Biology subjects

Lam, E. Y.

Publications and source records attributed to Lam, E. Y..

3 recordsLinked to original sources

bioRxiv2024

Catalytic inhibition of KAT6/KAT7 enhances the efficacy and overcomes primary and acquired resistance to Menin inhibitors in MLL leukaemia

Understanding the molecular pathogenesis of MLL fusion oncoprotein (MLL-FP) leukaemia has spawned epigenetic therapies that have improved clinical outcomes in this often-incurable disease. Using genetic and pharmacological approaches, we define the individual and combined contribution of KAT6A, KAT6B and KAT7, in MLL-FP leukaemia. Whilst inhibition of KAT6A/B is efficacious in some pre-clinical models, simultaneous targeting of KAT7, with the novel inhibitor PF-9363, increases the therapeutic efficacy. KAT7 interacts with Menin and the MLL complex and is co-localised at chromatin to co-regulate the MLL-FP transcriptional program. Inhibition of KAT6/KAT7 provides an orthogonal route to targeting Menin to disable the transcriptional activity of MLL-FP. Consequently, combined inhibition rapidly evicts the MLL-FP from chromatin, potently represses oncogenic transcription and overcomes primary resistance to Menin inhibitors. Moreover, PF-9363 or genetic depletion of KAT7 can also overcome acquired genetic/non-genetic resistance to Menin inhibition. These data provide the molecular rationale for rapid clinical translation of combination therapy in MLL-FP leukaemia.

cancer biology↗

bioRxiv2023

BARtab & bartools: an integrated Nextflow pipeline and R package for the analysis of synthetic cellular barcodes in the genome and transcriptome

Cellular barcoding using heritable synthetic barcodes coupled to high throughput sequencing is a powerful technique for the accurate tracing of clonal lineages in a wide variety of biological contexts. Recent studies have integrated cellular barcoding with a single-cell transcriptomics readout, extending the capabilities of these lineage tracing methods to the single-cell level. However there remains a lack of scalable and standardised open-source tools to pre-process and visualise both population-level and single-cell level cellular barcoding datasets. To address these limitations, we developed BARtab, a portable and scalable Nextflow pipeline that automates upstream barcode extraction, quality control, filtering and enumeration from high throughput sequencing data; and bartools, an open-source R package that streamlines the analysis and visualisation of population and single-cell level cellular barcoding datasets. BARtab contains additional methods for the extraction and annotation of transcribed barcodes from single-cell RNA-seq and spatial transcriptomics experiments, thus extending this analytical toolbox to also support novel expressed cellular barcoding methodologies. We showcase the integrated BARtab and bartools workflow through comparison with previously published toolsets and via the analysis of exemplar bulk, single-cell, and spatial transcriptomics cellular barcoding datasets.

bioinformatics↗

bioRxiv2022

Transcription factors use a unique combination of cofactors to potentiate different promoter-dependent steps in transcription

Transcription factors use DNA binding domains to recognise specific sequences and transactivation domains to recruit the cofactor proteins necessary for transcription. However, how specific cofactors contribute to transactivation at different genes remains unclear. Here, we couple Gal4-transactivation assays with comparative CRISPR-Cas9 screens to identify the cofactors required by nine different transcription factors and nine different core promoters in human cells. We classify cofactors as ubiquitous or specific, discover novel transcriptional co-dependencies and demonstrate that submodules within large co-activator complexes, such as the tail 2 and kinase modules of Mediator, facilitate transcriptional elongation. Rather than displaying discrete mechanisms of action, we discover that each TF requires a unique combination of cofactors, which influence its ability to potentiate distinct steps in the transcriptional process. Our findings help reconcile models of cofactor-promoter compatibility by demonstrating that transcription at different classes of promoters is constrained by either initiation or pause release. These differences dictate cofactor compatibility and the dynamic range of gene expression. Overall, our screens provide insight into TF-cofactor relationships and their ability to potentiate different steps in transcription at different classes of promoters.

molecular biology↗