Multi-dimensional transcriptomic profiling reveals novel tumor microenvironment landscape and subtype-specific therapeutic Vulnerabilities of MALT lymphomas

Abstract Introduction: Mucosa-associated lymphoid tissue (MALT) lymphoma is the most prevalent subtype of marginal zone lymphomas and can primarily occur in various sites. Despite generally favorable prognosis, patients with MALT lymphoma may still experience poor outcome due to relapse, progression or aggressive transformation. However, the biological characteristics that underlie the different origins and clinical evolutions of MALT lymphoma remain poorly understood. Methods: We collected the largest cohort of formalin-fixed paraffin-embedded (FFPE) tissue samples of MALT lymphoma patients from a series of sites for bulk RNA, single-nucleus and spatial transcriptomic sequencing, including the ocular adnexa, stomach, intestine, lung, liver, salivary gland, nasal sinus and lymph node. Results: A total of 120 MALT lymphoma bulk RNA sequencing datasets were first collected and integrated. To assess tumor microenvironment (TME) classification metrics, we employed non-negative matrix factorization (NMF) to categorize the samples into three distinct TME subtypes: Mesenchymal, characterized by an abundance of endothelial cells and fibroblasts; Inflammatory, enriched in lymphocytes; and Depleted, defined by high proliferative activity. Utilizing single-nucleus RNA sequencing (snRNA-seq) data, we further explored the cellular and molecular differences across the identified subtypes. Through NMF clustering, we identified two key meta programs (MPs) within tumor-infiltrating B cells. Notably, the immune regulatory MP was more prevalent in the Inflammatory subtype, while the cell cycle-related MP was predominantly enriched in the Depleted subtype. Drug sensitivity analysis suggested that tumor cells in the Mesenchymal subtype exhibited greater sensitivity to anti-angiogenic agents, whereas those in the Depleted subtype were more responsive to cell cycle-targeting therapies. By leveraging cellular proportion correlations from snRNA-seq and spatial domain analysis from spatial transcriptomics data, we elucidated the spatial colocalization patterns of different cell types. Cell-cell communication analysis further revealed that in the Mesenchymal subtype, neutrophils and MACRO+ tumor-associated macrophages (TAM) cells played key roles in promoting angiogenesis via the VEGF pathway. In contrast, the formation of tertiary lymphoid structures (TLSs) and the recruitment of Treg cells were more pronounced in the Inflammatory subtype, highlighting potential therapeutic targets for different tumor microenvironment subtypes. Conclusions: Our study firstly described the tumor microenvironment characteristics of multi-site MALT lymphomas by multi-dimensional transcriptomic sequencing, providing potential therapeutic targets for different tumor microenvironment subtypes and offering important insights for the development of personalized treatment strategies.