̽��ֱ�� of Cambridge - microscopy

Driving force behind cellular ‘protein factories’ could have implications for neurodegenerative disease

erh68 — Wed, 16 Dec 2020 19:00:00 +0000

In a study published today in Science Advances, researchers from the ̽��ֱ�� of Cambridge show that tiny components within the cell are the biological engines behind effective protein production.

̽��ֱ��endoplasmic reticulum (ER) is the cell’s protein factory, producing and modifying the proteins needed to ensure healthy cell function. It is the cell’s biggest organelle and exists in a web-like structure of tubes and sheets. ̽��ֱ��ER moves rapidly and constantly changes shape, extending across the cell to wherever it is needed at any given moment.

Using super-resolution microscopy techniques, researchers from Cambridge’s Department of Chemical Engineering and Biotechnology (CEB) have discovered the driving force behind these movements – a breakthrough that could have significant impact on the study of neurodegenerative diseases.

“It has been known that the endoplasmic reticulum has a very dynamic structure – constantly stretching and extending its shape inside the cell,” said Dr Meng Lu, research associate in the Laser Analytics Group, led by Professor Clemens Kaminski.

“ ̽��ֱ��ER needs to be able to reach all places efficiently and quickly to perform essential housekeeping functions within the cell, whenever and wherever the need arises. Impairment of this capability is linked to diseases including Parkinson’s, Alzheimer’s, Huntington’s and ALS. So far there has been limited understanding of how the ER achieves these rapid and fascinating changes in shape and how it responds to cellular stimuli.”

Lu and colleagues discovered that another cell component holds the key – small structures, that look like tiny droplets contained in membranes, called lysosomes.

Lysosomes can be thought of as the cell’s recycling centres: they capture damaged proteins, breaking them down into their original building blocks so that they can be reused in the production of new proteins. Lysosomes also act as sensing centres – picking up on environmental cues and communicating these to other parts of the cell, which adapt accordingly.

There can be up to 1,000 or so lysosomes zipping around the cell at any one time and with them, the ER appears to change its shape and location, in an apparently orchestrated fashion.

What surprised the Cambridge scientists was their discovery of a causal link between the movement of the tiny lysosomes within the cell and the reshaping process of the large ER network.

“We could show that it is the movement of the lysosomes themselves that forces the ER to reshape in response to cellular stimuli,” said Lu. “When the cell senses that there is a need for lysosomes and ER to travel to distal corners of the cell, the lysosomes pull the ER web along with them, like tiny locomotives.”

From a biological point of view, this makes sense: ̽��ֱ��lysosomes act as a sensor inside the cell, and the ER as a response unit; co-ordinating their synchronous function is critical to cellular health.

To discover this surprising bond between two very different organelles, Kaminski’s research team made use of new imaging technologies and machine learning algorithms, which gave them unprecedented insights into the inner workings of the cell.

“It is fascinating that we are now able to look inside living cells and see the marvellous speed and dynamics of the cellular machinery at such detail and in real time,” said Kaminski. “Only a few years ago, watching organelles going about their business inside the cell would have been unthinkable.”

̽��ֱ��researchers used illumination patterns projected onto living cells at high speed, and advanced computer algorithms to recover information on a scale more than one hundred times smaller than the width of a human hair. To capture such information at video rates has only recently become possible.

̽��ֱ��researchers also used machine learning algorithms to extract the structure and movement of the ER networks and lysosomes in an automated fashion from thousands of datasets.

̽��ֱ��team extended their research to look at neurons or nerve cells – specialised cells with long protrusions called axons along which signals are transmitted. Axons are extremely thin tubular structures and it was not known how the movement of the very large ER network is orchestrated inside these structures.

̽��ֱ��study shows how lysosomes travel easily along the axons and drag the ER along behind them. ̽��ֱ��researchers also show how impairing this process is detrimental to the development of growing neurons.

Frequently, the researchers saw events where the lysosomes acted as repair engines for disconnected or broken pieces of ER structure, merging and fusing them into an intact network again. ̽��ֱ��work is therefore relevant for an understanding of disorders of the nervous system and its repair.

̽��ֱ��team also studied the biological significance of this coupled movement, providing a stimulus – in this case nutrients – for the lysosomes to sense. ̽��ֱ��lysosomes were seen to move towards this signal, dragging the ER network behind so that the cell can elicit a suitable response.

“So far, little was known on the regulation of ER structure in response to metabolic signals,” said Lu. “Our research provides a link between lysosomes as sensors units that actively steer the local ER response.”

̽��ֱ��team hopes that their insights will prove invaluable to those studying links between disease and cellular response, and their own next steps are focused on studying ER function and dysfunction in diseases such as Parkinson’s and Alzheimer’s.

Neurodegenerative disorders are associated with aggregation of damaged and misfolded proteins, so understanding the underlying mechanisms of ER function is critical to research into their treatment and prevention.

“ ̽��ֱ��discoveries of the ER and lysosomes were awarded the Nobel Prize many years ago – they are key organelles essential for healthy cellular function,” said Kaminski. “It is fascinating to think that there is still so much to learn about this system, which is incredibly important to fundamental biomedical science looking to find the cause and cures of these devastating diseases.”

Reference:
Meng Lu et al. ' ̽��ֱ��structure and global distribution ofthe endoplasmic reticulum network is actively regulated by lysosomes.' Science Advances (2020). DOI: 10.1126/sciadv.abc7209

Researchers have identified the driving force behind a cellular process linked to neurodegenerative disorders such as Parkinson’s and motor neurone disease.

There is still so much to learn about this system, which is incredibly important to fundamental biomedical science

Clemens Kaminski

Inducing lysosome (green) anterograde motion with light leads to a rapid and significant extension of ER network (magenta).

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. Images, including our videos, are Copyright © ̽��ֱ�� of Cambridge and licensors/contributors as identified. All rights reserved. We make our image and video content available in a number of ways – as here, on our main website under its Terms and conditions, and on a range of channels including social media that permit your use and sharing of our content under their respective Terms.

Yes

New virtual reality software allows scientists to ‘walk’ inside cells

sc604 — Mon, 12 Oct 2020 15:00:15 +0000

̽��ֱ��software, called vLUME, was created by scientists at the ̽��ֱ�� of Cambridge and 3D image analysis software company Lume VR Ltd. It allows super-resolution microscopy data to be visualised and analysed in virtual reality, and can be used to study everything from individual proteins to entire cells. Details are published in the journal Nature Methods.

Super-resolution microscopy, which was awarded the Nobel Prize for Chemistry in 2014, makes it possible to obtain images at the nanoscale by using clever tricks of physics to get around the limits imposed by light diffraction. This has allowed researchers to observe molecular processes as they happen. However, a problem has been the lack of ways to visualise and analyse this data in three dimensions.

“Biology occurs in 3D, but up until now it has been difficult to interact with the data on a 2D computer screen in an intuitive and immersive way,” said Dr Steven F Lee from Cambridge’s Department of Chemistry, who led the research. “It wasn’t until we started seeing our data in virtual reality that everything clicked into place.”

̽��ֱ��vLUME project started when Lee and his group met with the Lume VR founders at a public engagement event at the Science Museum in London. While Lee’s group had expertise in super-resolution microscopy, the team from Lume specialised in spatial computing and data analysis, and together they were able to develop vLUME into a powerful new tool for exploring complex datasets in virtual reality.

“vLUME is revolutionary imaging software that brings humans into the nanoscale,” said Alexandre Kitching, CEO of Lume. “It allows scientists to visualise, question and interact with 3D biological data, in real time all within a virtual reality environment, to find answers to biological questions faster. It’s a new tool for new discoveries.”

Viewing data in this way can stimulate new initiatives and ideas. For example, Anoushka Handa – a PhD student from Lee’s group – used the software to image an immune cell taken from her own blood, and then stood inside her own cell in virtual reality. “It’s incredible - it gives you an entirely different perspective on your work,” she said.

̽��ֱ��software allows multiple datasets with millions of data points to be loaded in and finds patterns in the complex data using in-built clustering algorithms. These findings can then be shared with collaborators worldwide using image and video features in the software.

“Data generated from super-resolution microscopy is extremely complex,” said Kitching. “For scientists, running analysis on this data can be very time-consuming. With vLUME, we have managed to vastly reduce that wait time allowing for more rapid testing and analysis.”

̽��ֱ��team is mostly using vLUME with biological datasets, such as neurons, immune cells or cancer cells. For example, Lee’s group has been studying how antigen cells trigger an immune response in the body. “Through segmenting and viewing the data in vLUME, we’ve quickly been able to rule out certain hypotheses and propose new ones,” said Lee. This software allows researchers to explore, analyse, segment and share their data in new ways. All you need is a VR headset.”

Reference:
Alexander Spark et al. ‘vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy.’ Nature Methods (2020). DOI: 10.1038/s41592-020-0962-1

Virtual reality software which allows researchers to ‘walk’ inside and analyse individual cells could be used to understand fundamental problems in biology and develop new treatments for disease.

Biology occurs in 3D, but up until now it has been difficult to interact with the data on a 2D computer screen in an intuitive and immersive way

Steven Lee

Alexandre Kitching

DBScan analysis being performed a mature neuron in a typical vLUME workspace.

Yes

Calcium may play a role in the development of Parkinson’s disease

sc604 — Mon, 19 Feb 2018 10:00:00 +0000

̽��ֱ��international team, led by the ̽��ֱ�� of Cambridge, found that calcium can mediate the interaction between small membranous structures inside nerve endings, which are important for neuronal signalling in the brain, and alpha-synuclein, the protein associated with Parkinson’s disease. Excess levels of either calcium or alpha-synuclein may be what starts the chain reaction that leads to the death of brain cells.

̽��ֱ��findings, reported in the journal Nature Communications, represent another step towards understanding how and why people develop Parkinson’s. According to the charity Parkinson’s UK, one in every 350 adults in the UK – an estimated 145,000 in all – currently has the condition, but as yet it remains incurable.

Parkinson’s disease is one of a number of neurodegenerative diseases caused when naturally occurring proteins fold into the wrong shape and stick together with other proteins, eventually forming thin filament-like structures called amyloid fibrils. These amyloid deposits of aggregated alpha-synuclein, also known as Lewy bodies, are the sign of Parkinson’s disease.

Curiously, it hasn’t been clear until now what alpha-synuclein actually does in the cell: why it’s there and what it’s meant to do. It is implicated in various processes, such as the smooth flow of chemical signals in the brain and the movement of molecules in and out of nerve endings, but exactly how it behaves is unclear.

“Alpha-synuclein is a very small protein with very little structure, and it needs to interact with other proteins or structures in order to become functional, which has made it difficult to study,” said senior author Dr Gabriele Kaminski Schierle from Cambridge’s Department of Chemical Engineering and Biotechnology.

Thanks to super-resolution microscopy techniques, it is now possible to look inside cells to observe the behaviour of alpha-synuclein. To do so, Kaminski Schierle and her colleagues isolated synaptic vesicles, part of the nerve cells that store the neurotransmitters which send signals from one nerve cell to another.

In neurons, calcium plays a role in the release of neurotransmitters. ̽��ֱ��researchers observed that when calcium levels in the nerve cell increase, such as upon neuronal signalling, the alpha-synuclein binds to synaptic vesicles at multiple points causing the vesicles to come together. This may indicate that the normal role of alpha-synuclein is to help the chemical transmission of information across nerve cells.

“This is the first time we’ve seen that calcium influences the way alpha-synuclein interacts with synaptic vesicles,” said Dr Janin Lautenschläger, the paper’s first author. “We think that alpha-synuclein is almost like a calcium sensor. In the presence of calcium, it changes its structure and how it interacts with its environment, which is likely very important for its normal function.”

“There is a fine balance of calcium and alpha-synuclein in the cell, and when there is too much of one or the other, the balance is tipped and aggregation begins, leading to Parkinson’s disease,” said co-first author Dr Amberley Stephens.

̽��ֱ��imbalance can be caused by a genetic doubling of the amount of alpha-synuclein (gene duplication), by an age-related slowing of the breakdown of excess protein, by an increased level of calcium in neurons that are sensitive to Parkinson’s, or an associated lack of calcium buffering capacity in these neurons.

Understanding the role of alpha-synuclein in physiological or pathological processes may aid in the development of new treatments for Parkinson’s disease. One possibility is that drug candidates developed to block calcium, for use in heart disease for instance, might also have potential against Parkinson’s disease.

̽��ֱ��research was funded in part by the Wellcome Trust, the Medical Research Council, Alzheimer’s Research UK, and the Engineering and Physical Sciences Research Council.

Reference
Janin Lautenschläger, Amberley D. Stephens et al. ‘C-terminal calcium binding of Alpha-synuclein modulates synaptic vesicle interaction.’ Nature Communications (2018). DOI: 10.1038/s41467-018-03111-4

Researchers have found that excess levels of calcium in brain cells may lead to the formation of toxic clusters that are the hallmark of Parkinson’s disease.

This is the first time we’ve seen that calcium influences the way alpha-synuclein behaves.

Janin Lautenschlӓger

Janin Lautenschläger

Tyrosine hydroxylase positive neuron stained with a synaptic marker

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. For image use please see separate credits above.

Yes

Researchers identify when Parkinson’s proteins become toxic to brain cells

sc604 — Mon, 14 Mar 2016 19:00:00 +0000

Researchers have used a non-invasive method of observing how the process leading to Parkinson’s disease takes place at the nanoscale, and identified the point in the process at which proteins in the brain become toxic, eventually leading to the death of brain cells.

̽��ֱ��results suggest that the same protein can either cause, or protect against, the toxic effects that lead to the death of brain cells, depending on the specific structural form it takes, and that toxic effects take hold when there is an imbalance of the level of protein in its natural form in a cell. ̽��ֱ��work could help unravel how and why people develop Parkinson’s, and aid in the search for potential treatments. ̽��ֱ��study is published in the journal Proceedings of the National Academy of Sciences.

Using super-resolution microscopy, researchers from the ̽��ֱ�� of Cambridge were able to observe the behaviour of different types of alpha-synuclein, a protein closely associated with Parkinson's disease, in order to find how it affects neurons, and at what point it becomes toxic.

Parkinson’s disease is the second-most common neurodegenerative disease worldwide (after Alzheimer’s disease). Close to 130,000 people in the UK, and more than seven million worldwide, have the disease. Symptoms include muscle tremors, stiffness and difficulty walking. Dementia is common in later stages of the disease.

“What hasn’t been clear is whether once alpha-synuclein fibrils have formed they are still toxic to the cell,” said Dr Dorothea Pinotsi of Cambridge’s Department of Chemical Engineering and Biotechnology, the paper’s first author.

Pinotsi and her colleagues from Cambridge’s Department of Chemical Engineering & Biotechnology and Department of Chemistry, and led by Dr Gabriele Kaminski Schierle, have used optical ‘super-resolution’ techniques to look into live neurons without damaging the tissue. “Now we can look at how proteins associated with neurodegenerative conditions grow over time, and how these proteins come together and are passed on to neighbouring cells,” said Pinotsi.

̽��ֱ��researchers used different forms of alpha-synuclein and observed their behaviour in neurons from rats. They were then able to correlate what they saw with the amount of toxicity that was present.

They found that when they added alpha-synuclein fibrils to the neurons, they interacted with alpha-synuclein protein that was already in the cell, and no toxic effects were present.

“It was believed that amyloid fibrils that attack the healthy protein in the cell would be toxic to the cell,” said Pinotsi. “But when we added a different, soluble form of alpha-synuclein, it didn’t interact with the protein that was already present in the neuron and interestingly this was where we saw toxic effects and cells began to die. So somehow, when the soluble protein was added, it created this toxic effect. ̽��ֱ��damage appears to be done before visible fibrils are even formed.”

̽��ֱ��researchers then observed that by adding the soluble form of alpha-synuclein together with amyloid fibrils, the toxic effect of the former could be overcome. It appeared that the amyloid fibrils acted like magnets for the soluble protein and mopped up the soluble protein pool, shielding against the associated toxic effects.

“These findings change the way we look at the disease, because the damage to the neuron can happen when there is simply extra soluble protein present in the cell – it’s the excess amount of this protein that appears to cause the toxic effects that lead to the death of brain cells,” said Pinotsi. Extra soluble protein can be caused by genetic factors or ageing, although there is some evidence that it could also be caused by trauma to the head.

̽��ֱ��research shows how important it is to fully understand the processes at work behind neurodegenerative diseases, so that the right step in the process can be targeted.

“With these optical super-resolution techniques, we can really see details we couldn’t see before, so we may be able to counteract this toxic effect at an early stage,” said Pinotsi.

̽��ֱ��research was funded by the Medical Research Council, the Engineering and Physical Sciences Research Council, and the Wellcome Trust.

Reference:
Dorothea Pinotsi et. al. ‘Nanoscopic insights into seeding mechanisms and toxicity of α-synuclein species in neurons.’ Proceedings of the National Academy of Sciences (2016). DOI: 10.1073/pnas.1516546113

Observation of the point at which proteins associated with Parkinson’s disease become toxic to brain cells could help identify how and why people develop the disease, and aid in the search for potential treatments.

̽��ֱ��damage appears to be done before visible fibrils are even formed.

Dorothea Pinotsi

Zoomed-in super-resolution (dSTORM) images of the fibrils inside the neuron formed of exogenous ‘’seed’’ fibrils (green) elongated by endogenous α-synuclein (red).

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. For image use please see separate credits above.

Yes

̽��ֱ��super-resolution revolution

lw355 — Fri, 27 Feb 2015 09:30:07 +0000

There has been a revolution in optical microscopy and it’s been 350 years in the making. Ever since Robert Hooke published his Physiological Descriptions of Minute Bodies in 1665, the microscope has opened up the world in miniature. But it has also been limited by the wavelength of light.

Anything smaller than the size of a bacterial cell (around 250 nanometres) appears as a blurred blob through an optical microscope, simply because light waves spread when they are focused on a tiny spot. As a result, resolving two tiny spots that lie close together has been tantalisingly out of reach using an optical microscope. Unfortunately, many biological interactions occur at a spatial scale much smaller than this.

But, thanks to recent breakthroughs, a new era of super-resolution microscopy has begun. ̽��ֱ��developments earned inventors Eric Betzig and William E Moerner (USA) and Stefan Hell (Germany) the 2014 Nobel Prize for Chemistry, and are based on clever physical tricks that work around the problem of light diffraction.

Professor Clemens Kaminski, whose team in the Department of Chemical Engineering and Biotechnology designs and builds super-resolution microscopes to study Alzheimer’s disease, explained: “ ̽��ֱ��technology is based on a conceptual change, a different way of thinking about how we resolve tiny structures. By imaging blobs of light at separate points in time, we are able to discriminate them spatially, and thus prevent image blur.”

Imagine taking a photo of a tree lit by the glow of ten thousand tiny lights scattered over its branches. ̽��ֱ��emission from each light would overlap. At best you would see a fuzzy, glowing shape lacking in detail. But if you were to switch on only a few lights at a time, locate the centre of each glow and take a picture, and then repeat this process thousands of times for different lights, the composite image would resolve into a myriad of distinguishable dots, denoting the exact position of each individual light on the tree.

This is analogous to the techniques developed by the Nobel Prize winners: in one technique, a sample is tagged with light-activated markers called fluorophores that can be switched on and off with pulses of light, like a switchable light bulb; in another, the light at the outer edges of each blob of light is selectively blocked.

Either way, by imaging a sparse subset of lights, they can be localised with nanometre precision. When combined, a picture starts to emerge that features a resolution that is 10 to 100 times better than previously possible.

“It’s been hailed as revolutionary because it means that biologists can validate some of their hypotheses for the first time,” said Dr Kevin O’Holleran who co-leads the Cambridge Advanced Imaging Centre (CAIC), which is currently building two super-resolution microscopes. “Although electron microscopy has very high resolution, it can’t be performed on live cells. With super-resolution optical microscopy, scientists can track molecular processes as they happen and in three dimensions.”

Meanwhile, Dr Steven Lee and Professor David Klenerman in the Department of Chemistry have built what they believe is the first 3D super-resolution microscope of its kind in Europe. They are using the machine to watch the organisation of cell-surface proteins at the point when an immune cell is triggered into action. Before super-resolution, they needed to artificially reduce the number of proteins on the cell surface to make visualisation easier; now, they can work with normal levels of up to 10,000 proteins at a time on the cell surface.

“These exciting discoveries have emerged through years of painstaking research by physical scientists trying to better understand how light interacts with matter at a fundamental level,” explained Lee. “This work has enabled us to gain insight into biological processes by simply ‘looking’ at dynamic events at spatial scales that much better approximate the physical dimension that biomolecules interact on.”

Kaminski’s team has been visualising the ultrastructure of the clumps of misfolded proteins that cause Alzheimer’s disease. “We’d like to study what causes proteins to become toxic when they aggregate, and visualise them as they move from cell to cell to see whether there are opportunities early in the process to halt their progression.”

Like any fast-moving and transformative technology, super-resolution microscopy has required researchers to drive forward the capabilities of the lenses and light sources, as well as the chemistry of the fluorophores and the mathematical algorithms for image analysis. As a result, designing and building their own microscopes, rather than waiting for commercial devices to become available, has been the best option.

“ ̽��ֱ��field is dynamic and no instrument is exactly right for the questions you want to answer. We have to build the instrument around the science,” explained Dr George Sirinakis, who works with Professor Daniel St Johnston in the Gurdon Institute. His machines will be used to understand cell polarity and visualise the movement of thousands of tiny sacs called vesicles as they transport their cargo within cells. This process has never been seen before because the vesicles are so small and move fast.

No longer are these benchtop machines. Super-resolution microscopes resemble an army of lenses and mirrors marching across a table top, each minutely turning, concentrating and shaping the light beam that falls onto the sample stained with fluorescence markers. Tens of thousands of images are collected from any one sample – creating a deluge of ‘big data’ that requires complex mathematical algorithms to make sense of the information.

Quite simply, super-resolution microscopy is a feat of engineering, physics, chemistry, mathematics, computer science and biology, and it’s therefore out of reach to researchers who lack the necessary expertise or funds to take a step into this field.

CAIC has recently been created to meet super-resolution and other microscopy needs in the biological sciences. “We are a research and development facility. We have state-of-the- art commercial microscopes and we build our own, tailoring them to the needs of the biologists who come to us as a service facility or as a collaborative venture,” explained O’Holleran, who estimates that around 100 researchers will become part of the CAIC community.

“We’re also a hub. We connect researchers who’ve built their own devices and we train PhD students in the cross-disciplinary skills needed for cutting-edge imaging.”

CAIC, Klenerman, Kaminski and others have now been awarded funding as part of the Next Generation Microscopy Initiative Programme led by the Medical Research Council to help establish Cambridge as a national centre of excellence in microscopy. Part of this funding is being used for the two new super-resolution microscopes currently being built in CAIC.

̽��ֱ��researchers hope that super-resolution microscopes will one day become the workhorse of biology, allowing ever-deeper probing of living structures. Breaking the diffraction barrier of light had seemed an insurmountable barrier until recent years. With continuing advances, biologists are beginning to look beyond imaging single cells to the possibility of moving through tissues, tracking the movement of molecules in three dimensions and visualising the process of life unfolding.

Inset image: What was once a fuzzy glow (left of image) can now be super-resolved (right) even if, as here, the structures are smaller than the wavelength of light; credit: Laurie Young, Florian Stroehl and Clemens Kaminski

Cambridge scientists are part of a resolution revolution. Building powerful instruments that shatter the physical limits of optical microscopy, they are beginning to watch molecular processes as they happen, and in three dimensions.

These exciting discoveries have emerged through years of painstaking research by physical scientists trying to better understand how light interacts with matter at a fundamental level

Steven Lee

̽��ֱ��Super-Resolution Revolution

̽��ֱ��text in this work is licensed under a Creative Commons Licence. If you use this content on your site please link back to this page. For image rights, please see the credits associated with each individual image.

Yes

Watching the death throes of tumours

cjb250 — Wed, 25 Feb 2015 12:49:11 +0000

There was a time when diagnosing and treating cancer seemed straightforward. Cancer of the breast was breast cancer, for example, and doctors could only choose treatments from a limited arsenal.

Now, the picture is much more complicated. A study published in 2012, led by Carlos Caldas, showed that breast cancer was actually at least ten different diseases. In fact, genome sequencing shows that even one ‘type’ of breast cancer differs between individuals.

While these developments illustrate the complexity of cancer biology, they also offer the promise of drugs tailored to an individual. Chemotherapy is a powerful, but blunt, instrument – it attacks the tumour, but in doing so also attacks several of the body’s other functions, which is why it makes patients so ill. ̽��ֱ��new generation of cancer drugs aim to make the tumour – and not the patient – sick.

But telling if a patient is sick is easy; telling if the tumour is sick is more challenging. “Conventionally, one assesses whether a tumour is responding to treatment by looking for evidence of shrinkage,” explained Professor Kevin Brindle from the Cancer Research UK (CRUK) Cambridge Institute, “but that can take weeks or months. And monitoring tumour size doesn’t necessarily indicate whether it is responding well to treatment.”

Take brain tumours, for example. They can continue to grow even when a treatment is working. “ ̽��ֱ��thing is that a tumour is not just tumour cells. There are lots of other cells in there, too.”

For some time now, oncologists have been interested in imaging aspects of tumour biology that can give a much earlier indication of the effect of treatment. Positron emission tomography (PET) can be used for this purpose. ̽��ֱ��patient is injected with a form (or analogue) of glucose labelled with a radioactive isotope. Tumours feed on the analogue and the isotope allows doctors to see where the tumour is.

An alternative technique that doesn’t expose the patient to ionising radiation is magnetic resonance imaging (MRI), which relies on the interaction of strong magnetic fields with a property of atomic nuclei known as ‘spin’. ̽��ֱ��proton spins in water molecules align in magnetic fields, like tiny bar magnets. By looking at how these spins differ in the presence of magnetic field gradients applied across the body, scientists are able to build up three-dimensional images of tissues.

In the 1970s, scientists realised that it was possible to use MR spectroscopy to see signals from metabolites such as glucose inside cells. “Tumours eat and breathe. If you make them sick, they don’t eat as much and the concentration of some cell metabolites can go down,” said Brindle.

Around the same time, scientists hit upon the idea of enriching metabolites with a naturally occurring isotope of carbon known as carbon-13 to help them measure how these metabolites are used by tissues. But carbon-13 nuclei are even less sensitive to detection by MRI than protons, so the signals are boosted using a machine developed by GE Healthcare, called a hyperpolariser, which lines up a large proportion of the carbon-13 spins before injection into the patient.

In 2006, Cambridge was one of the first places to show that this approach could be used to monitor whether a cancer therapy was effective or not. Combined with the latest genome sequencing techniques, this could become a powerful way of implementing personalised medicine. What’s more, because no radioactive isotopes are involved, an individual could be scanned safely multiple times.

“Because of the underlying genetics of the tumour, not all patients respond in the same way, but if you sequence the DNA in the tumour, you can select drugs that might work for that individual. Using hyperpolarisation and MRI, we can potentially tell whether the drug is working within a few hours of starting treatment. If it’s working you continue, if not you change the treatment.”

̽��ֱ��challenge has been how to deliver the carbon-13 to the patient. ̽��ֱ��metabolite has to be cooled down to almost absolute zero (–273°C), polarised, warmed up rapidly, passed into the MRI room and injected into the patient. And as the polarisation of the carbon-13 nuclei has a half-life of only 30–40 seconds, this has to be done very quickly.

This problem has largely been solved and, with funding from the Wellcome Trust and CRUK, Brindle and colleagues will this year begin trialling the technique with cancer patients at Addenbrooke’s Hospital. If successful, it could revolutionise both the evaluation of new drugs and ultimately – and most importantly – the treatment of patients.

“Some people have been sceptical about whether we could ever get a strong enough signal. I’m sure we will. But will we be able to do something that is clinically meaningful, that is going to change clinical practice? That’s the big question we hope to answer in the coming years.”

Inset image: Kevin Brindle and Stefanie Reichelt.

A clinical trial due to begin later this year will see scientists observing close up, in real time – and in patients – how tumours respond to new drugs.

Using hyperpolarisation and MRI, we can potentially tell whether the drug is working within a few hours of starting treatment

Kevin Brindle

Kevin Brindle; published in Nature Medicine (2014) 20, 93-97

An abdominal tumour (outlined in white) 'feeding on' carbon-13-labelled glucose (orange) provides a means of testing when cancer drugs are effective enough to affect the health of the tumour

Lighting up the body

In many ways, light microscopy is a much better imaging technique than MRI and PET to study the nature of biological materials: it provides higher resolution and higher specificity as fluorescent markers can be used to highlight specific cancer cells and molecules in cells and tissues.

However, as Dr Stefanie Reichelt, Head of Light Microscopy at the Cancer Research UK Cambridge Institute, points out, there’s an obvious drawback: “Light doesn’t penetrate tissue, so we can’t see deep beneath the skin.”

Reichelt and colleagues are working on ways to correlate light microscopy with Kevin Brindle’s medical imaging techniques. One technique that shows promise for bridging the gap is light sheet microscopy, a fluorescence microscopy technique with an intermediate optical resolution.

A thin slice of the sample is illuminated perpendicularly to the direction of observation; this reduces photo damage, thus allowing high-speed, high-resolution, three-dimensional imaging of live animals and tissues.

“ ̽��ֱ��key for us is to be able to image whole biopsy samples or tumours rapidly and at a high level of detail.”

Reichelt is also exploring new techniques such as Coherent Anti-Raman Stokes, which uses the nuclear vibrations of chemical bonds in molecules. This can provide a highly specific but label-free imaging contrast. This capability will allow the investigation of unlabelled live tissues from tumour biopsies with high specificity.

Yes

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Attribution

Imaging: interpreting the seen and discovering the unseen

lw355 — Mon, 02 Feb 2015 09:59:56 +0000

We humans are visual creatures. An image aims to depict reality to us, but also invokes our imagination. It speaks more than a thousand words. We live in a world saturated with images and images allow us to see this world – from brain cells to distant galaxies – as never before. Advanced imaging techniques enable us to ask new research questions, break down disciplinary boundaries and extend our knowledge across an immense variety of fields.

Scientists have always used images of various kinds – drawings, pictures, photographs and videos, to name a few – to make discoveries, describe processes in nature, catalogue and achieve specimens, and illustrate observations and ideas. In scientific discoveries, images are often the scientific finding itself.

A work of art, an image in itself, can be analysed and its making can be understood with the help of advanced scientific imaging techniques. New images are created by this analysis, and the worlds of arts and science are becoming increasingly overlapping.

Scientific imaging has never been as exciting as it is now, with new technologies emerging all the time. ̽��ֱ��resolution limit in light microscopy, which had seemed unbreakable, is now less than 100 nanometres. These advances in super-resolved fluorescence microscopy were recognised in 2014 by the awarding of the Nobel Prize in Chemistry to Eric Betzig and W. E. Moerner in the USA and Stefan Hell in Germany.

Cambridge is home to a wealth of research which includes developing tools for acquisition, visualisation, automated processing and analysis of images. In January 2014, a group was formed to connect, present, discuss and advance research on or with images. IMAGES brings together leading academics from across the disciplines, as well as international experts and research-led industries that work on pioneering imaging technologies and analytical algorithms.

̽��ֱ��complex process, from acquiring images, to their interpretation and problem-solving applications, requires multi-expertise partnerships. Different problems and image applications inform similar methodologies and interpretative strategies. Cross-disciplinary collaboration is needed to analyse the image information not explicit in machine-generated data.

Mathematicians, physicists, chemists and biologists work together to develop new instruments, chemical dyes and model systems to interrogate biological questions with more precision and at greater resolution.

At CRUK Cambridge Institute and the Department of Applied Mathematics and Theoretical Physics, microscopists and mathematicians are developing new ways of tracking cells and analysing the effect of cancer drugs in tissues and whole organisms.

At the Cambridge Biomedical Campus, clinicians use magnetic resonance, positron emission tomography, and acoustic imaging as tools for looking into our internal organs. ̽��ֱ��challenge here is to produce a high quality description of patients and their ailments from data that is necessarily limited by the capability of scanners and the need to minimise exposure to harmful radiation.

Mathematicians and engineers create automated image-processing and analysis algorithms that extract meaningful, essential information from often large-scale, high-dimensional and imperfect image data.

̽��ֱ��importance of reliable image analysis extends to astronomy, the arts, seismology, surveillance and security. Image de-noising and image restoration algorithms are also essential pieces of any further image analysis pipeline such as object segmentation and tracking, pattern recognition, in fact any quantitative and qualitative analysis of image content.

At the Fitzwilliam Museum and the Hamilton Kerr Institute, spectroscopy methods underpin the non-invasive analyses of artists’ materials and techniques, informing the conservation and cross-disciplinary interpretation of paintings, illuminated manuscripts and Egyptian papyri. ̽��ֱ��research unites imaging scientists, chemists, physicists, mathematicians, biologists, conservators, artists and historians. Thanks to cutting-edge imaging techniques, we can now see art works as never before, uncovering centuries-long secrets of their production and ensuring their preservation into the future.

̽��ֱ��IMAGES group aims to stimulate new inquiries and focused dialogues between these many disciplines across the sciences, arts and humanities by providing them with a platform for communication. As collaborations across the ̽��ֱ�� show, art and science are not disparate, but complementary ways of seeing the world. Both depend on the subtle observations of life and attempt to interpret the seen and discover the unseen.

Dr Stella Panayotova (Fitzwilliam Museum Cambridge), Dr Stefanie Reichelt (Cancer Research UK Cambridge Institute) and Dr Carola-Bibiane Schönlieb (Department of Applied Mathematics and Theoretical Physics) lead IMAGES

From visualising microscopic cells to massive galaxies, imaging is a core tool for many disciplines, and it’s also the basis of a surge in recent technical developments – some of which are being pioneered in Cambridge. Today, we begin a month-long focus on research that is exploring far beyond what the eye can see, introduced here by Stella Panayotova, Stefanie Reichelt and Carola-Bibiane Schönlieb.

IMAGES

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Imaging the genome: cataloguing the fundamental processes of life

jfp40 — Mon, 27 Oct 2014 16:14:11 +0000

̽��ֱ��team of researchers, led by Dr Rafael Carazo Salas from the Department of Genetics, combined high-resolution 3D confocal microscopy and computer-automated analysis of the images to survey the fission yeast genome with respect to three key cellular processes simultaneously: cell shape, microtubule organisation and cell cycle progression. Microtubules are small, tube-like structures which help cells divide and give them their structure.

Of the 262 genes whose functions the team report in a study published today in the journal Developmental Cell, two-thirds are linked to these processes for the first time and a third are implicated in multiple processes.

“More than ten years since the publication of the human genome, the so-called ‘Book of Life’, we still have no direct evidence of the function played by half the genes across all species whose genomes have been sequenced,” explains Dr Carazo Salas. “We have no ‘catalogue’ of genes involved in cellular processes and their functions, yet these processes are fundamental to life. Understanding them better could eventually open up new avenues of research for medicines which target these processes, such as chemotherapy drugs.”

Using a multi-disciplinary strategy that took the team over four years to develop, the researchers were able to manipulate a single gene at a time in the fission yeast genome and see simultaneously how this affected the three cellular processes. Fission yeast is used as a model organism as it is a unicellular organism – in other words, it consists of just one cell – whereas most organisms are multicellular, yet many of its most fundamental genes carry out the same function in humans, for example in cell development.

̽��ֱ��technique enabled the researchers not only to identify the functions of hundreds of genes across the genome, but also, for the first time, to systematically ask how the processes might be linked. For example, they found in the yeast – and, importantly, validated in human cells – a previously unknown link between control of microtubule stability and the machinery that repairs damage to DNA. Many conventional cancer therapies target microtubular stability or DNA damage, and whilst there is evidence in the scientific literature that drugs targeting both processes might interact, the reason why has been unclear.

“Both the technique and the data it produces are likely to be a very valuable resource to the scientific community in the future,” adds Dr Carazo Salas. “It allows us to shine a light into the black box of the genome and learn exciting new information about the basic building blocks of life and the complex ways in which they interact.”

All the data from the study is being published online as an open resource for researchers to use. It will be available online at www.sysgro.org.

̽��ֱ��research was largely funded by the European Research Council, the Swiss Initiative in Systems Biology and the Swiss National Foundation.

A new study at the ̽��ֱ�� of Cambridge has allowed researchers to peer into unexplored regions of the genome and understand for the first time the role played by more than 250 genes key to cell growth and development.

It allows us to shine a light into the black box of the genome and learn exciting new information about the basic building blocks of life and the complex ways in which they interact.

Dr Rafael Carazo Salas

Image credit: L. Wagstaff, E. Piddini

Cells with damage in their DNA (green) assemble abnormally stable microtubule structures (purple to white). This new link between microtubule control and the response to DNA damage, originally discovered in yeast, can be observed also in human cells.

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