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Abstract
Cilia are hair-like projections lining the respiratory tract that move microbes and debris out of theairways. The coordinated beating of cilia provides the driving force for mucociliary clearance, which
is the primary defense mechanism of the lung. Cilia are also an important entry site for viral infection
including SARS-CoV-2, which is the causative agent of the COVID-19 pandemic. SARS-CoV-2 enters
host cells by interacting with angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease
2 (TMPRSS2) receptors, which are localized to respiratory cilia. The localization of ACE2 on these cilia
has important implications in SARS-CoV-2 transmission and the development of therapeutic strategies
to treat COVID-19. However, the specific localization of ACE2 in cilia and whether ACE2 plays a role
in ciliary function remain unknown. To investigate the localization of ACE2 in cilia, we performed
immunofluorescence staining and imaged with a super-resolution microscope using commercial ACE2
antibodies. We found that ACE2 localizes to the proximal region of cilia while TMPRSS2, an ACE2
sheddase, localizes to the distal region of cilia, which may in part explain the proximal distribution of the
ectodomain of ACE2 on respiratory cilia. To study ciliary function, we built a large-scale video dataset
of ciliary motion phenotypes under several categories (temperatures, drugs, and ACE2 manipulation).
This validation dataset consists of 872 videos and ground-truth masks labelling the ciliary area. We also calculated the ciliary beat frequency as a benchmark metric. Cilia segmentation is important for ciliary
waveform analysis, which will help in the diagnosis of ciliopathies. We built a deep learning pipeline that
incorporated Gabor filters into a the U-Net model for automated cilia segmentation. Our framework
improved the performances of the baseline model in terms of Intersection over Union (IoU), accuracy,
F1, and precision scores. Our work is crucial to understanding the precise nature of ACE2, SARS-CoV-2
pathogenesis, and ciliary motility.