{"id":1937,"date":"2012-04-13T00:35:39","date_gmt":"2012-04-13T00:35:39","guid":{"rendered":"http:\/\/occamstypewriter.org\/vwxynot\/?p=1937"},"modified":"2012-04-13T00:42:18","modified_gmt":"2012-04-13T00:42:18","slug":"a-very-retro-seminar","status":"publish","type":"post","link":"https:\/\/occamstypewriter.org\/vwxynot\/2012\/04\/13\/a-very-retro-seminar\/","title":{"rendered":"A very retro seminar"},"content":{"rendered":"

(now that Big Complicated Grant has progressed to the next stage and I can draw breath again, let’s see if I can remember how to write about anything other than hockey!)<\/em><\/p>\n

I believe I’ve mentioned in the past that I work in the same building as my postdoc supervisor; this proximity means that I often run into her and other old friends from my old lab. It’s always great to catch up and find out what everyone’s up to, both socially and scientifically, but these chance encounters are never quite long enough to learn many of the details of the latter. I read all the group’s papers when they show up in my automatic PubMed search RSS feeds, of course – just like I still read everything my PhD supervisor publishes, and even have a Google Alert RSS feed set up for news items that mention the company I worked for between my postdoc and my current job – but I very rarely get to hear about their new research directions and work in progress. This is a shame, because they do some really cool work on human endogenous retroviruses (HERVs), virally-derived pieces of our chromosomes that I described<\/a> in one of my first ever (and still most Google-searched) blogposts – see also two of my favourite<\/a> papers<\/a> (published under my maiden name) from my time in that lab. So, when I saw my postdoc supervisor’s name show up on the weekly building-wide seminar list, I transferred the notification email straight into my calendar and was sitting in my customary seat like the eager beaver I am when the talk began.<\/p>\n

I found myself surrounded by members of my old lab: a couple had overlapped with me; I’d met some of the others since leaving the lab, through the first two people; and I also got to meet some completely new people, including my former student’s new student! I felt like I’d gone seven years back in time, especially when photos of former lab members who’ve moved on to other cities and countries showed up on some of the data slides. It was a very nicely structured overview talk; the first part stimulated some lovely self-indulgent nostalgia (and even contained a brief mention of some of my own work), while the second brought me up to speed on what the lab’s doing now.<\/p>\n

The really interesting part is how much overlap is developing between the HERV field and the main research focus of my main boss in my current job, i.e. using next-generation sequencing (NGS) techniques<\/a> to characterise the genomic evolution of human cancer (cool paper #1<\/a> (2009), cool paper #2<\/a> (2012)) both before and during treatment. I’d been interested in this field, which itself represents an area of overlap between my PhD and postdoctoral fields, for a while (and blogged about it here<\/a>), but didn’t know a huge amount about the nitty gritty technical details before starting this job. When I first joined my current department I asked my new boss whether the dataset described in his 2009 paper could be used to assess changes in HERV mobility and expression as cancer progresses, and he said that it depended on the length of the sequence reads – he thought it might be possible to get a feel for large-scale changes in the activity of families<\/em> of HERVs and other repetitive elements, but probably not to look at individual HERVs.<\/p>\n

Well, sequencing technology has progressed scarily quickly since then, and NGS-based HERV studies are now a reality, despite the technical challenges<\/a> posed by the sequencing of highly repetitive elements. There had already been a couple of very intriguing studies about the role of HERVs in cancer that used more traditional molecular techniques (yes, I’m classing RNA interference as traditional – deal with it): for example, expression of HERV genes was shown to be required for melanoma growth in mice<\/a> and in human melanoma cell lines<\/a> grown in culture and as xenografts. As with multiple sclerosis (blogged here<\/a> and here<\/a>), these studies began to question the prevailing belief from my own time in the lab that the activation of HERVs that is often seen in human disease is a symptom, rather than a cause, of cellular disruption. As with so many other fields, NGS technology will really open up the data floodgates – and once all those data have been processed and analysed, we’re going to learn a LOT more about what those awesome-but-dangerous HERVS are up to in our genome. The first such results from my old lab – using some of the same datasets and collaborators as do the PIs with whom I work now – are very preliminary, and I’m obviously not going to blog about them until they’re published. But things look very, very interesting – watch this space!<\/p>\n

I’m also hoping that this new research direction will make other groups in my old department take the HERV group’s work a bit more seriously. We were always the only group doing work not directly related to cancer in a department that focused mostly on leukemia and lymphoma, and our trainees’ talks were always noticeably underattended compared to those of the other labs – people just didn’t seem to care much about research so very different to their own*. Judging by the turnout at my former supervisor’s talk, however, that attitude looks to be changing, as people wake up to the scary awesomeness of the virus inside.<\/p>\n

~~~~~~~~~~~~~~~~<\/p>\n

*I was once chatting to a grad student from another group just before his labmate’s talk began, and he said, as if realising it for the first time, “are ALL the talks in this department as out of your field as your lab’s talks are for the rest of us?” I said “yes, and look at how we always attend!” But it didn’t seem to help much.<\/p>\n","protected":false},"excerpt":{"rendered":"

(now that Big Complicated Grant has progressed to the next stage and I can draw breath again, let’s see if I can remember how to write about anything other than hockey!) I believe I’ve mentioned in the past that I … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":10,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[97,7,10,98,13,3,54],"tags":[],"class_list":["post-1937","post","type-post","status-publish","format-standard","hentry","category-cancer-research","category-career","category-evolution","category-genomics","category-original-research","category-science","category-technology"],"_links":{"self":[{"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/posts\/1937","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/users\/10"}],"replies":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/comments?post=1937"}],"version-history":[{"count":0,"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/posts\/1937\/revisions"}],"wp:attachment":[{"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/media?parent=1937"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/categories?post=1937"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/tags?post=1937"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}