Browsing by Subject "Chemosensitivity"

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Open Access
A-To-I RNA editing events, potential biomarkers for prognosis and chemosensitivity in gastric cancer
(2022-09) Çela, Isli
Gastric cancer (GC) is one of the leading causes of cancer mortality, and it frequently presents in advanced stages with a poor prognosis and response to treatment. Although extensive research has identified many potential biomarkers in GC, the heterogeneity of the disease is an impediment to validation, so only a small number find limited application in clinics. RNA editing is an epigenetic modification that results in nucleotide changes in the RNA sequence. Adenosine to Inosine (A-to-I) substitutions are the most common editing events in humans, and they are mediated by Adenosine deaminases acting on RNA (ADAR) enzymes. Inosine (I) mimics Guanosine (G) and creates pairs with Cytidine (C), resulting in changes in RNA structure and stability, amino acid substitutions, alternative splicing, or gene expression regulation via miRNA target site modifications.RNA editing dysregulations have been found in breast, lung, kidney, brain, and gastric cancers, but the utility of specific editing events as biomarkers is largely unexplored. In this study we investigate the potential of A-to-I editing events as chemosensitivity and prognostic biomarkers in GC. Across multiple datasets, our analysis shows that RNA editing events at 305 unique positions correlate with drug sensitivity measures of 17 approved chemotherapeutics in GC cell lines.The most significant editing event-drug sensitivity correlations indicate that higher editing levels are associated with higher chemosensitivity. Interestingly, the expression levels of genes with identified editing events have a weaker or no correlation with drug sensitivity, implying that editing events are biomarkers independent of transcript levels. We show that, while ADAR enzymes mediate editing events, ADAR expression levels are not interchangeable with editing frequencies as chemosensitivity biomarkers in GC. We discovered a non-synonymous editing event in the C11orf80 coding sequence, resulting in an amino acid substitution (S.p133G). Also, we identified an editing event in the 3'UTR of SOGA1 that correlates with increased SOGA1 expression. The presence of this editing site in a putative target site of miR-9-5p suggests that gene expression might be regulated by miRNA target site modifications. In the TCGA and Singapore cohorts, the prognostic role of editing events in GC was investigated. Overall, higher levels of editing are associated with better survival in GC patients. In both cohorts, we found an editing event in the CLPX gene at the position 65442098 to be an independent good prognostic factor. We chose editing events that would best categorize our patients into "High" and "Low" edited groups using the Log Rank Multiple Cut-off (LRMC) plot distribution. In each dataset, we propose two editing events, one good and one bad prognostic factor that independently correlate with survival in GC patients. In the Singapore Cohort, high editing levels in ZNF587 are associated with a good prognosis, while those in DCAF16 are associated with a poor prognosis.High editing levels in CTSB correlate with better overall survival (OS) in the TCGA cohort, while those in NUP43 correlate with worse OS. Because transcript levels do not correlate with survival, the prognostic effects of these editing events are unaffected by gene expression levels.We believe that editing levels at specific positions can be used as prognostic biomarkers in a significant way, providing a more cost-effective and applicable alternative to prognostic editing signature models. Our findings suggest that editing events could be used as independent biomarkers for chemosensitivity and prognosis in gastric cancer, however more investigation is required to elucidate the mechanisms underlying the observed relationships.
Open Access
Phenotype-based variation as a biomarker of sensitivity to molecularly targeted therapy in melanoma
(Royal Society of Chemistry, 2017) Senses, K. M.; Ghasemi M.; Akbar, M. W.; Isbilen, M.; Fallacara, A. L.; Frankenburg, S.; Schenone, S.; Lotem, M.; Botta, M.; Gure, A. O.
Transcriptomic phenotypes defined for melanoma have been reported to correlate with sensitivity to various drugs. In this study, we aimed to define a minimal signature that could be used to distinguish melanoma sub-types in vitro, and to determine suitable drugs by which these sub-types can be targeted. By using primary melanoma cell lines, as well as commercially available melanoma cell lines, we find that the evaluation of MLANA and INHBA expression is as capable as one based on a combined analysis performed with genes for stemness, EMT and invasion/proliferation, in identifying melanoma subtypes that differ in their sensitivity to molecularly targeted drugs. Using this approach, we find that 75% of melanoma cell lines can be treated with either the MEK inhibitor AZD6244 or the HSP90 inhibitor 17AAG.