Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification

J Ryu, S Barkal, T Yu, M Jankowiak, Y Zhou… - Nature Genetics, 2024 - nature.com
CRISPR base editing screens enable analysis of disease-associated variants at scale;
however, variable efficiency and precision confounds the assessment of variant-induced …

Preclinical Anticipation of On-and Off-Target Resistance Mechanisms to Anti-Cancer Drugs: A Systematic Review

PJ Dziubańska-Kusibab, E Nevedomskaya… - International Journal of …, 2024 - mdpi.com
The advent of targeted therapies has led to tremendous improvements in treatment options
and their outcomes in the field of oncology. Yet, many cancers outsmart precision drugs by …

A mutational atlas for Parkin proteostasis

L Clausen, V Voutsinos, M Cagiada… - Nature …, 2024 - nature.com
Proteostasis can be disturbed by mutations affecting folding and stability of the encoded
protein. An example is the ubiquitin ligase Parkin, where gene variants result in autosomal …

Analyzing the functional effects of DNA variants with gene editing

S Cooper, S Obolenski, AJ Waters, AR Bassett… - Cell Reports …, 2024 - cell.com
Continual advancements in genomics have led to an ever-widening disparity between the
rate of discovery of genetic variants and our current understanding of their functions and …

Base editor scanning reveals activating mutations of DNMT3A

EM Garcia, NZ Lue, JK Liang, WK Lieberman… - ACS chemical …, 2023 - ACS Publications
DNA methyltransferase 3A (DNMT3A) is a de novo cytosine methyltransferase responsible
for establishing proper DNA methylation during mammalian development. Loss-of-function …

Accelerated drug-resistant variant discovery with an enhanced, scalable mutagenic base editor platform

KM Dorighi, A Zhu, JP Fortin, JHH Lo, J Sudhamsu… - Cell Reports, 2024 - cell.com
Personalized cancer therapeutics bring directed treatment options to patients based on their
tumor's genetic signature. Unfortunately, tumor genomes are remarkably adaptable, and …

Forward Genetic Screens Identify Mechanisms of Resistance to Small-Molecule Lactate Dehydrogenase Inhibitors

AR Frank, F Vandiver, DG McFadden - ACS chemical biology, 2024 - ACS Publications
Altered metabolism is a hallmark of cancer; however, it has been difficult to specifically target
metabolism in cancer for therapeutic benefit. Cancers with genetically defined defects in …

Helicase-assisted continuous editing for programmable mutagenesis of endogenous genomes

XD Chen, Z Chen, G Wythes, Y Zhang, BC Orr, G Sun… - bioRxiv, 2024 - biorxiv.org
A major challenge in human genomics is to decipher the context specific relationship of
sequence to function. However, existing tools for locus specific hypermutation and evolution …

Asymmetric Engagement of Dimeric CRL3KBTBD4 by the Molecular Glue UM171 Licenses Degradation of HDAC1/2 Complexes

MJR Yeo, O Zhang, X Xie, E Nam, NC Payne… - bioRxiv, 2024 - biorxiv.org
UM171 is a potent small molecule agonist of ex vivo human hematopoietic stem cell (HSC)
self-renewal, a process that is tightly controlled by epigenetic regulation. By co-opting …

Engineering computational single-cell and CRISPR-based functional genomics tools to study dynamic gene regulation in hematopoietic development and disease

ME Vinyard - 2024 - dash.harvard.edu
Mammalian hematopoiesis, the process by which blood cells develop from a common
progenitor cell, is evolutionarily conserved and unfolds continuously over the lifetime of an …