About

P. Todd Stukenberg is a Professor of Biochemistry and Molecular Genetics at the University of Virginia School of Medicine. His educational background includes a BA in Molecular Biology from Colgate University, a PhD in Biochemistry from Sloan-Kettering Cancer Institute and Cornell Medical School, and a postdoctoral fellowship in Cell Biology at Harvard Medical School. His research focuses on the mechanisms of chromosome segregation in mitosis and the generation of chromosomal instability in tumors. His work investigates how defects in chromosome segregation can lead to aneuploidy, a condition prevalent in human tumors and a major cause of miscarriages and birth defects. The Stukenberg lab studies the pathways that power chromosome movements, ensure proper microtubule attachments, and regulate the transcription at inner centromeres during mitosis. A significant aspect of his research involves the Aurora B kinase, a critical mitotic regulator that localizes to the inner centromere region and is a target for chemotherapeutics. His team has characterized the subunits of the Ndc80 complex, essential for kinetochore-microtubule attachments, and studies how kinetochores move chromosomes and how the spindle checkpoint is coupled to microtubule attachments. Additionally, his research explores how tumors exhibit higher rates of chromosome missegregation, known as chromosomal instability, using bioinformatic approaches and model systems to understand these changes.

Research topics

• Biology
• Genetics
• Medicine
• Internal medicine
• Bioinformatics
• Computational biology
• Pathology
• Cell biology
• Cancer research
• Oncology

Selected publications

• Cahn-Hilliard dynamical models for condensed biomolecular systems

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-17

  preprintOpen access

  Biomolecular condensates create dynamic subcellular compartments that alter systems-level properties of the networks surrounding them. One model combining soluble and condensed states is the Cahn-Hilliard equation, which specifies a diffuse interface between the two phases. Customized approaches required to solve this equation are largely inaccessible. Using two complementary numerical strategies, we built stable, self-consistent Cahn-Hilliard solvers in Python, MATLAB, and Julia. The algorithms simulated the complete time evolution of condensed droplets as they dissolved or persisted, relating critical droplet size to a coefficient for the diffuse interface in the Cahn-Hilliard equation. We applied this universal relationship to the chromosomal passenger complex, a multi-protein assembly that reportedly condenses on mitotic chromosomes. The fully constrained Cahn-Hilliard simulations yielded dewetting and coarsening behaviors that closely mirrored experiments in different cell types. The Cahn-Hilliard equation tests whether condensate dynamics behave as a phase-separated liquid, and its numerical solutions advance generalized modeling of biomolecular systems.

  PublisherOA PDFDOI

• Abstract 2406 Inhibition of Aurora B kinase autoactivation by lysine methylation of the activation loop

  Journal of Biological Chemistry · 2024-03-01

  articleOpen accessSenior author

  Most protein kinases are capable of autoactivating by phosphorylating their activation loops, but their activities in cells are tightly constrained. The factors responsible for fine-tuning kinase activity are clinically significant because many human diseases are driven by kinase hypo- or hyperactivation. The phosphatase-mediated inactivation of an already active kinase by dephosphorylation of the activation loop is well understood, but significantly less attention has been paid to a complementary and fundamentally distinct mode of regulation, in which an inactive kinase is outright prevented from undergoing autoactivation. This kind of regulation has been shown to modulate the activities of several kinases in cells, and it often proceeds by modification of the activation loop, rendering it a poorer substrate for the kinase. Here, we document a new example of such regulation for the mitotic kinase Aurora B, demonstrating that its autoactivation can be blocked by methylation of a single lysine residue within its activation loop. We show, using in vitro biochemistry with purified components, that Aurora B kinase is a substrate for the lysine methyltransferases (KMTs) G9a and SETD6, which are recently established regulators of related mitotic kinase Plk1. Incubation of initially inactive Aurora B with either KMT yields a methylated kinase, which, upon addition of ATP, fails to phosphorylate its own activation loop as well as other substrates. We find that the activity of Aurora B in synchronized, mitotic human RPE-1 cells is increased by the addition of inhibitors against the same KMTs. We provide evidence that this regulation is conferred by a single lysine residue within the activation loop of Aurora B, because purified Aurora B harboring an arginine substitution at the position of the critical lysine is not inhibited by KMTs. We conclude that the activation loop of Aurora B kinase contains an unexpected site for negative regulation of autoactivation, allowing fine-tuning of Aurora B activity during mitosis. We speculate that similar mechanisms may be important for the regulation of other kinases. Our findings strengthen our emerging understanding of how KMTs modulate kinase signaling during mitosis. We anticipate that continued investigation of how other kinases might be similarly regulated will broaden our understanding of complex cellular signaling networks and potentially reveal new therapeutic targets. Luke Eldredge was supported by 5T32GM008136-35. Todd Stukenberg was supported by 5R35GM148181-02.

  PublisherOA PDFDOI

• Author response: Structural basis for the phase separation of the chromosome passenger complex

  2024-02-05

  peer-reviewOpen access
  PublisherDOI

• Structural basis for the phase separation of the chromosome passenger complex

  eLife · 2024-03-08 · 7 citations

  articleOpen access

  The physical basis of phase separation is thought to consist of the same types of bonds that specify conventional macromolecular interactions yet is unsatisfyingly often referred to as ‘fuzzy’. Gaining clarity on the biogenesis of membraneless cellular compartments is one of the most demanding challenges in biology. Here, we focus on the chromosome passenger complex (CPC), that forms a chromatin body that regulates chromosome segregation in mitosis. Within the three regulatory subunits of the CPC implicated in phase separation – a heterotrimer of INCENP, Survivin, and Borealin – we identify the contact regions formed upon droplet formation using hydrogen/deuterium exchange mass spectrometry (HXMS). These contact regions correspond to some of the interfaces seen between individual heterotrimers within the crystal lattice they form. A major contribution comes from specific electrostatic interactions that can be broken and reversed through initial and compensatory mutagenesis, respectively. Our findings reveal structural insight for interactions driving liquid-liquid demixing of the CPC. Moreover, we establish HXMS as an approach to define the structural basis for phase separation.

  PublisherDOI

• Chromosomal passenger complex condensates generate parallel microtubule bundles in vitro

  Journal of Biological Chemistry · 2024-01-23 · 14 citations

  articleOpen accessSenior authorCorresponding

  The mitotic spindle contains many bundles of microtubules (MTs) including midzones and kinetochore fibers, but little is known about how bundled structures are formed. Here, we show that the chromosomal passenger complex (CPC) purified from Escherichia coli undergoes liquid-liquid demixing in vitro. An emergent property of the resultant condensates is to generate parallel MT bundles when incubated with free tubulin and GTP in vitro. We demonstrate that MT bundles emerge from CPC droplets with protruding minus ends that then grow into long and tapered MT structures. During this growth, we found that the CPC in these condensates apparently reorganize to coat and bundle the resulting MT structures. CPC mutants attenuated for liquid-liquid demixing or MT binding prevented the generation of parallel MT bundles in vitro and reduced the number of MTs present at spindle midzones in HeLa cells. Our data demonstrate that an in vitro biochemical activity to produce MT bundles emerges after the concentration of the CPC and provides models for how cells generate parallel-bundled MT structures that are important for the assembly of the mitotic spindle. Moreover, these data suggest that cells contain MT-organizing centers that generate MT bundles that emerge with the opposite polarity from centrosomes.

  PublisherOA PDFDOI

• Integrative single-cell meta-analysis reveals disease-relevant vascular cell states and markers in human atherosclerosis

  Cell Reports · 2023 · 99 citations

  • Biology
  • Computational biology
  • Bioinformatics

  Coronary artery disease (CAD) is characterized by atherosclerotic plaque formation in the arterial wall. CAD progression involves complex interactions and phenotypic plasticity among vascular and immune cell lineages. Single-cell RNA-seq (scRNA-seq) studies have highlighted lineage-specific transcriptomic signatures, but human cell phenotypes remain controversial. Here, we perform an integrated meta-analysis of 22 scRNA-seq libraries to generate a comprehensive map of human atherosclerosis with 118,578 cells. Besides characterizing granular cell-type diversity and communication, we leverage this atlas to provide insights into smooth muscle cell (SMC) modulation. We integrate genome-wide association study data and uncover a critical role for modulated SMC phenotypes in CAD, myocardial infarction, and coronary calcification. Finally, we identify fibromyocyte/fibrochondrogenic SMC markers (LTBP1 and CRTAC1) as proxies of atherosclerosis progression and validate these through omics and spatial imaging analyses. Altogether, we create a unified atlas of human atherosclerosis informing cell state-specific mechanistic and translational studies of cardiovascular diseases.

  PublisherOA PDFDOI

• Aurora kinases: Generators of spatial control during mitosis

  Frontiers in Cell and Developmental Biology · 2023-03-13 · 23 citations

  reviewOpen accessSenior author

  Cell division events require regulatory systems to ensure that events happen in a distinct order. The classic view of temporal control of the cell cycle posits that cells order events by linking them to changes in Cyclin Dependent Kinase (CDK) activities. However, a new paradigm is emerging from studies of anaphase where chromatids separate at the central metaphase plate and then move to opposite poles of the cell. These studies suggest that distinct events are ordered depending upon the location of each chromosome along its journey from the central metaphase plate to the elongated spindle poles. This system is dependent upon a gradient of Aurora B kinase activity that emerges during anaphase and acts as a spatial beacon to control numerous anaphase/telophase events and cytokinesis. Recent studies also suggest that Aurora A kinase activity specifies proximity of chromosomes or proteins to spindle poles during prometaphase. Together these studies argue that a key role for Aurora kinases is to provide spatial information that controls events depending upon the location of chromosomes or proteins along the mitotic spindle.

  PublisherOA PDFDOI

• Author Reply to Peer Reviews of Structural Basis for the Phase Separation of the Chromosome Passenger Complex

  2023-07-23

  peer-review
  PublisherDOI

• Structural Basis for the Phase Separation of the Chromosome Passenger Complex

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-05-22 · 3 citations

  preprintOpen access

  The physical basis of phase separation is thought to consist of the same types of bonds that specify conventional macromolecular interactions yet is unsatisfyingly often referred to as 'fuzzy'. Gaining clarity on the biogenesis of membraneless cellular compartments is one of the most demanding challenges in biology. Here, we focus on the chromosome passenger complex (CPC), that forms a chromatin body that regulates chromosome segregation in mitosis. Within the three regulatory subunits of the CPC implicated in phase separation - a heterotrimer of INCENP, Survivin, and Borealin - we identify the contact regions formed upon droplet formation using hydrogen/deuterium-exchange mass spectrometry (HXMS). These contact regions correspond to some of the interfaces seen between individual heterotrimers within the crystal lattice they form. A major contribution comes from specific electrostatic interactions that can be broken and reversed through initial and compensatory mutagenesis, respectively. Our findings reveal structural insight for interactions driving liquid-liquid demixing of the CPC. Moreover, we establish HXMS as an approach to define the structural basis for phase separation.

  PublisherOA PDFDOI

• Contributors

  Elsevier eBooks · 2022-11-11

  book-chapter
  PublisherDOI

Recent grants

• Expanding the Xenopus ORFeome to genome-scale by de novo cloning of protein-coding gene models

  NIH · $2.3M · 2017–2021

• Mechanisms to move and steer chromosomes

  NIH · $1.7M · 2018–2023

• NIH Grant R01HD069352

  NIH · $3.6M · 2017

• NIH Grant R01GM081576

  NIH · $1.2M · 2013

• Molecular Mechanisms of Mitotic Regulation

  NIH · $1.8M · 2017–2022

Frequent coauthors

• Mike O’Donnell

  Rockefeller University

  46 shared

• Marc W. Kirschner

  Harvard University Press

  35 shared

• Minhui Shen

  Sun Yat-sen University

  20 shared

• Jian Kuang

  19 shared

• Michael B. Yaffe

  Massachusetts Institute of Technology

  19 shared

• Harrison Echols

  16 shared

• Jian Xu

  16 shared

• Kathleen Mc Entee

  Université Libre de Bruxelles

  16 shared

Education

• PhD, Microbiology

  Joan and Sanford I Weill Medical College of Cornell University

  1993

• BA

  Colgate University

  1986