Dinis Pedro Calado

Genome stability depends on the accurate repair of DNA double-strand breaks (DSBs). While chromatin-based mechanisms have been well studied, emerging evidence reveals that nuclear mechanics actively shape repair outcomes, although the mechanisms remain unclear. Here we identify microtubule acetylation as a regulator of nuclear mechanics that promotes DSB repair via homologous recombination (HR). DNA damage induces progressive tubulin acetylation, leading to displacement of the perinuclear vimentin cage. Loss of the vimentin cage softens the nucleus and renders the nuclear envelope responsive to microtubule forces, which drives transient nuclear shape fluctuations, localized DSB mobility and repair. Inhibiting tubulin acetylation abolishes these fluctuations, restricts DSB mobility and negatively impacts the homology search during HR, leaving non-homologous end joining intact. Consequently, persistent DSBs coalesce and cluster at the nuclear periphery, triggering cell-cycle arrest and senescence and increasing sensitivity to DNA-damaging agents. Removal of the vimentin cage is sufficient to rescue these effects, with restored nuclear fluctuations and repair efficiency. Thus, we propose that nuclear fluctuations act as a mechanical strategy to accelerate error-free repair. These findings reveal how cytoskeletal forces shape nuclear function and establish nuclear fluctuations as a fundamental principle for maintaining genome stability.

Summary: Germinal centers (GCs) support physiological B-cell mutagenesis and are considered lymphoma-permissive; nevertheless, lymphoma development is uncommon. Human in situ follicular neoplasia (ISFN) captures this paradox: premalignant B-cells can persist within GCs for prolonged periods without progressing to overt lymphoma. We found that human ISFN, but not normal GCs, are infiltrated by CD8⁺ T-cells, suggesting that premalignant GC B-cells are locally immune-surveilled. Using mouse models that separate early premalignant fitness from lymphoma-associated evolution, we show that fitness-enhanced premalignant GC B-cells expand transiently but are selectively eliminated by infiltrating cytotoxic CD8⁺ T-cells, while normal GC B-cells are spared. By contrast, evolved premalignant GC B-cells retain their fitness but disable productive CD8⁺ T-cell cytotoxic differentiation, allowing persistence and lymphoma-like transcriptional and genomic evolution. These findings establish GCs as active immune-surveillance sites and show that progression from premalignancy to lymphoma requires both enhanced GC fitness and escape from local immune control. Key findings: GCs undergo active immune-surveillance to detect premalignant B-cells. Premalignant GC B-cells trigger cytotoxic CD8⁺ T-cell responses. Lymphoma-associated evolution enables immune-escape within GCs. Fitness and immune-escape drive evolution from premalignancy to lymphoma. Blurb: Germinal centers are considered lymphoma-permissive; however, progression from premalignancy is uncommon. Using models of human in situ follicular neoplasia, Zhang et al. demonstrate that infiltrating CD8⁺ T-cells actively eliminate premalignant GC B-cells. Co-occurrence of lymphoma-like alterations blocks this cytotoxic T-cell response, driving immune escape and lymphoma evolution.

Follicular lymphoma (FL) is an incurable, prototypical relapse-remitting cancer, implying the existence of therapy-persistent cells that survive frontline treatment and seed disease recurrence1-3. However, these persister cells remain difficult to study directly in patients because immediate post-treatment sampling is ethically and practically challenging. Using a genetically defined mouse model that allows sampling of persistent cells immediately after frontline R-CHOP therapy, we prospectively isolate and functionally define relapse-founding cancer persister cells (CPC). The CPC is an IgM⁺ memory-like B-cell with high germinal center re-entry capacity. This state represents a discrete component of a heterogeneous residual pool indicating that residual disease is polytypic and that relapse potential may depend on which cells persist rather than on residual tumour burden alone. By integrating mouse CPC with human FL datasets, we show that an analogous transcriptional programme is detectable at diagnosis and is enriched in patients with inferior clinical outcome across independent cohorts4,5. These findings support the concept that relapse risk is linked to a conserved, genotype-agnostic CPC programme present before therapy. To explore therapeutic vulnerabilities, we developed a scalable in-vitro platform that models the CPC-like state and used it to identify sensitivity to histone deacetylase inhibition. Romidepsin and panobinostat killed CPC-like cells in-vitro, and decreased therapy-persistent cells after R-CHOP treatment in-vivo and in patient-derived organoids. Together, these data define a tractable CPC state in FL, with a validated clinical readout and an immediately testable therapeutic entry point, opening CPC-directed strategies for durable FL control.

Booster vaccination can restore antibody titres and protection, but whether it improves long-term durability by expanding plasma cell (PC) numbers or also by shifting PC fate toward intrinsically longer-lived states remains unclear. Here we established longitudinal in vivo ground truth for PC persistence by combining PC-specific genetic timestamping, clonal tracking, and multi-timepoint single-cell profiling across spleen and bone marrow. We resolved PC longevity as a layered, non-binary architecture comprising short-, intermediate-, and long-lived programs, and showed that program identity is specified early in secondary lymphoid tissues and largely maintained as PCs populate bone marrow niches. Primary vaccine responses initiated from naive B-cells generated a prominent intermediate-lived wave, whereas memory B-cell recall during boosting redistributed output toward long-lived programs rather than recreating the intermediate-lived compartment characteristic of priming. Conserved longevity signatures projected onto early circulating PCs provide a cross-species framework to infer durability programs, supporting benchmarking of vaccine regimens by predicted persistence rather than peak titres.

How plasma cells (PCs) shape anti-tumor immunity is unclear. We hypothesized that conflicting prognostic associations reflect differences in immune context and PC ontogeny. We identify extrafollicular (EF)-PCs as an antibody-independent checkpoint that aborts priming by disabling the cDC1→CD8 ⁺ T-cell axis in tumor-draining lymph nodes (td-LNs). EF-PCs blunt cDC1 activation and CCR7-guided repositioning into T-cell zones, precluding formation of TCF1⁺ stem-like CD8⁺ T-cells. Depleting EF-PCs in vivo restores cDC1 trafficking, expands the stem-like reservoir, increases intratumoral CD8⁺ infiltration, and restrains tumor growth; benefit is lost with CD8 T-cell ablation. Neither serum transfer nor Fcγ receptor blockade reverses tumor control, supporting a non-canonical, antibody-independent mechanism. Across independent triple-negative breast cancer cohorts, we find EF-PC hyperplasia in td-LNs and tumors; and within immune-cold cases, EF-PC burden stratifies poor prognosis and metastatic risk. A cross-species EF-PC signature maps to a conserved PC-state across cancer types that is linked to poor outcome and immune-checkpoint blockade resistance. EF-PCs thus relocate the dominant failure point to td-LNs and offer a tractable upstream target to convert immune-cold tumors into immune-responsive disease.

Immunotherapy has transformed cancer treatment, including early triple-negative breast cancer (TNBC), yet most patients with advanced TNBC fail to respond to immune checkpoint blockade (ICB) plus chemotherapy. Durable control likely requires not only tumour cell killing but also immunogenic cell death (ICD) that activates antitumour immunity. Using a Brca1 ^⁻/⁻ p53 ^⁻/⁻ organoid-derived TNBC model that recapitulates the immune landscapes of basal-like tumours, we show that RIPK1-driven ICD synergises with anti-PD-1 therapy to induce durable tumour control and immune memory in immune-infiltrated tumours. Mechanistically, both tumour-intrinsic and stromal necroptosis are required. Deletion of Ripk1 or Mlkl in tumour cells, or Mlkl in the stromal compartment, markedly impairs therapeutic efficacy. Moreover, immunologically “cold” tumours can be rendered responsive to ICD-based therapy by STING agonists. These findings demonstrate that the benefit of IAP antagonism with checkpoint blockade critically depends on coordinated necroptosis in both tumour and stromal cells, underscoring the need to integrate tumour microenvironmental context when designing ICD-targeted immunotherapies.

Table S4 contains the individual mutations of PPMBC and MBC lymphomas.

Table S6 contains clinical parameters and sequencing results of human DLBCL samples.

Table S3 contains B cell receptor repertoire sequencing data and lists the individual sublcones of the dominant clones of MBC, SMBC and PPMBC lymphomas.

Table S1 contains the p values of comparisons of the V gene usage in non-malignant GC B cells between the individual genotypes. These comparisons were done on the family, gene and allele level. V usage was compared for all BCR sequences as well as for isotype subsets.