EML4 Deficiency Causes Alveolar Macrophage Dysfunction and Interstitial Lung Disease

We report a novel inborn error of immunity in two siblings born to consanguineous parents who presented with short stature, failure to thrive, eosinophilic esophagitis, severe eczema, and early onset, progressive interstitial lung disease with lipoid pneumonia or pulmonary alveolar proteinosis (PAP)-like features. Genetic testing revealed both affected siblings harbored a homozygous deletion of a region of the EML4 gene, which encodes for echinoderm microtubule-associated protein-like 4 (EML4). Further analysis confirmed a lack of EML4 RNA or protein expression. EML4 deficiency has not been reported in the literature and very little is known about its physiological function. Thus, we generated EML4-deficient mice by CRISPR/Cas9 gene editing of EmL4 to examine the role of EML4 in immune function and lung disease. Consistent with the short stature of the patients, EML4-deficient mice were runted compared with wild-type (WT) mice. We also examined the lungs of EML4-deficient mice, particularly the alveolar macrophage (AMs) population, as defects in AM number or function are known to be associated with PAP. This revealed that EML4-deficient mice had significantly decreased alveolar macrophages (AMs) compared with WT mice, but no change in the frequencies of other immune cell populations. scRNA-seq demonstrated that among lung cells, EML4 deficiency had the greatest impact on the gene expression program of AMs. EML4-deficient AMs also showed increased lipid accumulation consistent with the foamy macrophages observed in the bronchioalveolar lavage of the patients. Under specific pathogen–free (SPF) conditions, EML4-deficient mice did not demonstrate lung pathology or fibrosis. However, colonization of EML4-deficient mice with more diverse microbiota by cohousing with “dirty” mice led to florid immune infiltration and fibrosis. Together, our results reveal that EML4 deficiency results in defects in AM which combined with microbial exposure may trigger inappropriate inflammatory responses and subsequent lung fibrosis.