Cecilia Lindskog – A spatio-temporal single-cell type map of human tissues

The aim of the research in my group is to utilize transcriptomics, large scale antibody-based proteomics, data integration and machine learning to generate a high-resolution spatio-temporal map of human tissues at the single cell type level.

During the last two decades, several large-scale efforts have been performed to map the biology of humans at different levels, including the mapping of all genes and proteins encoded within the human genome. However, the continuous emergence of new or upgraded technologies within the field of omics enable analysis with an ever increasing width and depth. Analysis of gene expression has gone from studies at the level of organs and tissues to distinguishing differences between single cells.

In our research we employ a multiomics systems biology approach, integrating different omics methods to study the spatio-temporal expression of proteins. We mainly utilize RNA sequencing data in combination with antibody-based imaging techniques to map the expression of proteins. One of the benefits with antibody-based proteomics is the possibility to localize proteins in their natural environment in intact tissue sections, making it possible to distinguish the spatial distribution of a protein in different cell types or subcellular structures.

Our lab has established a multiplex immunostaining method based on fluorescently labeled antibodies that enables simultaneous staining of six proteins in the same tissue section. Analyzing the co-localization between an unknown protein and five known cell type-specific markers makes it possible to study the expression of proteins within hard-to-distinguish cell types and novel cell states. Although we are involved in the exploration of protein expression in tissues across the entire human body, the main focus of our research is on healthy reproductive organs and cancers within the ovary and prostate.

Our research group is also affiliated with the Human Protein Atlas (HPA) project, initiated in 2003 with the aim to map all human proteins in tissues, cells and blood, both in health and disease. The HPA project is a collaboration between Uppsala University, Royal Institute of Technology and Karolinska Institute, and the open-access database (www.proteinatlas.org) has grown to become one of the world’s largest biological online resources. Our research group contributes with the profiling of human genes and proteins in healthy and diseased tissues, mainly utilizing antibody-based proteomics integrated with transcriptomics at the tissue and single-cell type level.

Read more about our research and the HPA project

Our research projects

Human Protein Atlas website

Methods for tissue profiling in the Human Protein Atlas project