Division of Pulmonary Medicine | Research Activities

Fellows in Pediatric Pulmonology pursue a research project during the second and third years of their training. This project can involve clinical, translational, basic science, or educational research. Selection of a project is guided by consultation with the Fellowship Director, the Division Chief, and other members of the Division. The goal is to have fellows choose an area of research that interests them and also provides strong mentorship.

General Research Activities

The BCH Division of Pulmonary Medicine is actively engaged in a wide range of basic, translational, clinical and educational research initiatives developed to advance our understanding of pediatric lung disease that will ultimately lead to new diagnostic and therapeutic strategies for our patients. Supported by more than $8.0 million in awarded research funds this past year, the Division has published 98 peer-reviewed manuscripts in a wide range of academic journals, including Pediatrics, the American Journal of Respiratory and Critical Care Medicine, Cell Stem Cell, Lancet Respiratory Medicine, the Journal of Allergy and Clinical Immunology, the Journal of Cystic Fibrosis, and many others.

The Division’s laboratories occupy 6,650 square feet of space on the 4th floor of the John Enders Research Building of Boston Children’s Hospital. The division labs also house six NIH-supported pulmonary investigators. As members of Boston Children’s Hospital and Harvard Medical School, our fellows have access to all our institutions’ core facilities, including a state-of-the-art animal facility, a Cell Imaging and Phenotyping Core (with access to two confocal microscopes, multichannel flow cytometers, and other imaging and cell sorting platforms), and a transgenic animal core. To make research more accessible to our fellows and all our faculty, the Division has in place multiple resources to assist with study organization and grant development including a dedicated grants administrator, a Translational Research Operations Manager, a Clinical Research Manager overseeing clinical trials, a biostatistician, a bioinformatics and data management team, and a number of Research Assistants and Research Coordinators.

Our Division is a world-leader in conducting clinical trials in pediatric populations. This is possible due to the extraordinary work of our Clinical Trials Group, Directed by Dr. Jonathan Gaffin. Staffed by our Clinical Research Coordinator and Clinical Research Nursing Managers and research personel, this team conducts at any given time between 15 and 30 clinical trials, including studies in CF, Childhood Interstitial Lung Disease, Asthma, Primary Ciliary Dyskinesia, Pulmonary Artery Hypertension, and Bronchopulmonary Dysplasia.

Collaborative research arrangements within the Harvard Medical area are extensive and include the Divisions of Newborn Medicine, Immunology, Allergy, Gastroenterology, Informatics, and others within Boston Children’s Hospital; the Respiratory Division of Brigham & Women’s Hospital; the Physiology Department of the Harvard School of Public Health; Harvard Medical School and the Channing Laboratories at Brigham and Women’s Hospital. The research progress of the fellow is monitored and facilitated through biannual presentations before the fellow’s Scholarship Oversight Committee.

Grant awards:

The Division of Pulmonary Medicine is highly competitive for grant external support, with numerous successful applications this year to the National Institutes of Health (NIH), the American Thoracic Society (ATS), the Cystic Fibrosis Foundation (CFF), and the National Organization for Rare Diseases (NORD), among others.

Recent Pulmonary Fellow grant awards:

Amanda Nelson: 1st and 2nd year Fellowship Award (CF Foundation)

Bob Sun: Pediatric Scientist Development Program Award

Taylor Baumann: 1st and 2nd year Fellowship Award (CF Foundation)

Kristen Richard: 1st and 2nd Year Fellowship Award (CF Foundation)

Kristen Richard: BCH Academy Health Professionals Education Innovation

Julia Lee: BCH Alumni Association Academic Development Award

Po-Yang Tsou: ATS ASPIRE (Academic Sleep Pulmonary Integrated Research/Clinical) Fellowship Program (ATS)

Stuart Rollins: 3rd and 4th year Fellowship Award (CF Foundation)

Dorothy Curran: 1st and 2nd year Fellowship Award (CF Foundation)

Jaclyn Davis: 1st year Fellowship Award; 2nd Year Fellowship Award, 3rd year Fellowship Award, 4th year Fellowship Award (CF Foundation)

Alexandra Kass: 3rd year fellowship award (CF Foundation)

Ryan Perkins: Developing Value Based Care in CF (CF Foundation)

Sigfus Gunnlaugsson ATS Aspire Fellowship (ATS)

Fran Flanagan: NORD ACDMPV Research Grant (NORD)

Eleanor Muise: NIH Loan Repayment Award. Establishment of a Reliable and Translatable Metric to Score Tracheobronchomalacia in Children with Esophageal Atresia with or without Tracheoesophageal Fistula

Tim Klouda: BWH/BCH T32 Research Fellowship (NHLBI)

Faculty grant awards (2022-2023)

Alicia Casey: A Phase 3, 2-part, Open-label Study to Evaluate the Safety and Pharmacokinetics of Lumacaftor/Ivacaftor (Vertex)

Benji Raby: Distinct and Overlapping Pathways of Fibrosis and Emphysema in Cigarette Smokers (NIH)

Greg Sawicki: A Phase III, randomized, double-blind, placebo-controlled study of AeroVanc for the treatment of persistent methicillin-resistant Staphylococcus aureus lung infection in cystic fibrosis patients (Savara)

Ahmet Uluer: A Phase 2 Study Evaluating the Safety and Efficacy of VX-121 Combination Therapy in Subjects with Cystic Fibrosis Aged 18 Years and Older (VX18-121-101) (Vertex)

Greg Sawicki: A Phase II, Randomized, Double-Blind, Placebo-Controlled Study of Aerovanc for the Treatment of Persistent Methicillin-Resistant Staphylococcus aureus Lung Infection in Cystic Fibrosis Patients

Greg Sawicki: A Phase 3, 2 Part, Open-label Study to Evaluate the Safety, Pharmacokinetics, and Pharmacodynamics of Ivacaftor in Subjects With Cystic Fibrosis Who Are Less Than 24 Months of Age at Treatment Initiation and Have a CFTR Gating Mutation (Vertex)

Ahmet Uluer: A Study to Evaluate Safety, Efficacy, and Tolerability of TEZ/IVA in Subjects With Cystic Fibrosis (CF) Who Have Previously Discontinued Orkambi (Vertex)

Gary Visner: Microbial Dysbiosis in Chronic Lung Allograft Dysfunction (NIH)

Carolyn Snell: Success with Therapies Research Consortium: Years 7, 8, and 9 (Cystic Fibrosis FD Therapeutics INC)

Ahmet Uluer: A Study Evaluating the Safety and Efficacy of VX-659 Combination Therapy in Subjects With Cystic Fibrosis (Vertex)

Jon Gaffin: A Phase 3, Open-label, Rollover Study to Evaluate the Safety and Efficacy of Long-term Treatment With Tezacaftor in Combination With Ivacaftor in Subjects With Cystic Fibrosis Aged 6 Years and Older, Homozygous or Heterozygous (Vertex)

Gary Visner: Targeting Inflammation and Alloimmunity in Lung Transplant Recipients With Clazakizumab (NIH)

Greg Sawicki: DESIGN CF: Developing e-Health Systems to Improve Growth and Nutrition in CF (Cystic Fibrosis FD Therapeutics INC)

John Kennedy: Program for Adult Care Excellence (CFF)

Jackie Davis: QI Screening Improvement Process for CF (CFF)

Steve Freedman: A Multi-Center Study of Non-Invasive Colorectal Cancer Evaluation in Cystic Fibrosis (NICE-CF) (CFF)

Benji Raby: Clinical Genetics and Screening for Pulmonary Fibrosis (NIH)

Ruby Wang: Using Induced Pluripotent Stem Cells to Characterize Cystic Fibrosis-Kboos (CFF)

Leah Ratner: Adult CF PACE Grant (CFF)

Alicia Casey: A master protocol to test the impact of discontinuing chronic therapies in people with cystic fibrosis on highly effective CFTR modulator therapy (SIMPLIFY): FIXED PRICE PORTION of PROJECT (CFF)

John Kennedy: Inflammatory Childhood Interstitial Lung Disease Cell Atlas (Chan Zuckerberg Initiative)

Pyong Park: ECM Regulation of Ocular Surface Disease (NIH)

Ryan Perkins: Program for Adult Care Excellence (PACE) (CFF)

Greg Sawicki: Observational Study of Telehealth for Remote Endpoint Assessment (OUTREACH) Protocol Number: OUTREACH-OB-22 (CFF)

Greg Sawicki: A Phase 3, 2-Arm, Open-label Study to Evaluate the Safety and Pharmacodynamics of Long-term Ivacaftor Treatment in Subjects With Cystic Fibrosis Who Are Less Than 24 Months of Age at Treatment Initiation and Have a CFTR Gating Mut (Vertex)

Pyong Park: HSPG Interactions in Liver Disease (NIH)

Jon Gaffin: Indoor Air Quality and Respiratory Morbidity in School-Aged Children with Bronchopulmonary Dysplasia (NIH)

Stuart Rollins: The effect of cystic fibrosis modulator therapy on the intrinsic airway epithelial response to SARS-CoV-2 using iPSC derived airway epithelium (CFF)

Ahmet Uluer: Outpatient Clinical Pharmacy Services: Award for a Pharmacist and a Pharmacy Technician (CFF)

Ruby Wang: High-throughput Phenotyping of iPSC-derived Airway Epithelium by Multiscale Machine Learning Microscopy (NIH)

Ahmet Uluer: Award for a Physical Therapist 2022 (E. Moulis) (CFF)

Ke Yuan: Pericytes differentiate into smooth muscle cells through HIF2a/SDF1 activation (NIH)

Carolyn Snell: Predictors of Mental Health Risk and Resilience in Caregivers of Children with CF (CFF)

Ryan Perkins: A prospective study to evaluate biological and clinical effects of significantly corrected CFTR function (the PROMISE Study) (Cystic Fibrosis FD Therapeutics INC)

Greg Sawicki: Qualitative Understanding of Experiences with the SIMPLIFY Trial (QUEST) (CFF)

Ruby Wang: Characterizing cystic fibrosis epithelial response to Pseudomonas aeruginosa with iPSC-airways (BCH)

Jackie Davis: Innovative Care Delivery in Cystic Fibrosis: assessing patient perspectives on the role of telehealth and the impact of remote patient monitoring. (BCH)

Tim Klouda: Integrated Training in Respiratory Research (NIH)

Benji Raby: Integrative Genomics of Acute Asthma Control (NIH)

Cathy Sheils: Implementation of Effective Home Oxygen Weaning Strategies in Premature Infants (PATIENT-CENTERED OUTCOMES RESEARCH INSTI)

Jon Gaffin: Early Childhood Diet, Growth, Gut Microbiome and Lung Health in Cystic Fibrosis (NIH)

Jackie Davis: Home Spirometry in Patients with CF: Acceptability and Feasibility of At-Home Monitoring (CFF)

Ahmet Uluer: Therapeutic Development Network (TDN) Protocol Review Committee (PRC) (CFF)

Greg Sawicki: Study Management Core for the Cystic Fibrosis Foundation’s Success with Therapies Research Consortium (Cystic Fibrosis FD Therapeutics INC)

Ahmet Uluer: Cystic Fibrosis Learning Network- Adult Program (CFF)

Greg Sawicki: Men’s Sexual and Reproductive Health in Cystic Fibrosis (CFF)

Greg Sawicki: Cystic Fibrosis Learning Network (CFF)

Jon Gaffin: Impact of Early Malnutrition on Lung Disease Development in Cystic Fibrosis (CFF)

Hank Dorkin: A Multicenter, Randomized, Double-Blinded, Placebo-Controlled Phase 2 Trial to evaluate Efficacy and Safety of Lenabasum in Cystic Fibrosis (CORBUS PHARMACEUTICALS)

Ke Yuan: Pericyte plasticity and its role in vascular inflammation in CTD-PAH (BAYER HEALTHCARE PHARMACEUTICALS, INC.)

Lystra Hayden: Genetic Epidemiology of Respiratory Function in Former Preterm Children: Salary Billing Agreement for Research Techs. (NIH)

Greg Sawicki: Co-Chair of the Success with Therapies Research Consortium (CFF)

Ruby Wang: Using Induced Pluripotent Stem Cells to Characterize Cystic Fibrosis (NIH)

Greg Sawicki: Project UPLIFT to Reduce Anxiety and Depression in CF Patients (Cystic Fibrosis FD Therapeutics INC)

Faculty grant awards (2021-2022)

Greg Sawicki: DESIGN CF: Developing e-Health Systems to Improve Growth and Nutrition in CF (Cystic Fibrosis FD Therapeutics, INC)

Jonathan Gaffin: Early Childhood Diet, Growth, Gut Microbiome and Lung Health in Cystic Fibrosis-Administrative Supplement (NIH)

Ke Yuan: Pericyte plasticity and its role in vascular inflammation in CTD-PAH  (Bayer Healthcare Pharmaceuticals)

Katie Krone: High Resolution Ventilation and Perfusion MRI Assessment of Neuroendocrine Cell Hyperplasia of Infancy (NEHI) in Infants and Young Children: Technical Feasibility and Direct Clinical Application (Orphan Disease Center)

Ryan Perkins: Program for Adult Care Excellence (PACE) (CFF)

Tregony Simoneau: Improving Asthma Morbidity by Virtual Home Visits for Children with Severe Asthma (Boston Children’s Hospital)

Faculty grant awards (2020-2021)

Jon Gaffin, Greg Sawicki, Benjamin Raby: Respiratory Disease Cluster (BCH)

Umakanth Katwa: Medical Staff Organization’s 2021 Faculty Innovated Research Award
“Evaluation of Breathing Dysfunction in Infants Undergoing Car Seat Testing” (BCH)

Pyong Park: R21 “Subversion of Syndecan-1 Functions in Listeriosis” (NIH/NHLBI)

Benjamin Raby: R01 “Integrative Genomics of Acute Asthma Control” (NIH/NHLBI)
R01 “Clinical Genetics and Screening for Pulmonary Fibrosis”

Greg Sawicki: Patient Safety and Quality Telehealth Grant “Home spirometry to augment telehealth for individuals with cystic fibrosis” (BCH)

Carolyn Snell: “Development of the CF Stress Questionnaire: Testing and Validation” (CFF)

Ahmet Uluer: “Therapeutic Development Network Protocol Review Committee” (CFF)

Ruby Wang: K08 “Mentored Clinical Scientist Development Award” (NIH/NHLBI)
“Using induced pluripotent stem cells to model long-term nonprogressive phenotype associated with F508del CFTR mutations” (Gilead)
SARS-CoV-2 and Cystic Fibrosis Research Award entitled “iPSC-airway to assess CF intrinsic epithelial response to SARS-CoV-2” (CFF)
“De-Novo Generation of Pulmonary ionocytes from Human Pluripotent Stem Cells” (CFF)

Ke Yuan: R01 “Pericytes differentiate into smooth muscle cells through HIF2a/SDF1” activation (NIH/NHLBI)
The Aldrighetti Research Award for Young Investigators (ATS/PHA)
Equipment grant for purchase of Vibrating Blade Microtome (BCH)

Faculty grant awards (2019-2020)

Ke Yuan: ATS Aldrighetti Research Award for young Investigators (ATS)
Lung Pericytes: A Novel Source of Pathogenic Smooth Muscle Cells in PAH (Francis Family Foundation)

Benjamin Raby: Pulmozyme to Improve COVID-19 ARDS outcomes (MassCPR)
Link: https://hms.harvard.edu/news/lung-link

John Kennedy: Program for Adult Care Excellence (CF Foundation)

Greg Sawicki: 2020 Program for Patient Safety and Quality Telehealth Grants Program (BCH).

Ahmet Uluer: Assessment of contraceptive safety and effectiveness in CF (University of Washington/CFF Foundation)

Levent Midyat: Whitetulip Global Health Grant (Whitetulip Health Foundation)

Tregony Simoneau: Creating an Asthma Network: Improving Asthma Management (Connecticut Children’s Medical Center/CIGNA)

Gaffin/Simoneau: Medical Staff Organization Innovation Award (BCH internal)

Ruby Wang: Using induced pluripotent stem cells to model long-term nonprogressive phenotype associated with F508del CFTR mutations (Gilead)

Current Research Programs

Pulmonary Genetics Program-
Dr. Raby is a pulmonologist and a genetic epidemiologist known internationally as an expert on the genetics and genomics of asthma, rare lung disease, and as a leader in the integration of genetic diagnostics in the clinical practice of pulmonary medicine. He leads an active NIH-funded laboratory that combines population-based integrative genomics with functional genetics to define the molecular determinants of asthma. He has been continuously NIH funded for nearly two decades and his laboratory is currently supported by four NIH R01 awards. Most recently, Dr. Raby’s group has published new findings demonstrating the importance of activation of the TREM-1 signaling pathway in poorly controlled and severe asthma (now the most replicated gene expression signature of poor asthma control) and the value of screening at-risk relatives of patients with ILD for pre-clinical evidence of ILD. Current projects are focused on understanding the functional mechanisms by which asthma variants confer disease, single-cell RNA-sequencing and biomarker studies in poor asthma control, gene mapping of rare childhood lung disease, and the development of novel computational approaches for the study of complex genetic disorders.

Extracellular Matrix Biology in Lung Health and Disease- Dr. Pyong Park
Dr. Pyong Park is an authority on the proteoglycans – extracellular matrix components that regulate receptor-ligand interactions, cellular communication, and tissue remodeling in health and disease. Most recently, his lab discovered that syndecans regulate the anti-inflammatory activity of mesenchymal stem cells (MSCs) in acute lung injury and that glypicans modulate the pathogenesis of pneumonia. His team is currently pursuing the molecular and cellular mechanisms of how syndecans and glypicans function in these manners.

Pluripotent Stem Cells- Dr. Ruby Wang
Dr. Ruobing Wang is developing approaches to use induced pluripotent stem cells (iPSC) and CRISPR-cas9 gene-editing tools to model Cystic Fibrosis (CF). Using samples obtained from CF patients with extreme phenotypes of lung function decline, Dr. Wang has derived 19 viable iPSC lines, has CRISPR-corrected the mutant CFTR gene in 5, and has successfully helped to develop a cell-based model based on in vitro differentiation of patient derived iPSCs to 1) airway epithelium both as 3D-organoids and 2D pseudostratified epithelium plated on air-liquid interface, and 2) functional putative macrophages. The iPSC-airway epithelium grown as 2D pseudostratified layer on air-liquid interface is capable of tight junction barrier formation, and mucociliary differentiation, and generates both the major airway cell types, as well as the rare cell types, including pulmonary ionocytes. She has shown that this platform is useful to model cystic fibrosis by demonstrating restoration of Cl- activities in CF iPSC after correction of CFTR via Ussing chamber assay. Recently, she has been using this platform to study CFTR-deficient epithelial response to SARS-CoV-2 and other CF relevant pathogens.

Computational Biology- Dr. Sung Chun
Dr. Sung Chun is a geneticist and computational biologist with an interest in complex trait genetics. He has developed approaches for co-localization of clinical phenotype and regulatory genetic (eQTL) associations and for using polygenic risk scores in the study of pulmonary disease. Current projects include applying these approaches in a clinical setting to improve risk stratification among at-risk relatives of patients with ILD, rare variant mapping in childhood interstitial lung disease, and genome-wide association studies in Eosinophilic Granulomatosis and Polyangiitis (EGPA, formerly called Churg-Strauss Syndrome). Dr. Chun and his team provide bioinformatic and statistical support to fellows and faculty across the division.

Vascular Biology- Dr. Ke Yuan
Dr. Ke Yuan is a vascular biologist whose research focuses on the role of the lung pericytes in the muscularization of pulmonary arterioles in response to regional hypoxia and the development of pulmonary arterial hypertension. She has published foundational papers in this area, including one of her most recent publications in Circulation that is the first to directly implicate Wnt5a in the pathogenesis in pulmonary arterial hypertension, demonstrating that endothelial cells derived from patients with pulmonary hypertension exhibit defective Wnt5a production, resulting in diminished pericyte recruitment and vessel loss (Yuan et al. Circulation. 2019). In addition, using lineage tracing transgenic animal models, she discovered that pericytes could become smooth muscle-like and contribute to abnormal muscularization and vascular obstruction (Yuan et al. AJRCMB, 2020). Her laboratory has a strong record of consistent contribution to a better and clinically relevant understanding of pericyte biology and facilitates new avenues of therapeutic targeting in PAH.

Clinical Trials Program-
Our pulmonary clinical research team remains among the most active clinical trials group in the country, continuing to enroll large numbers of subjects across a diverse set of clinical trials. We serve the Northeastern U.S. and all of New England as a major referral center for clinical trials in pulmonary disease, both for pediatrics and adults. We have participated in pivotal clinical trials for cystic fibrosis and continue to perform clinical trials in CFTR-modulating agents, anti-inflammatory and anti-bacterial drugs, as well as novel gene therapies for CF. The outcomes of these trials have had major impact on the health and quality of life of the majority of patients with CF. We continue to diversify our disease portfolio with clinical trials to treat asthma, interstitial lung disease, ciliary dyskinesia, and pulmonary hypertension. Our research portfolio also includes many cutting edge research projects led by our own Pulmonary Division clinician-scientists, including gene mapping efforts in Childhood Interstitial Lung Disease (Drs. Alicia Casey and Martha Fishman); several initiatives in the areas of Bronchopulmonary Dysplasia (BPD) and asthma (Drs. Lystra Hayden, Catherine Sheils, and Jonathan Gaffin), sleep disordered breathing syndromes (Drs. Katwa, Rosen and Katz); severe respiratory infections due to viral illness, and genetics/genomics of rare lung diseases (Dr. Raby).The clinical trials program provides personnel, informatics, and regulatory oversight to facilitate patient enrollment, sample collection and processing, and data management.

Childhood Interstitial Lung Disease (ChILD) Research-
Through the Pulmonary Biobank and BCH Sequencing Cohort Initiatives, the ChILD team utilizes a pipeline for whole exome sequencing analysis to evaluate undiagnosed cases and continue to grow a local patient registry to facilitate translational research. This collaboration has led to the identification of mutations in multiple known and novel genes in cases of unexplained diffuse lung disease. Our ChILD program has also conducted multiple clinical and genotype phenotype correlation studies. BCH is a major contributor of patients to the national chILD registry – a multicenter collaborative developed to accelerate scientific investigation and clinical trials research of these understudied diseases.

Bronchopulmonary Dysplasia Research-
Dr. Gaffin’s ongoing research examines the environmental determinants of impaired lung function and respiratory health in children. He currently has support from the NIH/NIEHS to assess the impact of indoor air quality on respiratory outcomes in children with BPD. Dr. Hayden continues progress on her NHLBI K23 funded studies of respiratory genomics and the early life determinants of obstructive pulmonary disease. She is the PI of the Preterm Lung Patient Registry and Biobank, which follows longitudinal outcomes among over 1,100 patients in BPD clinic. Studies in this cohort led by Dr. Levin, a dual trained neonatologist and pulmonologist with expertise in clinical informatics, have demonstrated worsening obstructive lung function pattern with age, revealing that former premature infants are at risk for ongoing abnormal pulmonary development in childhood. Dr. Sheils has led the BCH arm of the multi-center implementation protocol of home oximetry, which will improve and revolutionize home monitoring of patients with BPD. BCH participated in the PASSIVE study (PrevAlence Study of Severe BPD VEntilation), a multicenter point prevalence study describing ventilation strategies in infants with severe BPD. The BPD team are major contributors​​ to the advancement of BPD care including active participation in the international BPD Collaborative, which includes pulmonologist and neonatologists from 28 academic medical centers dedicated to supporting research and quality improvement in BPD. Fellows have been actively involved in all these efforts and the BPD team welcomes future fellow-initiated investigations. 

Sleep-disordered Breathing Research-
Our sleep faculty have made several noteworthy advances this past year. Dr. Umakanth Katwa published an algorithm for management of infants with Pierre Robin sequence. Dr. Dennis Rosen completed a study that identified a much-higher prevalence of periodic limb-movements of sleep in children with Down syndrome than in typical patients. This has resulted in the launching of a joint QI initiative with the Down syndrome program at BCH to improve the screening for and treatment of this condition in children with Down syndrome. This is expected to improve their overall health and to have a positive impact on their ability to integrate into mainstream educational frameworks. Dr. Eliot Katz published two studies on the evaluation and stratification of infants having brief resolved unexplained events.

Medical Education Research-
Fellows and faculty have conducted medical education research including related to curriculum design, feedback, and simulation. An example of a recent medical education-related fellowship project was conducting a needs assessment of the pediatric pulmonary fellowship curriculum, which was then used to inform specific teaching initiatives. One of our fellows recently surveyed pediatric pulmonary fellows across the country on the perceived effectiveness of virtual pulmonary fellowship interviews. Another one of our fellows was recently accepted into the Virtual Program for Post-Graduate Trainees: Future Academic Clinical Educators program. Opportunities for medical education related grant funding are available through the institution, with several recent fellows receiving these awards.