Biological and Health Sciences

Francisco Alvarez, PhD

PROFESSOR, SCHOOL OF MEDICINE, CELL BIOLOGY

GABA synaptic function promotes motor axon regeneration

Motor nerve regeneration after axotomy is very slow affecting recovery in the 200,000+ patients that undergo nerve reconstructive surgeries in the US every year. Improved knowledge on mechanisms to enhance motor axon growth is critical. After injury, motoneurons change gene expression towards protein synthesis for axon growth and recent studies highlighted the role of activity accelerating this process. However, this is paradoxical because until recently, most authors thought that regenerating motoneurons were kept in an electrophysiological “silent state” to redirect metabolic resources towards protein synthesis and transport. This was supported by the shedding of most excitatory synapses from the cell body, while partially keeping inhibitory synapses creating an E/I imbalance that was assumed to dampen motoneuron firing. However, this rises two fundamental questions, 1) how does motoneuron activity promotes regeneration? 2) what synaptic drives provide the necessary excitation? Two recent papers from our lab support the hypothesis that the “inhibitory” synapses retained on the cell body promote regeneration. First, we and others found that the potassium chloride co-transporter isoform 2 (KCC2) is removed after axotomy suggesting that “inhibitory” synapses change from hyperpolarizing to depolarizing on regenerating motoneurons. Second, in a recent manuscript we demonstrated that GABA synaptic release on axotomized motoneurons promotes regeneration. The purpose of this URC is to generate new data for an NIH grant application to study the mechanisms by which GABA enhances regeneration. We propose to genetically manipulate KCC2 regulation after axotomy to test its influence on motor axon regeneration, motoneuron function and gene expression

Erin Buckley, PhD

ASSOCIATE PROFESSOR, SCHOOL OF MEDICINE, BIOMEDICAL

Validation of broadband absorption spectroscopy measures of brain water content

Cerebral edema refers to an increase in brain water content that leads to an expansion in brain volume. Edema is a common complication following numerous pathologies, including traumatic brain injury and stroke, that is a significant contributor to morbidity and mortality. As edema progresses, it can distort vital brain structures, alter function, and increase intracranial pressure, resulting in secondary brain damage beyond that of the initial injury. Unfortunately, current clinical evaluation of cerebral edema relies on indirect and intermittent assessment via qualitative imaging or invasive pressure sensors. There is an urgent need for a non-invasive bedside monitor of brain water content to improve the diagnosis of edema and to assess the efficacy of treatments aimed at reducing edema. Broadband absorption spectroscopy (BAS) is a non-invasive optical tool that may provide such a monitor. We have taken the first steps to use BAS to measure regional cerebral water content in adults, showing that BAS is feasible in the intensive care unit and highly repeatable. In a small validation study (3 healthy and 2 stroke), we demonstrated strong correlation between BAS-measured water content and quantitative MRI-measured water. This proposal will increase our samples sizes to demonstrate that these exciting results are generalizable to a variety of edema etiologies. Successful completion of these aims will provide the foundation first steps towards a bedside tool that could have a powerful impact to address a major deficit in the clinical management of critically-ill patients suffering from cerebral edema.

Debayan Dey, PhD

ASSISTANT PROFESSOR, SCHOOL OF MEDICINE, BIOCHEMISTRY

EffluxStop- A Novel Framework for Targeting Efflux Pumps in Pseudomonas aeruginosa

This study addresses the critical challenge of antibiotic resistance in Pseudomonas aeruginosa, focusing on the targeting the MexXY-OprM efflux pump. The functional redundancy of multiple efflux pump paralogs, coupled with the structural flexibility of MexXY-OprM’s large efflux channel, presents unique challenges for inhibitor design, as efflux pump inhibitors (EPIs) can be expelled by other paralogous pumps within the pathogen and lack a traditional fixed substrate-binding pocket. To overcome these barriers, we propose EffluxStop, an integrated experimental and computational strategy to identify and optimize inhibitors for specific efflux pumps. This framework is broadly adaptable but focuses here on MexXY-OprM, a key player in aminoglycoside resistance. EffluxStop employs a short three-phase approach, completing within the grant proposal timeline, transitioning from hit identification to lead development, aiming to restore aminoglycoside efficacy. Lead compounds will be evaluated for their synergy with aminoglycosides through computational pipelines and microbiological assays, including FIC/MIC synergy tests. A multidisciplinary approach integrates computational modeling, MD simulations with experimental assays, using isoquinoline-based compounds to assess MexXY-OprM inhibition in engineered and clinically relevant P. aeruginosa strains. Anticipated outcomes include identifying lead compounds with efflux inhibitory properties, paving the way for long term planned SAR studies which will lead to targeted therapies against resistant P. aeruginosa infections. Long-term, the EffluxStop framework can be extended to other efflux pumps, addressing broader clinical challenges of antibiotic resistance and delivering impactful solutions in diverse settings.

Yue Feng, MD, PhD

PROFESSOR, SCHOOL OF MEDICINE, PHARMACOLOGY AND CHEMICAL BIOLOGY

Elucidating human-specific function of MIR137HG and its roles in schizophrenia risk

MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are two classes of noncoding RNAs (ncRNAs) that regulate broad gene networks through distinct mechanisms, essential for normal brain development and function. Genetic alterations and dysregulation of ncRNA genes are found in various neuropsychiatric disorders, represented by schizophrenia (SCZ) that affects 21 million people worldwide. MIR137HG, the host gene of miR-137, is a leading risk gene of SCZ that harbors various disease-associated genetic variants, including a human-specific variable number of tandem repeat (VNTR). How MIR137HG is dysregulated in SCZ brains remains unknown. The highly conserved miR-137 derived from MIR137HG is extensively studied, which is essential for neuronal development and brain function. However, MIR137HG also produces human-specific lncRNAs and miR-2682 that are markedly increased during brain development, which should also be affected by SCZ-associated genetic alterations and contribute to SCZ risk yet have never been investigated. The biased ignorance of these human-specific MIR137HG ncRNAs has left a prevailing knowledge gap regarding MIR137HG function in normal brains and the risk of SCZ. This URC application represents our first step efforts in understanding human-specific function and cooperation of MIR137HG ncRNAs. We propose to elucidate: 1) how the SCZ risk-associated human-specific VNTR affects biogenesis of MIR137HG miRNAs and lncRNAs; 2) how MIR137HG miRNAs and lncRNAs cooperatively regulate human neuronal gene networks that are affected in SCZ brains. Successful completion of these well-focused studies will provide novel clues regarding human-specific mechanisms of MIR137HG in SCZ risk and generate key preliminary data for our planned NIH grant submission.

Ezequiel Gleichgerrcht, MD, PhD

ASSISTANT PROFESSOR, SCHOOL OF MEDICINE, NEUROLOGY

Revealing the Neuroanatomy of Episodic Simulation through Temporal Lobe Epilepsy

Episodic simulation is the ability to imagine personal future events in vivid detail, such as planning a birthday celebration or envisioning a career milestone. This important cognitive skill allows us to set goals, solve problems, and regulate emotions. However, in people with temporal lobe epilepsy (TLE)—a common form of epilepsy that often does not respond to medications—this ability may be impaired. While surgery can effectively reduce or eliminate seizures for many TLE patients, it also poses a risk to memory and other cognitive functions. Despite its importance, episodic simulation in TLE has rarely been studied, leaving a critical gap in our understanding of its neurobiological basis and surgical outcomes.

This study aims to explore how TLE affects future-thinking abilities and identify the brain regions responsible for episodic simulation. By using advanced neuroimaging techniques and detailed episodic simulation tests, we will compare the performance on these abilities between patients with TLE patients and healthy individuals. For patients undergoing epilepsy surgery, we will also investigate how surgery-related brain changes impact their capacity to imagine the future.

The findings from this study will advance our understanding of how specific brain regions support future-thinking, offering insights into the complex relationship between the brain, memory, and imagination. Additionally, they will help improve counseling for TLE patients, allowing for more informed decisions about surgery and better management of cognitive challenges.

Chuan Huang, PhD

ASSOCIATE PROFESSOR, SCHOOL OF MEDICINE, RADIOLOGY AND IMAGING SCIENCES

Development of a Novel MR-Compatible Robotic System for PET/MR-Guided Breast Biopsies: Advancing Precision in Cancer Diagnostics

Breast cancer remains a leading cause of morbidity and mortality, emphasizing the critical need for precise diagnostic tools. While MR-guided breast biopsies have improved diagnostic accuracy, current workflows are hampered by procedural inefficiencies and high false-negative rates. This study aims to address these challenges by developing a novel PET/MR-compatible robotic biopsy system designed to enhance precision, efficiency, and minimally invasive sampling of diagnostically significant tumor regions. The proposed system integrates advanced functional imaging, using PET tracers like 18F-FLT and 18F-FES, with high-resolution MR imaging for accurate lesion characterization and biopsy guidance.

The robotic platform introduces innovations such as a compact, MR-compatible design and a nitinol-based steerable biopsy needle, enabling real-time targeting within the MRI bore. By eliminating the need for repeated patient repositioning, the system reduces procedural time and patient discomfort. Preliminary results demonstrate sub-2 mm targeting accuracy and effective tissue sampling in phantom studies, validating the system’s potential for clinical application.

The proposed PET/MR-guided robotic system represents a paradigm shift in imaging-guided breast biopsies. By integrating molecular and anatomical imaging with robotic precision, this approach addresses limitations of traditional methods, particularly in dense breast tissue and low-FDG-avid tumors. The project has transformative implications for personalized cancer diagnostics, offering a pathway to improved diagnostic accuracy, reduced false negatives, and enhanced patient care. These advancements pave the way for future large-scale clinical studies and adoption of this innovative system in routine breast cancer diagnostics.

Jie Jiang, PhD

ASSOCIATE PROFESSOR, SCHOOL OF MEDICINE, MEDICINE, CELL BIOLOGY

Deciphering Cell-Type Specific Proteomic Alterations in ALS

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease caused by the loss of upper and lower motor neurons, leading to progressive muscle weakness and paralysis. Currently, there is no cure for ALS. Strong evidence supports that non-neuronal cells including astrocytes play an important role in the disease. However, the underlying molecular mechanisms for cell autonomous and non-cell autonomous toxicity in ALS are not well established. Previous efforts to address this question either rely on physical enrichment of target cells with potential contamination from neighboring environment, or focus on transcriptomic changes, which only modestly correlate with protein-level changes. In addition, mechanisms proposed by studying cell cocultures do not capture age-dependent disease course in vivo. We have recently generated a mouse line for cell type-specific expression of biotin ligase TurboID which allows for in vivo biotinylation of proteins. In this study, we propose to determine proteomic changes within spinal cord motor neurons and astrocytes during the course of disease in an ALS mouse model using this newly established TurboID mice. Completion of this study will shed light on developing novel therapies for this fatal disease.

Jessica Konen, PhD

INSTRUCTOR, SCHOOL OF MEDICINE, HEMATOLOGY AND MEDICAL ONCOLOGY

The role of autotaxin and lysophosphatidic acid in suppressing stem-like T cell functions in lung cancer

Immune checkpoint inhibitors (ICI), which work to promote anti-tumor immune activity, have vastly improved the outlook for lung cancer over the last decade, with response rates reaching ~35% in the KRAS/p53 (KP) mutant subset of patients. However, most patients demonstrate primary or acquired resistance to treatment, limiting its efficacy. Therefore, identifying targetable mechanisms of resistance is a critical need. We previously discovered that autotaxin (ATX) is upregulated in lung cancer models with ICI resistance, and co-targeting ATX with ICI can significantly repress tumor growth. The work proposed herein aims to build on these data by analyzing the impact of ATX on the CD8+ T cell subsets that are vital for ICI response. We hypothesize that increased ATX activity promotes ICI resistance by negatively regulating the proliferation and differentiation of CD8+ stem-like T cells in the tumor microenvironment. This proposal will address this with two Specific Aims. First, we will examine the effects of combination therapy on TCF1+ stem-like CD8+ T cell subsets via flow cytometry and multiplex-IHC, as well as examine the LPAR5-dependent effects on TCF1 expression (Aim 1). Next, we will evaluate tumor progression and ICI response as a function of ATX in a clinically relevant genetically engineered mouse model (GEMM) (Aim 2). We generated a novel GEMM with conditional ATX depletion in the KP background to further characterize ATX effects on immune microenvironment in an autochthonous model. Together, these studies will provide a thorough examination of ATX-dependent effects on the immune landscape and ICI response in lung cancer.

Bo Liang, PhD

ASSOCIATE PROFESSOR, SCHOOL OF MEDICINE, BIOCHEMISTRY

Structures and Mechanisms of Borna Disease Virus RNA SynthesisTop of Form

This project aims to elucidate the molecular mechanisms of RNA synthesis in non-segmented negative-sense (NNS) RNA viruses, focusing on the Borna disease virus (BDV) as a model system. BDV is uniquely suited for this study due to its compact genome (8.9 kb), nuclear replication strategy, and ability to establish persistent infections while evading immune clearance. Unlike other NNS viruses, BDV replicates in the nucleus, a feature with implications for mRNA-based gene therapy, as it can sustain gene expression without modifying host genomes. We aim to investigate the BDV RNA-dependent RNA polymerase (RdRP), which consists of the catalytic L protein and the essential cofactor phosphoprotein (P). L performs nucleotide polymerization, cap addition, and cap methylation, while P enhances L’s activity on the viral genome. Using an integrative approach that combines biochemistry, enzymology, mutagenesis, virology, crystallography, and cryo-EM, we will define the minimal functional requirements for RdRP activity and examine the evolutionary aspects of NNS RNA viruses. This research addresses fundamental questions about BDV nuclear RNA synthesis and replication dynamics. The anticipated insights will significantly advance our understanding of NNS RNA virus biology and inform the development of antiviral strategies. The novel structural and mechanistic findings will provide a robust framework for therapeutic innovation targeting BDV and related viruses.

Marie-Claude Perreault, PhD

ASSOCIATE PROFESSOR, SCHOOL OF MEDICINE, CELL BIOLOGY

Neural Circuit Mechanisms of Early Motor Dysfunctions in ASD

Autism Spectrum Disorder (ASD) is a group of neurodevelopmental disorders characterized by deficits in communication and social behaviors, often preceded by deficits in early motor behaviors, such as low muscle tone, impaired trunk-limb coordination, and impaired balance. Emerging evidence links early motor deficits to ASD progression, yet the neural mechanisms underlying these impairments remain unexplored. Early motor behaviors are regulated by early-maturing supraspinal (brainstem) and spinal circuits, making these prime candidates for investigation.

This project tests the hypothesis that supraspinal and spinal motor circuits are altered in early ASD, focusing on reticulospinal, vestibulospinal and sensorimotor circuits. Preliminary data from an environmental mouse model of ASD (VPA-exposed) reveal early motor deficits, reduced functional connectivity between reticulospinal neurons and lumbar motoneurons (MNs), and fewer lumbar MNs. To strengthen findings, we will obtain comparable data in a genetic ASD model (16p11.2del).

Using an integrative approach combining behavioral assessments, electrophysiology, calcium imaging and stereology, we will address three aims: (1) longitudinally assess motor abilities in 16p11.2del animals and their correlation with later social behaviors, (2) determine the competency of functional connections between supraspinal neurons, sensory afferents, and MNs, to test if reduced competency correlates with early motor deficits, and (3) assess integrity of lumbar MN populations to determine whether a lower MN number contributes to early motor impairments.

By identifying circuit-level alterations, this study aims to provide insights into the neural basis of early motor dysfunction in ASD, informing diagnostic tools and interventions to improve motor function and developmental outcomes of children with ASD.

Sunil Raikar, MD

Associate Professor, SCHOOL OF MEDICINE, Pediatrics

Next generation CD5-CAR gamma delta T cells for T-cell acute lymphoblastic leukemia

There is an unmet need to develop improved therapies for the treatment of relapsed/refractory (R/R) T-cell acute lymphoblastic leukemia (T-ALL), as long-term survival is less than 30%. Targeted cellular therapies, like chimeric antigen receptor (CAR) T-cell therapy, have shown significant benefit in the R/R setting for B-cell malignancies. However, we have not seen the same success in T-ALL, mainly due to the shared antigen expression among leukemic, healthy, and CAR T cells, resulting in off-tumor toxicity and CAR T-cell fratricide. To address these concerns, we propose to utilize gamma delta (GD) T cells as a cytotoxic alternative to traditional alpha beta (AB) T cells, investigating efficacy of CD5 CAR modification in the two main subtypes of GD T cell: Vdelta1 (Vd1, Aim 1) and Vdelta2 (Vd2, Aim 2). While a subset of Vd1 GD T cells do not express CD5, eliminating risk of CAR T fratricide, Vd2 T cells do express CD5, and will thus require further modification through CRISPR-Cas9 knockout (KO) of CD5. This will not only eliminate CAR T fratricide, but recent literature suggests CD5 KO enhances efficacy of T-cell immunotherapy. Finally, as GD T cells act independently of the major histocompatibility complex (MHC), we can easily utilize this product in an allogeneic, “off-the-shelf” setting, quickening access to R/R T-ALL patients whose aggressive disease is often a limiting factor to the cumbersome traditional cell therapy manufacturing process. Ultimately, we aim to advance the use of CAR GD T cell therapy for the treatment of pediatric R/R T-ALL patients.

Chang Su, PhD

ASSISTANT PROFESSOR, ROLLINS SCHOOL OF PUBLIC HEALTH, BIOSTATISTICS AND BIOINFORMATICS

Novel statistical methods for uncovering the genetic basis of Alzheimer's disease

Alzheimer’s disease (AD) affects over 6 million individuals in the U.S., with cases expected to double by 2060. Although genome-wide association studies (GWAS) have identified numerous AD-associated genetic variants, the functional mechanisms underlying these variants remain elusive, limiting therapeutic advances. Transcriptome-wide association studies (TWAS) have emerged as a powerful statistical approach to identify genes associated with AD risk through genetic regulation, providing deeper insights into functional mechanisms. However, most existing statistical methods on TWAS rely on bulk gene expression data, which aggregate gene expression across brain cell types. As a result, these methods fail to capture the cell-type-specific (CTS) genetic regulation critical to AD mechanisms.

Recent advances in single-cell RNA-sequencing (scRNA-seq) provide an unprecedented opportunity to study CTS AD genes, especially in microglia and other low-abundance cell types vulnerable in AD. Nevertheless, the unique challenges of scRNA-seq data—such as high noises and technical variations—render existing statistical methods inadequate.

This proposal aims to develop innovative statistical methods for CTS TWAS, focusing on two goals: (1) developing a novel multi-task learning framework to model shared and specific genetic regulation across brain cell types using scRNA-seq data, and (2) integrating bulk and scRNA-seq data via transfer learning to maximize statistical power and discovery of CTS AD genes. These methods will be applied to population-scale datasets, leveraging complementary information from bulk and scRNA-seq data. By addressing key limitations in current TWAS approaches, this work will uncover CTS mechanisms of AD pathogenesis and inform new therapeutic targets for AD.