About

The Bugaj Lab at the University of Pennsylvania applies optogenetics and synthetic biology to study cell signaling and how proper cell signaling breaks down in cancer.

Research topics

• Neuroscience
• Cell biology
• Biology
• Computer Science
• Genetics
• Computational biology
• Physics
• Nanotechnology
• Materials science
• Chemistry

Selected publications

• A familiar newcomer to the thermogenetic toolset

  Nature Chemical Biology · 2026-04-16

  articleSenior authorCorresponding
  PublisherDOI

• Abstract A003: Adaptor sequestration and drug-induced potentiation of EGFR are widespread features of oncogenic RTK fusions

  Cancer Research · 2026-01-13

  articleSenior author

  Abstract Regulation of cancer cells by their environment contributes to tumorigenesis and drug response, though the extent to which the oncogenic state can alter a cell’s perception of its environment is not clear. EML4-ALK is a receptor tyrosine kinase (RTK) fusion oncoprotein that suppresses transmembrane EGFR signaling in cancer cells. ALK inhibition restores signaling through EGFR, thereby promoting survival and drug tolerance. Here we tested whether such modulation of EGFR activity was common among other RTK fusions, which collectively are found in ∼5% of all cancers. Using live- and fixed-cell microscopy in isogenic and patient-derived cell lines, we found that a wide variety of RTK-fusions suppress transmembrane EGFR and sequester essential adaptor proteins in the cytoplasm, as evidenced by the localization of endogenous Grb2. Targeted therapies rapidly released Grb2 from sequestration and potently reactivated EGFR. Engineered optogenetic analogs of RTK fusions confirmed that cytoplasmic sequestration of Grb2 was sufficient to suppress perception of extracellular EGF and could do so independent of driving signaling from the optogenetic fusion itself, demonstrating that fusion signaling and suppression of EGFR could be functionally decoupled. Our study uncovers that a large number of RTK fusions simultaneously act as both activators and suppressors of signaling, the mechanisms of which could be exploited for new biomimetic therapies that enhance cell killing and suppress drug tolerance. Citation Format: Yuzhi Gao, David Gonzalez-Martinez, Sofia Wissert, Hana Bader, Nidhi Sahni, Anh Le, Robert Doebele, Lukasz Bugaj. Adaptor sequestration and drug-induced potentiation of EGFR are widespread features of oncogenic RTK fusions [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Fusion-Positive Cancer: From Discovery to Therapy; 2026 Jan 13-15; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86(1_Suppl):Abstract nr A003.

  PublisherDOI

• Synthetic budding morphogenesis by optogenetic receptor tyrosine kinase signaling

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-02

  articleOpen access

  Summary The mammalian kidney relies on a branched network of collecting ducts for fluid transport and homeostasis. Replicating this network in vitro would parallelize function in synthetic replacement kidneys, yet current organoids have limited branching capacity. Here, we establish a developmentally-informed strategy to control organoid budding through optogenetic control of a receptor tyrosine kinase, RET. We first show pharmacological manipulation of RET signaling controls the extent of branching in mouse embryonic kidneys and human stem cell-derived kidney organoids. Next, we develop an optogenetic RET receptor (optoRET) that signals in a ligand-independent manner via blue light-mediated clustering. Epithelial cells expressing optoRET reproduce stereotyped RET signaling, scattering, and symmetry breaking in response to blue light. Human kidney organoids undergo budding with controllable orientation in response to spatially patterned optoRET stimulation. Our results establish ligand-free optogenetic control of branching and inspire new synthetic biology strategies for epithelial organoid design. Highlights GDNF-RET controls branching and tip cell state in mouse and human kidney tissues. OptoRET reproduces endogenous RET signaling and morphogenesis in cell lines. OptoRET enables ligand-free budding in human renal epithelial organoids. Spatially patterned optoRET stimulation controls budding orientation.

  PublisherOA PDFDOI

• Optogenetic Translocation to Subcellular Compartments through Regulation of Protein Avidity

  ACS Synthetic Biology · 2026-01-30

  articleSenior authorCorresponding

  Inducible translocation to subcellular compartments is a common strategy for protein switches that control a variety of cell behaviors. However, existing switches achieve translocation through induced dimerization, requiring constitutive anchoring of one component into the target compartment and optimization of relative expression levels between the two components. We present a simpler, single-component strategy called Avidity-assisted targeting (Aviatar). Aviatar achieves translocation with only a single protein by converting low-affinity monomers into high-avidity assemblies through inducible clustering. We demonstrated the Aviatar concept and its generality using optogenetic clustering to drive translocation to the plasma membrane, endosomes, golgi, endoplasmic reticulum, and microtubules using binding domains for lipids or endogenous proteins that were specific to those compartments. Aviatar recruitment regulated actin polymerization at the cell periphery and revealed compartment-specific signaling of receptor tyrosine kinase fusions associated with cancer. Finally, GFP-targeting Aviatar probes allowed inducible localization to any GFP-tagged target, including endogenously tagged stress granule proteins. Aviatar is a straightforward platform that can be rapidly adapted to a broad array of targets without the need for their prior modification or disruption.

  PublisherDOI

• Abstract 330: EGFR suppression and drug-induced potentiation are widespread features of oncogenic RTK fusions.

  Cancer Research · 2026-04-03

  articleSenior author

  Abstract Regulation of cancer cells by their environment contributes to tumorigenesis and drug response, though the extent to which the oncogenic state can alter a cell’s perception of its environment is not clear. Prior studies found that EML4-ALK, a receptor tyrosine kinase (RTK) fusion oncoprotein, suppresses transmembrane receptor signaling through EGFR. Moreover, suppression was reversed with targeted ALK inhibition, thereby promoting survival and drug tolerance. Here we tested whether such modulation of EGFR was common among other RTK fusions, which collectively are found in ∼5% of all cancers. Using live- and fixed-cell microscopy in isogenic and patient-derived cell lines, we found that a wide variety of RTK fusions suppress transmembrane EGFR and sequester essential adaptor proteins in the cytoplasm, as evidenced by the localization of endogenous Grb2. Targeted therapies rapidly released Grb2 from sequestration and potentiated EGFR. Synthetic optogenetic analogs of RTK fusions confirmed that cytoplasmic sequestration of Grb2 was sufficient to suppress perception of extracellular EGF and could do so without driving signaling from the synthetic fusion itself, demonstrating that fusion signaling and suppression of EGFR could be functionally decoupled. Our study uncovers that a large number of RTK fusions simultaneously act as both activators and suppressors of signaling, the mechanisms of which could be exploited for new biomimetic therapies that enhance cell killing and suppress drug tolerance. Citation Format: Carol Gao, David Gonzalez Martinez, Sofia Wissert, Hana Bader, Nidhi Sahni, Anh T. Le, Robert C. Doebele, Lukasz Bugaj. EGFR suppression and drug-induced potentiation are widespread features of oncogenic RTK fusions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 330.

  PublisherDOI

• Abstract B007: Low-order assemblies drive RTK fusion signaling without condensation

  Cancer Research · 2026-01-13

  articleSenior author

  Abstract Receptor tyrosine kinase (RTK) fusions are a diverse class of oncoproteins that have been identified in ∼5% of cancers. RTK fusions are chimeric proteins where the intracellular domain of an RTK is fused to an oligomeric domain from an unrelated protein. Such fusions can drive oncogenic signaling from the RTK fragment despite their cytoplasmic localization, away from the plasma membrane where normal transmembrane RTK signaling occurs, thus posing mechanistic questions of how RTK fusions transmit oncogenic signals. Recent studies have suggested that condensation is essential for signaling from RTK fusions because condensates can organize the necessary signaling machinery in the cytoplasm. In our study we tested this hypothesis using live cell fluorescent imaging, quantitative analysis of condensation, single-cell analysis, and synthetic biology, focusing on condensates of EML4-ALK, a granule-forming RTK fusion that is found in ∼5% of non-small cell lung cancer. We found weak correspondence between condensate formation and downstream signaling. Although signaling (Erk activation) was a direct function of oncogene expression, condensation was maximal only at intermediate expression levels, resulting in high-expressing cells that had the strongest signaling but no condensation as assessed under high magnification confocal microscopy. Furthermore, increasing the magnitude of condensation through multiple methods did not result in increase in downstream signaling. We then constructed synthetic fusions to test the lower limit of multimerization that could trigger signaling. While monomers of the ALK domain did not signal, dimers triggered signaling to approximately the same magnitudes as EML4-ALK and promoted colony formation in soft agar and tumor formation in xenograft models, but notably did not form condensates. Finally, a survey of 9 distinct oncogenic RTK fusions found that only few other fusions formed condensates, while most appeared diffuse. Nevertheless, all fusions could strongly activate signaling, independent of condensate formation. Our work thus suggests that condensation is not essential for RTK fusion signaling and that strong signaling and cell transformation can result from fusions that appear diffuse under fluorescence microscopy, from both synthetic and natural fusions. These results suggest a more nuanced role of condensation in RTK fusion signaling and call for further mechanistic studies to understand how cytoplasmic fusions can productively trigger oncogenic signals. Citation Format: David Gonzalez-Martinez, Thomas R. Mumford, Delaney Wilde, Sofia Wissert, Yuzhi (Carol) Gao, Emily Brackhahn, Richard Kriwacki, Elizabeth Rhoades, Lukasz J. Bugaj. Low-order assemblies drive RTK fusion signaling without condensation [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Fusion-Positive Cancer: From Discovery to Therapy; 2026 Jan 13-15; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86(1_Suppl):Abstract nr B007.

  PublisherDOI

• Intramolecular competition generates pulsatory protein activity shaped by light, temperature, and evolution

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-14 · 2 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Proteins are information processors, but their computations are typically considered at steady state. Here we find that individual proteins can dynamically encode information about their environment and that such response dynamics have been conserved throughout evolution. The fungal protein BcLOV4 exhibits pulsatory light responses shaped by the magnitude of environmental light and temperature. Response adaptation resulted from competitive interactions between domains that sensed either light or temperature. Temperature-sensing was encoded in a modular domain and could be tuned by mutations within co-evolved loops. Photo-thermal response dynamics were conserved in homologues from fungi that diverged >300 million years ago, and the characteristic temperature of pulsatory responses had adapted to match the ecological niche of the hosts, ranging from Antarctica to thermal ponds. These findings uncover a class of dynamic proteins, determine molecular principles of time-varying protein activation, and suggest functional importance for light- and temperature-conditioned protein activity pulses. One-Sentence Summary Individual proteins can dynamically encode information through interactions between their component domains, revealing principles for complex signal processing in natural and engineered proteins.

  PublisherOA PDFDOI

• EGFR suppression and drug-induced potentiation are widespread features of oncogenic RTK fusions

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-19

  preprintSenior author

  Regulation of cancer cells by their environment contributes to tumorigenesis and drug response, though the extent to which the oncogenic state can alter a cell's perception of its environment is not clear. Prior studies found that EML4-ALK, a receptor tyrosine kinase (RTK) fusion oncoprotein, suppresses transmembrane receptor signaling through EGFR. Moreover, suppression was reversed with targeted ALK inhibition, thereby promoting survival and drug tolerance. Here we tested whether such modulation of EGFR was common among other RTK fusions, which collectively are found in ∼5% of all cancers. Using live- and fixed-cell microscopy in isogenic and patient-derived cell lines, we found that a wide variety of RTK fusions suppress transmembrane EGFR and sequester essential adaptor proteins in the cytoplasm, as evidenced by the localization of endogenous Grb2. Targeted therapies rapidly released Grb2 from sequestration and potentiated EGFR. Synthetic optogenetic analogs of RTK fusions confirmed that cytoplasmic sequestration of Grb2 was sufficient to suppress perception of extracellular EGF and could do so without driving signaling from the synthetic fusion itself, demonstrating that fusion signaling and suppression of EGFR could be functionally decoupled. Our study uncovers that a large number of RTK fusions simultaneously act as both activators and suppressors of signaling, the mechanisms of which could be exploited for new biomimetic therapies that enhance cell killing and suppress drug tolerance.

  PublisherDOI

• Quantifying cancer- and drug-induced changes in Shannon information capacity of RTK signaling

  Scientific Reports · 2025-11-10

  articleOpen access

  Cancer can result from abnormal regulation of cells by their environment, potentially because cancer cells may misperceive environmental cues. However, the magnitude to which the oncogenic state alters cellular information processing has not been quantified. Here, we apply pseudorandom pulsatile optogenetic stimulation, live-cell imaging, and information theory to compare the information capacity of receptor tyrosine kinase (RTK) signaling pathways in EML4-ALK-driven lung cancer (STE-1) and in non-transformed (BEAS-2B) cells. The average information rate through RTK/ERK signaling in STE-1 cells was less than 0.5 bit/hour, compared to 7 bit/hour in BEAS-2B cells, but increased to 3 bit/hour after oncogene inhibition. Information was transmitted by 50-70% of cells, whose channel capacity (maximum information rate) was estimated through in silico protocol optimization. In BEAS-2B cells, channel capacity of the parallel RTK/calcineurin pathway surpassed that of the RTK/ERK pathway. This study highlights information capacity as a sensitive metric for identifying disease-associated dysfunction and evaluating the effects of targeted interventions.

  PublisherOA PDFDOI

• Quantifying cancer- and drug-induced changes in Shannon information capacity of RTK signaling

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-05 · 3 citations

  preprintOpen access

  Abstract Signaling pathways transmit and process information, enabling cells to respond accurately to external cues. Disease states like cancer can corrupt signal transmission, though the magnitude to which they reduce information capacity has not been quantified. Here we apply pseudo-random pulsatile optogenetic stimulation, live-cell imaging, and information theory to compare the information capacity of receptor tyrosine kinase (RTK) signaling pathways in EML4-ALK-driven lung cancer cells (STE-1) and non-transformed lung epithelial cells (BEAS-2B). The information rate through the RTK/ERK pathway in STE-1 cells was below 0.5 bit/hour but increased to 3 bit/hour after oncogene inhibition. Information was transmitted by only 50–70% of cells, whose channel capacity (maximum information rate) was estimated through in silico protocol optimization. Although oncogene inhibition increased the capacity of the RTK/ERK pathway in STE-1 cells (6 bit/hour), capacity remained lower than in BEAS-2B (11 bit/hour). The capacity of the parallel RTK/calcineurin pathway in BEAS-2B exceeded 15 bit/hour. This study highlights information capacity as a sensitive metric for identifying disease-associated dysfunction and evaluating effects of targeted interventions.

  PublisherOA PDFDOI

Recent grants

• CAREER: Engineering thermal biosensors for remote control of mammalian cells

  NSF · $595k · 2022–2027

• NIH Grant S10OD026986

  NIH · $439k · 2022

• NIH Grant R21GM132831

  NIH · $410k · 2022

• Harnessing protein clustering to understand, identify, and manipulate cellular systems

  NIH · $2.8M · 2020–2030

Frequent coauthors

• William Benman

  University of Pennsylvania

  21 shared

• Thomas R. Mumford

  University of Pennsylvania

  18 shared

• David Gonzalez-Martinez

  University of Pennsylvania

  15 shared

• David V. Schaffer

  University of California, Berkeley

  13 shared

• Brian Y. Chow

  University of Pennsylvania

  12 shared

• Wendell A. Lim

  University of California, San Francisco

  11 shared

• Juan Guan

  Austin College

  9 shared

• Dan E. Berkowitz

  University of Alabama at Birmingham

  9 shared

Labs

• THE BUGAJ LABPI