Biology subjects

Edgar, B. A.

Publications and source records attributed to Edgar, B. A..

5 recordsLinked to original sources

bioRxiv2025

Rare codon translation regulates growth factor-dependent cell proliferation

In animal cells, growth factor signaling promotes both cell cycle progression and cell growth, but the connection between these two processes is not well understood. Here, we investigated whether cell cycling and cell growth are coupled through protein translation. Using ribosome profiling and mRNA sequencing we examined changes in translational activities in human Retinal Pigment Epithelial (RPE-1) cells as they entered the cell cycle in response to serum growth factor stimulation. We found that, in addition to mRNAs encoding factors in ribosome biogenesis and translational initiation, mRNAs encoding many DNA replication factors were translationally upregulated by serum. We also noted increases of snoRNAs and tRNAs, which facilitate translation. By analyzing the distribution of 21nt mRNA ribosome footprints, produced by stalled ribosomes that lack amino-acyl-tRNAs, we found that growth factor withdrawal promoted ribosome stalling preferentially at specific rare codons. DNA replication factor genes that were translationally upregulated by serum and essential for cell cycle progression were enriched in many of these rare codons, and the cognate tRNAs that read these codons were induced by growth signaling. The serum-dependent induction of translation was more mTOR-dependent than MEK-dependent. Our results support a novel regulatory mechanism wherein growth factor signaling promotes cell proliferation by inducing tRNAs that decode rare codons, which in turn promote translational elongation of mRNAs encoding DNA replication factors to accelerate G1/S progression. Significance StatementWe present a mechanistic explanation for the longstanding question of how cell cycle progression is coupled to cell growth. Our findings emphasize the role of translation machinery and reveal a "growth checkpoint" that ensures that DNA replication gene translation occurs only when growth signaling has activated the protein translation machinery. Our work complements the textbook model of the Growth Factor-Cyclin D-Rb-E2F transcriptional mechanism for cell cycle entry and is a fundamental advance for the fields of cell proliferation and growth factor signaling.

cell biology↗

bioRxiv2024

Bwa, an ortholog of alkaline ceramidase-ACER2, promotes intestinal stem cell proliferation through pro-inflammatory cytokine signaling in Drosophila melanogaster

Sphingolipids, including ceramides, are an important component of high-fat diets. These molecules can regulate fatty acid oxidation and intestinal stem cell proliferation, predisposing the gut to tumorigenesis. However, the molecular mechanisms involved in ceramide metabolism-mediated intestinal stem cell (ISC) proliferation and tumorigenesis are poorly understood. To understand how changes in sphingolipid metabolite flux affect intestinal stem cells, we manipulated the activities of each of the enzymes of the ceramide synthetic pathway using cell type-specific over-expression or depletion of the corresponding mRNAs in each intestinal cell type of the Drosophila midgut. We documented cell-autonomous and non-cell-autonomous effects, including alterations in cell size, number, differentiation, and proliferation. In our screen, the altered expression of several ceramide metabolism enzymes led to changes in ISC proliferation, cell sizes, and overall cellularity. Among other genes, over-expression of ceramidase homolog, Brain washing (bwa) in gut enteroblasts (EB) increased EB cell size and caused a non-cell-autonomous, 7-8-fold increase in ISC proliferation. Our analysis confirmed previous reports that bwa does not have ceramidase activity, and lipidomic studies indicated that bwa increases the saturation status of sphingolipids, free fatty acids, and other lipids. The pro-proliferative effects of bwa could be counter-acted by depleting a serine palmitoyltransferase, Lace, or a sphingosine acyltransferase, Schlank, which are needed for ceramide synthesis, or by co-expressing a ceramide desaturase enzyme, ifc, indicating that increased saturated ceramides were causal for ISC proliferation and the disruption of gut homeostasis. Accumulating saturated sphingolipids and fatty acids induced inflammatory signaling in the gut, and activated ISC proliferation through the pro-inflammatory cytokines, Upd3 and Upd2. We propose that saturated sphingolipids promote ISC proliferation through pro-inflammatory pathways.

cell biology↗

bioRxiv2024

Mating and ecdysone signaling modify growth, metabolism, and digestive efficiency in the female Drosophila gut

Adaptive changes in organ size and physiology occur in most adult animals, but how these changes are regulated is not well understood. Previous research found that mating in Drosophila females drives not only increases in gut size and stem cell proliferation but also alters feeding behavior, intestinal gene expression, and whole-body lipid storage, suggesting altered gut metabolism. Here, we show that mating dramatically alters female gut metabolism and digestive function. In addition to promoting a preference for a high-protein diet, mating also altered levels of TCA cycle intermediates and fatty acids in the gut, increased total gut lipids and protein, reduced relative carbohydrate levels, and enhanced the efficiency of protein digestion relative to carbohydrate digestion. The expression of genes that mediate each of these metabolic processes was similarly altered. In addition, we noted the mating-dependent downregulation of oxidative stress response and autophagy genes. Mating-dependent increases in ecdysone signaling played an important role in re-programming many, but not all, of these changes in the female gut. This study contributes to our understanding of how steroid signaling alters gut physiology to adapt to the demands of reproduction.

physiology↗

bioRxiv2021

An improved organ explant culture method reveals stem cell lineage dynamics in the adult Drosophila intestine

In recent years, live-imaging techniques have been developed for the adult midgut of Drosophila melanogaster that allow temporal characterization of key processes involved in stem cell and tissue homeostasis. However, current organ culture techniques are limited to imaging sessions of [≤]16 hours, an interval too short to track dynamic processes such as damage responses and regeneration, which can unfold over several days. Therefore, we developed a new organ explant culture protocol capable of sustaining midguts ex vivo for up to 3 days. This was made possible by the formulation of a culture medium specifically designed for adult Drosophila tissues with an increased Na+/K+ ratio and trehalose concentration, and by placing midguts at an air-liquid interface for enhanced oxygenation. We show that midgut progenitor cells can respond to gut epithelium damage ex vivo, proliferating and differentiating to replace lost cells, but are quiescent in healthy intestines. Using ex vivo gene induction to promote stem cell proliferation, we demonstrate that intestinal stem lineages can be traced through multiple cell divisions using live imaging. Both asymmetric and symmetric divisions can be identified in the reconstructed lineages. We find that daughter cells of asymmetric divisions remain in close proximity of each other, while the progeny of symmetric divisions actively move apart, with implications for cell differentiation and tissue organization. We show that the same culture set-up is useful for imaging adult renal tubules and ovaries for up to 72 hours. By enabling both long-term imaging and real-time ex vivo gene manipulation, our simple culture protocol provides a powerful tool for studies of epithelial biology and cell lineage behavior.

cell biology↗

bioRxiv2021

Remodeling of oxygen-transporting tracheoles drives intestinal regeneration and tumorigenesis

The Drosophila tracheal system, as the functional equivalent of mammalian blood vessels, responds to hypoxia and transports oxygen throughout the body. Although the signaling pathways involved in tracheal development and the hypoxic response are well-studied, how adult tracheae interact with their target tissues is largely unknown. Here we show that the tracheae that serve the adult intestine are dynamic and respond to enteric infection, oxidative agents, and the development of gut tumors with increased terminal branching. Increased tracheation is necessary for efficient damage-induced intestinal stem cell (ISC)-mediated midgut regeneration and sufficient to drive ISC proliferation in the absence of damage. Gut damage or tumors induce Hif-1/Sima, which, in turn, stimulates tracheole branching via the FGF(Brachless/Bnl)/FGFR(Breathless/Btl) signaling cascade. Bnl/Btl signaling is required both in the intestinal epithelium and the tracheal system for efficient damage-induced tracheal remodeling and ISC proliferation. We show that chemical or Pseudomonas-generated ROS directly affect the trachea and are necessary for branching and intestinal regeneration. Similarly, tracheole branching and the resulting increase in oxygen supply are essential for tumor growth in the midgut. Thus, we have identified a novel mechanism of visceral tracheal-intestinal tissue communication, whereby oxidative damage and tumors induce neo-tracheogenesis in adult Drosophila. This process is reminiscent of cancer-induced neo-angiogenesis in mammals.

cell biology↗