Ari M. Melnick

Constitutive activation of the B-cell receptor (BCR) pathway drives non-Hodgkin lymphomas. MALT1 is a key mediator of NF-κB signaling downstream of B- and T-cell receptors. Herein, we report development of safimaltib (JNJ-67856633), a selective, allosteric inhibitor of MALT1 protease. The crystal structure of safimaltib bound to MALT1 was determined, and enzyme kinetic studies were performed to characterize its inhibitory mechanism. Sub-micromolar doses of safimaltib inhibited growth of diffuse large B-cell lymphoma (DLBCL) and mantle cell lymphoma (MCL) cell lines with activation of NF-κB signaling and models mimicking BTK inhibition resistance. Notably, activating mutations in BCR-pathway components were strongly associated with safimaltib response in vitro. Safimaltib demonstrated efficacy in DLBCL and MCL mouse models and synergy with a BTK inhibitor. Safimaltib was well tolerated in preclinical immunocompetent animal models with a safety profile supporting MALT1 targeting in humans. Overall, these results provide rationale for the first-in-human MALT1 inhibitor clinical trial.

The BAF (also known as mammalian SWI/SNF) chromatin remodelling complexes are essential regulators of nucleosome positioning and transcription factor binding ^1,2 . Loss-of-function (LOF) mutations in genes encoding components of the BAF complexes are among the most frequent across cancer types ³ . However, a unifying mechanism that explains their widespread disruption remains unclear. Here we disrupted BAF function through pharmacological inhibition and ARID1A deletion across various mammalian cell types and tissues and observed a conserved chromatin response: increased accessibility at CTCF-binding sites. ARID1A LOF alone was sufficient to drive these changes, which demonstrates that canonical BAF (cBAF) disruption is the key driver of CTCF gain. Genomic profiling showed increased CTCF and SMC3 occupancy, which reveals an antagonistic relationship between cBAF and CTCF–cohesin complexes. Furthermore, cBAF loss restructured 3D genome organization, which led to a strengthening of topologically associating domain boundaries and subdivision of large domains into smaller insulated structures. Long-range enhancer–promoter loops were replaced by shorter, promoter-proximal loops anchored at CTCF-enriched sites. To determine how CTCF function is enabled following cBAF loss, we profiled CTCF-interacting cofactors and found that CTCF binds directly to fully assembled PBAF. After cBAF depletion, PBAF was recruited to sites of increased CTCF occupancy, which demonstrates that there is an antagonistic switch between SWI/SNF subcomplexes. In vivo, conditional Arid1a deletion in primary mouse cells resulted in the expansion of a highly proliferative population marked by elevated accessibility at CTCF sites. This phenotype was fully reversed by either Ctcf or Pbrm1 deletion, which establishes that cBAF and the activity of CTCF and PBAF have contrasting roles.

Here we present DynaVelo, a generative neural ordinary differential equation model that learns the joint dynamics of gene expression and transcription factor (TF) motif activity from single-cell multiome data. DynaVelo learns a functional form of the vector field, such that the model can be perturbed in silico and not only used to draw trajectories. We show that DynaVelo recovers the bifurcating in vivo dynamics of wild-type murine germinal center (GC) B cells and reveals how these dynamics change under heterozygous loss of epigenetic regulators Arid1a and Ctcf . In silico perturbation yields dynamic and cell-state-specific gene regulatory networks (GRNs) that recover known TF-to-gene edges in the wild-type GC GRN and predicts those that are disrupted in mutants. Perturbing Arid1aHet GCs in silico identified Ctcf , Stat3 and Bcl6 as rescue targets for Arid1a loss. In vivo experiments in double-heterozygous mice confirmed rescue of the Arid1aHet dark-zone phenotype in all three cases, and multiome profiling of Arid1aHet ; CtcfHet GCs validated the predicted shift toward wild-type dynamics.

Table S1 shows Overlap of differential regulated genes in EZH2high vs EZH2low and EZH2i vs vehicle of EZH2high cells comparisons identifies 12 common genes.

Supplementary Figure S1 shows correlation of EZH2 gene expression with FGA in METABRIC and TCGA breast cancer cohort suggests a link between EZH2 and CIN. Supplementary Figure S2 shows correlation between fraction genome altered (FGA) and EZH2 gene expression in TCGA LUAD cohort. Supplementary Figure S3 shows increased CIN in various TNBC, non-TNBC and and RPE1 cells and impact of EZH2 inhibition. Supplementary Figure S4 shows EZH2 inhibition and cell cycle analysis. Supplementary Figure S5 shows CUT & RUN seq and RNA-seq analysis. Supplementary Figure S6 shows visualization and experimental validation of EZH2 target genes. Supplementary Figure S7 shows EZH2 mediated TNKS regulates CIN. Supplementary Figure S8 shows multipolar mitosis and supernumerary centrosome analysis of the TNKS KO cells. Supplementary Figure S9 shows correlation of EZH2, CPAP and aneuploidy and effect of EZH2 inhibition on CPAP expression and cell cycle analysis of TNKSWT and TNKSKO LM2 cells. Supplementary Figure S10 shows impact of CIN modulation on proliferation and metastatic progression in EZH2 WT and EZH2 KO cells.

Supplementary materials include materials and methods, supplementary Figure S1 to S10, figure legends and references.

DNA replication fidelity depends on the integrity of the replication fork to prevent DNA damage and preserve genome stability. Disruptions to this process can trigger replication stress, leading to the accumulation of single-strand DNA (ssDNA) and double-strand breaks (DSBs), which drive mutagenesis and ultimately contribute to disease. While the roles of core histones and their post-translational modifications in this context have been more well-studied, far less is known about how linker histones regulate the replication stress response. Here, we demonstrate that the S-phase–phosphorylated form of the linker histone H1 (pH1) plays a key role in DNA damage repair at collapsed replication forks, both in vitro and in cells. Using phosphomimic and phosphonull H1 mutants, we show that phosphorylation enhances H1 assembly with ssDNA. Utilizing intein chemistry for the site-specific incorporation of a photocrosslinker to the C-terminus of H1, we map the direct interactors of H1. We identify phosphorylated H1 at replication forks, where it engages replication machinery and DNA damage response factors, including Histone PARylation Factor 1 (HPF1). We further demonstrate that ssDNA induces pH1-HPF1 interactions that promote liquid-like assemblies, correlating with reduced DNA damage and histone PARylation. Consistent with this role, reduction of total H1 increases cellular sensitivity to DNA damage, a phenotype that is partially rescued by reintroduction of H1.4. Together, these findings establish pH1 as a new regulator of DNA damage repair at collapsed replication forks through the controlled sequestration of repair factors.

Combined SpenLOF and Notch2GOF mutations induce formation of a non-canonical AiBC with MZB features.

Combined SpenLOF and Notch2GOF mutations lead to increased fitness of female AiBC.