Case Western Reserve University

NIH Research Projects · FY 2026 · 2020-05

ABSTRACT Recent large genome wide association studies (GWAS) have identified hundreds to thousands of genetic variants associated with complex traits. The resulting GWAS summary statistics, together with large Biobank data, provide an unprecedented opportunity to understand the genetic mechanisms of complex traits. Inferring causal effects of risk factors on disease is the major challenge of observational epidemiology studies, which now can be addressed using genomic data through the cost-efficient Mendelian Randomization (MR) approach. However, current MR approaches suffer from bias due to multiple sources, including weak instrument variables (IVs), sample overlap, horizontal pleiotropy, and linkage disequilibrium (LD) among IVs. Novel statistical methods that can unbiasedly infer causality and estimate causal effects are therefore needed. On the other hand, one of the dominant views in the field is that genetic variation of complex disease is largely explained by additive effects. Even though gene-environment and gene-gene interactions have been well documented in experiment studies, the contribution of interactions is still unclear, partially because of limitations of current analytic approaches. The current methodological development focuses on improving computational efficiency to overcome the burden from the large number of interaction tests at the genome wide level, but the fundamental method is based on standard linear regression that often has low statistical power. In this project, we will develop, (1) novel unbiased multivariable MR with application to large genomics data and Biobank data, (2) novel powerful gene-environment interaction (𝐺 × 𝐸) methods with application to large genomics and Biobank data, (3) a novel powerful gene-gene interaction (𝐺 × 𝐺) method with application to large genomics and Biobank data, (4) corresponding software that will be made publicly available. We will apply these methods and software to UK Biobank, TOPMED WGS and All of Us, as well as many existing GWAS summary statistic datasets. We request support to develop statistical methods and software to address these goals. The proposed novel multivariable MR methods and 𝐺 × 𝐸 and 𝐺 × 𝐺 methods would speed up the new discoveries and improve our understanding of genetic architecture of complex traits, which aligns with the National Human Genome Research Institute mission.

NIH Research Projects · FY 2026 · 2020-05

SUMMARY Many of the 100 billion neurons in the human central nervous system require a protective and insulating coating called myelin to function properly. Loss or damage of this myelin coating underlies many neurological disorders and therefore regeneration of new myelin is an important part of improving health for patients with multiple sclerosis (MS), neuromyelitis optica (NMO), and other myelin diseases such as the pediatric leukodystrophies. Without myelin, certain nerve cells cannot properly conduct electrical impulses, leading to weakness, fatigue, loss of vision, cognitive decline, and physical incapacity. We have developed a novel regenerative approach to identify important new potential treatments for patients with myelin loss or dysfunction that is built upon our expertise in stem cell biology. Our overall goal is to utilize the in vitro mouse and human stem cell platforms that we have developed to define the central mechanisms responsible for preventing myelin development and function across the full range of myelin disorders. We seek to discover novel therapeutic interventions that can modulate the function or regeneration of oligodendrocytes and astrocytes to restore myelination and neurological function. For multiple sclerosis, we have already defined a central mechanism to stimulate myelin regeneration and identified potent small molecules that can reverse paralysis in mouse models of disease. Moving forward, we seek to leverage our innovative technologies and experience in multiple sclerosis to identify disease- and context-specific effectors of myelin dysfunction and provide the basis for new therapies.

NIH Research Projects · FY 2026 · 2020-01

PROJECT SUMMARY/ABSTRACT The overarching objectives of this research program are to determine the molecular basis of allosteric mechanisms that govern gating and modulation in pentameric ligand-gated ion channels (pLGICs). The pLGIC superfamily governs crucial physiological processes such as gastrointestinal functions, motor coordination, and pain transmission. Aberrant channel functions are implicated in neurological disorders, addiction, and chronic pain. Currently used therapeutic strategies suffer from our limited knowledge of pLGIC assemblies in their native environment, the origin of their functional diversity, and the downstream regulatory events. Over the last five years, we have made significant discoveries in two pLGIC members- serotonin (3) receptor (5HT3R), an excitatory channel, and glycine receptor (GlyR), an inhibitory channel. We have determined molecular details of neurotransmitter recognition, channel gating, desensitization, and drug modulation. Building on these advancements, we will probe the architecture and functional mechanisms in heteromeric pLGIC assemblies and dig deeper into their post-translational regulation and functional interactomes comprising of synaptic binding partners. To achieve these goals we will use cutting-edge multidisciplinary techniques, including cryo-electron microscopy (cryo-EM), protein dynamics measurements, mass spectrometry, molecular dynamic simulations, and electrophysiology. Taken together, our proposed work is expected to provide molecular blueprints of the channel in physiologically relevant conformations for therapeutic targeting and unravel mechanisms underlying channel function. These findings will in turn pave the way for the design of novel therapeutic agents that are safer and more effective.

NIH Research Projects · FY 2025 · 2020-01

Project Summary/Abstract: Breast cancer is the most common cancer in women, with an estimated 246,660 cases (and 40,450 deaths) in the US during 2015. Due to better screening techniques cancers are caught earlier and 75% of patients are candidates for breast conserving surgery (BCS) to remove the cancer. BCS is cosmetically preferable to the alternative (mastectomy) and long-term survival rates are equivalent [1]. The success of BCS is assessed post-operatively by pathology. The status of the microscopic margins of excision of the lumpectomy specimen is still the most important prognostic and risk factor for local recurrence [2,3]. A positive margin indicates that invasive carcinoma or ductal carcinoma in situ is touching a tissue edge of a lumpectomy specimen. Among patients treated by BCS and radiation therapy, positive margins are associated with a 2-fold increase in the risk of local recurrence when compared with negative margins [4]. A finding of positive margins is estimated to occur between 8% to 86% of the time, requiring patients to return for further treatment often associated with poorer cosmetic results and increases in local and distant recurrence of the disease. Current pathology methods only assess about 1/10 of 1% of the entire volume of the removed specimen. A consequence of margin undersampling is that local recurrence occurs in 5-16% of patients with pathologically clean margins, suggesting that one or more regions of tumor had not been sampled during pathological analysis resulting in tumor remaining in the patient. In addition, there is still no universal agreement among breast surgeons on what constitutes an adequate negative margin for patients undergoing BCS [5]. Together these data demonstrate the unmet clinical need for technologies that rapidly and globally identify cancerous tissues in the surgical cavity and can be used to guide their surgical resections during the procedure. Molecular imaging guided resections of tumors during surgeries are now being developed. However, most approaches employ IV administration of optical imaging agents, which require hours or days to highlight tumor tissues. Moreover, infiltrating cancer cells in tissues surrounding the main mass may not have developed a vasculature and likely would not be identified using injected agents. Finally, illuminating the entire cancer mass may create a high background signal from tumor that is not “at the margin” of the lumpectomy. Exploiting increased protease expression at the edge of breast cancers we introduce the novel concept of in vivo topical administration of quenched fluorescent molecular imaging probes to identify cancer that may remain in the surgical cavity after standard-of-care resection. This builds on years of preclinical studies and seeks to characterize, perform toxicology, and finally a Phase 1A & B clinical trial to demonstrate the utility of this novel approach. It has the potential to reduce re-excisions as well as the false negative rate from pathology undersampling, with a consequent savings in healthcare costs and, enhancement in patient life quality.

NIH Research Projects · FY 2026 · 2020-01

Project Summary/Abstract Breathing is a vital motor behavior which is controlled by neural circuits within the brainstem and spinal cord. Degeneration of these circuits leads to respiratory disorders, such as central sleep apneas, and, eventually, respiratory failure. In mammals, contraction of the diaphragm muscle is essential for driving airflow into the lungs during inspiration. At the core of respiratory circuits are Dbx1-derived interneurons in the brainstem, which generate the rhythm and pattern of breathing, and phrenic motor neurons (MNs) in the spinal cord, which provide the final motor output that drives diaphragm muscle contractions during inspiration. Despite their critical function, the principles that dictate how respiratory circuits assemble are largely unknown. We have found that sustained activity of Hox5 transcription factors is required in both phrenic MNs and Dbx1- derived brainstem neurons to generate normal breathing behaviors and robust respiratory motor output. In this proposal we will investigate the function of Hox5 genes in determining respiratory neuron specification, connectivity and maintenance. In Aim 1 we will define how Hox5 gene expression underlies the specification and connectivity of Dbx1-derived brainstem neurons at distinct time points. In Aim 2 we will test the hypothesis that sustained, cell-autonomous Hox5-dependent programs drive and maintain phrenic MN connectivity. In Aim 3 we will utilize a novel mouse model to define the molecular mechanisms that control the specification and development of brainstem respiratory neurons. We have developed an integrative methodology combining genetic models, next-generation sequencing approaches, retrograde viral tracing, and electrophysiology to address these questions in vivo. The overarching goal of this proposal is to uncover the basic principles underlying respiratory circuit assembly so that we can begin to consider alternative treatment methods for respiratory dysfunction.

NIH Research Projects · FY 2025 · 2019-10

PROJECT SUMMARY/ABSTRACT Limited data are available on the effects of antenatal opioid exposure on the brain and neurodevelopment. Most studies are limited by methodologic flaws in study design, including small sample sizes and difficulty controlling for important environmental variables. The OBOE (Outcomes of Babies with Opioid Exposure) study, an ongoing NICHD-funded longitudinal study enrolling infants with and without antenatal opioid exposure at birth and following them to 2 years of age, attempts to improve on the limitations of previous research by collecting comprehensive exposure data including infant umbilical cords, advanced neuroimaging data to evaluate brain development, and standardized and thorough information on the home environment, maternal mental health, and parenting. The OBOE consortium, comprised of 4 high performing centers, a data coordinating center, and a neuroimaging core, has completed our goal enrollment of 200 opioid-exposed and 100 unexposed infants. In response to RFA-HD-24-014, we now propose to complete follow-up to age two in our OBOE cohort, to fulfill our main study objectives. The Case site has contributed to the OBOE study by enrolling 29 infants (24 opioid-exposed and 5 controls), completing 25 MRIs thus far, and contributing to the publication of multiple abstracts and three manuscripts using OBOE data. For this renewal grant, we will continue progress toward our aims to : 1) determine the impact of antenatal opioid exposure on brain structure and connectivity over the first two years of life; 2) define medical, developmental and behavioral trajectories over the first two years of life in exposed infants; and 3) determine how the home environment, maternal mental health, and parenting modify trajectories of brain connectivity and neurodevelopment over the first two years of life. Our progress so far, with enrollment completed and success in following this difficult population, shows that we have the ability to successfully complete the objectives of the OBOE study. Contact PD/PI: Wilson-Costello, Deanne Project Summary/

NIH Research Projects · FY 2025 · 2019-09

PROJECT SUMMARY Over 20.3 million adults in the U.S. are estimated to have a substance use disorder (SUD); and, an estimated 2 million Americans have had an opioid use disorder (OUD) involving prescription opioids and about 600,000 have had an OUD involving heroin. The number of overdose deaths from illicit opioids including heroin and synthetic opioids has tripled from 2011 to 2015 in the U.S. Among the more than half-million adults entering addiction treatment for prescription opioid abuse every year, 50%-60% report co-morbid chronic pain and 80% report that pain triggers relapse. High rates of relapse are not surprising because substance misuse may cause adverse structural and functional brain changes in the same brain regions that need to be engaged to initiate recovery and maintain abstinence. Exercise has been shown to reduce substance cravings and reduce depression and anxiety and may help reduce weight gain induced by methadone and anti-psychotic drug treatments; and, exercise, particularly at higher intensities, may produce an analgesic effect improving pain measures in chronic pain patients. Exercise may act by increasing growth and brain-derived neurotrophic factors that stimulate endogenous dopaminergic, opioidergic and serotoninergic systems that, in turn, enhance plasticity, learning and memory. These effects may help repair the structural and functional brain changes caused by substance abuse and chronic pain and help “offset” reward seeking and craving of substances while improving physical and mental health. However, most residential drug treatment programs do not currently offer a structured exercise program. We have developed an ‘assisted’ exercise technology that enables active patient engagement and mechanical assistance to help patients pedal faster than their voluntary rates. We have previously shown that ‘assisted’ exercise on a stationary cycle provides global improvements in motor function and increased activity in cortical and subcortical brain regions consistent with neural activation patterns after applying a dopamine agonist in Parkinson’s disease patients, suggesting that ‘assisted’ exercise may be modulating dopamine levels in the brain. In addition, we have shown that ‘assisted’ cycling improves motor function and recovery in stroke patients. We have also developed a novel self-regulation/cognitive behavioral therapy (CBT) program that co-addresses opioid addiction and pain (STOP), which has shown efficacy on pain tolerance, cravings and functional engagement in daily activities in outpatients. In response to RFA-AT-19-006, we propose to take a multi-phase optimization strategy (MOST) approach to refining our intervention protocols and testing feasibility with our community partners (R61 Phase) and evaluating the effects of exercise and I-STOP (STOP modified for inpatients) as adjunctive treatments to Medication Assisted Treatment (MAT) in adults with an OUD and chronic pain enrolled in residential treatment programs to decrease drug cravings and pain and increase adherence to MAT (methadone, buprenorphine) (R33 Phase).

NIH Research Projects · FY 2024 · 2019-08

Abstract The standard approach to TB control relies on detection and treatment of Mycobacterium tuberculosis (Mtb) disease. This approach may have limited effectiveness in areas where the high burden of TB leads to high levels of transmission. To curb the TB epidemic, new cases must be prevented. Preventive therapy is an effective intervention as it reduces the risk of progression to disease by 65 – 85% in both HIV-positive (HIV+) and negative (HIV-) individuals. A monumental challenge still remains: one-quarter of the world's population is infected with Mtb. Treating all individuals with LTBI is not feasible: a strategy to identify those at highest risk for progression to TB is required. Contacts who are newly infected experience a period of high risk for progressive disease that lasts about 2 to 3 yrs. Our recent cohort study in urban Uganda measured the annual rate of Mtb infection in the community as close to 10%/yr. For most individuals with latent Mtb infection (LTBI), the timing of infection is unknown and biomarkers of recent infection would help identify persons at greatest risk for disease progression. A proteomic analysis of serum from TB household contacts who converted their tuberculin skin test (TST) identified a protein signature for new Mtb infection. Improving upon this signature and determining its use in the community to identify persons who recently developed LTBI would allow for targeted preventive therapy and “halt Mtb transmission”. The overall hypothesis for this proposal is that serum/plasma biomarker signatures of new Mtb infection can identify HIV+ and HIV- adults in high Mtb transmission areas and targeting these individuals for preventive therapy will reduce TB and Mtb transmission in the community. There are 3 aims. Aim 1 will test and enhance a host protein signature as biomarker for new Mtb infection in HIV-infected and non-infected persons. We will use plasma collected in an ongoing TB household contact study in Kampala, Uganda in which TST-/IGRA- HIV+ and HIV- adults are enrolled and followed for IGRA/TST conversion. We will determine if serum cytokines enhance the predictive accuracy of this protein signature. Aim 2 will identify new Mtb infection in high risk environments in an urban African setting. GPS tracking technology will be used to trace and longitudinally map subjects to locate areas of high Mtb transmission, i.e. “hot-spots”. Subjects will be enrolled and followed for IGRA/TST conversion every 3 months over 1 yr with serial sampling of plasma. Aim 3 will determine if the protein signature(s) developed in Aim 1 can identify new Mtb infections in the community. This project builds on more than 20 years of experience by this investigative team studying Mtb transmission in TB households and community in Kampala, Uganda, and host responses to Mtb infection and disease in HIV+ and HIV- persons. This proposal brings together expertise in Mtb epidemiology (Drs. Whalen, Kiwanuka, Joloba, Stein), immunology (Drs. Mayanja, Boom) and biomarker development (Drs. Bark, Paramithiotis) at CWRU, Makerere University, University of Georgia, and Caprion Inc.

NIH Research Projects · FY 2024 · 2019-07

Project Summary/Abstract: Patients with head and neck, lung, esophageal, rectal, and anal cancers typically undergo rigorous, intense, combined-modality treatment (radiation, surgery, and/or chemotherapy) and experience high symptom burden, functional impairment, and complex psychosocial issues. Positive treatment outcomes and avoidance of complications are dependent largely on the adequacy of care provided by family members. However, family caregivers (CGs) report feeling unprepared to assume the multiple, complex tasks of caregiving, including tangible help with tracheostomy care, tube feedings, wound and colostomy care, pain management, and ongoing emotional support. Despite being a critical extension of the oncology healthcare team, training of CGs to manage symptoms, deal with communication issues with care recipients, and take care of their own physical and emotional health, is not integrated into clinical practice. This study will measure the effect of a psychoeducational and skills training intervention that incorporates structured simulation or experiential learning to improve CG, patient, and healthcare utilization outcomes. Simulation is effective in training healthcare professionals, but little is known about its effectiveness in training family CGs. The intervention is designed for the period of active cancer treatment and the immediate transition to posttreatment survivorship, a time when the CG and patient are most vulnerable. The specific aims of this 2-group, prospective, randomized controlled trial are to: (1) evaluate the effect of a CG intervention, as compared to a control group, on CG primary (anxiety) and secondary (depression, health-related quality of life [HRQOL], and fatigue) outcomes; (2) measure the effect of the intervention on patient outcomes (HRQOL and interrupted treatment course) and healthcare utilization outcomes (unplanned hospital admission, unplanned emergency room visits, and unplanned use of intravenous fluids); (3) determine if CG self-efficacy mediates the effect of the intervention on CG anxiety; (4) determine if patient illness factors, care demands, and patient and CG demographic factors moderate the relationship between the intervention and CG outcomes; and (5) compare the costs of healthcare utilization between the intervention and control groups. We will recruit 180 CGs from University Hospitals Seidman Cancer Center at the Case Comprehensive Cancer Center. The intervention involves three in-person, one-on-one sessions during radiation treatments, followed by a telephone contact 2 weeks posttreatment. Data will be collected at baseline, at the end of radiation treatment, and 4 and 20 weeks postradiation treatment. The analysis will consist of linear mixed model repeated measures, mediation and moderation tests, and Poisson regression methods. The proposed project addresses National Cancer Institute's Division of Cancer Control and Population Sciences mission of improving the delivery of care to individuals and family members affected by cancer. The study findings will provide crucial information for translating the psychoeducational and simulation methods used in this intervention to other CG populations and clinical settings.

NIH Research Projects · FY 2026 · 2019-04

ABSTRACT This collaboration develops a comprehensive mathematical model of phosphorylation-dependent cardiac myosin binding protein C (cMyBP-C) regulation. The resulting model will be leveraged to predict how to best manipulate cMyBP-C phosphorylation to prevent or reverse contractile dysfunction in heart failure with reduced, or preserved ejection fraction. Recent attempts to treat cardiac disease by modifying myofilament-level function have been mostly disappointing. The main problem is that it has been difficult to enhance contraction without compromising relaxation, and vice versa. In vivo, of course, autonomic control can enhance both contraction and relaxation at the same time. During exercise, for example, the heart contracts more forcefully and it also relaxes faster to allow time for the ventricles to fill as heart rate increases. While numerous mechanisms contribute to this behavior, cMyBP-C is one of the main sarcomere-level effectors. It’s therefore possible that cMyBP-C could be strategically manipulated to create innovative new treatments for cardiac disease. The main barrier to developing these treatments is that cMyBP-C’s function is complex and regulated by at least 9 phosphorylation residues. The functional roles of the individual residues are not equivalent and the large number of potential combinations means that approaches based solely on cell and animal-based experiments are impractical. This challenge will be overcome by developing computational models that can capture and predict cMyBP-C’s complex impact on contractile function at both the sarcomere and whole organ levels. The multidisciplinary team comprises three experienced investigators with complementary skills: Julian Stelzer, PhD, Kenneth Campbell, PhD, and Brett Colson, PhD. The proposal has 3 Aims: Aim 1 combines high-throughput screens and computer modeling to predict cMyBP-C phospho-variants that enhance contraction and relaxation. Aim 2 tests these predictions in mice using AAV9 gene delivery. Aim 3 determines whether phospho-variants of cMyBP-C can rescue contractile function in mice and in samples of myocardium isolated from patients with disease. The proposal is innovative and advances understanding of cMyBP-C biology and clinical translation. The team’s commitment to sharing open-source code and experimental data will benefit research focused on heart failure.

NIH Research Projects · FY 2026 · 2019-03

Modified Project Summary/Abstract Section This project represents the comprehensive efforts of the oncology community at Case Western Reserve University School of Medicine and its three major teaching affiliate hospitals (University Hospitals, Cleveland Clinic, and MetroHealth) to participate as a Lead Academic Participating Site in the National Clinical Trials Network (NCTN). The NCTN, funded and directed by the National Cancer Institute (NCI), is the major consortium for performing federally-funded, national multicenter clinical trials that aim to improve outcomes for cancer patients. The emphasis of NCTN trials is late phase (phase III and relatively large Phase II) trials that address scientific questions that usually cannot be answered by other means such as a single-institution study or an industry company study. The results of these trials often set the standards of care for cancer treatment in the U.S. and the world. This includes clinical trials research in rare cancers and across all patient populations. Our specific aims for this project are 1) to participate in NCTN trials with exceptionally high levels of accrual volume and quality of data generation and submission for approximately 260 new patients per year; 2) to serve the NCTN and the cancer community by providing scientific and administrative leadership in the (Cooperative) Groups that design and operate these NCTN clinical trials in the entire broad portfolio of cancers; in particular we are full members with many investigator leaders within NRG Oncology, ECOG-ACRIN and SWOG; and 3) to perform and present hypothesis-based, investigator-led research that benefits future NCTN research. This includes secondary clinical and biorepository translational analyses from NCTN data and pilot studies from our institution. We achieve these aims by assembling an outstanding core of investigators representing all the major cancer specialties (surgical, radiation, medical and diagnostic oncology) and disease sites (hematologic, lung, breast, gastrointestinal, genitourinary, brain, gynecologic and melanoma). We have also developed a robust infrastructure of clinical trials operations in support of the NCTN, including the centralized facilities at Case Western and the hospital-based clinical trials units. They ensure timely activation of, and education about, NCTN trials, accrual enhancement, regulatory management and a high quality of research procedures and data submission. Finally, a major priority is the recruitment, development and mentoring of new investigators’ involvement within the NCTN, including their participation in the Groups’ activities such as their semi-annual meetings and committee assignments.

NIH Research Projects · FY 2026 · 2018-12

The goal of this project is to develop smart targeted lipid ECO/siRNA nanoparticles (ELNP) to target oncogenic long non-coding RNAs (lncRNAs) as a novel therapy to treat triple-negative breast cancer (TNBC). Metastasis and drug resistance are the main causes for the high mortality rates of women diagnosed with TNBC worldwide. Although targeted therapies have been developed to treat some subtypes of breast cancer, the TNBC subtype is particularly refractory to these therapies. Oncogenic lncRNAs play a critical role in tumorigenesis, metastasis, drug resistance, and immune suppression of cancer by simultaneously manipulating multiple cancer-associated signaling pathways. We have demonstrated in this project that onco-lncRNAs are promising therapeutic targets to treat TNBC, and that downregulation of an onco-lncRNA with systemic delivery of targeted ECO/siRNA nanoparticles results in significant suppression of TNBC proliferation. We have identified a novel lncRNA BORG, which is associated with TNBC development, metastasis, drug resistance and immune invasion, as a compelling therapeutic target to treat TNBC. It is overexpressed in invasive BC, including TNBC, but not in normal tissues. Downregulation of BORG with targeted ECO/siRNA nanoparticles has potential to inhibit metastasis, sensitize TNBC to chemotherapy, and enhance antitumor immunity for curative treatment of TNBC. In this project, we will optimize and develop the smart ECO/siBORG nanoparticles to efficiently deliver siBORG in TNBC to silence the cancer-promoting lncRNA. We will also explore the combination therapy of silencing BORG with a tumor-specific peptide drug conjugate and/or immunotherapy to treat TNBC and to eventually eradicate this deadly disease. The specific aims of this project are 1) to optimize and develop smart siBORG-ELNP for efficient and specific gene silencing in breast cancer cells; 2) to determine the efficacy of targeted siBORG-ELNP as single therapy and in combination with targeted chemotherapy in animal TNBC models; and 3) to determine the efficacy of targeted siBORG-ELNP in modulating TIME for improved immunotherapy in animal TNBC models. Our long-term goal is to develop a novel and feasible therapy based on the smart nanoparticles to treat life-threatening breast cancer.

NIH Research Projects · FY 2026 · 2018-09

PROJECT SUMMARY/ABSTRACT Acute kidney injury (AKI) is a severe clinical syndrome that develops in up to 15% of all hospitalized patients and up to 50% intensive care unit patients. Severe AKI results in tubulointerstitial fibrosis and progressive loss of kidney function, which are associated with increased long-term morbidity and mortality. Productive kidney repair (also called kidney adaptive repair) can restore nephron function and avoid tubulointerstitial fibrosis; therefore, promoting productive repair is an attractive target in therapeutic treatment of AKI. Nitric oxide (NO) is an established mediator in repair of skin, nerve, skeletal muscle, liver, heart, bone, and vessels, but its role in kidney repair remains entirely unknown. NO-based signaling is conveyed in large part by protein S-nitrosylation. We have discovered a novel protein S-nitrosylation system in kidney consisting of the novel nitrosylase SCAN and its cognate denitrosylase SCoR, which add and remove SNO groups on target proteins, respectively. Pyruvate Kinase M2 (PKM2) is a critical regulator of cell metabolism, and is a major S- nitrosylation target of the SCAN/SCoR system during kidney injury. We now find that SCAN/SCoR and PKM2 are also important during kidney repair. Deletion of SCoR in mice, which increases SCAN mediated S-nitrosylation, promotes adaptive repair through multiple beneficial effects: 1) alleviating oxidative stress; 2) increasing availability of biosynthetic macromolecules; 3) increasing cell cycle re- entry; 4) reversal of G2/M arrest; 5) reducing AKI-associated kidney fibrosis. Reduced SCoR activity and increased SCAN expression are observed in human AKI kidney compared with healthy kidney, suggesting that S-nitrosylation regulated by the SCAN/SCoR system is important in human kidney repair. We have developed a specific SCoR inhibitor as a tool to assess the therapeutic potential of SCoR inhibition in productive kidney repair. To explore the role of PKM2 S-nitrosylation regulated by the SCAN/SCoR system in kidney repair, and to assess the efficacy of SCoR inhibition in repair, we will: 1) define the role of SCoR in productive kidney repair; 2) delineate the role of SCAN and S- nitrosylation of PKM2 in kidney repair; 3) determine the clinical significance of SCoR and SCAN in kidney repair. Successful completion of our studies not only will reveal the physiological function of PKM2 S-nitrosylation catalyzed by SCAN and SCoR enzymes in productive repair, but also will define and validate new drug targets to repair the kidneys after AKI.

NIH Research Projects · FY 2025 · 2018-09

Cancer has been a major focus of biomedical research since the war on cancer began with the National Cancer Act of 1971. Despite this focus, nearly 10 million people die of cancer each year, worldwide. To help ensure that the nations’ biomedical, clinical, and behavioral cancer research workforce remains strong, we have developed the Cancer-focused Summer Undergraduate Research (CanSUR) Program, with the goal of recruiting highly motivated undergraduate students to foster their passion for a future career in cancer research and oncology. The CanSUR Program supports 32 undergraduate scholars each year, recruited from national and regional colleges/universities for a 10-week period, to participate in a cancer research experience with members of the Case Comprehensive Cancer Center (Case CCC). Key objectives of the CanSUR Program are to: (1) provide a hands-on, cancer research experience including project development, execution, interpretation, and reporting of research results in a Case CCC member’s laboratory; (2) develop the communication skills necessary to understand and present research in a variety of settings; (3) educate participants about cancer research career opportunities; (4) provide scientific enrichment and professional skills development curricula to help prepare Scholars for graduate and/or medical school; (5) evaluate all aspects of the Program. Three major components have been developed to meet these objectives. First, a Week 1 Cancer Immersion Bootcamp has been developed that includes interactive lectures/discussions, HoloLens virtual reality education modules, social outings to build community, discussions of cancer career paths, campus and Case CCC core facility tours, and research ethics and lab safety training. Second, Scholars will be engaged in an individual mentored research project. Finally, a Career and Scientific Enrichment Curriculum has been developed to help Scholars learn about hot topics in cancer research, build communication skills, develop professional habits, and prepare for the next step in their cancer-focused career path. Given the importance of our objectives, we have been pledged substantial institutional support and have 70 Case CCC members and institutional leaders who focus on cancer education prepared to continue recruiting and training outstanding undergraduates in this summer program. As such, we are well-positioned to convert highly motivated undergraduates into the nation’s next cancer research workforce.

NIH Research Projects · FY 2025 · 2018-08

ABSTRACT The fat-soluble vitamin A (all-trans-retinol) is distributed in the body to maintain retinoid signaling in peripheral tissues and vision in the eyes. This transport occurs via an extrinsic pathway for the distribution of dietary vitamin A in the form of retinyl esters in chylomicrons and an intrinsic pathway for the distribution of vitamin A from hepatic stores bound to the retinoid binding protein RBP4. Cellular uptake of vitamin A from these two transport modes is facilitated by lipoprotein lipase and by the RBP4 receptor STRA6 (Stimulated by Retinoic Acid 6), respectively. Disrupted vitamin A transport is a serious health problem and is associated with blinding diseases ranging from night blindness to complex ophthalmic syndromes. We propose to study the etiology of ocular diseases states that are associated with perturbed ocular vitamin A uptake homeostasis by comparing the eyes of STRA6-deficient and that of control mice. In Aim 1, we will examine the role of STRA6 in the functioning of the outer blood-retinal barrier. We will study whether ocular vitamin A deficiency in Stra6 knockout mice impairs the structural integrity and functioning of this barrier. Additionally, we will examine whether retinoid signaling regulates the expression of key components of both the outer blood-retina barrier in mice and human retina pigment epithelium cells derived from inducible pluripotent stem cells. In Aim 2, we will use Stra6 knockout mice to analyze the consequences of imbalances in ocular retinoid concentrations on rod and cone photoreceptor function and ultrastructure. We will generate novel transgenic mouse lines to examine the competition between rods and cones for limited chromophore in the STRA6-deficient eyes. This research will address the question whether the STRA6/RBP4-dependent transport system is an adaption to the high chromophore demand from rod photoreceptors. In Aim 3, we will study whether manipulation of the extrinsic pathway can rescue cone and rod photoreceptor function in STRA6-deficiency and whether the STRA6/RBP4 uptake system provides selectivity for the uptake of canonical retinoids. Collectively, our proposed studies will advance knowledge about ocular vitamin A homeostasis by elucidating its mechanisms in the physiological state and by studying the consequences of its loss-of-function in disease states.

NIH Research Projects · FY 2026 · 2018-07

Project Summary/Abstract. In the mammalian nervous system, a heightened level of plasticity is observed during early postnatal development that enables the neural circuit to change according to environmental stimuli. We have discovered that the mammalian olfactory sensory neurons (OSNs) undergoes a developmental switch during a critical period of development. OSNs born during the perinatal period exhibit high levels of plasticity, exuberant axon growth, and can alter their innervation targets following prolonged odor stimulation. Neurons born after the critical period no longer exhibit these characteristics. The objective of this application is to determine the molecular control of the critical period in olfactory system development. In particular, we will study the role of Fzd1, which have multiple functions in regulating cellular and developmental processes in neural and non- neuronal tissues, in regulating the critical period. By combining genetic manipulation, transcriptome analyses, protein interaction assays, imaging, and behavioral assays, we will determine the requirement of Fzd1 in regulating developmental plasticity of the OSNs. We will further determine at the molecular level how Fzd1 interact with other partners to increase neuronal plasticity during early phase of development and how it regulates a transcriptional program to close the critical period. These studies will provide mechanistic insights into axon pathfinding during OSN development and during adult neurogenesis.

NIH Research Projects · FY 2025 · 2018-07

PROJECT ABSTRACT The heterogeneity of pancreatic β-cells has been reported in many studies, but the field still lacks a consensus about its molecular signature and disease relevance. Our recent single cell multiome analysis suggested that HNF1A is a principal driver of a T2D-associated heterogeneity among the -cells from the same individual. By leveraging single cell Patch-seq data, we also discovered that HNF1A activity is associated with lower Na+ currents in β-cells and nominated a HNF1A target, FXYD2, as the primary mitigator. Since mutations in HNF1A are known to cause early onset diabetes (MODY3), there is a strong likelihood that HNF1A plays a causal role in T2D via governing -cell heterogeneity. In fact, many literatures studied HNF1A and its mutations due to the connection to MODY3, but little is known about its role in common diabetes in the context of -cell heterogeneity. It should be noted that although our previous work has demonstrated the power of single cell multiome to study -cell heterogeneity, the data did not allow us to directly compare the HNF1Ahi and HNF1Alo -cell populations due to technical difficulties. In this project we will develop new single cell multiome integration strategy to directly survey HNF1A function in -cell heterogeneity. We will establish stem cell models to manipulate HNF1A dosage in hESC-derived -cells, which will not only provide mechanistic insights into how HNF1A mediates MODY3 and -cell heterogeneity, but also offer new opportunity to improve the functionality of hPSC-derived -like cells for therapeutical benefits. We will also develop new cell line model to allow genetic and chemical screens for the upstream regulators of HNF1A in -cells. Taken together, our project will establish a new concept linking MODY3 gene HNF1A to common diabetes in the context of -cell heterogeneity.

NIH Research Projects · FY 2022 · 2018-06

PROJECT SUMMARY. The nervous system constantly adjusts how it processes sensory information based on the experience and physiological state of an animal. This flexibility is enabled by the release of neuromodulators, which alter the biophysical properties and synaptic interactions between neurons within a network. Neuromodulatory dysfunction is associated with many neurological disorders, yet despite its importance for healthy sensory processing, the effects of neuromodulation on sensory processing are often heterogeneous and difficult to predict. This is due to the diversity of receptors for a given neuromodulator, and the complexity of cell-class specific receptor expression patterns. For example, there are 14 serotonin receptors that differ in their intracellular signaling targets, time course of action and binding affinity for serotonin. When this is combined with the diversity of cell types within a neural network, understanding the impact of serotonin on sensory processing becomes challenging. We propose to address the topic of the receptor basis sensory modulation using the olfactory system of Drosophila as there is comprehensive understanding of sensory network connectivity and the modulatory receptors expressed by each class within that network. We previously demonstrated that serotonergic neurons primarily synapse upon inhibitory neurons that affect different aspects of olfactory coding in Drosophila. Our objective is to determine how the serotonin receptors expressed by each class of inhibitory neuron alter olfactory coding and odor-guided behavior. Our proposed experiments will establish how receptor expression patterns dictate the effects of serotonin on information coding, thus addressing a critical gap in our knowledge of healthy sensory processing. Ultimately this will reveal the mechanisms by which serotonin regulates how information about the external world is processed.

NIH Research Projects · FY 2024 · 2018-03

The proposed work is focused on restoration of hand and reaching functions for people with cervical level spinal cord injury. For individuals who have sustained this injury, restoration of hand function is their top priority, and existing alternatives are limited. Neuroprostheses are the most promising method for significant gain in hand and arm function. In this CREATE project, we propose to prepare for a future pivotal clinical trial by transfer of a third-generation neuroprosthetic, the Networked Neuroprosthesis, to two clinical trial sites. The effort will enable the development and evaluation of a clinical training program, establish the effectiveness of device transferability, and bring valuable clinical and patient experience into the product development cycle. The work represents an interim step between our Early Feasibility IDE experience which is currently underway, and a future Pivotal Clinical Trial. In the first phase of the proposed work, we will harden the implantable system for manufacture, and complete the verification and validation that will be necessary to perform a pivotal clinical trial. In the second phase, we will extend our Early Feasibility study by selecting and training two beta sites to test the feasibility of our training materials and procedures, our technology and medical/surgical procedures of implementation, and our outcome evaluations, in order to establish our system’s readiness for further translation to a Pivotal Clinical Trial. Following this work, our intent would be to undertake further expansion of the study to a Pivotal Clinical Trial in order to collect the definitive dataset necessary for full regulatory approval and market release that would enable successful commercialization and broader access for people with spinal cord injuries. This effort is coupled with an overall strategy for sustainable dissemination of this technology to the SCI population. Thus, the impact from this study is not only to demonstrate the benefits of a single clinical application, but the impact also extends to the entire field of SCI and similar orphan diseases through the establishment of a sustainable entity that can assure the availability of implanted neuroprostheses to the individuals who can benefit from them.

NIH Research Projects · FY 2026 · 2018-02

PROJECT SUMMARY (ABSTRACT) Mitochondria are double-membrane organelles that change shape, size and abundance in response to specific stimuli. Protein interactions that control mitochondrial division are tightly regulated and directly impact ATP production, Ca2+ homeostasis, and regulation of programmed cell death. Therefore, mitochondrial dynamics has recently come to the forefront as a therapeutic target in several degenerative diseases, including neurodegeneration, cancer, and cardiovascular disease. But the lack of insight into the regulation of this process is a major limitation. The major driver of mitochondrial division is a cytosolic GTPase, dynamin-related protein 1 (Drp1). To mediate membrane scission, Drp1 recruitment and self-assembly is coordinated through combinatorial interactions with lipids, proteins and nucleotides at the surface of mitochondria. This proposal seeks to identify key attributes of the mitochondrial division machinery and how dysregulation of Drp1 leads to organelle damage and cellular degeneration. This will be accomplished using a multifaceted approach that combines molecular studies with functional cell experiments to provide a comprehensive evaluation of Drp1 interactions that govern membrane remodeling. Under Specific Aim 1 of the renewal, cryo-EM studies will examine auto-inhibitory interactions that limit Drp1 oligomerization in a cytosolic state. Distinct conformations will be studied to identify and characterize intermediate structures during recruitment and assembly of Drp1 into a functional fission complex. We propose that regulated rearrangements “open” the molecule for functional assembly at defined sites of mitochondrial division. For Specific Aim 2, reconstitution experiments provide a means to evaluate macromolecular interactions that drive mitochondrial membrane remodeling. Specific mitochondrial cues, including lipids and partner proteins, will be studied to evaluate the contribution of each component to membrane remodeling. Constriction of protein-lipid tubules will be encouraged to evaluate the magnitude of constriction using advanced structural methods. Liquid-EM will visualize dynamic narrowing of Drp1-lipid tubules in real time, and cryo-ET will be used to resolve 3D structures of assorted Drp1 constriction events in parallel. In Specific Aim 3, defects in mitochondrial fission will be examined at the cellular level to establish how deleterious changes in Drp1 can directly influence mitochondrial bioenergetics. The integrity of ETC complexes will be studied to reveal how altered organelle morphology informs metabolic stress. Concurrently, the impact of this stress on ROS signaling and mitophagy will be monitored. In summary, the structural and functional insight gained from this proposal will catalyze directed therapeutic strategies that counteract mitochondrial damage in various disease states.

NIH Research Projects · FY 2026 · 2017-12

PROJECT SUMMARY This competitive renewal application focuses on continued development of cancer cell-specific nanobubble (NB) ultrasound contrast agents for real-time guidance of prostate biopsies using transrectal ultrasound (TRUS). In the current clinical workflow, prostate cancer (PCa) biopsies are almost always performed using TRUS guidance. However due to poor soft tissue contrast of the B-mode ultrasound scans, the delineation of tumors within the prostate using TRUS is not clear. Because only 1% of the prostate tissue is sampled with a typical 8-12 core biopsy, a lack of direct guidance of the biopsy to suspicious lesions has led to high false negative rates and rising morbidity from current standard of care. The development of a new tool to accurately depict cancer within the prostate in real-time using TRUS is thus urgently needed to aid in biopsy guidance. To provide a practical tool for clear identification of potential malignancies during prostate biopsies, we have developed a nanoparticle-based ultrasound contrast agent (called a nanobubble) targeted to the prostate specific membrane antigen (PSMA) which is significantly over-expressed in most prostate cancers. The PSMA-NBs, are similar in structure to clinically used microbubbles (MB) and are clearly visible on clinical US. In contrast to MB, which remain in the vasculature, the small size, deformable shell and gas core, enable NBs extravasate and directly bind to cancer cells. This results in highly specific accumulation of contrast at the tumor itself leading to better resolution and detection of PCa. During our initial award, we developed an entirely new platform NB formulation which has been rigorously vetted and tested extensively in animal models of PCa. The objective of the next phase of research proposed in this renewal is to continue working toward clinical translation by performing IND-enabling studies. Here, we will scale up the NB formulation, test batch-to-batch reproducibility, conduct toxicology studies and engineer viable long-term storage techniques. Concurrently we will develop multiparametric US imaging biomarkers unique to NBs and acquisition pulse sequences optimized for use with the NBs to further enhance the sensitivity and specificity of the PSMA-NB technology; there are currently no NB specific image acquisition or processing tools for contrast enhanced ultrasound. We will then test the sensitivity and specificity of PSMA-NB enabled TRUS biopsies in a large animal model of prostate cancer in dogs, which can accommodate clinical TRUS transducers and a near-identical workflow to clinical standard of care. These steps are critical to the advancement of the proposed imaging techniques to clinical use. The proposed research feasibility is supported by strong preliminary data generated by an integrated research team with complementary expertise in NB formulation and PSMA (Exner, Basilion), bubble-US interactions (Kolios), image processing (Wilson), and clinical prostate imaging (Bittencourt). The project outcomes will benefit diagnosis, biopsy, and care of prostate cancer using TRUS and complement the existing clinical workflow.

NIH Research Projects · FY 2025 · 2017-09

The overall objective of this R25 Youth Enjoy Science (YES) Grant Application from the Case Comprehensive Cancer Center (Case CCC), Case Western Reserve University (CWRU), Cleveland Ohio, aims to support, develop and implement exciting education, research immersion, outreach and curriculum development activities to attract and mentor students from the Cleveland area in middle and high school progressing to college undergraduate and science teachers to enhance the future cancer healthcare and research workforce. This program is a partnership between the Case CCC, supporting all cancer related research efforts at CWRU with the surrounding Cleveland area schools, particularly the Cleveland Metropolitan School District and East Cleveland Schools, both of which are economically and academically challenged urban school districts. Cleveland is recognized as being one of the poorest major cities in the U.S. This R25 program for students, their teachers and families builds and expands on our successful high school student targeted, Scientific Enrichment and Opportunity Program and our experience with the R25 YES Program. These programs have been developed to engage promising Cleveland area high school students to interact with the SOM faculty, to participate in exciting, longitudinal research experience, to enhance student interest in pursuing careers in biomedical research and healthcare professions, especially as they relate to cancer. The R25 YES Program extends and enhances our efforts to provide a coordinated sequentially integrated approach consisting of 1) Learn to Beat Cancer, a program targeted to engage Cleveland area middle school students, their families and teachers to become knowledgeable about cancer prevention and cancer research opportunities; 2) Research to Beat Cancer, a program designed to attract promising Cleveland area high school and undergraduate students to cancer education and research immersion opportunities at the Case CCC; and 3) Teach to Beat Cancer, a program designed to provide special research and education opportunities for teachers of Cleveland area students to enhance their cancer related knowledge and education skills, engage in curriculum development and enhance their enthusiasm and ability to promote careers in cancer research and in the biomedical work force as well as to further engage the community for increased interaction with the Case CCC.

NIH Research Projects · FY 2026 · 2017-08

Project Abstract Mapping the gene-regulatory chromatin interactions within topologically associated domains (sub- TAD) remains a major challenge in 3D genome research. It is generally believed that multibillion-read sequencing depth are required for Hi-C analysis at kilobase-resolution due to the complex bias structure and severe data sparsity. However, we recently discovered that this is problem can be largely solved computationally without the need for ultradeep-sequencing. We developed a new pipeline named DeepLoop that can robustly identify high-resolution chromatin interactions from low-depth Hi-C data. The conceptual innovation of DeepLoop is to handle systematic biases and random noises separately: we used HiCorr to improve the rigor of bias correction, and then applied deep-learning techniques for noise reduction and loop signal enhancement. Preliminary results showed that DeepLoop significantly improves the sensitivity, robustness, and quantitation of Hi-C loop analyses, and can be used to reanalyze most published low-depth Hi-C datasets. Remarkably, DeepLoop can identify chromatin loops with Hi-C data from a few dozen single cells. These successes motivate us to further optimize, benchmark, simplify and upgrade DeepLoop into a versatile tool for the 3D genome field. Aim 1 will optimize and benchmark DeepLoop performance, improve its compatibility with a variety of different Hi-C protocols, and expand its utility to ultra-resolution analysis. Aim 2 will develop new DeepLoop-based pipelines to enable robust mapping of dynamic chromatin loops at high-resolution, including the identification of homolog-specific loops and loops affected by structure variants. Aim 3 will develop a full-package solution for high- resolution loop analysis of complex tissues with single cell Hi-C, a significant amount of data will be generated in this project as a resource for the scientific community.

NIH Research Projects · FY 2025 · 2017-08

PROJECT SUMMARY/ABSTRACT Undertaking innovative cancer research requires input from teams of scientists with a mixture of backgrounds, including molecular biology, oncology, medicine, epidemiology, biostatistics, genomics/genetics, bioinformatics, computer science and artificial intelligence. Researchers with interdisciplinary training across these fields are extremely valuable to such teams, as they can act as conduits for the integrated work necessary to accomplish some of the most promising and forward-looking cancer research. Due to the exclusive nature of training within these fields, however, there are limited opportunities for investigators to obtain the knowledge that bridges these disciplines. To help remedy this problem, we propose here the continuation of this T32 program to provide postdoctoral training in the Computational Genomic Epidemiology of Cancer (CoGEC) at the Case Comprehensive Cancer Center. The CoGEC training program defines a novel, transdisciplinary area of training at the intersection of cancer research, epidemiology, biostatistics, genetics, and computer science. The program’s structure is defined by three key requirements. First, all trainees will have the opportunity to take a specialized core curriculum of five courses to fill in the gaps of their previous training if necessary. Second, the trainees will undertake additional didactic experiences selected to complement their educational and research background. Third, all trainees will obtain research experience by collaborating with multiple mentors on high-level computational genomic epidemiology of cancer projects. As an extension of this research experience, each trainee will be required to write and defend an NIH grant proposal. Cancer researchers obtaining training in this program will have the skills vital to deciphering the complex pathways comprising genetic and environmental risk factors for disease. In doing so, their knowledge and findings will be translated into improved cancer understanding, prevention and treatment.

NIH Research Projects · FY 2026 · 2016-12

PROJECT SUMMARY The therapeutic benefit of transfusion presumes a direct correlation between blood oxygen carrying capacity and oxygen delivery. However, our preclinical and clinical studies show that stored blood loses its ability to oxygenate tissues. The sequelae that can occur after transfusion (renal injury, myocardial infarction, death) are consistent with the idea that banked blood may exacerbate rather than correct anemia-induced hypoxia. We have discovered that banked blood has markedly diminished levels of nitric oxide/S-nitrosothiol (NO/SNO) bioactivity including the S-nitrosylated form of hemoglobin (SNO-Hb), a major mediator of blood flow and peripheral oxygen delivery. This decline in SNO provides a mechanistic basis for the impaired vasodilatory activity of stored red blood cells (RBCs) and an explanation for why transfusion of even small amounts of blood may impair tissue perfusion. We have built on this novel finding by demonstrating that restoration of SNO-Hb levels (renitrosylation) corrects storage-induced deficiencies in RBC oxygen delivery and transfusion-induced organ dysfunction in multiple preclinical transfusion paradigms, and we have initiated clinical studies to assess the effects of transfusion on tissue oxygenation. We have also developed first-in-class renitrosylating agents that are already undergoing clinical testing. We are positioned to provide critically needed data on the effects of transfusion on tissue oxygenation in humans and to advance the benefits of renitrosylation therapy on oxygen delivery through the following aims: 1. To further advance understanding of the molecular mechanisms by which RBCs export SNO bioactivity to regulate tissue oxygenation; 2. To develop a device for controlled ex vivo renitrosylation; 3. To determine if renitrosylation can improve post-surgical outcome in an animal model of pediatric bypass; and 4. To conduct an autologous transfusion study in humans to determine the benefits of renitrosylation on tissue oxygenation. Collectively, our studies should provide much-needed insight into the effects of transfusion on tissue oxygenation, shed light on the mechanistic basis of adverse ischemic events associated with transfusion, and accelerate development of therapeutic approaches (repletion of SNO-Hb). Restoration of the oxygen delivery capabilities of banked blood should result in blood transfusion achieving its clinical purpose: vasodilation in the microcirculation to improve end-organ oxygen delivery in the anemic patient. To the extent that the world’s supplies of banked RBCs are deficient in SNO-Hb, renitrosylation may hold significant therapeutic promise.