Figure 1: Illustration of Immuno-SABER approach for multiplexed signal amplification using DNA-barcoded antibodies and its application to enable 10-colour imaging of marker proteins with high sensitivity in mouse retina sections.

Figure 1: Illustration of Immuno-SABER approach for multiplexed signal amplification using DNA-barcoded antibodies and its application to enable 10-colour imaging of marker proteins with high sensitivity in mouse retina sections.

Figure 2: Multiparametric investigation of the cell state by integrating spatial information, subcellular morphology, and molecular make-up of cells to understand how they respond to perturbations and disease factors.

Figure 2: Multiparametric investigation of the cell state by integrating spatial information, subcellular morphology, and molecular make-up of cells to understand how they respond to perturbations and disease factors.

+++ At EMBL from January 2021 +++

The Saka group develops new tools and methods to investigate the spatial and molecular organisation of cells across scales. The group harnesses new labelling approaches, fluorescence and super-resolution microscopy methods, and DNA nanotechnology.

Previous and current research

We aim to understand the spatial features and organisational principles of biological structures ranging from nanoscale complexes to subcellular compartments, cells, and tissues. To enable comprehensive investigation, we develop molecular tools and methods for conventional and super-resolution imaging and employ multimodal approaches.

Previously, we have combined metabolic labelling, bioorthogonal click chemistry, cell fusion assays, and super-resolution microscopy to understand the universal principles of protein organisation in cellular membranes. We have also developed a correlative optical and isotopic super-resolution imaging modality (COIN) that makes it possible to study the turnover of proteins in subcellular compartments of neurons.

Recently, we have been harnessing the barcoding capacity and programmability of DNA to generate powerful tools for single-molecule imaging and multiplexed detection of proteins and nucleic acids in cells and tissues. We are applying these tools to visualise the 3D structure of chromatin at super-resolution and uncover how it spatially and functionally organises around nuclear structures such as nucleoli.

Broadening DNA-based detection further for the tissue scale, we have developed a new signal amplification method called signal amplification by exchange reaction (SABER) for immunofluorescence (Immuno-SABER) and fluorescence in situ hybridisation (SABER-FISH) to enable high-throughput multiplexed profiling of single cells in their native tissues. We are currently utilising SABER to reveal the spatial organisation of cell types in human tissues and to visualise cell cycle abnormalities in tumours.

Future projects and goals

  • We will expand our technology suite to create a high-throughput single-cell platform for spatial multi-omic profiling of cell states utilising integrated imaging, sequencing, and machine learning.
  • We will establish new reporters and approaches to probe and modulate the organisation of membraneless assemblies and investigate how the liquid–liquid phase separation (LLPS) intertwines with the molecular cell state and response to stress factors.
  • We aim to apply these approaches to address the fundamental question of how single cell identity relates to spatial and molecular organisation. These efforts will help to uncover the complexity of intricate diseases like cancers and neurodegeneration at the single-cell level, and will provide new insights into drug response, disease formation, and ageing.