Week 2 - Karin

In continuation of my last post, I finally received Copath access this week. Copath is a database of patient surgeries and work-ups (histology diagnosis, hormone assays, etc). I'm working with some other people to create a breast cancer tumor bank; extracting information such as how a specimen was obtained (excision, mastectomy, etc.), what the diagnosis was (invasive carcinoma, ductal carcinoma in situ, etc.), what other follow-up tests were performed (hormone assays: % estrogen receptor (ER), % progesterone receptor (PR), %HER2/neu, %Ki-67), etc. It's interesting going through these reports and seeing how a pathologist comes to a certain diagnosis by looking at the morphological features and the stain intensities on a slide - occasionally a clear diagnosis can't be made, so further tests are performed. Once this database is complete, plenty of statistical analyses can be performed which would allow us to see how certain aspects of a specimen discovered during diagnosis correlate to specific breast pathologies.

Aside from extracting data from Copath, I also met with Dr. Shin and Dr. Timothy D'Alfonso (fellow) to discuss other projects to work on. Dr. Shin would like us to submit two abstracts to the 2012 USCAP (United States and Canadian Academy of Pathology) conference. Our first project is a continuation of another BME immersion students' project (Shawn Carey): to review cases of in situ breast carcinoma in needle core biopsy and see how well key microscopic features predict "pathologic upgrade" (such as invasive carcinoma) in subsequent excisional biopsies. To aid my understanding of the histological samples I'll be reviewing with Dr. Shin and Dr. D'Alfonso, I'll be reading Rosen's "Breast Pathology: Diagnosis by Needle Core Biopsy." Our second project will be to compare how Axl gene expression in triple negative phenotype (TNP) breast tumors (tumors that do not express genes for ER, PR, or HER2/neu - aggressive tumors that do not respond well to standard treatments and are associated with poor prognosis) compare with that of non-TNP tissue microarray (TMA) samples and their associated subtypes (Luminal A, Luminal B, Luminal-HER2, HER2 enriched, Basal-like which categorize certain criteria such as %ER, %PR, %HER2/neu, %Ki-67, CK5/6, EGFR). I will be going through the literature to understand how Axl signaling was found to represent undesirable cellular traits associated with cancer, while we wait for IRB approval for this study.

Also, I have a few shadowing opportunities scheduled for next week! More to come... :D