June 16, 2014 in Blog by jmeyer

By Dr. Joanne Elliot

Thirteen years after the completion of the Human Genome Project, we now have the first drafts of the human proteome. The goals of the Human Proteome Project were to “…..characterize all 20,300 genes known in the genome, to generate a map of the protein based architecture of the human body and to become a useful resource to help elucidate biological and molecular function to advance diagnosis and treatment of disease”.

Thanks to the efforts of two independent research teams, we now have access to vast quantities of data that will hopefully revolutionize our understanding of the human proteome. One group, based in Germany (led by Professor Kuster), analyzed protein isolated from 60 human tissues, 13 body fluids and 147 cancer cell lines. The other, with research teams in Baltimore and Bangalore (led by Professor Pandey), isolated proteins from 30 healthy human tissues including 7 fetal tissues, 6 types of hematopoeitic cells and 17 adult tissues. Both groups used mass spectrometry to create a catalogue of proteins in the sample mix and similarly, both published their findings in the same journal of Nature on May 29th, 2014. For the benefit of the scientific community, both teams have made their results available online in searchable databases. Data from Prof Kuster’s group can be found freely at proteomicsdb.org while results from the Prof. Pandey’s team is available at humanproteomemap.org.

Prof Kuster’s team successfully detected 92% of proteins predicted to be encoded by the gnome, while Prof Panday’s group confirmed 84%. Interestingly, the initial findings of the human proteome have identified 193 novel proteins. These newly identified proteins seem to be transcribed from sections of DNA that were previously characterized as non-coding. In contrast, researchers were unable to locate approximately 2000 proteins that should be present according to genome analysis. These results ultimately raises questions about our understanding of how genes are transcribed and translated. Likewise, although we now have a comprehensive list of proteins, we cannot fully appreciate the function of each protein without considering how protein function may be altered by post-translational modifications, structure and protein-protein interactions.

Looking ahead, it is hoped that the expression profile of each protein may give researchers clues to their function. For example, if expression of a particular protein is restricted to a certain cell type, this may highlight which proteins are involved in development or homeostasis. Moreover, the human proteome may also give us a remarkable insight into how protein expression may be altered in disease. This information may help our understanding of disease development and progression. In the long term, the expression profile of certain proteins may even be used to determine the sensitivity of cells to a particular therapy or predict possible side effects of treatment. This would ideally lead to a more targeted therapeutic regime or personalized treatments for each patient.

As well as being an incredible achievement, the availability of the data generated by the Human Proteome Project will certainly mold and direct current and future research into protein expression and function in health and disease.