Biology subjects

Burugula, B. B.

Publications and source records attributed to Burugula, B. B..

3 recordsLinked to original sources

bioRxiv2026

Multimodal functional characterization of the LDLR noncoding landscape

The expression level of the low-density lipoprotein receptor (LDLR) gene is a critical determinant of circulating low-density lipoprotein concentrations and the corresponding risk of atherosclerotic cardiovascular disease. While the importance of sterol response elements in LDLR transcriptional regulation has been firmly established, the functional contribution of other potential cis-regulatory elements (CREs) remains poorly understood. In this study, we developed and applied a variety of high throughput functional genomic tools to systematically interrogate the noncoding space at the LDLR locus. These included saturation CRISPR nuclease, CRISPR activation, and CRISPR inhibition screening as well as a massively parallel reporter assay. With each approach, we observed robust discrimination of control sequences and significant effects for other regions with a previously unrecognized influence on LDLR expression. The CREs identified by each modality were overlapping but distinct, both in relation to each other and to those regions predicted to harbor CRE activity. Collectively, our findings clarify the functional landscape of the LDLR locus and highlight the complementary nature of different functional genomic approaches to CRE identification.

genomics↗

bioRxiv2021

Clonal hematopoiesis is driven by aberrant activation of TCL1A

A diverse set of driver genes, such as regulators of DNA methylation, RNA splicing, and chromatin remodeling, have been associated with pre-malignant clonal expansion of hematopoietic stem cells (HSCs). The factors mediating expansion of these mutant clones remain largely unknown, partially due to a paucity of large cohorts with longitudinal blood sampling. To circumvent this limitation, we developed and validated a method to infer clonal expansion rate from single timepoint data called PACER (passenger-approximated clonal expansion rate). Applying PACER to 5,071 persons with clonal hematopoiesis accurately recapitulated the known fitness effects due to different driver mutations. A genome-wide association study of PACER revealed that a common inherited polymorphism in the TCL1A promoter was associated with slower clonal expansion. Those carrying two copies of this protective allele had up to 80% reduced odds of having driver mutations in TET2, ASXL1, SF3B1, SRSF2, and JAK2, but not DNMT3A. TCL1A was not expressed in normal or DNMT3A-mutated HSCs, but the introduction of mutations in TET2 or ASXL1 by CRISPR editing led to aberrant expression of TCL1A and expansion of HSCs in vitro. These effects were abrogated in HSCs from donors carrying the protective TCL1A allele. Our results indicate that the fitness advantage of multiple common driver genes in clonal hematopoiesis is mediated through TCL1A activation. PACER is an approach that can be widely applied to uncover genetic and environmental determinants of pre-malignant clonal expansion in blood and other tissues.

genetics↗

bioRxiv2020

Massively parallel functional testing of MSH2 missense variants conferring Lynch Syndrome risk

The lack of functional evidence for the majority of missense variants limits their clinical interpretability, and poses a key barrier to the broad utility of carrier screening. In Lynch Syndrome (LS), one of the most highly prevalent cancer syndromes, nearly 90% of clinically observed missense variants are deemed "variants of uncertain significance" (VUS). To systematically resolve their functional status, we performed a massively parallel screen in human cells to identify loss-of-function missense variants in the key DNA mismatch repair factor MSH2. The resulting functional effect map is substantially complete, covering 94% of the 17,746 possible variants, and is highly concordant (96%) with existing functional data and expert clinicians interpretations. The large majority (89%) of missense variants were functionally neutral, perhaps unexpectedly in light of its evolutionary conservation. These data provide ready-to-use functional evidence to resolve the [~]1,300 extant missense VUSs in MSH2, and may facilitate the prospective classification of newly discovered variants in the clinic.

genetics↗