Profiling Immune Cells in Lymphoma and Lung Cancer

All patient samples in this study were reviewed and approved by the Stanford Institutional Review Board in accordance with the Declaration of Helsinki. Tonsils were collected as part of routine tonsilectomy procedures at Lucile Packard Children’s Hospital at Stanford University with informed consent for research use, and then mechanically disaggregated before cell suspensions were cryopreserved (Supplementary Fig. 3b). Peripheral blood mononuclear cells (PBMCs) were isolated from specimens taken before and immediately following four weekly doses of infusional rituximab (375 mg m⁻²) monotherapy for extranodal marginal zone lymphoma (EMZL) in a subject without measurable circulating disease (patient 1 in Supplementary Fig. 4c). PBMCs were respectively isolated from specimens taken immediately following four cycles and six cycles of RCHOP immunochemotherapy for treatment of DLBCL (patients 2 and 3 in Supplementary Fig. 4c). PBMCs were also isolated from a subject following four cycles of Rituximab for treatment of FL (patient 4 in Supplementary Fig. 4c); this subject had ~2% circulating lymphoma cells at diagnosis, which were undetectable by CIBERSORT and flow cytometry following four Rituximab infusions. Specimens of adjacent normal lung tissue were obtained during surgical resection of early stage non-small cell lung tumors (Fig. 2h). Surgical tissue biopsies were obtained from untreated FL patients enrolled in a Phase III clinical trial (NCT00017290^{18 (link)}) (Fig. 2i and Fig. 3c). Lastly, PBMCs were obtained from 20 adults of varying ages receiving influenza immunization (NCT01827462) (Fig. 3a), and from seven adults consisting of patient 4 in Supplementary Fig. 4c and six healthy subjects (Fig. 3b, which includes patient 4).