Unveiling the autoreactome: Proteome-wide immunological fingerprints reveal the promise of plasma cell depleting therapy

The prevalence and burden of autoimmune and autoantibody mediated disease continues to rise, yet the etiologies of many of these diseases remain unclear. Despite numerous new targeted immunomodulatory therapies, comprehensive approaches to apply and evaluate the effects of these treatments longitudinally are lacking. Here, we leverage advances in PhIPseq methodology to explore the modulation, or lack thereof, for autoreactive antibodies proteome-wide in both health and disease. We demonstrate that each individual, regardless of disease state, possesses a distinct set of autoreactivities constituting a unique immunological fingerprint, or \"autoreactome”, that is remarkably stable over years. In addition to uncovering important new biology, the autoreactome can be used to better evaluate the relative effectiveness of various therapies in altering autoantibody repertoires. We find that therapies targeting B-Cell Maturation Antigen (BCMA) profoundly alter an individual’s autoreactome, while..., All PhIP-Seq was performed similar to our previously published multichannel protocol, with minor adjustments as outlined in our new protocol: https://www.protocols.io/view/derisi-lab-phage-immunoprecipitation-sequencing-ph-czw7x7hn?step=14.1
Our human peptidome library consists of a custom-designed phage library of 731,724 unique T7 bacteriophage each presenting a different 49 amino-acid peptide on its surface. Collectively these peptides tile the entire human proteome including all known isoforms (as of 2016) with 25 amino-acid overlaps. 1 milliliter of phage library was incubated with 1 microliter of human serum overnight at 4C and immunoprecipitated with 25 microliters of 1:1 mixed protein A and protein G magnetic beads (Thermo Fisher, Waltham, MA, #10008D and #10009D). These beads were than washed, and the remaining phage-antibody complexes were eluted in 1 milliliter of E.Coli (BLT5403, EMD Millipore, Burlington, MA) at 0.5-0.7 OD and amplified by growing in 37C incubator. This new..., , # Individuals harbor a unique and longitudinally stable autoreactome maintained by plasma cells and altered by anti-BCMA CAR-T therapy

[https://doi.org/10.5061/dryad.w3r2280z6](https://doi.org/10.5061/dryad.w3r2280z6)

**Attached are the complete PhIP-Seq results for the 6 cohorts analyzed in the associated manuscript. There are 7 total datasets:**

-***\"HC_fc\"*** is the complete gene-level fold-change over mock-IP signal for all 79 healthy controls.

-***\"HC_reps\"*** is the complete gene-level raw sequencing reads for the 24 sets of duplicates among the 79 healthy controls.

-***\"Healthy_Longitudinal_fc\"*** is the complete gene-level fold-change over mock-IP signal for the 35 longitudinal healthy samples from 7 individuals.

-***\"IVIG_fc\"*** is the complete gene-level fold-change over mock-IP signal for the 4 sets of pre- and post-IVIG samples.

-***\"Ritux_fc\"*** is the complete gene-level fold-change over mock-IP signal for the 32 samples from the 7 individuals longitudinally tacked ...