Discovery of progenitor cell signatures by time-series synexpression analysis during Drosophila embryonic cell immortalization

Abstract

The use of time series profiling to identify groups of functionally related genes (synexpression groups) is a powerful approach for the discovery of gene function. Here we apply this strategy during RasV12 immortalization of Drosophila embryonic cells, a phenomenon not well characterized. Using high-resolution transcriptional time-series datasets, we generated a gene network based on temporal expression profile similarities. This analysis revealed that common immortalized cells are related to adult muscle precursors (AMPs), a stem cell-like population contributing to adult muscles and sharing properties with vertebrate satellite cells. Remarkably, the immortalized cells retained the capacity for myogenic differentiation when treated with the steroid hormone ecdysone. Further, we validated in vivo the transcription factor CG9650, the ortholog of mammalian Bcl11a/b, as a regulator of AMP proliferation predicted by our analysis. Our study demonstrates the power of time series synexpression analysis to characterize Drosophila embryonic progenitor lines and identify stem/progenitor cell regulators.

Cell Lines for Honey Bee Virus Research

“…Such differences in cell line establishment may relate to fundamental cellular biology. We plan to investigate the point in detail by tracing gene expression patterns during the establishment process, using cell lines from lepidopterans and coleopterans that are routinely established, and from recalcitrant species, similar to work in Drosophila melanogaster cell lines [69].…”

Generating and working with Drosophila cell cultures: Current challenges and opportunities

“…The Ras V12 lines were derived from embryos ubiquitously expressing Ras V12 and their cellular origins were not clear initially (A. Simcox et al, ). Expression profiling revealed that these cells have characteristic signatures that most resemble ML‐DmD8 (Ui et al, ), a wing disc cell line with adult muscle precursor's characteristics (Cherbas et al, ; Dequeant et al, ). Ras V12 cells retain the ability to differentiate into muscle cells when treated with ecdysone (Dequeant et al, ).…”

“…Expression profiling revealed that these cells have characteristic signatures that most resemble ML‐DmD8 (Ui et al, ), a wing disc cell line with adult muscle precursor's characteristics (Cherbas et al, ; Dequeant et al, ). Ras V12 cells retain the ability to differentiate into muscle cells when treated with ecdysone (Dequeant et al, ). The basis for the proliferative and undifferentiated state of Ras V12 lines may be attributed to the increased activity of genes in the E2 promoter binding factor/retinoblastoma (E2F/Rb) and the Polycomb Group (PcG) pathways, respectively (Dequeant et al, ).…”

Oncogenic transformation of Drosophila somatic cells induces a functional piRNA pathway

“…We therefore established primary cell cultures from embryos with Ras activation (Dequéant et al 2015), SWH pathway inactivation, Wts-RNAi, or the combined alterations (Simcox et al 2008). These lines could be grown continuously in culture for >100 passages, and, upon transplantation in vivo, Ras V12 and Wts-RNAi; Ras V12 formed tumors in flies (Wts-RNAi alone was not tested) (Simcox et al 2008; data not shown).…”