Immunology: article synopsis
The article, “Extensive RNA Editing and Splicing Increase Self-Representation Diversity in Medullary Thymic Epithelial Cells,” by Danan-Gotthold (2016) describes the process of establishing a central tolerance in the thymus. The immature T cells are trained by the thymic stroma to be immunocompetent. The prepared cells become capable of identifying recognizing invaders. The process which involved instruction of the T cells to discriminate between self and non–self while being potentially harmless. The experiment aims to determine the levels of medullary thymic epithelial cells. The article uses various research methods to analyze and describe the findings from the experiments conducted. The present review will examine the experimental approach, justification, and significance of the research.
Experimental approach and justification
From the article, the researchers used various controlled measures to test their hypothesis. The hypothesis of the research aimed at proofing that extensive RNA editing and gene splicing would increase self-representation diversity in mTECs. The approaches included;
RNA sequencing
This process of RNA sequencing is used in the measurement of a transcriptome. The researchers placed three different gene sample populations through this procedure to achieve their findings; this included; mTECs1 one which included the population with immature genes, mTECs2; which was composed of mature gene population, and (AireKO); which comprised of a population with severe impaired promiscuity of gene expression. mTECs1 and mTECs2 differed in that mTECs1
Justification: the RNA sequencing methodology is considered to be accurate in the measurement of immunology experiments. However, the level of accuracy will be determined by the variables used in the experiment. Thus, the researchers used the three sample to increase the conclusions from the finding of the research. Using the genes from various tissue parts was important to the experiment as it helped single out the mTECs response to the RNA sequencing compared to genes from other tissues.
Alternative splicing
The alternative splicing was used to determine the differences in frequency between the cell type as and cell types and the tissues under examination. The method was significant in the comparison of the detected junctions within each cell and expressing them in mTECs. Like the RNA sequencing method, the researchers also used three different sample variables i.e. the genes with an immature population, the population consisting of mature genes and the population with a severe deficiency in the promiscuity of gene expression.
Justification: The alternative splicing methods used similar sample variables like those used in the RNA sequencing method to ensure consistency. Since the aim of the experiment was to determine the effect of RNA sequencing and Alternative Splicing, similar samples were necessary to avoid inconsistency. Also, the various sample various were necessary to ensure the accuracy of the experiment.
Findings and Methodology
The experiment included the use of various sample variables hence various findings were attained. The researchers’ finding on this experiment included;
mTECs Express High Coding Genome
From the analysis using the above two methods, the research obtained that; most body tissues had a 60-65% of the coding genome. Some parts also expressed a higher percentage of coding genome, i.e., the testes and the brain at approximately 85% coding gene. However, the testes and brain tissues with Aire-deficient mTECs expressed a relatively lower genome of 75%. This was, however, larger than the overall percentage of the other peripheral tissues. From this analysis, it was clear that mTECs expressed much of the coding genome. The mTECs population which is not Aire-deficient expressed a higher coding gene as compared to the Aire-deficient mTECs population.
Tissue Self-shadow in mTECs
The results indicated that the peripheral tissues had a high tissue overlap with a 60-100% tissue signature. The tissues in parts such as the brain and testis expressed a low percentage of tissue overlap of approximately 31%. However, the overlap of the mTECs and other tissues was low in the Aire-deficient mTECs. The central tolerance of the testis in the brain and tests indicate a low tolerance as compared to periphery tissues. Self-shadow cells from these areas escape to the periphery where they are controlled by antigen sequestering. For instance, when cells from areas such as the brain or testis are exposed to antigens, i.e. after an injury, the T cells that escaped the central tolerance may be activated to attack these areas.
Alternative Splicing Events per Gene
An alternative splicing of a single gene gives rise to various protein variants. These variants differ in amino acid sequences. The use of alternative splicing of a gene leads to an increase in the diversity of antigens in these tissues. The difference in tissue antigens helps in a reduction in immune system self-reactivity. The experiment also obtained that mTECs displayed a high splicing propensity to events per gene. For example, mTECs various variants which are tissue restricted, these variants are often expressed in different alternative forms in the hematopoietic system as well as the brain.
Methodology
Leave-One-out Analyses
This expression analysis was utilized in this research to help compare the mTECs genes with other tissues. The research created samples which were randomly aligned. For instance, the research assessed the TRA gene expressions by mTECs by comparing a whole sample of FPKM values. The leave-one-out analysis was used to obtain the size of variable samples. This technique was important to the experiment as it helped assess the TRA genes using the mTECs.
Authors’ conclusion
From the findings, the authors of this article concluded that the high rate of RNA processing expressed in the sample populations with mature genes was responsible for the low rate of differences in antigens of mTECs found in the peripheral tissues. Also from the results indicating a high level of RNA editing, the levels were concluded to include the A -to-I and C -to -U. The authors thus can be said to have achieved good results to support their hypothesis that the use of RNA editing procedure can lead to an increase in gene self-representation. Also, from the results based on alternative splicing, the authors concluded that Aire conditions contributed a limited role in the in the high diversity of genes as a result of alternative splicing.
Indeed, from the findings, I agree with this position due to the results from the various variable samples used in the experiment. The procedures used were accurate as well as the various findings which were critical to the conclusions made. However, the authors fail to mention, in their conclusion, the challenges they encountered that may affect the accuracy of the conclusions. Although the experiments were extensive, few challenges such as the disease may affect the expression of tissue genes from a particular sample hence affecting the overall conclusions.
Significance of the research to immunology
Immunology studies are important as they provide an important insight into the nature of body cells to ensure survival. This research, for instance, seeks to highlight the nature of medullary thymic epithelial cells compared to other cells from the periphery tissues. Thus, the research is significant in explaining the ability of the body to maintain resistance to external disturbances such as injury or disease. As observed from the findings of this experiment, the mTECs have a high rate of diversity through the process of alternative splicing; this helps the cells to multiply various genes which do not exhibit harmful self-reaction. However, in the case of an injury or distance of this medullary cells, the cells from the periphery would produce antigens that with react with these cells. This observation is significant to the medical procedures involving tissues with medullary cells. For instance, cases of injury to the medullary cells will require fast action before the cells react with antigens from the periphery tissues which might cause more damage to the cells.
Understanding of the nature of medullary cells is also important as it helps in the development of drugs to curb damage to the cells as a result of injury or disease. Most of the medullary cells from the experiment were found in tissues from the brain and testis regions. This is delicate parts of the human body and may result in death if not attended to fast. The findings from the experiments thus will contribute significantly to the development of vaccines to control cell damaging diseases such as meningitis or even in developing a fast procedure to attend to injury to ensure saving of lives.
Lastly, the research findings were significant the continued research in immunology. The key aim of all medical researchers from the past is to acquire a better understanding of the human body. As we advance in the medical research, various diseases emerge that pose a threat to human life for instance; HIV/AIDS virus which attacks the cells and reduces the body immunity and other viral diseases such as bird flu. The success of these research thus indicates that despite the increasing nature of new diseases, an increased understanding in the field of immunology hopes to give an answer to these ailments. The research also serves as a reference to future studies that may conduct on the similar topics.