Donald Fox

Overview:

Please visit www.foxlabduke.com

Research overview:
Genomic extremes in organ development and repair.

The genome provides the blueprint for life. To achieve specialized cell or tissue function, specific genome features can be altered or exploited in extreme ways. My research program focuses on two such extreme genome variations: polyploidy and codon usage bias (defined below). In multicellular organisms with specialized organ systems, the function and regulation of these two extreme genome variations remains largely mysterious. We established accessible models where these two extreme genome variations impact cell and tissue biology.

1) Polyploidy. In numerous tissues or whole organisms, one nucleus can contain tens to thousands of genomes. Such whole genome duplication, or polyploidy, massively alters the transcriptome, proteome, and metabolome. We are only just beginning to understand the purposes of polyploidy in three crucial settings: organ development, organ repair, and ectopic polyploidy that can contribute to disease. My laboratory established accessible models of these processes using Drosophila. Our goal is to uncover fundamental functions and distinguishing regulation of polyploidy.

2) Codon usage bias. The genetic code is redundant, with 61 codons encoding 20 amino acids. Despite this redundancy, synonymous codons encoding the same amino acid occur at varying frequencies. “Rare” codons occur least often while other “common” codons occur most often. Altering codon bias across evolution affects mRNA translation and has biological consequences. The impact of codon bias on tissue-specific differentiation has been largely unexplored. In Drosophila, we discovered that the ability to express genes enriched in rare codons is a defining characteristic of at least two specific organs. We are uncovering evidence that these organs express rare codon-enriched genes to achieve cell and tissue-specific identity. We are thus well-poised to define, for the first time, the role of codon bias in tissue-specific development.

Positions:

Associate Professor of Pharmacology & Cancer Biology

Pharmacology & Cancer Biology
School of Medicine

Assistant Professor in Cell Biology

Cell Biology
School of Medicine

Associate of the Duke Initiative for Science & Society

Duke Science & Society
Institutes and Provost's Academic Units

Member of the Duke Cancer Institute

Duke Cancer Institute
School of Medicine

Affiliate of the Duke Regeneration Center

Regeneration Next Initiative
School of Medicine

Education:

B.S. 2000

College of William and Mary

Ph.D. 2006

University of North Carolina - Chapel Hill

Grants:

Hypertrophy vs. Proliferation Following Tissue Injury: A Drosophila Model

Administered By
Pharmacology & Cancer Biology
Awarded By
American Heart Association
Role
Principal Investigator
Start Date
End Date

Impact of polyploidy on establishing an HIV-1 reservoir in the kidney

Administered By
Medicine, Infectious Diseases
Awarded By
University of Alabama at Birmingham
Role
Principal Investigator
Start Date
End Date

Par-4 Regulation and Function in Breast Cancer Dormancy and Recurrence

Administered By
Pharmacology & Cancer Biology
Awarded By
National Institutes of Health
Role
Co Investigator
Start Date
End Date

Polyploidy after tissue injury: a Drosophila model

Administered By
Pharmacology & Cancer Biology
Awarded By
National Institutes of Health
Role
Principal Investigator
Start Date
End Date

Broken chromosome segregation during mitosis: a Drosophila model

Administered By
Pharmacology & Cancer Biology
Awarded By
National Institutes of Health
Role
Principal Investigator
Start Date
End Date

Publications:

Conserved Chamber-Specific Polyploidy Maintains Heart Function in Drosophila.

Developmentally programmed polyploidy (whole-genome-duplication) of cardiomyocytes is common across evolution. Functions of such polyploidy are essentially unknown. Here, we reveal roles for precise polyploidy levels in cardiac tissue. We highlight a conserved asymmetry in polyploidy level between cardiac chambers in Drosophila larvae and humans. In Drosophila , differential Insulin Receptor (InR) sensitivity leads the heart chamber to reach a higher ploidy/cell size relative to the aorta chamber. Cardiac ploidy-reduced animals exhibit reduced heart chamber size, stroke volume, cardiac output, and acceleration of circulating hemocytes. These Drosophila phenotypes mimic systemic human heart failure. Using human donor hearts, we reveal asymmetry in nuclear volume (ploidy) and insulin signaling between the left ventricle and atrium. Our results identify productive and likely conserved roles for polyploidy in cardiac chambers and suggest precise ploidy levels sculpt many developing tissues. These findings of productive cardiomyocyte polyploidy impact efforts to block developmental polyploidy to improve heart injury recovery.
Authors
Chakraborty, A; Peterson, NG; King, JS; Gross, RT; Pla, MM; Thennavan, A; Zhou, KC; DeLuca, S; Bursac, N; Bowles, DE; Wolf, MJ; Fox, DT
MLA Citation
Chakraborty, Archan, et al. “Conserved Chamber-Specific Polyploidy Maintains Heart Function in Drosophila.Biorxiv, Feb. 2023. Pubmed, doi:10.1101/2023.02.10.528086.
URI
https://scholars.duke.edu/individual/pub1566938
PMID
36798187
Source
pubmed
Published In
Biorxiv
Published Date
DOI
10.1101/2023.02.10.528086

Measuring Cellular Ploidy In Situ by Light Microscopy.

Determining cellular DNA content is valuable in the study of numerous biological processes, including organ development and injury repair. While FACS analysis of dissociated cells is a widely used method for assaying ploidy in a tissue cell population, for many tissue samples, it is possible and convenient to measure ploidy in situ using light microscopy. Here, we present two protocols for measuring cellular ploidy in tissues. These protocols are based on our studies in Drosophila melanogaster, but these are applicable to other settings as well. We present example results from Drosophila hindgut, midgut, and wing imaginal disc as examples. The first protocol focuses on measuring DNA content from decondensed interphase nuclei, while the second protocol details the visualization of condensed chromosomes for ploidy determination, either from mitotic cells or from interphase cells with drug-induced chromosome condensation. These techniques can be completed in 1 day and require standard lab supplies as well as a fluorescence light microscope.
Authors
Clay, DE; Stormo, BM; Fox, DT
MLA Citation
Clay, Delisa E., et al. “Measuring Cellular Ploidy In Situ by Light Microscopy.Methods Mol Biol, vol. 2545, 2023, pp. 401–12. Pubmed, doi:10.1007/978-1-0716-2561-3_21.
URI
https://scholars.duke.edu/individual/pub1565029
PMID
36720825
Source
pubmed
Published In
Methods Mol Biol
Volume
2545
Published Date
Start Page
401
End Page
412
DOI
10.1007/978-1-0716-2561-3_21

Physiology, Development, and Disease Modeling in the Drosophila Excretory System.

The insect excretory system contains two organ systems acting in concert: the Malpighian tubules and the hindgut perform essential roles in excretion and ionic and osmotic homeostasis. For over 350 years, these two organs have fascinated biologists as a model of organ structure and function. As part of a recent surge in interest, research on the Malpighian tubules and hindgut of Drosophila have uncovered important paradigms of organ physiology and development. Further, many human disease processes can be modeled in these organs. Here, focusing on discoveries in the past 10 years, we provide an overview of the anatomy and physiology of the Drosophila excretory system. We describe the major developmental events that build these organs during embryogenesis, remodel them during metamorphosis, and repair them following injury. Finally, we highlight the use of the Malpighian tubules and hindgut as accessible models of human disease biology. The Malpighian tubule is a particularly excellent model to study rapid fluid transport, neuroendocrine control of renal function, and modeling of numerous human renal conditions such as kidney stones, while the hindgut provides an outstanding model for processes such as the role of cell chirality in development, nonstem cell-based injury repair, cancer-promoting processes, and communication between the intestine and nervous system.
Authors
Cohen, E; Sawyer, JK; Peterson, NG; Dow, JAT; Fox, DT
MLA Citation
Cohen, Erez, et al. “Physiology, Development, and Disease Modeling in the Drosophila Excretory System.Genetics, vol. 214, no. 2, Feb. 2020, pp. 235–64. Pubmed, doi:10.1534/genetics.119.302289.
URI
https://scholars.duke.edu/individual/pub1430411
PMID
32029579
Source
pubmed
Published In
Genetics
Volume
214
Published Date
Start Page
235
End Page
264
DOI
10.1534/genetics.119.302289

Accelerated cell cycles enable organ regeneration under developmental time constraints in the<i>Drosophila</i>hindgut

<h4>Summary</h4> Individual organ development must be temporally coordinated with development of the rest of the organism. As a result, cell division in a developing organ occurs on a relatively fixed time scale. Despite this, many developing organs can regenerate cells lost to injury. How organs regenerate within the time constraints of organism development remains unclear. Here, we show the developing Drosophila hindgut regenerates by accelerating the mitotic cell cycle. This process requires JAK/STAT signaling and is achieved by decreasing G1 length during the normal period of developmental mitoses. Mitotic capacity is then terminated by the steroid hormone ecdysone receptor. This receptor activates a hindgut-specific enhancer of fizzy-related , a negative regulator of mitotic cyclins. We further identify the Sox transcription factor Dichaete as an important negative regulator of injury-induced mitotic cycles. Our findings reveal how mitotic cell cycle entry mechanisms can be adapted to accomplish developmental organ regeneration.
Authors
MLA Citation
URI
https://scholars.duke.edu/individual/pub1432701
Source
epmc
Published Date
DOI
10.1101/2020.02.17.953075

Cytoplasmic sharing through apical membrane remodeling

<h4>ABSTRACT</h4> Multiple nuclei sharing a common cytoplasm are found in diverse tissues, organisms, and diseases. Yet, multinucleation remains a poorly understood biological property. Cytoplasm sharing invariably involves plasma membrane breaches. In contrast, we discovered cytoplasm sharing without membrane breaching in highly resorptive Drosophila rectal papillae. During a six-hour developmental window, 100 individual papillar cells assemble a multinucleate cytoplasm, allowing passage of proteins of at least 27kDa throughout papillar tissue. Papillar cytoplasm sharing does not employ canonical mechanisms such as failed cytokinesis or muscle fusion pore regulators. Instead, sharing requires gap junction proteins (normally associated with transport of molecules <1kDa), which are positioned by membrane remodeling GTPases. Our work reveals a new role for apical membrane remodeling in converting a multicellular epithelium into a giant multinucleate cytoplasm. <h4>ONE SENTENCE SUMMARY</h4> Apical membrane remodeling in a resorptive Drosophila epithelium generates a shared multinuclear cytoplasm.
Authors
Peterson, N; Stormo, B; Schoenfelder, K; King, J; Lee, R; Fox, D
MLA Citation
Peterson, Nora, et al. Cytoplasmic sharing through apical membrane remodeling. 2020. Epmc, doi:10.1101/2020.02.22.960187.
URI
https://scholars.duke.edu/individual/pub1432702
Source
epmc
Published Date
DOI
10.1101/2020.02.22.960187

Research Areas:

Aneuploidy
Cell Cycle
Gene Dosage
Genome
Genomic Instability
Image Processing, Computer-Assisted
Microscopy, Confocal
Polyploidy
Transcriptome