Leïla Perié

Heterogeneous Differentiation Patterns of Individual CD8+ T Cells

Dynamic Protection During an immune response, CD8+ T cells are recruited to provide protection. Most cells differentiate into short-lived effectors that help to clear the pathogen, whereas others form long-lived memory cells to protect against reinfection. Gerlach et al. (p. 635, published online 14 March) and Buchholz et al. (p. 630, published online 14 March) used in vivo fate mapping of mouse T cells with a defined specificity during a bacterial infection to show that the dynamics of the single-cell response are not uniform. The response of a particular T cell population is the average of a small number of clones that expand greatly (“large clones”) and many clones that only proliferate at low amounts (“small clones”). The memory pool arises largely from small clones whereas effectors are primarily made up of large clones. The single-cell dynamics as cytotoxic T cells respond to a bacterial infection are analyzed in mice. Upon infection, antigen-specific CD8+ T lymphocyte responses display a highly reproducible pattern of expansion and contraction that is thought to reflect a uniform behavior of individual cells. We tracked the progeny of individual mouse CD8+ T cells by in vivo lineage tracing and demonstrated that, even for T cells bearing identical T cell receptors, both clonal expansion and differentiation patterns are heterogeneous. As a consequence, individual naïve T lymphocytes contributed differentially to short- and long-term protection, as revealed by participation of their progeny during primary versus recall infections. The discordance in fate of individual naïve T cells argues against asymmetric division as a singular driver of CD8+ T cell heterogeneity and demonstrates that reproducibility of CD8+ T cell responses is achieved through population averaging.

Diverse and heritable lineage imprinting of early haematopoietic progenitors

Haematopoietic stem cells (HSCs) and their subsequent progenitors produce blood cells, but the precise nature and kinetics of this production is a contentious issue. In one model, lymphoid and myeloid production branch after the lymphoid-primed multipotent progenitor (LMPP), with both branches subsequently producing dendritic cells. However, this model is based mainly on in vitro clonal assays and population-based tracking in vivo, which could miss in vivo single-cell complexity. Here we avoid these issues by using a new quantitative version of ‘cellular barcoding’ to trace the in vivo fate of hundreds of LMPPs and HSCs at the single-cell level. These data demonstrate that LMPPs are highly heterogeneous in the cell types that they produce, separating into combinations of lymphoid-, myeloid- and dendritic-cell-biased producers. Conversely, although we observe a known lineage bias of some HSCs, most cellular output is derived from a small number of HSCs that each generates all cell types. Crucially, in vivo analysis of the output of sibling cells derived from single LMPPs shows that they often share a similar fate, suggesting that the fate of these progenitors was imprinted. Furthermore, as this imprinting is also observed for dendritic-cell-biased LMPPs, dendritic cells may be considered a distinct lineage on the basis of separate ancestry. These data suggest a ‘graded commitment’ model of haematopoiesis, in which heritable and diverse lineage imprinting occurs earlier than previously thought.

Cellular barcoding: A technical appraisal

Cellular barcoding involves the tagging of individual cells of interest with unique genetic heritable identifiers or barcodes and is emerging as a powerful tool to address individual cell fates on a large scale. However, as with many new technologies, diverse technical and analytical challenges have emerged. Here, we review those challenges and highlight both the power and limitations of cellular barcoding. We then illustrate the contribution of cellular barcoding to the understanding of hematopoiesis and outline the future potential of this technology.

Citizen Science Toward Transformative Learning

Citizen science can raise people’s understanding of science while helping scientists conduct their research. Yet its potential for driving transformative learning is empirically underexplored. We present the results of a preliminary study with secondary school students engaged in a long-term citizen science project, from the formulation of the research questions to data analysis and discussion. Students learnt about and increased their interest in neuroscience. They were also able to reflect on the role of science for society and valued their involvement as active participants in the research. We discuss the opportunities and challenges of approaching citizen science for transformative learning.

Retracing the in vivo haematopoietic tree using single‐cell methods

The dynamic process by which self‐renewing stem cells and their offspring proliferate and differentiate to create the erythroid, myeloid and lymphoid lineages of the blood system has long since been an important topic of study. A range of recent single cell and family tracing methodologies such as massively parallel single‐cell RNA‐sequencing, mass cytometry, integration site barcoding, cellular barcoding and transposon barcoding are enabling unprecedented analysis, dissection and re‐evaluation of the haematopoietic tree. In addition to the substantial experimental advances, these new techniques have required significant theoretical development in order to make biological deductions from their data. Here, we review these approaches from both an experimental and inferential point of view, considering their discoveries to date, their capabilities, limitations and opportunities for further development.

Inferring average generation via division-linked labeling

For proliferating cells subject to both division and death, how can one estimate the average generation number of the living population without continuous observation or a division-diluting dye? In this paper we provide a method for cell systems such that at each division there is an unlikely, heritable one-way label change that has no impact other than to serve as a distinguishing marker. If the probability of label change per cell generation can be determined and the proportion of labeled cells at a given time point can be measured, we establish that the average generation number of living cells can be estimated. Crucially, the estimator does not depend on knowledge of the statistics of cell cycle, death rates or total cell numbers. We explore the estimator’s features through comparison with physiologically parameterized stochastic simulations and extrapolations from published data, using it to suggest new experimental designs.

Straight into conflict zones, scientific research empowers the minds

Sharing scientific knowledge in conflict zones may not sound as a priority. Still science communicators can contribute to address social issues by inviting people to experience the research practice, engaging them in scientific questioning and constructive dialog. Do nails grow at the same speed on each finger? Why does the moon seem to move with us as we walk at night, while stars stay still? Why, as girls, do we have to cover our heads? These questions were raised by kids in 2013 in Palestinian schools, during questioning workshops we facilitated2 during the Science Days of Palestine. Through these workshops, young Palestinians questioned their environment and daily experience, including the ongoing regional troubles, and were guided to seek for rational answers by themselves. This is the same very first step as in any scientific journey. Such questioning scaffolds research practice, together with rejection of arguments based on authority and criticism of established ideas based on reproducible proofs. We contend that these practices shared by members of the research community are similar to those that grounded our modern democracies. Thus, letting people experience scientific research and its values can be used as a tool for empowerment. This is particularly relevant whenever the target population is experiencing poverty, segregation, ongoing conflicts or their aftermath, and needs to collectively find answers to their problems. In this context, we take advantage of the relative neutrality of science, while having a realistic vision of science. We acknowledge that scientific research is not ideal and is also affected by misconducts and ethical abuses. Scientific research coexists with other knowledge systems, which altogether guide societal choices. However scientific questioning invites us to adopt intellectual attitudes that prevent from running straight into emotional conflicts. 10 years of experience support our claim and we foresee that this “tool” has an untapped potential. It can be implemented by practitioners of scientific research, from natural sciences 1All authors contributed equally, ranked by alphabetical order. 2How to stimulate open questions?, workshop tools. JCOM 13(02)(2014)C05 Licensed under Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 2 L. Perié, L. Riboli-Sasco and C. Ribrault and humanities, and actors from scientific institutions. For example, science centres and museums could contribute to address social issues, by inviting youth and citizens to experience scientific investigation [1, 2]. We first experimented this approach when creating the Science Académie program.3 It offers internships in research labs to high-school students from impoverished suburbs of France. We select participants based only on their motivation, in order to reach those who may not fit with the school system but express great curiosity. During a week, mentored by PhD students, they take part in the daily life of the lab (experiments, data analysis, lab meeting, coffee breaks, etc.). This provides a transparent vision on the way research proceeds, both in terms of pure management and intellectual challenges. Evaluation of this program revealed that some participants show empowerment as they set up NGO’s, become social entrepreneurs or join political action. Though we lack a control population to rigorously demonstrate efficiency of this program, these empowered participants cite participation to Science Académie as a key determinant of their social commitment. Following these internships, they are offered the possibility to perform science communication workshops in a festival in France4 or abroad. We observe that sharing passion for science with a wide audience strengthens self-confidence on a long term.5 This approach gets close to what the Exploratorium in San Francisco has been doing since 1969,6 with its explainers being recruited among youth who have abandoned their home or dropped out of school. Using research-based activities to empower people is complementary to other approaches addressing social and political issues: for instance, in 2009 in Vukovar — a Croatian city where young Serbs & Croats still live quite apart — we performed research-based activities which fruitfully combined with sport and theatre activities.7 Although we consider research-based activities to be relevant to address exclusion and conflict, these activities need to be finely tailored to each context: there is no ready-to-use universal “tool”. This shall not be understood as a limitation, but rather as a fantastic driver for innovation in science communication and science education. For instance, we are experimenting at a European scale a process of co-creation of new fundamental research programs. The co-creation involves professional scientists and citizens, youth and adults, in particular from poor or isolated communities, such as favelas in Lisbon suburbs.8 In addition, it should be noted that going towards populations living in conflictual or deprived areas does not imply simplification of scientific knowledge for mere entertainment or cultural purposes, but rather sharing the essence of the production of this knowledge. It allows new knowledge to be produced, meaningful for these communities. Incidentally, this approach, far from requiring technological or fashionable tools, merely relies on old-style genuine human interactions. 3Science Académie: http://www.scienceacademie.org. 4Festival in France: http://www.paris-montagne.org. 5Bilans: http://paris-montagne.org/science-academie/bilans. 6Program overview: http://explainers.exploratorium.edu/highschool/program. 7http://www.con-sol.org. 8Nouveaux Commanditaires — Science: http://www.joursavenir.org/ncs/en. Straight into conflict zones, scientific research empowers the minds 3 In order to engage more communities into a similar path we have performed capacitybuilding workshops for community educators, teachers, and university students from Europe and Middle-East.9 One crucial aspect highlighted in these workshops is the absolute necessity to involve active researchers. Indeed the process relies on mobilizing the values that are at the core of the research practice and kept alive by the research community. These researchers shall also be trained to avoid a “deficit model” stand and to face skepticism when communicating their involvement in conflict zones to their institutions. In addition, developing such activities also requires lots of patience, for both scientists and participants to scaffold an indispensable reflexivity about science. Last but not least, we must be careful when claiming to promote social inclusion. Claiming its achievement too early may lead to disappointment, and damage the necessary trust relationship with the targeted communities. Hopefully standard schemes of evaluation shall be produced in the next years, as more initiatives may take place. We will close this brief note with the words of Albert Camus, “one must imagine Sisyphus happy”. Even if strengthening peace in conflict areas is a difficult task, the community of science workers can have an impact through research-based activities, maybe small, but which will be bring some happiness for those involved.