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Waite, K.

Publications and source records attributed to Waite, K..

2 recordsLinked to original sources

The MIF SNP rs755622 is a germline determinant of tumor immune activation in Glioblastoma

While immunotherapies have shown durable responses for multiple tumors, their efficacy remains limited in some advanced cancers, including glioblastoma. This may be due to differences in the immune landscape, as the glioblastoma microenvironment strongly favors immunosuppressive myeloid cells, which are linked to an elevation in immune-suppressive cytokines, including macrophage migration inhibitory factor (MIF). We now find that a single-nucleotide polymorphism (SNP) rs755622 in the MIF promoter associates with increased leukocyte infiltration in glioblastoma. Furthermore, we identified lactotransferrin expression as being associated with the rs755622 SNP, which could also be used as a biomarker for immune infiltrated tumors. These findings provide the first example in glioblastoma of a germline SNP that underlies differences in the immune microenvironment and identifies high lactotransferrin as a potential factor promoting immune activation.

cancer biology↗

Inference of CRISPR Edits from Sanger Trace Data

Efficient precision genome editing requires a quick, quantitative, and inexpensive assay of editing outcomes. Here we present ICE (Inference of CRISPR Edits), which enables robust analysis of CRISPR edits using Sanger data. ICE proposes potential outcomes for editing with guide RNAs (gRNAs) and then determines which are supported by the data via regression. Additionally, we develop a score called ICE-D (Discordance) that can provide information on large or unexpected edits. We empirically confirm through over 1,800 edits that the ICE algorithm is robust, reproducible, and can analyze CRISPR experiments within days after transfection. We also confirm that ICE strongly correlates with next-generation sequencing of amplicons (Amp-Seq). The ICE tool is free to use and offers several improvements over current analysis tools. For instance, ICE can analyze individual experiments as well as multiple experiments simultaneously (batch analysis). ICE can also detect a wider variety of outcomes, including multi-guide edits (multiple gRNAs per target) and edits resulting from homology-directed repair (HDR), such as knock-ins and base edits. ICE is a reliable analysis tool that can significantly expedite CRISPR editing workflows. It is available online at ice.synthego.com, and the source code is at github.com/synthego-open/ice

bioinformatics↗