Yale Center for Pulmonary Infection Research and Treatment (CPIRT)

The Center for Pulmonary Injury, Repair and Therapeutics (CPIRT) is a multidisciplinary academic hub and international leader in advancing innovative, cutting-edge basic, translational, and clinical research focused on chronic lung injury, repair, and disease. Under the direction of Dr. Naftali Kaminski, CPIRT's primary goal is to deepen the field's understanding of the mechanisms driving pulmonary injury and fibrosis, and to translate that knowledge into more effective diagnostic tools and therapies.

Current therapies for chronic lung diseases, including pulmonary fibrosis and other advanced lung conditions remain limited, underscoring an urgent need for novel therapeutic strategies. CPIRT develops new approaches to study the molecular, cellular, and systems-level mechanisms of chronic lung injury and repair, integrating single cell profiling, spatial 'omics, artificial intelligence (AI), and machine learning to accelerate discovery and clinical translation. The Center's research maps the basic biological pathways underlying lung fibrosis, identifies novel biomarkers, and translates scientific outcomes into improved diagnostic and therapeutic modalities.

CPIRT focuses its efforts in both exploratory and targeted research in three specific areas:

1. Exploring the basic science of key molecular and cellular mechanisms driving chronic lung injury and aberrant repair, with emphasis on fibrogenesis using mutliple model systems and tools including model organisms, cellular systems and 3d model system such as organoids, and precision cut lung slices.
2. Investigating the pathways and processes that cause or exacerbate chronic lung diseases using basic, translational, genomic, and epidemiological approaches, enhanced by AI-driven data analysis, and sophisticated computrational approaches.
3. Developing and applying the bases for novel approaches to diagnose, prevent, allevoiatre and eventually cure progressive fibrotic and other advanced lung diseases.

CPIRT's objectives seek to:

• Promote systematic and interdisciplinary research into the mechanisms of chronic pulmonary injury, fibrosis, and repair in animal models and human cohorts, leveraging cutting edge research methodologies resolve disease mechanisms at unprecedented resolution;
• Bring together an integrated network of investigators who develop, test, and apply innovative interventions in chronic lung disease;
• Establish and maintain a rich and diverse pool of patient cohorts with chronic pulmonary conditions for both research and clinical practice;
• Leverage AI, machine learning, single cell profiling, and spatial 'omics to accelerate translational discovery, from biomarker identification to therapeutic target development;
• Educate the next generation of scientists and clinicians skilled in pulmonary injury and fibrosis research, including training in model organisms, 3d translational models and cutting-edge 'omics and computational methods;
• Promote public understanding and awareness of chronic lung disease, including prevention and treatment advances.

The Center complements and expands the disease-research unites, groups and center within the Pulmonary, Critical Care and Sleep Medicine Section, including current work in YCAAD, interstitial lung disease, cystic fibrosis, as well as P²MED. The Center also integrates expertise from members of other Departments of the Yale University School of Medicine (Pathology, Immunobiology, Genetics, Pediatrics) and the Yale University School of Public Health (Chronic Disease Epidemiology, Biostatistics). The Center generates independent funding from federal sources, foundation grants, industry sponsors, and patient donations, and hosts a yearly State-of-the-Art symposium on pulmonary injury, repair, and fibrosis.

The Center for Pulmonary Injury, Repair and Therapeutics, led by Dr. Naftali Kaminski, brings together investigators from within Yale PCCSM and disciplines across Yale School of Medicine and Yale University whose expertise and research interests intersect with chronic lung injury, fibrosis, repair, and translational therapeutics. The Center harnesses AI, computational approaches, single cell profiling, and spatial 'omics as cross-cutting resources to enhance research across all programs. The Center is also at the forefront of educating and mentoring early-career medical scientists, including clinical and postdoctoral fellows, residents, and medical students.

Research at Yale CPIRT encompasses a comprehensive infrastructure aimed at understanding the fundamental mechanisms of chronic lung injury, aberrant repair, and fibrosis. Studies explore the molecular and cellular drivers of lung remodeling, innate and adaptive immune contributions to fibrogenesis, and the biology of repair and regeneration following chronic lung injury.

Central to the Center's research program are single cell profiling and spatial 'omics technologies, which enable the dissection of lung disease at the resolution of individual cells and their precise anatomical context within tissues. These platforms reveal the cellular heterogeneity of fibrotic lungs, identify novel disease-associated cell states and intercellular signaling networks, and spatially resolve the molecular landscape of injury and repair across the lung parenchyma.

Complementing these approaches is the integration of AI and machine learning into discovery pipelines, from the analysis of large-scale genomic, proteomic, and spatial datasets to the development of predictive models for disease progression and therapeutic response. Studies combine cell-based assays, fibrosis animal modeling, and human biospecimens obtained from subjects recruited through the Center and its local and outside collaborators. The Center's investigators span a wide range of disciplines at Yale, bringing substantial and complementary expertise to the study of chronic pulmonary injury and repair.