Human Protein Atlas

The Human Protein Atlas (HPA) is a Swedish-based program started in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome. In November 2020, version 20 was launched along with a celebratory publication of the 20 year history of HPA. Version 20 introduces an additional sub-atlas, the Single Cell Type Atlas, showing expression of protein-coding genes in single human cell types, in addition to the existing sub-atlases; the Tissue Atlas showing the distribution of the proteins across all major tissues and organs in the human body, the Pathology Atlas showing the impact of protein levels for survival of patients with cancer, the Blood Atlas showing the expression profiles of blood cells and actively secreted proteins, the Brain Atlas showing the distribution of proteins in human, mouse, and pig brain, and the Cell Atlas showing the subcellular localization of proteins in single cells. Version 20 also included updates of the preexisting sub-atlases, a major update of the Dictionary tool, eleven educational 3D videos and a section regarding SARS-CoV-2 interacting human proteins. The Human Protein Atlas program has already contributed to several thousands of publications in the field of human biology and disease and was selected by the organization ELIXIR as a European core resource due to its fundamental importance for a wider life science community. The HPA consortium is funded by the Knut and Alice Wallenberg Foundation.
Six major projects.
The Human Protein Atlas consists of six sub-atlases:
Additional features.
In addition to the six sub-atlases of HPA, exploring gene and protein expression, there are various features available at the HPA website to assist the research community, including integrated external resources, such as Metabolic Atlas, educational material and free downloadable data.
History.
The Human Protein Atlas program was started in 2003 and funded by the non-profit organization Knut and Alice Wallenberg Foundation (KAW). The main site of the project is the Royal Institute of Technology (KTH), School of Engineering Sciences in Chemistry, Biotechnology and Health (Stockholm, Sweden). Additionally, the project involves research groups at Uppsala University, Karolinska Institutet, Chalmers University of Technology and Lund University, as well as several present and past international collaborations initiated with research groups in Europe, the United States, South Korea, China, and India. Professor Mathias Uhlén is the director of the program.
The research underpinning the start of the exploration of the whole human proteome in the Human Protein Atlas program was carried out in the late 1990s and early 2000s. A pilot study employing an affinity proteomics strategy using affinity-purified antibodies raised against recombinant human protein fragments was carried out for a chromosome-wide protein profiling of chromosome 21. Other projects were also carried out to establish processes for parallel and automated affinity purification of mono-specific antibodies and their validation.
Research.
Antibodies and antigens, produced in the Human Protein Atlas workflow, are used in research projects to study potential biomarkers in various diseases, such as breast cancer, prostate cancer, colon cancer, diabetes, autoimmune diseases, ovarian cancer and renal failure.
Researchers involved with Human Protein Atlas projects, are sharing protocols and method details in an open-access group on protocols.io. A large effort is put into validating the antibody reagents used for profiling of tissues and cells, and the HPA has implemented stringent antibody validation criteria as suggested by the International Working Group for Antibody Validation (IWGAV).
Collaborations.
The Human Protein Atlas program has participated in 9 EU research projects ENGAGE, PROSPECTS, BIO_NMD, AFFINOMICS, CAGEKID, EURATRANS, ITFoM, DIRECT and PRIMES.