About

Kevin A. Janes is a Professor in the Department of Biochemistry and Molecular Genetics at the University of Virginia School of Medicine. He holds a BS in Biomedical Engineering from Johns Hopkins University and a PhD in Bioengineering from the Massachusetts Institute of Technology. He completed a postdoctoral fellowship in Cell Biology at Harvard Medical School. His research focuses on systems-biology approaches to cancer biology and virology, emphasizing the study of changes in cellular behavior that underlie development, disease, and homeostasis. Professor Janes's group develops experimental and computational techniques to quantitatively monitor signaling networks activated by diverse stimuli and perturbations. His work involves collecting complex datasets and analyzing them through data-driven modeling to understand network-level questions about signal transduction. His research aims to elucidate how signaling networks enable cells to respond to their environment, which is particularly relevant to diseases such as cancer where molecular signal processing is disrupted. His current research interests include studying tissue responses of colonic epithelia and the morphogenetic responses of 3D-cultured mammary epithelia in vitro.

Research topics

• Biology
• Cancer research
• Genetics
• Cell biology
• Internal medicine
• Medicine
• Chemistry

Selected publications

• PCSK5M452I Is a Recessive Hypomorph Exclusive to MCF10DCIS.com Cells

  Molecular Cancer Research · 2025-10-28 · 2 citations

  articleSenior author

  The most widely used cell line for studying ductal carcinoma in situ (DCIS) premalignancy is the transformed breast epithelial cell line, MCF10DCIS.com. During its original clonal isolation and selection, MCF10DCIS.com acquired a heterozygous M452I mutation in the proprotein convertase PCSK5, which has never been reported in any human cancer. The mutation is noteworthy because PCSK5 matures GDF11, a TGFβ superfamily ligand that suppresses progression of triple-negative breast cancer. We asked here whether PCSK5M452I and its activity toward GDF11 might contribute to the unique properties of MCF10DCIS.com. Using an optimized in-cell GDF11 maturation assay, we found that overexpressed PCSK5M452I was measurably active but at a fraction of the wild-type enzyme. In a PCSK5-/- clone of MCF10DCIS.com reconstituted with different PCSK5 alleles, PCSK5M452I was mildly defective in anterograde transport. However, the multicellular organization of PCSK5M452I addback cells in three-dimensional Matrigel cultures was significantly less circumscribed than wild-type and indistinguishable from a PCSK5T288P-null allele. Growth of intraductal MCF10DCIS.com xenografts was similarly impaired along with the frequency of comedo necrosis and stromal activation. In no setting did PCSK5M452I exhibit gain-of-function activity, leading us to conclude that it is hypomorphic and thus compensated by the remaining wild-type allele in MCF10DCIS.com. IMPLICATIONS: This work reassures that an exotic PCSK5 mutation is not responsible for the salient characteristics of the MCF10DCIS.com cell line.

  PublisherDOI

• Ten simple rules for developing a training program

  PLoS Computational Biology · 2025-07-11

  articleOpen accessCorresponding
  PublisherDOI

• Systems virology at scale

  Current Opinion in Systems Biology · 2025-10-15

  articleOpen accessSenior authorCorresponding
  PublisherOA PDFDOI

• Fast, flexible, learning-free organoid quantification and tracking with OrganoSeg2

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-16

  preprintOpen accessSenior authorCorresponding

  Organoids are routinely imaged by brightfield microscopy at low magnification, but these images are challenging to analyze quantitatively at scale. Given differences in organoid-culture format and image acquisition among research groups, there is a general need for versatile segmentation algorithms that refine for specific applications. Here, we introduce OrganoSeg2, an overhauled software that substantively advances the multi-window adaptive thresholding of its predecessor. OrganoSeg2 gives users access to additional segmentation parameters that were latent in OrganoSeg, and common operations are accelerated ~10-fold. Using data from six organoid types, we find that the generalized segmentation accuracy of OrganoSeg2 surpasses multiple alternatives, including segmenters based on deep learning. OrganoSeg2 adds longitudinal single-organoid tracking and multicolor fluorescence quantification, which we use to examine growth trajectories and radiotherapy responses in luminal breast cancer organoids. OrganoSeg2 is shared freely as installation packages for current users and source code for future developers (https://github.com/JanesLab/OrganoSeg2).

  PublisherOA PDFDOI

• Age-dependent topoisomerase I depletion alters recruitment of rDNA silencing complexes

  Journal of Biological Chemistry · 2025-12-17

  articleOpen access

  Genomic instability and loss of proteostasis are two of the primary Hallmarks of Aging. Although these hallmarks are well-defined in the literature, the mechanisms that drive genomic instability and loss of proteostasis as cells age are still incompletely understood. Using budding yeast replicative lifespan as a model for aging in actively dividing cells, we identify nuclear proteins that are depleted in the earliest stages of aging. We find that many age-depleted proteins are involved in ribosome biogenesis, specifically in ribosome processing, or in maintenance of chromatin stability. We focus on topoisomerase I (Top1) as a novel age-depleted nuclear protein and determine that its depletion in the early stages of aging is not a result of transcriptional changes or changes in protein turnover. Despite the stark depletion of Top1 in early aging, we find that rescue of this age-dependent depletion is harmful to replicative lifespan. When overexpressed, Top1 disrupts the stoichiometry of the RENT complex by pulling Sir2 away from the ribosomal DNA (rDNA), a phenotype that is further enhanced when the overexpressed Top1 is catalytically dead. Loss of Sir2 from the rDNA via the overexpression of catalytically dead Top1 decreases RNA Pol II silencing of a reporter gene inside or adjacent to the rDNA, consistent with the lifespan defect. Finally, we show that the catalytic activity of Top1 plays an important role in the establishment of rDNA silencing, raising the possibility that rDNA secondary structure/DNA topology is important for RNA Pol I-dependent spreading of silent chromatin across the rDNA locus.

  PublisherDOI

• PCSK5 ^M452I is a recessive hypomorph exclusive to MCF10DCIS.com cells

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-07

  preprintSenior author

  ABSTRACT The most widely used cell line for studying ductal carcinoma in situ (DCIS) premalignancy is the transformed breast epithelial cell line, MCF10DCIS.com . During its original clonal isolation and selection, MCF10DCIS.com acquired a heterozygous M452I mutation in the proprotein convertase PCSK5, which has never been reported in any human cancer. The mutation is noteworthy because PCSK5 matures GDF11, a TGFβ-superfamily ligand that suppresses progression of triple-negative breast cancer. We asked here whether PCSK5 M452I and its activity toward GDF11 might contribute to the unique properties of MCF10DCIS.com . Using an optimized in-cell GDF11 maturation assay, we found that overexpressed PCSK5 M452I was measurably active but at a fraction of the wildtype enzyme. In a PCSK5 −/− clone of MCF10DCIS.com reconstituted with different PCSK5 alleles, PCSK5 M452I was mildly defective in anterograde transport. However, the multicellular organization of PCSK5 M452I addback cells in 3D matrigel cultures was significantly less compact than wildtype and indistinguishable from a PCSK5 T288P null allele. Growth of intraductal MCF10DCIS.com xenografts was similarly impaired along with the frequency of comedo necrosis and stromal activation. In no setting did PCSK5 M452I exhibit gain-of-function activity, leading us to conclude that it is hypomorphic and thus compensated by the remaining wildtype allele in MCF10DCIS.com . Implications This work reassures that an exotic PCSK5 mutation is not responsible for the salient characteristics of the MCF10DCIS.com cell line.

  PublisherDOI

• Acid ceramidase inhibition enhances BCL-2 targeting in venetoclax-resistant acute myeloid leukemia via a cytotoxic integrated stress response

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-07

  preprintOpen access

  Abstract Resistance to combination regimens containing the BCL-2 inhibitor venetoclax in acute myeloid leukemia (AML) is a growing clinical challenge for this extensively utilized agent. We previously established the anti-leukemic properties of ceramide, a tumor-suppressive sphingolipid, in AML and demonstrated that upregulated expression of acid ceramidase (AC), a ceramide-neutralizing enzyme, supported leukemic survival and resistance to BH3 mimetics. Here, we report the anti-leukemic efficacy and mechanisms of co-targeting AC and BCL-2 in venetoclax-resistant AML. Analysis of the BeatAML dataset revealed a positive relationship between increased AC gene expression and venetoclax resistance. Targeting AC enhanced single-agent venetoclax cytotoxicity and the venetoclax + cytarabine combination in AML cell lines with primary or acquired venetoclax resistance. SACLAC + venetoclax was equipotent to the combination of venetoclax + cytarabine at reducing cell viability when evaluated ex vivo across a cohort of 71 primary AML patient samples. Mechanistically, SACLAC + venetoclax increased ceramide to levels that trigger a cytotoxic integrated stress response (ISR), ISR-mediated NOXA protein upregulation, mitochondrial dysregulation, and caspase-dependent cell death. Collectively, these data demonstrate the efficacy of co-targeting AC and BCL-2 in AML and rationalize targeting AC as a therapeutic approach to overcome venetoclax resistance.

  PublisherOA PDFDOI

• Cahn-Hilliard dynamical models for condensed biomolecular systems

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

  preprintOpen accessSenior authorCorresponding

  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

• Age-dependent topoisomerase I depletion alters recruitment of rDNA silencing complexes

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-01

  preprintOpen access

  Genomic instability and loss of proteostasis are two of the primary Hallmarks of Aging. Although these hallmarks are well-defined in the literature, the mechanisms that drive genomic instability and loss of proteostasis as cells age are still largely unknown. Using budding yeast replicative lifespan as a model for aging in actively dividing cells, we identified nuclear proteins that were depleted in the earliest stages of aging. We found that many age-depleted proteins were involved in ribosome biogenesis, specifically in ribosome processing, or in maintenance of chromatin stability. We focused on topoisomerase I (Top1) as a novel age-depleted nuclear protein and found that its depletion in the early stages of aging was not a result of transcriptional changes or changes in protein turnover. Despite the stark depletion of Top1 in early aging, rescue of this age-dependent depletion was actually harmful to replicative lifespan. We found that Top1, when overexpressed, disrupts the stoichiometry of the RENT complex by pulling Sir2 away from the ribosomal DNA (rDNA), a phenotype which is further enhanced when the overexpressed Top1 is catalytically dead. Loss of Sir2 from the rDNA via the overexpression of catalytically dead Top1 decreases RNA Pol II silencing of a reporter gene inside or adjacent to the rDNA, consistent with the lifespan defect. Finally, we found that the catalytic activity of Top1 plays an important role in the establishment of rDNA silencing, raising the possibility that rDNA secondary structure/DNA topology is important for RNA Pol I-dependent spreading of silent chromatin across the rDNA locus.

  PublisherOA PDFDOI

• Cells of the Maternal–Fetal Interface May Contribute to Epidural-Related Maternal Fever After Administration of Ropivacaine: The Role of Phosphatases DUSP9 and PHLPP1

  International Journal of Molecular Sciences · 2025-06-09

  articleOpen access

  Epidural-related maternal fever (ERMF) occurs with significant incidence in women receiving local anesthetics such as ropivacaine via epidural catheter for pain relief during labor. The causal mechanism behind this phenomenon is still not fully resolved, but evidence suggests that these anesthetics cause sterile inflammation. In this observational study, we investigated a possible contributory role of the dual-specificity phosphatase-9 (DUSP9) controlling the activity of mitogen-activated protein kinases (MAPK), and also PH-domain and Leucine-rich repeat phosphatase (PHLPP) regulating AKT kinases. The data show that ropivacaine differentially affects the expression of these phosphatases in distinct cell types of the umbilical cord and placenta. The gene expression of DUSP9 was almost completely switched off in the presence of ropivacaine in HUVECs and extravillous trophoblasts for up to 6 h, while the expression of PHLPP1 was upregulated in HUVECs and syncytiotrophoblasts. Extravillous trophoblasts were identified as a source of pro-inflammatory mediators and regulatory miRNAs in response to ropivacaine. Placentae at term exhibited a distinct DUSP9 expression pattern, whether the patients belonged to the control group or received epidural analgesia with or without elevated body temperature. The observed data imply that ropivacaine induces complex effects on the MAPK and AKT pathways at the feto-maternal interface, which contribute to the ERMF phenomenon.

  PublisherOA PDFDOI

Recent grants

• Heterogeneous Loss of GDF11 Tumor Suppression in Triple-negative Breast Cancer

  NIH · $1.4M · 2018–2024

• Heterogeneous Loss of GDF11 Tumor Suppression in Triple-negative Breast Cancer

  NIH · $361k · 2018–2022

• (PQB4) Stochastic Profiling of Functional Single-Cell States Within Solid Tumors

  NIH · $1.8M · 2015–2020

• Outreach Core

  NIH · $17.8M · 2022–2027

• NIH Grant R21AI105970

  NIH · $426k · 2015

Frequent coauthors

• Shambhavi Singh

  Massachusetts General Hospital

  54 shared

• Matthew D. Sutcliffe

  52 shared

• Kristen A. Atkins

  University of Virginia

  44 shared

• Jennifer A. Harvey

  University of Queensland

  28 shared

• Kathy Repich

  University of Virginia Health System

  27 shared

• Douglas A. Lauffenburger

  Massachusetts Institute of Technology

  26 shared

• Hui Zong

  University of Virginia Health System

  25 shared

• Michael B. Yaffe

  Massachusetts Institute of Technology

  22 shared