Microbiology & Molecular Genetics
School of Medicine

Developmental & Cell Biology
School of Biological Sciences

developmental genetics; cell competition; ribosomal protein; ribosomopathy; aneuploidy; cancer

HHMI & Dept. of Molecular Cell Biology, University of California at Berkeley 1986-1990

Creating and maintaining a complex body plan involves cooperation and coordination between cells. Sometimes, however, cells don’t cooperate, but instead compete and even kill one another. What are the mechanisms and meaning of such cell competition? Does it represent counterproductive, selfish cell behavior, or is it somehow productive, contributing to the fitness of the organism? Does cell competition occur in disease? Can cell competition be exploited to replace cells in regenerative medicine? Our group employs multiple genetic and molecular approaches to answer these questions. We've found that cell competition optimizes tissue fitness by recognizing and eliminating abnormal cells, such as aneuploid cells. We seek to elucidate the molecular mechanisms by which abnormal cells are recognized and eliminated, the contributions of cell competition to genomic integrity, cancer and aging, and whether cell competition could be exploited to replace cell populations in regenerative medicine. We use genetic manipulations and genome-wide and single-cell molecular genetic approaches in both Drosophila and mammalian cells and tissues.

Harold and Muriel Block Chair of Genetics, Albert Einstein College of Medicine, 2013-2024
Senior Investigator Award, Research to Prevent Blindness, 2013
Visiting Professor, Chinese Academy of Sciences
Career Scientist Award, Irma T Hirschl Trust

Dr. Baker received his PhD from the MRC Laboratory of Molecular Biology in Cambridge, England, and did postdoctoral research in Molecular Cell Biology at UC Berkeley. He is interested in the signals that control development. During his PhD, he cloned and characterized the wingless gene, co-founder of the Wnt gene family. His postdoctoral work with Dr. Gerry Rubin at UC Berkeley investigated signaling mechanisms during neuronal fate specification in the Drosophila eye. Dr. Baker’s lab at the Albert Einstein College of Medicine in New York made many contributions to understanding cell signaling processes that regulate neuronal development, including how Notch signaling interacts with transcription factors to direct cells to neuronal cell fate, using genetics, confocal microscopy, transcriptomics and mathematical modeling. His research later addressed the mechanisms of cell proliferation and survival that act in concert with development to control the number of progenitor cells available for development, developing one of the most complete understandings of organ cell number in the case of the developing Drosophila eye. Observing how cell competition between cells with different growth rates affected cell survival inspired genetic screens designed to elucidate the molecular mechanisms of cell competition, which are the focus of his lab at UC Irvine.

For complete publication list, please see:
http://www.ncbi.nlm.nih.gov/sites/myncbi/nicholas.baker.1/bibliography/40803749/public/?sort=date&direction=ascending

Nair, S. and Baker, N.E. (2024) Extramacrochaetae regulates Notch signaling in the Drosophila eye through non- apoptotic caspase activity. Elife 12: RP91988.

Reddy, V., Bhattacharya, A., and Baker, N.E. (2024) The Id protein Extramacrochaetae restrains the E-protein Daughterless to regulate Notch, Rap1, and Sevenless within the R7 equivalence group of the Drosophila eye. Biol Open 13(8):bio060124

Baker, N.E. (2024) Founding the Wnt gene family: how wingless was found to be a positional signal and oncogene homolog. Bioessays 2024 Feb;46(2):e2300156.
doi: 10.1002/bies.202300156

Kiparaki, M. and Baker, N.E. (2023) Protocol for assessing translation in living imaginal discs by O-propargyl puromycin incorporation. STAR Protocols 4: 102653

Kiparaki, M. and Baker, N.E. (2023) Ribosomal protein mutations and cell competition: autonomous and nonautonomous effects on a stress response. Genetics 224: iyad080.

Folgado-Marco, V., Ames, K., Chuen, J., Gritsman, K., and Baker, N.E. (2023) Haploinsufficiency of the essential gene RpS12 causes defects in erythropoiesis and hematopoietic stem cell maintenance. Elife,12: e69322

Kumar, A., and Baker, N.E. (2022) The CRL4 E3 ligase mahjong/DCAF1 controls cell competition through the transcription factor Xrp1, independently of polarity genes. Development 149 dev.200795.

Baker, N.E., and Montagna, C. (2022) Reducing the aneuploid cell burden: cell competition and the ribosome connection. Dis Model Mech 15 dmm049673.

Kiparaki, M., Khan, C., Folgado Marco, V., Chuen, J., Moulos, P. and Baker, N.E. (2022) The transcription factor Xrp1 orchestrates both reduced translation and cell competition upon defective ribosome assembly or function. Elife, 11: e71705

Ji, Z, Chuen, J., Kiparaki, M., and Baker, N.E. (2021). Cell competition removes segmental aneuploid cells from Drosophila imaginal disc-derived tissues based on ribosomal protein gene dose. Elife 10:e61172.

Quiquand, M., Rimesso, G., Qiao, N., Suo, S., Zhou, C., Slattery, M., White, K.P., Han, J.J., and Baker, N.E. (2021) New regulators of Drosophila eye development identified from temporal transcriptome changes. Genetics, 217(4): iyab007

Blanco, J., Cooper, J.C., and Baker, N.E. (2020) Roles of C/EBP class bZip proteins in the growth and cell competition of Rp (“Minute”) mutants in Drosophila (2020). Elife, 9:e50535.?

Baker, N.E., Kiparaki, M., and Khan, C. (2019). A potential link between p53, cell competition and ribosomopathy in mammals and in Drosophila. Dev Biol 446: 17-19.

Baker, N.E. (2020) Emerging mechanisms of cell competition. Nature Reviews Genetics 21; 683-697

Lee, C.-H., Kiparaki, M., Blanco, J., Folgado, V., Ji, Z., Kumar, A., Rimesso, G., and Baker, N.E. (2018). A
regulatory response to ribosomal protein mutations controls translation, growth, and cell competition. Dev Cell. 46 456-469.

Ji, Z., Kiparaki, M., Folgado, V., Kumar, A., Blanco, J. Rimesso, G., Liu, Y., Zheng, D., and Baker, N.E. (2019) Drosophila RpS12 controls translation, growth, and cell competition through Xrp1. PLoS Genetics, 15(12):e1008513.?

Li, K. and Baker, N.E. (2019) Transcriptional and post-transcriptional regulation of extra macrochaetae during Drosophila adult peripheral neurogenesis. Dev Biol 449: 41-51.?

Wang, L.-H. and Baker, N.E. (2019) Salvador-Warts-Hippo pathway regulates sensory organ development via caspase-dependent non-apoptotic signaling. Cell Death & Disease 10 669.?

Kale, A., Ji, Z., Kiparaki, M., Rimesso, G., Flibotte, S., and Baker, N.E. (2018). Ribosomal protein S12e has a distinct function in cell competition. Dev Cell 44, 42-55.

Baker, N.E., and Brown, N.L. (2018). All in the family: neuronal diversity and proneural bHLH genes.
Development, 145: dev159426

Li, K., and Baker, N.E. (2018) Regulation of the Drosophila ID protein Extra Macrochaetae by proneural dimerization partners. Elife 7: e33967.?

Wang, L.-H. and Baker, N.E. (2018) Spatial regulation of expanded transcription in the Drosophila wing imaginal disc. PLoS One 13,e0201317

Cellular and Molecular Biosciences

Mathematical and Computational Biology

UCI Chao Family Comprehensive Cancer Center

Link to this profile
https://faculty.uci.edu/profile/?facultyId=7245

Last updated
01/29/2025