I chose the in-class assignments to be a part of this file because they were really interesting cases to discuss with my group mates and it really forced me to learn but also defend my position to my groupmates if I thought I was right. So because of this I liked the in-class assignments and they are included. I chose the “If I were a developmental biologist/geneticist” as the fourth assignment because it forced me to think as well but also because I can’t think of any other assignment we did. I wasn’t there when the January 19th assignment took place in class so I couldn’t include it.
Archives: Assignments
BIOL 463 N&V presentation
BIOL 463 NandV presentation – Anik
Please click the link to see the slide I used to do my New and Views presentation. It was really difficult and apparently I was way above the time alloted 🙁
The Hippo effector YAP promotes resistance to RAF- and MEK-targeted cancer therapies
Increased activation of the RAF-MEK-ERK signaling pathway (also known as the MAPK signaling pathway) is a common hallmark of many human cancers. This is usually due to activating mutations in the RAF (serine-threonine protein kinase) or RAS (small GTPase) genes. MAPK-pathway targeted therapies such as BRAF and MEK inhibitors have been developed to counteract these cancers. However, these therapies are only transiently effective due to resistance. Thus, there is a need to identify the molecular targets which provide resistance to BRAF and MEK inhibitors within cancer cells. This will lead to the development of new therapeutic strategies which can enhance the treatment response.
To determine the molecular targets which regulate the response against RAF and MEK inhibitors, the authors devised a short hair-pin RNA (shRNA) screen in human non-small cell lung carcinoma (NSCLC) cells. These cells express an endogenous BRAF V600E (valine to glutamate substitution at position 600) allele. Their aim was to identify genes which, when inhibited, would display an enhanced response to the BRAF inhibitor Vermurafenib; this would indicate that the gene’s normal function is to provide resistance against the BRAF inhibitor. The best candidate from the shRNA screen was the Hippo signaling pathway effector YAP1. Based on this result, the authors hypothesized that YAP inhibition may increase the efficacy of RAF-targeted therapy.
Independent shRNA knockdown of YAP1 in HCC364 (NSCLC cell line with BRAF V600E allele) cells resulted in increased sensitivity of these cells to both Vermurafenib and the MEK inhibitor Trametinib. Stable overexpression of YAP1 in HCC364 cells resulted in substantially decreased sensitivity to both Vermurafenib and Trametinib, which confirmed the initial screening results.
To determine whether the YAP suppression effect was only limited to BRAF V600E forms of cancer, the authors silenced the YAP1 gene in Cal-12T human NSCLC cells which have normal MEK-ERK activation but encodes a BRAF with a G466V (glycine to valine) substitution. This cell line also displayed enhanced efficacy to Vermurafenib and Trametinib, which shows that YAP1 suppression can be a target to counteract RAF and MEK inhibitor resistance in human NSCLC.
Next, the authors wanted to investigate whether YAP1 regulates the response against inhibition of BRAF signaling in BRAF in other BRAF mutation-driven cancers such as human melanoma, colon, and thyroid cancer. YAP1 suppression increased the efficacy of both Vermurafenib and Trametinib in A2058/WM793 human melanoma cell lines, HT29/WiDr colon cancer cell lines, and KHM-5M and HTC-C3 thyroid cancer cell lines. This indicates that YAP1 suppression can be broadly used as a target in a wide spectrum of BRAF mutant cancers.
RAS mutant cancers work partly through MEK-ERK signalling. There is no effective therapy against this type of cancer, with MEK inhibitors providing variable results. The authors determined that YAP1 suppression also enhanced the sensitivity of multiple KRAS and NRAS mutant human NSCLC, melanoma, and pancreatic adenocarcinoma cell lines to Trametinib. This indicates that YAP1 suppression in conjunction with MEK inhibitors could be an effective therapeutic strategy in patients with mutant RAS.
The authors then wanted to determine the mechanism by which YAP regulates the response against RAF- and MEK-targeted therapy. Previous work had indicated that YAP regulates apoptosis; the authors postulated that YAP might regulate the expression of an anti-apoptotic factor such as BCL-xL to provide resistance against RAF and MEK inhibitors. YAP1 suppression indeed led to a decrease in BCL-xL levels; overexpression of BCL-xL rescued the effect of YAP1 silencing on the response to RAF and MEK inhibitors in HCC364 cells. Pharmacological BCL-xL inhibition using the drug Navitoclax and Tw37 led to increased efficacy of treatment with RAF and MEK inhibitors in several NSCLC, melanoma, and colon cancer models. Overall, these data indicate that YAP, via BCL-xL, acts as a signaling mechanism alongside the MAPK signaling pathway to promote resistance to RAF and MEK inhibitors. This research may lead to a new therapeutic strategy to enhance the efficacy of RAF and MEK inhibitors for patients suffering from a broad range of BRAF-and RAS-mutant cancers.
Lin, L., Sabnis, A.J, Chan, E… Bivona, T.G. (2015). The Hippo effector YAP promotes resistance to RAF-and MEK-targeted cancer therapies. Nature Genetics, 47, 250-256. doi:10.1038/ng.3218
March 9th in-class assignment: Studying SRS and BWS patients
Assignment #3
Monday March 9th in class assignment _edit
Please click the link to see the assignment. Thanks 🙂
March 2nd – In class assignment: The mystery of the lacZ transgene
Monday March 2nd in-class “assignment”: the mystery of the lacZ transgene
Assignment #2
Monday March 2nd-in class assignment (1)
Click the link to see the assignment. Thanks 🙂
HW 1: If I was a developmental biologist/geneticist…
This assignment is a very interesting and made me think about what problems I would be interested in solving. It got my mind working…to the point where I was dreaming about the questions whilst sleeping. You know something has really gotten to your core if you are dreaming about it. So here are some of the questions that really pique my interest and maybe your interest as well. Maybe one day we can collaborate and solve these problems once and for all.
- The dystrophin (DMD) gene codes for a cytoplasmic protein which forms a complex with other proteins to help attach the muscle fiber cell membrane to the extracellular matrix (ECM). Defects in these interactions to form complexes or deficiencies in expression for these muscle proteins can result in various forms of muscle dystrophy. It would be interesting to determine whether these genes share common cis-regulatory elements. It’s possible that a transcription factor or a group of transcription factors regulate this gene set by interacting with the same regulatory element. It’s also possible that these proteins share the same functional domain that allows them to interact with one another to form a complex. It would be interesting to elucidate further upon this mechanism.
2. Asthma is a chronic inflammatory disease that has increased in incidence significantly in the last few decades. It’s been hypothesized that the increased rate of asthma is due to increased epigenetically-derived changes being passed down to future generations. It would be really interesting to determine what sorts of epigenetic changes could be responsible for higher risk of asthma. Personally, I would find it interesting if some epigenetic markers could be directly attributed to a someone becoming asthmatic.
I really find the muscular dystrophy problem interesting as it is a condition that has huge adverse impacts on a person’s life. I have had the chance to volunteer with events that deal with Duchene’s Muscular Dystrophy and seeing firsthand what muscular dystrophy can do makes me really want to solve the problem.
If I was lucky enough to determine that a transcription factor or a group of transcription factors is responsible for directing dystrophin and other proteins to form complexes, it would be huge in the field of developmental genetics just as another example that highlights how much regulation is required in development to get to where we are as adults. The question I posed is one small step, which if solved, can lead to further developments; it may lead to a flurry of research from different labs . Maybe one day it can lead to actually being able to prevent muscular dystrophy (dare to dream), which would be an amazing feat. If this feat is possible, I’m sure it would make a big impact to the community, especially to people who may be affected by muscular dystrophy or knows someone who has been affected by this condition. There is a possibility that we can help people from going through this limiting genetic condition and possibly improve their quality of life, which is a great reward.
So this is my first stab at developing some questions that I would like to investigate. I look forward to the day that I can either solve this issue entirely or make some significant contribution to this issue with my research work.