Difference between revisions of "Team:MIT/Experiments/miRNA"

 
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<h1 style="color:#ff9715; text-align: center; font-size: 40px; line-height: 40px;">microRNA: Detecting a Cell Specific Profile</h1>
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<h1 style="color:#000000; background-color:#FF9733; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center; font-family: Trebuchet MS"> How can we detect endometriosis using miRNA? </h1>   
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<h1 style="color:#ffffff; background-color:#ff9715; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center"> How can we detect endometriosis using microRNA? </h1>   
 
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<h2 style="color:#FF9733; text-decoration:underline; font-family: Trebuchet MS;"> What is miRNA?</h2>
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<h2 style="color:#ff9715; text-decoration:underline"> What is miRNA?</h2>
 
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For those who are not familiar with miRNA, miRNA are small units of RNA <b>found in all mammalian cells</b> and play a regular role in <b>gene regulation</b>. miRNA is single stranded and only about 20 nucleotides long. With the help of other proteins(which form what is called the 'RISC complex'), miRNA is guided to a complementary part on the mRNA (miRNA target site) where miRNA binds and cleaves messenger RNA. This inhibits gene expression post transcriptionally.  
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microRNA (miRNA) are small units of RNA <b>found in all mammalian cells</b> and play a regular role in <b>gene regulation</b>. miRNA is single stranded and only about 20 nucleotides long. miRNA forms a RNA-induced silencing complex (RISC) with other proteins and guides RISC to the complementary sequence on the mRNA (the miRNA target site). RISC cleaves messenger RNA and inhibits gene expression post transcriptionally.  
 
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<img src = "https://static.igem.org/mediawiki/2016/7/70/T--MIT--miRNA_profile.PNG" style = 'padding: 5px 10px 5x 10px; width: 400px; height = 400px; float: right; border:10px;'>
 
<img src = "https://static.igem.org/mediawiki/2016/7/70/T--MIT--miRNA_profile.PNG" style = 'padding: 5px 10px 5x 10px; width: 400px; height = 400px; float: right; border:10px;'>
 
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<h2 style="color:#FF9733; text-decoration:underline; font-family: Trebuchet MS;"> Why is miRNA a good biomarker?</h2>
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<h2 style="color:#ff9715; text-decoration:underline"> Why is miRNA a good biomarker?</h2>
 
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There are hundreds of different miRNAs that can make up a specific cell's miRNA profile. The profile and activity of miRNA varies between different <b>cell types </b> and different <b>cells states</b>.This makes it is possible to tell the difference between cells from the uterus and liver, and the difference between healthy and diseased cells based on miRNA profiles.
 
There are hundreds of different miRNAs that can make up a specific cell's miRNA profile. The profile and activity of miRNA varies between different <b>cell types </b> and different <b>cells states</b>.This makes it is possible to tell the difference between cells from the uterus and liver, and the difference between healthy and diseased cells based on miRNA profiles.
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<h2 style="color:#FF9733; text-decoration:underline; font-family: Trebuchet MS;"> What is the miRNA profile of Endometriosis?</h2>
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<h2 style="color:#ff9715; text-decoration:underline"> What is the miRNA profile of Endometriosis?</h2>
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Cells from the uterus (referred to as 'eutopic endometiotic cells') of women with endometriosis have been found to have dysregulated miRNA in comparison to cells from the uterus of women who do not have endometriosis (referred to as 'eutopic endometrial cells')[]. In order to study the uses of these miRNAs in our circuit, eight candidates were chosen based on fold difference in miRNA level between the the endometrial biopsy from women with and without endometriosis. The eight candidates are shown in the table below:
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<img src = "https://static.igem.org/mediawiki/2016/b/bb/T--MIT--miRNA_candidates.PNG" style = 'padding: 5px'; width: 250px; height = 250px; float: right; border:5px;'></p>
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<p>Endometrial cells from women with endometriosis have been found to have dysregulated miRNA compared to endometrial cells from women who do not have endometriosis.(<a href=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2744474/>1,</a><a href=http://molehr.oxfordjournals.org/content/13/11/797.full>2,</a><a href=https://www.ncbi.nlm.nih.gov/pubmed/26370665>3</a>). In order to study the uses of these miRNAs in our circuit, eight candidates were chosen based on fold difference in miRNA level between the the endometrial biopsy from women with and without endometriosis. The eight candidates are shown in the table to the right:</p>
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<img src = "https://static.igem.org/mediawiki/2016/7/75/T--MIT--endometriosis_profile.PNG" style = 'padding: 5px 10px 5x 10px;        width: 400px; height = 400px; float: left; border:10px;'>
 
<img src = "https://static.igem.org/mediawiki/2016/7/75/T--MIT--endometriosis_profile.PNG" style = 'padding: 5px 10px 5x 10px;        width: 400px; height = 400px; float: left; border:10px;'>
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<figcaption><i> Figure Burney et. al 2009 </i> One of the graphs observed in order to choose miRNA candidates to characterize. The three miRNAs, miR-34c-5p, miR-9, miR-34-b are shown to be downregulated and have a significant fold difference (p*= p**=) compared to their respective levels in healthy eutopic endometrial cells, miR-7. These measurements were from an endometrial biopsy and taken using miRNA microarray, similar to the other sources we also studied.</figcaption>
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<figcaption><a href=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2744474/>(1)</a> One of the graphs observed in order to choose miRNA candidates to characterize. The three miRNAs, miR-34c-5p, miR-9, miR-34-b are shown to be downregulated and have a significant fold difference (*p=0.05 **p<0.05, error bars= standard error of mean) compared to their respective levels in healthy eutopic endometrial cells. These measurements were from an endometrial biopsy and taken using quantitative polymerase chain reaction (qPCR), similar to the other sources we also studied.</figcaption>
 
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<b> Eight miRNAs candidates were chosen to be characterized in order to determine their gene regulatory ability for the purposes of increasing the specificity of our circuit.</b>
 
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<h1 style="color:#000000; background-color:#FF9733; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center; font-family: Trebuchet MS"> How can our circuit sense miRNA activity? </h1>   
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<h1 style="color:#ffffff; background-color:#ff9715; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center"> How can our circuit sense miRNA activity? </h1>   
  
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<img src = "https://static.igem.org/mediawiki/2016/0/0e/T--MIT--miRNA_targetsites2.PNG" style = 'padding: 5px 10px 5x 10px; width: 500px; height = 500px; float: right; border:10px;'>
  
 
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Our circuit utilizes the natural function of miRNA to regulate gene expression. Depending on the miRNA activity in a cell, different levels of our desired gene will be expressed. This allows our circuit to produce a differential output depending on whether the cell has dysregulated miRNA. This is achieved by attaching 4 tandem sites complementary to the affected miRNA following a gene of interest. This is called the miRNA target site (miRNA-ts).
 
Our circuit utilizes the natural function of miRNA to regulate gene expression. Depending on the miRNA activity in a cell, different levels of our desired gene will be expressed. This allows our circuit to produce a differential output depending on whether the cell has dysregulated miRNA. This is achieved by attaching 4 tandem sites complementary to the affected miRNA following a gene of interest. This is called the miRNA target site (miRNA-ts).
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<b>As miRNA activity increases, the output of the desired gene decreases.</b>
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<a href="https://2016.igem.org/Team:MIT/Experiments/miRNA/more_background">Read more about our decision to use miRNA sensors</a>
 
<a href="https://2016.igem.org/Team:MIT/Experiments/miRNA/more_background">Read more about our decision to use miRNA sensors</a>
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<h1 style="color:#ffffff; background-color:#ff9715; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center"> Are the target sites sensitive to miRNA levels? </h1>
  
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<img src = "https://static.igem.org/mediawiki/2016/6/60/T--MIT--tHESC_siRNA_final1.PNG" style = 'padding: 5px'; width: 300px; height = 400px; float: right; border:5px;'>
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<img src = "https://static.igem.org/mediawiki/2016/c/cd/T--MIT--microRNAsensor.PNG" style = 'padding: 5px'; width: 400px; height = 400px; float: left; border:5px;'>
  
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<h1 style="color:#000000; background-color:#FF9733; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center; font-family: Trebuchet MS"> Are the target sites sensitive to miRNA levels? </h1>
 
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These 4 tandem sites for miRNA binding were tested by coding for them distal to the gene for red fluorescent protein. We were able to see a ten fold repression upon increasing the concentration of siRNA from 0 to 1 nM. Saturation appeared at about 10 nM.
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These 4 tandem sites for miRNA binding were tested by inserting them after a red florescent gene (mKate) in the 3' untranslated region. We were able to see a ten fold repression upon increasing the concentration of siRNA from 0 to 1 nM. Saturation appeared at about 10 nM.
  
 
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<a href="https://2016.igem.org/Team:MIT/Experiments/miRNA/more_experiments">Read more about our experiment testing miRNA target site sensitivity</a>
 
<a href="https://2016.igem.org/Team:MIT/Experiments/miRNA/more_experiments">Read more about our experiment testing miRNA target site sensitivity</a>
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<h1 style="color:#000000; background-color:#FF9733; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center; font-family: Trebuchet MS"> Probing tHESC for miRNA Levels </h1>
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<h1 style="color:#ffffff; background-color:#ff9715; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center"> Does miRNA activity in endometrial cells respond to hormones? </h1>
  
 
<p style="font-family: Verdana;"> <img src = "https://static.igem.org/mediawiki/2016/3/3b/T--MIT--tHESC_profile.PNG" style = "padding:10px; width: 250px; height = 250px; float: right; border:10px;">  
 
<p style="font-family: Verdana;"> <img src = "https://static.igem.org/mediawiki/2016/3/3b/T--MIT--tHESC_profile.PNG" style = "padding:10px; width: 250px; height = 250px; float: right; border:10px;">  
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Unlike more common cell lines like MCF7 and HEK293, tHESC is not a highly characterized cell line. This meant that the levels of our eight miRNA candidates were completely unknown in tHESC. We set out to characterize our miRNA target sites (miRNA-ts) in tHESC using a miRNA sensor.
 
 
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<a href="https://2016.igem.org/Team:MIT/Experiments/miRNA/more_background">What is tHESC?</a>
 
 
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<a href="https://2016.igem.org/Team:MIT/Experiments/miRNA/more_experiments">Read more about our experiment to characterize miRNA targets sites in tHESC</a>
 
  
  
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The eight miRNA candidate target sites were characterized in TERT-immortalized Human Endometrial Stromal Cells (tHESC).
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Unlike more common cell lines like MCF7 and HEK293, tHESC is not a highly characterized cell line.This meant that the levels of our eight miRNA candidates were completely unknown in tHESC. We set out to characterize our miRNA target sites (miRNA-ts) in tHESC using a miRNA sensor.
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<a href="http://press.endocrine.org/doi/10.1210/en.2003-1606?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed">What is tHESC?</a>
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<a href="https://2016.igem.org/Team:MIT/Experiments/miRNA/more_experiments">Read more about our experiment to characterize miRNA targets sites in tHESC</a>
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<a href="https://2016.igem.org/Team:MIT/Experiments"><h1 style="color:#FFFFFF; background-color:#ff9715;; -moz-border-radius: 15px; -webkit-border-radius: 15px; padding:15px; text-align: center; font-family: trebuchet MS"> Back to Experiments Home</h1></a>
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<p> References
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1.Burney, RO, et al. Molecular Human Reproduction (2009). 15(10):625-631.
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2.Pan, Q. Xiaoping, L. Toloubeydokhti, T. Chegini, N. Basic Science of Reproductive Medicine (2007). 13(11):797-806.
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3.Joshi, NR, et al. Human Reproduction (2015). 30(12):2881-91.
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Latest revision as of 01:11, 20 October 2016

microRNA: Detecting a Cell Specific Profile

How can we detect endometriosis using microRNA?




















What is miRNA?


microRNA (miRNA) are small units of RNA found in all mammalian cells and play a regular role in gene regulation. miRNA is single stranded and only about 20 nucleotides long. miRNA forms a RNA-induced silencing complex (RISC) with other proteins and guides RISC to the complementary sequence on the mRNA (the miRNA target site). RISC cleaves messenger RNA and inhibits gene expression post transcriptionally.



Why is miRNA a good biomarker?


There are hundreds of different miRNAs that can make up a specific cell's miRNA profile. The profile and activity of miRNA varies between different cell types and different cells states.This makes it is possible to tell the difference between cells from the uterus and liver, and the difference between healthy and diseased cells based on miRNA profiles.


Found in all mammalian cells


Unique to cell type


Unique to cell states


What is the miRNA profile of Endometriosis?

Endometrial cells from women with endometriosis have been found to have dysregulated miRNA compared to endometrial cells from women who do not have endometriosis.(1,2,3). In order to study the uses of these miRNAs in our circuit, eight candidates were chosen based on fold difference in miRNA level between the the endometrial biopsy from women with and without endometriosis. The eight candidates are shown in the table to the right:




(1) One of the graphs observed in order to choose miRNA candidates to characterize. The three miRNAs, miR-34c-5p, miR-9, miR-34-b are shown to be downregulated and have a significant fold difference (*p=0.05 **p<0.05, error bars= standard error of mean) compared to their respective levels in healthy eutopic endometrial cells. These measurements were from an endometrial biopsy and taken using quantitative polymerase chain reaction (qPCR), similar to the other sources we also studied.






Eight miRNAs candidates were chosen to be characterized in order to determine their gene regulatory ability for the purposes of increasing the specificity of our circuit.


How can our circuit sense miRNA activity?

Our circuit utilizes the natural function of miRNA to regulate gene expression. Depending on the miRNA activity in a cell, different levels of our desired gene will be expressed. This allows our circuit to produce a differential output depending on whether the cell has dysregulated miRNA. This is achieved by attaching 4 tandem sites complementary to the affected miRNA following a gene of interest. This is called the miRNA target site (miRNA-ts).

As miRNA activity increases, the output of the desired gene decreases.

Read more about our decision to use miRNA sensors







Are the target sites sensitive to miRNA levels?

These 4 tandem sites for miRNA binding were tested by inserting them after a red florescent gene (mKate) in the 3' untranslated region. We were able to see a ten fold repression upon increasing the concentration of siRNA from 0 to 1 nM. Saturation appeared at about 10 nM.

Read more about our experiment testing miRNA target site sensitivity



Does miRNA activity in endometrial cells respond to hormones?


















The eight miRNA candidate target sites were characterized in TERT-immortalized Human Endometrial Stromal Cells (tHESC). Unlike more common cell lines like MCF7 and HEK293, tHESC is not a highly characterized cell line.This meant that the levels of our eight miRNA candidates were completely unknown in tHESC. We set out to characterize our miRNA target sites (miRNA-ts) in tHESC using a miRNA sensor.

What is tHESC?

Read more about our experiment to characterize miRNA targets sites in tHESC

Back to Experiments Home

References
1.Burney, RO, et al. Molecular Human Reproduction (2009). 15(10):625-631.
2.Pan, Q. Xiaoping, L. Toloubeydokhti, T. Chegini, N. Basic Science of Reproductive Medicine (2007). 13(11):797-806.
3.Joshi, NR, et al. Human Reproduction (2015). 30(12):2881-91.