Dataset Information

Identification of lipid-binding lncRNAs in triple-negative breast cancer

ABSTRACT: To comprehensively identify RNA molecules that are naturally associated with cellular lipid components, we isolated lipid fractions and their bound RNAs from triple-negative breast cancer (TNBC) patient tissues. Fresh frozen TNBC tissues and their normal counterparts were subjected to total RNA extraction, or in parallel, to whole cell fractionation via Hydrostatic Pressure Cycling to form a lipid-containing upper phase, a denatured protein-containing lower phase, and an insoluble fraction containing DNA and RNA (PBI Inc.) The RNAs extracted from the lipid fractions were applied to LncRNA Array v3.0 (Arraystar).

ORGANISM(S): Homo sapiens

PROVIDER: GSE92414 | GEO | 2017/02/21

SECONDARY ACCESSION(S): PRJNA357495

REPOSITORIES: GEO

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Project description:We looked for the presence of prostatic cells and RNAs (cellular and acellular) of prostatic origin in the ejaculate semen from fertile and sterilized men and from men with prostate cancer, to ascertain the suitability of ejaculate semen for studying and monitoring prostate health. Methods. For prostatic cells, semen from fertile and sterile men and men with prostate cancer were subjected to density gradient centrifugation on a 60% cushion of Suprasperm™ and fractions containing somatic cells were washed and cytospun onto coated slides prior to fixation and immunocytochemistry with antibodies recognizing prostatic markers. Small RNAs were isolated from liquefied semen clarified of all cellular and other insoluble material by high-speed ultra-centrifugation. Sequencing libraries were prepared from fractions isolated by PAGE, corresponding to small non-coding (snc) RNAs in the 18-23 nt and 30-35 nt size ranges. Libraries were interrogated by next generation sequencing and analysed to generate lists of differentially expressed RNAs associated with cancer and sterility. Results. Cells positive for cytokeratin 18, PSMA, NKX3.1 and CD24 were observed in most ejaculate samples by indirect immunocytochemistry as either discrete cellular entities or within clumps of cell containing material (DAPI+; antigen positive and negative) and cytoplasmic fragments (DAP–; antigen positive and negative). RNA from populations of cells enriched by differential density gradient centrifugation supported their immunocytochemical designation as prostatic cells. Small RNAs (18 - 43 nt) from seminal plasma were highly heterogeneous although tRNAs and 5SRNAs were the dominant forms. A degree of overlap between the respective differential expression profiles of small RNAs from sterile and cancer samples, suggested a common feature, perhaps indicating an inflammatory response. Conclusion. This study supports a wider appraisal of ejaculate semen for studying and monitoring prostate health.