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Immunology with numbers


Ramblings of a numerate immunologist


Archive for June, 2015

Single cells and their stochastic perambulations

By regfbec, on 30 June 2015

I returned last week from a small but intense meeting entitled “Stochastic single-cell dynamics in immunology : experimental and theoretical approaches”. The meeting took place in the splendid 17th century Tripenhuis building in Amsterdam, the home of  the Royal Netherlands Academy of Arts and Science for over two centuries. The meeting was organised by Leïla Perié, Johannes Textor and  Rob de Boer (all from the University of Utrecht) and Ton Schumacher (NKI Amsterdam).

Perhaps unsurprisingly, the meeting was driven by technical and methodological advances, both experimental and computational. Dirk Busch (TUM, Munich) presented further results from his elegant  single cell adoptive transfer in vivo model system, which has already revealed the striking heterogeneity in both proliferative and differentiation fate which arise from different naïve T cells or the same specificity. A nice extension of the system was the introduction of dendritic cells carrying the diphtheria toxin receptor, which could be depleted at fixed time after immunisation, thus allowing the role of persistence of antigen to be dissected. Remarkably, perhaps, the mechanistic source of the stochastic variation remains incompletely understood, and both this group and other groups are looking to in vitro models to give a more precise handle on this fundamental question.

Another highlight of technological virtuosity was, as ever, Ido Amit’s (Weizmann Institute, Israel) presentation of his experimental system which allows global transcriptomic and chromatin modification analysis to be carried out on ever smaller numbers of cells. Single cell transcriptomics of blood has revealed an increasingly complex mixture of heterogenous “subpopulations”, although the challenge of conceptualising meaningful “shapes” in such vertiginously high dimensional space remains.

A very considerable effort from many groups focused on improving the length of time, and the precision, with which cells could be imaged in vitro. The prodigious ability of T cells to race around in three dimensions provide special challenges for imaging, which Philippe Bousso  (Institut Pasteur, France) tackled by forcing them to migrate up and down narrow microchannels (reminding me rather of Olympic swimmers in their allotted lanes), thus allowing very accurate quantitation of migration velocities in one dimension. Tim Schroeder (ETH, Switzerland) presented another very elegant experimental system to tackle the challenge arising from the very slow turnover kinetics of stem cells, which therefore requires very long tracking times (in the order of weeks) in order to follow cells through differentiation. Although perhaps relying less on technical virtuosity, I liked Gregoire Altan-Bonnet’s (Memorial Sloan-Kettering Cancer Centre, USA) approach of extracting information from the natural heterogeneity captured by most flow cytometry data sets, which is otherwise largely ignored by  the thousands of practitioners of flow cytometry. He illustrated how a combination of this data analysis with elegant and simple mathematical modelling can be used to extract functional regulatory networks from quite “low-tech” data sets.

Technology aside, what were the conceptual questions emerging from the meeting ? Questions of lineage loomed very large. Tracing cell family trees (questions of progenitors, descendants , branch points) has long exercised immunologists and haematologists, and new technologies have certainly promised to provide more accurate and detailed answers. In the context of the very real prospect of successful clinical stem cell therapies such questions are surely important, although the nagging concern over lineage stamp collecting remains for me a niggling concern. An idea raised by several speakers was the “stemness” properties of the T memory cell. For this writer, the idea that memory cell “self renew” seemed almost tautological.  And in this context, it seemed astonishing that teleomeres scarcely got a mention ! Another surprising emphasis was the re-emergence of the concept that T cells can affect neighbouring cells through cytokine secretion. This idea, which was in some way the fundamental concept underlying the prolonged era of cytokine discovery, has gradually been replaced by the concept of specific targeted secretion dominated by tight immunological junctions. But the wheel, it appears, is about to turn full circle. A particularly intriguing extension of this is the suggestion that cytotoxic T cell mediated killing is often mediated at a distance via interferon gamma secretion. Further experimental and quantifiable evidence on the importance of this process in vivo is urgently required.

I did not emerge from this meeting with the feeling of having heard any major specific breakthrough, but rather with the sensation that the meeting represented a gathering of pioneers  who are exploring the possibilities of a new type of immunology. The common theme among the participants was a willingness to engage at the frontier between computational and experimental science. The rules of this new subject, how to develop it, which approaches will be fruitful, and which will turn out to be relics of the physical sciences with little relevance to the world of cell biology : all these questions remain to be answered. But it is encouraging to find a group of scientists seriously engaged in this exciting challenge (discussion throughout the meeting was lively).  Many of the senior investigators told me they faced a continual battle to secure funding and to ensure high impact publication in the face of a scientific establishment which often pays lip service to interdisciplinary research, but doesn’t understand or appreciate it when it actually finds some. In this context, one can hardly avoid mention of the enormous influence of Rob de Boer and his ever growing school of talented and imaginative disciples on the field as a whole.

I finish with a plea to conference organisers. Can we introduce a rule that any talk must present one, or at absolute maximum, two key findings ?  Perhaps its my limited attention span, but learning one really important new thing from a talk is about as much as I can take in or remember. And anyway, how many of us have the privileges of discovering more than one really important thing at a time?