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Disease and treatment

New method reveals which cells resist chemotherapy

When cancer attacks the body, the body needs to combat the cancer cells while sparing the healthy ones. Conversely, cancer cells develop mechanisms to escape both the body’s response to cancer and chemotherapy. The natural differences between humans and between tumours influence how effectively the body can fight cancer cells, including the response to chemotherapy. Researchers have now developed a method of differentiating between cancer cells and healthy cells – based solely on the composition of the proteins in cells. This method can also show how cells react to external stimuli such as chemotherapy.

Cancer cells are basically ordinary cells that are out of control. The usual regulation of the cells fails, which causes them to divide and proliferate abnormally. This faulty regulation also significantly changes the distribution of the 20,000 proteins in the cells. Swiss researcher Ruedi Aebersold and his research team have specialized in spotting this imbalance. They have become so expert that they not only can distinguish between cancer cells and healthy cells but also can determine how cancer cells react to chemotherapy.

“People who have prostate cancer often initially respond positively to chemotherapy, and this gives the impression that the treatment is working. However, resistance often emerges, indicating the need for multiple drugs in combination therapy. Our new method can monitor the molecular response very precisely, enabling us to constantly measure how the internal processes of cancer cells react to chemotherapy,” explains Ruedi Aebersold, Professor, Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich.

Millions of fragments

Ruedi Aebersold is a pioneer in proteomics research. Genomics examines an organism’s DNA, whereas proteomics focuses on the final product of a gene: proteins, which are both the building blocks of cells and the enzymes that catalyse cellular processes. Proteomics therefore provides a snapshot of the actual state of a cell and is therefore also very suitable for spotting changes in cellular health and the difference between healthy cells and cancer cells.

“Researchers previously assumed that they only need to screen the messenger RNA patterns cells that use in transcribing proteins from DNA. Now we know that RNA has many other cellular functions, so measuring RNA does not provide a conclusive snapshot of the state of the cells. Further, the quantity of protein translated from a specific transcript cannot be accurately predicted. Therefore, we need to measure the proteins directly to obtain an accurate indication of the biochemical state of the cell.”

Screening a library of multiple thousands of proteins encoded by the approximately 20,000 coding genes of the human genome and expressed in the human cells that are produced at a specific time and especially in a given quantity is no trivial task. Nevertheless, in the past 20 years, Ruedi Aebersold and his laboratory have developed and refined several methods for fragmenting the thousands of proteins in cells and labelling them using the isotope-coded affinity tag (ICATTM) reagent process or, more recently, with the massively parallel targeting proteomic method SWATH-MS. The researchers then analyse the millions of fragments using mass spectrometry and advanced computer programs.

“These snapshots show which cells contain abnormal levels of certain proteins, but we can also differentiate cells in various states and systematically examine how the cells react to external stimuli. We recently completed a study investigating how effective different types of therapy are on prostate cancer. This enables us to determine how well specific therapies work and whether each individual develops resistance to the treatment.”

Suspected cheating may not be cheating

The new method is expected to lead to the development of new diagnostic markers for diseases. Equally important, this method will provide more comprehensive understanding of the biochemical processes that control and comprise the physiology of human cells.

“Research was previously carried out on one protein at a time. Our technology enables many proteins to be identified and quantitatively analysed simultaneously and directly in biological cell tissue and biological fluids and such analyses to be performed on high numbers of samples with a high degree of reproducibility. This means that complex samples can be analysed on a large scale, and shortly after taking a sample from a person we can produce a comprehensive snapshot of how each cell deviates from the normal state.”

Ruedi Aebersold and his research group encountered one unexpected side-effect of this very precise analytical method when they attempted to analyse samples from HeLa cancer cells, an immortal cell line used in research. The cells should actually have been identical, apart from being cultured in laboratories in different countries. However, the researchers analysed these cells and discovered major differences.

“We were very surprised to find such major differences. However, this clarified something researchers had been wondering about for decades: why they could not repeat identical experiments carried out in cells of the same type, here HeLa, and obtain the same results as colleagues elsewhere in the world. Now we know that the probable reason is minor differences in the molecular make-up of the cells, which causes different responses, rather than someone trying to cheat or being incompetent.”

Ruedi Aebersold gave a presentation in October 2018 at Protein Signaling – from Pathways to Networks, a Copenhagen Bioscience Conferences sponsored by the Novo Nordisk Foundation. “Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer” has been published in Systems Biology and Applications.

Ruedi Aebersold
Professor Dr.
Prof. Ruedi Aebersold is one of the pioneers in the field of proteomics. He is known for developing a series of methods that have found wide application in analytical protein chemistry and proteomics like a new class of reagents termed Isotope Coded Affinity Tag (ICAT) reagents used in quantitative mass spectrometry. Prof. Dr. Aebersold and his team of researchers use the protein profiles determined by this method to differentiate cells in different states, such as noncancerous versus cancerous cells, and to systematically study how cells respond to external stimuli. These "snapshot" profiles indicate which cells contain abnormal levels of certain proteins. This is expected to lead to new diagnostic markers for disease and to a more complete understanding of the biochemical processes that control and constitute cell physiology. Prof. Aebersold serves on the Scientific Advisory Committees of numerous academic and private sector research organizations and is a member of several editorial boards in the fields of protein science, genomics, and proteomics. Prof. Aebersold is a native of Switzerland and obtained his Ph.D. in Cellular Biology at the Biocenter of the University of Basel in 1983. Since that time, he is a faculty member of the Universities of Washington and British Columbia, until 2000, when he co-founded the Institute for Systems Biology in Seattle. In 2004, he accepted a position as full professor at the Institute of Biotechnology at the Swiss Federal Institute of Technology (ETH) in Zurich, where in January 2005, his research group became the first integral part of the newly founded Institute of Molecular Systems Biology.