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Tracing the lineage of replicative RNAs in the process of KRAS (S17N) evolution

ABSTRACT: Tracing the lineage of replicative RNAs in the process of KRAS (S17N) evolution

PROVIDER: PRJNA1133787 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29759500_subreads.fastq.gz	Fastqsanger.gz
	SRR29759501_subreads.fastq.gz	Fastqsanger.gz
	SRR29759502_subreads.fastq.gz	Fastqsanger.gz
	SRR29759503_subreads.fastq.gz	Fastqsanger.gz
	SRR29759504_subreads.fastq.gz	Fastqsanger.gz

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Tracing the lineage of replicative RNAs in the process of KRAS (S17N) evolution

Project description:A dominant-negative gene therapy approach has been proposed and tested on proto-oncogene KRAS, wherein the oncogenic activity (and cell proliferation) of KRAS can be suppressed by introducing a dominant-negative KRAS allele (S17N). We employed REPLACE to conduct continuous evolution on KRAS (S17N) and examined its potential pathways for conferring resistance in this gene therapy methodology.To explore the accumulation of mutations in various RNAs during the KRAS (S17N) evolution experiment, we established a barcoded library and conducted lineage tracing of replicative RNAs carrying KRAS (S17N) throughout the evolution process.

2024-09-30 | GSE271874 | GEO

Tracing the lineage of replicative RNAs carrying MEK1 in the evolution of drug resistance

Project description:Drug resistance poses a significant clinical challenge, and comprehending the mechanisms underlying this resistance can facilitate the design of novel inhibitors and advance cancer treatment. The REPLACE system was employed to examine resistance mutations in MEK1 during the administration of 3 allosteric inhibitors. To explore the accumulation of mutations in various RNAs during the MEK1 evolution experiment, we established a barcoded library and conducted lineage tracing of replicative RNAs carrying MEK1 throughout the drug resistance evolution process.

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Tracing the lineage of replicative RNAs carrying MEK1 in the evolution of drug resistance

Project description:Tracing the lineage of replicative RNAs carrying MEK1 in the evolution of drug resistance

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Analyzing the process of mutation accumulation in KRAS evolution experiment using amplicon sequencing

Project description:Directed evolution in mammalian cells can facilitate the engineering of mammalian-compatible biomolecules and can enable synthetic evolvability for mammalian cells. We engineered an orthogonal alphaviral RNA replication system to evolve synthetic RNA-based devices, enabling RNA replicase-assisted continuous evolution (REPLACE) in live mammalian cells. Using REPLACE, we attempted continuous intracellular evolution of the negative dominant mutant KRAS (S17N). To analyze the process of mutation accumulation, we performed amplicon sequencing on experimental materials at different stages and under different treatment conditions. The results indicated that the mutations generated by this system were primarily induced by Monanunavir, and the addition of Monanunavir significantly accelerated the rate of evolution.

2024-07-07 | GSE235327 | GEO

Analyzing the process of mutation accumulation in KRAS evolution experiment using amplicon sequencing

Project description:Analyzing the process of mutation accumulation in KRAS evolution experiment using amplicon sequencing

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Evolution of drug resistance enabled by replicative RNAs carrying MEK1

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KRAS-Dependent Sorting of miRNAs and other small RNAs to secreted vesicles

Project description:Although long thought to act cell autonomously, mutant KRAS colorectal cancer (CRC) cells release protein-laden exosomes that can alter the tumor microenvironment. We have previously shown that mutant KRAS induces EGFR-ligand trafficking to exosomes and drastically alters exosomal protein contents, leading to activities that contribute to neoplastic growth. We have performed small library RNAseq analysis on cells and matched exosomes from isogenic CRC cell lines differing only in KRAS status to determine whether mutant KRAS regulates the composition of secreted small RNAs. Exosomal small RNA profiles were distinct from cellular profiles, with principle component analysis showing clusters of mutant KRAS cell-derived exosomes distinct from wild type KRAS cell-derived exosomes. Secreted RNA species encompassed several different classes of small RNAs, including ribosomal and tRNA fragments, as well as mature miRNA sequences. miR-10b, was selectively increased in wild type KRAS-derived exosomes, whereas miR-100 was selectively increased in mutant KRAS-derived exosomes. Ceramide inhibition resulted in accumulation of miR-100 in mutant KRAS cells, suggesting KRAS-dependent miRNA export. In Transwell cell culture experiments, mutant, but not wild type, KRAS donor cells conferred miR-100-mediated target repression in wild type KRAS recipient cells miRNAseq deep sequencing for both cell and exosome mirnas of Dks-8, DLD-1, and DKO-1 cell lines. The DKs-8 line contains a wild type KRAS alleles, the DLD-1 line contains both wild type and mutant (G13D) KRAS alleles, and the DKO-1 line contains only a mutant KRAS allele.

2015-08-28 | E-GEOD-67004 | biostudies-arrayexpress

KRAS-Dependent Sorting of miRNAs and other small RNAs to secreted vesicles

2015-08-28 | GSE67004 | GEO

Methylation of KRAS by SETD7 promotes KRAS degradation in non-small cell lung cancer

Project description:Oncogenic KRAS mutations are a key driver for initiation and progression in non-small-cell lung cancer (NSCLC). However, how post-translational modifications (PTMs) of KRAS, especially methylation, modify KRAS activity remain largely unclear. Here, we show that SET domain containing histone lysine methyltransferase 7 (SETD7) interacts with KRAS and methylates KRAS at lysines 182 and 184. SETD7-mediated methylation of KRAS leads to degradation of KRAS and attenuation of the RAS/MEK/ERK signaling cascade, endowing SETD7 with a potent tumor-suppressive role in NSCLC, both in vitro and in vivo. Mechanistically, RABGEF1, a ubiquitin E3 ligase of KRAS, was recruited and promoted KRAS degradation in a K182/K184 methylation-dependent manner. Notably, SETD7 is inversely correlated with KRAS at the protein level in clinical NSCLC tissues. Low SETD7 or RABGEF1 expression is associated with poor prognosis in lung adenocarcinoma patients. Altogether, our results elucidate a tumor-suppressive function of SETD7 that operates via modulating KRAS methylation and degradation.

2023-07-19 | PXD043931 |

KRAS is required for placenta development

Project description:Besides its well-known roles in cancer, KRAS is important for embryogenesis, as its absence causes embryonic lethality. The precise mechanisms underlying the developmental functions of KRAS is still incompletely characterized. To address this issue, we analyzed Kras-/- mouse embryos. We observed that Kras-/- embryos show a lethality that starts around E13.5. Interestingly, a placental phenotype was observed in Kras-/- embryos. This phenotype was associated with a small placental size, and a marked decrease in glycogen trophoblast cells. It was related to the presence of hypoglycaemia and hypoxia in Kras-/- embryos. Thus, our study reveals hidden functions of KRAS4. Importantly, it identifies for the first time a role for KRAS in the differentiation process of a specific cell type and the biological defects caused by a loss of KRAS.

2023-09-17 | GSE243258 | GEO

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