A human cell is an organized place, with different compartments isolating biochemical processes into subcellular locations. Defining the proteome of each compartment, or organelle, can yield insights into the functioning of the cell. Techniques such as microscopy and mass spectrometry on biochemical fractions have yielded some insights, however, the proteomic information remains incomplete.

Now, researchers from Sinai Health provide an ultra-detailed look at the organization of a living human cell using the proximity-dependent biotinylation technique known as BioID. A new paper presents a BioID-based map of a human cell on the basis of 192 subcellular markers, and defines the intracellular locations of 4,145 unique proteins in HEK293 cells.

The work, published in Nature in the paper, “A proximity-dependent biotinylation map of a human cell,” provides a new tool that can help scientists around the world better understand what happens during disease.

“The Human Cell Map was able to predict the localization of 4,000 proteins across all compartments in living human cells,” said Christopher Go, one of the co-first authors on the paper. Go is a graduate student in the laboratory of Anne-Claude Gingras, PhD, a senior investigator at the Lunenfeld-Tanenbaum Research Institute (LTRI) and professor in the department of molecular genetics at the University of Toronto.  “We sampled all the major organelles of the human cell,” noted Go, “and used innovative analysis to create the highest resolution map to date, with high accuracy in predicting novel localizations for many unmapped proteins.”

Earlier approaches to elucidate which proteins are in an organelle often used methods that first kill the cells before trying to separate the organelles from one another. “These approaches,” said Go, “tend to provide only crude views of the organization of a cell.”

The Gingras lab purified the proteins that are “tagged” by organelle markers and identified each of them by mass spectrometry. The team then used computational tools to reconstruct the human cell.

“Through our research, we have shown that we can precisely localize thousands of proteins at a time with relatively little effort,” said James Knight, PhD, a bioinformatician in the Gingras lab. “Previous methods for localizing a protein required each protein to be investigated individually, or required a limited focus.”

In addition to conducting the research, the team also created an analysis portal to allow researchers access to the data. Users can scan each of the 192 markers in detail and compare their own data on protein localization to predictions made in the Human Cell Map.

Knight said while this work provides a greater understanding of the organization within the human cell, it also can be leveraged to better understand what happens during disease.

“Human diseases are typically characterized at the molecular level by proteins with aberrant behavior that causes the cell to behave in pathological ways. In these situations, proteins will often change where they reside in the cell,” said Knight. “Our research is a first step in addressing this challenge in normal cells and we can use it for comparisons against altered cell states, such as disease conditions, to identify proteins with unexpected localizations that may help us understand a diseased cell better.”

The team said the map will now be used in a variety of projects to help shed additional light on protein localization in human cells. Future efforts will include using chemical, viral, and disease conditions to better characterize how cells adapt structurally to these stressors. This can inform future research efforts towards a mechanistic understanding of diseased states and the development of future therapeutics.