Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Translation dysregulation in cancer as a source for targetable antigens.

ABSTRACT: We used MULTI-seq (McGinnis, Patterson, et al., Nature Methods, 2019) to perform multiplexed single-cell RNA-sequencing analysis of cryopreserved primary melanoma tumor samples isolated from mice inoculated with TYW2 WT or KO tumors. Presented data represent CD45+ immune cells isolated from both tumor backgrounds at two timepoints (D18 and D21).

ORGANISM(S): Mus musculus

PROVIDER: GSE272996 | GEO | 2024/09/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

The temporal progression of lung immune remodeling during breast cancer metastasis

Project description:The dynamics of immune reprogramming in the breast cancer lung metastastic niche remains incomplete. We used MULTI-seq (McGinnis, Patterson, et al., Nature Methods, 2019) to perform multiplexed single-cell RNA-sequencing analysis of cryopreserved lung immune cells isolated from PyMT mice, freshly-isolated lung immune cells isolated from PyMT mice, and cryopreserved lung immune cells isolated from 4T1 tumor-bearing mice from the onset of primary tumorigenesis through the formation of macrometastatic lesions. Cryopreserved PyMT samples were collected from 6-14 weeks of age, fresh PyMT samples were collected at 6, 10 and 13 weeks of age (with age-matched wild-type controls)

2024-04-22 | GSE263963 | GEO

Noncoding regions are the main source of targetable tumor-specific antigens

Project description:Purpose: Tumor-specific antigens (TSAs) represent ideal targets for cancer immunotherapy, but very few of them have been identified. Therefore, the goal of this study was to develop a novel approach, combining RNA-Sequencing and mass spectrometry, to enlarge the landscape of actionable TSAs in seven human primary samples, namely 4 B-ALL and 3 lung tumor biopsies. Methods: We performed RNA-Sequencing on each primary tumor sample (unreplicated) with the Illumina HiSeq200. Using those RNA-Sequencing data to build a global cancer database for each sample, we performed a transcriptomic-informed mass spectrometry analysis of their MHC I-associated peptides to identify TSAs. Results: We identified a total of 30 TSAs, 90% of which derived from allegedly non-coding regions and would have been missed by standard approaches. Moreover, most of these TSAs derived from non-mutated yet cancer-restricted transcripts that can be shared by multiple tumors. Conclusions: In conclusion, the strategy reported herein is readily applicable to human tumors and should considerably enlarge the landscape of actionable TSAs.

2019-11-20 | GSE127825 | GEO

Fetal lung development

Project description:Fetal lung development is a complex biological process, which involves temporal and spatial regulations of many genes. To understand molecular mechanisms of this process, we investigated gene expression profiling of lungs at gestational day 18, 19, 20, 21, new born, and adult rats using in-house rat DNA microarray containing 6,000 known genes and 4,000 ESTs. 1,512 genes passed SAM test and 583 genes (402 known genes and 181 ESTs) had a 2-fold change at least at one time point. K-means cluster analysis revealed 7 major expression patterns. Furthermore, using GeneMapp, we identified 3 regulatory pathways: TGF beta signaling pathway, cell cycle, and G-protein signaling; and 2 metabolism pathways: proteasome degradation and glycolysis. Our results suggest a complex regulatory pathway for fetal lung development. Loop Design as following: D18-D19-D20-D21-NB-AD-D18

2010-07-01 | E-GEOD-3302 | biostudies-arrayexpress

Whole-genome resequencing of wildtype and EMS-treated fission yeast Schizosaccharomyces pombe

Project description:This experiment aims at analyzing crossover distribution genome-wise, in the fission yeast. S. pombe strains PR109 (h- leu1-32 ura4-D18) and PR110 (h+ leu1-32 ura4-D18) were used for three successive rounds of mutagenesis with Ethylmethane Sulfonate Mutagenesis. Five independent clones of the first round of mutagenesis were at the root of two subsequent similar rounds of mutagenesis. Each clone used was checked for its ability to mate and sporulate. Eventually, five mutagenized clones from each of the PR109 and PR110 backgrounds were sequenced to identify de novo mutations and determine the optimal combinations of mutation patterns for recombination analyses.

2023-03-03 | E-MTAB-12514 | biostudies-arrayexpress

Translation dysregulation in cancer as a source for targetable antigens.

Project description:Translation dysregulation in cancer as a source for targetable antigens.

| PRJNA1139766 | ENA

Noncoding regions are the main source of targetable tumor-specific antigens

Project description:Noncoding regions are the main source of targetable tumor-specific antigens

| PRJNA525590 | ENA

Whole-genome resequencing of 90 tetrads of EMS-treated fission yeast Schizosaccharomyces pombe

2023-03-03 | E-MTAB-12516 | biostudies-arrayexpress

Methylation changes occurring in early postnatal liver development

Project description:Genomic DNA is isolated from C57BL6/J mice at E17.5 and postnatal d21, and we used MCAM to identify genes undergoing methylation change during late fetal to early postnatal mouse liver development.

2009-04-15 | GSE15634 | GEO

MEK inhibition enhances presentation of targetable MHC-I tumor antigens in mutant melanomas.

Project description:Combining multiple therapeutic strategies in NRAS/BRAF mutant melanoma-namely MEK/BRAF kinase inhibitors, immune checkpoint inhibitors (ICIs), and targeted immunotherapies-may offer an improved survival benefit by overcoming limitations associated with any individual therapy. Still, optimal combination, order, and timing of administration remains under investigation. Here, we measure how MEK inhibition (MEKi) alters anti-tumor immunity by utilizing quantitative immunopeptidomics to profile changes in the peptide major histocompatibility molecules (pMHC) repertoire. These data reveal a collection of tumor antigens whose presentation levels are selectively augmented following therapy, including several epitopes present at over 1,000 copies per cell. We leveraged the tunable abundance of MEKi-modulated antigens by targeting four epitopes with pMHC-specific T cell engagers and antibody drug conjugates, enhancing cell killing in tumor cells following MEK inhibition. These results highlight drug treatment as a means to enhance immunotherapy efficacy by targeting specific upregulated pMHCs and provide a methodological framework for identifying, quantifying, and therapeutically targeting additional epitopes of interest.

| S-EPMC9894220 | biostudies-literature

Transcriptomic analysis of PHHs isolated from hCLiP-transplanted mouse chimeric liver

Project description:Transcriptome of PHHs isolated from hCLiP-transplanted mouse chimeric liver was compared with those of cryopreserved PHHs.

2019-07-04 | GSE133779 | GEO