The Interplay between Lipid Nanodomains, Protein Clusters and Cell Topography in Cell Signalling

Research group

Short description

Signal transduction from the environment to cell interior is a fundamental biological process acting across a membrane. Using superresolution microscopy of the type that was awarded a Nobel Prize in 2014, Ingela Parmryd's group studies how signalling molecules in T cells, a cell type specialized in immune defence, are organized before and after the signalling has been initiated. We study the prevalence of molecular clusters, how the clusters are related to the properties of the membrane and change depending on the cellular environment. To interpret the results, we develop image analysis methods of use also for a wide range of other research areas. Increased knowledge on how signalling is initiated is of importance for therapeutical intervention of the aberrant signalling that is a hallmark of multiple serious diseases, including cancer.

The Functional Organisation of the Plasma Membrane in T cell Signalling

The plasma membrane of eukaryotic cells contains nanodomains, commonly referred to as lipid rafts, which are more ordered than the rest of the plasma membrane. The high order is generally considered equivalent to the tight packing of cholesterol and sphingolipids observed in model membranes. However, we have demonstrated that lipid rafts form when actin filaments are pinned to the plasma membrane via phosphoinositides and when extracellularly exposed receptors are pinned by antibodies (Dinic et al., 2013), suggesting that the mechanism for lipid raft formation is lipid-protein interactions.

We have shown that T cell signalling is initiated upon lipid raft aggregation that can be triggered by cold stress and changes in the plasma membrane lipid composition (Magee et al., 2005; Mahammad et al. 2010) and that the T cell receptor in resting T cells resides in lipid rafts that are brought together upon receptor engagement (Dinic et al., 2015). We are now investigating what triggers the formation of lipid rafts in more detail and how membrane order affects the molecular clustering that accompanies T cell signalling using techniques like super resolution microscopy and fluorescence correlation spectroscopy. The cell studies are accompanied by the development of methods for cluster analysis.

Cell Topography and Plasma Membrane Models

The cell surface is neither flat nor smooth but this is rarely acknowledged. Using high resolution topographical maps of live cells, we and our collaborators have demonstrated that apparent topographical trapping can be behind phenomena described as hop diffusion and transient anchorage in diffusion studies (Adler et al., 2010). Even binding could be the result of apparent topographical trapping when single particle tracks are interpreted in 2D when the molecules are moving over 3D surface. We have shown that ignoring membrane topography causes a consistent underestimation of diffusion and that membrane topography itself can cause anomalous diffusion. Our conclusion is that disentangling apparent from genuine diffusion requires surface characterisation (Adler et al., 2019; Gesper et al., 2020).

Different measures of movement in a folded membrane.
Using conventional 2D and 3D analysis methods allows the molecule to leave the membrane. Lipids and proteins tend to remain in the membrane and movement therefore needs to be analysed using the shortest within surface distance.


Co-localisation Analysis

We develop image analysis methods to get quantitative and objective answers to biological questions. We have developed and patented the method RBNCC (replicate based noise corrected correlation) where image noise, which is unavoidable and leads to the underestimation of any underlying correlation, can be eliminated from correlation measurements (Adler et al. 2008). RBNCC forms the basis for our company No More Noise.

We have performed detailed studies on coefficients developed for use in colocalisation analyses revealing that several are of doubtful value (Adler & Parmryd, 2010; Adler & Parmryd, 2018, Adler & Parmryd, 2019). We were the first to suggest that colocalisation analysis should be divided into the two subgroups co-occurrence and correlation (Adler & Parmryd, 2007; Adler & Parmryd, 2013) and that only pixels where both fluorophores are present should be included in correlation analyses (Adler et al. 2008; Adler & Parmryd, 2014). We now investigate how deconvolution affects correlation analysis and how different intracellular distributions of molecules are represented by our division of colocalisation analysis into co-occurrence and correlation.

Tumour Cell Killing Vδ2Vγ9 T Cells

Vδ2Vγ9 T cells are a T cell subset that recognise and kill cancer cells that accumulate high levels of phosphoantigens, small organic compounds with phosphate groups. There is a positive correlation between the Vδ2Vγ9 T cell number and tumour cell death making Vδ2Vγ9 T cells appealing candidates for immunotherapy. A pilot study indicated that colon cancer patients have lower numbers of circulating Vδ2Vγ9 T cells than healthy individuals.

Together with collaborators at the Uppsala University Hospital we address how the prevalence of Vδ2Vγ9 T cells in colon cancer patients at the four different cancer stages varies and characterise the Vδ2Vγ9 T cells regarding differentiation status, tumour homing potential, proliferation and cytotoxicity.

Together with collaborators at Stockholm University we found that media from erythrocytes infected with P. falciparum can stimulate Vδ2Vγ9 T cell proliferation (Lindberg et al., 2013) suggesting that phosphoantigens both are produced in and released from these cells. In a recent study we show that this occurs at all parasite blood stages and not only, as previously thought, when the erythrocytes rupture and release parasites (Liu et al., 2018). 

  • Otrygga villkor för forskare med STs förslag

    Authors: Ingela Parmryd

    Publication type:Newspaper article

    Publication year:2009

    Published in:ST Press

  • Protein Prenylation in Higher Eukaryotes

    Authors: Ingela Parmryd

    Publication type:Doctoral thesis

    Publication year:1998

  • Cholesterol homeostasis in T cells. Methyl-beta-cyclodextrin treatment results in equal loss of cholesterol from Triton X-100 soluble and insoluble fractions

    Authors: Saleemulla Mahammad, Ingela Parmryd

    Publication type:Journal article, reviewed

    Publication year:2008

    Published in:BBA - Biomembranes

  • In support of the Pearson correlation coefficient

    Authors: Jeremy Adler, Ingela Parmryd

    Publication type:Journal article, reviewed

    Publication year:2007

    Published in:Journal of Microscopy

  • Quantifying colocalization: the MOC is a hybrid coefficient - an uninformative mix of co-occurrence and correlation.

    Authors: Jeremy Adler, Ingela Parmryd

    Publication type:Journal article, reviewed

    Publication year:2019

    Published in:Journal of cell science

  • Interleaflet Coupling, Pinning, and Leaflet Asymmetry—Major Players in Plasma Membrane Nanodomain Formation

    Authors: Toyoshi Fujimoto, Ingela Parmryd

    Publication type:Review article, reviewed

    Publication year:2017

    Published in:Frontiers in Cell and Developmental Biology

  • Methods applicable to membrane nanodomain studies?

    Authors: Parham Ashrafzadeh, Ingela Parmryd

    Publication type:Book chapter, reviewed

    Publication year:2015

    Published in:Essays in Biochemistry

  • Quantifying colocalization thresholding, void voxels and the H-coef

    Authors: Jeremy Adler, Ingela Parmryd

    Publication type:Journal article, reviewed

    Publication year:2014

    Published in:PLoS ONE

  • Quantifying Colocalization by Correlation : The Pearson Correlation Coefficient is Superior to the Mander's Overlap Coefficient

    Authors: Jeremy Adler, Ingela Parmryd

    Publication type:Journal article, reviewed

    Publication year:2010

    Published in:Cytometry Part A

  • Protein prenylation in spinach chloroplasts

    Authors: Ingela Parmryd, B. Andersson, G. Dallner

    Publication type:Journal article, reviewed

    Publication year:1999

    Published in:Proceedings of the National Academy of Science of the United States of America

  • Actin filaments attachment at the plasma membrane in live cells cause the formation of ordered lipid domains

    Authors: Jelena Dinic, Parham Ashrafzadeh, Ingela Parmryd

    Publication type:Journal article, reviewed

    Publication year:2013

    Published in:BBA - Biomembranes

  • The T Cell Receptor Resides in Ordered Plasma Membrane Nanodomains that Aggregate Upon T Cell Activation

    Authors: Ingela Parmryd, Astrid Riehl, Jelena Dinic, Jeremy Adler

    Publication type:Journal article, reviewed

    Publication year:2015

    Published in:Scientific Reports

  • Laurdan and di-4-ANEPPDHQ do not respond to membrane-inserted peptides and are good probes for lipid packing

    Authors: Jelena Dinic, Henrik Biverståhl, Lena Mäler, Ingela Parmryd

    Publication type:Journal article, reviewed

    Publication year:2011

    Published in:BBA - Biomembranes

  • Conventional analysis of movement on non-flat surfaces like the plasma membrane makes Brownian motion appear anomalous.

    Authors: Jeremy Adler, Ida-Maria Sintorn, Robin Strand, Ingela Parmryd

    Publication type:Journal article, reviewed

    Publication year:2019

    Published in:Communications biology

  • Chloroplastic prenylated proteins

    Authors: Ingela Parmryd, C. A. Shipton, E. Swiezewska, G. Dallner, B. Andersson

    Publication type:Journal article, reviewed

    Publication year:1997

    Published in:FEBS Letters

  • Lipid rafts : cell surface platforms for T cell signaling

    Authors: Tony Magee, Niina Pirinen, Jeremy Adler, Stamatis N. Pagakis, Ingela Parmryd

    Publication type:Review article, reviewed

    Publication year:2002

    Published in:Biological Research

  • Proteomics of Synechocystis sp strain PCC 6803 - Identification of plasma membrane proteins

    Authors: Fang Huang, Ingela Parmryd, Fredrik Nilsson, Annika L. Persson, Himadri B. Pakrasi, Bertil Andersson, Birgitta Norling

    Publication type:Journal article, reviewed

    Publication year:2002

    Published in:Molecular & Cellular Proteomics

  • Isoprenylation of plant proteins in vivo Isoprenylated proteins are abundant in the mitochondria and nuclei of spinach

    Authors: C. A. Shipton, Ingela Parmryd, E. Swiezewska, B. Andersson, G. Dallner

    Publication type:Journal article, reviewed

    Publication year:1995

    Published in:Journal of Biological Chemsitry

  • Vγ9Vδ2 T cells proliferate in response to phosphoantigens released from erythrocytes infected with asexual and gametocyte stage Plasmodium falciparum.

    Authors: Chenxiao Liu, S Noushin Emami, Jean Pettersson, Lisa Ranford-Cartwright, Ingrid Faye, Ingela Parmryd

    Publication type:Journal article, reviewed

    Publication year:2018

    Published in:Cellular immunology

  • Identification of spinach farnesyl protein transferase : Dithiothreitol as an acceptor in vitro

    Authors: Ingela Parmryd, C. A. Shipton, E. Swiezewska, B. Andersson, G. Dallner

    Publication type:Journal article, reviewed

    Publication year:1995

    Published in:European Journal of Biochemistry

Group members

Jeremy Adler, PhD, Research Engineer

Sven-Göran Eriksson, BSc, Statistician

Chi-wen Huang, PhD student

Issac Thiria


Dr. Helgi Birgisson, Uppsala University Hospital, Sweden

Dr. Stefan Wennmalm, ALMI, SciLifeLab Stockholm, Sweden

Dr. Patrick Happel and Ms. Astrid Gesper, Ruhr-Universität Bochum, Germany

Prof. Benedikt Kost & Ms. Carolin Fritz, Universität Erlangen-Nürnberg, Germany

Prof. Gunilla Westermark, Uppsala University, Sweden