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Bulk RNA-seq of U251N orthotopic glioblastoma xenografts in athymic RNU/RNU rats before and after MRI-guided laser interstitial thermal therapy (LITT)

ABSTRACT: Laser interstitial thermal therapy (LITT) is increasingly used for deep-seated and recurrent glioblastoma, but the transcriptional state of cells that survive the sublethal thermal penumbra and seed recurrence is poorly defined. We performed bulk RNA-seq on matched primary (pre-LITT) and recurrent (post-LITT) tumors from a U251N orthotopic xenograft in athymic RNU/RNU rats treated with MRI-guided LITT. Reads were sorted into human (graft) and rat (host) streams with xengsort to isolate the human tumor transcriptome from host signal. Recurrent tumors showed a pronounced translational shutdown and integrated-stress-response activation, with a shift toward the Garofano Mitochondrial molecular subtype, nominating the translation/ISR axis as a candidate target for LITT-adjuvant therapy.

ORGANISM(S): Rattus norvegicus Homo sapiens

PROVIDER: GSE338105 | GEO | 2026/07/17

REPOSITORIES: GEO

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Project description:The goal of this study was to use global gene expression as a diagnostic tool to compare hepatic gene expression patterns in both male and female FHM in streams with the lowest and highest reproductive success, and potentially identify a suite of mRNA transcripts indicative of reproduction in a population The goal of this study was to compare differences in hepatic mRNA expression between gender at high and low egg-producing streams, not differences between individual streams. A k-means cluster analysis was performed using eggs/pair/day on the original 17 streams to delineate 3 clusters: high, medium and low. From that analysis, FHM from 6 of the original 17-streams used in Crago et al. (2010) were chosen for the microarray experiment (Fig. 1, Table 1). In this study the experimental condition is reproductive success; High versus Low reproductive success. The streams grouped into High Reproductive Success were Oak Creek-2007 (2313 eggs), Point Creek (1277 eggs), Meeme Creek (1164 eggs) and Baird Creek (967 eggs). The streams grouped into Low Reproductive Success were: Ashwaubenon Creek (0 eggs), Devils Creek (541 eggs) and Oak Creek-2006 (642 eggs). Multiple regression analysis using the 22 sediment and water quality characteristics measured in the 6 streams with the highest (n = 4 and lowest (n = 3) streams demonstrated that there were no differences amongst the streams in regards to measure sediment and water variables. .5 One array was run for each gender from each stream. So that Males from Point Creek were pooled and run on one array, males from Ashwaubenon Creek were run on a separate array, and so forth. There were 14 arrays used in this study, 7 for males, 7 for females from individual rivers. So that Males from Point Creek were pooled and run on one array, males from Ashwaubenon Creek were run on a separate array, and so forth. In the case of Oak Creek, which was sampled in both years, there was a large difference in egg production between two years. Therefore separate arrays were run for Oak Creek 2006 and Oak Creek 2007. All streams chosen had overall survival rates of at least 80% through the 21-day sampling period, except Devils River. The survival rate for Devils River was at 100% until four days prior to the end of the experiment when six fish died or escaped.

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Bulk RNA-seq of U251N orthotopic glioblastoma xenografts in athymic RNU/RNU rats before and after MRI-guided laser interstitial thermal therapy (LITT)

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