Comprehensive Characterization of the Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis

• DOI: 10.1158/2767-9764.crc-22-0022
• Publication Date: 2022-08-31T13:51:44Z
• Authors: Lijun Yao; Reyka G. Jayasinghe; Brian H. Lee; Swati S. Bhasin; William Pilcher; Deon Bryant Doxie; Edgar Gonzalez-Ko...; Surendra Dasari; Mark A. Fiala; Yered Pita-Juarez; Michael Strausbauch; Geoffrey Kelly; Beena E. Thomas; Shaji K. Kumar; Hearn Jay Cho; Emilie Anderson; Michael C. Wendl; Travis Dawson; Darwin D'souza; Stephen T. Oh; Giulia Cheloni; Ying Li; John F. DiPersio; Adeeb H. Rahman; Kavita M. Dhodapkar; Seunghee Kim-Schulze; Ravi Vij; Ioannis S. Vlachos; Shaadi Mehr; Mark Hamilton; Daniel Auclair; Taxiarchis Kourelis; David Avigan; Madhav V. Dhodapkar; Sacha Gnjatic; Manoj K. Bhasin; Li Ding
• Keywords: Concordance; Mass cytometry

As part of the Multiple Myeloma Research Foundation (MMRF) immune atlas pilot project, we compared cells multiple myeloma bone marrow samples from 18 patients assessed by single-cell RNA sequencing (scRNA-seq), mass cytometry (CyTOF), and cellular indexing transcriptomes epitopes (CITE-seq) to understand concordance measurements among techniques. Cell type abundances are relatively consistent across three approaches, while variations observed in T cells, macrophages, monocytes. Concordance correlation analysis cell marker gene expression different modalities highlighted importance choosing genes best suited particular modalities. By integrating data these assays, found International Staging System stage 3 exhibited decreased CD4+ T/CD8+ ratio. Moreover, upregulation RAC2 PSMB9, natural killer fast progressors with those nonprogressors, as revealed both scRNA-seq CITE-seq measurement. This detailed examination microenvironment using technologies markers associated rapid progression which will be further characterized full-scale project. Significance: scRNA-seq, CyTOF, increasingly used for evaluating heterogeneity. Understanding their concordances is great interest. To date, this study most comprehensive measurement identified predicted significantly progression.