Genetic Analysis for Correlation with Preeclamptic Progression
Clinical data is analyzed for glycolysis, TCA, and PPP genes to find any variance between expression in healthy and preeclamptic patients. Eventually, the findings will be applied to in vitro modeling using the novel BEASTS platform.
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[00:00:01.530]My name is Noha Algahimi and I am a
junior chemical engineering major at the
[00:00:05.070]University of Nebraska
[00:00:08.580]PE is a major disease of human pregnancy
characterized internally by high
[00:00:12.980]placental stiffness and affects roughly
3 to 8% of women worldwide.
[00:00:17.820]It remains one of the few fatal
complications of pregnancy to date.
[00:00:21.990]There is no cure for
PE and in severe cases,
[00:00:24.450]it often requires premature labor
induction, which carries with it
[00:00:28.380]the inherent risks of premature
neonates. PE manifests in the pregnant
[00:00:33.330]mother as high blood pressure, headaches,
nausea, and breathing difficulties.
[00:00:37.620]Under preeclamptic conditions,
[00:00:39.130]placental development is
inhibited preventing the fetus
from receiving nutrition
[00:00:42.690]necessary for healthy
development. Molecular mechanisms
[00:00:46.080]that account for the maternal placental
stiffness associated with PE are
[00:00:49.890]underexplored and the full extent of
the stiffness effects on trophoblast
[00:00:53.820],otherwise known as, placenta cells
remains a gap in scientific knowledge
[00:01:00.360]The goal of my research this year has
been to explore clinical data for patients
[00:01:05.010]with preeclampsia to determine
any significant difference
that might exist from
[00:01:09.180]the healthy controls.
Three clinical data sets
[00:01:12.690]including genetic expression information
for a variety of genes in preeclampsia
[00:01:17.160]patients and healthy controls
were assessed. These datasets G S
[00:01:22.020]E three five five seven four
G S E two five nine Oh six and
[00:01:26.460]GSE one Oh five
[00:01:27.780]eight eight were processed using geo2R software provided through NCBI
[00:01:33.270]log two fold change,
[00:01:34.500]which provides the logarithmic ratio of
genetic expression between the control
[00:01:38.670]and the diseased state was found
for all genes of interest.
[00:01:42.720]This included 15 causes related genes,
[00:01:45.450]three tricarboxylic acid genes,
[00:01:48.270]and three pentose phosphate pathway genes.
[00:01:51.690]The results were initially mapped
using Microsoft Excel to give an initial
[00:01:55.980]picture of how log two fold change data could
potentially be assessed.
[00:02:00.930]The initial mapping of log2 fold change
showed that the values calculated for
[00:02:04.980]dataset GSE one Oh five, eight,
[00:02:07.020]eight were unusually large when compared
to the other two datasets. While
[00:02:11.490]the reason for this is
not explicitly known,
[00:02:14.280]it could be the result of the method
in which the data was collected or the
[00:02:17.730]varied quantities of gene samples
analyzed. To remedy the negative effects of
[00:02:22.260]having such a large difference
in values between datasets,
[00:02:25.800]all three data sets were
compared against each other once.
[00:02:29.130]And then data says G S E
three five five seven four,
[00:02:32.580]and GSE25906 were compared separately.
[00:02:36.960]This made it easier to note which genes
had a potential significant difference
[00:02:40.590]in genetic expression between the
control and the pre-eclamptic state.
[00:02:45.600]This is shown in figure two,
[00:02:47.070]a with all three data sets and figure
two b with only the two aforementioned
[00:02:53.700]it must be noted that TCA and PPP genes
were only found in two of the three
[00:02:58.110]datasets GSE, three five, five,
seven, four, and GSE one Oh five,
[00:03:03.970]So in analyzing the log2 fold change
for these two metabolic pathways only
[00:03:08.260]the two mentioned data sets are used,
[00:03:10.630]this potentially means the findings for
TCA and PPP do not have enough collected
[00:03:15.070]data to reasonably reach a conclusion.
[00:03:18.160]The data was then formatted into heat
maps using prism software to present a
[00:03:21.970]visualization of potential
significance. Once again,
[00:03:25.510]G S E 105 eight eight was admitted in a
single visualization of glycolysis data
[00:03:30.220]to accurately maintain the variability
within the other two datasets. Because the
[00:03:34.870]TCA and PPP genes were only found
in two of the three datasets,
[00:03:39.280]one of which being the set with abnormally
large log2 fold change values,
[00:03:43.540]it was not possible to create heat maps
[00:03:45.640]omitting said dataset
from the two pathways.
[00:03:49.330]It was determined from heat maps
that for the glycolysis pathway,
[00:03:52.780]Hexokinase 2 and glyceraldehyde-3-phosphate dehydrogenase showed
[00:03:57.280]potential significance in the
variability of genetic expression between
[00:04:01.090]preeclampsia patients and
healthy patients. In PPP
dehydrogenase shows some promise,
[00:04:10.510]but due to lack of data, it is
hard to draw a definite conclusion.
[00:04:14.470]The same can be said for pyruvate
[00:04:16.060]dehydrogenase in TCA. To further explore
the potential significance of these
[00:04:21.010]It is pertinent that more data be
analyzed so that the unusually large log
[00:04:24.910]two-fold change values
in G S E one Oh five,
[00:04:28.240]eight eight are no longer an issue.
Additionally, in future exploration,
[00:04:34.270]using ANOVA in prism software, will be
conducted to determine whether it worth
[00:04:39.250]creating in vitro essays
of the indicated genes,
[00:04:43.150]or if it would be more appropriate
to observe other genes. In the
[00:04:47.890]focus lab biomimetic stiffness modeling
is conducted using the novel bio
[00:04:51.610]engineered adhesive siloxane
substrate with tuneable stiffness (BEASTS)
[00:04:56.470]platform. To construct the platform polydimethylsiloxane
[00:05:01.450]mixed in ratio to produce variable stiffness plates.
[00:05:03.700]Stiffnesses are at eight kilo pascals,
[00:05:06.460]25 kilo pascals and 55 kilo pascals.
[00:05:10.210]These are then used to coat welled
plates in seven millimeter increments.
[00:05:14.680]This can be seen in figure three,
[00:05:17.290]coated plates are incubated
overnight at 65 degrees Celsius,
[00:05:21.190]and then treated with oxygen plasma
to create a hydrophilic surface.
[00:05:25.510]The last step is to create 10 bi
layers, alternating the positive
[00:05:33.880]and the negative suphonated
polystyrene (SPS) polymers. Upon bilayer
[00:05:39.490]Placenta cells are seeded on the plates
and subjected to experimentation.
[00:05:43.780]This will be the platform I use
in the next steps of my research,
[00:05:46.840]as I run in vitro assays of the genes
of interest found through clinical data
[00:05:52.750]The noting of potential genetic
variance occurring in the glycolysis
[00:05:56.080]metabolic pathway indicates the
possibility that energy production and
[00:06:00.200]consumption in the placenta cells are
negatively affected by the changing
[00:06:03.920]environment under preeclamptic conditions.
[00:06:06.350]This could aid in closing the knowledge
gap associated with the progression
[00:06:09.620]and treatment of preeclampsia
in pregnant women.
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