Boldly Going

When you come across a very successful, middle-aged scientist jumping up and down shouting “This is going to be just amazing” you can only conclude that either the pressures of the life scientific have finally got to him and he’s flipped or there is something really remarkable going on. Thus my feeling this week when I noted the behaviour of Greg Hannon who now works at the Cancer Research Institute in Cambridge.

Probing further, it emerged that Hannon, who is collaborating with Xiaowei Zhuang at Harvard University in the ‘other’ Cambridge, has just been awarded a five-year grant of £20 million by the London-based charity Cancer Research UK as part of its Grand Challenge initiative – more than enough to get your jumping genes going.

But it’s the aim of the project rather than its monetary size that is truly astonishing and has almost a feel of science fiction about it. The plan is nothing less than to come up with an interactive virtual-reality map of breast cancers. That is, to reconstruct every cell that makes up a tumour, showing the different types of cell and what they are up to at any given time – meaning that the model will display the expression level of thousands of genes in each cell and the different proteins being made. Staggering.

What’s the point?

The project is driven by the fact that we have gradually come to realize that tumours are a complex mixture of cells (what’s been called the tumour microenvironment) and the signals that these cells send out and receive determine the extent of tumour growth and whether it can spread to other sites in the body (i.e. metastasize).

Where have we got to?

One approach to mapping what’s going on was laid out a couple of years ago by the converging studies of Rahul Satija and colleagues of the Broad Institute of MIT and Harvard and Kaia Achim et al. from labs in Heidelberg, Cambridge and Oxford using zebrafish embryos and worm brains, respectively.

The method has two parts:

  1. The tissue is dissociated into single cells and the power of sequencing is applied to obtain RNA sequences from each cell (revealing which genes are ‘switched on’ in that cell).
  2. The second step visualizes specific RNAs using tagged probes (fluorescently labeled RNAs that enter cells and bind to target RNAs molecules).

In essence a reference map is made by overlaying the intact tissue with a grid and matching a cell to a grid area by comparing expression of a number of ‘landmark’ genes with the fluorescence marker signal.

To do all this they devised a computational package that, using fewer than 100 landmark genes, maps hundreds of sequenced cells to their location in the tissue. In that arty way that scientists have, they named their package after Georges-Pierre Seurat, the French chappie who came up with the idea of painting in small dots of colour (though his weren’t fluorescent).

Cellular pointillism has just taken another step forward with Keren Bahar Halpern, Ido Amit and Shalev Itzkovitz at the Weizmann Institute of Science, Rehovot, Israel producing a cell-by-cell map of mouse liver, complete with RNA sequences from each cell. To be precise they mapped the hexagon-shaped units called lobules that are repeated to make up mammalian liver.

The shapes of things to come

So the next step for Hannon and his colleagues is an interactive map of a human tumour and, if you can’t wait, CLICK HERE to see their mock-up to give you some idea of what’s in store. In this synthetic video tumour cells are green, macrophages are blue and blood vessels are red.

Overwhelming?

So it’s warp factor 9 for Captain Hannon and his crew. It may be that the 3D images of tumours will look a bit the virtual graphics that the astrophysicists fob off on us whilst pretending they have some idea what a star’s doing umpti-zillion light years away. But in fact, rather than boldly going where no man has gone before“, this cellular journey is better summed up by Marcel Proust The real voyage of discovery consists not in seeking new landscapes, but in having new eyes” – the new eyes being the stunning combination of methods that permits 3D interrogation of individual cells.

Will this phase of the Grand Challenge produce overwhelming amounts of data? Undoubtedly. But, if we are to understand how living things work we have to front up to the complexity of nature. We then have to hope we are smart enough to resolve the crucial from the detail.

References

Satija, R. et al. (2015). Spatial reconstruction of single-cell gene expression data. Nature Biotechnology 33, 495–502.

Achim, K. et al. (2015). High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin. Nature Biotechnology 33, 503–509.

Halpern, K. B. et al. (2017). Nature 542, 352–356.

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New Era … Or Déjà vu?

 

Readers who follow events in the US of A – beyond the bizarre unfolding of the selection of the Republican Party’s nominee for President of the United States – may have noticed that the presidential incumbent put forward another of his bright ideas in the 2016 State of the Union Address. The plan launched by President Obama is to eliminate cancer and to this end $1 billion is to go into a national initiative with a strong focus on earlier detection, immunotherapy and drug combinations. It’s called a Moonshot’, presumably as a nod to President Kennedy’s 1961 statement that America should land a man on the moon (and bring him back!).011316_SOTU_THUMB_LARGE

A key aim of Moonshot is to improve all-round collaboration and to ‘bring about a decade’s worth of advances in five years.’ Part of this involvesbreaking down silos’ – which apparently is business-speak (and therefore a new one on me) for dealing with the problem of folk not wanting to share things with others in the same line of work. So someone’s spotted that science and medicine are not immune to this frailty.silo_mentality

On the home front …

In fact the President could be said to be slightly off the pace as, in October 2015, Cancer Research UK launched ‘Grand Challenges’ – a more modest (£100M) drive to tackle the most important questions in cancer. They’ve pinpointed seven problems and, helpfully, six of these will not be new to dedicated readers of these pages. They are:

  1. To develop vaccines (i.e. immunotherapy) to prevent non-viral cancers;
  2. To eradicate the 200,000 cancers caused each year by the Epstein Barr Virus;
  3. To understand the mutation patterns caused by different cancer-causing events;
  4. To improve early detection;
  5. To map the complexity of tumours at the molecular and cellular level;
  6. To find a way of targetting the cancer super-controller MYC;
  7. To work out how to target anti-cancer drugs to specific cells in the body.

{No/. 2 is the odd one out so it clearly hasn’t been too high a priority for me but we did talk about Epstein Barr Virus in Betrayed by Nature – phew!}.

But wait a minute

Readers of a certain age may be thinking this all sounds a bit familiar and, of course, they’re right. It was in 1971 that President Richard Nixon launched the ‘war on cancer’, the aim of which was to, er, to eliminate cancers. Given that 45 years on in the USA there’ll be more than 1.6 million new cases of cancer and 600,000 cancer deaths this year, it’s tempting to conclude that all we’ve learned is that things are a lot more complicated than we ever imagined.

Well, you can say that again. Of the several hundred genes that we now know can play a role in cancers, two are massively important MYC (‘mick’) and P53. Screen the scientific literature for research publications with one of those names in the title and you get, wait for it, over 50,000 for ‘MYC’ and for P53 over 168,000. It’s impossible to grasp how many hours of global sweat and toil went into churning out that amount of work – and that’s studies of just two bits of the jigsaw!

So 45 years of digging have yielded astonishing detail of the cellular and molecular biology – and that basis will prove essential to any rational approach to therapy. It’s a slow business this learning to walk before you run! But we can be rather more up-beat. Alongside all the science there have come considerable improvements in treatments. Thirty years ago one in four of those diagnosed with a cancer survived for more than 10 years. Now it’s almost one in two. But it’s a hugely variable picture: for breast cancer the 10 year overall survival rate is nearly 80% and for testicular cancer it’s over 98%. However, for lung cancer and cancer rates remain below 5% 1%, respectively. For these and other cancers there has been very little progress.

So 45 years of digging away have yielded astonishing detail of the cellular and molecular biology – and that basis will prove essential to any rational approach to therapy. It’s a slow business this learning to walk before you run! But we can be rather more up-beat. Alongside all the science there have come considerable improvements in treatments. Thirty years ago one in four of those diagnosed with a cancer survived for more than 10 years. Now it’s almost one in two. But it’s a hugely variable picture: for breast cancer the 10 year overall survival rate is nearly 80% and for testicular cancer it’s over 98%. However, for lung cancer and pancreatic cancer rates remain below 5% and 1%, respectively. For these and other cancers there has been very little progress.

All systems go?

Well, maybe. Moonshot is aimed at better and earlier diagnosis, more precise surgery and radiotherapy, and more drugs that can be better targeted. Oh, and bearing in mind that one in three cancers could be prevented, keeping plugging away at lifestyle factors.

How will it fare? Well, now we’re in the genomic era we can be sure that the facts mountain resulting from 45 years of collective toil will be as a molehill to the Everest of data now being mined and analysed. From that will emerge, we can assume with some confidence, a gradual refinement of the factors that are critical in determining the most effective treatment for an individual cancer.

Just recently we described in The Shape of Things to Come the astonishingly detailed picture that can be drawn of an individual tumour when it’s subjected to the full technological barrage now available. As we learn more about the critical factors, immunotherapy regimens will become more precise and the current response rate of about 10% of patients will rise.

Progress will still be slow, as we noted in The Shape of Things to Come – don’t expect miracles but, with lots of money, things will get better.

The Shape of Things to Come?

One of the problems of trying to keep up with cancer – and indeed helping others to do so – is that you (i.e. ‘I’) get really irritated with the gentlemen and ladies of the press for going over the top in their efforts to cover science. I have therefore been forced to have a few rants about this in the past – actually, when I came to take stock, even I was a bit shocked at how many. Heading the field were Not Another Great Cancer Breakthough, Put A Cap On It and Gentlemen… For Goodness Sake. And not all of these were provoked by The Daily Telegraph!

If any of the responsible reporters read this blog they probably write me off as auditioning for the Grumpy Old Men tv series. But at least one authoritative voice says I’m really very sane and balanced (OK, it’s mine). Evidence? The other day I spotted the dreaded G word (groundbreaking) closely juxtaposed to poor old Achilles’ heel – and yes, it was in the Telegraph – but, when I got round to reading the paper, I had to admit that the work referred to was pretty stunning. Although, let’s be clear, such verbiage should still be banned.

A Tumour Tour de Force

The paper concerned was published in the leading journal Science by Nicholas McGranahan, Charles Swanton and colleagues from University College London and Cancer Research UK. It described a remarkable concentration of current molecular fire-power to dissect the fine detail of what’s going on in solid tumours. They focused on lung cancers and the key steps used to paint the picture were as follows:

1. DNA sequencing to identify mutations that produced new proteins in tumour cells (called tumour-associated antigens or ‘neoantigens’ – meaning molecular flags on the cell surface that can provoke an immune response – i.e. the host makes antibody proteins that react with (stick to) the antigens). Typically they found just over 300 of these ‘neoantigens’ per tumour – a reflection of the genetic mayhem that occurs in cancer.

2 tumoursVariation in neoantigen profile between two multi-region sequenced non-small cell lung tumours. There were approximately 400 (left) and 300 (right) neoantigens/tumour

  • Blue: proportion of clonal neoantigens found in every tumour region.
  • Yellow: subclonal neoantigens shared in multiple but not all tumour regions.
  • Red: subclonal (‘private’) neoantigens found in only one tumour region.
  • The left hand tumour (mostly blue, thus highly clonal) responded well to immunotherapy (from McGranahan et al. 2016).

2. Screening the set of genes that regulate the immune system – that is, make proteins that detect which cells belong to our body and which are ‘foreign.’ This is the human leukocyte antigen (HLA) system that is used to match donors for transplants – called HLA typing.

3. Isolating specialised immune cells (T lymphocytes) from samples of two patients with lung cancer, growing them in the lab to expand the population and testing how good these tumour-infiltrating cells were at recognizing the abnormal proteins (neo-antigens) on cancer cells.

4. Detecting proteins released by different types of infiltrating T cells that regulate the immune response. These include so-called immune checkpoint molecules that limit the extent of the immune response. This showed that T cell subsets that were very good at recognizing neo-antigens – and thus killing cancer cells (they’re CD8+ T cells or ‘killer’ T cells) also made high levels of proteins that restrain the immune response (e.g., PD-1).

5. Showing that immunotherapy (using the antibody pembrolizumab that reacts with PD-1) could significantly extend survival of patients with advanced non-small cell lung cancer. We’ve already met this approach in Self-help Part 1.

The critical finding was that the complexity of the tumour (called the clonal architecture) determines the outcome. Durable benefit from this immunotherapy requires a high level of mutation but a restricted range of neo-antigens. Put another way, tumours that are highly clonal respond best because they have common molecular flags present on every tumour cell.

6. Using the same methods on some skin cancers (melanomas) with similar results.

What did this astonishing assembly of results tell us?

It’s the most detailed picture yet of what’s going on in individual cancers. As one of the authors, Charles Swanton, remarked “This is exciting. This opens up a way to look at individual patients’ tumours and profile all the antigen variations to figure out the best ways for treatments to work. This takes personalised medicine to its absolute limit where each patient would have a unique, bespoke treatment.”

He might have added that it’s going to take a bit of time and a lot of money. But as a demonstration of 21st century medical science it’s an absolute cracker!

References

McGranahan et al. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science 10.1126/science.aaf490 (2016).