Enriched protein screening of human bone marrow mesenchymal stromal cell secretions reveals MFAP5 and PENK as novel IL-10 modulators

Abstract

The secreted proteins from a cell constitute a natural biologic library that can offer significant insight into human health and disease. Discovering new secreted proteins from cells is bounded by the limitations of traditional separation and detection tools to physically fractionate and analyze samples. Here, we present a new method to systematically identify bioactive cell-secreted proteins that circumvent traditional proteomic methods by first enriching for protein candidates by differential gene expression profiling. The bone marrow stromal cell secretome was analyzed using enriched gene expression datasets in combination with potency assay testing. Four proteins expressed by stromal cells with previously unknown anti-inflammatory properties were identified, two of which provided a significant survival benefit to mice challenged with lethal endotoxic shock. Greater than 85% of secreted factors were recaptured that were otherwise undetected by proteomic methods, and remarkable hit rates of 18% in vitro and 9% in vivo were achieved.

Figure 1

Enriched protein screening (EPS). A generalized schematic of EPS methodology. Protein products are derived from various cell types in the form of conditioned media and screened for activity in an in vitro potency assay. Based on the activity of the conditioned media from the cells, differential gene expression profiling is performed to select for genes uniquely upregulated in the cell type with the highest activity in the potency assay. Recombinant protein products of the enriched gene list are then screened in the same potency assay and candidates with the highest activity are assessed for activity in vivo.

Figure 2

In vitro blood inflammation assay. (a) An IL-10 in vitro potency assay for this study. This assay entails incubating primary human PBMCs in the presence of protein products (e.g., conditioned medium from a cell) for 16 hours, followed by stimulation of the PBMCs with (LPS) for 5 hours, and measurement of IL-10 secretion into the supernatant via ELISA. (b) Time course of IL-10 expression from PBMCs when incubated with either bone marrow stromal cell conditioned medium (BM-MSC-CM) or unconditioned medium (DMEM) in the potency assay. (c) Dose response of the potency assay to increasing concentration of BM-MSC-CM. 15× CM was either diluted or concentrated further to generate the different concentrations. N = 3 independent trials. *P < 0.001 compared to DMEM. BM-MSC, bone marrow mesenchymal stromal cell; CM: conditioned medium; DMEM, Dulbecco's modified Eagle's medium; LPS, lipopolysaccharide; PBMC, peripheral blood mononuclear cells.

Figure 3

Gene contrast hierarchy and generation of screening library. (a) Comparison of potency assay activity of conditioned medium from FB-CM and BM-MSC-CM. *P < 0.001 compared to FB-CM. N = 3 independent trials. (b) The top five ontological gene clusters for the contrast set of BM-MSC>FB. N = 3 independent microarrays per group. (c) Effect of preconditioning BM-MSCs with stimulatory ligands on the activity of BM-MSC-CM in the potency assay. N = 2 independent trials. (d) Comparison of potency assay activity of conditioned medium from BM-MSC-CM and BM-MSCs preincubated with LPS prior to conditioning (BM-MSC_LPS-CM). *P < 0.001 compared to BM-MSC-CM. N = 3 independent trials. (e) Top five ontological gene clusters for the contrast set of BM-MSC_LPS≥BM-MSC. N = 3 independent microarrays per group. (f) Schematic of the gene expression comparison scheme. Genes correlating with anti-inflammatory activity were selected by taking the intersection of the sets of all genes upregulated in BM-MSCs compared to FBs and all genes expressed equally or upregulated in BM-MSC_LPS compared to BM-MSCs. (g) Gene expression profiling revealed 22 genes responsible for secreted proteins that were upregulated by BM-MSCs stimulated with LPS compared to BM-MSCs and FBs. BM-MSC: bone marrow mesenchymal stromal cell; FB, normal human dermal fibroblasts; LPS: lipopolysaccharide.

Figure 4

Screening of the enriched recombinant protein candidates. Enriched recombinant protein screen of 22 candidates using the potency assay. N = 2 independent trials for the entire screen, with N > 4 for hits.

Figure 5

Assessment of BM-MSC secretion of the candidate proteins and gene expression evaluation of known therapeutic molecules produced by BM-MSCs. (a) ELISA and western blotting of FB-CM, BM-MSC-CM, and BM-MSC_LPS-CM for LGALS3BP, MFAP5, GALNT1, and PENK. *P < 0.001 compared to FB-CM. (b) Partial list of proteins contained in 150× FB-CM, BM-MSC-CM, and BM-MSC_LPS-CM detected by proteomic mass spectrometry. (c) Contrast gene expression data for known therapeutic molecules expressed by BM-MSCs. N = 2 independent batches of BM-MSCs. BM-MSC, bone marrow mesenchymal stromal cell; FB, normal human dermal fibroblasts; GALNT1, polypeptide N-acetylgalactosaminyltransferase 1; LPS, lipopolysaccharide; LGALS3BP, soluble galectin-3 binding protein; MFAP5, microfibrillar-associated protein 5; PENK, proenkephalin.

Figure 6

In vivo hit screen and survival study. Proteins were administered IP at the concentration that elicited the strongest effect in vitro, followed by IP administration of LPS in conjunction with a second dose of the proteins 16 hours later. Two days after the combined LPS and second protein dose, the mice were sacrificed and assessed for changes in serum cytokines and tissue histology. (a) Serum IL-10 and serum TNF-α levels of BALB/cJ mice subjected to the in vivo LPS assay. *P < 0.001 IL-10 expression compared to saline. #P < 0.001 TNF-α compared to saline, ##P < 0.05 TNF-α compared to BM-MSC-CM. N = 4 mice per group. (b) Representative micrographs of lung tissue from mice subjected to the in vivo LPS assay stained with hematoxylin and eosin. A table below quantifies alveolar space and mononuclear cell infiltrate per high per field in H&E sections as a % change compared to saline treated mice. A positive % change in alveolar space equates to a more normalized tissue state. A negative % change in mononuclear infiltrate would equate to normalization to a healthier tissue state. (c) Survival of mice subjected to a lethal dose of LPS i.p. (350 µg) concurrently with i.p. saline vehicle (bold dark blue line, n = 20), 300 µg/kg Anti-TNF-α antibody (thin dark blue line, n = 5), 200 µg/kg PENK (bold light blue line, n = 5) or 200 µg/kg MFAP5 (thin light blue line, n = 5). *P < 0.005 compared to vehicle control, **P < 0.001 compared to vehicle control. Scale bar = 200 µm. i.p., intraperitoneal; LPS, lipopolysaccharide; MFAP5, microfibrillar-associated protein 5; PENK, proenkephalin; TNF, tumor necrosis factor.

Figure 7

Identification of cellular targets of MFAP5 and PENK. (a) Flow cytometry of CD14⁺ cells from whole human PBMCs incubated with either MFAP5-GST, PENK-GST or no protein and then stained for GST. (b) LPS potency assay with PBMCs or enriched human monocytes from PBMCs and MFAP5 or PENK. BM-MSC, bone marrow mesenchymal stromal cell; FITC, fluorescein isothiocyanate; LPS, lipopolysaccharide; MFAP5, microfibrillar-associated protein 5; PBMC, peripheral blood mononuclear cells; PENK: proenkephalin.