Highlights d Single-cell signaling map of lung development identifies inter-lineage crosstalk d Lung-resident basophils are broadly interacting cells located near alveoli d Lung environment imprints the gene signature of basophils via IL33 and GM-CSF d Basophils regulate alveolar macrophage maturation and immunomodulation functions

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Multiple myeloma (MM), a plasma cell (PC) malignancy, is the second most common blood cancer. Despite extensive research, disease heterogeneity is poorly characterized, hampering efforts for early diagnosis and improved treatments. Here, we apply scRNA-seq to study the heterogeneity of 40 individuals along MM progression spectrum including 11 healthy controls, demonstrating high interpatient variability that can be explained by expression of known MM drivers and additional putative factors. We identify extensive sub-clonal structures for 10/29 patients. In asymptomatic patients with early disease and in minimal residual disease post-treatment, we detect rare tumor-PC with similar molecular characteristics of active myeloma, with possible implications for personalized therapies. Single cell analysis of rare circulating-tumor-cells (CTC) allows for accurate liquid biopsy and detection of malignant PC, which reflect the patient BM disease. Our work establishes scRNA-seq for dissecting blood malignancies and devising detailed molecular characterization of tumor cells in symptomatic and asymptomatic patients.

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