Lost in Durham – A Scouser’s tale of Science

Two blog posts in the space of a month? You lucky readers you!

Recently, as part of the BBSRC DTP experience, I went on lab rotation to the wonderful Durham University, where I spent 4 days working with my third supervisor, the legendary Prof (uncle) Roy Quinlan. Roy and his former PhD student, and my new favourite former PhD student, Fred gave me the opportunity to learn how to extract a lens basement membrane from a cow eye (see videos below). While super squeamish at first, with all the blood and what not, it was amazing to get the chance to learn such a cool and useful technique from one of the leading lens scientists in the world! “But why is this such a cool technique?” I imagine I’d hear you ask if it was in fact possible for me to hear you through a computer screen as you read this blog.

The len’s basement membrane is quite a unique basement membrane, as it comprises only one cell type, in addition to being one of the thickest basement membranes in the body. This is particularly useful as we believe we can decellularise this basement membrane and use it to culture our Pierson syndrome cell models on, providing an ex vivo model of the basement membrane. Another cool aspect of using cow eyes for this model is that the animals were already being used for meat, so no part of the animal has went to waste!

After many, many goes, and the wonderful patience of the lovely Fred, I successfully managed to extract the basement membrane from the cow lens. I was also able to decellularise the lens surprisingly easily! I’d like to thank the lovely Quinlan lab for helping me out while I was in Durham and helping me take some really useful skills back to Liverpool, with special thanks to Roy (for organising the trip), Fred (for showing me the ways of cow dissection), and Alexia (for being super friendly to a weird scouser and showing me around, and also being camera woman for the videos above!).

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Another Brucey Bonus point, I couldn’t have went to Durham on a more Christmassy weekend! I drove up in the middle of a snow blizzard, so Durham was a winter wonderland for the weekend I was there. While there, I purchased the newest member of the Hamill Lab at the Durham Christmas Markets. I know Derek the Reindeer will play a huge role in keeping me sane during my PhD!

Derek the Reindeer

Welcome to the lab Derek!

So that was my weekend in Durham! It was a fabulous five days or so, and I look forward to many more days in the Quinlan lab!

Thanks for reading science homies!

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New content; introduction to laminins

I’ve added a “non-scientist”-friendly introduction to laminins to the site today. Kinda wikipedia-like but with more connection to what we work on. If you have 5 mins, can you have a look via the link above and provide a bit of feedback about whether I have managed to write this in a way that works to effectively introduce this protein family in an accessible way.

They grow up so fast – graduation edition

Today marked another milestone for some of the lab members and another day of immense pride and paternal type feelings for myself!

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L-R Kevin, Valentina and Carl

First up Dr Iorio received her PhD. Valentina is my first student to complete the emotional rollercoaster that is a PhD, and it was fantastic to be able to share this final step with her family. I’ve posted lots of things about Vale and her journey, you can check some of those out here, here and here.

Valentina also brought me a hard copy of her thesis which now sits next to mine on my bookshelf. There is something extra special about seeing img_0484the thoroughly impressive body of work in “proper” book form that really cements the magnitude of the undertaking and underscores the effort that has gone in to getting to this stage.

The red cover is also lots cooler than my boring black one!

Also graduating in the same ceremony were the MRes students from last year. This included Conro and Liam, who are now continuing in the Hamill lab doing PhDs. I really like our MRes program, if gives the students a solid taste of a variety of lab projects and sets them up well for continuing their academic journey (which is why I keep on recruiting PhD students from the courses). Liam and Conro have each written their own blog posts that tell of their MRes experiences here (Liam) and here (Conro). They are competing for most hits of their link so pick a team…

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Conro “Conor” Sugden and Liam Shaw

Quite depressingly, the University spelt Conro incorrectly on his certificate so, according to Liam, his degree doesn’t count as it refers to somebody

24879187_10215041319246530_851600222_oelse! I think we will let you off “Conor”

Also celebrating today were the other recent PhD and MRes graduates from the previous year. Including Holly Smith who did some nice work with my team for her third project.

Holly also wins in all the best photo comps (click the link above, you’ll see what I mean)!

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And finally, I too am celebrating a milestone; I was promoted to Senior Lecturer yesterday. These steps up the ladder aren’t really down to me, they are absolutely dependent on the hard work of my team generating the outputs needed for the University to value my contribution. I have been lucky to have a group of excellent students and staff working with me that have allowed our research to move forward and days like today are a fantastic time to acknowledge that.

A late introduction into the mind of a new PhD student

Howdy Hey Blogareenos! I’m Liam (the tiger from previous blog posts) and I have recently started my PhD with the Hamill lab, where my project looks at the role of LN domains in basement membrane integrity and signalling. Much like Conro, this isn’t my first rodeo in the Hamill lab, but it is my first year as a PhD student. Over the past year, Dr Hamill was my supervisor for a 9 month MRes project (and for some reason, he decided to keep me!)

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Squad Goals! The Sunscreen challenge OG Team. From Left to right: Your very own tiger, Conro, Lee and the Big boss man!

So a bit of background. It seems as though I shall never escape Liverpool or its University. I completed a 3 year undergraduate in Biochemistry, where I experienced “real” research for the first time. During my third year dissertation, I spent 12 weeks investigating the effects of oxidation on a number of anti-cancer therapeutics, such as Cetuximab and Rituximab. How very Biochemistry! During my undergraduate degree, I also completed a 3 month summer placement in the lab of Dr Dada Pisconti, where the team were investigating the role of serpin B1 in Duschenne Muscular Dystrophy.

Following my 3 years in Liverpool, I very clearly fancied a change. So I went straight back to Liverpool to complete an MRes. This was when I was introduced to the world of laminins and LaNts (and poor Kevin was introduced to the world of me)! I was part of a 9 month project in the Hamill Lab investigating the potential of peptides to disrupt laminin polymerisation (see some cool images below!) It was during this time that I realised my love for the world of matrix biology, and I was lucky enough to get a place on this current PhD programme, funded by the BBSRC DTP for Durham-Newcastle-Liverpool (Try saying that 5 times really fast!)

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A spoiler free selection of some of the coolest LAMA3 and LAMC1 staining from my MRes project!

And that led me to here. I’m 1 month and 22 days into my PhD (at the time of writing) and I couldn’t be more excited! One of the key processes in early basement membrane formation is the assembly of the laminin network, through the N-terminal domains of laminin. But besides their role in polymerisation of laminin, not much else is known about the laminin N-terminal (or LN) domains. There is clinical evidence of these domains being absolutely vital as well, with mutations in the LN domain resulting in numerous nasty diseases such as muscular dystrophy (LAMA2) and Pierson Syndrome (LAMB2). During my project, I will use the disease Pierson syndrome as a model to investigate the roles of the LN domains, and how these roles are compromised in the diseased phenotype. One particularly cool aspect of my project is the potential it has to open up the door for future stem cell research! The laminins I will mainly be focussing on during my project are LM511 and LM521, which have been shown to play an important part in stem cell maintenance. So the potential to investigate one of the key events in matrix biology is something that really excites me!

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Pierson Syndrome, a disease caused by the mutation of LM β2’s LN domain, which results in glomerular dysfunction and ocular malformation, as shown above. Source: Zenker, et al. 2004.

Outside of the lab (yes I do sometimes leave, contrary to popular belief), I was part of the now award winning Sunscreen Challenge as part of Team Hamill’s Meet the Scientist outreach event, and I plan on taking it to a high school in Durham in the near future. I was also lucky enough to attend a number of super cool conferences including the ‘Assembly, Dynamics and Organisation of Filaments and Cellular Responses’ workshop in Durham, and the recent CCI workshop at Liverpool, where Dr Teng-Leong Chew of Janelia Farm gave a particularly amazing talk into super microscopy! Outside the lab AND science, I’ll continue playing and coaching table tennis to keep me sane during my PhD (if you’re interested in lessons, hit me up)!

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Some extracurricular activities: Left to right – Lee and Conro getting hands on experience with children’s entertaining at the Sunscreen Challenge in May. The amazing ‘Assembly, Dynamics and Organisation of Filaments’ workshop at Durham University, hosted by the wonderful Uncle Roy (my third and Durham based Supervisor). Shameless evidence that I do actually play table tennis, with the lads from Crosby’s Southport and Lancashire League and Cup double winning side from September 2017.

The next four years are looking very exciting. The team, as well as the atmosphere in the lab in general, are all fantastic and like no lab I’ve worked in before. I’m lucky to be working in a field that I am so interested in, and can’t wait for the opportunity to contribute to the field myself!

Also, I will beat Conro in the lab wars lab wars by any means necessary, his 1-0 lead means nothing. As a Liverpool fan, I know a 1-0 lead is meaningless.

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Thanks for reading!

Liam (aka, Chocolate thunder bear)

Big laminin paper: Gene therapy for junctional epidermolysis bullosa

When I started this blog I envisaged it as a way to acknowledge lab achievements and celebrate the successes of the Hamill lab team members. As we have gone on it has developed and changed (and I would like to think got better) and its time for the next evolution; “Big laminin papers” (wondering what a laminin is? See the video at the bottom of the page)

First up is a laminin story that made it to the mainstream media as the implications are pretty huge! A case report describing a junctional epidermolysis bullosa patient  receiving effective treatment for their debilitating disase. Bit strange, picking a case report? Well the treatment is pretty awesome; skin transplant of ex vivo repaired cells to effectively cure someone who had no other treatment options left and would have died soon. Original article in Nature by Hirsch et al from Michele De Luca’s group available here (paywall).

Paper choice

In many ways picking a translational science paper for the first “big laminin paper” feels a bit strange. So far this year there have been over 100 papers with “laminin” in the title including some thoroughly impressive papers that are much closer to what my lab work on (eg important potential therapy for muscular dystrophy based on laminin polymerisation from Peter Yurchenco’s group, a comprehensive investigation of netrin-4 effects on laminin matrixes, crystal structures from the Hohenester group, and  useful papers using laminins to improve culture conditions for stem cells including for limbal epithelial stem cells and pericytes that we grow), any or indeed all of which are worth commenting on and are directly relevant to what we are doing. However, this one touched me in a different way.

Junctional epidermolysis bullosa (JEB) is a rare but truly horrible disease. Patients present with  horrendous all over blistering in response to really mild mechanical trauma; indeed, they get referred to as “butterfly children” as their skin is as fragile as a butterfly’s wing. You can read more about it at DEBRA: the charity dedicated to researching the disease and therapeutic interventions to treat and hopefully, ultimately cure, the disease (or technically diseases). JEB itself is rare but there are a variety of other variations in the epidermolysis spectrum that mean the overall incidence is about 5000 people in the UK, 1/17000 births.

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Electron micrographs of the hemidesmosomes in normal skin (left); often described as “spot welds” their job is to button down the epidermis onto the underlying stromal tissue. On the right you can see what happens in epidermolysis bullosa, where the split in the middle results from a failure to assemble this structure.

As most the people who are reading this will probably be aware (as I have no doubt told you about laminins at some point whether you wanted to hear or not!). I have been directly and indirectly working on projects related to JEB and the proteins involved for the past 15 years. Indeed my first postdoctoral position was supported by DEBRA so its always been a subject that is close to my heart. Indeed my first real contribution to a paper and  a chapter in my doctoral thesis was dedicated to identifying the mutation that causes a rare form of JEB.

What makes this paper such a big deal?

In this paper, the authors treated a patient who had lost 80% of their skin to the blistering and sloughing off the skin that results from the weakness in the junction between the epidermal layers and the stroma. If you think how painful one blister is, can you imagine how bad losing the skin on most of your body is? Indeed, here, the disease was so bad that the treatments were essentially limited palliative.

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Laryngo-onycho-cutaneous syndrome; a variant of JEB where patients overproduce granulation tissue. This disease was the starting point for my PhD and my entry into the world of laminins!

So, what they did was take a biopsy from a region of non-blistered skin, grew up the cells in culture and used a retrovirus to correct the mutation in the laminin beta 3 gene. They then expanded the cells in culture and grafted the repaired cells back onto the patient. Lots and lots more rounds of treatments, more grafts and more cells, and 2+ years later the boy they treated has essentially normal skin. Safe to touch, to the extent his parents are now even able to hug their 7 year old for the first time.

It should be noted that smaller grafts with longer follow up have been done before, indeed Prof De Luca’s group reported the approach in Nature Medicine in 2006. However, the difference now is the scale. This is the real proof that this approach is viable for patients who otherwise at best case would be in for a life of pain.

Importantly, it proves concept; gene correction and grafting can be done even in really bad cases and it actually provides hope for patients living with some of the multitude of other diseases where gene correction could be the answer.

Its not all good

The stories in the news carry the excitement but there are some issues.

The gene editing process itself introduces a whole bunch of additional genetic changes, the practical upshot of which is that there is a real potential that some of those mutations can lead to additional, different problems, most obviously cancer. As you would expect, the incidence and pathways in which genetic changes occurred in this patient were mapped in order to determine how big a problem this is. These data showed that were indeed many including  mutations in coding regions of numerous genes (though apparently not in the key cancer pathways). However, 2 years out, the patient has no sign of cancer in any of his new skin and his quality of life has improved enormously.

Another point to note; although more than 40% of patients with JEB die in childhood, if they survive to adulthood, they have much higher incidence of skin cancers than the general public so am increased* cancer risk isn’t something that would put patients off.

*possibly increased; this is a fear rather than proven increased risk at this point.

Another current limitation is that its only the surface epithelium that was treated. With this disease other epithelium eg the linings of the wind pipe and GI tract are affected. Often these aspects of this disease are more manageable but the patient will still require extensive medical care.

Bench to bedside. It’s a journey.

Why I really chose to highlight this paper is because, even though it is an endpoint paper, it effectively highlights the importance and massive value fundamental research has. To be clear, when I read this type of research, while I appreciate the vital work the clinicians who delivered the final therapy have done, I read it with the understanding that it marks an important step within a long journey that was absolutely dependent on lab based research.

In no uncertain terms, this treatment could not have been achieved without the seminal work identifying the pathogenic mutations more than 20 years ago, and indeed the work that started 10 years before, that identified the hemidesmosome  (that my postdoctoral mentor Jonathan Jones was massively important in this), and ultimately their protein constituents that helped direct the search for the mutation. This current development also required more recent discoveries that identified the strategies to edit the genome and the subsequent hard graft needed to optimise the approach so that you could make the change you want without massive other problems. It also took the identification, isolation and expansion of stem cells in culture and development of scaffolds upon which to expand epithelial sheets to allow grafting. So while this paper is indeed huge and worthy of press attention (and hopefully increased donations to DEBRA that will come from it), it is not just the authors that should be feeling proud but also all the scientists that allowed the treatment to get to this stage. The preceding research may not have made it onto the BBC but it’s no less sexy in grand scheme of things.

Keep on researching!

People sometimes describe fundamental research as “basic” science but none of this stuff is or was basic. Without “discovery” science (a much more appropriate term) the science that underpins the next big therapy will never get developed. Developments like these that reflect more than just an incremental advance, that took hundreds of groups working over many decades, require and are worth the investment in time and effort that they take.

To students on a discovery track, this work also shows that you don’t have to work on a project that is translatable tomorrow for it to be worthwhile. Indeed, the most worthwhile research might take longer than the extent of your current project.

A final point

This treatment doesn’t mean the story is over. Lots more work is required before other patients can benefit and this treatment will not necessarily work for all types of EB. Indeed, even for people with the same exact mutation this therapy may not work if the disease has progressed so far that the underlying stroma is so damaged that grafts are no longer possible. So, if you want to help support a charity that not only works tirelessly toward supporting patients with the disease but also are committed to supporting the discovery science needed to provide a cure for all, you can do so here; DEBRA.

 

Introduction to laminins

New review article out; anti angiogenic applications for corneal neovascularization

Just a quick post to say our recent review article on “Gene based anti-angiogenic applications for corneal neovascularization” is now available; link to pubmed here

The first author for this article is Siyan (Shane) Liu who did a couple of MRes projects with my  and  Colin Willoughby groups a couple of years ago, and the basis of this article is one of the “short review” topics that he was assigned during the year.

The resultant article is worth a read if you want a good overview of anti angiogenic approaches especially if you are new to the field. Co authors Vito, Bernie and Profs Kaye and Willoughby have ensured its all clinically relevant with some lovely eye images.

Presentation2You can read about Shane’s lab work in my posts from

They grow up so fast: MRes Spring 2016 edition, They grow up so fast – MRes Jan’16 edition

Team photo – Oct 2017

Today the whole team were together for our lab meeting so we took the opportunity to grab a lab photo. We have definitely reached critical mass; my head is struggling to cope with everything that is going on in the 10 projects but it’s worth it as it’s really exciting to see them all progressing. We certainly have lots to talk about at lab meetings.

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L to R: Lizzy, Laura, Lizzie, Conro, John, Nikitha, Lee, Kevin, Valentina, Liam, Thanos

In fairness, we are only temporarily at this size as we have 4 MRes students who are only with us until end of Jan but it’s still pretty cool while it lasts!

Liam vs Conro; the lab challenge round 1

Liam and Conro started their PhD studies in the Hamill lab in October, Liam on a BBSRC DTP and Conro supported by the IACD managed Crossley Barnes endowment. Unsurprisingly, both are working on laminin related projects but asking different questions in different contexts. Additionally , and also unsurprisingly, there is a bit of competition between them so it seemed only appropriate that we would welcome them to the lab with a series of games with the two guys being team captain in every game but with different other lab mates to support them.


First up; a lllama themed game! A mixture of charades, articulate and Pair matching game. Great fun. Conro’s team, despite some amazing acting by JohnJohn (in video he is acting out Nicolas Cage falling off a stage), lost comprehensively. Some might think a key example of how his team was let down was lee struggling to guess otter from a description of the “best animal that holds hands as it floats away” but really it was that Liam had the advantage of having Karen and myself in his team.


Next, a super quick game of beer pong while waiting for a taxi. how this game went is summed up by the video above… Liam , lee and JohnJohn were off their game and conro ultimately won easily. 2 games down , score 1 – 1.


Next, a couple of games of pool. Both captains won one each principally driven by whichever team had lee on it! 2 – 2

And then, the main event; Shuffleboard. On the sandiest table I’ve ever played on. Here you could tell that the presssure was beginning to get to the boys as stones were flying off in all directions. However, as a team game, Liam streaked into an early lead only for conro to pull it back so it was close going into the final ends.


Cometh the hour, cometh the man. Conro took the win and the championship (or at least round 1!) with the shot below… what a way to win. At this point I would mention the staff vs students game but I don’t feel that it is necessary to point out how much better Valentina Karen and I were…

All in all. Awesome fun, I’ve assembled a great team. It’s been awhile since we’ve been out together but I’m really glad this somewhat spontaneous night was arranged. Many thanks to all involved.

They grow up so fast – JohnJohn’s 1st year talk

Today JohnJohn Knox had his end of 1st year of PhD talk (upgrade seminar). JohnJohnJohn is working on trying to develop a new molecular therapeutic for glaucoma on a project sponsored by UK charity Fight for Sight. He has three supervisors; Colin Willoughby, George Bou Gharios and myself and while Colin is the real driver behind this project (it is his grand plan), George and I contribute our expertise to guidance. and are likely to take a bigger role as he enters the next phase of his project.

JohnJohnJohnJohn did really well in his talk, presenting to a packed seminar room with most of the faculty from IACD in attendance. He did particularly well in dealing with some tricky questions in a really confident and effective way. He got some nice comments and suggestions for future work too so should be off designing new experiments as I write this!

There is some cool stuff coming here so expect more news about JohnJohnJohnJohnJohn’s progress in the near future.

 

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JohnJohn adopting the “intense stare at supervisor” approach to presentation giving

 

If anyone is wondering where they have seen JohnJohn before… he was the face of the sunscreen trial! Famous throughout the land after featuring in most major newspapers and on ITV!

Pratt Figure 1c

 

Sunscreen challenge; article in press

Today the primary research that led to the sunscreen challenge, and all the posts (and TV shows) that you have must seen by now, was published.

The link to the paper at the PLOS one site is here. Have a look, download the paper, make a comment, tweet directly from the site (rather than retweeting this). Will all boost our altmetrics and help the article get some attention. If you prefer a the press release version, check out this link to the University of Liverpool website from when we were promoting this work in relation to the British Association of Dermatologists meeting. camera

Want to see more about our public engagement events related to this work? Check out these posts here, here (filming for ITV), here and here