# Single-molecule localization microscopy reveals the molecular organization of endogenous membrane receptors

**Authors:** Patrick Eiring, Maximilian J. Steinhardt, Nele Bauer, Cornelia Vogt, Umair Munawar, Seungbin Han, Thomas Nerreter, Hermann Einsele, K. Martin Kortüm, Sören Doose, Markus Sauer

PMC · DOI: 10.1126/sciadv.aea2310 · 2026-02-04

## TL;DR

This paper introduces a new method using super-resolution microscopy to study the organization of membrane receptors in cells, which could improve personalized immunotherapy.

## Contribution

The study introduces an optimized protocol for immunolabeling and analysis to accurately quantify and identify membrane receptor stoichiometry.

## Key findings

- The method successfully resolved the molecular organization of CD45, CD69, and CD38 on Jurkat T cells.
- The approach was applied to study interactions between multiple myeloma cells and therapeutic antibodies.
- The protocol could enhance diagnostics and treatment using therapeutic antibodies.

## Abstract

Super-resolution microscopy in combination with genetic labeling methods allows imaging of single proteins in cells. However, visualizing endogenous proteins on primary cells remains challenging due to the use of sterically demanding antibodies for labeling. Here, we demonstrate how immunolabeling conditions and antibody cross-linking influence the quantification and identification of membrane receptor stoichiometry on cells using single-molecule localization microscopy. We developed an optimized immunolabeling and analysis protocol and demonstrate the performance of the approach by resolving the molecular organization of endogenous CD45, CD69, and CD38 on Jurkat T cells. To demonstrate the usefulness of the method for immunotherapy applications, we investigated the interaction of primary multiple myeloma cells with the therapeutic monoclonal antibodies daratumumab and isatuximab and a polyclonal anti-CD38 antibody. Our approach might lay the foundation for improved personalized diagnostics and treatment with therapeutic antibodies.

Single-molecule localization microcopy quantifies the expression and resolves the stoichiometry of endogenous membrane receptors.

## Linked entities

- **Proteins:** PTPRC (protein tyrosine phosphatase receptor type C), CD69 (CD69 molecule), CD38 (CD38 molecule)
- **Diseases:** multiple myeloma (MONDO:0009693)

## Full-text entities

- **Genes:** CD69 (CD69 molecule) [NCBI Gene 969] {aka AIM, BL-AC/P26, CLEC2C, EA1, GP32/28, MLR-3}, ZAP70 (zeta chain of T cell receptor associated protein kinase 70) [NCBI Gene 7535] {aka ADMIO2, IMD48, SRK, STCD, STD, TZK}, PDCD1 (programmed cell death 1) [NCBI Gene 5133] {aka ADMIO4, AIMTBS, CD279, PD-1, PD1, SLEB2}, CD38 (CD38 molecule) [NCBI Gene 952] {aka ADPRC 1, ADPRC1, cADPR1}, PTPRC (protein tyrosine phosphatase receptor type C) [NCBI Gene 5788] {aka B220, CD45, CD45R, GP180, IMD105, L-CA}, AMBP (alpha-1-microglobulin/bikunin precursor) [NCBI Gene 259] {aka A1M, EDC1, HCP, HI30, IATIL, ITI}
- **Diseases:** hematological malignancies (MESH:D019337), inflammatory conditions (MESH:D007249), MM (MESH:D009101), IgA lambda myeloma (MESH:D017098), autoimmune disorders (MESH:D001327), bone marrow cancer (MESH:D001859), tumor (MESH:D009369)
- **Chemicals:** PIPES (MESH:C008916), EGTA (MESH:D004533), ISA (MESH:C000599209), sodium bicarbonate (MESH:D017693), ethanol (MESH:D000431), streptomycin (MESH:D013307), PFA (MESH:C003043), penicillin (MESH:D010406), oil (MESH:D009821), CO2 (MESH:D002245), KOH (MESH:C029943), MEA (MESH:D003543), methanol (MESH:D000432), DARA (MESH:C556306), GA (MESH:D005976), FA (MESH:D005557), AF647 (MESH:C569686), thiol (MESH:D013438), MgCl2 (MESH:D015636), AF647-N-hydroxysuccinimide (-)
- **Species:** Homo sapiens (human, species) [taxon 9606]
- **Mutations:** A to C, L153H, D to F, Arg140   Gly, (A) at 280
- **Cell lines:** OPM-2 — Homo sapiens (Human), Plasma cell myeloma, Cancer cell line (CVCL_1625), Jurkat T — Homo sapiens (Human), Childhood T acute lymphoblastic leukemia, Cancer cell line (CVCL_0065), MM — Homo sapiens (Human), Plasma cell myeloma, Cancer cell line (CVCL_M492), Jurkat E6-1 — Homo sapiens (Human), Childhood T acute lymphoblastic leukemia, Cancer cell line (CVCL_0367)

## Figures

4 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12871438/full.md

---
Source: https://tomesphere.com/paper/PMC12871438