John Sulston: Biologist, Geneticist and Guardian of our Heritage

 

Sir John Sulston died on 6 March 2018, an event reported world-wide by the press, radio and television. Having studied in Cambridge and then worked at the Salk Institute in La Jolla, California, he joined the Laboratory of Molecular Biology in Cambridge to investigate how genes control development and behaviour, using as a ‘model organism’ the roundworm Caenorhabditis elegans. This tiny creature, 1 mm long, was appealing because it is transparent and most adult worms are made up of precisely 959 cells. Simple it may be but this worm has all the bits required for to live, feed and reproduce (i.e. a gut, a nervous system, gonads, intestine, etc.). For his incredibly painstaking efforts in mapping from fertilized egg to mature animal how one cell becomes two, two becomes four and so on to complete the first ‘cell-lineage tree’ of a multicellular organism, Sulston shared the 2002 Nobel Prize in Physiology or Medicine with Bob Horvitz and Sydney Brenner.

Sir John Sulston

It became clear to Sulston that the picture of how genes control development could not be complete without the corresponding sequence of DNA, the genetic material. The worm genome is made up of 100 million base-pairs and in 1983 Sulston set out to sequence the whole thing, in collaboration with Robert Waterston, then at the University of Washington in St. Louis. This was a huge task with the technology available but their success indicated that the much greater prize of sequencing of the human genome — ten times as much DNA as in the worm — might be attainable.

In 1992 Sulston became head of a new sequencing facility, the Sanger Centre (now the Sanger Institute), in Hinxton, Cambridgeshire that was the British component of the Human Genome Project, one of the largest international scientific operations ever undertaken. Astonishingly, the complete human genome sequence, finished to a standard of 99.99% accuracy, was published in Nature in October 2004.

As the Human Genome Project gained momentum it found itself in competition with a private venture aimed at securing the sequence of human DNA for commercial profit — i.e., the research community would be charged for access to the data. Sulston was adamant that our genome belonged to us all and with Francis Collins — then head of the US National Human Genome Research Institute — he played a key role in establishing the principle of open access to such data, preventing the patenting of genes and ensuring that the human genome was placed in the public domain.

One clear statement of this intent was that, on entering the Sanger Centre, you were met by a continuously scrolling read-out of human DNA sequence as it emerged from the sequencers.

In collaboration with Georgina Ferry, Sulston wrote The Common Thread, a compelling account of an extraordinary project that has, arguably, had a greater impact than any other scientific endeavour.

For me and my family John’s death was a heavy blow. My wife, Jane, had worked closely with him since inception of the Sanger Centre and not only had his scientific influence been immense but he had also become a staunch friend and source of wisdom. At the invitation of John’s wife Daphne, a group of friends and relatives gathered at their house after the funeral. As darkness fell we went into the garden and once again it rang to the sound of chatter and laughter from young and old as we enjoyed one of John’s favourite party pastimes — making hot-air lanterns and launching them to drift, flickering to oblivion, across the Cambridgeshire countryside. John would have loved it and it was a perfect way to remember him.

Then …

When John Sulston set out to ‘map the worm’ the tools he used could not have been more basic: a microscope — with pencil and paper to sketch what he saw as the animal developed. His hundreds of drawings tracked the choreography of the worm to its final 959 cells and showed that, along the way, 131 cells die in a precisely orchestrated programme of cell death. The photomontage and sketch below are from his 1977 paper with Bob Horvitz and give some idea of the effort involved.

Photomontage of a microscope image (top) and (lower) sketch of the worm Caenorhabditis elegans showing cell nuclei. From Sulston and Horvitz, 1977.

 … and forty years on

It so happened that within a few days of John’s death Achim Trubiroha and colleagues at the Université Libre de Bruxelles published a remarkable piece of work that is really a descendant of his pioneering studies. They mapped the development of cells from egg fertilization to maturity in a much bigger animal than John’s worms — the zebrafish. They focused on one group of cells in the early embryo (the endoderm) that develop into various organs including the thyroid. Specificially they tracked the formation of the thyroid gland that sits at the front of the neck wrapped around part of the larynx and the windpipe (trachea). The thyroid can be affected by several diseases, e.g., hyperthyroidism, and in about 5% of people the thyroid enlarges to form a goitre — usually caused by iodine deficiency. It’s essential to determine the genes and signalling pathways that control thyroid development if we are to control these conditions.

For this mapping Trubiroha’s group used the CRISPR method of gene editing to mutate or knock out specific targets and to tag cells with fluorescent labels — that we described in Re-writing the Manual of Life.

A flavor of their results is given by the two sets of fluorescent images below. These show in real time the formation of the thyroid after egg fertilization and the effect of a drug that causes thyroid enlargement.

Live imaging of transgenic zebrafish to follow thyroid development in real-time (left). Arrows mark chord-like cell clusters that form hormone-secreting follicles (arrowheads) during normal development. The right hand three images show normal development (-) and goiter formation (+) induced by a drug. From Trubiroha et al. 2018.

John would have been thrilled by this wonderful work and, with a chuckle, I suspect he’d have said something like “Gosh! If we’d had gene editing back in the 70s we’d have mapped the worm in a couple of weeks!”

References

International Human Genome Sequencing Consortium Nature 431, 931–945; 2004.

John Sulston and Georgina Ferry The Common Thread: A Story of Science, Politics, Ethics and the Human Genome (Bantam Press, 2002).

Sulston, J.E. and Horvitz, H.R. (1977). Post-embryonic Cell Lineages of the Nematode, Caenorhabitis elegans. Development Biology 56, 110-156.

Trubiroha, A. et al. (2018). A Rapid CRISPR/Cas-based Mutagenesis Assay in Zebrafish for Identification of Genes Involved in Thyroid Morphogenesis and Function. Scientific Reports 8, Article number: 5647.

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Making Movies in DNA

Last time we reminded ourselves of one of the ways in which cancer is odd but, of course, underpinning not just cancers but all the peculiarities of life is DNA. The enduring wonder is how something so basically simple – just four slightly different chemical groups (OK, they are bases!) – can form the genetic material (the instruction book, if you like) for all life on earth. The answer, as almost everyone knows these days, is that there’s an awful lot of it in every cell – meaning that the four bases (A, C, G & T) have an essentially infinite coding capacity.

That doesn’t make it any the less wonderful but it does carry a huge implication: if something you can squeeze into a single cell can carry limitless information it must be the most powerful of all storage systems.

A picture’s worth a thousand words

We looked at the storage power of DNA a few months ago (in “How Does DNA Do It?”) and noted that its storage density is 1000 times that of flash memories, that it’s fairly easy to scan text and transform the pixels into genetic code and that, as an example, someone has already put Shakespeare’s sonnets into DNA form.

Now Seth Shipman, George Church and colleagues at Harvard have taken the field several steps forward by capturing black and white images and a short movie in DNA. Moreover they’ve managed to get these ‘DNA recordings’ taken up by living cells from which they could subsequently recover the images.

Crumbs! How did they do it?

First they used essentially the text method to encode images of a human hand: assign the four bases (A, C, G & T) to four pixel colours (this gives a grayscale image: colours can be acquired by using groups of bases for each pixel). These DNA sequences were then introduced into bacteria (specifically E. coli) by electroporation (an electrical pulse briefly opens pores in the cell membrane).

The cells treat this foreign DNA as though it was from an invading virus and switch on their CRISPR system (summarized in “Re-writing the Manual of Life”). This takes short pieces of viral DNA and inserts them into the cell’s own genome in the form of ‘spacers’ (the point being that the stored sequences confer ‘adaptive immunity’: the cell has an immunological memory so it is primed to respond effectively if it’s infected again by that viral pathogen).

In this case, however, the cells have been fooled: the ‘spacers’ generated carry encoded pictures, rather than viral signatures.

Because spacers are short it’s obvious that you’ll need lots of them to carry the information in a photo. To keep track when it comes to reassembling the picture, each DNA fragment was tagged with a barcode (and fortunately we explained cellular barcoding in “A Word From The Nerds”).

Once incorporated in the bugs the information was maintained over many bacterial generations (48 in fact) and is recoverable by high-throughput sequencing and reconstruction of the patterns using the barcodes.

And the movie bit?

Simple. In principle they used the same methods to encode sequential frames.

Pictures in DNA.

Top: Using triplets of bases to encode 21 pixel colours. Images of a human hand (top) and a horse (bottom) were captured. For the movie they used freeze frames taken in 1872 by the English photographer Eadweard Muybridge. These showed that, for a fraction of a second, a galloping horse lifts all four hooves off the ground. Seemingly this won a return for the sometime California governor, Leland Stanford (he of university-founding fame) who had put a wager on geegees doing just that. From Shipman et al., 2017. You can see the movie here.

Getting the picture clear

To recap, in case you’re wondering if this is some scientific April Fools’ prank. What Church & Co. did is scan pictures and transform pixel density into the genetic code (i.e. sequences of the four bases A, C, G & T). They then made DNA carrying these sequences, persuaded bacteria to take up the DNA and incorporate it into their own genomes and, after growing many generations of the bugs, extracted their DNA, sequenced it and reconstructed the original images. By scanning sequential frames this can be extended to movies.

It’s not science fiction – but it is pretty amazing. With a droll turn of phrase Seth Shipman said “We want to turn cells into historians” and the work does have significant implications in showing something of the scope of biological memory systems.

Won’t be long before the trendy, instead of birthday presents of electronic family photo albums, are giving small tubes of bugs!

References

Shipman, S.L., Nivala, J., Macklis, J.D. & Church, G.M. (2017). CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria. Nature 547, 345–349.