Biology subjects

Denny, N.

Publications and source records attributed to Denny, N..

4 recordsLinked to original sources

bioRxiv2026

Single-cell CRISPR activation screens in primary B cells discover gene regulatory mechanisms for hundreds of autoimmune risk loci.

Genome-wide association studies (GWAS) have discovered thousands of genetic variants linked to autoimmune disease, and yet the molecular pathways underlying autoimmunity have remained elusive. A key challenge is that >90% of identified GWAS risk loci are in non-coding genomic regions making it difficult to predict their relevance to disease. Here, we have curated fine-mapped non-coding risk variants from over 30 different autoimmune traits including common conditions such as systemic lupus erythematosus (SLE), Crohns disease, and multiple sclerosis, and reveal shared genetic signatures between diverse autoimmune diseases. We subsequently performed a high-throughput single-cell multi-omic CRISPR activation screen targeting 763 autoimmune risk loci in primary human B cells (a highly relevant cell type to autoimmune diseases) and discover 524 cis-regulatory target gene effects for 378 risk loci, with many risk loci regulating multiple gene targets. This Single Cell Analysis of Non-coding Distal Autoimmune Loci (SCANDAL) provides a powerful experimental resource linking non-coding risk loci to many disease-relevant genes, including lowly-expressed cytokines and transcription factors for which perturbation effects can be difficult to quantify with other CRISPR-based strategies. We reveal how increased transcriptional activity at one non-coding risk locus can drive transcription at other risk loci within the same regulatory landscape that may be relevant to understand genetic pleiotropy of autoimmune diseases. Finally, we quantified allele-specific effects on target gene expression with massive parallel reporter assays and prime editing to discover a gain-of-function variant associated with SLE that controls expression of the transcription factor REL/cREL which subsequently binds dozens of risk loci and target genes associated with different autoimmune diseases. Our study provides a valuable resource linking non-coding risk loci with their cis-regulatory target genes and advances our understanding of the shared genetic networks and mechanisms involved in autoimmunity.

genomics↗

bioRxiv2026

Menin maintains enhancer-promoter interactions in a leukemia-specific manner

Inhibition of the protein-protein interaction between Mixed Lineage Leukemia (MLL) and Menin is a promising therapy for both high-risk MLL-rearranged and NPM1-mutant (NPM1c) acute leukemias, yet the mechanistic basis of this dependency in distinct contexts remains unclear. By comparing the transcriptional responses of MLL::AF4 and NPM1c leukemia models to Menin inhibition, we find broad, acute transcriptional dysregulation in MLL::AF4 cells, but minor transcriptional consequences in NPM1c cells, despite similarities in Menin promoter occupancy. Using high-resolution Micro Capture-C, we discover that Menin drives enhancer activity and maintains enhancer-promoter contacts in MLL::AF4 cells but not in NPM1c cells. Crucially, Menin is also essential for patient-specific enhancer function in primary MLL-rearranged leukemia samples. Proteomic analysis further demonstrates that Menin associates with distinct transcriptional and elongation complexes in MLL::AF4 compared to NPM1c cells, supporting a context-dependent mechanism of action. Together, these findings establish that Menin is not a uniform transcriptional cofactor, but a context-dependent regulator of enhancer connectivity, and identifies enhancer-promoter architecture as a selective vulnerability in MLL-rearranged leukemia.

cancer biology↗

bioRxiv2025

Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions

Transcription factors (TFs) are key effectors of enhancer activity. MYB is a critical hematopoietic TF that is frequently dysregulated in cancer. Despite its well-established role, the exact mechanisms by which MYB influences enhancer function--and the specific stages of enhancer activation at which it operates--remain poorly understood. Using high resolution Micro-Capture-C, we show that upon MYB degradation, highly defined enhancer-promoter interactions at specific MYB binding sites are lost. Loss of these interactions, together with other hallmarks of enhancer activity--reduced H3 lysine-27 acetylation and enhancer RNA transcription--correlates with significant downregulation of target gene expression in leukemia, indicating that MYB mediates transcription activation via maintenance of enhancer function. When anchored to DNA within a gene desert region that is devoid of histone marks and active transcription, the MYB transactivation domain is sufficient and necessary for the nucleation of an enhancer-like region. This results in the activation of transcription from distal cryptic elements and the establishment of long-range chromatin interactions up to 400 kb away from the anchor point. Together, these results indicate that MYB activity alone is sufficient to induce long-range interactions and transcription, achieving this through highly precise enhancer-promoter crosstalk.

genomics↗

bioRxiv2024

Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression between patients

Genetic alterations alone cannot account for the diverse phenotypes of cancer cells. Even cancers with the same driver mutation show significant transcriptional heterogeneity and varied responses to therapy. However, the mechanisms underpinning this heterogeneity remain under-explored. Here, we find that novel enhancer usage is a common feature in acute lymphoblastic leukemia (ALL). In particular, KMT2A::AFF1 ALL, an aggressive leukemia with a poor prognosis and a low mutational burden, exhibits substantial transcriptional heterogeneity between individuals. Using single cell multiome analysis and extensive chromatin profiling, we reveal that much transcriptional heterogeneity in KMT2A::AFF1 ALL is driven by novel enhancer usage. Using high resolution Micro-Capture-C in primary patient samples, we also identify patient-specific enhancer activity at key oncogenes such as MEIS1 and RUNX2, driving high levels of expression of both oncogenes in a patient-specific manner. Overall, our data show that enhancer heterogeneity is highly prevalent in KMT2A::AFF1 ALL and may also be a mechanism that drives transcriptional heterogeneity in cancer more generally. Key PointsO_LILeukemia patients with the same driver mutations often display gene expression differences C_LIO_LIUsing chromatin profiling and high resolution 3C methods we show that enhancer heterogeneity drives gene expression differences C_LI

cancer biology↗