High multiplex analysis of the immune microenvironment in bone marrow trephine samples using GeoMX™ digital spatial profiling

Abstract

Background: To date, studies into the bone marrow (BM) immune microenvironment have been limited due to reliance on the analysis of BM aspirates in which the microenvironmental context is lost. GeoMX™ digital spatial profiling (DSP) is a new technique developed for the analysis of formalin-fixed paraffin-embedded tissue samples which allows high multiplex analysis of protein expression in multiple user-defined regions within a tissue section. We examined the applicability of this technique to the analysis of protein expression in diagnostic BM trephine samples. Materials and methods: Archival BM trephines were obtained from patient groups (normal, myelodysplasia and aplastic anaemia). Regions of interest in each section were identified by dual CD3þ/CD45þ immunohistochemistry staining to identify immune infiltrates, and DSP was applied. Results: Due to variability in cell number within regions of interest and differing cellular composition of the BM trephines, raw protein expression counts were normalised by internal controls and nuclei count to determine the expression level of each protein within each region of interest. In heat map analysis using Spearman's rank correlation, aplastic anaemia samples clustered away from both normal and myelodysplasia samples, demonstrating significant differences in their BM immunology. Conclusions: GeoMX™ DSP is an innovative new technique that, for the first time, allows the analysis of archival BM trephines at an unprecedented level of detail. It will allow investigations in large cohorts of patients with haematological malignancies to identify new biomarkers, new mechanisms of disease pathogenesis and new drug targets.

Arecanut (Areca catechu L.) Seed Polyphenol-Ameliorated Osteoporosis by Altering Gut Microbiome via LYZ and the Immune System in Estrogen-Deficient Rats

“…The gut microenvironment and inflammatory changes of the immune system are closely related . The expression of LYZ, which was implicated with Paneth cells, directly affected the gut microorganisms, , and the immune response associated with the gut microenvironment could significantly affect the dynamics of bone metabolism. − In this study, the ovariectomized rats after being treated by ACP and E2 with normalized bone mass acquired an altered gut microbiota and maintained the number of Paneth cells compared to OVX, revealing that osteoporosis drugs may alter the intestinal bacteria of ovariectomized rats by influencing the expression of Paneth cells. The Paneth cell-derived antimicrobial peptides, including LYZ, plays an important role in the regulation of gut microbiota.…”

Transcriptional Spatial Profiling of Cancer Tissues in the Era of Immunotherapy: The Potential and Promise

“…Thus, it seems that DSP has the potential to be an accurate and reproducible tool for determining patient prognosis following checkpoint inhibition. The usefulness of DSP is not just limited to fresh-frozen or FFPE tissue samples; indeed, one study showed how DSP could be extended to bone marrow trephine samples with unprecedented high-plex spatial profiling of the bone marrow microenvironment [ 96 ]. This finding means that DSP might serve to identify biomarkers and potential drug targets specific to haematological malignancies.…”

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Clinical features, pathophysiology, and therapy of poor graft function post–allogeneic stem cell transplantation

“…Larger longitudinal-assessment studies comparing those with persisting PGF vs those with resolution are required. Utilization of other novel techniques such as digital spatial profiling applied to bone marrow trephines 73 and gene-expression profiling will give further insight to the immunobiology of PGF.…”