blood cells specific somatic mutations that are frequently associated with clonal hematopoiesis in aging humans. Mutations will be induced in situ, in discrete subsets of endogenous blood cells of otherwise normal young or aging mice, using a lineage-selective, virus-based gene editing system. We will then monitor these animals over time for the emergence of mutant blood cell clones and of well- characterized, age-associated pathologies in three different non-hematopoietic organ systems – the skeletal muscle, heart and brain. Each of these organs shows profound and well-defined alterations with advancing age, and prior studies demonstrate that aging pathologies that arise in each of these non-blood organs shows responsiveness to blood-borne (systemic) signals. Our proposed studies also will compare the possible differential effects of different mutations occurring in distinct target genes, each associated with aging of the human blood system, and evaluate whether the lineage restriction (cell type) or timing (age of onset) of the mutagenic event has any impact on subsequent organismal pathology. Finally, we will apply rigorous single cell sequencing, heterochronic parabiosis and serum analyte assays to uncover the molecular mediators of aging-relevant blood-to-non-blood organ communication networks. In this way, our experiments will directly test the hypothesis that age-associated clonal mutagenesis is a mechanistic driver of aging pathologies that disrupts interorgan communication between the hematopoietic system and other tissues, identifying the specific cellular contexts and mutagenic events occurring in the aging blood system that can drive dysfunction in the cardiovascular, neurologic and skeletal muscle systems through cell non- autonomous signals. Ultimately, the results of these studies will offer new guidance for the clinical interpretation and management of individuals identified to harbor clonal hematopoiesis, estimated to represent more than 20% of individuals over the age of 70 (and potentially nearly all individuals who reach very old age) and important new insights into the significant interorgan communication mechanisms that contribute to aging and disease.

NIH Research Projects · FY 2025 · 2024-06

Project Summary/Abstract The neurotransmitter dopamine (DA) is thought to play a central role in reward-based learning. The leading theory posits that DA release acts as a reward prediction error (RPE) which incrementally updates the brain’s predictions about future rewards. Recently, however, this hypothesis has come under attack, with two distinct alternatives suggested related to learning rate and retrospective inference. However, these models make similar predictions for patterns of DA release in standard classical conditioning tasks, making them difficult to separate. Additionally, these studies, as well as some supporting RPE, suffer from several caveats: (1) Rewards generate movements, which confound the interpretation of neural signals related to learning; (2) Rewards activate many learning systems in parallel, not just the DA system, limiting the ability to attribute learning to DA itself; (3) DA neurons have diverse functions that depend on their projection target, but prior studies often mixed these diverse populations when recording or stimulating DA neurons. Thus, the algorithm(s) by which DA drives reward learning and how this may be implemented in neural circuits remain unknown. The central idea of this proposal is to use artificial conditioning tasks in which natural rewards have been replaced with calibrated optical stimulation of dopamine axons (cDAS) in specific striatal subregions in head-fixed mice. By design, this approach (1) limits movements, (2) isolates the effect DA release itself, and (3) targets a projection-specific population of DA neurons, thus limiting caveats that hindered prior studies. Aim 1 uses this approach to identify the algorithm of DA-driven learning within the lateral nucleus accumbens (lNAc), a site with concentrated signatures of RPE in DA release. Artificial conditioning tasks were designed to arbitrate between RPE and alternative models. Preliminary data suggest that cDAS in lNAc generates changes in DA activity that are consistent with RPE but not alternatives. In Aim 2, cell type-specific electrophysiological recording and optical stimulation in lNAc will be used to answer how DA release alters striatal activity to drive RPE learning. Aim 3 expands these studies to the dorsal striatum (DS), where DA release is thought to shape and reinforce movements during addiction and other forms of habit formation. Multisite cDAS and projection- specific optotagging of DA neurons will be combined with cutting-edge video processing techniques to test the hypothesis that DA-driven learning spreads from lNAc to DS to shape movements (an “actor-critic” model). Together, these reductionist studies will enable the algorithmic and neural circuit basis of DA-driven learning in the striatum to be dissected with unprecedented precision. The proposed research will be conducted in the Uchida Lab at Harvard, an excellent environment with all the necessary resources at hand. The candidate has assembled an expert advisory committee and has made detailed plans to acquire the additional technical and professional skills needed to complete the proposed project and launch his successful transition to an independent research career.

NIH Research Projects · FY 2026 · 2024-05

ABSTRACT Our vision is to unravel and ultimately reverse the intricate network of causal factors throughout the life course that disrupts biological homeostasis to promote colorectal cancer (CRC) among individuals younger than age 50 years. Uniting leading scientific minds in early-onset colorectal cancer (EOCRC) research and complementary fields, we have embraced disruptive, transdisciplinary approaches spanning cells to individuals to populations to address the core Grand Challenge to “Determine why the incidence of early-onset cancers is rising globally”. We will address specific questions of “the mechanisms linking lifetime exposures with cancer initiation and promotion” by focusing on EOCRC as an ideal model for early-onset cancer due to the availability of well- characterized animal models and a well-established and prevalent precursor lesion, the adenomatous polyp (adenoma), offering a unique opportunity for interception and prevention. Our work will transform the field by directly addressing our overarching goal to “identify and understand the processes through which different biological and environmental factors cause early-onset cancers”, and reverse the burden in a timely, effective, and feasible fashion. Our team, both working independently and in collaboration, has uncovered several risk factors that are likely to be drivers for the rising incidence for EOCRC. We are now uniquely positioned to translate etiologic understanding to actionable prevention by identifying novel factors, including environmental determinants, and deepening our understanding into overlooked dimensions of exposure throughout the life course. The unprecedented scope and scale of our proposal can only be supported through Cancer Grand Challenges since our “high-risk” disruptive approach requires deep interactions between work packages (WP)s led by leaders in distinct disciplines. This will enable incorporation of fresh perspectives to move beyond traditional risk-factor epidemiology toward an integrated, mechanistically-informed model with population scale and cellular resolution of the multiple and cumulative “hits” that promote EOCRC to inform the development of actionable prevention. Our innovations intersect epidemiology, small molecule discovery, genomics, stem cell biology, immunology, and computational biology with these key features: 1) harmonization of cohorts with data and biospecimens collected across the lifecourse; 2) innovative and reliable analysis of small molecules to detect novel exposures; 3) high-resolution technologies for analysis of target tissues; 4) model systems capable of interrogating accumulating exposures across the lifespan and their impact on the cellular ecosystem; 5) prevention through risk assessment and pharmacologic/lifestyle interventions. Collectively, our work will serve as an exemplar for transforming research into other early-onset cancers.

NIH Research Projects · FY 2025 · 2024-04

PROJECT SUMMARY/ABSTRACT Humans have evolved an expanded and elaborated brain capable of higher-order cognition. However, the sequence variants and resulting neural specializations that distinguish humans from other mammals are commonly dysregulated in diseases such as autism spectrum disorder (ASD). This suggests that human-specific non-coding variants are enriched for neural functions and may underlie genetic and phenotypic disease vulnerabilities. Thus, there is a critical need to identify and characterize the non-coding variants that underlie human neural specializations. However, identifying the causal variants that contribute to human neural specializations is a daunting challenge that has been likened to searching for needles in a haystack. In this proposal, Dr. Janet Song will improve prioritization of human-specific variants for further functional analysis using two complementary approaches (Aims 1 and 2) and determine whether prioritized variants regulate nearby gene expression in a high-throughput manner (Aim 3). Dr. Song will use the human-chimpanzee tetraploid system to link regulatory regions that are differentially accessible between species to nearby differential genes in neural progenitor cells and excitatory neurons, two cell types that are profoundly changed in humans and are commonly dysregulated in neurological diseases (Aim 1 – K99 phase). As a complementary approach, Dr. Song will identify constrained human-specific insertions and assess their contribution to ASD risk (Aim 2 – K99/R00 phase). Dr. Song will then evaluate the effects of human-specific variants on nearby gene expression in neural cell types using CRISPR inhibition screens (Aim 3 – K99/R00 phase). This K99/R00 proposal will support Dr. Janet Song in her pursuit of the genetic basis of human neural specializations and allow her to acquire new skills in comparative and functional genomics that will open up innovative approaches to explore this problem. This proposal will be initiated during the mentored period in Dr. Christopher Walsh’s lab at Boston Children’s Hospital / Harvard Medical School and continue in Dr. Song’s own lab upon securing an independent position. In addition to providing immediate insights into the genetic basis of human neural specializations, the proposed research will lay the foundation for Dr. Song’s independent research program. It will provide a framework for future studies in additional cell types or paradigms, pinpoint high-priority loci for single-locus studies, and identify a corpus of human-evolved elements that may contribute to genetic risk for neurodevelopmental and neuropsychiatric diseases. Long-term, Dr. Song’s independent research program will dissect how sequences that changed in humans relative to other mammals result in human-specific neural phenotypes, and ultimately, contribute to neurodevelopmental and neuropsychiatric diseases.