Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Contact versus contactless signatures in myeloma

ABSTRACT: The intracellular pathways regulated by intercellular interactions within the myelomatous bone marrow (BM) were studied by analysis of the changes in gene expression profile (GEP) following interruption of the natural interactions due to BM aspiration. Among numerous changes in GEP evolved, a subset of genes exhibited prompt and sustained switch in expression reproducibly. The switch in GEP was reversible and turned “off” and on” in culture conditions resuming cell-cell-matrix contact versus re-spread onto suspension, respectively. Although similar changes in GEP were recorded during remission, various changes were restricted to either the normal or tumor cells. Interestingly, the contact signature was accompanied in culture conditions by stasis as opposed to invasive/expansive potential recognized within the contactless genetic program. This dataset, being unique in disclosing the authentic GEP of MM cells, uncovered contact regulated genes capable of controlling homing, expansion and cell fate. Comparative gene expression profiling of whole bone marrow samples from myeloma patients fixed either immediately following aspiration or after delayed RNA fixation (for 17, 120, 300, 420, 540, 660 minutes). Comparison was also made between cultured bone marrow cells fixed immediately following spread from the bottom well or after maintenance in suspension (for 60, 120 minutes) as well as between malignant pleural fluid sediment fixed before or after cell spread from the bottom tube and maintenance in suspension (for 270 minute).

ORGANISM(S): Homo sapiens

SUBMITTER: Yossi Cohen

PROVIDER: E-GEOD-36036 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Goal was to identify yeast genes whose expression changed as a function of the shift from growth in bulk culture to growth in an air-liquid interfacial biofilm. Experiment Overall Design: Cells were grown 24 h at 30 C in YEPD to a density of about 500,000,000 cells/ml. At harvest, sugar was found to be depleted as measured by an enzymatic dip stick (Diastic, Bayer). Cells were pelleted and washed twice in sterile distilled water by centrifugation and then diluted 10-fold into 100 ml of Flor medium (YNB + 4% ethanol + leucine + histidine + uracil) in triplicate 250 ml beakers. Cultures were then grown statically in Flor medium at 27 C. Within a few hours following inoculation, the bulk liquid appeared to be clear, no biofilm was evident by visual observation, and a layer of settled cells was evident at the bottom of the beakers. After 48 h, a visible air-liquid interfacial biofilm covered the entire surface while the thickness of the layer of settled cells appeared unchanged. After 48 h, biofilm cells (floaters) were collected by aseptic aspiration. Once the biofilm cells were removed, cells at the bottom of the beaker (sinkers) were collected similarly. Cells from both populations were washed once in sterile distilled water by centrifugation prior to RNA isolation. Significant cell clumping was evident in both populations of cells by microscopic observation. While cell viability was estimated by plating on YEPD, the resultant cfu/ml values could not be directly correlated with cell counts in a hemacytometer because clumps of cells containing at least one viable cell presumably produced only a single colony. Further, counting individual cells accurately in the numerous clumps containing large numbers of cells was not possible. Nonetheless, when cells were counted (clumps were counted as single cells) and compared to cfu/ml for the same suspension, the cfu/ml values were about 2-fold higher than the corresponding values for cell counts using the hemacytometer for both biofilm and bottom layer cells.

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Contact versus contactless signatures in myeloma

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