Dataset Information

Proteomics of WT and bleached Euglena

ABSTRACT: In this study, the whole-genome proteome with dark-adapted E. gracilis strain (WT) and permanently ofloxacin-bleached mutant (B2) was compared under the light exposure after 0 h, 12 h, and 72h.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Euglena Gracilis

TISSUE(S): Photosynthetic Cell

SUBMITTER: Jiangxin Wang

LAB HEAD: Jiangxin Wang

PROVIDER: PXD030414 | Pride | 2022-04-04

REPOSITORIES: Pride

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Publications

Proteomic Responses of Dark-Adapted Euglena gracilis and Bleached Mutant Against Light Stimuli.

Chen Zhenfan Z Chen Zixi Z Zhu Jiayi J He Jiayi J Liu Qiong Q Zhu Hui H Lei Anping A Wang Jiangxin J

Frontiers in bioengineering and biotechnology 20220303

Euglena gracilis (E. gracilis) has secondary endosymbiotic chloroplasts derived from ancient green algae. Its chloroplasts are easily lost under numerous conditions to become permanently bleached mutants. Green cells adapted in the dark contain undeveloped proplastids and they will develop into mature chloroplasts after 3 days of light exposure. Thus, E. gracilis is an ideal model species for a chloroplast development study. Previous studies about chloroplast development in E. g ...[more]

PMID: 35309998

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Project description:Background: Epithelial-stromal crosstalk plays a critical role in invasive breast cancer (IBC) pathogenesis; however, little is known on a systems level about how epithelial-stromal interactions evolve during carcinogenesis. Results: We develop a framework for building genome-wide epithelial-stromal co-expression networks composed of pairwise co-expression relationships between mRNA levels of genes expressed in the epithelium and stroma across a population of patients. We apply this method to laser capture micro-dissection expression profiling datasets in the setting of breast carcinogenesis. Our analysis shows that epithelial-stromal co-expression networks undergo extensive re-wiring during carcinogenesis, with the emergence of distinct network hubs in normal breast, ER-positive IBC, and ER-negative IBC, and the emergence of distinct patterns of functional network enrichment. In contrast to normal breast, the strongest epithelial-stromal co-expression relationships in IBC mostly represent self-loops, in which the same gene is co-expressed in epithelial and stromal regions. We validate this observation using an independent laser capture micro-dissection dataset and confirm that self-loop interactions are significantly increased in cancer by performing computational image analysis of epithelial and stromal protein expression using images from the Human Protein Atlas. Conclusions: Epithelial-stromal co-expression network analysis represents a new approach for systems-level analyses of spatially-localized transcriptomic data. The analysis provides new biological insights into the re-wiring of epithelial-stromal co-expression networks and the emergence of epithelial-stromal co-expression self-loops in breast cancer. The approach may facilitate the development of new diagnostics and therapeutics targeting epithelial-stromal interactions in cancer. 36 flash-frozen human primary breast cancer samples were subjected to laser capture microdissection to separately isolate matched tumor epithelial and tumor-associated stromal components. RNA was isolated, subjected to 2 rounds of amplification, and hybridized on Agilent 4x44K microarrays along with a common reference (single round-amplified commercially obtained Universal Human Reference RNA) in a dyeswap design. For two samples of tumor-associated stroma, a second technical replicate was performed. Samples were labelled as ER-positive based on ESR1 gene expression levels in the tumor epithelium, using univariate Gaussian mixture model-based clustering via the mclust package in R.

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	Ori_quantification.xlsx	Xlsx
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	P64A-12.raw	Raw

Dataset Information

Proteomics of WT and bleached Euglena

Dataset's files

Publications

Proteomic Responses of Dark-Adapted <i>Euglena gracilis</i> and Bleached Mutant Against Light Stimuli.

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