ABSTRACT
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
ABSTRACT
High-throughput CRISPR-Cas9 knockout screens using a tiling-sgRNA design permit in situ evaluation of protein domain function. Here, to facilitate de novo identification of essential protein domains from such screens, we propose ProTiler, a computational method for the robust mapping of CRISPR knockout hyper-sensitive (CKHS) regions, which refer to the protein regions associated with a strong sgRNA dropout effect in the screens. Applied to a published CRISPR tiling screen dataset, ProTiler identifies 175 CKHS regions in 83 proteins. Of these CKHS regions, more than 80% overlap with annotated Pfam domains, including all of the 15 known drug targets in the dataset. ProTiler also reveals unannotated essential domains, including the N-terminus of the SWI/SNF subunit SMARCB1, which is validated experimentally. Surprisingly, the CKHS regions are negatively correlated with phosphorylation and acetylation sites, suggesting that protein domains and post-translational modification sites have distinct sensitivities to CRISPR-Cas9 mediated amino acids loss.
Subject(s)
Computational Biology/methods , Protein Domains/genetics , Algorithms , CRISPR-Cas Systems/genetics , Cell Line, Tumor , Datasets as Topic , Gene Knockout Techniques , High-Throughput Screening Assays , Humans , Models, Genetic , Protein Processing, Post-Translational/genetics , RNA, Guide, Kinetoplastida/genetics , SMARCB1 Protein/genetics , SoftwareABSTRACT
BACKGROUND: The rising cost of healthcare requires responsible allocation of resources. Not all trauma centers see the same types of patients. We hypothesized that patients with blunt injuries require more resources than patients with penetrating injuries. METHODS: This was a retrospective analysis of all highest-level activation trauma patients at our busy urban Level I Trauma Center over five years. Data included demographics, injuries, hospital charges, and resources used. A p valueâ¯<â¯0.05 was significant. RESULTS: 4578 patients were included (2037 blunt and 2541 penetrating). Blunt patients were more severely injured, more often admitted, required more radiographic studies, had longer hospital, intensive care unit, and mechanical ventilation days, and therefore, higher hospital charges. CONCLUSIONS: Within one center, patients with blunt injuries required more resources than those with penetrating injuries. Understanding this pattern will allow trauma systems to better allocate limited resources based on each center's mechanism of injury distribution.
