About

Joerg Bewersdorf is a Professor of Cell Biology and of Biomedical Engineering at Yale University. He received his Master's degree (Dipl. Phys., 1998) and his doctoral degree in physics (Dr. rer. nat., 2002) training with Dr. Stefan W. Hell at the Max Planck Institute for Biophysical Chemistry in Goettingen, Germany. After four years at The Jackson Laboratory in Bar Harbor, Maine, he relocated his research group to Yale University in 2009. An optical physicist and biophysicist by training, Dr. Bewersdorf has contributed extensively to the development of super-resolution light microscopy techniques and their application to cell biological questions. His research focuses on visualizing 3D structure and dynamics at the molecular scale, addressing the critical need for high-resolution imaging of sub-cellular features such as organelle morphology and chromatin organization. His laboratory develops and improves fluorescence microscopy methods, including Stimulated Emission Depletion (STED) microscopy, Single-molecule Localization Microscopy, and pan-Expansion Microscopy, aiming to enhance spatial and temporal resolution, speed, robustness, and multicolor labeling capabilities. These advanced imaging techniques are applied in collaboration with various research groups at Yale and beyond to investigate biological questions related to the endoplasmic reticulum, Golgi complex, cell nucleus, and cytokinesis.

Research topics

• Physics
• Optics
• Materials science
• Biology
• Biophysics
• Chemistry
• Nanotechnology
• Artificial Intelligence
• Biochemistry
• Computer Science
• Anatomy
• Optoelectronics
• Cell biology

Selected publications

• pan-ASLM: Axially Swept Light Sheet Microscopy for Fast and High-Resolution Imaging of Expanded Samples

  npj Imaging · 2026-03-23

  articleOpen accessSenior authorCorresponding

  Abstract Expansion microscopy, a super-resolution fluorescence microscopy technique in which samples are expanded up to ~8000 times (after 20-fold expansion) their original volume, places high demands on the microscopes used to image the expanded samples. To reveal nanoscale cellular ultrastructure in meaningful sample volumes, the instruments need to feature a large field of view and working distance. Simultaneously, they need to offer a high three-dimensional resolution to avoid counteracting the resolution improvement achieved by the expansion process. Here, we present pan-ASLM, a high resolution, large field-of-view light-sheet microscope developed for expanded samples, based on the Axially Swept Light Sheet Microscopy (ASLM) technique. pan-ASLM allows imaging over a 640 x 640 µm 2 field of view with lateral and axial resolutions of 586 and 428 nm, respectively, and features an image acquisition speed of up to 20 fps (183 Mvoxels/sec). It offers ~1200× higher imaging speed, a ~7× larger field of view, and ~2× better axial resolution than the standard confocal microscopes typically used for expanded samples. We validate the new microscope design through imaging of pan-expanded HeLa cells as well as mouse kidney and brain tissue.

  PublisherOA PDFDOI

• Reviewer #1 (Public review): ATG2A engages RAB1A and ARFGAP1 positive membranes during autophagosome biogenesis

  2026-03-13

  peer-reviewOpen access

  Autophagosomes form from seed membranes that expand through bulk-lipid transport via the bridge-like lipid transporter ATG2. The origins of the seed membranes and their relationship to the lipid transport machinery are poorly understood. Using proximity labeling and a variety of fluorescence microscopy techniques, we show that ATG2A localizes to extra-Golgi ARFGAP1 puncta during autophagosome biogenesis. ARFGAP1 itself is dispensable during macroautophagy, but among other proteins associating to these membranes, we find that RAB1 is essential. ATG2A co-immunoprecipitates strongly, albeit indirectly, with RAB1A, and siRNA-mediated depletion of RAB1A/B blocks autophagy downstream of LC3B lipidation, similar to ATG2A depletion. Further, when either autophagosome formation or the early secretory pathway is perturbed, ARFGAP1 and RAB1A accumulate at ectopic locations with autophagic machinery. Our results indicate that ATG2A engages a RAB1A complex on select early secretory membranes in support of autophagosome biogenesis.This study elucidates the role of early secretory membranes in autophagosome biogenesis. The authors demonstrate that RAB1/ARFGAP1 positive membranes are essential to autophagy and are recruited to the phagophore assembly site at an early step of autophagosome biogenesis. These membranes interact with the bridge-like lipid transport protein ATG2A and are positive for LC3B and WIPI2, suggesting that RAB1 membranes are a direct source for autophagosome formation.

  PublisherDOI

• Fluorogenic speed-optimized DNA-PAINT probes enable super-resolution imaging of whole cells

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-25

  articleOpen access

  Super-resolution microscopy with DNA-PAINT enables molecular-scale, multiplexed, and quantitative imaging, but its throughput is limited by slow binding kinetics and elevated background at high probe concentrations. Recent speed-optimized and fluorogenic probes improve performance but impose strong constraints on sequence design, revealing a fundamental tradeoff between fast binding and efficient quenching. Here, we introduce a modular probe architecture that spatially decouples binding kinetics from fluorophore-quencher interactions by integrating speed-optimized sequence motifs with PEG spacers. Using DNA origami nanostructures, we demonstrate enhanced localization rates, signal-to-background ratios, and imaging efficiency compared to state-of-the-art probes. We validate our approach in cells, demonstrating its capability to image nuclear targets and enabling three-dimensional imaging of the endoplasmic reticulum using standard widefield illumination. Our work establishes a general framework for fast, multiplexed, and low-background super-resolution imaging.

  PublisherOA PDFDOI

• ATG2A engages RAB1A and ARFGAP1 positive membranes during autophagosome biogenesis

  eLife · 2026-03-13

  articleOpen access

  Autophagosomes form from seed membranes that expand through bulk-lipid transport via the bridge-like lipid transporter ATG2. The origins of the seed membranes and their relationship to the lipid transport machinery are poorly understood. Using proximity labeling and a variety of fluorescence microscopy techniques, we show that ATG2A localizes to extra-Golgi ARFGAP1 puncta during autophagosome biogenesis. ARFGAP1 itself is dispensable during macroautophagy, but among other proteins associating to these membranes, we find that RAB1 is essential. ATG2A co-immunoprecipitates strongly, albeit indirectly, with RAB1A, and siRNA-mediated depletion of RAB1A/B blocks autophagy downstream of LC3B lipidation, similar to ATG2A depletion. Further, when either autophagosome formation or the early secretory pathway is perturbed, ARFGAP1 and RAB1A accumulate at ectopic locations with autophagic machinery. Our results indicate that ATG2A engages a RAB1A complex on select early secretory membranes in support of autophagosome biogenesis.

  PublisherDOI

• Reviewer #3 (Public review): ATG2A engages RAB1A and ARFGAP1 positive membranes during autophagosome biogenesis

  2026-03-13

  peer-reviewOpen access

  Autophagosomes form from seed membranes that expand through bulk-lipid transport via the bridge-like lipid transporter ATG2. The origins of the seed membranes and their relationship to the lipid transport machinery are poorly understood. Using proximity labeling and a variety of fluorescence microscopy techniques, we show that ATG2A localizes to extra-Golgi ARFGAP1 puncta during autophagosome biogenesis. ARFGAP1 itself is dispensable during macroautophagy, but among other proteins associating to these membranes, we find that RAB1 is essential. ATG2A co-immunoprecipitates strongly, albeit indirectly, with RAB1A, and siRNA-mediated depletion of RAB1A/B blocks autophagy downstream of LC3B lipidation, similar to ATG2A depletion. Further, when either autophagosome formation or the early secretory pathway is perturbed, ARFGAP1 and RAB1A accumulate at ectopic locations with autophagic machinery. Our results indicate that ATG2A engages a RAB1A complex on select early secretory membranes in support of autophagosome biogenesis.This study elucidates the role of early secretory membranes in autophagosome biogenesis. The authors demonstrate that RAB1/ARFGAP1 positive membranes are essential to autophagy and are recruited to the phagophore assembly site at an early step of autophagosome biogenesis. These membranes interact with the bridge-like lipid transport protein ATG2A and are positive for LC3B and WIPI2, suggesting that RAB1 membranes are a direct source for autophagosome formation.

  PublisherDOI

• Abstract 4758: MYC-BCL6 state transition drives metabolomic cycling and leukemia-initiating capacity in B-ALL

  Cancer Research · 2026-04-03

  article

  Abstract Background and significance: Stemness in AML is defined by a rare leukemia-initiating cell (LIC) population, but analogous LICs in B-ALL have remained elusive (Kelly 2007, Le Viseur 2008, Rehe 2013). Given that LICs in AML are drug-resistant and initiate relapses, identifying an LIC population in B-ALL would be consequential. Results: Time-lapse studies of patient-derived B-ALL cells revealed that most B-ALL cells were continuously proliferating, while subpopulations underwent periodic transitions between quiescent and proliferative states. Gene expression studies identified MYC as the top-ranking gene in ‘proliferative’ and BCL6 in ‘quiescent’ B-ALL cells. To dissect MYC-BCL6 dynamics, we knocked in dual reporters with mNeonGreen fused to MYC and mScarlet fused to BCL6 in patient-derived B-ALL (PDX). Time-lapse imaging revealed proliferative cells expressed MYC with no detectable BCL6, whereas PDX also included ‘alternating’ cells that underwent repeated transitions between MYC+ BCL6− and MYC− BCL6+ states. Approximately 30% of BCR-ABL1 B-ALL and >50% of RAS-pathway B-ALL consisted of ‘alternating’ cells. Transitions occurred independently of the ∼36-hour cell-division cycle, with ∼3-hour MYC phases and ∼6-hour BCL6 phases. Integrated ChIP-seq, RNA-seq, and metabolomics showed that MYC-high cells are much larger and activate glycolysis and protein-synthesis programs, whereas BCL6-high cells are small and enriched for phosphatidylethanolamine (PtdEtn) synthesis, essential for autophagosome formation. To directly link MYC-BCL6 dynamics with growth, we combined quantitative phase microscopy and time-lapse fluorescence to measure single-cell dry mass. MYC-high cells accumulated biomass at twice the rate of BCL6-high cells (0.018 vs 0.009 pg/min), producing stepwise trajectories aligned with each MYC/BCL6 state transition. To experimentally induce transitions, we engineered PDX with MYC-dTAG knock-in alleles and employed the BCL6 PROTAC ARV-393. Acute MYC degradation caused rapid shrinkage and reduced dry mass, whereas BCL6 degradation decreased autophagy and increased biomass, confirming opposing MYC-driven anabolic and BCL6-driven catabolic programs. To functionally study ‘steady’ (MYC-only) and ‘alternating’ (MYC/BCL6) B-ALL populations, we developed a cell-sorting strategy that enriched each of the two populations to a purity of 85% as confirmed by subsequent time-lapse imaging. Extreme limiting dilution and series transplantation experiments revealed MYC-BCL6 alternating B-ALL cells significantly enriched for LIC (1 in 124) compared to MYC-only population (1 in 574) and initiated fatal leukemia after short latency. Conclusion: These findings reveal a MYC-BCL6 state-transition program in B-ALL that coordinates quiescence-proliferation cycling, anabolic-catabolic metabolism, and leukemia-initiating potential. Citation Format: Zhangliang Cheng, Ruoyi Shi, Kohei Kume, Mark Robinson, Richard Kim, Kadriye Nehir Cosgun, Yujin Bao, Siyi Chen, Mina Xu, Joerg Bewersdorf, Markus Muschen, . MYC-BCL6 state transition drives metabolomic cycling and leukemia-initiating capacity in B-ALL [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 4758.

  PublisherDOI

• Reviewer #2 (Public review): ATG2A engages RAB1A and ARFGAP1 positive membranes during autophagosome biogenesis

  2026-03-13

  peer-reviewOpen access

  Autophagosomes form from seed membranes that expand through bulk-lipid transport via the bridge-like lipid transporter ATG2. The origins of the seed membranes and their relationship to the lipid transport machinery are poorly understood. Using proximity labeling and a variety of fluorescence microscopy techniques, we show that ATG2A localizes to extra-Golgi ARFGAP1 puncta during autophagosome biogenesis. ARFGAP1 itself is dispensable during macroautophagy, but among other proteins associating to these membranes, we find that RAB1 is essential. ATG2A co-immunoprecipitates strongly, albeit indirectly, with RAB1A, and siRNA-mediated depletion of RAB1A/B blocks autophagy downstream of LC3B lipidation, similar to ATG2A depletion. Further, when either autophagosome formation or the early secretory pathway is perturbed, ARFGAP1 and RAB1A accumulate at ectopic locations with autophagic machinery. Our results indicate that ATG2A engages a RAB1A complex on select early secretory membranes in support of autophagosome biogenesis.This study elucidates the role of early secretory membranes in autophagosome biogenesis. The authors demonstrate that RAB1/ARFGAP1 positive membranes are essential to autophagy and are recruited to the phagophore assembly site at an early step of autophagosome biogenesis. These membranes interact with the bridge-like lipid transport protein ATG2A and are positive for LC3B and WIPI2, suggesting that RAB1 membranes are a direct source for autophagosome formation.

  PublisherDOI

• Author response: ATG2A engages RAB1A and ARFGAP1 positive membranes during autophagosome biogenesis

  2026-03-13

  peer-reviewOpen access

  Autophagosomes form from seed membranes that expand through bulk-lipid transport via the bridge-like lipid transporter ATG2. The origins of the seed membranes and their relationship to the lipid transport machinery are poorly understood. Using proximity labeling and a variety of fluorescence microscopy techniques, we show that ATG2A localizes to extra-Golgi ARFGAP1 puncta during autophagosome biogenesis. ARFGAP1 itself is dispensable during macroautophagy, but among other proteins associating to these membranes, we find that RAB1 is essential. ATG2A co-immunoprecipitates strongly, albeit indirectly, with RAB1A, and siRNA-mediated depletion of RAB1A/B blocks autophagy downstream of LC3B lipidation, similar to ATG2A depletion. Further, when either autophagosome formation or the early secretory pathway is perturbed, ARFGAP1 and RAB1A accumulate at ectopic locations with autophagic machinery. Our results indicate that ATG2A engages a RAB1A complex on select early secretory membranes in support of autophagosome biogenesis.This study elucidates the role of early secretory membranes in autophagosome biogenesis. The authors demonstrate that RAB1/ARFGAP1 positive membranes are essential to autophagy and are recruited to the phagophore assembly site at an early step of autophagosome biogenesis. These membranes interact with the bridge-like lipid transport protein ATG2A and are positive for LC3B and WIPI2, suggesting that RAB1 membranes are a direct source for autophagosome formation.

  PublisherDOI

• Data from: Mitotic Cdc42 waves encode PI(3,4)P₂ signaling and Golgi morphological state to control spindle scaling

  DRYAD · 2026-04-30

  datasetOpen access

  Self-organizing waves are observed in numerous biological systems and may encode spatial and temporal information for cellular organization in the absence of pre-patterns. In mitotic mast cells, periodic cortical waves emerge prior to spindle assembly with wave periods that are proportional to cell size. Here, we investigate the mechanisms that govern cortical wave scaling and examine the consequences of wave perturbation on mitotic spindle size scaling. We find that the periods of mitotic waves are regulated by the turnover of phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2) on the plasma membrane, which depends on inositol polyphosphate-4-phosphatase type II (INPP4B). Genetic depletion of INPP4B increases cortical wave period and spindle length. Intriguingly, mitotic wave period could be tuned continuously during mitosis, indicating the existence of a fast, post-translational regulatory mechanism for wave scaling. We further find that the regulation of mitotic waves on the plasma membrane is controlled by the sequestering of INPP4B and PI(3,4)P2 upon mitotic Golgi fragmentation. Based on these findings, we propose a cell size-sensing mechanism in which cortical waves act like sonar waves, adjusting their timing and propagation based on the shuttling of signalling proteins between the cell cortex and intracellular organelles. This rapid communication scheme allows the cell to adjust spindle scaling dynamically, ensuring accurate cell division.

  PublisherDOI

• Scalable automated segmentation of pan-Expansion Microscopy data quantifies mitochondrial proteins and morphology at the nanoscale

  2025-07-28

  dataset
  PublisherDOI

Recent grants

• New Mechanisms of Heterotaxy and Congenital Heart Disease: Nucleoporins at Cilia

  NIH · $5.5M · 2015–2023

• Development of a Versatile Multiplexing Nanoscopy Platform for Cell Biology

  NIH · $1.8M · 2023–2027

• An Integrated Imaging System for High-throughput Nanoscopy of the 4D Nucleome

  NIH · $990k · 2015–2020

• Enabling Nanoscale Dynamic Imaging of Vesicles and Organelles

  NIH · $3.4M · 2016–2021

• An Integrated Imaging System for High-throughput Nanoscopy of the 4D Nucleome

  NIH · $660k · 2015–2020

Frequent coauthors

• David Baddeley

  University of Auckland

  41 shared

• Yongdeng Zhang

  Westlake University

  31 shared

• Edward S. Allgeyer

  Wellcome/Cancer Research UK Gurdon Institute

  31 shared

• Travis J. Gould

  Pfizer (United States)

  28 shared

• Mark D. Lessard

  Yale University

  24 shared

• Thomas D. Pollard

  Yale University

  24 shared

• Martin J. Booth

  24 shared

• Kevin Hu

  Yale University

  23 shared

Awards & honors

• Harvey and Kate Cushing Professor of Cell Biology (2022)