The ethnographic process: visiting the lab and learning about organoids in practice

by Dr. Sara Bea


Recently, I had the pleasure and privilege to visit a lab for a few weeks, the pandemic has made it difficult but at last I got the chance to do that which social scientists do when they go to labs: shadowing scientists, observing, learning and above all asking questions. The ethnographic process requires the generosity, both in time and disposition to help, from hard-working scientists already dealing with busy schedules. Their participation in our research project is fundamental and thus invaluable. It is through our observations and conversations about their everyday practices at the lab to grow human organoid models that we can begin to unpack the politics of the human in biomedical research.

The following is a fragment of a recorded conversation I had with a researcher that works with kidney and ureter organoids. We use interviews as a research method to complement and extend ethnographic observations. We focus on the trials and tribulations of modelling and approximating the human with in vitro technologies, and by drawing upon organoid researchers’ own experiences and accounts, we strive to attain a collaborative and in-depth understanding of how the humanness of organoids is defined and enacted in scientific practice. The findings of our work speak directly to longstanding and emerging issues both in scientific practice and in policy. Ultimately, our social scientific approach is placed to inform and improve the regulation and governance of stem cell-based biotechnologies. In what follows, some of the salient themes we explore within the project are being touched upon: validation, correspondence, variability and balancing emergence and engineering.

Validation is key

We depart from the premise that the humanness of organoids is not simply granted by the human origin of the starter cultures, rather it is a quality that requires a lot of work in the lab to be achieved. To inquire into the processes and materials involved in generating human organoids, I ask about the need for, and challenges of, validating the in vitro and in vivo correspondence of such multicellular living systems:

Researcher: They take a lot of validation, and I think even people who do publish their results making a certain organoid that resembles the corresponding organ, even after the publication, they continue modifying and verifying and it keeps going. You know, if you look at the publications and just search kidney organoids, you find different protocols to make kidney organoids, not only one protocol, However, in the human embryo the development that they all follow is one pathway, I think. Maybe there are individual differences and that’s accepted, but I don’t think that the differences are as considerable as those you find in the literature. Published studies might use different growth factors and signalling pathways but there are also significant differences that probably need to be validated to make a really optimised protocol for kidney organoids.

Achieving correspondence

The practical challenge of achieving a high degree of correspondence is a recurring theme during our talk. To probe on that I enquire about the documented fact in the literature that shows that mouse organoids present higher in vitro-in vivo correspondence than human organoids:

Researcher: Exactly, well I would assume that is because, the way that any protocol is made is based mainly on animals. So, they make the animal study, they apply it to the animal stem cells, and then when you compare them, they are very similar to each other. But when you take these data, and we just spoke about the interspecies differences, and just extrapolate them to the human that could be quite hard to achieve similar results. You achieve some similarity between the organoids and the organ of the human, but still, it requires a lot more work.

Accounting for variability

During lab visits, I have become aware that the arduous work of validation is often complicated by the intrinsic instabilities of iPS cells. However, there are other sources of variability that also need to be accounted for:

Researcher: That’s quite an issue. So, you know that I now work on ureter organoids and there is one type of my cultures that is quite variable in my results. The others are quite consistent. And it’s very hard to trace the cause of the variability. Is it because of the stem cells like you said, the instability? And, the other cell types are quite consistent in the results. So, if it’s an instability with the cells, why does it always happen with this type of the cells, but not with the others, you know? And I must also say that even with the mouse embryonic stem cells, which you know don’t have that issue that the human iPS cells have, I have heard of cases that had trouble differentiating them and they could not get the cell types they were after. It is not well understood why, if it’s related to the cells, but the same cells that don’t give them the results they want, maybe after a while they do get them. So maybe it’s not the cells, could be any of the factors they use, lot-to-lot variability, there are a lot of options and it’s hard to identify the cause of variability.

Sara: And what about the variability that might come from, you know, when you’re using human cells since there is no such thing as a universal human, human population is diverse and we’re all different. Does any of this person-to-person variability come into this confounding pot of factors?

Researcher: Well, because I use a certain cell line since I started, it’s probably hard for me to answer your question, I mean from my results. But I can say that I had very variable results in one direction and so that type of cells which I was also tracing in my PhD, and I was in quite a lot of trouble because sometimes I ended up by having this cell type and sometimes not having it, sometimes having very few of it, sometimes having a lot of it. That’s quite weird. But that’s all using the same cell line, doing the same technique, could be due to many reasons. The culture conditions, although we try to optimise the culture condition and stabilise them without any change. But who knows what happens? I mean, simple things like, changes in the incubator, errors that you don’t notice might have happened over the night or something like this. Maybe something in the culture conditions that’s out of our control, could also be any of the growth factors that shows variability every now and then, could be many different things and could be the cells themselves. But the inter-individual variability, which I’m sure exists, I don’t get to experience it in my own cultures.

Balancing emergence and engineering

Time spent at the lab has been very valuable and yielded some significant insights that bear upon the very nature of growing multicellular living systems in vitro. A task that can be described as a delicate balancing act between engineering and emergence. The researcher is always engineering from the outside – manipulating, guiding, and coaxing – but at the same she is dependent on the cells’ intrinsic ability to self-assemble and self-organize in vitro as they would do inside an organism:

Researcher: I would say that you know, just like I was saying, when I cannot get the specific cell type I want, I think that that has something to do with this balance you mention, that my control over the cells is quite limited. They would do what they want to do, so I try to control them and direct them in one direction, but they still have a chance to do what they want to do, not responding to the control totally, you know because they still have intrinsic directions that they follow. But yes, we try with the growth factors and inhibitory factors to control them and to optimise the direction to one specific cell type by following the developmental pathways they go through. But yes, cells sometimes have the chance to choose differently.