Patrick Cody, Ph.D.
Cody received his doctorate in bioengineering with a focus in neural engineering from the University of Pittsburgh, where he is now a research assistant professor in the department of otolaryngology. Cody is a recipient of a 2026 Elizabeth M. Keithley, Ph.D. Early Stage Investigator Award, generously funded by Zellis Family Foundation.
Gene replacement therapy has the potential to restore natural hearing in individuals with congenital deafness, by delivering a functional copy of affected genes to restore natural mechanisms of the inner ear. However, evaluations of current therapies fail to capture hearing recovery in complex listening situations and hearing restoration is limited due to imprecise targeting of the affected inner ear cell types. There are over 100 forms of congenital deafness that impact specific inner ear cell types, making treatments challenging to scale.
This project addresses these limitations through two innovations. First, using an established animal model of congenital deafness, we introduce a comprehensive approach to gene therapy evaluation that tracks how the auditory pathway adapts to complex sound environments and recovers over time. We will explore whether improved cell-type targeting of gene delivery can improve how the brain recovers and adapts to sound.
Second, we apply a model-based platform to design gene regulatory elements that target gene therapy to specific inner ear cell-types. This generalizable approach can be tailored to target various cell types for delivery at specific ages and thus can accelerate the development of therapies for other forms of gene-linked deafness. Current gene therapies in clinical trials solely address a single form congenital deafness. Our plan would mark a significant step for accelerating cochlear gene therapy development to benefit patients with a broad range of congenital hearing loss forms. Our proposed evaluations of central processing, sound context adaptation, and perception will fill a critical gap in both cochlear gene therapy development and our understanding of hearing loss recovery mechanisms.
Dr. Chris Cunningham and his lab developed an in situ platform using an established animal model to test and identify a novel promoter that specifically targets hair cells for gene therapy, aiming to restore hearing in cases of TOMT gene-linked hearing loss. This work is the foundation of our proposal. Given my experience in applied data science, Chris and his team invited me to contribute by applying a model-based approach to enhance gene therapy-mediated hearing recovery, specifically by refining targeting sequences to improve cell specificity and physiological expression throughout the cochlea.
This turned out to be a serendipitous confluence of events. Leading up to the collaboration with Chris, I had been running with a friend who was researching the model-based design of enhancer targeting sequences for spinal cord gene therapy to treat pain, under Dr. Andreas Pfenning. Their innovative strategies for designing targeting enhancers inspired me to consider how similar approaches could be adapted for the cochlea.
One of my high school biology classes required preparatory summer classwork. Summer work as a kid can be a drag, but this time I didn’t mind it because it involved collecting bugs and I already spent a lot of time in the dirt. We were instructed to determine whether pill bugs preferred an acidic, basic, or neutral environment. We used petri dishes which made it seem like official science work. It wasn’t rocket science, but it got me hooked on the process of coming up with an educated guess at an expected outcome (hypothesis), thinking up an experiment to test it, then considering the why.
I grew up on an old farm (prime pill bug collection area), where I spent many hours watching my grandfather take apart broken machines and put them back together in working order. Over time, he let me take the lead, guiding me as I learned to troubleshoot and repair things myself. I started with tools and equipment around the farm and eventually found myself applying the same mindset to computers and technology. This and the pill bug experiment was enough to make a science related career a safe bet for me.
I’ve had tinnitus, primarily in one ear, since my early 20s. Beyond the constant desire for relief from the ringing, it’s also been a driving force behind many of my educational and career choices. I’ve been deeply motivated to understand how the ear and brain work together to produce the experience of hearing.
During my graduate studies, I had the opportunity to work under the mentorship of Dr. Thanos Tzounopoulos, a leading researcher whose seminal work has advanced our mechanistic understanding of tinnitus. While my own research doesn’t focus directly on the condition, it falls within the same field, placing me in a rich environment of talks, collaborations, and discoveries that are steadily moving us closer to effective treatments.
A routine meeting with my first Ph.D. mentor to discuss my dissertation proposal became a decisive turning point in my research trajectory when I realized I wouldn’t propose a thesis in that lab. Although the lab offered an exciting opportunity to apply my background in neuroscience and biochemistry to innovative biomaterial solutions for neural implant biocompatibility, I found myself increasingly disconnected from the research questions.
Recognizing this, my mentor, along with a senior researcher in the lab, provided exceptional support that enabled me to explore other labs that might better align with my interests. It was during this period that I realized my passion lay in the science of hearing and sound. After meeting with several researchers, I joined an auditory neuroscience lab, which ultimately became a defining chapter in my research journey.
Growing up on a farm, I was always immersed in the natural world, exploring the woods, solving mechanical problems, and repairing equipment. This hands-on environment, combined with an early fascination with computers, made a research-adjacent career feel almost inevitable. The question was just what I would end up researching. Realistically, I might have continued working in data science within the healthcare industry, where I was before returning to academia. In another life, I could easily imagine myself in an ecology-related field, perhaps something like permaculture, where my interests in nature and systems thinking would also thrive.
I spend a lot of time listening to, thinking about, and experimenting with sound. Right now, I’m collaborating with a friend on an interactive sound project built as a web app. While the development is code-heavy, the goal is to create location-based sound experiences that connect people in the real world.
To give my eyes a break from the screen, I often listen to full albums from start to finish. For a more hands-on experience, I mix sounds, typically layering drone-like train noises, choral vocals, and pulsating beats. When I want more engagement, I’ll tweak parameters on sound-making modules. The connection to hearing research goes without saying. As my work has become increasingly computational, these outlets offer a kind of tactile experimentation and problem-solving that I once found in imaging-based auditory neuroscience. They help me stay grounded in the sensory experience that originally drew me to this field.
My first job out of college was a post-bac position at the NIH, no surprises there. However, my life outside of the lab, was a bit more unusual. After many trying group home open houses and interviews, I landed in a warehouse in the northeast part of town, a former DIY venue for hardcore music shows. It came with attractive amenities such as an auto mechanic downstairs and garden plots on a tarred rooftop (which housed our neighbor Fred, a rat).
Over the course of a year, we converted it into a gallery space complete with rented studios and an almost functional darkroom. For my room, I tore out the drop ceiling and installed a brass chandelier. Finding the right breaker was an adventure; I was convinced Fred was powering it with a hamster wheel in one of the walls. We eventually hosted local art exhibitions, music, and performance art shows. Besides the experience really putting the A in my post-baccalaureate STEAM education, it provided me a grounding community, continual inspiration, and lifelong friends.
This award represents a pivotal step toward my independence as a researcher. It will support the experiments and data collection necessary to prepare a competitive R21 application, and ultimately an R01. These applications will support my long-term (5+ year) goal of accelerating and comprehensively evaluating gene therapy approaches for various forms of genetically linked deafness.
I will continue building research infrastructure and collaborating with clinical experts to develop data-driven strategies that translate institutional healthcare data into improved treatments for hearing-related conditions. In both the near and long term, my goal is to implement these strategies in clinical settings and expand upon them through prospective research studies.
The Research
Patrick Cody, Ph.D. | University of Pittsburgh
Comprehensive hearing recovery evaluation of novel targeting sequences for cell-type–specific gene therapy for hearing loss
Gene replacement therapy has the potential to restore natural hearing in individuals with congenital deafness, potentially overcoming the limitations of cochlear implants. While cochlear implants provide substantial benefits, they rely on artificial signals to bypass affected inner ear structures that are essential for accurate speech perception in noisy environments.
In contrast, gene therapy treats congenital hearing loss by delivering a functional copy of affected genes to restore natural mechanisms of the inner ear. However, evaluations of current therapies fail to capture hearing recovery in complex listening situations and hearing restoration is limited due to imprecise targeting of the affected inner ear cell types. There are over 100 forms of congenital deafness that impact specific inner ear cell types, making treatments challenging to scale.
This project addresses these limitations through two innovations. First, using an established animal model of congenital deafness, we introduce a comprehensive approach to gene therapy evaluation that tracks how the auditory pathway adapts to complex sound environments and recovers over time. We will explore whether improved cell-type targeting of gene delivery can improve how the brain recovers and adapts to sound. Second, we apply a model-based platform to design gene regulatory elements that target gene therapy to specific inner ear cell types. This generalizable approach can be tailored to target various cell types for delivery at specific ages and thus can accelerate the development of therapies for other forms of gene linked deafness.
Long-term goal: Precise cell-type targeting is critical to the success of cochlear gene therapy for congenital deafness to avoid detrimental effects of off-target gene expression. Using analytical approaches, we have previously identified a promoter sequence that targets gene replacement therapy specifically to hair cells to recover hearing in deaf mice lacking the gene TOMT. This award will fund the validation of our proposed generalizable model-based approach in our established platform to identify novel gene regulatory sequences that target hair cells for gene therapy delivery at specific ages.
Upon validation of our scalable approach, we will next design gene regulatory elements that are optimized for physiological expression across the cochlea and target cell-types affected by other forms of congenital deafness. Current gene therapies in clinical trials solely address a single form of congenital deafness. This phase in our plan would mark a significant step for accelerating cochlear gene therapy development to benefit patients with a broad range of congenital hearing loss forms.
Validation of candidate targeting sequences using our current screening platform is limited to at most 3 candidates per delivery experiment. Concurrent with scaling to additional cell-types, within the next 2 years, we will work towards greater screening throughput using multiplexed screening methods that rely on candidate barcoding such as Xenium. This will enable screening of 80+ candidates in one run and would significantly accelerate therapy development.
Restoring natural hearing with biological therapies can translate to transformative benefits for those suffering from hearing loss by enhancing their ability to communicate effectively, reducing cognitive effort required for listening, and preventing the social isolation often associated with hearing impairment. Our proposed evaluations of central processing, sound context adaptation, and perception will fill a critical gap in both cochlear gene therapy development and our understanding of hearing loss recovery mechanisms. Our next step is to the evaluate therapeutic benefit on listening effort such as with a pupillometry based assay. This will mark a critical step to improving therapies for speech perception in challenging listening environments.
Finally, before safety studies and clinical implementation, the next stage of our plan is preclinical therapeutic optimization. To better optimize viral serotype and dosing parameters for the scale of the human cochlea, we will work with a department colleague with expertise in viral gene delivery in a porcine model.
Recipient of an Elizabeth M. Keithley, Ph.D. Early Stage Investigator Award, generously funded by Zellis Family Foundation