Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of murine Vg4+CD27-CD44+ and Vg4-CD27-CD44+ gamma delta from the lymph nodes of retinoic acid receptor deficient mice and littermate controls

ABSTRACT: The aim of this experiment was to decipher the role of retinoic acid receptor (RAR) on interleukin(IL)-17-producing gamma delta (gdT17) T cells. Therefore we generated mice where RAR activity is defective specifically in cells expressing the transcription factor RORgt, which is constitutively on in gdT17 cells. From these mice and their littermate controls we FACS-sorted the two major gdT17 populations from the lymph node (Vg4+ and Vg4-) and subjected them to RNA-seq.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Vasileios Bekiaris

PROVIDER: E-MTAB-8554 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Breast cancers contain a minority population of cancer cells characterized by CD44 expression but low or undetectable levels of CD24 (CD44+CD24-/low) that have higher tumorigenic capacity than other subtypes of cancer cells. METHODS: We compared the gene-expression profile of CD44+CD24-/low tumorigenic breast-cancer cells with that of normal breast epithelium. Differentially expressed genes were used to generate a 186-gene invasiveness gene signature (IGS), which was evaluated for its association with overall survival and metastasis-free survival in patients with breast cancer or other types of cancer. RESULTS: There was a significant association between the IGS and both overall and metastasis-free survival (P<0.001, for both) in patients with breast cancer, which was independent of established clinical and pathological variables. When combined with the prognostic criteria of the National Institutes of Health, the IGS was used to stratify patients with high-risk early breast cancer into prognostic categories (good or poor); among patients with a good prognosis, the 10-year rate of metastasis-free survival was 81%, and among those with a poor prognosis, it was 57%. The IGS was also associated with the prognosis in medulloblastoma (P=0.004), lung cancer (P=0.03), and prostate cancer (P=0.01). The prognostic power of the IGS was increased when combined with the wound-response (WR) signature. CONCLUSIONS: The IGS is strongly associated with metastasis-free survival and overall survival for four different types of tumors. This genetic signature of tumorigenic breast-cancer cells was even more strongly associated with clinical outcomes when combined with the WR signature in breast cancer. Expression profling was performed on 6 tumorigenic, 3 non tumorigenic samples of breast tumors and 3 normal breast samples on two different platforms GPL96 and GPL97. A gene signature was derived by comparing the gene expressions of 6 tumorigenic samples with 3 normal breast samples.

Dataset Information

RNA-seq of murine Vg4+CD27-CD44+ and Vg4-CD27-CD44+ gamma delta from the lymph nodes of retinoic acid receptor deficient mice and littermate controls

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