Week 8

During this last week, I was able to complete my primary research project for the summer, which was to elucidate the genetic basis for resistance to a novel proteasome inhibitor compound in plasmodium falciparum parasites.  Through sequencing of isolated proteasome beta subunit genes, I was able to identify several point mutations in resistant parasite strains that may be responsible for altering the conformational state of the proteasome and thus prevent the proteasome inhibitor from binding.  The next step will be to use CRISPR to induce the identified point mutations in wild type parasite strains and subsequently assessing for the induction of resistance.  Ultimately, knowledge accrued from these studies will facilitate the development of next generation anti-malarial compounds, for which there is a pressing need as current drugs such as artemisinin are becoming less and less effective. 

I also started a mini-project my last week which involved mimicking the mechanical filtration of the spleen in vitro using a matrix of metallic microspheres.  While normal red blood cells are highly deformable, red blood cells infected with plasmodium falciparum decrease in deformability as parasites mature.  This change is believed to be caused by interactions between parasite secreted proteins and the cellular cytoskeleton.  In vivo, the inter-endothelial slits of the spleen trap red blood cells with low deformability, which is the mechanism by which senescent red blood cells are removed from circulation.  This mechanism can be recapitulated in vitro using a matrix of microspheres of sizes 5-25 microns.  Red blood cells flowing through the matrix are forced to undergo dumbbell shaped deformations in the inter-sphere spaces, which is the same type of deformation that occurs during splenic filtration.  In this manner, normal red blood cells can pass through the matrix while red blood cells filled with late stage parasites have a high probability of being retained.  This filtration technique can be used as an alternative to sorbitol-based parasite stage synchronization and can also be used to study other hemolytic diseases such as babesia.  Preliminary experiments conducted using the set-up shown below showed that the microsphere matrix does retain a significant amount of late stage parasite containing red blood cells.  This was a good starting point and Dr. Kirkman’s group will continue to improve and optimize the process.

Filtration set-up

Metallic microsphere layer on pipette filter

Filtration in action

Overall, my immersion term has been an amazing experience and I had a blast spending the summer in New York City.  It was great having the opportunity to interact with clinicians, residents, and fellows and also just being able to enjoy activities the city has to offer during my downtime.  I was able to pick up some molecular biology knowledge through my research and the clinical shadowing portion has granted me extensive insight into how infectious disease care is implemented when an advanced medical infrastructure is available.  Hopefully, I’ll be able to use this knowledge to brainstorm clever ways to bring about equivalent levels of care in low-resource settings for my PhD work.    

Week 8: New York, New York

Bittersweet is the perfect oxymoron to describe the end of the immersion term. These past weeks have been nothing short of incredible. I strongly believe I was able to meet my goals of better understanding the process of care of cancer patients, particularly lymphoma patients, and of creating a more clinically translational aspect of my PhD project. However, it still feels like I have so much more to learn.

In my final week, I sought to maximize both my clinical hours and produced data. In the clinic, I was able to go into the OR and see an IORT - intraoperative radiation therapy- procedure on a patient receiving a lumpectomy. Through this procedure, after the tumor is removed following the usual lumpectomy procedure, the radiation probe is inserted to deliver radiation to the previous tumor site in hopes of killing microscopic cancerous remains. This intraoperative delivery mirrors the purpose of external beam radiation, which I have witnessed through my past few weeks in the radiation oncology department. With similar purposes and efficacy, IORT can be preferred by patients to prevent skin damage and for the simple matter of convenience. The daily struggle of a cancer patient to simply receive patient, as is the case for external radiation, is often overlooked for the sake of the final diagnosis. Through IORT, a patient is able to receive the best of both worlds - health and convenience. For further information,  please follow this link to watch a video of the procedure. 

In the lab, I finished producing data regarding the growth capacity and differential drug response for the vitally infected and non-infected DLBCL and BL organoids in the context of various integrin ligands. Although the analysis of the data is ongoing, I'm thrilled to report that the project will be continued as a collaboration. Extracting lymphocytes from tonsils also proves to be the second project that will be continued as a collaboration.

Overall, this past week serves as a microcosm of the entire immersion term. It has been a whirlwind of clinical perspective and immediately translating what I learned into the lab. Set against the backdrop of the city that never sleeps, the immersion program was the fast-paced, jumpstart I needed to further motivate me to move forward in my research and to help me understand that my long-term goal of translating my research to the clinic can come sooner than later. 

Week 7 and 8: This is the End, Beautiful Friend

These weeks have been a grind of arranging for patient urine samples, processing them into single cell suspensions, and then assessing cell concentration and viability in the hopes of meeting the quality control conditions for Drop-seq processing. The high sample to sample variability has made this quite challenging, but I was finally able to submit a sample. It remains to be seen if the cDNA library generated meets QC for sequencing.

I was also able to work with a graduate student who set up the Drop-seq system for the genomics facility and learn some of the subtleties in the protocol. This was incredibly beneficial for me as I finish setting up my own Drop-seq in my lab.

Unfortunately, I ended up not observing an actual transplantation surgery, but this is probably for the best as the last time I was in an operating room I ended up passing out. My other experiences working in the research lab, shadowing in the clinic, sitting in on consults and grand rounds, and observing inpatient rounds have made this clinical immersion more than worthwhile.

Until next time, New York.

Coming Back to reality!

It is time to go back to Ithaca and return to our original research and environment. Although it feels good to go back home and retake the routine, it is also hard to leave this place that was full of new experiences, learning, and a lot of fun. During my last week in NYC, I concentrated my last days on doing final research about the two approved HIFU technologies to base my report in a formal review and comparison for both of the methods. Since the technology is fairly new (not approved until 2015), there is not enough credible research to follow a formal publishable review, but it is fair enough to produce a good paper. I attended the last board meeting in which I learned uncountable material and a lot of interesting people working with cancer too but from a very different direction. I am so grateful to have the opportunity to live this experience and to work with Dr. Hu in such an amazing field.

On the other side, I also tried to enjoy my last days at NYC. I finally visited the 9/11 memorial and museum which was on my list since the beginning and was one of the couple places I had left to visit. I visited high line, and finally attended a Broadway show. Then, with all of these experiences, I felt like I got everything I wanted from NYC and I will miss this city a lot!!. Mentors/ students final dinner was wonderful, we had such a good time meeting the mentors and sharing our summer experiences. It was such a great end for this excellent experience!