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Current Projects

Project 1: Translational control of the cell cycle

Since ~2010 we’ve investigated a potentially ubiquitous mechanism of cell cycle control that’s been overlooked by the field. In this mechanism the growth- or growth factor-dependent translation (synthesis of protein from mRNA) of unstable cell cycle regulators limits cell proliferation. This has been suggested for yeasts1, 2 but barely touched on in animal cells3-8. We envision translational control as one of two “gates” that regulate cell proliferation, the other being programed transcription of cell cycle control genes (Fig 1A,B). Translation-dependent gating is important because it can couple metabolism to proliferation, providing a growth check point9, 10. Early in this project we discovered that E2F1, the transcription factor that activates DNA replication and mitosis genes, controls the cell cycle in most Drosophila cells11-15. Years later we found that E2F1 translation determines when and how fast cells divide16, 17. In some cell types nutrition-dependent Insulin/Pi3K/mTOR signaling regulates E2f1 translation, whereas in others stress-dependent EGFR/Ras/Erk signaling is the major growth stimulus16, 18-20. Recently we found that E2F1 monitors a cell’s growth status via a collection of small open reading frames (uORFs) in its mRNA 5’ UTR that attenuate translation, but which can be bypassed by mTOR or ERK activity53.

Figure 1. Growth-dependent regulation of the cell cycle (Drosophila model).
Figure 1. Growth-dependent regulation of the cell cycle (Drosophila model).

Future goals of this project are to understand how mTOR and ERK promote uORF read-thru, and to look beyond E2F1, using ribosome profiling to test whether different signaling inputs regulate the cell cycle via other “growth sensor” genes in other cell types. We are also extending this project to include translational control of the vertebrate cell cycle. As an entry we performed ribosome profiling21, 22 on human RPE-1 cells, and identified ~600 genes that are translationally activated by growth factors stimulation. Many of these are G1/S control and DNA replication genes that are rate-limiting for proliferation (e.g. CCNE2, CDC6, CDC45, POLE2, RAD51, ORC1, MCM10). Analysis of these genes revealed an interesting, novel mechanism in which serum- and mTOR-dependent induction of tRNAs that decode rare codons in the DNA replication genes regulates cell cycle progression.

Project 2: Intestinal stem cell control

Another major goal of my lab has been to understand how intestinal stem cell (ISC) proliferation is regulated. The seminal discovery for this project was our finding that the fly’s gut epithelium readily regenerates after damage, by mobilizing ISCs for rapid proliferation23-31. Using genetic screens, we found that damage-dependent Cytokine/Jak/Stat and EGFR/Ras/Erk signaling are responsible for activating ISC growth and division (Fig 2)18, 19, 24, and that the conserved ERK-dependent transcription factors Capicua (CIC), Ets21C, and Pnt (ETS2)16, 20 execute this function. Using mRNA expression, chromatin, and metabolome profiling we learned that these transcription factors promote mitochondrial biogenesis and drive a profound metabolic shift that is essential for stem cell growth and division. This metabolic appears to involve repurposing carbohydrates for the biosynthesis of nucleotides and amino acids (building blocks for cell growth), and at the same time mobilizing fatty acid oxidation to drive the TCA cycle maintain energy (ATP) production. Going forward, we will investigate how ERK signaling interfaces with the metabolic network to drive these changes, and how the metabolic switch impacts the ISC cell cycle. We are also translating this research with parallel studies in human cell culture and mouse intestinal epithelia. Overall, this project is deepening our understanding of how EGFR/RAS/ERK signaling, so important in human cancers, regulates cell growth and proliferation.

Project 3: Gut epithelial damage sensing

A related goal is to understand how gut epithelia sense damage. This process is poorly understood 32, 33, but critical because it initiates both inflammation and regeneration. Following our discovery that damage-dependent cytokine induction drives gut regeneration24, we determined that Jnk, p38MAPK, Fak/Src, and Hpo/Yki signaling relay damage cues to drive cytokine induction (Fig 2)24, 30, 34.

Figure 2. Regeneration in the fly gut epithelium (working model). Each red arrow represents a process that is under investigation.
Figure 2. Regeneration in the fly gut epithelium (working model). Each red arrow represents a process that is under investigation.

A ROS burst activates Jnk and p3824, 30, whereas mechano-sensing activates Hpo/Yki34 and Src/Fak signaling31, and all four are induced by epithelial disruption by tumors29, 31, 35. We developed an in vivo RNAi screen to identify genes required for gur epithelial damage sensing in a high-throughput format, something only possible in Drosophila. This screen identified 68 genes required for epithelial damage sensing, 51 of which have human orthologs, and 16 of which had no known function, until now. Characterizing these genes will extend our understanding of how stress-activated, inflammatory, and regenerative signaling is initiated and present new, clinically relevant approaches for controlling inflammation, stimulating regeneration, and managing tissue engineering.

Support: R01 DK125745

Project 4: Steroid signaling and adaptive growth of the intestine

In addition to regeneration, the fly’s ISCs mediate adaptive growth of the gut during cycles feeding and fasting36, and in response to the demands of reproduction37. A talented student in the lab discovered that mating-dependent gut growth in females is driven by the steroid hormone ecdysone, produced by the activated ovaries after fertilization38. This nearly doubles the size of the gut, enhancing nutrient influx and augmenting female fecundity. However, the hyper-proliferative nature of steroid-stimulated ISCs also increases female susceptibility to gut tumorigenesis, reducing lifespan. These discoveries highlight the fitness trade-offs incurred when inter-organ signaling alters stem cell behavior to optimize physiology. Our findings raise many questions about how steroid signaling alters stem cell function and metabolism, how it impacts gut and whole-body physiology, and whether sex steroids play similar roles in mammals. We are pursuing these questions through further studies in Drosophila, and parallel studies in mice and mouse intestinal organoids.


Edgar Lab citations in bold

  1. Daga RR, Jimenez J. Translational control of the cdc25 cell cycle phosphatase: a molecular mechanism coupling mitosis to cell growth. J Cell Sci. 1999;112 Pt 18:3137-46. PubMed PMID: 10462529.
  2. Polymenis M, Schmidt EV. Coupling of cell division to cell growth by translational control of the G1 cyclin CLN3 in yeast. Genes Dev. 1997;11(19):2522-31. PubMed PMID: 9334317; PMCID: 316559.
  3. Mullany LK, Nelsen CJ, Hanse EA, Goggin MM, Anttila CK, Peterson M, Bitterman PB, Raghavan A, Crary GS, Albrecht JH. Akt-mediated liver growth promotes induction of cyclin E through a novel translational mechanism and a p21-mediated cell cycle arrest. J Biol Chem. 2007;282(29):21244-52. doi: 10.1074/jbc.M702110200. PubMed PMID: 17517888.
  4. Nelsen CJ, Rickheim DG, Tucker MM, Hansen LK, Albrecht JH. Evidence that cyclin D1 mediates both growth and proliferation downstream of TOR in hepatocytes. J Biol Chem. 2003;278(6):3656-63. doi: 10.1074/jbc.M209374200. PubMed PMID: 12446670.
  5. Goggin MM, Nelsen CJ, Kimball SR, Jefferson LS, Morley SJ, Albrecht JH. Rapamycin-sensitive induction of eukaryotic initiation factor 4F in regenerating mouse liver. Hepatology. 2004;40(3):537-44. doi: 10.1002/hep.20338. PubMed PMID: 15349891.
  6. Faller WJ, Jackson TJ, Knight JR, Ridgway RA, Jamieson T, Karim SA, Jones C, Radulescu S, Huels DJ, Myant KB, Dudek KM, Casey HA, Scopelliti A, Cordero JB, Vidal M, Pende M, Ryazanov AG, Sonenberg N, Meyuhas O, Hall MN, Bushell M, Willis AE, Sansom OJ. mTORC1-mediated translational elongation limits intestinal tumour initiation and growth. Nature. 2015;517(7535):497-500. doi: 10.1038/nature13896. PubMed PMID: 25383520; PMCID: 4304784.
  7. Lai MC, Chang WC, Shieh SY, Tarn WY. DDX3 regulates cell growth through translational control of cyclin E1. Mol Cell Biol. 2010;30(22):5444-53. doi: 10.1128/MCB.00560-10. PubMed PMID: 20837705; PMCID: 2976371.
  8. Dowling RJ, Topisirovic I, Alain T, Bidinosti M, Fonseca BD, Petroulakis E, Wang X, Larsson O, Selvaraj A, Liu Y, Kozma SC, Thomas G, Sonenberg N. mTORC1-mediated cell proliferation, but not cell growth, controlled by the 4E-BPs. Science. 2010;328(5982):1172-6. doi: 10.1126/science.1187532. PubMed PMID: 20508131; PMCID: 2893390.
  9. Ginzberg MB, Kafri R, Kirschner M. Cell biology. On being the right (cell) size. Science. 2015;348(6236):1245075. doi: 10.1126/science.1245075. PubMed PMID: 25977557; PMCID: 4533982.
  10. Zatulovskiy E, Skotheim JM. On the Molecular Mechanisms Regulating Animal Cell Size Homeostasis. Trends Genet. 2020;36(5):360-72. Epub 2020/04/16. doi: 10.1016/j.tig.2020.01.011. PubMed PMID: 32294416; PMCID: PMC7162994.
  11. Britton JS, Edgar BA. Environmental control of the cell cycle in Drosophila: nutrition activates mitotic and endoreplicative cells by distinct mechanisms. Development. 1998;125(11):2149-58. PubMed PMID: 9570778.
  12. Neufeld TP, de la Cruz AF, Johnston LA, Edgar BA. Coordination of growth and cell division in the Drosophila wing. Cell. 1998;93(7):1183-93. PubMed PMID: 9657151.
  13. Reis T, Edgar BA. Negative regulation of dE2F1 by cyclin-dependent kinases controls cell cycle timing. Cell. 2004;117(2):253-64. PubMed PMID: 15084262.
  14. Britton JS, Lockwood WK, Li L, Cohen SM, Edgar BA. Drosophila's insulin/PI3-kinase pathway coordinates cellular metabolism with nutritional conditions. Dev Cell. 2002;2(2):239-49. Epub 2002/02/08. doi: S153458070200117X [pii]. PubMed PMID: 11832249.
  15. Shibutani ST, de la Cruz AF, Tran V, Turbyfill WJ, 3rd, Reis T, Edgar BA, Duronio RJ. Intrinsic negative cell cycle regulation provided by PIP box- and Cul4Cdt2-mediated destruction of E2f1 during S phase. Dev Cell. 2008;15(6):890-900. doi: 10.1016/j.devcel.2008.10.003. PubMed PMID: 19081076; PMCID: 2644461.
  16. Xiang J, Bandura J, Zhang P, Jin Y, Reuter H, Edgar BA. EGFR-dependent TOR-independent endocycles support Drosophila gut epithelial regeneration. Nat Commun. 2017;8:15125. doi: 10.1038/ncomms15125. PubMed PMID: 28485389; PMCID: PMC5436070.
  17. Zielke N, Kim KJ, Tran V, Shibutani ST, Bravo MJ, Nagarajan S, van Straaten M, Woods B, von Dassow G, Rottig C, Lehner CF, Grewal SS, Duronio RJ, Edgar BA. Control of Drosophila endocycles by E2F and CRL4(CDT2). Nature. 2011;480(7375):123-7. Epub 2011/11/01. doi: 10.1038/nature10579. PubMed PMID: 22037307.
  18. Jiang H, Edgar BA. EGFR signaling regulates the proliferation of Drosophila adult midgut progenitors. Development. 2009;136(3):483-93. doi: 10.1242/dev.026955. PubMed PMID: 19141677; PMCID: 2687592.
  19. Jiang H, Grenley MO, Bravo MJ, Blumhagen RZ, Edgar BA. EGFR/Ras/MAPK signaling mediates adult midgut epithelial homeostasis and regeneration in Drosophila. Cell Stem Cell. 2011;8(1):84-95. Epub 2010/12/21. doi: 10.1016/j.stem.2010.11.026. PubMed PMID: 21167805; PMCID: PMC3021119.
  20. Jin Y, Ha N, Fores M, Xiang J, Glasser C, Maldera J, Jimenez G, Edgar BA. EGFR/Ras Signaling Controls Drosophila Intestinal Stem Cell Proliferation via Capicua-Regulated Genes. PLoS Genet. 2015;11(12):e1005634. doi: 10.1371/journal.pgen.1005634. PubMed PMID: 26683696; PMCID: 4684324.
  21. Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc. 2012;7(8):1534-50. doi: 10.1038/nprot.2012.086. PubMed PMID: 22836135; PMCID: 3535016.
  22. Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science. 2009;324(5924):218-23. doi: 10.1126/science.1168978. PubMed PMID: 19213877; PMCID: 2746483.
  23. Buchon N, Broderick NA, Poidevin M, Pradervand S, Lemaitre B. Drosophila intestinal response to bacterial infection: activation of host defense and stem cell proliferation. Cell Host Microbe. 2009;5(2):200-11. doi: 10.1016/j.chom.2009.01.003. PubMed PMID: 19218090.
  24. Jiang H, Patel PH, Kohlmaier A, Grenley MO, McEwen DG, Edgar BA. Cytokine/Jak/Stat signaling mediates regeneration and homeostasis in the Drosophila midgut. Cell. 2009;137(7):1343-55. Epub 2009/07/01. doi: 10.1016/j.cell.2009.05.014. PubMed PMID: 19563763; PMCID: PMC2753793.
  25. Biteau B, Karpac J, Hwangbo D, Jasper H. Regulation of Drosophila lifespan by JNK signaling. Exp Gerontol. 2011;46(5):349-54. Epub 2010/11/30. doi: 10.1016/j.exger.2010.11.003. PubMed PMID: 21111799; PMCID: PMC3079798.
  26. Biteau B, Karpac J, Supoyo S, Degennaro M, Lehmann R, Jasper H. Lifespan extension by preserving proliferative homeostasis in Drosophila. PLoS Genet. 2010;6(10):e1001159. Epub 2010/10/27. doi: 10.1371/journal.pgen.1001159. PubMed PMID: 20976250; PMCID: PMC2954830.
  27. Buchon N, Broderick NA, Chakrabarti S, Lemaitre B. Invasive and indigenous microbiota impact intestinal stem cell activity through multiple pathways in Drosophila. Genes Dev. 2009;23(19):2333-44. Epub 2009/10/03. doi: 10.1101/gad.1827009. PubMed PMID: 19797770; PMCID: PMC2758745.
  28. Miguel-Aliaga I, Jasper H, Lemaitre B. Anatomy and Physiology of the Digestive Tract of Drosophila melanogaster. Genetics. 2018;210(2):357-96. Epub 2018/10/06. doi: 10.1534/genetics.118.300224. PubMed PMID: 30287514; PMCID: PMC6216580.
  29. Patel PH, Dutta D, Edgar BA. Niche appropriation by Drosophila intestinal stem cell tumours. Nat Cell Biol. 2015;17(9):1182-92. Epub 2015/08/04. doi: 10.1038/ncb3214. PubMed PMID: 26237646; PMCID: PMC4709566.
  30. Patel PH, Penalva C, Kardorff M, Roca M, Pavlovic B, Thiel A, Teleman AA, Edgar BA. Damage sensing by a Nox-Ask1-MKK3-p38 signaling pathway mediates regeneration in the adult Drosophila midgut. Nat Commun. 2019;10(1):4365. Epub 2019/09/27. doi: 10.1038/s41467-019-12336-w. PubMed PMID: 31554796; PMCID: PMC6761285.
  31. Kohlmaier A, Fassnacht C, Jin Y, Reuter H, Begum J, Dutta D, Edgar BA. Src kinase function controls progenitor cell pools during regeneration and tumor onset in the Drosophila intestine. Oncogene. 2015;34(18):2371-84. Epub 2014/07/01. doi: 10.1038/onc.2014.163. PubMed PMID: 24975577.
  32. Niethammer P. The early wound signals. Curr Opin Genet Dev. 2016;40:17-22. doi: 10.1016/j.gde.2016.05.001. PubMed PMID: 27266971.
  33. Hernandez C, Huebener P, Schwabe RF. Damage-associated molecular patterns in cancer: a double-edged sword. Oncogene. 2016;35(46):5931-41. Epub 2016/04/19. doi: 10.1038/onc.2016.104. PubMed PMID: 27086930; PMCID: PMC5119456.
  34. Shaw RL, Kohlmaier A, Polesello C, Veelken C, Edgar BA, Tapon N. The Hippo pathway regulates intestinal stem cell proliferation during Drosophila adult midgut regeneration. Development. 2010;137(24):4147-58. doi: 10.1242/dev.052506. PubMed PMID: 21068063; PMCID: PMC2990206.
  35. Cordero JB, Stefanatos RK, Myant K, Vidal M, Sansom OJ. Non-autonomous crosstalk between the Jak/Stat and Egfr pathways mediates Apc1-driven intestinal stem cell hyperplasia in the Drosophila adult midgut. Development. 2012;139(24):4524-35. Epub 2012/11/23. doi: 10.1242/dev.078261. PubMed PMID: 23172913.
  36. O'Brien LE, Soliman SS, Li X, Bilder D. Altered modes of stem cell division drive adaptive intestinal growth. Cell. 2011;147(3):603-14. Epub 2011/11/01. doi: 10.1016/j.cell.2011.08.048. PubMed PMID: 22036568; PMCID: PMC3246009.
  37. Reiff T, Jacobson J, Cognigni P, Antonello Z, Ballesta E, Tan KJ, Yew JY, Dominguez M, Miguel-Aliaga I. Endocrine remodelling of the adult intestine sustains reproduction in Drosophila. Elife. 2015;4:e06930. Epub 2015/07/29. doi: 10.7554/eLife.06930. PubMed PMID: 26216039; PMCID: PMC4515472.
  38. Ahmed SMH, Maldera JA, Krunic D, Paiva-Silva GO, Penalva C, Teleman AA, Edgar BA. Fitness trade-offs incurred by ovary-to-gut steroid signalling in Drosophila. Nature. 2020;584(7821):415-9. Epub 2020/07/10. doi: 10.1038/s41586-020-2462-y. PubMed PMID: 32641829; PMCID: PMC7442704.