Olink-based Protein Profiling in Metastatic Melanoma

Olink profiling of blood samples (collected using DF/HCC IRB approved Protocol 11–181) from patients with metastatic melanoma at MGH was performed as previously described^{21 (link)}. Olink Proximity Extension Assay (PEA) for high-multiplex analysis of proteins was performed as previously described^{57 (link)}. The full library (Olink ^® Explore 1536) consists of 1472 proteins and 48 control assays, divided into four 384-plex panels. Four overlapping assays of IL-6, IL-8 (CXCL8), and TNF are included for quality control (QC) purposes. In the immune reaction, 2.8 mL of sample is mixed with PEA probes and incubated overnight at 4°C. Olink’s relative protein quantification unit on a log2 scale and values are calculated from the number of matched counts on the NovaSeq run. Data generation of normalised protein expression (NPX) consists of normalisation to the extension control (known standard), log2-transformation, and level adjustment using the plate control (plasma sample).

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Revach O.Y., Cicerchia A.M., Shorer O., Petrova B., Anderson S., Park J., Chen L., Mehta A., Wright S.J., McNamee N., Tal-Mason A., Cattaneo G., Tiwari P., Xie H., Sweere J.M., Cheng L.C., Sigal N., Enrico E., Miljkovic M., Evans S.A., Nguyen N., Whidden M.E., Srinivasan R., Spitzer M.H., Sun Y., Sharova T., Lawless A.R., Michaud W.A., Rasmussen M.Q., Fang J., Palin C.A., Chen F., Wang X., Ferrone C.R., Lawrence D.P., Sullivan R.J., Liu D., Sachdeva U.M., Sen D.R., Flaherty K.T., Manguso R.T., Bod L., Kellis M., Boland G.M., Yizhak K., Yang J., Kanarek N., Sade-Feldman M., Hacohen N, & Jenkins R.W. (2024). Disrupting CD38-driven T cell dysfunction restores sensitivity to cancer immunotherapy. bioRxiv.

Publication Preprint 2024

Explore 1536

Corresponding Organization :

Other organizations : Center for Cancer Research, Harvard University, Massachusetts General Hospital, Broad Institute, Technion – Israel Institute of Technology, Boston Children's Hospital, Massachusetts Institute of Technology, Teikoku Pharma (United States), University of California, San Francisco, Cedars-Sinai Medical Center, Dana-Farber Cancer Institute

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Variable analysis

independent variables

Metastatic melanoma patient blood samples

dependent variables

Protein expression levels quantified using Olink Proximity Extension Assay (PEA)

control variables

Olink Explore 1536 library containing 1472 proteins and 48 control assays
Four overlapping assays of IL-6, IL-8 (CXCL8), and TNF for quality control (QC) purposes
Normalisation to the extension control (known standard)
Log2-transformation and level adjustment using the plate control (plasma sample)

positive controls

Plasma sample used for plate control

negative controls

Not explicitly mentioned

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