Tuesday, August 27, 2019

Revolutionising the CRISPR method

14.08.2019 | News

Researchers at ETH Zurich have refined the famous CRISPR-Cas method. Now, for the very first time, it is possible to modify dozens, if not hundreds, of genes in a cell simultaneously.
Genes and proteins in cells interact in many different ways. Each dot represents a gene; the lines are their interactions. For the first time, the new method uses biotechnology to influence entire gene networks in one single step. (Visualizations: ETH Zurich / Carlo Cosimo Campa)
Everyone’s talking about CRISPR-Cas. This biotechnological method offers a relatively quick and easy way to manipulate single genes in cells, meaning they can be precisely deleted, replaced or modified. Furthermore, in recent years, researchers have also been using technologies based on CRISPR-Cas to systematically increase or decrease the activity of individual genes. The corresponding methods have become the worldwide standard within a very short time, both in basic biological research and in applied fields such as plant breeding.
To date, for the most part, researchers could modify only one gene at a time using the method. On occasion, they managed two or three in one go; in one particular case, they were able to edit seven genes simultaneously. Now, Professor Randall Platt and his team at the Department of Biosystems Science and Engineering at ETH Zurich in Basel have developed a process that – as they demonstrated in experiments – can modify 25 target sites within genes in a cell at once. As if that were not enough, this number can be increased still further, to dozens or even hundreds of genes, as Platt points out. At any rate, the method offers enormous potential for biomedical research and biotechnology. “Thanks to this new tool, we and other scientists can now achieve what we could only dream of doing in the past.”

Targeted, large-scale cell reprogramming

Genes and proteins in cells interact in many different ways. The resulting networks comprising dozens of genes ensure an organism’s cellular diversity. For example, they are responsible for differentiating progenitor cells to neuronal cells and immune cells. “Our method enables us, for the first time, to systematically modify entire gene networks in a single step,” Platt says.
Moreover, it paves the way for complex, large-scale cell programming. It can be used to increase the activity of certain genes, while reducing that of others. The timing of this change in activity can also be precisely controlled.
This is of interest for basic research, for example in investigating why various types of cells behave differently or for the study of complex genetic disorders. It will also prove useful for cell replacement therapy, which involves replacing damaged with healthy cells. In this case, researchers can use the method to convert stem cells into differentiated cells, such as neuronal cells or insulin-producing beta cells, or vice versa, to produce stem cells from differentiated skin cells.

The dual function of the Cas enzyme

The CRISPR-Cas method requires an enzyme known as a Cas and a small RNA molecule. Its sequence of nucleobases serves as an “address label”, directing the enzyme with utmost precision to its designated site of action on the chromosomes. ETH scientists have created a plasmid, or a circular DNA molecule, that stores the blueprint of the Cas enzyme and numerous RNA address molecules, arranged in sequences: in other words, a longer address list. In their experiments, the researchers inserted this plasmid into human cells, thereby demonstrating that several genes can be modified and regulated simultaneously.
For the new technique, the scientists did not use the Cas9 enzyme that has featured in most CRISPR-Cas methods to date, but the related Cas12a enzyme. Not only can it edit genes, it can also cut the long “RNA address list” into individual “address labels” at the same time. Furthermore, Cas12a can handle shorter RNA address molecules than Cas9. “The shorter these addressing sequences are, the more of them we can fit onto a plasmid,” Platt says.


Campa CC, Weisbach NR, Santinha AJ, Incarnato D, Platt RJ: Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts. Nature Methods, 12 August 2019, doi: 10.1038/s41592-019-0508-6

Smart interaction between proteins

19.08.2019 | News

Very little was known till now about DNA repair by homologous recombination, which is fundamental for human health. Now an ETH research group has for the first time isolated and studied all the key proteins involved in this process, laying the foundation for investigating many diseases.

Which proteins are essential for cell division? The biochemist Philipp Wild (left) and his colleagues Ilaria Piazza and Christian Dörig examine the results from the mass spectrometer. (Photograph: ETH Zurich / Adrian Henggeler)

Within our body, the process of cell division is constantly creating new cells to replace old or damaged ones. The genetic information is also duplicated and passed on to the new cells. Complex interaction of many different proteins ensures a smooth process. This is because these proteins immediately repair any errors that creep in during DNA duplication. However, the same protein machinery also performs another function: in germ cells that divide to from gametes – egg cells and sperm – it is responsible for mixing the genetic information of the original maternal and paternal side during cell division. The same mechanism therefore has to resolve two conflicting problems: in normal cell division, called mitosis, it ensures genetic preservation, while in the cell division to produce gametes, or meiosis, it ensures genetic diversity. 
Both tasks are vital. If DNA repair does not work in mitosis, this can lead to cancer and other diseases. If, on the other hand, the exchange of DNA in meiosis does not function correctly, the fertility and health of the offspring may be damaged. “Although these processes are crucial for our health, very little was known till now about how the whole system functions and is regulated,” says Joao Matos, Professor for Biochemistry at ETH Zurich. His team has now studied the responsible proteins and discovered how they differentiate between the two tasks.

A complex task

The scientists began by cultivating a large number of yeast cells in the laboratory, as these cells only contain a minute quantity of the proteins involved. The production of the yeast cells was therefore extremely complex: the researchers cultivated cells in 120 6-litre containers in such a way that the division occurred simultaneously in all yeast cells. Mitosis and meiosis are highly complex processes that take place in precisely orchestrated phases. Only synchronized cell cultures can thus differentiate which proteins are important in which phase, and how they work together.
Scientists already knew that yeast, along with plants, animals and humans, have a group of seven enzymes involved in the reproduction of DNA: the recombination intermediates processing enzymes (RIPEs). For the first time, ETH scientists were able to isolate these RIPEs from the cell cultures and identify them in the mass spectrometer – from a specific phase of cell division in each instance. At the same time, they used this method to identify a series of other proteins that help regulate cell division.

The same components, but rewired

Joao Matos and his team were eventually able to identify which RIPEs are important for which phase of cell division and which helper proteins interact with the RIPEs in each case. The first unexpected result: the quantity of RIPEs remains almost constant in all phases of mitosis and meiosis. “Unlike many other processes, the cells do not regulate cell division and DNA repair through the production of the proteins involved,”  Matos explains. Instead, the helper proteins interact systematically with the RIPE enzymes in order to enable or disable them in a specific phase. “All the components are always there, but are rewired depending on the task”, says the ETH professor.
For example, the researchers discovered that three of the RIPEs lose almost all their interaction partners precisely in the so-called metaphase of meiosis, in other words when the maternal and paternal DNA is mixed. In return, another protein complex is formed at this point. “This must be responsible for mixing up the maternal and paternal DNA,” Matos concludes. In addition, ETH researchers have identified a number of new helper proteins whose role was previously unknown.

Key to understanding disease

The results from the yeast cells can be transferred to humans, as for every helper protein involved there is an equivalent in humans that functions in the same or very similar fashion. So the Matos research group and fellow scientists can build on this knowledge. They can now study specific proteins to discover whether, and how, they are involved in the development of diseases and ultimately find a remedy to combat them.

Wild P, et al. Network Rewiring of Homologous Recombination Enzymes during Mitotic Proliferation and Meiosis. Molecular Cell, available online 24 July 2019. doi: 10.1016/j.molcel.2019.06.022

Sunday, July 21, 2019

Chinese Scientists Say They’ve Found a Safer Alternative to CRISPR

Researchers from China’s Peking University have developed a new gene-editing technology —  and they think it shows promise as a CRISPR alternative for fighting human diseases.

According to a paper published on Monday in the journal Nature Biotechnology, this new technology, LEAPER, which stands for “leveraging endogenous ADAR for programmable editing of RNA,” works similarly to CRISPR-Cas13, targeting RNA molecules as opposed to DNA like the well-known CRISPR-Cas9.

But while CRISPR-Cas13 relies on both a guide RNA and the Cas13 enzyme to make its edits to RNA, the LEAPER system needs just one component known as an arRNA.

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Friday, July 12, 2019

Proton Therapy

There are more than 200 different types of cancers. According to the US National Cancer Institute, nearly 40% of Americans will be diagnosed with cancer during their lives. The World Health Organization names cancer as the second leading cause of death globally, causing nearly one in six deaths. In case anyone needs reminding, cancer is a big deal. Lung cancer is the leading cause of cancer deaths around the world, causing more deaths than prostate, breast and colon cancers combined. Only 18.5% of patients will survive five or more years after being diagnosed with lung cancer. So smokers, take note! Alongside chemotherapy and surgery to remove tumors, about 40% of cancer patients are treated with radiotherapy, which fires ionizing radiation into the body, killing malignant cells with X-ray photons. Roughly 17,000 clinics worldwide deliver X-ray radiotherapy treatment today.

The rise in popularity of proton therapy (vs X-ray) is continuing across the globe. It is estimated that more than 165,000 patients suffering from a variety of cancers, such as prostate cancer, brain tumors, etc. have already been successfully treated using this method. In fact, the proton therapy market is on track to become a multibillion-dollar industry by 2024. The number of proton therapy centers is increasing globally. Still, industry experts believe that players will miss out on a majority of cancer patients who can benefit with proton therapy, overlooking a huge multi-Billion-dollar potential market.

The proton therapy market is likely to almost double by 2024 from its current market value.  Globally, the numbers of patients treated with proton therapy is very low whereas the potential candidates for it are in the Millions.

Tuesday, January 31, 2017

Swiss Society for Biomaterials & Regenerative Medicine Annual Conference

Advances in Antimicrobial Biomaterials science, industry, physicians

The SSB+RM meetings are devoted to all aspects of biomaterials science including basic research, engineering, and medical applications. The 2017 conference is dedicated to Advances in Antimicrobial Materials. This conference will include keynote speakers who will give an overview of clinical and commercial translations of biomaterials. Selected sessions are devoted to the design, preparation, characterization, quality control and application of all types of antimicrobial materials from the viewpoints of academia, industry and the clinics.
Both oral and poster presentations are welcome. Those wishing to present are asked to submit an extended abstract (1 page maximum) by March 17th, 2017. Abstracts must be submitted as an electronic file in MS Word and must adhere to the abstract guidelines. The abstract template can soon be obtained from the conference website.
Dr Katharina Maniura
EMPA, Biointerfaces
Phone: +41 58 765 74 47

Thursday, November 3, 2016

Alzheimer's, a dementia disease of the past?

The BACE1 inhibitor verubecestat (MK-8931) reduces CNS β-amyloid in animal models and in Alzheimer’s disease patients

The discovery of BACE1 inhibitors that reduce β-amyloid peptides in Alzheimer’s disease (AD) patients has been an encouraging development in the quest for a disease-modifying therapy. Kennedy and colleagues now report the discovery of verubecestat, a structurally unique, orally bioavailable small molecule that potently inhibits brain BACE1 activity resulting in a reduction in Aβ peptides in the cerebrospinal fluid of animals, healthy volunteers, and AD patients. No dose-limiting toxicities were observed in chronic animal toxicology studies or in phase 1 human studies, thus reducing safety concerns raised by previous reports of BACE inhibitors and BACE1 knockout mice.
According to the World Health Organization over 36 million people world-wide are affected by dementia, of which the majority have Alzheimer’s. This number is forecast to double by 2030 and triple by 2050 if no treatment is discovered. So great hopes are placed on verubecestat. 

Monday, August 15, 2016

Nanoparticles to Break Up Plaque and Prevent Cavities

Philadelphia, PA (Scicasts) — The bacteria that live in dental plaque and contribute to tooth decay often resist traditional antimicrobial treatment, as they can "hide" within a sticky biofilm matrix, a glue-like polymer scaffold.
A new strategy conceived by University of Pennsylvania researchers took a more sophisticated approach. Instead of simply applying an antibiotic to the teeth, they took advantage of the pH-sensitive and enzyme-like properties of iron-containing nanoparticles to catalyze the activity of hydrogen peroxide, a commonly used natural antiseptic. The activated hydrogen peroxide produced free radicals that were able to simultaneously degrade the biofilm matrix and kill the bacteria within, significantly reducing plaque and preventing the tooth decay, or cavities, in an animal model.
"Even using a very low concentration of hydrogen peroxide, the process was incredibly effective at disrupting the biofilm," said Hyun (Michel) Koo, a professor in the Penn School of Dental Medicine's Department of Orthodontics and divisions of Pediatric Dentistry and Community and Oral Health and the senior author of the study, which was published in the journal Biomaterials. "Adding nanoparticles increased the efficiency of bacterial killing more than 5,000-fold."

Research Shows Gentle Cancer Treatment Using Nanoparticles Works

Copenhagen, Denmark (Scicasts) — Cancer treatments based on laser irradiation of tiny nanoparticles that are injected directly into the cancer tumour are working and can destroy the cancer from within.
Researchers from the Niels Bohr Institute and the Faculty of Health Sciences at the University of Copenhagen have developed a method that kills cancer cells using nanoparticles and lasers. The treatment has been tested on mice and it has been demonstrated that the cancer tumours are considerably damaged. The results are published in the scientific journal, Scientific Reports.
Traditional cancer treatments like radiation and chemotherapy have major side affects, because they not only affect the cancer tumours, but also the healthy parts of the body. A large interdisciplinary research project between physicists at the Niels Bohr Institute and doctors and human biologists at the Panum Institute and Rigshospitalet has developed a new treatment that only affects cancer tumours locally, therefore, much more gentle on the body. The project is called Laser Activated Nanoparticles for Tumor Elimination (LANTERN). The head of the project is Professor Lene Oddershede, a biophysicist and head of the research group Optical Tweezers at the Niels Bohr Institute at the University of Copenhagen in collaboration with Professor Andreas Kjær, head of the Cluster for Molecular Imaging, Panum Institute.

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Monday, May 9, 2016

Latest Advances in Nano-Oncology

Unique characteristics of nanoparticles make them highly attractive for various applications in oncology. They are able to function as carriers for chemotherapeutic drugs to increase their therapeutic index and lower their toxicity, as therapeutic agents in photodynamic, gene, and thermal therapy, as well as molecular imaging agents to detect and monitor cancer progression. Several nanoparticle-based agents for cancer therapy and diagnostics have been approved by FDA, more are in clinical trials, and even more are in the discovery and early development stages in academic and industry laboratories. Cambridge Healthtech Institute’s Latest Advances in Nano-Oncology symposium is designed to encourage open discussion and knowledge exchange in this exiting and rapidly developing area at the junction of nanobiotechnology and oncology.
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