What Is a Protein Expression Atlas and Why Is It Vital?

A protein expression atlas is a large-scale, public database that maps the location and abundance of proteins throughout the human body. It functions like a biological encyclopedia, providing detailed information on where each protein is present, from major organs down to individual cells. The purpose of such a resource is to accelerate scientific understanding of human biology and disease.

This comprehensive mapping provides a foundation for medical research worldwide. Scientists use the data to explore the complex networks that proteins form and to understand their roles in various biological processes, which helps speed up the development of new diagnostics and treatments.

Proteins and Their Expression: The Foundation

Proteins are the primary functional and structural molecules in every living cell. These complex molecules are responsible for nearly all tasks in cellular life, acting as enzymes to drive chemical reactions, providing structural support, and transmitting signals. Each of the approximately 20,000 protein-coding genes in the human genome holds the instructions for building at least one unique protein.

The process of creating these proteins is called gene expression. It begins with transcription, where information in a gene’s DNA is copied into messenger RNA (mRNA). The mRNA then travels to the cytoplasm for translation, where cellular machinery reads the code and assembles amino acids into a protein.

This process is tightly regulated, acting like a dimmer switch that controls when, where, and how much of a protein is made. Some proteins are needed in almost all cells for basic functions, while others are produced only in specific tissues or at certain times. Understanding these patterns of protein expression is fundamental to comprehending how cells acquire specialized functions and how disruptions can lead to disease.

Defining the Protein Expression Atlas

A protein expression atlas is a systematic catalog of protein distribution across various biological contexts. A leading example is the Human Protein Atlas (HPA), a Swedish-based program initiated in 2003. The mission of the HPA is to map all human proteins in cells, tissues, and organs using a combination of different technologies. This effort has generated millions of images and vast datasets covering the majority of human protein-coding genes. These atlases are not static; they are continuously updated with new data and features, serving as a foundational tool for biomedical research.

Exploring the Atlas: Data and Organization

Protein expression atlases are organized into distinct sections to make their information accessible. These databases are often structured as a collection of sub-atlases, each focusing on a different aspect of protein expression. This organization allows users to navigate from a whole-organism view down to the subcellular level.

A Tissue Atlas details the expression of proteins across all major organs and tissues, like the liver, brain, and kidneys. It shows which proteins are abundant in specific tissues, suggesting specialized roles in their function.

The Cell Atlas provides a higher-resolution view, focusing on the spatial distribution of proteins within different types of cells and their subcellular localization. Another section, the Pathology Atlas, is dedicated to exploring how protein expression changes in disease states, containing data from common forms of human cancer.

Techniques Behind Atlas Creation

Creating a protein expression atlas relies on several scientific techniques. A primary method is immunohistochemistry (IHC), which uses antibodies to visualize protein locations within tissue samples. This imaging shows which cells in a tissue are producing a particular protein.

For a more detailed subcellular view, a similar technique called immunofluorescence (IF) is used. This method also employs antibodies but adds fluorescent tags that light up under a microscope, revealing a protein’s location within structures like the nucleus. Millions of high-resolution images from these methods form the visual core of resources like the Human Protein Atlas.

These techniques are complemented by RNA sequencing (RNA-Seq), which measures the mRNA for every gene in a sample. Since mRNA is the template for proteins, its abundance can indicate gene activity. Atlases also incorporate data from mass spectrometry, a technology that directly identifies and quantifies proteins in a sample.

Applications and Scientific Value

Protein expression atlases have broad applications in basic science and clinical research. They help scientists understand the normal functions of proteins by revealing their location, which allows researchers to form hypotheses about their roles in biological processes.

In medicine, these resources aid disease research. The Pathology Atlas, for example, allows scientists to identify proteins overexpressed in tumors compared to healthy tissue. This information helps in understanding cancer mechanisms and discovering potential biomarkers for diagnosis or prognosis.

The atlases also support drug discovery. By identifying proteins uniquely expressed in a disease, researchers can pinpoint new targets for therapies. Knowing a target protein’s location helps predict a drug’s efficacy and side effects. The open-access nature of these atlases ensures this data can be used by researchers worldwide to advance biomedical science.