Integration of Mutational Signature Analysis with 3D Chromatin Data Unveils Differential AID-Related Mutagenesis in Indolent Lymphomas

Activation-induced cytidine deaminase in tertiary lymphoid structures: dual roles and implications in cancer prognosis

Activation-induced cytidine deaminase (AID) serves as a critical molecular orchestrator in the germinal center (GC) reaction within secondary lymphoid organs (SLOs), driving the production of high-affinity antibodies through somatic hypermutation. While its pathological implications are well-documented - including ectopic expression in non-B cell populations and transcriptional dysregulation linked to hematological malignancies and solid tumorigenesis - the cellular provenance of AID in solid tumors remains an unresolved paradox. This review advances two principal hypotheses: (1) AID may derive from tertiary lymphoid structures (TLSs), ectopic immune niches mirroring SLO organization, and (2) exhibits context-dependent transcriptional duality, capable of both potentiating and suppressing gene expression based on microenvironmental cues. Through systematic analysis of AID/GC involvement across cancer subtypes, we delineate mechanistic connections between lymphoid neogenesis and tumor progression. Our examination extends to TLS architecture, revealing three critical dimensions: (i) structural organization and cellular heterogeneity, (ii) developmental trajectories, and (iii) bidirectional interactions with tumor microenvironments. Crucially, we establish functional parallels between tumor-infiltrating B cells (TIL-Bs) in SLOs versus TLSs, while elucidating the differential roles of AID in canonical GC versus TLS-associated GC formation. This synthesis ultimately proposes that AID's functional dichotomy - acting as both oncogenic collaborator and tumor suppressor - underlies the paradoxical prognostic associations observed with TLS presence across malignancies. The review thereby provides a conceptual framework reconciling AID's dual functionality with the context-dependent immunobiology of tumor-associated lymphoid structures.

Chromatin and the Cellular Response to Particle Radiation-Induced Oxidative and Clustered DNA Damage

Exposure to environmental ionizing radiation is prevalent, with greatest lifetime doses typically from high Linear Energy Transfer (high-LET) alpha particles via the radioactive decay of radon gas in indoor air. Particle radiation is highly genotoxic, inducing DNA damage including oxidative base lesions and DNA double strand breaks. Due to the ionization density of high-LET radiation, the consequent damage is highly clustered wherein ≥2 distinct DNA lesions occur within 1–2 helical turns of one another. These multiply-damaged sites are difficult for eukaryotic cells to resolve either quickly or accurately, resulting in the persistence of DNA damage and/or the accumulation of mutations at a greater rate per absorbed dose, relative to lower LET radiation types. The proximity of the same and different types of DNA lesions to one another is challenging for DNA repair processes, with diverse pathways often confounding or interplaying with one another in complex ways. In this context, understanding the state of the higher order chromatin compaction and arrangements is essential, as it influences the density of damage produced by high-LET radiation and regulates the recruitment and activity of DNA repair factors. This review will summarize the latest research exploring the processes by which clustered DNA damage sites are induced, detected, and repaired in the context of chromatin.