We previously reported that the phosphate exporter XPR1 is required to prevent toxic phosphate accumulation in ovarian cancer cells. To guide therapeutic development, we sought to systematically compare potential strategies to inhibit XPR1: directly targeting the phosphate efflux channel, targeting its partner protein...
Daniel P. Bondeson, David Husselbee, Saoirse Hanbury et al.· bioRxiv· 0 citations
DNA methylation regulates transcription, yet the demethylation of canonical elements like promoter CpG islands exhibits inconsistent correlations with gene activation. We hypothesize that causal regulatory elements are defined by biophysical hypersensitivity. Profiling 24 whole-genome bisulfite sequencing samples acros...
Y.-V. Liu, J. Suryatenggara, H. Wong et al.· Nature Communications· 0 citations
Findings indicate that the Cas12a system does not yield locus excision at the efficiency required for sensitive negative selection assays, and showed no meaningful correlation between gRNA efficiency, orientation, GC content, or cut site geometry and the success of locus excision.
N. Anvar, Zsofia M. Szegletes, R. Steger et al.· bioRxiv· 0 citations
It is demonstrated that machine learning applied to transcriptomic data can uncover novel cancer vulnerabilities and actionable targets in individual tumors, even in the absence of functional screening, which may represent a scalable approach to advance precision oncology in rare and/or under-characterized cancer types...
Ananthan Sadagopan, Bingchen Li, Jiao Li et al.· Cancer Research· 0 citations
An selective, on-target, and well-tolerated DHODH inhibitor, GLIO-1, that is effective in IDH-mutant gliomas is developed and nominated as a new pan-cancer biomarker and targeted therapy pairing, KDM6A inactivation and GLIO-1, that is poised for clinical translation.
Alexander C-Y. Tsai, Mathew D. Lin, V. Puliyappadamba et al.· Clinical Cancer Research· 0 citations
An selective, on-target, and well-tolerated DHODH inhibitor, GLIO-1, that is effective in IDH-mutant gliomas is developed and nominated as a new pan-cancer biomarker and targeted therapy pairing, KDM6A inactivation and GLIO-1, that is poised for clinical translation.
Alexander C-Y. Tsai, Mathew D. Lin, V. Puliyappadamba et al.· Clinical Cancer Research· 0 citations
CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) are two workhorse technologies for loss-of-function studies, yet direct comparisons between the two are scant relative to their widespread adoption. Here, we establish benchmarking libraries for Cas9-based CRISPRko and CRISPRi screens using Perturb-seq as the...
Laura M Drepanos, Berta Escude Velasco, Abigail J Chase et al.· bioRxiv· 1 citation
This work compares the performance of multiple KRAB domain systems, develops an updated CRISPRi-specific on-target scoring scheme, and quantitatively characterize off-target effects associated with seed-sequence patterns.
Smriti Srikanth, Fengyi Zheng, Laura M Drepanos et al.· Cell Genomics· 0 citations
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