Cass Nordmann - Dr. Sandra Demaria - Week 3

 One of the lab’s post-docs was on vacation this week so somebody had to present in her place during lab meeting. Dr. Demaria asked Diego, one of the medical students in the lab, and me to present on Tuesday morning, so I spent the majority of my Monday working on my presentation. Diego also went over his experimental timeline with me and the other medical student. This week, some of his organoids were ready to harvest so he worked on irradiating the different treatment groups and collected conditioned media for protein level testing and RNA sequencing of the samples. The other medical student, Marvin, also placed some samples in a hypoxic chamber. This is intended to model the state of tumor cells in the core of a tumor, which becomes hypoxic due to lack of vasculature to deliver oxygen.

Tuesday morning, Diego presented some bulk RNA sequencing data collected by another lab member that he continued the analysis on. Part of the purpose of this study was to look at cell death after radiotherapy (RT). Traditionally, clonogenic assays are used to study RT, which feature irradiated cells being grown in colonies, where each colony represents the clones of an original cell that received treatment. However, these assays really measure the cells’ proliferative ability and not necessarily their death. The study that Diego presented looked at gene expression for genes related to ATP metabolism to measure metabolic cell death.

My own presentation went fairly well. I’m really unused to talking about my research with people outside of biomedical engineering but are still cancer researchers. I had been assuming some things were common knowledge before now realizing that they really are specific to my niche field. I think it was a valuable opportunity to practice my communication skills. I tried to explain the basics of what microfluidics are and how they’re made and also discussed some of the importance of mechanics on tumor cells. Dr. Demaria’s lab does similar in vitro immunotherapy work to our own, but they mostly look at the biochemical aspects of their system and not the mechanics, which I think our lab could contribute to. I also tried to explain the basics of how our imaging techniques like FRET (Forster resonance energy transfer) and TFM (traction force microscopy) work. At the end of the presentation, I showed some data that our lab’s recent graduate Dr. Brian Cheung collected on the effect of RT on natural killer (NK) cell killing efficacy and received some helpful suggestions for where this study could go. We talked about potentially using regular cell counting protocols using trypan blue to measure NK cell death after radiation and the potential of using antibodies to block certain NK cell ligands to see if radiation is upregulating their expression in the tumor cells.

Also on Tuesday, I got to see the department’s irradiator in use by a postdoc from another lab. It wasn’t anything too exciting. The postdoc just put her well plate on a platform, used a crosshair to aim the beam of radiation, and pushed a button to start it. I wanted to see their machine mostly so that if I eventually get to use the one in the vet school in Ithaca, I can compare the two. I think Brian said that the irradiator he used rotates the sample, which this one did. I’d like to know the differences and how that might be affecting whatever data I wind up collecting there.

Thursday and Friday I shadowed Dr. Demaria and one of the pathology residents, Carla, during sign-offs. In pathology, after the histology slides for a case are prepared, a resident will look at them and write up a preliminary report, and then they’ll go over the case with an attending to make suggestions on further testing or sign off that the report is ready to submit. On Thursday Dr. Wang also joined us for sign-offs. That day, most of the cases were benign fibroadenomas. The two most interesting cases we saw were a case in which, after a mastectomy, the cancer had unfortunately invaded into the skeletal muscle of the chest wall, and a tumor with phyllodes features. Phyllodes means “leaf-like” and I think it gets that name due to the round protrusions at the end and the structures that look like the veins of a leaf that permeate through the tumor. Friday's cases were a little more varied and included a lot of malignancies. I know I saw both ductal carcinoma and lobular carcinoma, but I don’t think I can really tell the difference between their morphologies. I’m still no expert, but I think at this point I can at least recognize cancer when it is very obvious and can tell breast tissue from skeletal muscle or nerves. I’ve also seen a lot of cysts in the breast tissue samples and can identify those.

I’ve been learning about some of the terminology that pathologists use and the sorts of tests that they order. In the case with skeletal muscle invasion, they ordered a sort of test called Oncomine which uses DNA from the samples to look for potential genetic targets for treatment. In a few cases, they ordered cytokeratin staining. I’m still not sure of the purpose of this stain when looking at breast tissue, but I do understand why it’s used on lymph nodes. Cytokeratin is normally found in breast tissue, but not in the lymph nodes. If a lymph node stains positive for cytokeratin, that is a sign that breast cancer cells have metastasized there. On some samples, they ordered biomarkers. I haven’t gotten the chance to ask what those are yet, but my guess is that they’re estrogen and progesterone receptors and HER2 expression levels, which are commonly used to assess breast cancers and make treatment decisions.