single-molecule-localization-microscopy-membrane-proteins-using

Single-Molecule Localization Microscopy of Membrane Proteins using Single-Antibody Labeling

The plasma membrane defines the cell shape and serves as the interface that governs intercellular communication. Membrane proteins constitute a major ...

University of Illinois Chicago

T cells coordinate intercellular communication through the meticulous regulation of cytokine secretion. Direct visualization of vesicular transport and intracellular distribution of cytokines provides valuable insights into the temporal and spatial mechanisms involved in regulation. Employing Jurkat E6-1 T cells and interleukin-2 (IL-2) as a model system, we investigated vesicular dynamics using single-particle tracking and the nanoscale distribution of intracellular IL-2 in fixed T cells using superresolution microscopy. Live-cell imaging revealed that in vitro activation resulted in increased vesicular dynamics. Direct stochastic optical reconstruction microscopy and 3D structured illumination microscopy revealed nanoscale clustering of IL-2. In vitro activation correlated with spatial accumulation of IL-2 nanoclusters into more pronounced and elongated clusters. These observations provide visual evidence that accelerated vesicular transport and spatial concatenation of IL-2 clusters at the nanoscale may constitute a potential mechanism for modulating cytokine release by Jurkat T cells.

Increased vesicular dynamics and nanoscale clustering of IL-2 after T cell activation.

The transcription factor GATA-binding protein 3 (GATA-3) and the transcriptional program it regulates have emerged as oncogenic drivers across diverse T-cell lymphomas (TCLs), many of which are resistant to conventional chemotherapeutic agents and characterized by recurrent losses of key tumor suppressor genes, including TP53 and PTEN, both of which are clients of the nuclear export protein XPO1. Here, we demonstrated that XPO1 is highly expressed by malignant T cells expressing GATA-3 and by lymphoma-associated macrophages (LAMs) within their tumor microenvironment (TME). Using complementary genetically engineered mouse models, we demonstrated that TP53- and/or phosphate and tensin homolog (PTEN)-deficient TCLs, and LAMs within their TME, are sensitive to the selective exportin-1 (XPO1) antagonist selinexor. In an effort to identify TP53- and PTEN-independent mechanisms, we used complementary and orthogonal approaches to investigate the role of eIF4E and XPO1-dependent messenger RNA nuclear export in these TCLs. We identified a novel role for eIF4E/XPO1 in exporting GATA-3 and GATA-3-dependent transcripts from the nucleus in TCLs, and in the export of therapeutically relevant transcripts, including colony-stimulating factor-1 receptor, from LAMs. Therefore, XPO1 antagonism, by impairing oncogenic transcriptional programs in TCLs and depleting LAMs from their TME, is a novel approach to target 2 independent dependencies in a group of therapeutically challenging TCLs.

The GATA-3-dependent transcriptome and tumor microenvironment are regulated by eIF4E and XPO1 in T-cell lymphomas.

Dynamic protein distribution within and across the plasma membrane is pivotal in regulating cell communication. However, rapid, high-density labeling methods for multiplexed live imaging across diverse cell types remain scarce. Here, we demonstrate N-hydroxysuccinimide (NHS)-ester-based amine crosslinking of fluorescent dyes to uniformly label live mammalian cell surface proteins. Using model cell systems, we capture previously elusive membrane topology and cell-cell interactions. Live imaging shows transient membrane protein accumulation at cell-cell contacts and bidirectional migration patterns guided by membrane fibers in DC2.4 dendritic cells. Multiplexed superresolution imaging reveals the biogenesis of membrane tunneling nanotubes that facilitate intercellular transfer in DC2.4 cells, and caveolin 1-dependent endocytosis of insulin receptors in HEK293T cells. 3D superresolution imaging reveals membrane topology remodeling in response to stimulation, generation of microvesicles, and phagocytic activities in Jurkat T cells. Furthermore, NHS-labeling remains stable in vivo, enabling visualization of intercellular transfer among splenocytes using a T cell lymphoma mouse model.

Unveiling cellular communications through rapid pan-membrane-protein labeling.

Rapid and uniform labeling of plasma membrane proteins is essential for high-resolution imaging of dynamic membrane topologies and intercellular communication in live mammalian cells. Existing strategies for labeling live cell membranes, such as fluorescent fusion proteins, enzyme-mediated tags, metabolic bioorthogonal labeling, and lipophilic dyes, face trade-offs in the requirement of genetic manipulation, the presence of non-uniform labeling, the need for extensive preparation times, and limited choices of fluorophores. Here, we present a streamlined protocol that leverages N-hydroxysuccinimide (NHS)-ester chemistry to achieve rapid (≤5 min), covalent conjugation of synthetic small-molecule dyes to surface-exposed primary amines, enabling pan-membrane-protein labeling. This workflow covers dye stock preparation, labeling for suspension and adherent cells, multiplex live-cell imaging, fusion protein co-staining (including insulin-triggered receptor endocytosis), 3D membrane visualization, and in vivo assays for visualizing membrane-derived material transfers between donor and recipient cells using a lymphoma T-cell mouse model. This high-density labeling approach is compatible with various cell types across diverse imaging platforms. Its speed, versatility, and stability make it a broadly applicable tool for studying plasma membrane dynamics and intercellular membrane trafficking. Key features • Rapid high-density membrane labeling with small-molecule fluorescent dyes. • Enables live-cell multiplexed imaging, amenable to primary cells and cells expressing fluorescent fusion proteins, and supports in vivo studies of membrane-associated cell-cell communications. • Compatible with various fluorescence imaging modalities.

Rapid and Uniform NHS-Ester-Based Membrane Protein Labeling of Live Mammalian Cells.

The transcription factor GATA-binding protein 3 (GATA-3) regulates oncogenic transcriptional programs across diverse T-cell lymphomas, including subsets of both peripheral and primary cutaneous T-cell lymphomas. These GATA-3 dependent transcriptional programs, in collaboration with the genetic landscape, promote cell growth and survival, and confer resistance to conventional chemotherapeutic agents. We observed that transcriptional cyclin dependent kinase 9 (CDK9) activation regulates diverse oncogenic transcriptional programs in these aggressive T-cell lymphomas and is thus a novel therapeutic vulnerability. Using complementary and orthogonal approaches, we identified multiple independent mechanisms by which CDK9 promotes T-cell lymphomagenesis, including a mechanism by which GATA-3 promotes CDK9 activation at GATA-3 dependent loci. We also identify novel mechanisms by which GATA-3 and CDK9 regulate rRNA transcription and processing, respectively, collaboratively promoting ribosome biogenesis. Therefore, CDK9 is a therapeutic vulnerability across genetically and transcriptionally diverse T-cell lymphomas, including those for which GATA-3 is oncogenic.

CDK9 is a dependency in GATA-3 driven and MCL-1 independent T-cell Lymphomas.

The diffraction limit of visible light governs the spatial resolution of optical microscopy to roughly half the wavelength of the light, typically around 200 nm in the lateral dimension and 500 nm in the axial dimension. However, many subcellular structures and processes occur on a much smaller length scale. Technological solutions beyond the optical diffraction limit are needed to study subcellular organizations of proteins and their related functions. Super-resolution microscopy (SRM) represents a family of techniques capable of resolving structures and objects below the optical diffraction limit. This chapter provides an overview of three super-resolution techniques, stimulated emission depletion (STED) microscopy, structured illumination microscopy (SIM), and single-molecule localization microscopy (SMLM), and their applications in investigating subcellular protein organizations and related functions in immune cells.

Article	Year
Increased vesicular dynamics and nanoscale clustering of IL-2 after T cell activation. Biophysical journal\| PubMed ID: 38532626	2024
The GATA-3-dependent transcriptome and tumor microenvironment are regulated by eIF4E and XPO1 in T-cell lymphomas. Blood\| PubMed ID: 39652777	2025
Unveiling cellular communications through rapid pan-membrane-protein labeling. Nature communications\| PubMed ID: 40234465	2025
Rapid and Uniform NHS-Ester-Based Membrane Protein Labeling of Live Mammalian Cells. Bio-protocol\| PubMed ID: 41080442	2025
CDK9 is a dependency in GATA-3 driven and MCL-1 independent T-cell Lymphomas. Blood cancer journal\| PubMed ID: 41309546	2025
Single-Molecule and Super-Resolution Techniques for Investigating Protein Organizations and Biological Functions of Immune Cells. Advances in experimental medicine and biology\| PubMed ID: 41652169	2026

Alyssa Burgess

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