Cass Nordmann - Dr. Sandra Demaria - Week 4

 This week in the pathology lab, I sat in for some more sign-offs with Dr. Demaria and Carla, the resident, on Tuesday and Friday. I was able to bring my notebook with me this time, so I could take more detailed notes on the proceedings rather than writing up my recollections after the fact. I’m glad I did so as I feel like I got a lot of insight into what breast pathologists are looking for and got to ask lots of questions in these two days. Dr. Demaria was so patient and generously made an effort to include me by asking whether I recognized different features or my opinion on some stains. Some of the new types of tissues I got to see this week include: a lymph node with metastasis from the breast, nipple, blood vessels with invading tumor cells, intramammary lymph nodes, mucinous carcinoma of the breast, and a radial scar. The lymph nodes stood out to me because I could instantly tell it looked different from a regular lymph node (there were a lot fewer dark nuclei and granules and some tissue that looked a bit like breast stroma) and because of the importance of lymph nodes to my research on immune responses and immunotherapy. Lymphatics isn’t an area that my lab has looked too far into, even though we’ve begun working on immunotherapy research. Not only are the lymph nodes often sites of metastasis for breast cancer, infiltration into the lymph nodes could also impact the efficacy of future immunotherapies. I also found it really interesting to actually be able to see tumor cells undergoing intravasation to enter the bloodstream. Our lab has done a lot of work on tumor cell invasion, so I’m familiar with the process, but it was still surprising to see the tumor cells actually squeezed between the layers of the blood vessel walls.

It was a bit of a slow week on the research side of things. Last week, Diego, one of the medical students, tried to extract RNA from some patient-derived organoids for sequencing but got hardly any RNA from one of the organoid lines. I pointed out that that line is cultured in Matrigel while the other two, which RNA was successfully collected from, were cultured in Cultrex, a similar but distinct basement membrane extract product. Cultrex became more prevalent in research and was adopted by Dr. Demaria’s lab during the COVID-19 pandemic, which interfered with the supply chain for the normally ubiquitous Matrigel. After doing some literature searches and discussing it with the medical students and Dr. Demaria, she suggested they try running a small troubleshooting experiment wherein they cultured the problem organoid in both Cultrex and Matrigel and see if they got more RNA out of the organoids in Cultrex. The medical students finished that experiment while I was in the pathology lab this morning and unfortunately got some strange results. Not only did they get plenty of RNA out of the organoids in Matrigel this time, but they also got more out of the samples in Matrigel than the ones in Cultrex. As far as Diego knows, the only thing that might have changed since last time is that the organoids used in this last experiment were not as confluent when they were harvested, but Maud, the postdoc, and I are skeptical that would have been the sole source of trouble. For now, it’s still a mystery. In the meantime, I’ve begun doing some of my own research into the literature on the differences between Matrigel, Cultrex, and other basement membrane extracts, along with other biological matrices like rat tail collagen I, which is what my lab uses. Products like Matrigel contain a mix of all sorts of proteins and their contents can vary from lot to lot. The companies that make them are also not entirely transparent about what goes into them and how they’re made. They honestly seem like a bit of a black box to me. I’m wary of how these products could impact results. Them being a mix of proteins also would probably make the mechanics of the matrix more difficult to characterize and model, which is important for my lab. I asked Dr. Demaria why they use basement membrane extracts instead of just collagen I, and she said they were just following the precedent set out by previous organoid research. I’m obviously no expert but I think the reliance on Matrigel could really be a weakness in this kind of research and something that should be looked into more.