Research On Global Gene Expression In Human Skeletal Muscle By Aerobic Exercise And Its Sanatory Molecular Mechanism

Exercise is one of the most important enviroment factors to maintain fitness, and lack of physical exercise would induce chronic disease. Scientific aerobic exercise can bring better effect to the people with chronic disease than medicine. So research on gene expression influenced by aerobic exercise of different people and different chronic disease can provide idea for developing gene medicine. These years, because of drug resistance, drug price, side effect of drug and individual difference to drug, people pay more attention to prevent disease and those with chronic disease hunger green treatment, however, these all are very closely contacted with aerobic exercise. To reveal molecular mechanism of enhancing health and preventing disease is becoming a popular research topic. There are many reports about biochemistry mechanism of aerobic exercise enhancing health, but reports on molecular mechanism of aerobic exercise are very few. With developing of gene chip, people pay more and more attention to research on aerobic exercise and gene expression. Many foreign research institutes have got great magnanimity of datum by using gene chip in sudying aerobic exercise and global gene expression. Lacking of good algorithm and analyzing tools, there are few reports about synthetic analyzing of datum from different labs which include redundant bioinformation waiting for being further mined.In order to reveal molecular mechanism of enhancing health in view of molecular biology, we used key word of exercise to search and screen the databases in GEO Datasets, at last we download two datum, GSE1786 and GSE1295. With 32 GSM and 24 GSM belonging to GSE1295 and GSE1786 respectively, these two datasets involved with a total of 21 participants: 6 healthy people, 9 COPD patients and 9 people with obesity and hyperinsulinemia (6 male and 3 female). BRB-ArrayTools version 3.4 was the main data analysis tool to mine the datasets mentioned above. The class comparison method was used to screen the differentially expressed genes which were then assessed by hierarchial clustering analysis according to its expression pattern. Gene Ontology(GO) analysis was used to determine the functional categories of genes. KEGG and the online analyzing tool DAVID were applied to search for the associated biologic pathways of the genes of interest. We tried to establish a set of method system ob genechip bioinformation, reveal the sanatory mechanism of aerobic exercise to provide scientific evidence for designing exercise prescription and provide molecular rationale for health-protective remedy.This study includes the following three parts:Part 1 . Influence of aerobic exercise on global gene expression in skeletal muscle of healthy elderly people. BRB-Array Tools 3.4 was used to analyze the data about global gene expression profile in skeletal muscle of 6 healthy elderly people saved in dataset GSE1786. KEGG was applied to search for the biological pathways of the differentially expressed genes. We attempted to resolve two problems, i.e. whether the gene expression pattern would change with aerobic exercise and what were the metabolic pathways linking to the differentially expressed genes. Among the 725 genes which had passed the filtering criteria, 20 were picked out as the significantly differentially expressed genes, of which 3 were up-regulated and 17 down-regulated. After two-dimensional hierarchial clustering analysis, genes with the common expression pattern were found. According to GO annotation, the most differentially expressed genes were involved in the following 8 categories: mitochondria structure(4 genes), cellular organelle(14 genes), endoplasmic reticulum (14 genes), membrane structure(14 genes),cellular component and energetic metabolism(44 genes), carbohydrate metabolism(19 genes), reverse regulation of metabolism(7 genes) and cell transportation(6 genes). 4 metabolic pathways of certain genes were found after KEGG online search. Systemic and routine aerobic exercise could up-regulate genes concerning energy metabolism, especially enzymes in TCA cycle and down-regulate those related to protein synthesis in muscle and sphingolipid metabolism. It suggested that aerobic exercise could help to maintain neuron's integrity, to counter senescence and to accelerate the aerobic metabolism of the lipids, which is good for losing weight and keep figure. Except for these benefits, aerobic exercise, however, is not beneficial to enhance muscle flexibility. Therefore, if the elderly men's flexibility of skeletal muscle will be maintained, adequate strength training is indispensable through the aerobic exercise training .Part 2. Influence of aerobic exercise on global gene expression in skeletal muscle of elderly COPD patients. In this section we attempted to explore the molecular mechanism of aerobic exercise in improving the manifestation of the COPD patients through the analysis of the gene expression profile in skeletal muscle of 6 COPD patients included in the dataset GSE 1786. By BRB-Array Tools analysis, 55 genes with 10 down-regulated and 45 up-regulated were found to be most differentially expressed after screening 736 genes which had passed the filtering criteria. According to GO annotation, 273 genes are linked to the molecular function (MF) of ion transporter activity, transition metal ion binding, cofactor binding and coenzyme binding. And their biologic processes were mainly involved in 16 GO categories such as cellular carbohydrate metabolism, energy derivation by oxidation of organic compounds, main pathways of carbohydrate metabolism, regulation of enzyme activity, acetyl-CoA metabolism, coenzyme metabolism, cofactor metabolism, generation of precursor metabolites and energy, cellular macromolecule metabolism, carbohydrate metabolism and cellular component (CC) of mitochondrion and mitochondrial matrix. Clustering analysis of the 55 most differentially expressed genes and correspondant DAVID online searching were then performed to comprehensively explore the molecular mechanism of aerobic exercise in improving the manifestation of the COPD patients. Aerobic exercise could down-regulate the expression of some ribosomal protein genes( PRL28, PRS19, SNRPF, RPS21, SNRPE ) ,hence inhibited the growth of inflammatory cells in COPD patients. It could also down-regulate the genes controlling the programming cell death so to improve the vitality of normal cells and life span. The up-regulation of CREBBP/EP300 inhibitor 1 (CRI1) induced by aerobic exercise might partially explain why it was beneficial to the health of COPD patients. It was reported that the TNF-αgene would be up-regulated in COPD patients, which, however, was not confirmed in this study. Nevertheless, the up-regulation of PIK3R1 in our analysis might lead to the expression alteration of TNF-α. Among various regulation mechanisms and metabolic pathways, PIK3R1 might play the pivotal role in helping COPD patients recover, because its up-regulation was connected to almost all the expression alterations of the related genes. This may imply that PIK3R1 is the major factor in all the pathways capable of influencing expression of many other genes and all these genes should cooperate in order to help improve COPD patients' health. A long term of systemic aerobic exercise would induce expression changes of several sensitive genes in COPD patients and then provoke series of biological process beneficial to health.Part 3. Influence of aerobic exercise on global gene expression in skeletal muscle of patients with obesity and hyperinsulinemia. This section analyzed the dataset GSE1295 which included 30 GSMs(after excluding 2 incomplete GSMs from the original 32), among which 6 GSMs were generated on microarray platform GPL91 and other 24 GSMs were generated on microarray platform GPL96. The datasets based on the two different microarry platforms were comparatively analyzed to asses their gene expression levels at various sampling time, and the levels both before and after aerobic exercise as well as that between males and females. Class Comparison, Cluster analysis, GO comparison of BRB-Array Tools, DAVID online searching tool were all used to find pathways of significance. The list of most differentially expressed genes and their clustering map and scatter plot were generated. It is known that different microarray platforms are likely to generate different results even when they are used to explore similar problems. The reasons for it might be the difference of research targets or protocol details in experiments. In this study, we compared the data based on two platforms namely GPL91 and GPL96, and found some genes sharing the similar expression pattern on both platforms. After a comprehensive analysis, we believe that it's better to use a high density microarray but a low density one to study gene expression on the whole scale to ensure data integrity. The GPL96 platform generated more accurate data with less false positive or negative results and slighter data deviation than GPL91. This may suggest to some degree that GPL96 is superior than GPL91.The molecular mechanism of human body's response and adaptability to aerobic exercise are not exactly the same for different groups of people, e.g. males and females. The Influence of aerobic exercise is also individual oriented, so the exercise remedy should be individuated. Scientific and proper aerobic exercise can help people of obesity to lose weight and people with hyperinsulinemia or COPD to recover. As the adaptability at the transcription level will lose again if the breaks of aerobic exercise last too long, it's necessary to carefully design an exercise plan to ensure the best effect. It's better to do some aerobic exercise once a day, i.e. the intervals between two times of exercise should be about 24hours to 72 hours. The Influence of exercise will not be apparent if the interval is over 72 hours. Compared to healthy people, those with obesity and hyperinsulinemia have some significantly differentially expressed genes concerning metabolism disorder even at the base level and also some abnormality of genes associated with immune system. After aerobic exercise, the abnormal differentially expressed genes would decrease , the fatty acids oxidation and aerobic oxidation of carbohydrate enhanced, which improved the economy of energy metabolism, and so the lactic acid reduced, muscle glycogen and hepatic glycogen increased, which may prevent the hyperinsulinemia from developing to non-insulin dependent diabetes(NIDD). Aerobic exercise made AMPK activity in hyperinsulinemia patients recover to normal level, and made three types of AMPK (1, 2 andβ1) express normally, which provide a good idea for producing gene drug to regulate AMPK activity and targeted therapy of NIDD. If genes of CTAP III t-PA and tetranectin expressed abnormally, metabolic syndrome would be very likely to emerge, which is a main factor to induce disease of blood vessel and thrombosis. Fortunately, the expression of CTAP III, t-PA and tetranectin could change after aerobic exercise, which make it practical that aerobic exercise can help to enhance human's health.This study combined BRB-ArrayTools with KEGG and DAVID to analyze gene expression datasets, which created a new way to mine data of gene expression generated from microarray experiments and helped to establish the subject of microarray bioinformatics. Additionally, this research classified and compared the gene expression datasets from different labs and different platforms, screened the differentially expressed genes of healthy people, COPD patients, and people with obesity and hyperinsulinemia after aerobic exercise, clustered and analyzed gene expression patterns and sanatory molecular mechanism of aerobic exercise. We established a set of method system of genechip bioinformation, revealed the sanatory mechanism of aerobic exercise to provide scientific evidence for designing exercise prescription and provide molecular rationale for health-protective remedy. But in this paper there isn't any experimental testing for the analyzing results, and mining bioinformation of some genes are not very profound, which will be a very important task to be solved in the following researching work.