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\begin{document}

\title{Comprehensive Profiling of the Human Fecal Proteome from IBD Patients
with DIA-MS Enables Evaluation of Disease-Relevant Proteins}



\author[1]{Brandon Harder}%
\author[1]{Annemarie Lekkerkerker}%
\author[1]{Ellen Casavant}%
\author[1]{Jason Hackney}%
\author[1]{Allen Nguyen}%
\author[1]{Jacqeline McBride}%
\author[1]{W. Rodney Mathews}%
\author[1]{Veronica Anania}%
\affil[1]{Genentech Inc}%


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  \date{June 18, 2024}


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\begin{abstract}
Inflammatory bowel disease (IBD), which includes ulcerative colitis (UC)
and Crohn's disease (CD), is characterized by chronic gastrointestinal
inflammation. A high unmet need exists for non-invasive biomarkers in
IBD to detect mucosal inflammation to monitor changes in disease
severity and guide treatment decisions. Fecal proteomics has the
potential to allow frequent, non-invasive monitoring of biomarkers in
stool of IBD patients, however the fecal proteome remains under
explored. Here a data-independent acquisition LC-MS/MS approach was used
to profile the human fecal proteome in two independent cohorts of IBD
patients and healthy controls (HC) to identify non-invasive biomarkers
reflective of disease activity. 688 human proteins were quantified, with
523 measured in both cohorts. In UC stool 96 proteins were
differentially abundant and in CD stool 126 proteins were differentially
abundant compared to HC stool (absolute log2 fold change
\textgreater{}1, p-value \textless{}0.05). Many of these fecal proteins
are associated with infiltrating immune cells and ulceration/rectal
bleeding, which are hallmarks of IBD pathobiology. Mapping of the
identified fecal proteins to a whole blood single-cell RNA sequencing
data set revealed the involvement of various immune cell subsets to the
IBD fecal proteome. Findings from this study not only confirmed the
presence of established fecal biomarkers for IBD, such as calprotectin
and lactoferrin, but also revealed new fecal proteins from multiple
pathways known to be dysregulated in IBD. These novel proteins could
serve as potential non-invasive biomarkers to monitor specific aspects
of IBD disease activity which could expedite clinical development of
novel therapeutic targets.%
\end{abstract}%



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