2020 Annual Laboratory Research Report

 

Anthony Ricci, PhD
Edward C. and Amy H. Sewall Professor of Otolaryngology — Head & Neck Surgery (OHNS) and, by courtesy, of Molecular and Cellular Physiology
Chief of Research

     December 10, 2020

2020 is a year of challenges that makes us all appreciate the privilege we have as scientists at Stanford and the responsibilities that come with that privilege. It has been a year of uncertainty where a global pandemic, economic downturns, social unrest, political strife and massive wildfires have shaken the very fabric of our society. However, the same issues that have taken so much of our time and energy, have brought our community together, bringing out the resilience and compassion in each of us. There have been many successes and silver linings to 2020. Our department has pushed forward successfully this year on many fronts. Research has continued through the shutdown; through each stage of reopening we have adapted, and we continue to thrive. The summaries of research accomplishments below attest to the character of our programs, the will of our scientists and the brightness of our future.

It would be remiss to discuss research progress without first acknowledging three major events in the past year. Rob Jackler is stepping down as department chair. Rob created this department and the research division, and it is his vision that has made possible the major accomplishments of this group. It is not possible to express our gratitude at the opportunities his efforts have provided. We have completed a search for a new chairperson, with Konstantina Stankovic joining us early next summer. We look forward to working with Dr. Stankovic as she develops a vision for the 21st century. And finally, a culmination of years of work by Dr. Jackler is our garnering new research space in the Biomedical Innovation Building. Many of us have moved into this state-of-the-art research facility, despite the pandemic and are excited to begin a new stage of research.

Research in OHNS crosses many boundaries from basic science to clinical studies, from cancer research to cell biology to big data RNAseq to single molecule tracking, from hearing to smell to larynx to new surgical technologies. This breadth continues to grow and with the recruitment of a new chairperson will expand further. In the past year, the research teams have published more than 45 basic science/translational research papers and countless clinically relevant papers across a wide range of journals. A brief list of selected publications is presented at the end as a sample. Complete lists can be found on individual lab websites. A departmental core facility serves as a training center for many of our junior scientists, as the water cooler meeting spot for many of us (particularly during non-covid times) but largely as a major resource for access to high end technologies. This year we added a new imaging system for live cell imaging that also allows for lifetime imaging and incorporates the newest white laser technology and hybrid gasp photomultiplier detectors for maximal sensitivity and flexibility. Our core facility exists at the generosity of our philanthropic supporters and is central to our research efforts.

 

 

Rosenthal Lab

The Rosenthal lab conducts bench to bedside translational studies in targeted therapy and molecular imaging.  He has conducted over a dozen early phase clinical trials for diagnostic and therapeutic agents for the treatment of solid tumors.  He is part of a multidisciplinary team of clinicians and basic scientists that perform preclinical animal studies including nonhuman primate IND-enabling studies, and first-in-human clinical trials. The team assesses near infrared fluorescent contrast agents for use in the operating room to make the cancer visible. Ongoing clinical trials include brain, lung, pancreas, skin and head and neck tumors.  The lab also focuses on molecular imaging of fluorescently labeled therapeutic antibodies to measure cellular delivery of therapies to tumors and adjacent tissues. Although it had ups and downs, 2020 was highly successful for the Rosenthal Lab. We published a total of 26 manuscripts and some in high impact journals including Lancet Gastroenterol Hepatol (IF 13.4), Nature Biomedical Engineering (IF 10.3), Cancer Research (IF 9.1), and Nature Biocommunications (IF 13.4).

Sunwoo Lab

The John Sunwoo laboratory is focused on understanding how the immune system recognizes and interfaces with head and neck cancer and on ways to translate this to the clinical care of patients. They are focused on three major questions: (1) What are tumor-intrinsic mechanisms that determine tumor cell resistance to immune pressure? (3) How can we induce neoantigens (or target molecules) on tumors for immune targeting? (4) How can we enhance the function of immune cells to treat oral cancer. For this work, Dr. Sunwoo was selected to receive an R35 Outstanding Investigator Award this year from the National Institute for Dental and Craniofacial Research (NIDCR) at the National Institutes of Health (NIH). The NIDCR funds the vast majority of the nation’s oral cancer research, and Dr. Sunwoo is the first otolaryngologist to have the honor of receiving this award from the NIDCR. The overall goal of this new grant mechanism is to provide sustained and flexible support to NIDCR-funded investigators with outstanding records of research productivity entering their mid-career stage, to conduct exceptionally innovative research, with unusual potential for improving dental, oral and craniofacial health.

Valdez Lab

2020 was a good year for the Valdez Laboratory.  Overall, we have very much directed our attention to transtympanic drug delivery and molecular probes for diagnosis of bacterial and inflammatory processes, now with 1 full time postdoc postdocs (Raana Kashfi Sadabad) focusing on this project. One additional postdoc (Aimen Zlitni from the Ghambir lab) is exploring the development of probes using maltriose to detect bacterial infections using Short wave infrared (SWIR) sensors and Photoacoustic imaging.  This exciting new direction is a piece of exploratory research that started in 2020 and if successful, it will allow us to obviate the need for CT scans and radiation in pediatric patients. Other projects focus on the chemical sensing mechanisms that allow detection of ototoxic chemicals in the inner ear using Raman spectroscopy.  We were able to publish our work in good journals including the ANALYST, ACS sensors and Scientific Reports in the past year and were able to add more patents to our innovation portfolio. We were granted a SPADA award for Ototopical Delivery of Smart Optical Contrast Agents for Diagnosis of Middle Ear Infections and an AHEAD program by the Fraunhofer institute for the development of our SWIR otoscope.

Pepper Lab

Facial paralysis is a debilitating condition that affects hundreds of thousand people each year.  The mission of research in the Pepper Laboratory at the Stanford Facial Nerve Center is to identify new ways to treat facial paralysis.  We have three areas of active scientific work: 1) molecular and genetic pathway analysis of the facial nerve after injury in a mouse model; 2) bioengineered nerve tissue in vitro and in vivo; 3) a machine learning algorithm to improve our understanding of human facial nerve injury, recovery, and the outcomes of existing treatments.  Over the past year, we have furthered this work through successful publication of our findings in academic journals and continued federal grant support for our research. 

The Voice Research Lab, led by Dr. Elizabeth Erickson-DiRenzo, integrates research from the basic and clinical sciences to improve the prevention and management of voice disorders. One line of research aims to assess the effect of deep brain stimulation (DBS) on essential vocal tremor (EVT). By employing a battery of objective and subjective measures, found a benefit of DBS for the treatment of EVT and specifies the acoustic and physiologic mechanisms that mediate its positive effect. We also uncovered a relationship between lead location and EVT outcomes, laying the foundation for future studies to clarify the optimal DBS target for the treatment of EVT.

Patel Lab

Dr. Zara Patel’s lab continues to perform research in chronic sinusitis, endoscopic skull base surgery and olfactory disorders. The COVID-19 pandemic has led to challenges in both the clinical and scientific arenas around the world, but the silver lining has been the increased attention and empathy for those with loss of smell and taste, as a result of this being one of the classic early symptoms of the disease. Even before millions of people experienced this disorder as a result of COVID-19 infection, Dr. Patel had begun enrollment in a clinical trial using platelet enriched plasma directed at helping those with post-viral olfactory loss, based on a successful pilot study completed last year, and recruitment is ongoing. She also made a significant breakthrough in her lab research, showing for the first time that electrical stimulation applied to damaged olfactory neurons can help improve regeneration of those nerves. She is continuing to build on that first step in her quest to eventually cure olfactory loss.

Ó Maoiléidigh Lab

In 2020, Dáibhid Ó Maoiléidigh’s group contributed to three talks at the 42nd Annual MidWinter Meeting of the Association for Research in Otolaryngology (2020). The talks described sounds emitted from the ear by Dáibhid Ó Maoiléidigh, analysis of the auditory system’s electrical activity by a medical resident working in our lab, George Liu (Stanford), and computational modeling and experimental observations of hair-bundle motion by a graduate student in Tony Ricci’s lab (Stanford), Alex Scharr. We are continuing the work on sounds emitted by the ear in collaboration with Chris Bergevin (York University) and Yuttana Roongthumskul (Chulalongkorn University). A rotation student in our group, Lawrence Chiou (Stanford), is continuing the work on the ear’s electrical activity in collaboration with Matt Fitzgerald (Stanford) and Gabriella Musacchia (University of the Pacific). A postdoc in our group, Zenghao Zhu (Stanford), a former research assistant, Wisam Reid (Harvard), and a graduate student in our group, Victoria Ou (Stanford), are building computational models of the ear’s sensory hair bundles and have produced preliminary data we are using to secure extramural funding. Next year, we will resubmit an R01 grant on hair bundles to the National Institutes of Health and publish our preliminary findings. Our collaboration with Tony Ricci (Stanford), supported by his R01 grant, has produced results combining experimental observations and computational modeling of hair-bundle motion. Together, we will submit a paper on this subject by the end of the year.

Grillet Lab

This year the Grillet lab discovered that a gene causing hearing loss in human and mice affects the process of sound-detection by the sensory cells of the inner ear in a new and unique way. This work is now at the revision stage of publication. The Grillet lab submitted a NIH grant application about a new approach to localize proteins at high-resolution by electronic microscopy. The grant has been well ranked by the peer-reviewers, and the funding decision will happen in January 2021. Finally, Dr. O Maoileidigh and Dr. Grillet created a new course at Stanford about the inner ear biology. The class combine theory and experimental aspects used in this research field to better educate graduate students and post-docs. This class will be offered every fall and spring quarters to Stanford students.

Santa Maria Lab

The Santa Maria lab focusses upon Chronic Suppurative Otitis Media (CSOM) is a neglected tropical disease that afflicts 330 million people worldwide and is the most common cause of persistent hearing loss among children in the developing world. It is characterized by a chronically infected and discharging middle ear, and there is currently no effective medical therapy or cure. While we know CSOM is associated with SHL, we do not yet understand how or why. Our lab has developed this model, optimized it to mimic the human infection, validated it against standard microbiological benchmarks and adopted it to include real time in vivo tracking of bacteria. In CSOM, this recalcitrance is not caused by multidrug resistant (MDR) bacteria, but by the inability of fluoroquinolone to target a subpopulation of metabolically inactive bacteria known as persister cells within biofilms. Persister cells repopulate the biofilm niche after the fluoroquinolone therapy is discontinued, causing a relapse of CSOM. As there is no effective treatment against these persister cells, the end result is multiple rounds of surgery to debride the biofilm and a lifelong struggle with this disease. We are developing therapeutics targeted at persister cells in biofilms of CSOM. This past year the lab has begun a Multicenter Phase 1 clinical trial commenced for tympanic membrane regenerative treatment. The lab has also received NIH support to investigate a nanoparticle therapy against middle ear disease. The Santa Maria lab published two manuscripts, one focused upon prevention of radiation induced oral mucositis and the other on a novel animal model for investigating chronic supporative otitis media. Peter was also named the Tashia and John Morgridge Endowed Faculty Scholar in Pediatric Translational Medicine.

Blevins Lab

The Blevins Surgical Simulation Lab has had a productive 2020 despite the limitations and restrictions that we have all faced.  We have been able to maintain the multidisciplinary efforts that define our team and have been able to significantly advance our efforts in developing simulation and extended reality technology to improve the planning and performance of surgical procedures.  This year, we strengthened and refined the efforts of our multi-specialty and multi-institutional collaborations to further development of an integrated platform for immersive rehearsal of patient-specific skull base surgery.  This system allows surgeons to perform virtual procedures in a simulated environment using routine preoperative imaging studies to experience the opportunities and constraints that will be faced during the actual procedure. This method imparts additional understanding of anatomic interrelationships not possible through the use of traditional methods of preparation.  We are on-track to introduce this system for clinical use in a number of selected North American academic sites in early 2021. Through the year, we have focused on a number of computational methods to improve the efficacy and safety of complex surgical procedures.  This includes the use of artificial intelligence to extract anatomic data from patient imaging studies, promising to greatly improve accuracy and efficiency of developing patient-specific simulation environments. Additionally, the technology allows the objective analysis of anatomic variations that influence surgical outcomes.  We are currently using this approach to refine the selection of cochlear prostheses to treat hearing loss.  We have also used machine learning and computer vision techniques to assist surgeons in differentiating tissues using multispectral imaging techniques. In addition, we have demonstrated the efficacy of using augmented reality systems for planning surgical approaches more effectively, allowing the surgeon to see beyond the normal limits available in the operating room. Our work has been made possible by generous grants from the Kaufer Family Fund, as well as an endowment from the Malcolmson Family.  We gratefully acknowledge this support as we enthusiastically plan for additional advances in 2021.

Cheng Lab

The Cheng Lab is interested in mechanisms of hair cell development, regeneration and protection and continued to made progress in these areas in 2020. First, hair cells are precisely patterned as a checkerboard in the cochlea and normal hearing critically depends on this organization and also their integrity. In the developing cochlea, we have successfully pinpointed mechanisms by which Wnt signaling coordinate with intrinsic proteins to regulate hair cell polarity (Huarcaya Najarro et al., Development 2020). This study builds on our previous work that Wnt signaling can regulate proliferation and hair cell formation and as a potential tool useful to stimulate regeneration. In a long-term collaboration with the Ricci lab, we have been studying approaches to alleviate hearing loss caused by a class of antibiotics called aminoglycosides. In evaluating a commonly used aminoglycoside gentamicin, we found that components of the gentamicin formula were sufficient to act as antibiotics. Importantly, we found that these components were also less ototoxic, thereby potentially providing another less ototoxic antibiotic for patients in the future (O’Sullivan et al., Proc Natl Acad Sci USA 2020). 

Nicolson Lab

The Nicolson lab uses the genetic tractability of the zebrafish model system to investigate the molecular underpinnings of the inner ear auditory and vestibular system. The vestibulospinal reflex is initiated by the inner ear and is important for adjusting the position of the body in response to rotation of the head. This reflex is key to everyday life and evolved very early in vertebrates. From fish to man, the basic neural circuitry that mediates this reflex is highly conserved. Recently we developed a new method for examining the vestibulospinal reflex in young zebrafish larvae. For our experiments, we film tail movements of fish on a moving platform and then use a custom software program to analyze how robust the response is in wild type and mutant fish. Using this new behavioral assay, we took a closer look at the motor functions in a synaptojanin zebrafish mutant. The synaptojanin enzyme is vital for synaptic transmission and mutations in synaptojanin are associated with Parkinson's Disease, which has profound effects on walking and balance. We found that synaptojanin zebrafish mutants can respond normally at first while the platform rotates, but then the vestibulospinal reflex quickly declines over time. To our knowledge, this is rare demonstration of synaptic fatigue of a behavioral reflex in vertebrates and our work has potential implications for the understanding of the impaired balance seen in Parkinson's patients.

Heller Lab

The focus for the Heller Lab in 2020 has been writing manuscripts and finishing papers that were almost done at the onset of the year.  We contributed serendipitously to a finding on generating human skin from embryonic stem cells (Lee et al., 2020, Nature), which builds on a previous collaboration with Karl Koehler’s laboratory at Harvard.  One study reported the successful generation of human hair cell-like cells from progenitor cells that we isolated from the adult human inner ear (Senn et al., 2020, Anatomical Records).  This project has been a focus of the lab for more than 16 years and the slow progress shows the inherent difficulties of working with human inner ear samples.  One review was published that focuses on novel therapies in the inner ear (Roccio et al., 2019, Hearing Research).  Nevertheless, the core of 2020 went into four papers that are currently all “in review” or “in revision” at the journal Cell Reports.  Two papers represent the first batch of single cell analysis data from our laboratory aimed at describing the process of cochlear hair cell regeneration in the chicken cochlea (Janesick et al., and Benkafadar et al., – in review, Cell Reports).  With respect to the characterization of stem/progenitor cells in the mouse cochlea, we have revised a manuscript that identified a very specific cell population in the mouse cochlea with a very high regenerative capacity (Kubota et al., - in revision, Cell Reports).  Finally, we have a paper in the final stages that represents a collaboration with Alan Cheng’s laboratory (Jan et al., - in revision, Cell Reports).  Additional manuscripts are still in various stages of completion and we hope that they will be submitted before the end of the year.  In addition to papers, we submitted three NIH grant applications and multiple fellowship applications. Besides these successes with scholarly work, we are highly optimistic to shift our efforts next year towards more experimental work on core questions related to inner ear cell regeneration.

Ricci Lab

The Ricci lab continues to focus upon understanding the molecular and mechanical underpinnings of hair cell mechanotransduction, the first step in signal processing for both the auditory and vestibular systems. 2020 represents a transition year for our group with two graduate students finalizing their projects and preparing submissions while transitioning into new positions. Long-term collaborator Mike Schnee retired after twenty years of work. Postdoctoral Scholar Marry O’Sullivan completed her training and has moved on to an industry position. Sara Talaei is another postdoctoral scholar is transitioning into an industry position. New recruit, Sriram Hemachandran with exquisite timing joined the laboratory just prior to the shutdown! He is a promising scientist focused on investigating hearing loss modulation of synaptic activity.  We also have a new postdoctoral scholar joining the lab at the start of the year, Jamis McGrath whom we are all excited to get to know. The majority of the year has been spent finalizing manuscripts leading to 3 publications, two other papers that are in review and the likelihood of three more submissions before years end. These publications are the premise for the new directions within the lab and the new funding that is needed to move the program forward. One publication leverages some new chemistry to isolate subtypes of the aminoglycoside gentamicin to demonstrate that the major component of hospital gentamicin is the most ototoxic and lacks antimicrobial activity, while identifying a small subtype that is considerably less ototoxic but equally good as an antimicrobial agent. The second publication demonstrates for the first time that the lipid bilayer mechanical properties are important for translating force to the mechanically gated ion channels in the stereocilia. This surprising finding is the basis for a new direction of work in our laboratory. And finally, with the collaboration of an outstanding and highly motivated resident Jason Qian, we published a paper demonstrating that hearing loss exacerbates cognitive decline in an age dependent manner. Dr. Ricci was also named Associate Dean of Graduate Education and Postdoctoral Affairs.