An isogenic cell line panel for sequence-based screening of targeted anticancer drugs

NXPE1 alters the sialoglycome by acetylating sialic acids in the human colon

Mild periodic acid Schiff staining (mPAS) of human colonic tissue has been used to answer a variety of fundamental questions in germline and somatic genetics. mPAS stains sialic acids except when these glycans are modified by O-acetylation, but a full accounting of the genes contributing to sialoglycan acetylation is incomplete. Using haplotypes derived from whole genome sequencing, we identify a region on chromosome 11 that is associated with inherited differences in mPAS staining. Of the genes in this region, only haplotypes containing NXPE1 correlate perfectly with mPAS staining in the original cohort used for whole genome sequencing, as well as in a validation cohort. Transcriptomic analysis indicates that linked haplotypes are associated with altered expression of NXPE1 suggesting a possible genetic mechanism. Genetic manipulation of a common single nucleotide polymorphism observed in the haplotype region and located in NXPE1's promoter alters expression and causes changes to modified sialic acid levels supporting this mechanism. Finally, high-performance liquid chromatography (HPLC) confirms that enzymatically active NXPE1 is capable of transferring an acetyl group from acetyl coenzyme A to sialic acid in vitro. These findings suggest that NXPE1 is the long-sought gene responsible for differences in colon mPAS staining and may be the prototype of a new family of sialic acid O-acetylation-modifying genes.

Selective Modulation of PAR-2-Driven Inflammatory Pathways by Oleocanthal: Attenuation of TNF-α and Calcium Dysregulation in Colorectal Cancer Models

Colorectal cancer (CRC) remains a principal contributor to oncological mortality worldwide, with chronic inflammation serving as a fundamental driver of its pathogenesis. Protease-activated receptor-2 (PAR-2), a G-protein-coupled receptor, orchestrates inflammation-driven tumorigenesis by potentiating NF-κB and Wnt/β-catenin signaling, thereby fostering epithelial-mesenchymal transition (EMT), immune evasion, and therapeutic resistance. Despite its pathological significance, targeted modulation of PAR-2 remains an underexplored avenue in CRC therapeutics. Oleocanthal (OC), a phenolic constituent of extra virgin olive oil, is recognized for its potent anti-inflammatory and anti-cancer properties; however, its regulatory influence on PAR-2 signaling in CRC is yet to be elucidated. This study interrogates the impact of OC on PAR-2-mediated inflammatory cascades using HT-29 and Caco-2 CRC cell lines subjected to lipopolysaccharide (LPS)-induced activation of PAR-2. Expression levels of PAR-2 and TNF-α were quantified through Western blotting and RT-PCR, while ELISA assessed TNF-α secretion. Intracellular calcium flux, a pivotal modulator of PAR-2-driven oncogenic inflammation, was evaluated via Fluo-4 calcium assays. LPS markedly elevated PAR-2 expression at both mRNA and protein levels in CRC cells (p < 0.01, one-way ANOVA). OC administration (20-150 μg/mL) elicited a dose-dependent suppression of PAR-2, with maximal inhibition at 100-150 μg/mL (p < 0.001, Tukey's post hoc test). Concomitant reductions in TNF-α transcription (p < 0.01) and secretion (p < 0.001) were observed, corroborating the anti-inflammatory efficacy of OC. Additionally, OC ameliorated LPS-induced calcium dysregulation, restoring intracellular calcium homeostasis in a concentration-dependent manner (p < 0.01). Crucially, OC exhibited selectivity for PAR-2, leaving PAR-1 expression unaltered (p > 0.05), underscoring its precision as a therapeutic agent. These findings position OC as a selective modulator of PAR-2-driven inflammation in CRC, disrupting the pro-tumorigenic microenvironment through attenuation of TNF-α secretion, calcium dysregulation, and oncogenic signaling pathways. This study furnishes mechanistic insights into OC's potential as a nutraceutical intervention in inflammation-associated CRC. Given the variability in OC bioavailability and content in commercial olive oil, future investigations should delineate optimal dosing strategies and in vivo efficacy to advance its translational potential in CRC therapy.

Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape

Despite exciting developments in cancer immunotherapy, its broad application is limited by the paucity of targetable antigens on the tumor cell surface. As an intrinsic cellular pathway, nonsense-mediated decay (NMD) conceals neoantigens through the destruction of the RNA products from genes harboring truncating mutations. We developed and conducted a high-throughput screen, based on the ratiometric analysis of transcripts, to identify critical mediators of NMD in human cells. This screen implicated disruption of kinase SMG1's phosphorylation of UPF1 as a potential disruptor of NMD. This led us to design a novel SMG1 inhibitor, KVS0001, that elevates the expression of transcripts and proteins resulting from human and murine truncating mutations in vitro and murine cells in vivo. Most importantly, KVS0001 concomitantly increased the presentation of immune-targetable human leukocyte antigens (HLA) class I-associated peptides from NMD-downregulated proteins on the surface of human cancer cells. KVS0001 provides new opportunities for studying NMD and the diseases in which NMD plays a role, including cancer and inherited diseases.

Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape

Despite exciting developments in cancer immunotherapy, its broad application is limited by the paucity of targetable antigens on the tumor cell surface. As an intrinsic cellular pathway, nonsense-mediated decay (NMD) conceals neoantigens through the destruction of the RNA products from genes harboring truncating mutations. We developed and conducted a high throughput screen, based on the ratiometric analysis of transcripts, to identify critical mediators of NMD. This screen implicated disruption of kinase SMG1's phosphorylation of UPF1 as a potential disruptor of NMD. This led us to design a novel SMG1 inhibitor, KVS0001, that elevates the expression of transcripts and proteins resulting from truncating mutations in vivo and in vitro . Most importantly, KVS0001 concomitantly increased the presentation of immune-targetable HLA class I-associated peptides from NMD-downregulated proteins on the surface of cancer cells. KVS0001 provides new opportunities for studying NMD and the diseases in which NMD plays a role, including cancer and inherited diseases.

One Sentence Summary

Disruption of the nonsense-mediated decay pathway with a newly developed SMG1 inhibitor with in-vivo activity increases the expression of T-cell targetable cancer neoantigens resulting from truncating mutations.

CRISPR single base-editing: in silico predictions to variant clonal cell lines

Engineering single base edits using CRISPR technology including specific deaminases and single-guide RNA (sgRNA) is a rapidly evolving field. Different types of base edits can be constructed, with cytidine base editors (CBEs) facilitating transition of C-to-T variants, adenine base editors (ABEs) enabling transition of A-to-G variants, C-to-G transversion base editors (CGBEs) and recently adenine transversion editors (AYBE) that create A-to-C and A-to-T variants. The base-editing machine learning algorithm BE-Hive predicts which sgRNA and base editor combinations have the strongest likelihood of achieving desired base edits. We have used BE-Hive and TP53 mutation data from The Cancer Genome Atlas (TCGA) ovarian cancer cohort to predict which mutations can be engineered, or reverted to wild-type (WT) sequence, using CBEs, ABEs or CGBEs. We have developed and automated a ranking system to assist in selecting optimally designed sgRNA that considers the presence of a suitable protospacer adjacent motif (PAM), the frequency of predicted bystander edits, editing efficiency and target base change. We have generated single constructs containing ABE or CBE editing machinery, an sgRNA cloning backbone and an enhanced green fluorescent protein tag (EGFP), removing the need for co-transfection of multiple plasmids. We have tested our ranking system and new plasmid constructs to engineer the p53 mutants Y220C, R282W and R248Q into WT p53 cells and shown that these mutants cannot activate four p53 target genes, mimicking the behaviour of endogenous p53 mutations. This field will continue to rapidly progress, requiring new strategies such as we propose to ensure desired base-editing outcomes.