Reprogramming of type 2 alveolar epithelial cells in idiopathic pulmonary fibrosis and regulation by TGFb1.

Idiopathic Pulmonary Fibrosis (IPF) is the most common fibrotic interstitial lung disease among adults.

The cause of IPF is not fully understood, and it is frequently progressive, often leading to death within several years of diagnosis.

In IPF, there is loss of alveolar epithelial cells, including type 1 cells (AEC1s), which line the alveolar airspace surface, and type 2 (AEC2s), which secrete surfactant, self-renew, and give rise to AEC1s and development of honeycomb cysts.

These cysts are lined by bronchiolized epithelium, so-called because of expression of airway and secretory cell markers such as p63, KRT5, KRT17, and MUC5B.

The origin of the cells lining these cysts is not understood, but have generally been thought to be the result of migration of airway epithelial cells (basal and/or club), in a failed attempt at alveolar repair.

Recent single-cell RNA (sc-RNA) sequencing studies have uncovered widespread AEC2 and other epithelial cell abnormalities in end-stage IPF tissue, such as intermediate/transitional cell states and ectopic expression of genes associated with airway cells (such as KRT5+ AEC2s).

Our lab has recently shown that AEC2s are capable of reprogramming into KRT5+ basal-cell like cells in in vitro organoid cultures.

These suggest a new hypothesis that the bronchiolized epithelium lining honeycomb cysts may actually be derived from reprogrammed AEC2s.

This study seeks to characterize whether the epithelial abnormalities present in end-stage IPF tissue are also present earlier in the IPF disease course and to determine the role of TGF?1 in regulating the aforementioned reprogramming.

Samples from patients undergoing surgical biopsy for the purpose of clinical diagnosis will be analyzed by sc-RNA sequencing, to characterize the AEC2 and other epithelial cell populations and reconstruct estimated lineages, especially surrounding the induction of the basal-cell differentiation master- regulator Sox2 within AEC2s.

These samples will be compared to normal and end-stage IPF tissue, in order to test the hypothesis that AEC2 reprogramming is an early feature of IPF.

In addition, diagnostic biopsy samples will be obtained from patients who took epigallocatechin gallate (EGCG) for two weeks prior to biopsy.

EGCG is a mesenchyme-specific inhibitor of TGF? signaling under study in humans and will therefore allow us to examine the hypothesis that AEC2 reprogramming abnormalities seen in diagnostic biopsies can be reversed by TGF? blockade.

Finally, organoid co-cultures and precision-cut lung slices cultures will be used to examine the contribution of important signaling pathways, such as TGF?, Wnt, and Notch, in driving AEC2 reprograming towards a SPC-/KRT5+ basal-cell like state.

Knowledge of the mechanisms driving AEC2 reprograming in IPF may provide fundamental insight into the cause of this disorder and contribute to the development of targeted therapies for this incurable and frequently fatal disease.

This proposed project will be performed as part of the research phase of Pulmonary & Critical Care Medicine Fellowship at UCSF and utilizes comprehensive institutional support and resources, in order to prepare the applicant for an independent research career.