A group of researchers from the Lomonosov Moscow State University in collaboration with their Irish colleagues from the University College Cork has studied the early response of cells to ischemia, which is a restriction in blood supply to tissues causing the death of the cell. The article describing the results of their studies is published in Genome Biology.
Dmitry Andreev, PhD, senior research fellow at the A.N. Belozersky Institute Of Physico-Chemical Biology and Ivan Shatsky, PhD, professor at the same institute, described the results.
"The study became possible due to the development of techniques like next-generation sequencing (NGS), which made a real revolution in the life sciences. In particular, we used the ribosome profiling technique which allows the capture of a "snapshot" of all protein synthesis in the cell at a given time. The protein synthesis in the cell is driven by ribosomes, which are huge macromolecular machines capable of reading the information encoded in the messenger RNA and synthesizing corresponding proteins. At any time thousands of various proteins, are being synthesized by ribosomes. When a change in external conditions occurs, ribosomes can quickly switch to the other messenger RNA and begin to synthesize the proteins necessary for adaptation to new conditions.
"We decided to use this method to study the changes in gene expression in the cells upon oxygen and glucose deprivation," Dmitry Andreev explains. "This is a model for studying ischemia."
Prolonged exposure to ischemia always leads to irreversible tissue damage, and as a consequence to the cell death. However, within a short time after the stress cells are still viable, what means they can rescued and thereby prevent the devastating effects of ischemia. That is why understanding of the processes occurring in a cell in the early hours, or even minutes after ischemia, can have a very important fundamental and practical significance.
We have studied the early response to ischemia in the first hour after stress. It appeared that within 20 minutes after the stress significant changes in the synthesis of proteins occur. It is interesting that the most significant changes occur in the synthesis of proteins involved in mitochondrial respiratory chain. Apparently, the cell tries dramatically to adapt to new conditions and to switch to "alternative" energy sources in order to avoid death.
The main paradigm of regulation of respiration in the cell signaling pathway is a family of transcription factors known as HIF (Hypoxia Inducible Factor). This transcription factor activates expression of several genes involved, for example, in glucose transport or in the formation of new blood vessels. Under normal conditions, when the oxygen in the cell is sufficient, specific prolyl hydroxylase enzymes constantly modify regulatory subunits of HIF sending it to the destruction. Thereby HIF remains turned off. Once the oxygen level in the cell falls below a threshold, prolyl hydroxylase, which requires oxygen for activity, turns off, while HIF stabilizes and begins to work.
The HIF signaling cascade is also important because its activity is necessary for the survival of a variety of tumors as many cancer cells face with chronic shortage of oxygen due to defects in the blood supply, and in order to survive they have to adapt to the conditions of hypoxia. Therefore HIF is a very promising target for cancer therapy.
As a indication of the scientific interest in this family, there are more than 12,000 scientific studies on the subject, since it was first identified in 1995.
Importantly, we have found that the early changes in genes expression observed upon oxygen and glucose deprivation precede the response of the HIF transcription factors and do not overlap with it. Moreover, the new ways of regulation may directly affect the HIF signaling pathway. For example, one of the most striking cases of regulation is an increase in synthesis of UBE2S protein, which is directly involved in the degradation of regulatory HIF subunit. This is an early system of regulation that was not previously appreciated. There were no approaches that could reliably detect these early changes prior to the development of the ribosomal profiling method.
"We have many plans how to develop this subject, but at the moment we prefer not to share them as in this area of research there is a very serious competition, including scientists from the world's leading research centers. It is necessary to note that a very large contribution of all members of the team took place in this work and we look forward to continuing the collaboration with our colleagues", Dmitry Andreev summed.
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Dmitry E Andreev, Patrick B.F. O’Connor, Alexander V. Zhdanov, Ruslan I. Dmitriev, Ivan N. Shatsky, Dmitri B. Papkovsky, Pavel V. Baranov. Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes. Genome Biology, Published May 6 2015. doi: 10.1186/s13059-015-0651-z