Pharmacogenomics of radiation therapy

In class we recently read:

Genetic analysis of radiation-induced changes in human gene expression.

Smirnov DA, Morley M, Shin E, Spielman RS, Cheung VG.

Nature. 2009 May 28;459(7246):587-91. Epub 2009 Apr 6.

Howard Hughes Medical Institute, USA.

Abstract
Humans are exposed to radiation through the environment and in medical settings. To deal with radiation-induced damage, cells mount complex responses that rely on changes in gene expression. These gene expression responses differ greatly between individuals and contribute to individual differences in response to radiation. Here we identify regulators that influence expression levels of radiation-responsive genes. We treated radiation-induced changes in gene expression as quantitative phenotypes, and conducted genetic linkage and association studies to map their regulators. For more than 1,200 of these phenotypes there was significant evidence of linkage to specific chromosomal regions. Nearly all of the regulators act in trans to influence the expression of their target genes; there are very few cis-acting regulators. Some of the trans-acting regulators are transcription factors, but others are genes that were not known to have a regulatory function in radiation response. These results have implications for our basic and clinical understanding of how human cells respond to radiation.

This paper described the reseachers efforts to identify classes of genes that may serve as potential markers of radiation sensitivity. To accomplish this the investigators started with a series of transcription factors that they used to then pull other sets of genes from radiation exposed cells.

How did the reseachers do this? What cells did they use and why? Describe one of the genes they found and which transcription factor it is regulated by.

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25 thoughts on “Pharmacogenomics of radiation therapy

  1. This article was rather dense to read particularly because it is packed with vocabularies and is written in a way that does more to confuse the reader. Nonetheless it is an article about individual reaction to a toxin in this case radiation, and how each person’s reaction may differ due to the different gene expressions of human genomes.

    The researcher used immortalized B cells collected from a special group of people in Utah, who are known for their inbreeding and well kept family medical histories. The researchers microarrayed 10,174 genes and eliminated all possible genes besides the 3,280 that react to ionizing energy after 2 hours and 6 hours of exposure, by at least 1.5 fold. For each time of exposure they calculated a ratio of irradiation compare to expression level at baseline. They first looked for individual variable in gene expression response to ionizing radiation and discovered that gene like TRIAP1 has very little individual variation in gene expression than other genes such as JUN. From this they were able to identify the regulators that control these genes and trace the nature of these regulators to either cis acting or tans acting. They performed a genetic analysis, first using a standard SNP based linkage panel to obtain 4,6000 SNP markers, then using S.A.G.E, a computer program to carry out genome wide linkage analysis for each of the 3,280 for both 2hour and 6hour exposures.

    They found that FAM57A and GADD45B are both linked to influence radiation response and apoptosis. Out of all the significant links 20% of the phenotypes had cis regulators and the other 80% contained trans regulators. However, another phenomenon known as co regulation of genes was also evident in the study, where if the target genes has regulators that are located close to each other, that will cause the genes to work together to carry out a specific action. RASL11B, RAP1GDS1 and RASA1 are three genes located around the regulatory region of chromosome 2 that encodes proteins. Another piece of evidence is CD70 and TNFSF14, which are located next to each other on chromosome 19 that have similar functions.

    One trans acting regulator in particular is the VDR, which also acts like a transcription factor that cause apoptosis and cytotoxicity, Its major allele is the Adenine (A)and whose SNP location rs4760658, AG. In addition to this finding, CD44 a cell surface receptor as well as other genes with few known functions also affect gene expression.

    Overall this research was successful at explaining the regulatory roles certain genes and regulators possess. But can these results be used to predict individual sensitivity and allow medical professionals to develop more radiosensitizers that irradiate tumors and improve radiotherapy? Thought this study may serve as the beginning to this long journey towards personalizing medicine, but in time it will be accomplished.

  2. According to the article, the researchers used microarrays to measure the expression levels of genes from radiated B-cells collected from 15 Morman families after 0, 2, and 6 hours of exposure. They then narrowed down their list of expressed genes by focusing only on the genes that had an activation difference between 2 and 6 hours of radiation. The researchers then used a genome wide linkage analysis to find “hot spots”, cooresponding transcription factors that possibly regulate the found gene’s expression. Researchers then examined other genes that were close to the found transcription factors, that may also affect the first gene’s response, by using what they called a quantitative transmission disequilibrium test (QTDT). Afterwards, they ran the program “Chilibot” to identify the genes possible regulators from a database of primary research data. Using this compiled list, they confirmed the presence or absence of each regulator by using the process of siRNA knockout.
    The researchers found the gene RFX3, which codes for a DNA binding protein, and its potential regulator HIVEP2, on the posterior end of chromosome 6, that regulates transcription.

  3. The researchers in this paper are using radiation as a drug. They attempt to divide the patients into groups, such as sensitive, moderate, and insensitive. Patients respond differently to radiation. Radiation is commonly used in cancer treatment and in X-rays to kill cells by destroying the genetic material or DNA in the cell. It induces apoptosis, programmed cell death, and necrosis, death due to cell damage. Regulators can effect gene expression of the genes involved in the radiation process. Cis regulators are near the specific focus of interest and a trans regulator is distant from the focus of interest. Hot spots are regions that show high relevance to the area of interest.
    In this study, the researchers used irradiated B cells, which were taken from people in the CEPH pedigree, and collected data every 2 and 6 hours. 3,280 genes out of 10,174 genes were found to be expressed 1.5 fold at the 2 hour and 6 hour intervals. One of the genes found in the paper to be radiation induced was HRAS. The potential regulator for this phenotype is RB1 and was expressed after the 2 hour interval. The gene was found on chromosome 13. The transcription factor RB1 is a trans- acting regulator.
    A series of cultures are used and the relations between these cultures are known. The cell cultures cover 15 different pedigrees. Table 1 shows the most significant changes. They looked for a change in gene expression by correlating the irradiation of transcription factors. Table 2 states the hot spots and the changes in phenotype expressed in irradiation. Linkage scans looked for genes that co-segregate between parents or siblings. Unrelated people were used as the control. QTDT looks for neighboring genes that affect the mutated gene. The trans-regulators were found to be mostly transcription factors.

  4. To identify regulators that influence expression levels of radiation – responsive genes, the researchers treated radiation –induced changes in gene expression and conducted genetic linkage and association studies to map their regulator. They used microarrays to measure the expression levels of genes in irradiated immortalized B cells from members of Polymorphisme Humain CEPH Utah pedigrees because these families are efficient at preserving the medical records (genetic) about their ancestors which helps the research in order to trace the ailing transcription factor or gene causing a particular disease. The focus was primarily based on ionizing radiation responsive genes that show 1.5 fold changes in gene expression levels at 2 h and/or 6 h after irradiation relative to the baseline. The results showed the variation in gene expression response to ionizing radiation. TRIAP1 showed little gene variation as compared to the expression levels of JUN which led to identify the regulators which influence these individual differences in radiation – induced level.

    With the help of computer programming SAGE, genome wide-linkage analysis was carried out in 15 families which revealed the expression phenotypes with the most significant linkage results. FAM57A and GADD45B influence radiation response through the regulation of cell cycle and apoptosis. Trans acting regulator had 80% significant linkage while cis acting regulator showed 20%, therefore, trans-acting regulator is more abundant in the cells than cis. Later, the researchers co-regulated the genes that have similar functions or are closely linked and further followed up results of the linkage scans by family-based association analysis in order to confirm the linkage results and association of several markers near or within TP53BP2. This shows that genetic analysis allows the identification of polymorphic trans-acting regulators of gene expression.

    Then Chilibot was used to look for co-occurrence of the names of the regulator and target genes in the literature and relationship between them and the significant association was found between some radiation – induced expression phenotypes and SNP alleles in trans regulators which shows that polymorphisms in the trans regulators contribute to individual differences in radiation – induced gene expression. Therefore, siRNA was used to knock down the regulators and the expression of the target genes was measured. Changes in expression of the target genes after knockdown of the regulators support the regulator-target gene relationships identified by genetic mapping and by combining results from genetic mapping and molecular validation studies, the regulatory regions and regulators have been identified that influence radiation-induced changes in gene expression.

    RB1 is the transcription factor found in chromosome 13, that acts as a trans acting regulator whose gene expression phenotype is HRAS (potential markers of radiation sensitivity) and SNP location is rs198584 whereas remaining regulators include a cell surface receptor (CD44) and genes with few functions (DYNC2LI1 and UBA52). Many genes other than transcription factors also play a vital role in regulating gene expression.

    The results proved to reveal a medical implication and could also be helpful in determining the regulatory roles which certain genes adhere to and is a great breakthrough in the field of research.

  5. This paper focuses on the use of radiation as treatment in human cells and the reactions that the cells have to it. Humans tend to either be sensitive, moderate or not sensitive to radiation and this is caused by different gene expressions based off of transcription factors that turn on specific genes. These transcription factors are what are being studied in this paper. When exposed to radiation, these transcription factors can be altered, causing the regulation of some of the genes to change such as having other genes not turned on by that specific transcription factor that should have. This creates what appears as a condition of being sensitive, moderate or not sensitive to radiation in humans.

    In this paper, immortalized human beta cells were used to study the transcription factors. These cells were obtained from Mormon families due to their accurate ancestral records. These records allow for scientists to know the genotypes and the alleles that they are therefore dealing with in these cells and what diseases that may exist that would be responsible for gene expression. Also, these cells will contain DNA that is very similar to the primary cell culture because of the interbreeding rituals done in this type of culture. The transcription factors of study were then determined by exposing these cells to radiation for 2 hour and 6 hour intervals. These intervals were used because it would capture the cell’s gene expression right before it the cell begins to die. From these gene expressions, hotspots are able to be identified. These hotspots are areas within the genome or transcription factors that set off other genes that are important. At these hotspots, chromosomes are analyzed to see if they co segregate with one another in parents or sibling generations; meaning that the scientists are looking for groups of chromosomes that are related to one another.

    After the transcription factors are determined as to what genes they control, scientists tested their results by using siRNAs to see if the gene expression would be blocked when the transcription factor is blocked. It was found that mostly trans regulators had an effect on gene expression such as the trans regulator HIVEP2 which is located on chromosome 6. This function is to regulate transcription.

    Overall, I thought that this paper was very interesting and the background behind as to why they used the samples that they did was very enlightening and interesting as well. I did find this paper a little hard to read and to understand at first but I definitely think that it is a paper that explains why radiation can be so bad to our cells and DNA.

  6. The articles is based on reasearch done using radiation as a drug therapy. The population of test subjects were broken up intro groups of sensitive, moderate, or insensitive to the influence of radiation. The levels of gene expresssion changed based on the damage caused by radiation. The regulators were predominantly in trans when influencing their target genes. There is differential response to the therapy because of each person’s genome, however the most common response to radiation is apoptosis which is programmed cell death. Apoptosis is partly beneficial in that even though the cell commits suicide, it feeds nearby cells the nutrients that he had stored. Radiation kills the cells by destroying the cell’s genetic material.

    The experiment was conducted using microarray to measure the levels of gene expression before and between 2 and 6 hours after exposure to radiation. At this time they would get the best differential expression. The genes that were focused on were those that had 1.5-fold change in their levels of expression. The B cells used came from a group of individuals in a CEPH pedigree in Utah who keep a good record of family history (including deaths). The more that the researchers know about a family’s history, the better they can understand how and why the genes respond in a particular manner.
    One of the genes that were found was JUN which is regulated by LCP2 that was validated molecularly. Changes in the gene support the concept of genetic mapping where the knockdown shows that there is a relationship between the regulators and the target gene.

  7. This paper is actually an example of what we did in our last lab except instead of analyzing the affects of radiation, our experiment had to do with the affects of lead. In this paper they found what influences expressions of radiation-responsive genes. They found how human cells react to radiation. They conducted an experiment using what we did in lab: microarray. They got adiated B-cells collected from 15 Polymorphisme Humain CEPH Utah families after 0, 2, and 6 hours of exposure. They used ‘ionizingradiation-
    responsive’ genes because it showed a good amount of change in gene expression in result from the radiation. The results showed the variation in gene expression response to ionizing radiation. One gene they found is TP53BP2 (located on chromosome 1) which is a regulator of BAX 19. BAX is part of the radiation-induced expressions which plays a part in apoptosis. This showed that there are trans-acting regulator of gene expression which is significant because the article states that “few trans-acting regulators have previously been
    identified in studies of the genetics of human gene expression.” This article was pretty interesting especially since we did it in lab as well. Microarrays are a breakthrough in science and for the future as well. All I keep thinking is that I’m going to be doing the ELISA, PCR, and microarray techniques for the rest of my life and maybe one day write an article like the ones that I’m reading.

  8. Researchers here are concerned with developing a relationship between radiation and people. Currently radiation dosage is distributed based upon things such as location of target spot and body weight and these researchers are taking a step in the direction of one of our most discussed topics, personalized medicine, by identifying genes that are responsible for radiation tolerance and sensitivity to easily determine a person’s sensitivity to radiation. The goal of the researchers was to divide humans into the category of sensitive, moderate or insensitive to radiation exposure.

    The cell population of choice for this experiment was the immortalized B cells of the Mormon population of Utah due to their incestual background and well documented medical records. The researchers conducted this experiment using various technologies such as microarray which was used to identify the expression of genes after being exposed to radiation in two hour and six hour intervals narrowing the ten thousand genes being arrayed down to around three thousand genes. They also used computer program based technologies such as S.A.G.E and Chilibot, S.A.G.E was used to perform a genome-wide linkage and Chilibot is a program which scans through papers finding word associations, in this instance researches used to it identify the relationship between certain transcription factors and specific genes.

    Fortunately the researches were successful in this experiment; they found a number of genes such as ARHGDIA, HRAS, TNFSF9, HMMR and FAS which is located on chromosome 19 and serves purpose in the modification of the ribosome and proteins, its potential regulator was identified by researchers as the UBA52 regulator.

    This paper was definitely more difficult than the others and seemed to hold the interest of readers based on it’s interesting content but lose it at times based on the way the content was presented but overall it was rather successful at getting it’s point across.

  9. This article is about the effects of radiation and how people’s reactions may differ because of their different gene expressions. Radiation can induce apoptosis, which is programmed cell death, and necrosis. The researchers in this article used microarrays to measure the expression levels of genes from irradiated B cells collected from people in Utah, who inbreed and keep a well record of family medical histories. The researchers used irradiated B cells and collected data every 2 and 6 hours. They found 3,280 genes out of 10,174 genes to be expressed by 1.5 fold. The researchers then used a genome wide linkage analysis to find “hot spots”, corresponding transcription factors that possibly regulate the found gene’s expression.

    HRAS was a gene found in the paper that was radiation induced. The HRAS regulator for this phenotype is RB1 and was expressed after the 2 hour interval. The gene was found on chromosome 13. The transcription factor RB1 is a trans- acting regulator. The gene expression phenotype SNP location is rs198584 whereas the remaining regulators include a cell surface receptor called CD44 and DYNC2LI1 and UBA52, which are genes with few functions.

  10. The paper “Genetic analysis of radiation-induced changes in human gene expression”, it treats radiation therapy as the same way as toxins and drugs. The study went on to separate people into three distinct groups: sensitive, moderate and insensitive to the radiation exposure. These different sensitivities is base on the transcription factors that which on and off the gene. Exposures to radiation can destroy the genetic materials of the individual such as the DNA and a large amount of radiation can also affect the person’s cellular system because the cells are unable to make any response. This paper is trying to ask the question what genes are responsible for the different cell expressions after radiation.

    This research is based upon the immortalized human beta cells to study different transcription factors. These cells are from fifteen different pedigrees of Utah, because these families have very accurate ancestral history and great genetic phenotypes. Their cells are collected after two and six hours of radiation exposures, this interval can be able to capture cell expressions with “dying cells”. 3,280 radiation responsive genes showed to have at least 1.5 fold changes in gene expression in the immortalized B cells. Hotspots can be identified after series of cell expressions. Hotspots are regions that show up with the relevant information to the study. In this case are the cis and trans transcription factors. After the transcription factors are determined to the corresponding genes they turn on, the researchers confirmed with the testing results by siRNA to knock out the regulator when gene expression is blocked. It was found by siRNA knock out that there is a relationship between the regulators and their target genes and the trans regulators have much more gene expression effects than the cis regulators. One of the gene sthey found was the JUN and it was regulated by the LCP2 regulator, which is located on chromosome 5.

  11. This main goal of this paper was to figure out the genes that are responsible for the different responses to radiation. They tried to divide the population based on sensitivity to radiation: sensitive, moderately sensitive and insensitive. The researchers used immortalized B cells from 15 groups of Mormons in Utah. DNA collected from the Centre d’Etude du Polymorphisme Humain (CEPH) Utah members is very useful because they keep awesome phenotypic history and excellent records. The researchers know who is related to who and how each person died. The researchers performed numerous analysis and tests to understand which genes influence people’s reactions to radiation. They used microarrays to figure out the expressions levels after 2 and after 6 hours of radiation. To identify the regulators, or hotspots where the regulators might be, that influenced the differences in gene expression in individuals, the researchers carried out genome-wide linkage analysis using the computer program called S.A.G.E. Next, they performed family-based association analysis on the SNPs that were near the hotspots to zone in on the spot where the regulators might exactly be using the quantitative transmission disequilibrium test (QTDT). Chilbot was used to look for co-occurrences of certain genes and regulators and to examine how close these words appear near one another to identify which regulator control which genes. Afterwards, to confirm whether or not some of the genes identified as genes that influence the responses to radiation are regulated by cis or trans-regulators, they performed a differential allelic gene expression analysis for cis-regulators and short interfering RNA knockout for trans-regulators. If there was a change in gene expression after the regulators were eliminated or changed, then the regulators control those genes. One of the genes that they found that affects gene expression after radiation is JUN. According to the paper, a potential regulator for JUN is LCP2. JUN is found on chromosome 5, expressed after 2 hours of radiation, and its GO function is transmembrane receptor signaling pathway.

  12. Humans are exposed to radiation through environmental and medical settings, but there are also genetic expression responses that differ among all individuals. The researchers identified regulators responsible for expression levels of the genes that respond to radiation. Everyone varies in their sensitivity to radiation and researchers look at these chromosomal regions and genetic variants for the genetic mapping of regulatory codes that influence radiation induced changes in gene expression.
    Rephrasing this article is difficult because the terms and phrases used were complex and seemed countless. The researchers used irradiated immortalized B cells from a confined group of people that normally keep consistent records of their ancestors. Fifteen pedigrees between related groups were used for comparisons. Among these 15 groups, microarrays were used to measure expression levels of genes in these irradiated cells. In between 2 and 6 hours the exposure of cells to radiation shows the best differential expressions at these points. There was a 1.5 fold change in gene expression level between these time points of the 3,280 ‘ionizing-radiation-responsive’ genes that the researchers focused on. These genes were chosen out of 10,174 genes expressed from microarrays expressed in the B cells. The fold change varies upon different people within this time frame of these radiation-responsive genes.
    Radiation is related to toxins and drugs, in a sense, because it also has side effects for people. In order to maintain health within the organism that is exposed to bad entities, apoptosis occurs. The researchers tried to find out which genes govern the response to radiation. There are regions in the gene that have regulators which influence expression levels of many genes known as the “hot spots.” It was found that only 20% of the gens were cis-acting and 80% were trans-acting genes. An example of a 2-h-after- irradiation is of the BAX gene which shows radiation-induced expression through apoptosis. This gene has a known regulator known as the TP53BP2.
    They also found co-regulation of genes where two of the targeted genes in the regulatory region were next to each other. This shows that distance is an important factor in processes of regulation. The researchers also focused on SNP markers to with SNP-based linkage panel for each of the 3,280 genes using the S.A.G.E computer program. They did this because they could find an association with the trait of genes that respond to radiation with the SNP markers that “sit around the chromosome.” In the end maybe the pattern of SNPs that cause this response could be found and to be honest I have no idea what they want to do with that. Maybe they just want to observe on how the body responds to certain exposures by focusing on the genetic responses. Results from their study shows that polymorphisms in the trans regulators contribute to individual differences in radiation-induced gene expression, despite the small sample size used. They used siRNAs to confirm this result by knocking down potential trans acting regulators and measure the expression of the target genes but the results show the regulator-target-gene relationship (LCP2 (also known as SLP-76) as regulator of expression of JUN, CD44 as regulator of TNFSF9, FAS as regulator of TRAF4, SERPINE2 as regulator of ARHGDIA, and SSB as regulator of FAS).

  13. This article focuses on research done in using radiation as treatment in humans and their reactions to it. When humans are exposed to radiation, cells produce responses that rely on changes in gene expression, which differ among individuals. This is because individuals vary in sensitivity to radiation. The test subjects in this article were divided between sensitive, moderate, or insensitive to the influence of radiation, which is based on transcription factors that cause different gene expressions.
    In this paper transcription factors were studied by using immortalized beta cells. They conducted the experiment on these cells using microarray and they were exposed to radiation for 2 and 6 hour intervals, which is able to determine the cells gene expression before cells began to die. They used these cells because they were taken from Mormon families who have good medical records because they inbreed and are helpful because scientists can know the genotypes and diseases in the population beforehand.
    They used SAGE to carry out genome wide linkage analysis for the 2 and 6 hour radiation expression phenotypes. One of the genes they found is TP53BP2 located on chromosome 1. It is a known regulator of BAX which has a role in apoptosis. Its expression level is regulated by trans-acting regulators.

  14. This paper focuses on the effects of radiation exposure to human cells. Each person responds differently to radiation. People can either have sensitive, insensitive, or moderately sensitive reactions to radiation. These different reactions to radiation can be explained by gene expression levels of radiation-responsive genes. The researchers are trying to identify exactly which genes are responsible for these differing reactions among people. They do so by taking a closer look at transcription factors that influence expression levels of radiation-responsive genes.

    The researchers used immortalized beta cells from humans. The cells came from Mormons since they maintain extremely accurate and detailed information about their ancestors and causes of death. Using cells from Mormons helps the researchers determine who is related, what diseases could affect gene expression, and whether there is a common allele that affects how a person responds to radiation. The cells underwent microarrays to measure expression levels of the genes after being exposed to radiation. The researchers looked at the cells at two specific time intervals: 2 hours and 6 hours after exposure to radiation because at these time intervals, there was at least a 1.5-fold change in gene expression levels. Upon examining expression levels at 2 hours and 6 hours after radiation, the authors were able to identify specific hotspots. Hotspots indicate a transcription factor process, where a certain transcription factor leads to the expression of other genes. The researchers also performed linkage scans to determine genes that cosegregate between parent and sibling relatedness. Although not very clear because of how technical the text is, it seems to me that the researchers definitely determined that trans-acting regulators (transcription factors) ultimately play a large role in the change in gene expression after exposure to radiation.

    Once specific transcription factors that affect gene expression levels were identified, the researchers tried to “knockdown” the regulators of radiation-responsive genes through the use of siRNAs. One of the gene/receptor pair they targeted was the TRAF4 gene. TRAF4 is a gene that plays a key role in neurulation, or the formation of the central nervous system, and its regulator is FAS.

    This paper was one of the most difficult to read for a few reasons. It was very technical and didn’t really have a sense of organization. Most papers have their text separated into sections: methods, results, discussion, etc. If the text wasn’t so “jargony” I believe it would’ve been much more interesting.

  15. This article seemed to concentrate a lot on the statistics of cell expression. The program called the “Chilabot” was used to gather as much information about the expressed genes as possible due to the fact that there were trans regulated genes involved. The genes expressed when irradiated were seen to be regulated in a cis and trans way. Due to the varied reactions toward radioactivity, genes from Polymorphisme Humain CEPH Utah pedigrees were irradiated and micro arrayed. The genes from the Utah pedigrees were significant because the lifestyles of that individual group gave scientists well documented family trees and information. A large number out of about 11,000 gene samples they took showed an increase in expression. The B cells that were irradiated and micro arrayed were seen to have increase in gene expression of cells that are going through apoptosis. The responding genes were expressed 1.5 fold when irradiated and left for 2-6 hours. The JUN gene was said to have increased in expression 2 hrs after exposure. Other genes such as those in the RAS family were seen to have changed in expression. The genes that were recorded were seen to be transcription factors and other factors that contributed to cell apoptosis.
    The genes that were seen to be inactivated or altered were mostly trans regulated as well. Trans regulated genes have the possibility of being shut off due to another inactivated gene in another region of the DNA, which would give unclear results.

  16. Radiation exposure to the human body can cause cytotoxic and genotoxic outcomes. Humans are usually exposed to radiation via therapeutic/medical causes or through environmental happenings. Either method one is exposed, radiation is extremely toxic and effects individuals according to the amount of radiation they were exposed to, the amount of time they were exposed, as well as several other factors.

    The factor that this paper focuses on is individual variation and sensitivity to radiation exposure. The paper discusses a research study in which scientists were attempting to classify SNP’s (single nucleotide polymorphism) as well as other genes that are potential markers that cause some people to be more susceptible to radiation toxicity after exposure. They treated changes in gene expression after radiation exposure as genetic phenotypes, then mapped out the gene regulators for association studies.

    The scientists used microarrays to measure the gene expression of genes in B cells that were immortalized. These genes were placed in the microarrays and the scientists calculated the ratio of expression after 2 hr intervals of irradiation. They used these cells because cellular processes and activities rely partly on alterations in genetic expression and the repressed genes can influence how a cell is impacted and changes due to ration exposure. They compared the cellular survival of different individual’s cells after radiation treatment and they found that the radiated expression of the T allele was higher than the expression of the C alleles.

    In order to test the truth to these findings the scientists used short interfering RNA to knockout potential gene regulators and then measure the expression the focused target genes. One of the genes they found was the cis-regulated phenotype CP110 gene. This gene has a transcription factor that helps enable it to encode a specific proteins involved with duplication of the centrosome in the cell. They found an exonic SNP known as rs179050 related to the process. They’re results help to contribute to the study that radiation toxicity is also subject to genetic differences and greatly related to the field of pharmacogenomics.

  17. In this paper, scientists attempt to discover the genes that cause the differential type of response to radiation. In order to achieve this attempt, they utilized methods similar to our Microarray Lab experiment performed during Pharmacogenomics Lab. Through microarrays, the genes of immortalized B cells were measured to determine the expression levels. Usually, it is common to find such an attempt to be rather difficult since it is very hard to determine the expression of thousands of genes. However, this research proves to be unique because they were able to obtain great genotype pedigrees from Mormons who voluntarily gave their cells in order to be studied. Once these cells were obtained, scientists exposed them to 10 Gy of ionizing radiation that were analyzed after 2 and 6 hours. As a result, 3,280 ionizing radiation-responsive genes out of 10,174, were focused on and these genes conveyed a 1.5 fold change in gene expression levels.

    In order to observe how cells deal with radiation exposure, they compared cellular survival rate in individuals and showed that individuals with low JUN induction had a higher survival rate than in those with high Jun induction. With this knowledge they were able to determine if the regulators were cis acting or trans acting. They carried out a genome-wide linkage analysis that utilized SNP markers on 3,280 expressed genotypes of 15 separate families.

    One of the genes that were found derived from a region that contains the gene TP53BP2, a known regulator of BAX19. Through family based association analysis, this linkage finding was confirmed and allowed it to be identified as a polymorphic trans-acting regulator of gene expression. This identification held great significance because there have only been a few trans-acting regulators that have been seen in the history of studying human gene expression. This paper was very difficult to read because the article appeared to assume that everyone should know their terminology. Few words like “hotspots” were clearly defined, while many were left without any form of explanation. As a result, it was hard to comprehend how the procedure was performed.

  18. Radiation is used in medicine as a treatment for many diseases, but radiation can also be found in the environment. The radiation found in the environment cannot be controlled in amounts like they are in a medical setting. Although scientists cannot control the environment they can surely keep control of it in a medical situation, which is the main pint of this paper. Scientists are trying to figure out how cells react to specific amounts of radiation and how gene expression affects radiation sensitivity.
    In order to do this research, scientists used immortalized B cells. They got their sample B cells from a group of individuals that are known to only breed with their own, a group named” Centre d’E ´ tude du Polymorphisme Humain”. This group is conformed of Mormons. They not only chose the Mormons for their inbreeding, but for their well kept medical records. Once they got their sample B cells they exposed them to 10 Gy ionizing energy, and they collected data from their samples in intervals of two and six hours. Scientist then used microarray and found out that from the 10,174 genes that the immortalized B cell expresses, there are only 3,280 genes that are responsive to ionizing radiation. They also found out that these genes have a 1.5 change of expression as the radiation exposure increases in time; at two hours and six. They then compared genes to see which were more affected by the ionizing radiation, and found out that the gene TRIAP1 suffers very little gene expression change when exposed, but that the gene JUN can suffer very serious changes in gene expression. Scientists then used the JUN gene as a target to see at the outcomes of high level expression and low. The conclusion was that high levels of expression of the JUN gene may lead an individual to have much greater cell death than an individual with low levels of expression.
    One particular gene they focused on was the FAM57A. They discovered that this gene is linked to another one, GADD45B, and are supposed to influence radiation response and the start of apoptosis. This was very interesting fact because the transcription factors transcribed these two genes together, because they are so close to each other. The transcription factors are RB1,
    HIVEP2 and VDR.

  19. During the past two decades it is evident that radiation has become a big part of our medical technology. We can find such technology in X-rays whether it be for detecting where a broken bones is to or to find cancers in the body. Radiation is also known to be carcinogenic and mutagenic due to its genotoxicity. This can also ultimately cause “DNA damage in the human cell”. Depending on one’s level of gene expression, people have different reactions to the exposure of radiation. In order to identify classes of genes that may serve as potential markers of radiation sensitivity, researchers performed genetic mapping of the regulatory elements that have a reaction to the markers of radiation in the gene expression.

    These researchers used microarray chips to determine the level of gene expression in the targeted gene, which are irradiated immortalized B cells. In the study they used 3,280 ‘ionizing radiation-
    responsive’ genes from the microarray. They came to the conclusion that there was a 1.5 fold in the levels of expression within the gene. A slight change in the gene expression can set the level or bar for the way a cell responds and in this case they way the genes are expressed or lack of being expressed determines how certain cells react to the exposure of radiation. Using SNP markers and the use of the S.A.G.E. computer program the researchers were able to map the genes that are markers to radiation sensitivity.

    One of the genes they found was FAM57A and GADD45B. These two genes may trigger a radiation response through the” regulation of cell cycle and apoptosis” and this is illustrated in figure 2. Another gene that they found was TP53BP2. This gene is mostly known to regulate BAX where it is considered to be a trans-acting regulator of gene expression.

    This paper was interesting because it was cool to see how researchers utilized microarrays, a technique that we learned to perform in our pharmacogenomics lab, where they target which genes that are most sensitive to radiation. Overall this paper was an easier read than the other papers because I was able to understand most of the terminology.

  20. This paper is about radiation and its effects on genes. People who are taking a toxin or drug have an individual reaction depending on their rate of metabolism. This study treats radiation like a drug and they try to break the population up to sensitive, moderate, or insensitive to the influence that radiation has on their body. Radiation has many uses; some are more common like x-rays and other are less common like radiation for the treatment of cancer. Through this study the researchers hope that they can give individual radiation treatments based on different things like the kind of tumor, age, body mass, and where it is located. Radiation is used for cell death of which there is two different kinds’ apoptosis (programmed cell death) and necrosis (cell death from damage). Radiation is genotoxic which is defined as something that is toxic to the genes or breaks up DNA at a level of destroying gene expression. As of now we do not know what classes of genes or the genes themselves that might be responsible for the differential response to radiation. This experiment breaks up their data into two time points, 2 and 6 hours, to try and best capture expression changes as the cells are on their way to death. They attempted to choose the time point where they would get the best differential expression. Transcription factors operate at the level of many genes. This study used 15 separate pedigrees from Utah Mormons. The Mormons provide great genetic phenotype history and give immortalized B cells which are kept as a culture. They are a great subject to test because you know about the people, where they come from and all about their families. If you mutate a transcription factor you expect the genes that the transcription factors regulate will get mutated as well. The mRNA knockdown method is used. For this they do their analysis, identify bins of genes that go together with some transcription factor so they have to prove that the transcription factor regulates these genes that are sensitive to radiation. They then go into a cell and mess up the transcription factor to see if it affects the gene. One of the genes they found was TNFSF9 whose potential regulator is CD44 and whose GO function was receptor. I feel that this paper was very hard to get through although it was much more interesting once I better understood all of the different types of terms being used throughout it. This paper was also a little more difficult because it was not broken down in to different sections, for example methods or discussion as most papers are. This made looking for information that much more difficult and frustrating. Overall though I thought it was a pretty interesting paper and I look forward to seeing if an individual based radiation treatments will be coming up in the near future.

  21. Radiation is one of the possible ways to cure cancer. In this paper, researchers studied the relationship between radiation and human gene expression. They consider radiation like a type of medicine, so they wanted to see how it would affect the human body.
    The researchers procured samples of immortalized B cells from a group of 15 people who were related to each other. This particular sample culture was specifically used because the 15 people are all family members and so genetically linked to each other. Because these cells are related, scientists can easily compare what type of gene is associated with each specific phenotype.
    First of all, they used microarrays to measure the level of gene expression. Among the 10,174 genes, they only focused on 3,280 ‘ionizing radiation-responsive’ genes, but the point of the experiment was that the genes had to show at least 1.5 fold change. Also, the researchers separated the cell group into two; one was a group of cells put under radiation for 2 hours and the other 6 hours. For next step, to find the relationship of phenotypes of the 15 family members, the scientists used the S.A.G.E method which is a form of genome-wide linkage analysis. As a result, they could limit and separate the 3,280 sample genes to 1,275 2-h-after-irradiation phenotypes and 1,298 6-h-after-irradiation phenotype with using a threshold of t=4. However, after the analysis, they found large amount of number of linkages, so then, they focused the experiment on cells that showed at least two fold change. Subsequently, 182 2-h-after irradiation phenotypes and 164 6-h-after irradiation phenotypes were left to test. Also, they used the quantitative transmission disequilibrium test (QTDT) to find cis regulated phenotypes, because the test also checked 5kb upstream and downstream of the target gene’s sequence. After they limited the possible trans- acting regulators, they used Chilibot, the program that scanned all the reported documents and found out the correlation of cell and condition. Moreover, they used quantitative PCR for the calculation of allele-specific changes and siRNA for knocking down the regulators and to find out what gene expression related to what kind of target genes.
    The genes that they found in this study are FAM57A and GADD45B in trans regulated phenotype. Those regulate cell cycle and apoptosis after expose to radiation.

  22. In this paper we discussed the effects of radiation on the expression of genes and the genetic material. Individuals respond differently to radiation and cells have their own mechanisms to recover from this stage of distortion. Gene expression responses differ greatly between individuals and contribute to individual differences in response to radiation.
    Scientist, used microarrays to measure the expression levels of genes in irradiated immortalized B cells from members of 15 Centre d’E ´ tude du Polymorphisme Humain (CEPH) Utah pedigrees. They used cell cultures that are coming from individuals with well documented family history of illnesses. Data were collected for cells at baseline and at 2 and 6 h after exposure to 10 Gy of ionizing radiation. Scientist documented that 3280 out of 10174 of these genes, had affected gene expression after exposure to 10 Gy radiation. One of the genes used in this experiment are genest that regulate gene expression in chromosome 2. They found out that this gene is FAM57A and that is closely related to another gene GADD45B, which is important because transcription factors transcribed them together in the process of transcription, in contrast to when the genes are nore far apart in the chromosome and where there are transcribed separately. Transcription factors involved are RB1,HIVEP2 and VDR.

  23. This paper examines the effects of radiation on the expression of genes and genetic sequences. Radiation is a possible attribute to the cure of cancer. Radiation is considered a type of “medication” and doctors monitor closely how it affects the human body. Radiation is a genotoxis which is used to break up DNA and destroy gene expression.
    Scientists used samples of immortalized B cells from 15 different people that were blood related to each other. They must be related so that they’re gene sequencing would be somewhat similar. Using microarrays, they were able to measure the level of gene expression. The experimental data was broken up into two time points, 2 hours and 6 hours, to measure expression on the journey to cell death.
    The result was 3,280 ionizing radiation-responsive genes out of 10,174 were seen to have a 1.5 fold change in expression level. One gene found (TNFSF9) who’s regulator is CD44 was found to be mutated. The microarray analysis targeted the genes most sensitive to radiation.
    This paper was particularly more difficult to comprehend due to the way they had broken it down. I feel as if it could have been separated and explained a little bit more elaborately.

  24. In order to test genes for radiation-induced expression, researchers have examined genetic studies to identify chromosomal regions and genetic variants that influence expression levels of many genes. First, microarray technology was utilized in order to measure the expression levels of immortalized B cells from 15 different individuals. After 10 Gy of ionizing radiation at 2 h and 6 h, the genes with a 1.5 fold change in gene expression levels of 3,280 ‘ionizing-gene expression’ genes were measured. 10,174 genes were analyzed in the microarray and only 3,280 were focused on because they were radiation responsive. For 2 h and 6 h after irradiation for these genes the fold change varied greatly between individuals. The expression level of JUN plays an important part in variable radiation-induced expression phenotypes and helps determine cellular survival compared to JUN induction. High JUN induction after exposure to 10 Gy of irradiation showed a decrease in cell survival and higher cell death while low JUN induction showed higher rate of cell survival and lower cell death. In order to identify individual differences in radiation-induced levels of JUN and other responsive genes, regulators influencing these differences were analyzed. A genome-wide linkage analysis for each of the 3,280 genes at 2 h and 6 h after irradiation for 15 individuals was carried out. The results showed 1,275 2-h-after-irradiation phenotypes and 1,298 6-h-after-irradiation phenotypes that exceeded the threshold of t=4 which corresponds to a P value of 4×10-5; and more than 1,250 phenotypes showed a significant linkage at a genome-wide threshold of 0.05. Some phenotypes had linkage far beyond the t=4 threshold. Furthermore, cis-regulatory and trans-regulatory expression phenotypes were quite different for radiation-induced gene expression at exposure to radiation. The cis regulators are those that are 5 megabase (Mb) of the target gene while all other linkages represented trans regulators. It was found that out of the 1,275 2-h-after-irradiation phenotypes, only 9 were cis regulated; and 12 out of 1,298 6-h-after-irradiation phenotypes were cis regulated. The rest were trans regulated. For the baseline (normal) gene expression phenotypes, about 20% were cis regulated and the rest 80% were trans regulated. This difference between the cis and trans regulated genes suggests Hotspots which are regions that probably contain regulators influencing gene expression levels, were identified by determining the number of regulators mapping to each of the 554 windows of 5 Mb each. Surprisingly, four hotspots with 18 or more hits were found for the 2-h-after-irradiation phenotypes and the 6-h-after-irradiation phenotypes had two such hotspots. The regulators that mapped to the same hotspots for the target genes seem to suggest co-regulation of genes and have similar functions or are closely related. Following the linkage analysis, family-based association analysis was used to confirm the linkage results and obtain a better view of the linkage regions. Due to many significant linkage findings, expression phenotypes with a twofold change in expression at 2 h and 6 h irradiation were analyzed. Of 346 total phenotypes, there were 182 2-h-after-irradiation phenotypes, 164 6-h-after-irradiation phenotypes, and 6 were cis regulated. In order to confirm association of these cis-regulated genes, quantitative transmission disequilibrium test (QTDT) using SNP markers proved that five of the six expression phenotypes are indeed cis regulated. The test suggests that the remaining 340 phenotypes (178 at 2 h and 162 at 6 h) are regulated by trans regulators. One trans-regulated radiation-induced expression phenotype is BAX found with a linkage on chromosome 1. It has a role in apoptosis. The region contains a known regulator of BAX, the gene TP53BP2. The results identified trans-acting regulators of gene expression which may be polymorphic. The identification of trans-acting regulators is important because none have been previously recognized as a candidate for inducing gene expression.

  25. This paper deals with researchers comparing radiation to genetically linked diseases. They used three levels of responsivness; severe, moderate, and nonresponsive to effects of radiation. So basically their goal was to find out what makes people react differently to radiation. They used cells from morman families, they were chosen because they are very “genetically pure” which means that mormans only marry within their community so you are basically able to analyze a realtivly isolated subset of genetics. The examnined the cells at 0 2 and 6 hours of exposure. From two hours to six hours there is a 1.5 fold change in gene expression levels. Major changes in gene expression allowed researchers to identify “hotspots” or areas that indicate changes in transcripton and thus changes in expression of other genes. Scans of other geneomes to look for the correlation and repetiton of hotspots in related genomes narrowed down what to research. One specifc gene receptor pair that was targeted was The genes that they found in this study are FAM57A and GADD45B in trans regulated phenotype. Those regulate cell cycle and apoptosis after expose to radiation.

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