The Human Protein Atlas (HPA) program was launched in 2003 and aims to map all human proteins across cells, tissues, and organs by combining various omics technologies, such as antibody-based imaging, mass spectrometry proteomics, transcriptomics, and system s biology.

“Our goal is to map all human protein-coding genes to understand the spatial distribution of proteins across tissues, cells, organelles, and blood, both in healthy and diseased states. This is crucial for deciphering protein function, as specific expression patterns can reveal tissue-specific roles or indicate disease such as cancer progression,” explains Cecilia Lindskog, Head of the tissue-based efforts of the HPA program. She is also Associate Professor and Group Leader of a research group focusing on cancer precision medicine at Uppsala University.

"My primary research interest is exploring the molecular mechanisms of reproductive organs, both in normal and diseased states,” she says.

Open source approach

The HPA resource is open access, enabling researchers in academia and industry to freely explore and utilize the data related to the human proteome.

This open-source approach enables researchers to utilize our data and publish their findings, enabling scientific progress.

“This open-source approach enables researchers to utilize our data and publish their findings, enabling scientific progress. We recognize that we cannot generate all ideas or projects on our own, so engaging the entire scientific community is essential. Our continuous improvements involve adding new data types and enhancing existing datasets for deeper analysis, as scientific advancement is an ongoing journey,” says Lindskog.

Understanding protein expression in different cell types helps identify the drivers of cancer, and blood proteins in patients may signal disease, offering potential diagnostic tools. "We believe the data is used for pharma companies and researchers as a starting point for further research," says Lindskog.

Cecilia Lindskog, Head of the tissue-based efforts of the HPA, and Associate Professor, Uppsala University. Photo: David Naylor

A comprehensive map

The data generated in the HPA project provides detailed information on the location of the 20,000 or so different human proteins within the body, showing where each is expressed – whether in a specific organ, cell type, or organelle.

“This creates a comprehensive map, so we call it an "Atlas." We present this data through microscopic images that are stained using antibody-based proteomics, allowing visualization of protein distribution across tissues,” says Lindskog.

The main challenges that the HPA has encountered along the path are connected to the fact that research is continually evolving, and new findings often prompt re-evaluation of previous analyses from different perspectives, says Lindskog.

“This means the work is never truly finished, there's always an opportunity to delve deeper and enhance the data in various ways. Even large projects can be expanded and refined over time, ensuring that improvements and advancements in research continue,” she explains.

The future

HPA releases new data every year and the next update was scheduled for the end of October 2024. Each year, Lindskog and her colleagues incorporate additional data types.

“We've recently added information on protein structure and interactions, sourced from external resources. We aim for the HPA to serve as the primary resource for protein information.”

HPA also utilizes artificial intelligence (AI) for its data analysis, predictive modeling, and image analysis to examine protein data from antibody-based images, allowing for comprehensive image evaluation. “This approach offers a broader overview of the data than traditional methods, enabling us to uncover new patterns and insights,” says Lindskog.

Identifying proteins can serve us as future diagnostic tools or be targets for future drugs, and we can understand how a drug works in the human body.

For the future, Lindskog hopes that the Human Protein Atlas will be able to continue to help scientists identify proteins exhibiting specific patterns in certain cells and tissues that may indicate disease.

“This information allows us to develop measurement methods and create diagnostic tools or new treatment approaches for specific diseases,” she says.

"Identifying proteins can serve us as future diagnostic tools or be targets for future drugs, and we can understand how a drug works in the human body. If you have a drug designed to work on a certain protein, it’s very important to know where that protein is in the human body because that can tell you the potential side effects of the drug.” 

Facts The Human Protein Atlas

The Human Protein Atlas (HPA) is a Swedish-based program with the aim to map all the human proteins in cells, tissues, and organs using an integration of various omics technologies. The atlas also consists of eight separate resources; tissue, brain, single cell, subcellular, cancer, blood, cell line, and structure and interaction.

The Human Protein Atlas (HPA) program was launched in 2003 and aims to map all human proteins across cells, tissues, and organs by combining various omics technologies, such as antibody-based imaging, mass spectrometry proteomics, transcriptomics, and system s biology.

“Our goal is to map all human protein-coding genes to understand the spatial distribution of proteins across tissues, cells, organelles, and blood, both in healthy and diseased states. This is crucial for deciphering protein function, as specific expression patterns can reveal tissue-specific roles or indicate disease such as cancer progression,” explains Cecilia Lindskog, Head of the tissue-based efforts of the HPA program. She is also Associate Professor and Group Leader of a research group focusing on cancer precision medicine at Uppsala University.

“My primary research interest is exploring the molecular mechanisms of reproductive organs, both in normal and diseased states,” she says.

Open source approach

The HPA resource is open access, enabling researchers in academia and industry to freely explore and utilize the data related to the human proteome.

This open-source approach enables researchers to utilize our data and publish their findings, enabling scientific progress.

“This open-source approach enables researchers to utilize our data and publish their findings, enabling scientific progress. We recognize that we cannot generate all ideas or projects on our own, so engaging the entire scientific community is essential. Our continuous improvements involve adding new data types and enhancing existing datasets for deeper analysis, as scientific advancement is an ongoing journey,” says Lindskog.

Understanding protein expression in different cell types helps identify the drivers of cancer, and blood proteins in patients may signal disease, offering potential diagnostic tools. “We believe the data is used for pharma companies and researchers as a starting point for further research,” says Lindskog.

Cecilia Lindskog, Head of the tissue-based efforts of the HPA, and Associate Professor, Uppsala University. Photo: David Naylor

A comprehensive map

The data generated in the HPA project provides detailed information on the location of the 20,000 or so different human proteins within the body, showing where each is expressed – whether in a specific organ, cell type, or organelle.

“This creates a comprehensive map, so we call it an “Atlas.” We present this data through microscopic images that are stained using antibody-based proteomics, allowing visualization of protein distribution across tissues,” says Lindskog.

The main challenges that the HPA has encountered along the path are connected to the fact that research is continually evolving, and new findings often prompt re-evaluation of previous analyses from different perspectives, says Lindskog.

“This means the work is never truly finished, there’s always an opportunity to delve deeper and enhance the data in various ways. Even large projects can be expanded and refined over time, ensuring that improvements and advancements in research continue,” she explains.

The future

HPA releases new data every year and the next update was scheduled for the end of October 2024. Each year, Lindskog and her colleagues incorporate additional data types.

“We’ve recently added information on protein structure and interactions, sourced from external resources. We aim for the HPA to serve as the primary resource for protein information.”

HPA also utilizes artificial intelligence (AI) for its data analysis, predictive modeling, and image analysis to examine protein data from antibody-based images, allowing for comprehensive image evaluation. “This approach offers a broader overview of the data than traditional methods, enabling us to uncover new patterns and insights,” says Lindskog.

Identifying proteins can serve us as future diagnostic tools or be targets for future drugs, and we can understand how a drug works in the human body.

For the future, Lindskog hopes that the Human Protein Atlas will be able to continue to help scientists identify proteins exhibiting specific patterns in certain cells and tissues that may indicate disease.

“This information allows us to develop measurement methods and create diagnostic tools or new treatment approaches for specific diseases,” she says.

“Identifying proteins can serve us as future diagnostic tools or be targets for future drugs, and we can understand how a drug works in the human body. If you have a drug designed to work on a certain protein, it’s very important to know where that protein is in the human body because that can tell you the potential side effects of the drug.” 

Facts The Human Protein Atlas

The Human Protein Atlas (HPA) is a Swedish-based program with the aim to map all the human proteins in cells, tissues, and organs using an integration of various omics technologies. The atlas also consists of eight separate resources; tissue, brain, single cell, subcellular, cancer, blood, cell line, and structure and interaction.