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A DNA-nanoassembly-based approach to map membrane protein nanoenvironments

https://doi.org/10.5878/jvvj-1688
Most proteins at the plasma membrane are not uniformly distributed but localize to dynamic domains of nanoscale dimensions. To investigate their functional relevance, there is a need for methods that enable comprehensive analysis of the compositions and spatial organizations of membrane protein nanodomains in cell populations. Here we describe the development of a non-microscopy based method for ensemble analysis of membrane protein nanodomains. The method, termed NANOscale DEciphEring of membrane Protein nanodomains (NanoDeep), is based on the use of DNA nanoassemblies to translate membrane protein organization information into a DNA sequencing readout. Using NanoDeep, we characterised the nanoenvironments of Her2, a membrane receptor of critical relevance in cancer. Importantly, we were able to modulate by design the inventory of proteins analysed by NanoDeep. NanoDeep has the potential to provide new insights into the roles of the composition and spatial organization of protein nanoenvironments in the regulation of membrane protein function. The methodology is described in the preprint article (see publications list). The methodology for this dataset is available in the preprint (see publication list) Software for data collection: Biacore T200 System Control software, NextSeq control software Software for data analysis: BIAevaluation v3.0, GraphPad Prism v8.2.1, Fiji ImageJ v1.0, Illumina Sequencing Analysis Viewer software, Python v3.8.0.
Download data and documentation (106 files / 31.58 GiB)

Data files

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Documentation files

  • Files description.xlsx
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Citation and access

Data access level:

Creator/​Principal investigator(s):

Research principal:

Data contains personal data:

No

Citation:

Language:

Method and outcome

Population:

cell membrane receptors

Study design:

  • Experimental study

Data format/​data structure:

Data collection Measurements and tests

Mode of collection:

Measurements and tests

Time period(s) for data collection:

2017-05-01 - 2020-07-15

Source of the data:

  • Biological samples

Administrative information

Responsible department/​unit:

Department of Medical Biochemistry and Biophysics [C2]

Funding

Funding agency:

Award number:

2015-03520_VR

Award title:

Spatial signalling in cell-to-cell communication

Funding information:

Cell-to-cell communication pathways coordinate cellular functions in multicellular organisms and are frequently dysregulated in cancer, allowing cells to acquire abnormal functions such as invasion of neighboring tissues. Membrane proteins are key sensor components in cell-to-cell communication and form the largest class of proteins in the druggable genome. We hypothesize that the spatial distribution of ligands and receptors contributes to defining the fundamental mechanisms of action of cell-to-cell communication pathways and their cellular outcomes. The research program relies on the development of tools that provide well-defined physical inputs to cells, not confounded by simultaneous changes in chemical inputs. Therefore, beyond state-of-the-art developments in nanotechnology are here integrated with cell biology. In particular, DNA origami technology is applied to the development of ligand nanoclusters with customized spatial organization and mechanical properties. We will focus on the ephrin/Eph and DSL/Notch cell-to-cell communication pathways, which regulate embryonic development and the homeostasis of adult organs. These pathways are commonly disrupted in cancer, showing tumour suppressing or tumour promoting character. The mechanisms that generate the diversity of outcomes in normal and disease settings are largely unknown. We will use DNA origami/ephrin ligand nanoclusters to investigate whether the spatial organization ligand assemblies impact receptor function. We aim to generate a knowledge foundation for the development of new rational therapeutic approaches that target ephrin ligand/Eph and Notch receptor signalling.

Topic and keywords

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Keywords:

Publications

Citation:

A DNA nanoassembly-based approach to map membrane protein nanoenvironments (preprint). Elena Ambrosetti, Giulio Bernardinelli, Ian Hoffecker, Leonard Hartmanis, View ORCID ProfileRickard Sandberg, Björn Högberg, Ana I. Teixeira doi: https://doi.org/10.1101/836049Opens in a new tab

Citation:

“A DNA-nanoassembly-based approach to map membrane protein nanoenvironments” E. Ambrosetti, G. Bernardinelli, I. T. Hoffecker, L. Hartmanis, G. Kiriako, A. de Marco, R. Sandberg, B. Högberg, A. I. Teixeira. Nat. Nanotechnol. 2020.

Metadata

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