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Ally Nguyen, Ph.D.

Assistant Professor

Ally Nguyen
E-mail Addressally.nguyen@cuanschutz.edu
Phone Number(303) 724.0620
DegreePh.D. Rutgers University, 2018
External Websitehttps://www.nguyenlab.org/

Graduate Program Affiliations:

 

Molecular Mechanisms of Genome Integrity

 

In the Nguyen Lab we are fascinated with understanding how cells organize and segregate their genomes and how these processes can be rewired across different cellular contexts. To answer these questions, we use mammalian cell lines and a combination of high-resolution microscopy, genetic and molecular techniques, and large-scale CRISPR-Cas9 based functional genetic screens. Our approach is to harness the context-specific gene requirements that are intrinsic to cell function as a way to uncover how cells regulate their genomes and understand how alterations in these processes influence disease, development, and evolution.

 

 

How does the cohesin complex maintain functional diversity?

A diagram of a cell.  AI-generated content may be incorrect.

 

The cohesin complex is a key regulator of genome integrity, contributing to multiple functions including DNA organization, DNA replication, transcription, the DNA damage response, and cell division. Misregulation of cohesin function is devastating and is a key contributor to cancer and genetic diseases. But how does the cohesin complex know where to go and what job to do?

 

We are using large-scale screening approaches combined with targeted genetic and molecular techniques to identify regulators of the cohesin complex and define their function. Using this approach, we recently discovered the cohesin regulatory protein PRR12. Current work seeks to understand the role of PRR12 in regulating cohesin stability and the DNA damage response.

 

 

How is cell division altered across cellular contexts?

Cell division is a fundamental process where cells duplicate and segregate their genomes. To achieve this, hundreds of proteins must function together in a carefully choreographed dance to ensure the chromosomes are segregated faithfully. We are fascinated in understanding how these mechanisms are rewired across diverse cellular contexts including in different cell types, cells states, in stress conditions, and within disease.

 

A diagram of cancer cells.  AI-generated content may be incorrect.

 

By harnessing differential gene requirements, we uncovered the functionof the enigmatic CENP-O complex in cell division and identified why these proteins are only required in select cancers. Current work builds on these approaches, investigating other selectively required cell division genes we have identified. We seek to define the function of these proteins, identify why they are selectively required, and determine how we can exploit these factors to target disease.

 

How do gene requirements change across species?

Mice and other mammals are often used as models for human disease, with the assumption that the proteins and pathways in these organisms will be highly conserved. However, our work and others has begun to reveal striking differences in gene requirements across even closely related mammalian species. Understanding these differences will help reveal the fundamental biology by which cells function and provide critical insight into the evolution of core cellular processes. To achieve this, we are performing pooled CRIPSR-Cas9 based functional genetic screens in cell lines from diverse animal models.

 

A diagram of a gene knockout.  AI-generated content may be incorrect.

Publications

 

  1. Nguyen, A.L. Smith, E., Cheeseman, I.M. (2025). Co-essentiality Analysis Identifies PRR12 as a Cohesin Interacting Protein and a Contributor to Genomic Integrity. Developmental Cell. PMID: 39742660.
  2. Dudka, D., Nguyen, A.L., Boese, K., Marescal, O. Akins, B., Black, B.E., Cheeseman, I.M., Lampson, M.A. (2025) Bi-directional modulation of centromere binding via evolutionary innovation in the CENPT histone fold domain. Current Biology. (Manuscript Accepted). 
  3. Nguyen, A.L. Fadel, M.D., Cheeseman, I.M. (2021). “Differential Requirements for the    CENP-O Complex Reveal Parallel PLK1 Kinetochore Recruitment Pathways”. Molecular Biology of the Cell. 32(8):712-721. PubMed PMID: 33596090.
  4. Blengini, C.S., Nguyen, A.L., Aboelenain, M., Schindler K. (2022). “Age-dependent integrity of the meiotic spindle assembly checkpoint in females requires Aurora kinase B”. Aging Cell. 20(11). e13489. PubMed PMID: 34704342.
  5. Nguyen, A.L., Drutovic, D., Gentilello, A., Malumbres, M., Solc, P., Schindler K.  (2018). “Genetic interactions between the Aurora kinases reveal new requirements for AURKB and AURKC during oocyte meiosis”. Current Biology. 28 (21): 3458-3468 PubMed PMID: 30415701.
  6. Marin, D.*, Nguyen, A.L*., Schindler, K. (2018). “Using mouse oocytes to access human gene function during Meiosis I”. *Equal contribution. J. Vis. Exp. (134). e57442. PubMed PMID: 29708548.
  7. Pascottini, O.B., Goszczynski, D.E., Nguyen, A.L. (2017). “Creating Chimeras: Embryonic stem cells incorporated”. Molecular Reproduction & Development. 85: 85-85.
  8. Nguyen, A.L., Marin, D., Zhou, A., Cao, Z., Fedick, A., Wang, Y., Taylor, D., Scott, R.T., Xing, J. Treff, N. Schindler, K. (2017). “Identification and characterization of Aurora Kinase B and C Variants associated with maternal aneuploidy”. Molecular Human Reproduction. 23(6): 406-416. PubMed PMID: 28369513.
  9. Nguyen, A.L. Schindler, K. (2017). “Specialize and divide (twice). Functions of the three Aurora kinase homologs in mammalian oocyte meiotic maturation”. Trends  in Genetics. 33(5): 349-363. PubMed PMID:28359584.
  10. Schang, G., Fernandez-Fuertes, B., Lean, S.C., Nguyen, A.L., Pascottini, O.B. (2017). “ Infinity sperm storage: The gift that keeps on giving”. Molecular Reproduction &. Development. 84(8). 667-667.
  11. Radford, S., Nguyen, A.L., Schindler, K., McKim, K. (2016). “The chromosome basis of       acentrosomal spindle assembly and function”. Chromosoma. 126(3): 351-364. PubMed PMID: 27837282.
  12. Balboula, A.Z., Nguyen, A.L., Gentilello, A.S., Quartuccio, S.M., Drutovic, D., Solc, P., Schindler, K. (2016). “Haspin kinase regulates microtubule-organizing center clustering and stability through Aurora kinase C in mouse oocytes”. Journal of Cell  Science. 129(19): 3648-3660. PubMed PMID: 27562071.
  13. Nguyen, A.L., Gentilello A., Balboula A., Shrivastava V., Ohring J., Schindler K. (2014). “Phosphorylation of Threonine 3 on Histone 3 by Haspin Kinase is Required  for Meiosis I in Mouse Oocytes”. Journal of Cell Science. 127(23): 5066-5078.  PubMed PMID: 25315835.
  14. Chu H., Liao Y., Novak J., Hu J., Merkin J.J., Shymkiv Y., Braeckman B., Dorovkov M., Nguyen A., Clifford P., Nagele R., Harrison D., Ellis R., Ryazanov A.G. (2014). “Germline quality control: eEF2K stands guard to eliminate defective oocytes”. Developmental Cell. 28(5): 561-572. PubMed PMID: 24582807.

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