Mass spectrometry-based proteomic characterization of peripheral immune cells

Abstract

The immune system is vital to the defense against external and internal threats to our health. Each immune cell subpopulation conducts specialized roles in relation to disease, thus making our understanding and characterization of these cells crucial in screenings, determining disease progression, and developing novel therapeutics. Protein biomarkers discovered through mass spectrometry (MS)-based proteomics, can be utilized to define immune cells. Through MS proteomics, the proteome of each cell type can be determined, and differential abundance analysis of these proteins can discover cell-type-specific proteins. In this study, optimization of the proteomic preparatory workflow was conducted with an aim to maximize protein identifications. These experiments show that continued developments within proteomics workflows of low analyte quantity are essential. The analysis and dataset on immune cells termed, ‘final-immune-cell’ analysis, on B-cells, B-naïve-cells, Monocytes, Natural Killer (NK)-active-cells, T-cells, CD8+T-cells, PBMCs, and a CD8+T-cell-Monocyte mixture revealed defined separation in a principal component analysis (PCA), showed differential abundance of various cell-surface markers used for fluorescence-activated cell sorting (FACS) cell isolation, developed a proof-of-concept for immune cell deconvolution, and determined differentially abundant proteins via cell-cell comparisons. Additionally, a comparison with a dataset from a similar study was conducted, revealing overlapping differentially abundant proteins from B-naïve-cells and CD8+T-cells between the datasets. This study shows that protein identification in low sample-size experiments continues to hamper MS-based proteomics and lists potentially promising markers for future identification and deconvolution, thus highlighting the need to develop low sample-size workflows and increase the scope of the study to include more cell types.

Popular Abstract

Heading:
Defining immune cells based on their collection of proteins.

Introduction:
What makes each cell type in our bodies unique from other cells? There are many answers to this question, such as what the function of the cell is, where it is located in the body, and where it comes from. The collection of all of the proteins in each cell type, called the ‘proteome’ also makes each cell type unique. This definition formed the theoretical backbone that this project is based on, where the levels of proteins in various immune cells were measured. This measurement was compared between cell types to find unique proteins, which can then be used to define the cells.

Main text:
The immune system is responsible for keeping us healthy and free from disease. Specialized immune cells are what make up the immune system and carry out its various functions, such as killing viruses or bacteria that invade our bodies. Learning more about these immune cells allows us to understand how our bodies respond to threats, or how we can use them to our advantage to treat disease. In order to learn more about each of these cells, though, we need to be able to distinguish them from one another. We can identify them based on the different proteins that they possess, also known as the ‘proteome’. Measuring the proteome of each cell type can be done with a technique called ‘mass spectrometry’, where the relative amount of proteins in each sample is determined.
Making sure that as many proteins are detected as possible is therefore critical. Different methods to prepare the cells for mass spectrometry were trialed to see which method could result in the greatest number of detected proteins. These experiments showed that further efforts are needed to make this preparation more effective for analyzing small amounts of cells.
The proteomes of the immune cells analyzed were compared to one another, which allowed us to find proteins that are more specific to certain cell types. We also compared our results to the results of a similar study to see if any of the proteins we found to be specific to a certain cell matched the results of that study.
Defining immune cells based on their proteins might allow us to determine how many immune cells of different types might be present in samples of diseased tissue, or tumors, which can help us determine the progression of disease. Such a technique is termed ‘deconvolution’. A proof-of-concept for this method was additionally tested in this project, with promising results.
In the future, more cell types will need to be analyzed to develop a comprehensive cell-protein dictionary, which will prove to be extremely useful in studying the progression of disease, and in developing new therapeutics to cure and treat disease.

• author: Andree, Sebastian Lucas
• supervisor: Fredrik Levander; Malin Lindstedt
• organization: Department of Immunotechnology; Educational programmes, LTH
• alternative title: Proteomics based immune-cell characterization
• course: KIMM01 20231
• year: 2023
• type: H2 - Master's Degree (Two Years)
• subject: Biology and Life Sciences
• keywords: Proteomics, Immunology, Mass Spectrometry, Characterization, Immune Cells, Immunotechnology
• language: English
• id: 9126022
• date added to LUP: 2023-06-19 12:08:41
• date last changed: 2023-06-19 12:08:41