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Transcriptomic analysis of a putative LysR family regulator, a putative Dps, and a cystine importer disrupted mutants in radiation resistant bacterium Deinococcus geothermalis

ABSTRACT: Transcriptomic analysis of a putative LysR family regulator, a putative Dps, and a cystine importer disrupted mutants in radiation resistant bacterium Deinococcus geothermalis

PROVIDER: PRJNA637617 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11935554_1.fastq.gz	Fastqsanger.gz
	SRR11935554_2.fastq.gz	Fastqsanger.gz
	SRR11935555_1.fastq.gz	Fastqsanger.gz
	SRR11935555_2.fastq.gz	Fastqsanger.gz
	SRR11935556_1.fastq.gz	Fastqsanger.gz

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Project description:Altered metabolism is an important part of malignant transformation of tumor cells. Oncogenic transformation may reprogram tumor metabolism and render tumor cells addicted to extracellular nutrients. Such nutrient addictions associated with oncogenic mutations may offer therapeutic opportunities; however, it remains difficult to predict these nutrient addictions. Here, we performed a nutrigenetic screen to determine the phenotypes of isogenic pairs of clear-cell renal cancer cells (ccRCC) with or without VHL upon the deprivation of individual amino acids. We identified that cystine deprivation triggered rapid programmed necrosis in VHL-deficient RCC, but not in their VHL-restored counterparts. Similar cystine addiction was also observed in VHL-deficient primary RCC tumors cells. Blockage of cystine uptake significantly delayed xenograft growth of ccRCC. Importantly, cystine deprivation triggered similar metabolic changes regardless of VHL status. Therefore, metabolic differences due to cystine deprivation are not different enough to readily explain the distinct fate of life vs. death in VHL-deficient and restored cell.. Instead, we found that increased levels of TNFÎ± associated with VHL loss in the VHL-deficient RCC force them to rely on intact RIPK1 to inhibit apoptosis. However, this pre-existing elevated TNFÎ± in the VHL-deficient ccRCC renders these cells susceptible to the necrosis signaling triggered by cystine deprivation. In addition, we identified that cystine-deprived necrosis in VHL-deficient RCC depends on reciprocal amplification of the Src-p38-Noxa signaling and TNFÎ±-RIP1/3-MLKL necrosis pathways that culminate in MLKL oligomerization and programmed necrosis. Together, our data reveal that the contextual cystine-addictions in VHL-deficient ccRCC is dependent on activating pre-existing oncogenic pathways to trigger programmed necrosis. RNA was extracted by RNAeasy kits (Qiagen) from the RCC4 Vec and VHL-reconstituted cells which were exposed to the control full DMEM or cystine deprived DMEM media for 6 hours (three replicates in each condition).

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Transcriptomic analysis of a putative LysR family regulator, a putative Dps, and a cystine importer disrupted mutants in radiation resistant bacterium Deinococcus geothermalis

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