Spatial Proteomics for Further Exploration of Missing Proteins: A Case Study of the Ovary

In the quest for “missing proteins” (MPs),
the proteins
encoded by the human genome still lacking evidence of existence at
the protein level, novel approaches are needed to detect this challenging
group of proteins. The current count stands at 1,343 MPs, and it is
likely that many of these proteins are expressed at low levels, in
rare cell or tissue types, or the cells in which they are expressed
may only represent a small minority of the tissue. Here, we used an
integrated omics approach to identify and explore MPs in human ovaries.
By taking advantage of publicly available transcriptomics and antibody-based
proteomics data in the Human Protein Atlas (HPA), we selected 18 candidates
for further immunohistochemical analysis using an exclusive collection
of ovarian tissues from women and patients of reproductive age. The
results were compared with data from single-cell mRNA sequencing,
and seven proteins (CTXN1, MRO, RERGL, TTLL3, TRIM61, TRIM73, and
ZNF793) could be validated at the single-cell type level with both
methods. We present for the first time the cell type-specific spatial
localization of 18 MPs in human ovarian follicles, thereby showcasing
the utility of the HPA database as an important resource for identification
of MPs suitable for exploration in specialized tissue samples. The
results constitute a starting point for further quantitative and qualitative
analysis of the human ovaries, and the novel data for the seven proteins
that were validated with both methods should be considered as evidence
of existence of these proteins in human ovary.