Single Cell Mass Cytometry for Phenotypic Analysis of Diffuse Large B-Cell Lymphoma
Authors: Kusakabe Manabu , Simkin Guillermo , Meskas Justin , Zhang Chaoran , Ennishi Daisuke , Boyle Merrill , Scott David W. , Steidl Christian , Gascoyne Randy D. , Brinkman Ryan R. , Weng Andrew P 
Published: November 2019

Diffuse Large B-cell Lymphoma (DLBCL) is the most common histologic subtype of non-Hodgkin Lymphoma (NHL). Despite its improved outcome with R-CHOP chemotherapy, 40% of patients still suffer with relapsed or refractory disease. Further investigation is needed to understand the complexity of DLBCL. Time-of-flight mass cytometry (CyTOF) is a recently developed technology that combines traditional flow cytometry with mass spectrometry and supports analysis of up to 30-40 parameters simultaneously at the single cell level with minimal spectral overlap (Bendall et al, Science 2011). In this study, we sought to develop a CyTOF method for phenotypic analysis of DLBCL to obtain high resolution profiles of the malignant clone(s) represented in individual tumor samples and resolve any underlying population substructure that might be informative in understanding the clinical and biologic heterogeneity of this disease.

We designed a two-tube assay for this study. Tube #1 contained 35 cell surface markers including CD45, CD19, CD20, CD22, CD79B, IgM, IgD, Ig Kappa, Ig Lambda, CD5, CD10, CD23, CD43, CD38, CD138, CD44, CD21, CD24, CD40, CD72, CD80, CD45RA, CD49D, CD49F, CD62L, CD25, CD27, CD30, CD127, CD184, CD194, CD200, CD34, HLA-DR, and CD3. Tube #2 contained 37 markers in total including 17 cell surface markers overlapping with Tube #1 plus an additional 20 intracellular markers (BCL2, BCL6, IRF4/MUM1, LMO2, MYC, MCL1, MEF2B, KAT3B/P300, CBP, FOXP1, RUNX1, Ikaros, EZH2, BMI1, NOTCH1, CARD11, IkBa, phospho-Rb, Ki67, and CyclinD2). Metal-conjugated antibodies were purchased from DVS Sciences or unconjugated antibodies labeled in-house using DVS MaxPar metal labeling kits. Data were acquired using a DVS CyTOF2 instrument. We examined both fresh and viably frozen single cell suspensions from diagnostic lymph node biopsy samples received for flow cytometric analysis at the BC Cancer Agency. We used SPADE (spanning-tree progression analysis of density-normalized events) for initial data analysis.

We first performed preliminary validation studies including cross-comparison of mass cytometry (CyTOF2) vs. flow cytometry (BD Canto2) datasets and fresh vs. previously frozen cell suspension material. Although individual marker intensities using matched antibody clones were in general lower by CyTOF, eight-parameter surface staining results were qualitatively comparable between the two platforms. Also there were essentially no differences observed in CyTOF staining profiles between fresh and previously frozen samples. Preliminary clustering analysis of cell populations using SPADE revealed clear separation between normal and malignant B cell populations as well as apparent substructure to the malignant population in a subset of DLBCL samples. These findings suggest intratumoral heterogeneity can be resolved by high dimensional CyTOF analysis. Ongoing efforts will focus on determining if phenotypically defined subsets show enrichment for subclonal mutations.

Disclosures

No relevant conflicts of interest to declare.