Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Characterization of human breast cancer xenografts

ABSTRACT: A bank of human breast tumor xenografts was established by serial passage of primary breast tumor fragments in the cleared mammary fat pads of immuno-compromised NOD-SCID-IL2Rgammac–/– mice. The 15 expression profiles from five different tumors were classified using the ClaNC method [1]. The training data set consisted of 94 samples from Herschkowitz et al. [2]; class labels were based on tumor subtype (Basal-like, Luminal A, Luminal B, Claudin-low, HER2+/ER- and Normal breast-like). [1] Dabney AR (2005) Classification of microarrays to nearest centroids. Bioinformatics 21:4148-4154. [2] Herschkowitz JI, et al. (2007) Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol 8:R76. Total RNA obtained from xenograft tumors from 5 different patients have been profiled in triplicate on the Illumina HT-12 BeadChip platform.

ORGANISM(S): Homo sapiens

SUBMITTER: Matthew Ritchie

PROVIDER: E-GEOD-28570 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Cotton (Gossypium hirsutum L.) fibres are specialised trichomes that extend from the seedcoat. To date only a few genes directly involved in the differentiation of these epidermal cells have been identified. We have identified a HD-ZIP transcription factor, GhHD-1, expressed in trichomes and early fibres that might play a role in cotton fibre initiation. Here we characterise GhHD-1 from G. hirsutum and show, using reporter constructs and qRT-PCR, that they are expressed predominantly in epidermal tissues during early fibre development and in other tissues bearing epidermal trichomes. GhHD-1 silencing caused reduced trichome formation and delayed the timing of fibre initiation whereas constitutive over-expression of GhHD-1 increased the number of fibres initiating on the seed, but did not affect leaf trichomes. Expression of GhHD-1 in transgenic cotton silenced for different fibre MYBs suggest that in ovules it acts downstream of GhMYB25-like. Microarray analysis of silencing and over-expression lines of GhHD-1 indicated that it potentially functions through a WRKY transcription factor and calcium-signalling pathway genes that are shared with some biotic stress reactions. Microarray analysis of 2 biological replicates each of GhHD-1 silenced and over-expression transgenic lines relative to wild-type were used to identify downstream targets of this transcription factor during early fibre development. 0 dpa (Days post anthesis) ovules from GhHD-1 silenced and over-expression lines and wild-type cotton plants were selected for RNA extraction and hybridisation on Affymetrix cotton arrays. Cotton fibre development initiates on the epidermal surface of each ovule within a cotton boll on the day of flowering and GhHD-1 has been shown to be most highly expressed at this stage (0 dpa). Ovules were obtained from 0dpa flowers for hybridisation to cotton arrays to identify genes that may be regulated by GhHD-1 during this early fibre development stage (initiation).

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Characterization of human breast cancer xenografts

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