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Hypoxia

Submitted by abnguyen on Thu, 03/23/2017 - 23:07

For this project our group will continue using non-small cell lung cancer.  NSCLC metastasizes to the adrenal gland, bone, brain, liver and the other lung.  For a tumor cell to grow and expand into other cells it needs a stable blood supply and a hypoxic environment.  In tumor cells, hypoxia is regulated by hypoxia-induced factor 1 alpha.  HIF1α can be translocated to the nucleus, bind with HIF1β and increase transcription of vascular endothelial growth factor (VEGF).  VEGF leads to the formation of more blood vessels which supply the tumor cells with more nutrients. 

            Hypoxia also stimulates growth factors such as IGF and EGF which inhibit apoptosis.  Cells can also escape death in the hypoxic areas by reducing cell division and lowering their metabolism.  Tumor cells also have their own level of selection occurring.  After generations of cell formation, the cells in the hypoxic areas are the ones that can survive hypoxia based apoptosis.  These tumors will have a more aggressive phenotype and be significantly harder to treat than their earlier stage counterparts.

            HIF1α can initiate apoptosis but can be overwhelmed in the hypoxic environment.  HIF1α has the ability to release proapoptotic proteins such as BNIP3 to stabilize p53 and start the process of apoptosis.  However, during hypoxia, IAP-2, an antiapoptotic protein is released. This neutralizes BNIP3 and other proapoptotic protein such as BAX are down regulated.  Our goal is to reduce the level of hypoxia in the environment for HIF1α to perform apoptosis while IAP-2 cannot function.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1770458/

https://www.cancer.gov/types/metastatic-cancer

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4821869/

Day back at work

Submitted by abnguyen on Tue, 03/14/2017 - 21:53

Yesterday at work I created a few sleeves of media.  The media created were TSB and FTM.  To start, I filled up beakers with .5L of milli-Q water and then added roughly 15 g of either TSB or FTM powder to each beaker.  These beakers were then put into autoclaves for an hour of sterility.  After an hour these beakers were moved to a hot water bath to keep warm.  While the beakers were sitting in the hot water bath, I cleaned a biological safety cabinat and prepared it for pouring.  Next I made sure that the safety cabinet was up to standards and set up a few sleeves of clean media plates inside.  The plates were poured to have around 25 mL of media each.  The media plates were then left to rest and solidify while the started the next batch of pouring.  Once solidified I stacked up the plates in towers of 20 and wrapped it up and placed them on the bench of the person who requested media plates.  In total I poured 80 plates and the total process took around 3 hours.  Yesterday at work I created a few sleeves of media.  The media created were TSB and FTM.  To start, I filled up beakers with .5L of milli-Q water and then added roughly 15 g of either TSB or FTM powder to each beaker.  These beakers were then put into autoclaves for an hour of sterility.  After an hour these beakers were moved to a hot water bath to keep warm.  While the beakers were sitting in the hot water bath, I cleaned a biological safety cabinat and prepared it for pouring.  Next I made sure that the safety cabinet was up to standards and set up a few sleeves of clean media plates inside.  The plates were poured to have around 25 mL of media each.  The media plates were then left to rest and solidify while the started the next batch of pouring.  Once solidified I stacked up the plates in towers of 20 and wrapped it up and placed them on the bench of the person who requested media plates.  In total I poured 80 plates and the total process took around 3 hours.  

Review article report

Submitted by abnguyen on Mon, 03/06/2017 - 21:41

The tumor microenvironment system regulates overall tumor growth, homeostasis and progression.  It also directs tumor development so that tissues can be altered at the structural, histopathological and molecular levels.  TME can be used for inflammation and wound healing if we can somehow control this cancer feature.  The cells from distant tissues can be mobilized to help such as the bone marrow and spleen tissue.  For the bone marrow factors, it is effected by CXCL12, CXCR4, cytokine G-CSF.  When mice were induced with tumors, G-CSF moved beneficial tumor cells from the bone marrow into the blood circulation and towards the tumor.  For this system, an option is bone marrow transplant, the infected bone marrow is removed and disposed of while new pure bone marrow can fill in the removed areas.

The angiogenesis is one of the key systems in keeping tumors alive.  This the creation of new blood vessels that lead directly into the tumor in order to provide the adequate amount of nutrients.  Some of the pathways used are the vascular endothelial growth factor (VGEF), placental growth factor (PIGF), and VEGFR-1.  Cancer-associated fibroblasts (CAFs) are abundant in many tumor microenvironments, and linked to angiogenesis.  CAFs release CXCL12 to mobilize stem cells from the bone marrow to assist the tumor and this triggers angiogenesis.  There are several drugs that specially inhibit VEGF that can be used in combination with several other treatments and surgeries. 

The microvesicles movement system is used to help the primary tumor communicate with distant tumors.  These vesicles carry lipids, proteins, mRNAs and miRNAs.  These messengers can also travel into normally functioning cells and alter their behavior to better support the tumor cells.  The pathways and genes responsible for distal tumor messaging include VEGF-A, EGF-beta, and TNF alpha.  For lung cancer, the tumor mobilizing pathways involve MCP1, and VCAN.  Drugs can be designed to pop the vesicles before they reach their destination but this could cause a problem of the harmful material inside of the vesicles to inhabit other cells.

McAllister SS. Weinberg RA. The tumour-induced systemic environment as a critical regulator of cancer progression and metastasis .  Nature Cell Biology.  <http://www.nature.com/ncb/journal/v16/n8/abs/ncb3015.html>.  Accessed 2017 Mar 6

Journal: Reading Response

Submitted by abnguyen on Sun, 03/05/2017 - 23:11

For my Advanced Genetics class, I had to read an article and respond to it.  This is my response below.

After reading this article I found it interesting that CRISPR is already being used for experiments like this one.  It did not surprise me that removing transcriptional factors also hindered the expression of certain genes.  However, I was surprised that this retrovirus spanned multiple mammalian lineages.  This is another branch in the evolutionary tree that links us closer to other species.  One question I have about this article is, if these endogenous retroviruses started out as virus, isn't there a chance that the virus used reverse transcriptase to incorporate itself into our genome?

Chuong EB. Elde NC. Feschotte C.  Regulatory evolution of innate immunity through co-option of endogenous retroviruses.  Science.  <http://science.sciencemag.org.silk.library.umass.edu/content/351/6277/10....  Accessed 2017 Mar 3. 

Journal: Methods Project Introduction

Submitted by abnguyen on Fri, 03/03/2017 - 11:23

The purpose of this project was to learn how a methods section of a scientific manuscript were created and the amount of thorough description needed in order for the experiment to be accurately recreated.  For this project, a methods section was created and followed by another student who was doing their own version of this project simultaneously.  The methods were to describe step by step how an individual came across a section of moss and to describe how a multi figure panel was to be created that reflected the results.  However, some restrictions were put in place to narrow the search for moss.  Some conditions required the moss to be located on the Umass campus and that it must include gametophytes and sporophytes.  Sporophytes are the part of the moss that reproduce asexually; they can be seen at the tip of moss.  In the winter weather sporophytes have an orange coloration and look as if they are dead but this is a cause of the cold weather.  Gametophytes are the part of the moss that can reproduce sexually.  These can be identified as the main body of the moss.  

    In addition to finding viable moss in this weather condition, a three panel figure was to be created by both the original author and by a random peer.  The panels should include the location the moss was found usually via a close up picture of the campus map with a circled location to narrow down the search.  The other panels should contain the moss itself with the sporophytes and gametophytes clearly labeled and a picture of the tree or plant off of which the moss was taken.  

    Since this project had to be created by another peer with a different schedule from me, I decided to choose a place where time was not a restriction.  Many greenhouses on campus have strict visiting hours and since I didn’t know my peers daily schedule I chose a place which had no time constraint, a tree in the middle of campus.  Other important factors that impacted this project were weather conditions, since it could snow again and cover up the moss I had chosen and the specificity of the directions given.  Since this was a tree outside, there is a possibility that multiple patches of moss can call this tree home and skew the comparisons if two different patches were photographed.

Moss Experiment

Submitted by abnguyen on Fri, 03/03/2017 - 09:49

Finding a peer reviewed article about moss was a slight challenge.  The main issue was that the first few hits I got when I google searched "moss experiment peer review" led me to articles from a man with the last name "Moss" talking about gender bias in science.  But after a few refined searches I came across an experiment performed on moss.  

In this experiment, moss samples were placed in petri dishes with varying amounts of chemicals for 7 days.  After the 7 days the dishes were photographed and analyzed to see how much nitric oxide gas and nitrate reductase the moss had accumulated over the experiment time frame.  The levels of chemicals were tested with electron paramagnetic resonance (EPR) and confocal laser scanning microscopy (CLSM).  

Medina-Andres R. Solano-Peralta A. Saucedo-Vazques JP. Napsucialy-Mendivil S. Pimentel-Cabrera JA. Sosa-Torres ME. Dubrovsky JG. Lira-Ruan V. 2015 Mar 5. The Nitric Oxide Production in the Moss Physcomitrella patens Is Mediated by Nitrate Reductase. <http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0119400>. Accessed 2017 Mar 3.

Perfect Paragraph: T790M mutations

Submitted by abnguyen on Mon, 02/27/2017 - 00:12

Since T790M is one of the most common forms of cancer resistant mutations in NSCLC (non small cell lung cancer), there are drugs available that combats the new strain. Osimertinib or Tagrisso, is a third generation EGFR-TKI (epidermal growth factor receptor tyrosine kinase inhibitor) drug developed by AstraZeneca Pharmaceuticals that specifically fights T790M mutations.  This drug was recently pushed into further testing so there is not much known about it's effectiveness but some results have come back positive.  Tagrisso is predicted to induce cell death and inhibit tumor growth in EGFR-overexpressed tumor cells.  Although this drug is designed for T790M it also works for the common EGFR mutations present in early stage of NSCLC so it could possibly be administered early on in the treatment process.

Journal: More cancer 1 project

Submitted by abnguyen on Mon, 02/27/2017 - 00:04

Once the original treatments of Erlotinib fail to show signs of improvement it can be assumed that EGFR has evolved to become more resilient to the administered drugs.  This usually occurs after 11 months of being on Erlotinib.  It can be best assumed that EGFR has evolved into a mutant variation called T790M but to be certain, a sample of the resilient cells should be extracted and tested for the mutation through a biopsy.  The biopsy can be a traditional surgery or be done by a new ctDNA testing.  ctDNA testing requires a small vial of blood and no operation.  The plasma in the blood will be analyzed with up to 94% accuracy if the patient does in fact have the T790M mutation.

However, there are ways to prevent EGFR from evolving further resistances.  MK-2206 when combined with erlotinib has been known to restore activity of erlotinib.  We also plan to add MEK inhibitors in our drug cocktail.  The main purpose of MEK inhibitors is to prevent them from sending signals downstream that trigger evolution and adaptive resistances.  In theory, MEK inhibition alongside MK-2206 addition, T790M should not be able to form and cause more problems.  

MK-2206 is an allosteric Akt inhibitor that has been combined with other anti-cancer drugs to show positive results.  Erlotinib has also been know to act synergistically with MK-2206.  Some forms of Akt can evolve immunity to Erlotinib but still be vulnerable to MK-2206 inhibitions.  When tested in live organisms, MK-2206 has demonstrated significantly more tumor suppression in combination with other drugs than when administered alone.  

The most promising downstream component of our growth pathway that we can attack is MEK. The two drugs at the forefront of MEK inhibition are selumetinib and trametinib.  Trametinib is a selective allosteric inhibitor of MEK1 and MEK2 while selumetinib is a highly selective non-ATP competitive inhibitor of MEK1 and MEK2. MEK1 and MEK2 triggers the activation of ERK1 and ERK2 which eventually leads to proliferation, survival and resistance.  With the addition of the two inhibitors, MEK1 and MEK2 can be disabled before reaching ERK1 and ERK2.  MEK1/2 inhibitors have been shown to be flexible with what drugs they are combined with.  The inhibitors are usually used along with chemotherapy and have shown positive results.  

One of the main goals is to prevent the cancer from adapting and developing future resistances.  ERK1 and ERK2 are the most notable proteins responsible for drug resistances.  Located further downstream are the exact proteins that cause further cancer mutations but attacking ERK1 and ERK2 will prevent the signals from going downstream in the first place.  With trametinib and selumetinib circulating a patient’s system, ERK1 and ERK2 will never have a chance to mutate with their previous activation signals nullified.

 

Sources 

http://arup.utah.edu/media/shortTopics/spot_bronner_t790m/t790m_video.html

http://clincancerres.aacrjournals.org/content/early/2015/06/23/1078-0432...

https://www.ncbi.nlm.nih.gov/pubmed/25257766

Manuscript Guidelines

Submitted by abnguyen on Thu, 02/23/2017 - 22:31

The journal that I picked is called "Genes, Chromosomes and Cancer".  The link to the guidelines can be viewed by this link http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1098-2264/homepage/ForAuthors.html.  Each article is usually in the same format that follows the order of title, abstract, key words, materials and methods, and finally references.  The title is no longer than 45 characters and gives a brief descriptive preview.  An abstract is a single paragraph with no more than 250 words that is a condensed summary of the journal.  Key words are the critically important words that raise visibility of the journal.  The materials and methods section should be described in sufficient enough detail that the experiment can be recreated.  Finally, 

Journal 9: Drugs used for cancer and their side effects

Submitted by abnguyen on Tue, 02/21/2017 - 01:04

Since T790M is one of the most common forms of cancer resistant mutations there is a drug available that combats the new strain. Osimertinib or Tagrisso, is a third generation EGFR TKI drug developed by AstraZeneca Pharmaceuticals that specifically fights T790M mutations.  This drug was recently pushed into further testing so there is not much confirmed public data about the outcomes yet.  Tagrisso is predicted to induce cell death and inhibit tumor growth in EGFR-overexpressed tumor expressed cells.  Although this drug is designed for T790M it also works for the common EGFR mutations present in early stage of NSCLC so it could possible be administered early on in the treatment process.

  

 A side growth process that is commonly abused in cancer cells is the forced creation of new and specific blood vessels, angiogenesis.  Some drugs that have been created specifically to combat angiogenesis in NSCLC are Bevacizumab (Avastin) and Ramucirumab (Cyramza).  

    

Avastin is a drug that interferes with cancer growth and can help slow down stage 4, spreading to non cancerous cells.  Avastin is best described as a tumor starving cancer treatment.  It is designed to block vascular endothelial growth factor (VEGF), a protein that creates new blood vessels.  Avastin is main used for nonsquamous cells and enter the body after tumors have been detected. Chemotherapy is used to attack the cell while Avastin is used to attack the blood supply of the cell and starve it.  It is recommended to be used along with carboplatin and paclitaxel.  

 

Cyramza is also an anti-angiogenic drugs similar to Avastin.  This drug is used to block VEGF in squamous and nonsquamous patients.  Both types of patients had an increased average of overall survival of about 1 month compared to patients that were given a placebo.

 

Known common side effects of Tagrisso can include anxiety, irregular heartbeats, slurred speech, vision changes, sudden headaches and sudden weakness or numbness.  Less than 1% of patients who took this drug suffered fatal reactions from lung disease and cerebral hemorrahages.  This drug hasn’t been administered along with other cancer prevention drugs so there is no knowledge of what the possible outcomes could be.

 

Avastin has a large laundry list of possible side effects. The most common ones are easier to bleed, dangerously high blood pressure, fever, chills, vomiting and swollen body parts.  Some other drugs have been known to interact with Avastin such as prescriptions, over the counter drugs, vitamins and herbal products.  Avastin has been used with other cancer medication with success so putting Avastin in our drug cocktail will allow for more treatment than harm.

 

https://www.cancer.org/cancer/non-small-cell-lung-cancer/treating/target...

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