Tag Archives: Telomere

Microbiology

Simple blood tests for telomeric protein could provide a valuable screen for certain cancers

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Reviewed by Emily Henderson, B.Sc.Feb 21 2023

Once thought incapable of encoding proteins due to their simple monotonous repetitions of DNA, tiny telomeres at the tips of our chromosomes seem to hold a potent biological function that’s potentially relevant to our understanding of cancer and aging.

Reporting in the Proceedings of the National Academy of Science, UNC School of Medicine researchers Taghreed Al-Turki, PhD, and Jack Griffith, PhD, made the stunning discovery that telomeres contain genetic information to produce two small proteins, one of which they found is elevated in some human cancer cells, as well as cells from patients suffering from telomere-related defects.

Based on our research, we think simple blood tests for these proteins could provide a valuable screen for certain cancers and other human diseases. These tests also could provide a measure of ‘telomere health,’ because we know telomeres shorten with age.”

Jack Griffith, PhD, the Kenan Distinguished Professor of Microbiology and Immunology and Member of the UNC Lineberger Comprehensive Cancer Center

Telomeres contain a unique DNA sequence consisting of endless repeats of TTAGGG bases that somehow inhibit chromosomes from sticking to each other. Two decades ago, the Griffith laboratory showed that the end of a telomere’s DNA loops back on itself to form a tiny circle, thus hiding the end and blocking chromosome-to-chromosome fusions. When cells divide, telomeres shorten, eventually becoming so short that the cell can no longer divide properly, leading to cell death.

Scientist first identified telomeres about 80 years ago, and because of their monotonous sequence, the established dogma in the field held that telomeres could not encode for any proteins, let alone ones with potent biological function.

In 2011 a group in Florida working on an inherited form of ALS reported that the culprit was an RNA molecule containing a six-base repeat which by a novel mechanism could generate a series of toxic proteins consisting of two amino acids repeating one after the other. Al-Turki and Griffith note in their paper a striking similarity of this RNA to the RNA generated from human telomeres, and they hypothesized that the same novel mechanism might be in play.

They conducted experiments – as described in the PNAS paper – to show how telomeric DNA can instruct the cell to produce signaling proteins they termed VR (valine-arginine) and GL (glycine-leucine). Signaling proteins are essentially chemicals that trigger a chain reaction of other proteins inside cells that then lead to a biological function important for health or disease.

Al-Turki and Griffith then chemically synthesized VR and GL to examine their properties using powerful electron and confocal microscopes along with state-of-the-art biological methods, revealing that the VR protein is present in elevated amounts in some human cancer cells, as well as cells from patients suffering from diseases resulting from defective telomeres.

“We think it’s possible that as we age, the amount of VR and GL in our blood will steadily rise, potentially providing a new biomarker for biological age as contrasted to chronological age,” said Al-Turki, a postdoctoral researcher in the Griffith lab. “We think inflammation may also trigger the production of these proteins.”

Griffith noted, “When you go against current thinking, you are usually wrong because you are bucking many people who’ve worked so diligently in their fields. But occasionally scientists have failed to put observations from two very distant fields together and that’s what we did. Discovering that telomeres encode two novel signaling proteins will change our understanding of cancer, aging, and how cells communicate with other cells.

“Many questions remain to be answered, but our biggest priority now is developing a simple blood test for these proteins. This could inform us of our biological age and also provide warnings of issues, such as cancer or inflammation.”

Source:

University of North Carolina Health Care

Journal reference:

Al-Turki, T., et al. (2023) Mammalian Telomeric RNA (TERRA) can be translated to produce valine-arginine and glycine-leucine dipeptide repeat proteins. PNAS. doi.org/10.1073/pnas.2221529120.

Microbiology

Highly accurate test for common respiratory viruses uses DNA as ‘bait’

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A new test that ‘fishes’ for multiple respiratory viruses at once using single strands of DNA as ‘bait’, and gives highly accurate results in under an hour, has been developed by Cambridge researchers.

The test uses DNA ‘nanobait’ to detect the most common respiratory viruses — including influenza, rhinovirus, RSV and COVID-19 — at the same time. In comparison, PCR (polymerase chain reaction) tests, while highly specific and highly accurate, can only test for a single virus at a time and take several hours to return a result.

While many common respiratory viruses have similar symptoms, they require different treatments. By testing for multiple viruses at once, the researchers say their test will ensure patients get the right treatment quickly and could also reduce the unwarranted use of antibiotics.

In addition, the tests can be used in any setting, and can be easily modified to detect different bacteria and viruses, including potential new variants of SARS-CoV-2, the virus which causes COVID-19. The results are reported in the journal Nature Nanotechnology.

The winter cold, flu and RSV season has arrived in the northern hemisphere, and healthcare workers must make quick decisions about treatment when patients show up in their hospital or clinic.

“Many respiratory viruses have similar symptoms but require different treatments: we wanted to see if we could search for multiple viruses in parallel,” said Filip Bošković from Cambridge’s Cavendish Laboratory, the paper’s first author. “According to the World Health Organization, respiratory viruses are the cause of death for 20% of children who die under the age of five. If you could come up with a test that could detect multiple viruses quickly and accurately, it could make a huge difference.”

For Bošković, the research is also personal: as a young child, he was in hospital for almost a month with a high fever. Doctors could not figure out the cause of his illness until a PCR machine became available.

“Good diagnostics are the key to good treatments,” said Bošković, who is a PhD student at St John’s College, Cambridge. “People show up at hospital in need of treatment and they might be carrying multiple different viruses, but unless you can discriminate between different viruses, there is a risk patients could receive incorrect treatment.”

PCR tests are powerful, sensitive and accurate, but they require a piece of genome to be copied millions of times, which takes several hours.

The Cambridge researchers wanted to develop a test that uses RNA to detect viruses directly, without the need to copy the genome, but with high enough sensitivity to be useful in a healthcare setting.

“For patients, we know that rapid diagnosis improves their outcome, so being able to detect the infectious agent quickly could save their life,” said co-author Professor Stephen Baker, from the Cambridge Institute of Therapeutic Immunology and Infectious Disease. “For healthcare workers, such a test could be used anywhere, in the UK or in any low- or middle-income setting, which helps ensure patients get the correct treatment quickly and reduce the use of unwarranted antibiotics.”

The researchers based their test on structures built from double strands of DNA with overhanging single strands. These single strands are the ‘bait’: they are programmed to ‘fish’ for specific regions in the RNA of target viruses. The nanobaits are then passed through very tiny holes called nanopores. Nanopore sensing is like a ticker tape reader that transforms molecular structures into digital information in milliseconds. The structure of each nanobait reveals the target virus or its variant.

The researchers showed that the test can easily be reprogrammed to discriminate between viral variants, including variants of the virus that causes COVID-19. The approach enables near 100% specificity due to the precision of the programmable nanobait structures.

“This work elegantly uses new technology to solve multiple current limitations in one go,” said Baker. “One of the things we struggle with most is the rapid and accurate identification of the organisms causing the infection. This technology is a potential game changer; a rapid, low-cost diagnostic platform that is simple and can be used anywhere on any sample.”

A patent on the technology has been filed by Cambridge Enterprise, the University’s commercialisation arm, and co-author Professor Ulrich Keyser has co-founded a company, Cambridge Nucleomics, focused on RNA detection with single-molecule precision.

“Nanobait is based on DNA nanotechnology and will allow for many more exciting applications in the future,” said Keyser, who is based at the Cavendish Laboratory. “For commercial applications and roll-out to the public we will have to convert our nanopore platform into a hand-held device.”

“Bringing together researchers from medicine, physics, engineering and chemistry helped us come up with a truly meaningful solution to a difficult problem,” said Bošković, who received a 2022 PhD award from Cambridge Society for Applied Research for this work.

The research was supported in part by the European Research Council, the Winton Programme for the Physics of Sustainability, St John’s College, UK Research and Innovation (UKRI), Wellcome, and the National Institute for Health and Care Research (NIHR) Cambridge Biomedical Research Centre.

  • Filip Bošković, Jinbo Zhu, Ran Tivony, Alexander Ohmann, Kaikai Chen, Mohammed F. Alawami, Milan Đorđević, Niklas Ermann, Joana Pereira-Dias, Michael Fairhead, Mark Howarth, Stephen Baker, Ulrich F. Keyser. Simultaneous identification of viruses and viral variants with programmable DNA nanobait. Nature Nanotechnology, 2023; DOI: 10.1038/s41565-022-01287-x

    • University of Cambridge
    Microbiology

    Antiviral defense regulates intestinal function and overall gut health

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    Besides the skin, the digestive tract is the tissue that is most exposed to environmental influences such as bacteria and viruses. Therefore, cells that form these barriers to the interior of the body also have special defence mechanisms. A research team led by Professor Dr Thorsten Hoppe has now shown that RNA interference, or RNAi for short, which is known to be a viral defence mechanism, also prevents the overproduction of the body’s own proteins in intestinal cells. The study ‘ER-Associated RNA Silencing Promotes ER Quality Control’ has been published in the journal Nature Cell Biology.

    RNAi is able to recognize, bind, and ultimately degrade RNA from viruses. This prevents the production of viral proteins. With the help of green fluorescent proteins and further analyses in the nematode Caenorhabditis elegans, the UoC research team was able to show that RNAi also intervenes in cells during protein production to maintain the protein balance (protein homeostasis) of the intestinal cells. The body’s own protein production starts with the copying of DNA and the creation of the template molecule, also known as the messenger RNA (mRNA), in the cell nucleus. The mRNA is then taken to the endoplasmic reticulum (ER), where a protein is produced from the template molecule. As in a factory, the manufactured proteins are subject to a strict quality control. Deficient proteins are exported from the ER and degraded to avoid cellular waste and extensive negative consequences for the physiology and functionality of the cell as well as the tissue.

    ‘We observed that the RNAi mechanism specifically degrades messenger RNAs at the ER before the protein is even produced. This serves to protect the ER from being overloaded by too much production,’ said Dr Franziska Ottens, one of the first authors of the study. The scientists thus found a new mechanism to regulate protein production.

    The interplay between RNAi and previously known ER quality control systems appears to be important for overall intestinal health. This is shown by the fact that simultaneous failure of both mechanisms impairs the important barrier function of the gut. The study results also suggest a link between ER functionality and quality control, which are important for protection against viral infection. For example, RNA viruses such as SARS-CoV use the ER for replication.

    ‘We were able to significantly suppress viral loads by specifically overstressing the ER. The interplay of protein homeostasis, RNAi, and viral infection could be an important approach for the prospective research and treatment of viral diseases,’ said doctoral candidate Sotirios Efstathiou, a member of Thorsten Hoppe’s team and another first author of the study.

    The research was conducted at the CECAD Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases at the University of Cologne. It was funded by the German Research Foundation (DFG) in the framework of the German Excellence Strategy and by the European Research Council. Furthermore, support from the Cologne Graduate School of Aging Research and the Alexander von Humboldt Foundation made the research possible.

    Story Source:

    Materials provided by University of Cologne. Note: Content may be edited for style and length.

    Journal Reference:

  • Sotirios Efstathiou, Franziska Ottens, Lena-Sophie Schütter, Sonia Ravanelli, Nikolaos Charmpilas, Aljona Gutschmidt, Jérémie Le Pen, Niels H. Gehring, Eric A. Miska, Jorge Bouças, Thorsten Hoppe. ER-associated RNA silencing promotes ER quality control. Nature Cell Biology, 2022; 24 (12): 1714 DOI: 10.1038/s41556-022-01025-4

    • University of Cologne
    Microbiology

    Molecular monitoring of RNA regulation

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    The better we understand cellular processes such as RNA regulation, the better molecular therapies can be developed. Until now, it has been especially difficult to track the regulation of non-coding RNA, which is RNA that is not further converted into proteins. A research team from Helmholtz Munich and the Technical University of Munich (TUM) has now developed a minimally invasive reporter system that enables highly sensitive monitoring of RNA production of both coding and non-coding RNA.

    For cellular processes, our genetic DNA information is transcribed into RNA, which then undergoes further processing before it either serves as a blueprint for proteins or performs a cellular function itself. Which types of RNA are produced and in which quantities reveals a lot about the condition of our cells. In case of an infection, for example, cells produce increased amounts of RNA molecules that code for proteins involved in the immune response.

    When DNA molecules are translated into proteins via RNA, researchers can track the process with existing reporter systems. However, not all human genes encode proteins. The majority of human genes is non-coding, including genes for long non-coding RNAs (lncRNA). These are RNA molecules with more than 200 building blocks that do not act as blueprints for proteins. Instead, they control important processes in cells. Initial research shows that lncRNA is involved in such processes as regulating RNA production, the organization of structures in the cell nucleus or in switching certain enzymes on and off.

    Despite their importance for cellular processes, it has been difficult to investigate lncRNAs with existing methods. So far, this was only partially possible, for example in fixed cells at specific time points, because classical reporter systems based on the translation into proteins cannot be used.

    INSPECT permits the monitoring of non-coding RNA

    A solution has now been found in the form of a new reporter system: INSPECT. A team working with Gil Westmeyer, Professor of Neurobiological Engineering at TUM and the Director of the Institute for Synthetic Biomedicine at Helmholtz Munich, has now published the newly developed reporter system in the journal Nature Cell Biology.

    “Unlike previous methods, INSPECT encodes sequences for reporter proteins in modified introns. These are sequences in the pre-mature RNA molecule that are removed naturally and eliminated by the cell during processing. INSPECT stabilizes the introns such that, rather than being degraded after removal, they are transported to the cellular cytoplasm where they are translated into reporter proteins,” explains first author Dong-Jiunn Jeffery Truong. The researchers can then use conventional methods to detect reporter protein signals such as fluorescence.

    INSPECT modifies neither the completed RNA nor the proteins

    The new molecular biology tool thus not only solves the problem of tracking the generation of non-coding RNA, but also offers advantages for studying coding RNA. Current reporter systems often run the risk of damaging the RNA or proteins under investigation, for example, because they must be fused directly to the RNA being studied in order to be co-translated into proteins. Rather than modifying the completed RNA or the proteins, INSPECT modifies the introns.

    The team has demonstrated the function of INSPECT using various examples of coding and non-coding RNA. They tracked the production of RNA for interleukin 2, a protein that is produced in larger quantities in response to infections. They have also achieved highly sensitive monitoring of the production of two lncRNAs and tracked changes in regulation during the investigation period.

    “INSPECT adds an important molecular biology tool to the biomedical toolbox. It makes it easier to study the role of certain non-coding RNA molecules in cell development and to explore how their regulation can be modulated, for example, to prevent them from turning into cancer cells,” says Prof. Westmeyer. “In combination with the minimally invasive reporter system EXSISERS, which we previously developed to study protein isoforms, it may be possible in the future to study an entire genetic regulation process from RNA processing to the production of specific protein variants in living cells.”

    Story Source:

    Materials provided by Helmholtz Munich. Note: Content may be edited for style and length.

    Journal References:

  • Dong-Jiunn Jeffery Truong, Niklas Armbrust, Julian Geilenkeuser, Eva-Maria Lederer, Tobias Heinrich Santl, Maren Beyer, Sebastian Ittermann, Emily Steinmaßl, Mariya Dyka, Gerald Raffl, Teeradon Phlairaharn, Tobias Greisle, Milica Živanić, Markus Grosch, Micha Drukker, Gil Gregor Westmeyer. Intron-encoded cistronic transcripts for minimally invasive monitoring of coding and non-coding RNAs. Nature Cell Biology, 2022; 24 (11): 1666 DOI: 10.1038/s41556-022-00998-6

  • Dong-Jiunn Jeffery Truong, Teeradon Phlairaharn, Bianca Eßwein, Christoph Gruber, Deniz Tümen, Enikő Baligács, Niklas Armbrust, Francesco Leandro Vaccaro, Eva-Maria Lederer, Eva Magdalena Beck, Julian Geilenkeuser, Simone Göppert, Luisa Krumwiede, Christian Grätz, Gerald Raffl, Dominic Schwarz, Martin Zirngibl, Milica Živanić, Maren Beyer, Johann Dietmar Körner, Tobias Santl, Valentin Evsyukov, Tabea Strauß, Sigrid C. Schwarz, Günter U. Höglinger, Peter Heutink, Sebastian Doll, Marcus Conrad, Florian Giesert, Wolfgang Wurst, Gil Gregor Westmeyer. Non-invasive and high-throughput interrogation of exon-specific isoform expression. Nature Cell Biology, 2021; 23 (6): 652 DOI: 10.1038/s41556-021-00678-x

    • Helmholtz Munich