Patrizia Mondello

Germinal center (GC)-derived lymphomas arise within a specialized immune ecosystem, yet whether malignant cells direct its remodeling remains unclear. Integrating genomic, transcriptomic, spatial, and functional analyses across follicular lymphoma and diffuse large B-cell lymphoma, we define a developmental framework linking malignant B-cell differentiation state to tumor microenvironment (TME) organization. Rather than segregating by histology, lymphomas align along a shared differentiation continuum in which proliferative dark zone (DZ) states associate with immune-depleted TMEs, whereas post-GC/memory B-cell (MBC) states drive inflamed but immunosuppressed TMEs. Spatial profiling reveals collapse of GC architecture and emergence of suppressive myeloid niches along this trajectory. Single-cell lineage reconstruction uncovers a DZ-to-MBC developmental axis underlying lymphoma evolution. Genetic reprogramming in vivo demonstrates that malignant differentiation state is sufficient to instruct TME remodeling. Collectively, these findings establish malignant differentiation state as a causal determinant of immune architecture across GC-derived lymphomas and identify lineage-directed immune reprogramming as a potential therapeutic strategy.

Waldenström macroglobulinemia (WM) is characterized by recurrent MYD88 and CXCR4 mutations, whose prognostic value in patients treated with chemoimmunotherapy remains unclear. Moreover, the typically prolonged progression-free survival (PFS) correlates inconsistently with overall survival (OS), underscoring the importance of examining other surrogates. Progression of disease within 24 months (POD24), an established early end point, delineates functionally high-risk patients in other indolent lymphomas. This international study evaluated 253 patients receiving frontline fixed-duration bendamustine-rituximab (BR), a common chemoimmunotherapy for WM. At a median follow-up of 5.9 years, 5-year PFS and OS were 65% and 87%, respectively; 5-year PFS was similar between MYD88L265P (90%) and MYD88wild-type (WT) subcohorts (64% each; P = .4). Among 89 patients with known CXCR4 status, the subcohort with CXCR4mutation (28%) had shorter PFS (median 3.3 vs 8.8 years; hazard ratio [HR], 2.8; P = .0036) and OS (HR, 2.6; P = .036) compared with CXCR4WT. POD24 occurred in 11.5% of patients who demonstrated inferior subsequent OS (5-year OS, 71% vs 86%; HR, 3.1; P = .005) and higher mortality (standardized mortality ratio [SMR], 3.7), unlike the non-POD24 group, whose mortality was comparable to the matched general population (SMR, 1.1). In conclusion, BR is effective irrespective of the MYD88 status, but CXCR4 mutations and POD24 portend worse outcomes. Patients without POD24 represent a cohort with distinctly favorable outcome.

Supplemental Fig. 2. Gene expression of non-tumor cells by cluster.

Supplementary Figure 5 A. Heat map of Spearman's correlation coefficients among paired proteins in the bone marrow (BM) supernatant and peripheral blood (PB) serum of 16 patients with WM (n=11) and IgM MGUS (n=5). Positive correlations are shown in red, whereas negative correlations are indicated in blue. B. Heat maps showing expression of (i) 12 proteins significantly different between C1 vs C2 plus C3, and (i) 74 proteins significantly different between C2 vs C1 plus C3 in the PB serum. The left bar shows correlation coefficients between BM and PB proteins. Gray squares indicate non significance.

Supplementary Figure 9 SPADE maps of CD4+ CTLA-4+ T cells from concatenated files (C1, n=7; C2, n=4). The dots in red and blue indicate high and low expression, respectively. The dot size is representative of cell events, with the big size containing more cell events.

Supplementary Figure 7 A. Heat map of Spearman's correlation coefficients among paired metabolites in the bone marrow (BM) supernatant and peripheral blood (PB) serum of 12 patients with WM. Positive correlations are shown in red, whereas negative correlations are indicated in blue. B. Heat map showing different expression of 44 metabolites in the BM supernatant among the three molecular clusters. The left bar shows correlation coefficients between BM and PB metabolites. Gray squares indicate non significance.

Supplementary Figure 3 Boxplot showing that 6q deletion resulted in decreased expression of TNFAIP3.

Supplementary Figure 4. Schematic representation of the mechanism associated with the three clusters.