Field, Jeffrey Michael
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Publication Targeting Hippo-YAP Signaling in Neurofibromatosis type 1 and Neurofibromatosis type 2 Tumors(2019-05-23) Yang, Yang; Field, Jeffrey MichaelNeurofibromatosis type 1 (NF1) and Neurofibromatosis type 2 (NF2) are both autosomal dominant tumor disorders that are caused by mutations in different genes. Individuals with NF1 develop neurofibromas and Malignant Peripheral Nerve Sheath Tumors (MPNSTs), while individuals with NF2 primarily develop tumors of Schwann cells. Mutations in NF1 cause hyper-activation of the RAS/RAF/MEK/ERK pathway. This pathway is one of the most commonly activated cancer signals. Inhibitors of pathway components RAF and MEK are now approved to treat melanoma, which is an aggressive form of tumor associated with NF1 mutations. Promising clinical results with the neurofibromas of NF1 patients have been reported with MEK inhibitors. However, clinical experience with melanomas show that malignant tumors become resistant to MEK inhibitors after a few months and tumors recur. Little is known about resistance to MEK inhibitors in NF1 tumors. Here, the mechanisms of adaption that occurred in the acquisition of MEK resistance by NF1 cells have been investigated to facilitate the design of long-term therapeutic strategies. Two MEK resistant NF1 cell lines were developed and screened extensively against a large variety of individual drugs and two-drug combinations to identify compensating signals. Two pathways that synergized with a MEK inhibitor were identified and examined. The first was the Hippo-YAP signaling pathway and the second was the receptor tyrosine kinase DDR1. Hippo-YAP signaling was upregulated in MEK resistant MPNST cells, suggesting a mechanism for the increased synergy of Hippo inhibitors when used in combination with MEK inhibitors and the increased expression levels of its target genes. Similarly, DDR1 was upregulated in MEK resistant cells, suggesting DDR1 expression is regulated by a common mechanism as Hippo-YAP signaling. Interestingly, the MEK resistant NF1 cells resembled NF2 cells in their appearance and their Hippo/MEK inhibitor synergy suggesting that NF1 cells become more dependent on NF2 signaling pathways when they become MEK inhibitor resistant.Publication Utilizing AI Models to Map Oxidative Damage on Telomere DNA from Oxford Nanopore Generated DNA sequence(2025-09-16) Jarrar, Sophia; Beytoughan, Zachary; Peddikuppa, Akhil; Romano, Joseph; Johnson, F. Brad; Field, Jeffrey MichaelTelomeres are long protective DNA repeats that cap each end of the chromosome and are highly vulnerable to damage from oxidative stress. The repeat contains many guanine residues, which, when oxidized, forms 8-oxo-2’-deoxyguanosine (8-oxo-dG). The presence of 8-oxo-dG causes cell apoptosis and senescence. This study aims to map these DNA adducts on telomeres using nanopore sequencing technology and AI modeling software. Telomere plasmids were amplified with oligonucleotides containing 8-oxo-dG adducts at positions along the sequence, and the resulting data were used for model training. Each sequence was “super accurately” basecalled and aligned, and the resulting datasets were utilized to create a training model that can recognize 8-oxo-dG. The training model was then given novel datasets to detect 8-oxo-dG, and Integrative Genomics Viewer (IGV) was used to visualize the model’s ability to detect 8-oxo-dG. We hypothesize that utilizing command-line interfaces with nanopore sequencing will accurately detect telomeric damage. In testing our hypothesis, we developed a workflow that involved library preparation of a training dataset, nanopore sequencing, basecalling and alignment with Dorado, and model training with Remora. Our findings suggest that neural networks can be trained to read 8-oxo-dG in nanopore data and map oxidative damage to telomere sequences at the single-nucleotide level.