Thoughts on lab rotations

The thing with first-year rotations in a Ph.D. program is that anxiety starts kicking in somewhere along the way when you consciously identify the lab that you want to join and want to get started right away. Having realized that this is going to be a long journey and rushing into things may not help, I am now gaining patience and perspective, and hope to make the most of the remaining time of my first year.

Rotations are a great way to learn about a lab and get involved in the nitty-gritty of research. I was warned at the beginning by a few seniors that I would either love a lab or reject it within the first few weeks of the rotation. Mind you – this has nothing to do with the science pursued in the lab (one wouldn’t decide to rotate in a lab if they didn’t find the research interesting in the first place). This is more about getting comfortable with the way a lab functions and deciding if the environment is a good fit for you. An eight-week lab rotation is really like an eight-week long interview with a potential PI and the lab! It is essential to identify the kind of relationship you foresee having with your advisor for the next couple of years (and beyond). This is perhaps one of the most important aspects of a rotation for me, next to the research work. A good mentor-mentee relationship can go a long way and can be extremely beneficial to one’s academic/professional career. I prefer having an open channel of communication with my mentor and learn as much as possible from him/her.

Not all graduate programs require laboratory rotations. Many departments or programs accept or reject students simply based on their application and/or an interview. In the UK for example, students are recruited to work on specific projects and grants as a part of their Ph.D. for the time period of around 3 years. This may not benefit the candidates who wish to propose their own ideas and develop their own thesis based on their individual research interests. In the US, for most graduate programs in the life sciences (mainly biology and chemistry), the average time for graduation is around 5-6 years. I believe that the freedom and independence of this system trump the short graduation time of the other systems. Although I am certain that both sides have their set of merits and demerits, at the end of the day, the journey is unique to each one of us and what we make of the experience matters the most.

Chasing cancer cells

Glioblastoma_-_MR_sagittal_with_contrast
Glioblastoma (astrocytoma) WHO grade IV – MRI sagittal view, post contrast. 15-year-old boy. Image courtesy: Wikimedia commons

Glioblastoma multiforme (GBM) is one of the most invasive forms of malignant brain tumors. By the time the tumor is removed from a region in the brain, the cancer cells rapidly metastasize and spread throughout the brain. Common treatment procedures such as chemotherapy and radiotherapy are not completely effective due to the aggressive nature of the tumor invasion. Therefore, many treatments also target the migratory properties of the tumor cells. Several proteins (focal adhesion kinase, paxillin, vinculin) are over-expressed in the extracellular matrix of the tumor microenvironment and help the GBM cells proliferate through the brain tissues. A treatment approach is to target these proteins and hopefully prevent -or at least reduce- the tumor cell invasion.

Studying this type of a cancer model is tricky. Most of the work that has been done in the traditional 2-dimensional cell culture environment cannot be translated into the 3-dimensional environment of the brain. We need a system that mimics the brain to realistically model the tumor cell growth and migration. As a part of my third rotation, I have been investigating the migration characteristics of GBM cells in tissue-engineered, 3-dimensional cell culture matrices that mimic the brain environment. The cells are grown in a collagen matrix containing components of the brain extracellular matrix (hyaluronan, astrocytes, etcetera) and the tumor cell migration is studied by tracking the focal adhesion proteins. However, this is not easy. Cancer cells have shown to modify their migratory patterns based on the physical conditions of the tumor microenvironment (Herrera-Perrez et al. 2015 Tissue Engineering Part A). This makes it more difficult to target the adhesion receptors to ultimately inhibit tumor invasion. It is also challenging to prevent the disruption of the cross-talk between the targeted receptor protein and other important signaling molecules during evaluation of the treatment procedures. Overall, new innovative strategies are required that focus on the diversity and adaptability of tumor cell invasion and migration.