Multiplexed measurements of protein-protein interactions and protein abundance across cellular conditions using Prod&PQ-seq

Xu, T.; Wang, J.; Shin, Y.; Cao, Y.; Zhang, L.; Modolo, E.; Dishon, T.; Fisher, J.; Norton, M.; Fry, C.; Farjoun, Y.; Mendenhall, E.; Heinz, S.; Benner, C.; Goren, A.

doi:10.64898/2026.01.01.697286

bioRxiv · 10.64898/2026.01.01.697286

Multiplexed measurements of protein-protein interactions and protein abundance across cellular conditions using Prod&PQ-seq

Xu, T.·Wang, J.·Shin, Y.·Cao, Y.·Zhang, L.·Modolo, E.·Dishon, T.·Fisher, J.·Norton, M.·Fry, C.·Farjoun, Y.·Mendenhall, E.·Heinz, S.·Benner, C.·Goren, A.

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Abstract

Methods to profile protein-protein interactions (PPIs) have limited scalability and can only study a handful of conditions and/or targets. Here, we introduce Prod&PQ-seq, a framework for multiplexed detection and quantification of PPIs and proteins. Our framework uses cross-linked cells, antibody-oligonucleotide conjugates (ab-oligos), and captures PPIs by the DNA-caliper, a specialized oligonucleotide for bidirectional priming of proximal ab-oligos. We benchmarked Prod&PQ-seq using recombinant complexes, titrations and cell mixture experiments and show that our framework is quantitative, reproducible, sensitive and specific. Applying Prod&PQ-seq to study Polycomb Repressive Complex 2 (PRC2) shows that EZH2 inhibition and expression of the oncohistone H3.3K27M weakens both PRC2-H3K27me3 interactions and PPIs within PRC2. Further, H3.1K27M and H3.3K27M variants lead to distinct PPI profiles such as the intensity of H3K27ac-K27M or H3K27ac-EED. Together, Prod&PQ-seq enables detection of changes in PPI composition and intensity and protein quantification across biological conditions, small molecule inhibition and genetic perturbations. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/697286v2_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@1ed0805org.highwire.dtl.DTLVardef@a9c0d9org.highwire.dtl.DTLVardef@b411fborg.highwire.dtl.DTLVardef@8a12e_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Xu, T., Wang, J., Shin, Y., Cao, Y., Zhang, L., Modolo, E., Dishon, T., Fisher, J., Norton, M., Fry, C., Farjoun, Y., Mendenhall, E., Heinz, S., Benner, C., Goren, A.. 2026-01-02. Multiplexed measurements of protein-protein interactions and protein abundance across cellular conditions using Prod&PQ-seq. https://doi.org/10.64898/2026.01.01.697286

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