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Transcriptomic data indicating differential expressed genes between HIV-1 Associated Nephropathy (HIVAN) mouse model (Tg26) and wildtype mice.

ABSTRACT: Tg26 mice are robust models of human immunodeficiency virus 1 associated nephropathy (HIVAN). These mice are useful for HIVAN pathology analysis, and recent studies suggest that the Tg26 mouse model is an excellent model of other chronic kidney diseases. We performed RNA seq analysis of differential gene expression in the kidneys of Tg26 mice. Kidneys were collected from Tg26 mice and wildtype (WT) littermates at 3 months of age. The raw data were analyzed for differential gene expression using a negative binomial generalized linear model in the DeSeq2 software package. We used P-Value ?0.05 and an absolute fold change of 1.5 to identify top 50 upregulated and top 50 downregulated differentially expressed genes between the WT and Tg26 mice. As expected inflammatory genes were among the top differentially regulated genes. Our data provides yet another level of information to help gain a more comprehensive understanding of disease progression and identify potential drug targets for HIVAN and chronic kidney diseases.

SUBMITTER: Chakravarthi VP

PROVIDER: S-EPMC7186506 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Transcriptomic data indicating differential expressed genes between HIV-1 Associated Nephropathy (HIVAN) mouse model (Tg26) and wildtype mice.

Chakravarthi V Praveen VP Yerrathota Sireesha S Radadiya Priyanka P Bloomer Clark C Gunewardhana Sumedha S Sharma Madhulika M

Data in brief 20200417

Tg26 mice are robust models of human immunodeficiency virus 1 associated nephropathy (HIVAN). These mice are useful for HIVAN pathology analysis, and recent studies suggest that the Tg26 mouse model is an excellent model of other chronic kidney diseases. We performed RNA seq analysis of differential gene expression in the kidneys of Tg26 mice. Kidneys were collected from Tg26 mice and wildtype (WT) littermates at 3 months of age. The raw data were analyzed for differential gene expression using ...[more]

PMID: 32368594

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Project description:BACKGROUND: Using the piggyBac-mediated GAL4/UAS transgenic system established in the silkworm, Bombyx mori, we have previously reported that overexpression of the Ras1(CA) oncogene specifically in the posterior silk gland (PSG) improved cell growth, fibroin synthesis, and thus silk yield. However, the detailed molecular mechanism remains to be fully elucidated. To achieve this goal, Illumina sequencing was used in the present study to compare the transcriptomes of the Ras1(CA)-overexpressed and wildtype PSGs. RESULTS: The transcriptomic sequencing results in 56 million reads following filtering steps. Most of the reads (~70%) are successfully mapped to the Bombyx genome. The mapped reads are situated within at least 9,133 predicted genes, covering 62.46% genes of the Bombyx genome. GO annotation shows that 2512 of the 2,636 differentially expressed genes (DEGs) are mostly distributed in metabolic process, cell and cell part, and binding, and KEGG annotation shows that 1,941 DEGs are mapped into 277 pathways. Importantly, Ras1(CA) overexpression in the PSG upregulated many DEGs distributed in "pathways in cancer", "insulin signaling pathway", and "MAPK signaling pathway" as well as "purine metabolism" and "pyrimidine metabolism". Transcriptional regulation of these DEGs was verified by quantitative real-time PCR. Moreover, injection of small-molecule chemical inhibitors of the Ras1 downstream effectors into the Ras1(CA)-overexpressed silkworms revealed that both Raf-MAPK and PI3K-TORC1 pathways are required for the Ras1-induced DEG expression. CONCLUSION: The transcriptomic analysis illustrates that, apart from phosphorylational regulation, Ras1 activates its downstream Raf-MAPK and PI3K-TORC1 pathways at the transcriptional level. Meanwhile, Ras1 increases DNA content and induces endoreplication, at least in part, by upregulating genes in "nucleotide metabolism" and "cell cycle". This study provides further insights into the molecular mechanism of how Ras1(CA) overexpression in the PSG improves silk yield.

Dataset Information

Transcriptomic data indicating differential expressed genes between HIV-1 Associated Nephropathy (HIVAN) mouse model (Tg26) and wildtype mice.

Publications

Transcriptomic data indicating differential expressed genes between HIV-1 Associated Nephropathy (HIVAN) mouse model (Tg26) and wildtype mice.

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