Blood proteome profiling using aptamer-based technology for rejection biomarker discovery in transplantation

Abstract

Face transplantation is a promising solution for patients with devastating facial injuries who lack other satisfactory treatment options. At the same time, this type of transplantation is accompanied with high risks of acute transplant rejection. The limitations of traditional skin biopsy and the need to frequently monitor the condition of face transplant call for less invasive biomarkers to better diagnose and treat acute rejection. Discovery of peripheral serum proteins accurately reflecting the transplant status would represent a reasonable solution to meet this demand. However, to date, there is no clinical data available to address the feasibility of this approach. In this study, we used the next generation aptamer-based SOMAscan proteomics platform to profile 1305 proteins of peripheral blood serum in twenty-four samples taken from 6 patients during no-rejection, nonsevere rejection, and severe rejection episodes. Also, we provide a detailed description of biosample processing and all steps to generate and analyze the SOMAscan dataset with hope it will assist in performing biomarker discovery in other transplantation centers using this platform.

High-Multiplex Aptamer-Based Serum Proteomics to Identify Candidate Serum Biomarkers of Oral Squamous Cell Carcinoma

“…Among these, 2-gel electrophoresis (2DE) coupled with matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF), as well as two-dimension liquid chromatography in combination with tandem mass spectrometry, were considered as state-of-the-art for almost a decade in discovery proteomics. However, the application of affinity-based, high multiplex methods such as the here-used aptamer-based SOMAscan, or the proximity extension assay (PEA, Olink), technologies are being applied increasingly with great success to an ever increasing number of clinically relevant studies [ 17 , 18 , 20 , 21 , 22 , 23 , 26 , 33 ]. So far, the SOMAscan technology has been linked to the biomarker discovery of various chronic and acute diseases [ 22 , 24 , 25 , 34 , 35 , 36 , 37 , 38 , 39 , 40 ].…”

“…All sample analyses were conducted with compliance to the Good Laboratory Practice (GLP). After transport, a SOMAscan ® analysis (SomaLogic, Boulder, CO, USA) quantifying 1305 distinct serum proteins (1305-plex) was performed using 55 μL of the anonymized serum samples at the Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Boston, MA, USA, according to the manufacturer’s standard protocol and as previously described [ 21 , 26 ]. Briefly, modified DNA aptamers (SOMAmers) composed of a unique 40-mer sequence of single stranded DNA were employed.…”

“…Using modified DNA-aptamers that bind to defined proteins or peptides allows the quantitative detection of 1305, more recently ~7000, proteins at a 30 fM detection level in a multiplex assay format. This way, even a difficult-to-analyze proteome such as from serum or plasma can be investigated with a small sample size and high reproducibility [ 18 , 19 , 20 , 21 ]. DNA-aptamers exhibit a versatile set of chemical and physical modifications that endow them with protein-like and other functional groups to allow selective binding to a given target protein according to a key and lock mechanism, while non-specific binding is reduced.…”

Proteomics of lung tissue reveals differences in inflammation and alveolar-capillary barrier response between atelectasis and aerated regions

“…SOMAscan was run on the samples to capture 1305 protein analytes, using SOMAmer reagents 50 . The samples were prepared following recommended sampling and handling procedure for both tissue types 50 , 51 . They were then run in the Somalogic certified assay site at the BIDMC genomics, proteomics, bioinformatics and systems biology center at Beth Israel Deaconess medical center along with pooled and quality control samples according to the manufacturer's well-established protocols.…”

Serum Protein Signatures Using Aptamer-Based Proteomics for Minimal Change Disease and Membranous Nephropathy

“…A 50 ml of patient serum was processed on the SOMAscan assay 1.3k for human serum, which measures the expression of 1305 human proteins using highly selective, single-stranded, modified Slow Offrate Modified DNA Aptamers and analyzed according to standard protocols for biological fluids from Soma-Logic that have been described elsewhere. 8,[13][14][15][16][17] In brief, fluorescence-labeled SOMAscan aptamers for the 1305 proteins, coupled with a photocleavable linker and biotin, were immobilized on beads and divided into 3 dilution bins (0.05%, 1%, 40%) corresponding to the abundance of their target proteins in serum. Then, the serum test samples, diluted to the 3 bin concentrations, were incubated with the corresponding highly specific SOMAmer-bead panel.…”