Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Allele imbalance in Reps1 and Adpgk

ABSTRACT: Effective anti-cancer immunity is associated with the presence of T cells directed at potentially immunogenic tumor neoantigens arising from tumor-specific mutation. We confirmed the expression of reported MC38 neoantigens (Nature 515: 572, 2014). MC38 cells in our laboratory had the same point mutation at amino acid position 299 in Adpgk (ASMTN[R/M]ELM), but did not have a point mutation at amino acid position 42 in Reps1 (AQL[P/A]NDVVL). The allele frequency of mutated Adpgk (ASMTNMELM) was 30%.

ORGANISM(S): Mus musculus

PROVIDER: GSE126280 | GEO | 2019/02/13

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

K120R mutation inactivates p53 by creating an aberrant splice site leading to nonsense-mediated mRNA decay

Project description:The point mutation that substitutes lysine with arginine at position 120 of human p53 has been characterized as a missense mutation. The K120R mutation renders the p53 protein disabled for acetylation and, as a result, defective for apoptotic function, which provides a mechanistic link between the missense mutation and tumorigenesis. However, we noticed the failures of tumorigenesis in mice with the mutation, and of the related studies to notice that it has arbitrarily reflected in amino acid change through a sequence modification (AGA) of the original tumor mutation (AGG) by codon degeneracy. Unlike this modified version, we also discovered a novel splicing site the original mutation, TP53 c.359A>G, may induce. Using a human induced pluripotent stem cell line that was engineered to be homozygous for the original mutation, we here identified that the accidental splicing site generates a defective transcript variant with a frame-shifted premature termination codon which is subjected to nonsense-mediated mRNA decay. The authentic splicing still occurs but in extremely low amounts. Taken together, this mutation causes depletion of cellular p53 via defective mRNA, suggesting a new link to tumorigenesis.

2018-09-14 | GSE119891 | GEO

A single N66S mutation in the PB1-F2 protein of influenza A virus increases virulence by inhibiting the early interferon response in vivo

Project description:This study used virological, histological, and global gene expression from an experimental murine model of influenza infection to study the contribution of a specific mutation in the PB1-F2 protein (PB1-F2 N66S) of influenza A to viral pathogenesis. 6-8 week old, wild-type, female, C57Bl/6 mice were inoculated individually with 30 μl (10^4 PFU) of virus (recombinant influenza A/WSN/33 carrying the PB1 gene segment from A/Hong Kong/156/97 (H5N1) or a PB1 mutant recombinant virus resulting in an amino acid change at position 66 in the PB1-F2 protein [N66S]) in phosphate-buffered saline (PBS) containing penicillin-streptomycin and bovine serum albumin (PBS-BA-PS). A total of 10^4 PFU of virus was given in all inoculations. Control mice were given PBS-BA-PS. Lung samples were taken for microarray analysis at 12h, 1d, 3d, and 5d post-infection (n=3 animals per group at each time point for virus infected animals; n=2 animals per time point for mock-infected animals).

2012-02-20 | E-GEOD-35940 | biostudies-arrayexpress

Intracellular expression of a chimeric antigen reverses resistance to cancer immunotherapy

Project description:The interaction of frameshift mutation-derived cancer neoantigens and cancer immunotherapy remains unknown. We found that live cell adjuvant or cDNA transfection in the muscle, which express MHC-class I and class II-restricted non-self-peptides, generated broad-spectrum anti-tumor immunity. Such chimeric peptides did not need to be tumor-neoantigens, but must be in a single chain (complete T cell antigen: CTA). Long product of frameshift mutation frequently contained CTA and the colon cancer patients with the long frameshift products (>120 amino acids) showed a good prognosis. Mechanistically, live cell adjuvant expressing CTA strengthened crosstalk between dendritic cells and CD8+ T cells in a CD4+ T cells-dependent manner. This cross talk suppressed CD8+ T cell exhaustion and produced stem-cell like progenitor CD8+ T cells in vivo. Combination of the live cell adjuvant conversed unresponsive tumors to responsive to PD-1 blockade therapy. Together, our findings provide a new broad-spectrum cancer immunotherapy, and clarify the type of frameshift neoantigens controlling the efficacy.

2024-10-16 | GSE245743 | GEO

Transcriptome anaylisis of WT and GFAT-1 G451E engineered N2a cells by RNA-Seq

Project description:Transcriptome of N2a cells carrying a GFAT-1 gain-of-function point mutation that results in a G451E amino acid substitution were compared to WT N2a transcriptome profiles. Three replicates of both cell lines were analyzed. Additionally WT N2a cells were treated with 10 mM GlcNAc for 24h prior to transcriptome analysis resulting in a third dataset with 3 replicates.

2019-11-14 | GSE140357 | GEO

Brain transcriptome of hereditary cerebral haemorrhage with amyloidosis–Dutch type (HCHWA-D)

Project description:HCHWA-D is an early onset hereditary form of Cerebral Amyloid Angiopathy (CAA) caused by a point mutation resulting in an amino acid change (NP_000475.1:p.Glu693Gln) in the Amyloid Precursor Protein (APP). Post-mortem brain tissue (9 patients and 9 age-related controls; frontal and occipital cortex) was used for next generation sequencing of RNA (RNA-Seq with ribosomal RNA depletion).

| EGAS00001002730 | EGA

Amino Acid Conjugated Surfaces and Controls 32 Hours

Project description:Amino Acid Conjugated Surfaces and Controls 32 Hours Time Point Keywords: parallel sample

2004-01-28 | GSE999 | GEO

Amino Acid Conjugated Surfaces and Controls 6 Hours

Project description:Amino Acid Conjugated Surfaces and Controls at Time point 6 hours Keywords: parallel sample

2004-01-28 | GSE998 | GEO

RNA-Seq and RNC-Seq of HeLa cells stably expressing NDV NP protein

Project description:The oncolytic potential of NDV has gained significant attention in the context of clinical trials. After systematically comparing the oncolytic activities of different NDV subtypes,we found that all subtypes, except for highly pathogenic genotype VII NDVs, display remarkable infectivity on tumor cell lines.A single amino acid mutation (F450L) in the NP protein at position 450 leads to an approximate 1000000-fold increase in the TCID50 value of genotype VII NDVs on tumor cells.Mechanistic inquiries unveiled that the amino acid at position 450 of the NP protein governs preferential translation of NDV mRNA.The preferential translation that regulates viral mRNA translation is often accompanied by modulation of the host translation machinery. Therefore, we established HeLa cell lines stably expressing NP protein from different NDV strains. Ribosome-bound mRNA was enriched to perform Ribosome Nascent-chain Complex sequencing(RNC-seq), while total cellular mRNA was enriched to conducted RNA-Seq . Untreated cells were used as controls. These experiments aimed to investigate the impact of NP on the host translation system.

2023-06-01 | GSE233617 | GEO

Neoantigen identification for 1956 and F244 murine MCA-sarcomas

Project description:This study was to predict neoantigens in 1956 and F244 murine MCA-sarcomas (female C57BL/6N and male 129S6 lines, respectively). Mutations were called by comparing tumor versus normal whole exome sequencing (WES) data, and filtered for expressing mutations using RNA-seq data. Out of expressing mutations, MHC class I or II neoantigens were predicted and screened by T cell reactivities (IFN-gamma ELISPOT and tetramer staining). Therapeutic vaccine confirmed an M50I mutation in Psmd6 and an R144S mutation in Cs to be the major MHC class I (H-2Kb) and II (I-Ab) neoantigens for 1956; and a G122A in Pex14 and a D2944Y mutation in Plec to be the major class I (H-2Kb) and class II (I-Ab) neoantigens for F244.

2024-05-20 | GSE267886 | GEO

Sarig et al. SOFT syndrome caused by a mutation in POC1A

Project description:Disproportionate short stature refers to a heterogeneous group of hereditary disorders, which are classified according to their mode of inheritance, their clinical skeletal and non-skeletal manifestations, and their radiological characteristics. In the present study, we report on a novel autosomal recessive osteocutaneous disorder that we termed short stature-onychodysplasia-facial dysmorphism-hypotrichosis (SOFT) syndrome. we identified a homozygous point mutation (p.L171P) in POC1A (Centriolar Protein Homolog A). The mutation affects a highly conserved amino acid residue and is predicted to interfere with protein function. To gain insight into the pathomechanisms underlying the deleterious effect of the causative mutation, we compared transcription profiles of patient and control fibroblasts.

2012-08-22 | E-MEXP-3650 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data