Purdue University

NIH Research Projects · FY 2026 · 2022-03

Tourette Syndrome (TS) is characterized by multiple, persistent motor and vocal tics and affects approximately 1% of children worldwide. There is no cure for TS and efforts to develop novel treatments are hampered by our limited understanding of the underlying neurobiology and brain structural and functional deficits. Although tics represent the hallmark feature of TS, up to 90% of patients present with additional neuropsychiatric disorders, including Obsessive Compulsive Disorder (OCD up to 50% of TS patients), Attention Deficit Hyperactivity Disorder (ADHD up to 54.3%), Autism Spectrum Disorders (ASD up to 20%), Major Depressive Disorder (MDD up to 26%), and Anxiety Disorders (AXD up to 36%). These comorbidities contribute to decreased quality of life and introduce etiological and phenotypic heterogeneity that further hampers efforts to elucidate the TS neurobiology. Here, we are proposing to investigate TS-related brain structure and function at a large scale but also to identify those factors that lead to high comorbidity with other disorders. Motivated by international collaborative studies on the genetics and neuroimaging of TS led by the PI, we bring together all major worldwide collaborative efforts on neuroimaging and genetics for TS and aim to integrate with equivalently large and already existing studies of highly comorbid OCD, ADHD, ASD, MDD, and AXD. We take advantage of access to data, resources and standardized pipelines from the ENIGMA (Enhancing Neuroimaging Genetics through Meta- Analysis) consortium and the Psychiatric Genomics Consortium (PGC). First, we will establish the ENIGMA-TS working group, for which PI Paschou has already laid the groundwork, with 17 sites from nine countries having agreed to contribute existing neuroimaging and clinical data from 1,930 cases and controls. We will pool together T1 structural imaging data as well as rsfMRI and DTI data. Second, we will pursue the largest neuroimaging studies for TS to date aiming to understand the pathophysiology of the disorder. Pursuing cross-disorder analysis, we will also integrate our TS neuroimaging data with existing ENIGMA data for the most frequently comorbid disorders in TS (OCD, ADHD, ASD, MDD, and AXD). Third, we will aim to uncover brain regions that correlate to genetic background in TS and related disorders. To do this we will analyze TS genomewide association studies (GWAS) but also pursue cross-disorder GWAS for TS and comorbid disorders. We will leverage our findings from the first large-scale cross-disorder GWAS meta-analysis for TS, OCD, ADHD, ASD (led by the PI), as well as access to data from ENIGMA GWAS on brain structure from more than 50,000 individuals and the UK Biobank on additional 10,000 individuals. Importantly, we will also leverage access to population-based cohorts (ABCD and Generation R), with longitudinal brain imaging, clinical but also genetic information in order to replicate our findings to diverse populations and explore correlations to behavioural profiles moving beyond strict diagnostic categories. Ultimately, our findings will help elucidate brain structure and function in TS but also disentangle relationships with comorbid OCD, ADHD, ASD, MDD, and AXD.

NIH Research Projects · FY 2026 · 2022-01

PROJECT SUMMARY When a mosquito-borne flavivirus encounters a cell, it must adhere to a receptor on the cell surface, endocytose, and finally fuse with the endosomal membrane. To accomplish this, flaviviruses use an exterior lattice of 180 E proteins arrayed in a herringbone arrangement of 90 antiparallel dimers at neutral pH. Acidification in the late endosome induces a widespread conformational rearrangement, resulting in 60 outward-facing trimeric E spikes that can embed into the host membrane and pull the membranes together, fusing them and releasing the viral RNA into the host cytoplasm. Although flavivirus lattices are canonically described as 90 dimers lying flat (mature state) or 60 trimers facing outward (immature and fusion states), up to 50% of Dengue virions have incomplete maturation that results in a mosaic pattern of E dimers and trimers with different orientations. It is unknown whether mosaic lattices are less functional than their perfect counterparts due to steric hindrance of the conformational rearrangements, or alternatively might have certain advantages that explain why evolution has conserved their heterogeneous arrangement. This has strong consequences for the design of therapeutics, as the mature and immature patches have different epitope exposure and possibly different binding affinities for antibodies that are not well understood. We will explore this question through a combination of structural and functional studies performed on mosaic Dengue and West Nile viruses, using cryo-electron tomography and subtomogram averaging to determine the position and orientation of individual E proteins within the viral lattices, and designing new analyses to describe the heterogeneity of the viral population. We will evaluate how the mosaic surface affects fusion and antibody binding, and directly visualize the structure-function relationship by imaging viruses interacting with target membranes and cells. This approach will allow us to identify which areas of a mosaic lattice participate in adhesion or fusion, and whether functional virions favor more heterogeneous or homogeneous surfaces. Current structural biology is usually performed on samples that contain a large number of inactive virions; by imaging functional states directly, inactive virions are eliminated from analysis to facilitate identification of the structural states of the virus that should be prioritized in structure-based therapeutic and vaccine design. While this work will focus on the flavivirus lattice, functional lattices are ubiquitous in all the domains of life and play integral roles in human health and disease. The methods and analyses we develop to study flaviviruses will directly apply to other viruses, but will also potentially aid in understanding processes as diverse as bacterial chemotaxis, carbon fixation, and human cardiac muscle contraction.

NIH Research Projects · FY 2025 · 2021-12

Emerging evidence implies that protein acetyltransferases play a crucial role in diverse biological processes and various human diseases including cancer. Protein N-terminal acetyltransferase D (NatD), also known as Naa40, Nat4, or Patt1, is a unique member of protein N-terminal acetyltransferases because it only acetylates histones H2A and H4 that share the identical N-terminal sequence of SGRGK. NatD has been reported to play an important role in a variety of processes including remodeling of chromatin structure, cell migration and invasion, and apoptosis. The elevated level of NatD in human lung and colorectal cancer tissues correlates with poor clinical outcomes. Moreover, loss of NatD suppresses human lung cancer cell invasion and decreases the tumor growth in colorectal cancer xenograft mice models. Hence, we hypothesize that NatD is a compelling target for the development of novel cancer therapeutics for lung and colorectal cancers. However, there are no specific small molecule probes available for NatD to decipher the functions of NatD acetyltransferase activity in cancer. To fill this gap, our long-term goal is to discover novel, potent, and selective small molecule NatD inhibitors. For this application, we will employ a series of facile and reproducible high-throughput screening (HTS) assays with orthogonal readouts to screen 400,000 diverse compounds from selected chemical libraries at the Chemical Genomics Facility at Purdue Institute for Drug Discovery. Then we will characterize active compounds in structural, mechanistic, selectivity, and cell-based studies. Upon completion of this project, we expect to identify potent and selective first-in-class NatD small molecule inhibitors as chemical probes for NatD function in cells. The knowledge gained from this project would expedite the development of NatD modulators and our understanding of NatD-regulated pathways in cancer patients.

NIH Research Projects · FY 2025 · 2021-09

PROJECT SUMMARY/ABSTRACT Corneal neovascularization (CNV), or the invasion of new blood vessels into the avascular cornea, remains one of the major causes of blindness worldwide. Topical eye drop therapy serves as the most easily accessible and noninvasive treatment of CNV, but its therapeutic efficacy is limited due to the corneal barriers and nasolacrimal drainage that quickly eliminates eye drops within a few minutes. Recent advances of biodegradable microneedles have led to the development of many strategies for intraocular drug delivery through the corneal barriers, which increases therapeutic efficacy. However, the clinical implementation of these microneedles in human eyes is often impeded due to their relatively large size for the human cornea and rapidly dissolving nature (typically, within 15 minutes-2 hours), which causes pain and limited therapeutic efficacy, respectively. The research endeavors of this project will focus on the development of a new class of intraocular drug delivery platform made from fully-miniaturized (i.e., at nanoscale) and slowly-biodegradable silicon nanoneedles that are > 30-fold smaller and provide > 10-fold slower degradation rate compared to current biodegradable microneedles. The silicon nanoneedles will be built upon a water-soluble contact lens that offers excellent biocompatibility, softness, rapid degradability in tear fluid (within no more than 30 seconds), and optimal curvature to fit a variety of corneal shapes (8.3-9.0 mm base curve radii). These aspects are essential to allow for the minimally-invasive, painless, and long-term (over days) sustained delivery of ocular drugs through the corneal barriers. In this project, we will reveal the structure-property-performance relationship of the silicon nanoneedles with various size, shape, aspect ratio, and surface porosity in vitro and ex vivo. We will also evaluate the biosafety, therapeutic efficacy, and side-effects of the silicon nanoneedles in a well-established rabbit CNV model in vivo, as compared to conventional anti-vascular endothelial growth factor therapy (anti- VEGF) and laser therapy. Because the materials used for both the nanoneedles and water-soluble contact lens are already in clinical use, this intraocular drug delivery platform can be rapidly translated into clinical practice for the treatment of CNV in human eyes. Furthermore, the established intraocular drug delivery platform will be also useful for the treatment of other chronic ocular diseases, including corneal, retinal, and choroidal neovascularization.

NIH Research Projects · FY 2025 · 2021-09

SUMMARY Industrial hygienists are tasked with protecting worker health. However, there are many hazardous substances which lack official guidelines related to their safe management. Thus, there is a need for professionals charged with protecting worker health to be able to increase their knowledge regarding these emerging contaminants, emerging technologies, and systems to protect worker health. This project was designed to address this need. The Distance Education and Training on Emerging Contaminants and Technologies (DETECT) project will implement online training modules and in-person research experiences to provide unique educational opportunities for education on emerging contaminants and technologies for prospective graduate students, graduate students, and industrial hygienists. The DETECT program will establish a consortium between established programs in industrial hygiene at Purdue University, the University of Toledo, the University of Oklahoma Health Sciences Center, and the University of South Florida. The DETECT program will focus on identifying and characterizing emerging contaminants, use of emerging technologies to assess and monitor hazardous chemicals, and safety management systems or strategies to mitigate and prevent potential hazards. Emerging contaminants to be discussed include, but are not limited to nanoparticles, bioaerosols, hazardous algal blooms, and ototoxic compounds. There will be three main educational components of the DETECT program: online educational modules, in-person research sessions, and online laboratories. First, we will create a series of for- credit and non-credit online lessons; these will be grouped together in three modules. The for-credit version of this online educational content will be incorporated into existing industrial hygiene graduate programs at the DETECT consortium institutions. The non-credit version will be available free of charge for anyone to access via the Purdue Online website. Second, we will develop and run in-person research based educational sessions. Each year, these will be hosted by a different DETECT consortium intuition and will feature a different topic. Prospective graduate students and graduate students from the DETECT consortium institutions and beyond will be encouraged to participate. These intensive sessions will include research training, laboratory tours, and the opportunity for participants to complete, analyze, and present a short research project. Third, we will develop five online laboratories and at least one virtual reality laboratory. The online laboratories will be accessible using an internet browser, and will be incorporated into the online educational modules. The virtual reality laboratory will be completed in-person by graduate students at the DETECT consortium institutions. Upon completion of this project, we will have developed and implemented training in key emerging contaminants and technologies to assess, mitigate, and prevent their impact via platforms that are accessible to a large population. This will have a significant impact on industrial hygienists and other professionals’ ability to protect workers and the public from health effects resulting from exposure to hazardous substances.

NIH Research Projects · FY 2025 · 2021-09

Lowe Syndrome (LS) is a disease caused by mutations in the OCRL1 gene that unfortunately leads to the early death of affected children and has no cure. However, this project aims to change such scenario. Further, since OCRL1 mutations also cause a related renal condition known as Dent-2 (D2) disease, this proposal will also benefit D2 patients. LS patients display mental retardation, ocular (e.g., glaucoma, cataracts) and renal (e.g., kidney stones, LMW proteinuria) abnormalities, while D2 patients show renal symptoms almost exclusively. Although most OCRL1 missense mutations found in patients alter the phosphatase domain of the encoded protein Ocrl1, about half of these changes do not affect residues involved in binding or modification of the substrate. In fact, our results indicate that a substantial number of patients express Ocrl1 mutated proteins with intact binding/catalytic sequences but locked in a conformation unable to process lipid substrates. Therefore, we HYPOTHESIZE that a subset of Ocrl1 patient mutated proteins can re-acquire functionality by action of drugs able to stabilize the enzymatically active conformer (allosteric activators). Indeed, as a result of a series of small molecule screens performed in our lab, we identified a group of compounds (including FDA-approved drugs) as able to restore catalytic activity of different Ocrl1 patient mutants and to suppress a readout LS/D2 cellular phenotype. To test our hypothesis, 4 allosteric activator candidates will be used along with a panel of LS and D2 Ocrl1 patient mutated variants to pursue the following specific aims focused on kidney function: AIM 1. To determine the in vitro effect of selected candidate drugs ON THE BIOCHEMICAL ACTIVITY of a panel of Ocrl1 LS/D2 patient mutated variants. AIM 2. To determine the effect of selected candidate drugs ON MULTIPLE LS PHENOTYPES observed in kidney cell lines, kidney organoids and a zebrafish animal model bearing LS/D2 patient OCRL1 mutations. AIM 3. To determine the effect of selected candidate drugs ON THE STABILITY AND STRUCTURE of the Ocrl1 LS/D2 mutated variants bound or not to substrate. This project is INNOVATIVE because it introduces the concept of LS and D2 as heterogenous conditions with some patients displaying a conformational/misfolding disease component and proposes a novel therapeutic approach using allosteric activators. Importantly, this project has high SIGNIFICANCE as it will address the lack of therapeutic approaches designed to suppress the upstream cause of a disease that affects tens of thousands of children in the US and worldwide. Further, FDA-approved candidate drugs currently used to ameliorate other conditions can be readily repurposed to LS/D2. Therefore, the translational IMPACT of this project is very high.

NIH Research Projects · FY 2025 · 2021-09

ABSTRACT In multicellular organisms including animals, plants and human beings, stem cells play conserved roles in maintaining themselves undifferentiated but continuously dividing to sustain organ development and body formation. Defects in stem cell function lead to abnormal organ development and diseases. On the other side, unraveling stem cell behavior and regulation can provide effective cell-based therapies including tissue regeneration for human diseases such as neurodegeneration, diabetes, and heart disease. To date, the regulatory mechanisms controlling the initiation, proliferation and termination of stem cell niches are still not fully understood. Here, we propose to determine the cellular and molecular basis underlying stem cell homeostasis using the Arabidopsis shoot apical meristem (SAM) as a model system. Because undifferentiated stem cells in Arabidopsis SAMs are at and near the surface and the living SAMs can maintain sessile during experiments, non-invasive time-lapse live imaging approaches are particularly effective in Arabidopsis, to follow the fate of each stem cell and their derivatives and to quantify cell dynamics in vivo. In addition, great genetic resources in Arabidopsis allow us to quantitatively dissect gene function through using an existing array of mutants with changed SAM sizes and stem cell numbers. Using this system, through a combination of in vivo time-lapse confocal imaging, transient and stable perturbations of gene function, in vitro biochemistry and in silico quantification and modeling approaches, we aim to uncover mechanisms by which a small group of key transcriptional regulators that are excluded from stem cells but determine the identity and activity of the stem cells in the SAMs. Our work will not only define the yet missing molecular linkage and cell-cell communication between differentiated and undifferentiated cells, but also elucidate a regulatory network underlying a cell non- autonomous phenomenon in control of stem cell homeostasis.

NIH Research Projects · FY 2025 · 2021-08

Abstract The main objective of this project is to advance our extensive preliminary results and develop novel protease inhibitor drugs for the effective treatment of COVID-19. The COVID-19 pandemic, caused by the highly transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV- 2), emerged in central China's Hubei Province, Wuhan in December 2019. The outbreak has spread at an alarming rate, creating a catastrophic global health crisis the likes of which the world has not witnessed in over 100 years. SARS-CoV-2 has spread to nearly every continent around the globe and has affected over 4.8 million individuals with more than 380,000 deaths. Thus far, there are no vaccines or approved effective drug treatments against COVID-19. The development of antiviral agents is the foremost priority for reducing morbidity and mortality around the world. SARS-CoV-2 encodes two classes of cysteine proteases, the 3-chymotrypsin-like protease (3CLpro) and the papain-like protease (PLpro), which are critical for coronavirus replication. These two proteases have been recognized as important targets for drug development against COVID-19 and related pathogenic coronaviruses. In our extensive collaborative work against SARS and MERS coronaviruses, we previously developed and reported the development of a variety of covalent and non-covalent small- molecule reversible inhibitors of SARS-CoV-3CLpro that showed significant antiviral activity. We also demonstrated that PLpro is a significant drug target by developing the first non-covalent, reversible and potent inhibitors of SARS-CoV-PLpro that show effective antiviral activity in cell culture and in an animal model. We carried out structure-activity and extensive X-ray structural studies to gain molecular insight into the 3CLpro and PLpro active sites of SARS, MERS and most recently SARS-CoV-2. Furthermore, we have now generated a number of new small molecule lead inhibitors of SARS-CoV-2 3CLpro and PLpro and determined several high- resolution X-ray structures of SARS-CoV-2 3CLpro inhibitor complexes. This work forms the basis of our proposed studies. We now plan to design, optimize and develop structurally novel drug- like and broad-spectrum protease inhibitors that show favorable pharmacological profiles and low toxicity. We will carry out a multidisciplinary research effort that will integrate X-ray structure- guided design, iterative medicinal chemistry, molecular modeling, biochemical and biophysical assays, antivirus and cell biological studies in combination with various physiochemical assays to optimize compounds for preclinical development against COVID-19.

NIH Research Projects · FY 2025 · 2021-08

Project Summary Implicit Structural Priming as a Treatment Component in Aphasia Impaired message-to-structure mapping is at the heart of communication deficits in persons with aphasia (PWA), resulting in impaired sentence production and comprehension. As of yet, the few treatment options available for the mapping deficits involve explicit metacognitive training of sentence production, yielding variable generalization and maintenance effects. Therefore, there remains a critical need to identify interventions that successfully improve mapping abilities in PWA. This project introduces implicit structural priming as a novel facilitator for language recovery in aphasia. Structural priming, a tendency to repeat or better process a current sentence because of its structural similarity to a previously experienced (“prime”) sentence, has been ubiquitously observed across decades of psycholinguistic research and viewed as a powerful tool to study the processes of implicit language learning. Preliminary studies reported in this application suggest that structural priming can be applied to PWA and might produce positive, enduring language recovery in PWA. The planned studies seek to test the hypothesis that implicit structural priming alters the central syntactic system in PWA, creating lasting and generalized improvements in both language production and comprehension. Aim 1 will determine the extent to which different manipulations of structural priming conditions modulate immediate and long-term improvement in sentence production. We integrate multiple theories of language learning and apply them to make predictions about the trajectory of priming-induced syntactic learning in PWA. In Aim 2, using a set of eyetracking sentence comprehension tasks, we investigate whether the effects of structural priming in production generalize to off-line (accuracy) and on-line (eye fixations) sentence comprehension and determine what learning conditions result in greater cross- modality generalization. In Aim 3, we develop and establish Phase I efficacy data of an implicit structural priming treatment, incorporating the crucial learning conditions supporting maximal retention from Aims 1 and 2. The outcomes of this work will lead to identification of a model of language (re-)learning in aphasia and the development of a novel treatment that capitalizes on the benefits of the implicit learning mechanisms underlying structural priming.

NIH Research Projects · FY 2025 · 2021-08

Project Summary Ebola (EBOV) and Marburg (MARV) filoviruses cause severe hemorrhagic fever in humans with up to 90% mortality rates. Their genome contains only seven genes including the viral matrix protein VP40 which, when expressed in mammalian cells, is sufficient to produce virus-like particles (VLPs) that are essentially indistinguishable from live virions. VP40 forms dimers, hexamers and octamers mediated by different protein-protein (PPI) and protein-lipid (PLI) interactions that fulfill different and essential roles in the viral lifecycle, making VP40 a “swiss army knife” of proteins. The fascinating dynamic equilibria of VP40 and the availability of VLPs as a model system for direct observations outside of a BSL4 laboratory make VP40 a unique system to rigorously study the biophysical basis for viral budding as well as PPIs and PLIs in general. The significance of these studies is further increased because VP40 is the most conserved protein upon virus passage through humans, but exploiting VP40 as a potential drug target is unlikely to succeed without understanding the physical basis for oligomerization and function of VP40. The Stahelin and Wiest laboratories, building on established collaborations with each other and several other collaborators supplying specific expertise, will use computational, experimental and structural biophysics methods to investigate the central hypothesis of this grant: that interdomain interactions of VP40 are key regulators of VP40 structures during the viral life cycle. In two specific aims, we will (i) Determine the biophysical mechanisms by which VP40 dimer, hexamer and octamers form in silico, in vitro and in human cells and (ii) determine how mutations of VP40 that arise in humans during the course of an outbreak as well as in animals during passage of virus contribute to VP40 conformational change and rearrangement into its separate oligomeric forms. These questions will be studied using a tightly integrated approach using multiscale molecular dynamics simulations on the µs timescale and free energy perturbation methods on the computational side and hydrogen-deuterium exchange, cellular imaging of VLPs as well as more traditional biophysical experiments such as ultracentrifugation and SPR to determine the binding constants of wildtype VP40 from EBOV and MARV as well as pertinent mutants. This innovate and integrated approach will not only provide careful validation of the results, but also provide detailed insights into the PPIs and PLIs governing the oligomerization equilibria across many time- and lengths scale, thus enabling a rigorous understanding of the biophysical principles for a biomedically very important filovirus protein that will have a significant impact on understanding other PPIs and PLIs.

NIH Research Projects · FY 2025 · 2021-08

PROJECT SUMMARY Triple-negative breast cancer (TNBC), the deadliest form of breast cancer, affects Black/African American women at twice the rate of white women. Additionally, the survival rate for TNBC is lower in Black/African women. To address the disparities associated with TNBC we need broadly applicable targeted therapies. Without targeted therapies, clinicians are left with chemotherapy, which has many negative side- effects and in many cases is ultimately ineffective in the treatment of TNBC. We have observed that a subset of TNBC cell lines are dependent on the expression of Adenosine Deaminase Acting on RNA (ADAR). ADAR is an enzyme that converts adenosine nucleotides in RNA to inosine in a process known as A-to-I editing. Loss of ADAR inhibits cellular proliferation and tumor formation for a subset of TNBC cell lines. Because ADAR is required for the growth of some TNBC cell lines it serves as a valuable therapeutic target for the treatment of TNBC. It has been observed that ADAR-dependent cell lines have elevated interferon signaling, potentially making it possible to classify ADAR-dependent tumors. Interferon signaling is higher in Black/African American breast tumors than tumors in white patients, which may make therapies targeting ADAR more effective for Black/African American patients. There are aspects of ADAR-dependence that we do not understand. For instance, we do not understand why some cells are dependent on ADAR expression while others are not. Here we will explore the mechanism of ADAR-dependency and develop a strategy for treatment of TNBC based on ADAR inhibition. In AIM 1 we will identify the factors that are required for ADAR-dependence, including identification of the immunogenic RNAs that contribute to the phenotype caused by ADAR depletion. In AIM 2 we will develop and assess a classification model to predict which tumors will be sensitive to ADAR inhibition. The accuracy of the classification model will be evaluated by knockdown of ADAR in patient derived xenograft models of TNBC. Importantly this AIM will provide the PI with training in mouse models of breast cancer, including tumor implantation and monitoring. Finally, in AIM 3, we will develop a high-throughput A-to-I editing assay and use it to identify a small molecule inhibitor of ADAR. In addition to the potential identification of a small molecule inhibitor of ADAR, this AIM will provide the PI with experience developing a high-throughput screen and the use of DNA-encoded chemical libraries. This work will advance our understanding of ADAR- dependency such that we can accurately classify ADAR-dependent TNBC, thus opening the door to treating this deadly form of breast cancer with the small molecules identified in AIM 3. Developing an effective targeted therapy for TNBC is essential to reducing the disparate effects of this disease on Black/African American women. Finally, the research and career development training included in this grant will facilitate the PIs transition into an independent investigator.

NIH Research Projects · FY 2025 · 2021-07

Project Summary/Abstract Genetic studies in humans revealed that gain-of-function variants of SCN2A are associated with epilepsy, whereas loss-of-function variants of SCN2A are associated with autism spectrum disorder (ASD). However, about a third of ASD children carrying SCN2A loss-of-function or nonsense variants (collectively referred to as SCN2A deficiency) develop intractable seizures, major comorbidity associated with ASD. How SCN2A deficiency contributes to seizure is largely unknown. To address this problem, we generated a Scn2a-deficient mouse model by gene-trap knockout (gtKO) strategy. Homozygous gene-trap knockout mice have only a quarter of the Scn2a expression level of WT mice, which model severe Scn2a deficiency. Our preliminary patch-clamp recordings reveal that neurons with severe Scn2a deficiency displayed neuronal hyperexcitability. This finding is unexpected, but could open the door for the understanding of the puzzling seizure comorbidity in SCN2A deficiency-related ASD. However, critical gaps exist regarding the possible mechanisms underlying Scn2a deficiency-related neuronal hyperexcitability, its consequences on neural network and seizures susceptibility, as well as the reversibility of seizures-related phenotypes. Filling these gaps would greatly enhance understanding of the mechanisms underlying seizure comorbidity in ASD; and shed new light on the development of effective therapeutic interventions. To this end, here we propose to test an overarching hypothesis that a substantial reduction of Scn2a expression results in increased neuronal excitability related to K channel downregulation, hypersynchronization of in vivo firing, and elevated seizure susceptibility that can be reversed by targeted genetic interventions. We will test our hypothesis at the cellular, circuit, and in vivo levels. In Aim 1, we will assess ex vivo neuronal excitability of Scn2a-deficient mice. In Aim 2, we will determine in vivo neuronal firings and seizure susceptibility of the Scn2a-deficient mice. In Aim 3, we will test targeted genetic interventions. Our study is significant in the following ways: i) SCN2A deficiency is among the leading monogenetic forms of ASD and seizure comorbidity occurs in about 30% of affected ASD patients; ii) The finding that severe SCN2A deficiency resulting in hyperexcitability is potentially paradigm-shifting, and the study of which could reveal key insights regarding seizure comorbidity associated with ASD; and iii) Targeted genetic interventions to be evaluated have clear translational relevance. Our study has the following innovations: i) the use of novel Scn2a deficient mice that reveal unexpected finding of neuronal hyperexcitability; ii) innovative ways to achieve genetic rescue; and iii) the use of cutting-edge technologies including high-density Neuropixels recordings. The applicant is an early stage investigator (ESI), whose team has extensive expertise in sodium channel physiology, genetics, electrophysiology, and pharmacology. The team is well suited to carry out the proposed work to its full completion within the project timeframe, and generate impactful outcomes to advance the field.

NIH Research Projects · FY 2026 · 2021-06

Undergraduate programs that train biomedical engineers to identify clinical user needs and to implement design processes toward innovative solutions are imperative. These programs also have opportunity to educate students on existing health disparities during their training and to instill informed decision making to advance medical innovation for all Americans. Since 2021, the (IN)SCRIBE Program, or INdiana Summer Clinical Residency in Innovation for Biomedical Engineers, has trained biomedical engineering (BME) students to identify and address urban health needs through clinical immersion and design training. The Program has engaged 32 students in over 6,000 hours of clinical experiences and has impacted senior capstone design teams, with one team winning the 2022 NIH DEBUT Challenge for Healthcare Technologies for Low-resource Settings. Participants report improved preparedness and sustained impact in their capstone projects. Our expanded program aims to train students to identify both urban and rural clinical needs while learning about existing health disparities (e.g., how food deserts may affect dietary habits, how geographic location may contribute to time-limiting access to care). Indiana reflects national demographics, with a substantial rural population and health issues that impact both urban and rural communities. Purdue University recently expanded its BME program to Indianapolis, positioning itself as a potential leader in integrating health disparities as a topic within BME design education. We will extend the (IN)SCRIBE Program’s immersive experiences to rural settings, develop and disseminate a health awareness survey, and empower students to incorporate identified needs into capstone projects. The Program will engage undergraduates in a seven-week summer clinical immersion and design experience that challenges teams to integrate socioeconomic considerations into clinically-relevant design without introducing new disparities. We will engage more than 20 key partners – Design & Innovation Collaborators, Health Experts, and Clinical Collaborators in delivery of educational and immersive experiences. The renewed program will be a blueprint for BME programs looking to integrate geographic considerations into their training. Specific Aim 1 is to update and implement the (IN)SCRIBE Program. We will immerse undergraduates in settings across urban and rural clinics, develop student design skills and self-efficacy, create student awareness of health disparities, and leverage partners in the Daniels School of Business to train students in business pitch development. Specific Aim 2 is to determine how the updated (IN)SCRIBE Program affects student abilities toward engineering design. We will identify how student teams articulate consideration of socioeconomic and geographic factors in design solutions, document how teams pursue design to meet rural and urban health needs beyond the Program, and measure changes in participant design self-efficacy and health disparity awareness. Successful achievement of the project’s aims will result in improved training for BME students and better health for residents of urban and rural areas.

NIH Research Projects · FY 2026 · 2021-04

ABSTRACT Exposure to manganese (Mn) through inhalation of welding fumes continues to be a health risk factor, resulting in accumulation of brain Mn and neurochemical changes in welders, which further lead to changes in mood, cognitive and motor function. Yet, not much is known about the dose-response relationships of uptake and elimination of Mn in specific brain regions of the human brain. Furthermore, while animal and cell studies strongly suggest oxidative stress as one of the primary mechanisms of Mn toxicity, markers of oxidative stress and their relation to symptoms have not yet been explored in the human brain. Our novel magnetic resonance imaging (MRI) and spectroscopy (MRS) techniques allow generating whole-brain maps of Mn deposition, as well as the measurement of glutathione (GSH), a marker of oxidative stress, and g- aminobutyric acid (GABA), the main inhibitory neurotransmitter in the human brain. Using these techniques, the primary objective of the proposed work is to elucidate the spatial-temporal uptake and elimination of manganese in the human brain of welders, and the relationship of oxidative stress markers and neurotransmitter imbalances in specific brain regions to mood, cognition and motor function. Our preliminary data suggest that diffusion along white matter tracts may contribute to Mn deposition in cortical areas, and that the time of elimination of brain Mn varies across the brain. Furthermore, exposure-induced increase of thalamic GABA seems to be reversible upon reduction of Mn exposure. Making use of a longitudinal study design, our unique access to a cohort of career welders for personal air sampling and accurate exposure assessment, and our state-of-the-art neuroimaging technology, this proposal will test the central hypothesis that the dose-response relationship of Mn deposition and elimination in the human brain varies across different brain regions and leads, via oxidative stress and neurotransmitter imbalance, to brain region specific symptoms. To test whether the uptake of brain Mn accumulation occurs sequentially across the brain, leading to oxidative stress and GABA imbalance, Aim 1 will study dynamic Mn brain deposition by following 20 new welding apprentices for two years into their welding career, using personal air sampling, whole-brain quantitative MRI and the novel MRS editing technique, HERMES. In Aim 2 we will recruit 40 active experienced welders and 40 control workers to probe GSH and GABA in the thalamus, the cerebellum and the frontal cortex. A test battery for changes in mood, cognition and motor function will be used to study associations with neurochemical changes. In Aim 3 the same methods will be used to study elimination of brain Mn by following 20 welders who cease to be exposed to Mn (retire, change job) for two years. Understanding the spatio-temporal characteristics of human brain Mn deposition, neurochemical responses and their relation to symptoms will have significant translational impact on our understanding of the Mn dose-response relationship in welding and will inform safe levels of occupational Mn exposure.

NIH Research Projects · FY 2025 · 2021-04

Project Summary/Abstract Autism spectrum disorder (ASD) is a neurodevelopmental disorder associated with impaired social communications and behavioral abnormalities, which affects ~1 in 54 children in the United States (CDC.gov). SCN2A, encoding neuronal voltage-gated sodium channel Nav1.2, has been identified as one of the leading genes associated with ASD. We have characterized a novel Scn2a-deficient mouse model that is generated via targeted gene-trap knockout (gtKO) strategy and possesses a built-in genetic rescue element. Our preliminary data revealed profound behavioral abnormalities in homozygous Scn2agtKO/gtKO mice including anxiety-like behaviors, impaired nesting and social deficits. We also identified elevated excitation-inhibition (E/I) balance in pyramidal neurons of mPFC, which has been implicated in ASD and social deficits. However, a critical gap exists regarding how in vivo neuronal firings in mPFC are affected by elevated E/I balance and to what extent the manipulation of E/I balance will alter the behavioral outcomes in Scn2agtKO/gtKO mice. To address this gap, we propose to test an overarching hypothesis that Scn2a deficiency increases E/I balance, impairs neuronal responses in mPFC, and results in social deficits that can be rescued with targeted genetic and pharmacological interventions. In Aim 1, we will assess the synaptic properties and in vivo firing of neurons in mPFC using brain- slice patch-clamp recording and Neuropixels in vivo recording. Our findings are expected to provide cellular-level and local network level neuropathological mechanisms of Scn2a deficiency. In Aim 2, we will determine neuronal firings and behavioral outcomes in response to manipulating E/I balance in mPFC microcircuit using optogenetics and chemogenetics. Our findings will bolster the significance of E/I balance modulation for correction of behavioral deficits. In Aim 3, we will evaluate the efficacy of timed genetic and pharmacological rescue to determine optimal windows for intervention. Our study is significant in the following ways: i) SCN2A deficiency to be studied is among the leading monogenetic forms of ASD; ii) Excitation and inhibition (E/I) balance of mPFC microcircuit to be thoroughly dissected is closely associated with social deficits; and iii) Genetic rescue and pharmacological intervention to be tested are of clear clinical relevance, and will provide translational basis to inform therapeutic development for the treatment of Scn2a-deficiency related disorders. Our study has the following innovations: i) use of novel Scn2agtKO/gtKO mice that display profound cellular and behavioral deficits; ii) innovative ways to achieve genetic and pharmacological rescue; and iii) use of cutting-edge technologies including high density Neuropixels in vivo recordings. The applicant is an early stage investigator (ESI), whose team has extensive expertise in sodium channel electrophysiology, animal behaviors, genetics and pharmacology. The team is well suited to carry out the proposed work to its full completion within the project timeframe, and generate impactful outcomes to advance the field.

NIH Research Projects · FY 2026 · 2021-03

Project Summary/Abstract Pulmonary infections caused by multidrug-resistant bacteria are extremely difficult to treat. Gram-negative `superbugs' are particularly worrisome in pulmonary infections and are often only susceptible to polymyxins. However, intravenous polymyxins have poor efficacy for pulmonary infections due to limited drug exposure in the airway. Inhaled polymyxins have been increasingly used in the clinic for the treatment of pulmonary infections; yet current inhalation therapies are empirical and have never been optimized using pharmacokinetics/pharmacodynamics/toxicodynamics approaches. No systematic evaluations have ever been conducted on the pulmonary toxicity of inhaled polymyxins. Furthermore, the currently used traditional jet nebulization has very low delivery efficiency (<15% of drug delivered to the lungs). Suboptimal use of inhaled polymyxins has caused unsatisfactory therapeutic efficacy, emergence of resistance, frequent adverse effects, and poor patient compliance. We have elucidated that polymyxin-induced pulmonary toxicity involves drug accumulation in human alveolar epithelial cells, particularly in mitochondria, which leads to oxidative stress, mitochondrial damage and apoptosis. Excitingly, we discovered that polymyxin combinations with aminoglycosides can significantly attenuate polymyxin-induced pulmonary toxicity, maximize antimicrobial activity and prevent resistance development. In this proposal, we will employ a multi-disciplinary approach to develop efficient powder aerosol delivery systems for these promising polymyxin combinations. The overarching hypothesis is that our optimized aerosol therapy of polymyxin combinations possesses superior delivery efficiency and PK/PD/TD to treat pulmonary infections; prevents bacterial resistance by synergistically inhibiting multiple key biochemical pathways; and minimizes toxicity in lung epithelial cells. The specific aims are: (1) To elucidate the mechanisms of attenuation of polymyxin-induced pulmonary toxicity by aminoglycosides using advanced imaging, CRISPR and transcriptomics; (2) To develop efficient aerosol delivery systems of polymyxin combinations using innovative manufacturing techniques; (3) To examine the tripartite relationships among human lung cells, Gram-negative pathogens, and superior polymyxin combinations using correlative multi-omics; and (4) To optimize the dosage regimens of superior inhaled polymyxin combination formulations using a machine learning-driven mechanism-based PK/PD/TD model. Our project responds in a timely manner to the recent National Action Plan for Combating Antibiotic-Resistant Bacteria (2020 – 2025).

NIH Research Projects · FY 2026 · 2021-03

Project Summary It is estimated that 10-20% of toddlers will experience early delays in their expressive communication skills, an experience termed Late-talking (LT). While many of these children will resolve this initial delay, others experience persistent challenges in communication, such as Developmental Language Disorder (DLD), that are associated with a host of negative health and academic consequences. This project addresses critical public-health needs regarding our understanding of the long-term profiles of children with a history of LT by: (1) Characterizing how trajectories of early language skills in toddlers with and without LT predict later school-age identification of language and literacy disorders and (2) documenting how language growth trajectories associate with domains outside of language, including in other academic skills and socio-emotional wellbeing within the child and family. We build on several promising assessments of lexico-semantic abilities in toddlers from the first project period, and adapt measures of these skills to school-age children, as lexico-semantic skills are a component of language which is affected in school-age children with developmental language disorders, and can also be reliably measured in toddlers. We plan to continue to follow a large group of children who were initially recruited at 18-months-old (half of whom were classified as LT at 18 months), and explore how continuously measured trajectories of lexico-semantic skills and other associated skills in speech / language that were assessed when children were between 18 months to 4 years, forecast school-age skills and outcomes when these same children are between 5;6 to 8;6 years old. To fully characterize how early skills and trajectories lead to later outcomes, we carry out several analyses on concurrent and predictive relations between skills. This project will advance our ability to detect early language disorders by evaluating the degree to which early skills in understanding relationships between word meanings might serve as a marker of longer-term language / literacy disorders, and also extend our understanding of how these early skills and experiences connect with broader academic and socio-emotional impacts that children with DLD frequently experience.

NIH Research Projects · FY 2025 · 2020-12

Chronic pain costs the US more than $635 billion per year, however, patients fail to receive adequate relief from the available drugs and often become drug-dependent. These observations highlight the importance for identifying new agents acting on unique targets to treat chronic pain. Genetic, neurobiological, and preclinical studies have suggested that adenylyl cyclase type 1 (AC1) may provide that new drug target. AC1 knock out mice (AC1-/-) show reduced or absent inflammatory and neuropathic pain when compared to littermate controls. Preclinical studies with a small molecule inhibitor of AC1, NB001 revealed that NB001 reduced chronic pain responses (i.e. inflammatory and neuropathic) in both mice and rats. Similarly, we have recently shown that a novel AC1 inhibitor, ST034307 also reduced inflammatory pain in a mouse model. These studies are consistent with the premise that AC1 is a new target for inhibitors of chronic pain. Unfortunately, both NB001 and ST034307 have significant issues and liabilities preventing further development. To that end, we have recently screened a chemical library collection that allowed us to identify a pyrimidinone scaffold for the development of novel AC1 inhibitors. This scaffold was prioritized for hit-to-lead optimization based on several promising criteria. Preliminary structure-activity relationship (SAR) studies have revealed for the first time compounds with sub-micromolar potency at AC1, as well as selectivity versus the closely-related AC8. Further, initial in vivo studies with a lead compound reveal activity in an animal model of chronic pain. Despite these promising observations, the lead compounds suffer from extremely low aqueous solubility. We propose medicinal chemistry optimization of this scaffold to develop potent and selective inhibitors of AC1 activity as novel probes under the following Specific Aims: Specific aim 1 will use medicinal chemistry optimization of the pyrimidinone scaffold to develop potent drug-like AC1-selective molecular probes. Specific aim 2 will establish the pharmacological specificity of the probe molecules using a set of in vitro model assays and explore the mechanisms for probe activity. Additionally, we will execute in vivo preclinical pharmacokinetic testing with iterative medicinal chemistry and pharmacology. Specific aim 3 will then use the best molecules to explore the in vivo pharmacological activity of the AC1 inhibitors in a mouse model of inflammatory pain, conditioned place preference, and opioid withdrawal. At the end of this study, we shall provide the research community with chemical probes with < 100 nM AC1 potency, > 30-fold selectivity vs other ACs and related CNS targets, and in vivo efficacy. These new probes will provide essential tools to validate AC1 as a new and safe drug target in the treatment of chronic pain.

NIH Research Projects · FY 2025 · 2020-09

Optimization of Clear Optically Matched Panoramic Access Channel Technique (COMPACT) for large-scale deep-brain neurophotonic interface With the advance of sensitive molecular indicators and actuators, neurophotonics has become a powerful paradigm for discovering the principles underlying neural circuit functions. However, a major obstacle of using light to study neurons located deep in the mammalian brain is the limited access depth. Even with the advance of multiphoton microscopy, the majority of implementation for imaging the mammalian brain is limited to ~ 1 mm in depth. The majority of the mouse brain still remains inaccessible to cellular resolution measurement, not to mention the brain of larger mammals. To image deep brain regions, invasive miniature optical probes are required. One key issue with these optical probes is the tiny tissue access volume which limits the number of neurons to be imaged and reduces the success rate of experiments. Towards large-scale deep-brain neurophotonic interface, we have recently developed Clear Optically Matched Panoramic Access Channel Technique (COMPACT), which can effectively increase the tissue access volume by ~ three orders of magnitude. To maximize the impact of the COMPACT platform, we propose to optimize COMPACT in three major areas. First, we will further miniaturize the implementation of COMPACT. Second, we will enable COMPACT based fiber photometry and optogenetics. For these two applications, we can further reduce the capillary diameter to 160 μm. Multiple capillaries can be inserted in the mammalian brain to create the neurophotonic interface “highway” system. This development will complement the existing paradigm of mesoscale sampling with electrode array probes by providing an optical version of whole-brain-access high-capacity recording and modulation system. Third, we will develop head-mounted two-photon COMPACT system for freely moving animal studies. To benchmark the system performance, we will carry out extensive in vivo measurement of neuronal structure and activity in the living mouse brain. Specifically, we will quantify and optimize the imaging resolution, signal-to-noise ratio, and maximum imaging depth outside capillary. Moreover, we will simplify and automate the operation procedure so that it can be easily adopted by neurobiologists. With the progress of the technology development, we will also work to broadly disseminate the COMPACT based technologies. In addition to scientific publication, we will develop a comprehensive website similar to that of the Miniscope project to include the detailed mechanical and optical design files, system calibration and alignment routines, surgical procedures, and customized control software. The ultimate goal is to make COMPACT robust, turn-key, and broadly available to transform how we use light to study mammalian brains.

NIH Research Projects · FY 2024 · 2020-09

SUMMARY ABSTRACT Although cervical cancer is an easily curable disease if detected early, it continues to claim the lives of hundreds of thousands of women worldwide. Healthcare disparities have resulted in cervical cancer incidence and mortality that are five times higher in low and middle income countries (LMICs) than in high-income countries. In the United States, cervical cancer mortality rates are twice as high among rural women than their urban counterparts. The wide disparity in cervical cancer incidence rates and deaths is attributed to both higher HPV infection rates and a lack of accessible screening and treatment of pre-invasive cervical lesions. The current standard of care in the US, a cytology-based Pap smear, requires resource intensive laboratory and clinical specialists with a long turnaround time from sample collection to result. Alternatives, such as visual inspection with acetic acid and emerging HPV-targeted tests, have poor specificity for cervical cancer, leading to overtreatment that can cause complications including infertility and pre-term births and that further the burden on limited healthcare resources. This proposal aims to create an integrated point-of-care screening test that can be used by healthcare providers in under-resourced settings to obtain relevant clinical insights, including cervical cancer risk stratification, and enable same-visit treatment of high risk cervical lesions. Building on our preliminary development of a highly sensitive paper-based immunoassay to test for the key cervical cancer biomarker, valosin containing protein (VCP), the objective of this proposal is to combine VCP detection with three other known cervical cancer protein biomarkers, in a sensitive and specific single-step point- of-care assay. Specific milestones include: 1) Integrating and optimizing multiplex detection of cervical cancer biomarkers into a simple paper-based sample-to-answer device. 2) Evaluating the operational and performance metrics of the test in retrospective cervical swab samples. The outcome of this proposal will be a highly characterized point-of-care test with high sensitivity (95%) and specificity (90%) to detect high-risk cervical intraepithelial neoplasia and invasive cervical cancer within 40 minutes. This affordable solution for cervical cancer screening and control programs will be applicable in LMICs and will provide highly sensitive monitoring of cervical intraepithelial neoplasia in the US, where it will be especially impactful in high-risk populations that are currently underserved by existing screening programs.

NIH Research Projects · FY 2024 · 2020-09

PROJECT SUMMARY Alzheimer’s disease (AD) is a progressive and fatal neurodegenerative disorder manifested by cognitive and memory deterioration. The characteristic pathology changes in AD are fibrin deposition in cerebral cortex, likely through the deposition of beta-amyloid (Aβ) in cell space and hyperphosphorylated Tau protein in cell. However, the exact molecular mechanism and pathogenic signaling of AD is not clear and researchers have been searching for new leads and reliable diagnosis for AD. In this R01 study that focuses on innovative and translational AD research, we will introduce novel strategies at the forefront of basic disease mechanism and clinical perspectives. The long term goal of this project is 1) to develop systematic strategies to dissect kinase-substrate signaling network related to onset of AD, with an emphasis on the identification and validation of direct kinase-substrate relationship in AD’s critical pathogenic pathways; and 2) to develop phosphorylated proteins in plasma extracellular vesicles (EVs) for potential clinical diagnosis. As phosphorylation is a major player in early onset and progression of diseases such as AD, EV phosphoproteins are expected to become actively pursued targets as indicators of cellular states and for in vitro disease diagnosis. We will integrate novel proteomic approaches to identify Aβ and Tau upstream kinases associated with the pathogenesis of AD and to dissect Aβ and Tau- associated signaling networks. The strategy, fluorescence complementation mass spectrometry (FCMS), will utilize protein complementation and quantitative proteomics to establish a high throughput screening method to identify direct upstream kinases of Aβ and Tau associated with the AD progression. Accordingly, we will achieve the following specific aims: 1): Understanding the driving force of AD progression through the construction of high resolution kinase-substrate network in Aβ and Tau associated signaling pathways; 2): Establishment of an analytical platform for targeted detection of known AD biomarkers in plasma EVs; and 3): Discovery of phosphoproteins from plasma EVs as novel biomarkers for AD detection and monitoring.

NIH Research Projects · FY 2025 · 2020-09

Tissue is extraordinarily complex, and new measurement tools are necessary to elucidate cellular function and composition at never-before-observed levels. The long-term goal of this research program is to develop nanoelectrochemical technologies for single cell and spheroid function and composition. The main focus will be on metabolomics (quantifying several metabolites simultaneously) and pharmacokinetics (quantifying analyte concentrations with time). We endeavor to make the most accurate measurements of cellular metabolites with sub- micrometer resolution while minimally perturbing cellular homeostasis. These measurements have the potential to open the door to unrealized sensitivity in sub-cellular metabolite quantification. Electrochemistry at nanoelectrodes has been used to interrogate cellular processes and quantify reactive species within cells. However, the amount of charge required to make an electrochemical determination can be detrimental to a cell, which comprises a rather small volume, within 100 milliseconds. Therefore, novel techniques must be developed to minimize the perturbation to cellular homeostasis to ensure accurate measurements of natural cellular processes. To achieve low-charge electroanalysis, our group has innovated novel potentiometric and aptamer-based sensing modalities. Over the next five years, metabolite- specific sensors will be miniaturized to the sub-micrometer scale for single cell and spheroid analyses. Multibarrel nanoelectrodes will be developed and optimized to quantify several metabolites in single cells and spheroids with high spatiotemporal resolution. These sensors will be deployed into single cells and spheroids for metabolomics and pharmacokinetics studies. Findings will be validated with microscopy and mass spectrometry. Finally, the sensing modalities will be extended to build onto a new bioimaging platform: the Hyperspectral-Assisted Scanning Electrochemical Microscope, a low-cost alternative to white light laser confocal microscopy. The overarching goal of this research program is to create the foundation for generalized metabolomics studies with nanoelectrode sensors, where the library of metabolites of interest depends only on the availability of an enzyme or a carefully designed aptamer.

NIH Research Projects · FY 2025 · 2020-09

PROJECT SUMMARY/ABSTRACT Our proposed efforts align directly with a goal of RFA-NS-18-019: optimization of transformative technologies for modulation in the nervous system. Specifically, we seek to optimize microelectrode arrays (MEAs) and ultra-microelectrode arrays (UMEAs) for large-scale circuit manipulation that will control neural activity at cellular resolution with high temporal resolution. Our goals are to 1) advance CNS MEA and UMEA electrical microstimulation by testing the separate hypotheses that MEAs and UMEAs can deliver safe, effective levels of cortical electrical stimulation and 2) advance research by generating transformative tools and technologies that will be widely used throughout the research community. Here we propose combining computational modeling, engineering optimization, and in vivo measurement to address these challenges and produce advances in microstimulation and tools for the community. Our Aims are to 1) engineer approaches to non-damaging charge, 2) engineer approaches to enable selective and graded activation of targeted neural elements, and 3) document the performance of the innovations from Aim 1 and Aim 2. Via an outstanding team working together to address this interdisciplinary problem, our innovative approach will result in 1) models to deliver non- damaging currents from MEAs and UMEAs; 2) evaluation of the models to optimize MEA and UMEA design for microstimulation; and 3) experimental assessment of the outcomes of our designs, both within our team and with our collaborators. Our transformative results will lead to model-based optimization of reliable and high- fidelity multichannel microstimulation technologies enabling sustainable, broad dissemination and user-friendly incorporation into regular neuroscience practice.

NIH Research Projects · FY 2024 · 2020-09

PROJECT SUMMARY The creation of highly innovative solutions to complex problems impacting human health requires research teams that are rich in cognitive diversity. Cognitive diversity represents the bringing together of people with different backgrounds, viewpoints, and life experiences and is a hallmark of highly innovative teams. Cognitive diversity correlates with identity diversity; it is thus imperative that the translational biomedical sciences workforce includes strong representation of Ph.D. scientists from diverse backgrounds that may imbue new ideas and perspectives to maximize scientific innovation. Unfortunately, cognitive diversity in research teams is currently limited because individuals from specific racial and ethnic groups, those with disabilities, and individuals with low socioeconomic backgrounds, remain significantly underrepresented (UR) in the biomedical sciences. Here, we propose to develop, apply, and evaluate a Postbaccalaureate Research Education Program (PREP) that will help prepare recent college graduates from UR backgrounds to enter and successfully complete a Ph.D. or dual- doctoral degree program in translational biomedical sciences. At Purdue University, PREP Scholars will have the opportunity to enhance their skill set in four main areas: research aptitude; academics; professional development and career planning; and community and resiliency. Scholars will engage in a yearlong, mentored research experience with an emphasis on preclinical translational studies. The Purdue PREP curriculum is adaptive; Scholars will use an Individual Development Plan (IDP) as a framework and will participate in the educational, professional development, and career planning activities that prepare them for admission to high caliber graduate programs and are aligned with their future career goals. Scholars will be introduced to the breadth of biomedical research and research- related careers along the translational pipeline available to a Ph.D. scientist. The Purdue PREP will adopt a multi-layered, hierarchical approach to mentoring in which each Scholar will work with a network of faculty and near-peer mentors with complementary skills that will provide a broad range of expertise and psychosocial support to enhance Scholars' success. PREP faculty mentors and Scholars will undergo parallel cultural competency training focused on issues of diversity and inclusion as they relate to the academic research environment in order to improve cross-cultural communication and enhance UR student experience. Success will be measured by > 75% of Scholars entering a high quality Ph.D. or dual-doctoral (e.g. DVM-Ph.D.; MD-Ph.D.) degree program upon completion of the one-year Purdue PREP. Formative and summative evaluations will be used to assess Scholars' persistence and progression to a Ph.D. and also the impact of the PREP on fostering an institutional climate of diversity that may enhance UR retention.

NIH Research Projects · FY 2024 · 2020-09

Summary: Dissecting host-pathogen interactions through the lens of genomics Current investigation of mechanisms underlying many diseases relies on the acquisition of multi-dimensional genomics data. The utility of these data is, however, offset by the lag in development of tools and models to fully interrogate them. In the context of infectious diseases, such data contains molecular information including gene transcription, regulation, and variations from both the infecting pathogen and the host cell, providing a snapshot of the host and pathogen interactions (HPIs). These HPIs determine infection outcomes. For instance, when a pathogen evades, or evolves resistance to defensive host immunity via a multifaceted HPI, it can result in persisting infection, chronic inflammation, malignant transformation, and/or elevated mortality. Recent successes in overcoming immune-evasion of infected tumor cells with checkpoint inhibitors exemplifies the clinical gains that can be made by identifying and specifically targeting essential mechanisms of HPIs. Hence, precisely identifying new mode(s) of HPIs is critical for development of effective and personalized interventions. The molecular mechanisms of HPIs underpinning disease can be identified from genomics data. For example, information on whether a transcription factor (TF) regulates genes from either host or pathogen, or both, can be captured by chromatin immunoprecipitation (ChIP) sequencing of infected host cells. This means that integrative analysis of genome-scale data can provide a platform for large-scale and unbiased detection of often multi- dimensional and novel facets of HPIs in host cells. However, there is a lack of data mining tools and models to extract such information. More importantly, the available analysis tools typically focus on data from either the host or the pathogen and not on the interactions occurring between the two, excluding us from investigating the full HPI spectrum. Thus, novel methods to determine HPIs by simultaneously modeling both host and pathogen data are critical for understanding key cellular mechanisms and developing treatment strategies. My lab specializes in developing computational models to construct HPI maps and to experimentally validate them. As proof-of-principle, we produced a comprehensive HPI map from sequencing samples from large numbers of tumors caused by Epstein–Barr virus. This map delivered unprecedented insights, identifying novel viral integrations, mutations linked to viral reactivation and providing molecular classification of tumors expected to yield individualized cancer therapy. Therefore, my lab is uniquely positioned to uncover mechanistic insights from HPIs. Our program seeks to develop new models and machine learning tools to construct HPI maps in several diseases by focusing on the following major questions: 1) how do expression, integration, and mutational landscapes of host and pathogen affect pathogenesis of disease?; 2) what is the nature of physical HPIs and cross-regulation by major host and pathogen factors that modulate gene expression, such as TFs and RNA binding proteins?; 3) how do HPIs define molecular subtypes to guide personalized treatments? We expect to identify novel HPIs and provide systems-level understanding of mechanisms critical to cell biology.