Tài liệu Potential gene network for the health effect of exposure to pcb fs on human diffuse large cell lymphoma

THAI NGUYEN UNIVERSITY UNIVERSITY OF AGRICULTURE AND FORESTRY NATIONAL TSING HUA UNIVERSITY THAVISACK MIVONGSACK TITLE: POTENTIAL GENE-NETWORK FOR THE HEALTH EFFECT OF EXPOSURE TO PCB/FS ON HUMAN DIFFUSE LARGE CELL LYMPHOMA BACHELOR THESIS Study Mode:Full-time Major: Environmental science and management Faculty:International Programs Office Batch: 2013-2017 Thai Nguyen, 21/12/2017 DOCUMENTATION PAGE WITH ABSTRACT Thai Nguyen University of Agriculture and Forestry Degree Program Bachelor of Environmental Science and Management Student name THAVISACK MIVONGSACK Student ID DNT 1253110103 Thesis Title Potential gene-network for the health effect of exposure to pcb/fs on human diffuse large cell lymphoma Supervisor (s) Prof. Chun-Yu Chuang, Associate. Prof. DRTran Van Dien Abstract: The thesis describes the Lymphoma is the most top cancers in the worldwide, and the incidence rises strikingly since the last half of 20thcentury. Lymphoma is a cancer affecting the immune system; the major risk factor is associated with exposure to occupational or environmental chemicals. Polychlorinated biphenyls (PCBS) are a class of organic chemicals, known as congeners that have been used in a variety of commercial products. PCBs were used in caulking, electronics, fluorescent light ballasts and other building materials from the 1950s to the late 1970s. Buildings built or renovated during that time may contain PCBs in caulking and other materials. PCBare very stable mixtures that are resistant to extreme temperature and pressure. PCBS were used widely in electrical equipment like capacitors and transformers. They also were used in hydraulic fluids, heat transfer fluids, lubricants, and plasticizers. i PCBs have been released into the environment through spills, leaks from electrical and other equipment, and improper disposal and storage. It is estimated that more than half of the PCBS produced have been released into the environment. Once in the environment, PCBS can be transported long distances and they bind strongly to soil and sediment so they tend to be persistent in the environment. They have been found in air, water,soil, and sediments throughoutthe world.PCBs can enter the body through inhalation, ingestion, and dermal routes of exposure. They are readily absorbed but are slowly metabolized and excreted. In particular, PCBs initially distribute to the liver and muscle tissues, but eventually accumulate in lipid-rich tissues. This leads to greater concentrations of PCBS in adipose tissue, breast milk, the liver, and skin. The data analysis was subsequently performed using Network Analyst, a standard web browser for network analysis and interactive exploration. Keywords TCDD, Furans, DBLCL, bioinformatics, GEO, Array Express Number of pages 59 Date of submission October,2017 Supervisor’s signature ii ACKNOWLEDGEMENT First of all, we know that knowledge is just only can be proved by our works, and internship is one of the best opportunity for a student whose can do their first project before they find their jobs to enroll in the future. Besides that, we are not only improving ourselves by knowledge in company environment, institute or laboratory but also making more friends whose are having many experiences in environment, and it will help us in the near future. From my perspective, this internship is absolutely needed, helpful and important. Because of that, and be assigned by the International Programs Office and also the allowed of Department of Biomedical Engineering and Environmental Sciences (National TsingHua University, Taiwan). To well done this thesis, I want to express profound gratitude to Advanced Education Program, the school administrators, the staffs in Department of Biomedical Engineering and Environmental Sciences, the staffs of YC laboratory, and particularly my supervisor,Associate. Prof. DRTran Van Dien and Prof Chun-Yu Chuang whose were always supporting me every single time I got troubles. I would like to send both of supervisors a warmly thanks for the supporting me, and for their sacrifice for education, as same as environmental issues in Taiwan and Vietnam as all countries in the world. Finally, I would like to say that I had tried my best to finish this thesis in the best way, I guess. However, to be honest, I partly believe that my thesis still have some problems because of the limitation of knowledge and reality experiences, especially in our environmental circumstances these days. It is totally happy if I can iii get feedbacks and comments from you, my Teachers, Professors, and Supervisors, to finish my thesis in a fantastic way, to get the best results. Sincerely, Thai Nguyen October, 2017 THAVISACK MIVONGSACK iv TABLE OF CONTENTS DOCUMENTATION PAGE WITH ABSTRACT ..........................................................i ACKNOWLEDGEMENT ............................................................................................. iii TABLE OF CONTENTS ................................................................................................v LIST OF FIGURES ...................................................................................................... vii ABBRIVIATION ...........................................................................................................ix PART I: INTRODUCTION ............................................................................................1 1.1. Rationale ...................................................................................................................1 1.2. Objectives .................................................................................................................3 PART II:LITERATURE REVIEW .................................................................................4 2.1. Polychlorinated biphenyls (PCBs) ..........................................................................4 2.1.1. Polychlorinated Biphenyls (PCBs) Toxicity .........................................................5 2.1.2. The industrial production of PCB..........................................................................6 2.1.3. PCBs and Environment .........................................................................................7 2.1.4. Health Effects of PCBs ..........................................................................................9 2.2. Lymphoma ..............................................................................................................12 2.3. Biological pathway .................................................................................................13 2.3.1. Diffuse large B cell lymphoma (DLBCL) ...........................................................15 2.4. Gene-network components .....................................................................................17 2.4.1 Gene-network database:Array Express and (GEO)..............................................18 2.4.2. Statistical analysis ...............................................................................................19 3.2. Gene network analysis and Cytoscape for gene-network analysis ........................24 v PART IV: RESULTS AND DISCUSSIONS ................................................................29 4.1. Genetic datasets ......................................................................................................29 4.1.1 Differentially expressed genes .............................................................................32 4.1.2. Gene-network construction of DLBCL and PCBs ..............................................35 4.2. Discussion ...............................................................................................................38 PART V: CONCLUSION AND RECOMMENDATION ............................................41 5.1. Conclusion ..............................................................................................................41 5.2. Recommendation ....................................................................................................42 REFERENCES ..............................................................................................................43 vi LIST OF FIGURES Figure 2.1: Diagram of Polychlorinated Biphenyls (PCBs)(Shoemaker, 2005) .............6 Figure2.2: Polychlorinated biphenyls – levels in foods ................................................11 Figure 2.3: Diffuse large Bcell lymphoma ....................................................................16 Figure 3.1: The flowchart of methodology....................................................................24 Figure 3.2: Cytoscape home page(Shannon P, 2003) ...................................................26 Figure 4.1: Diagram of Gene-network construction of DLBCL & PBCs Sources: (Rosenwald,2002) ..........................................................................................................37 Figure 4.2: The potential regulatory pathway of NHL progression in response to PCB exposure Source: (Miller, 2001) ....................................................................................38 vii LIST OF TABLES Table 4.1: Genetics Datasets of DLBCL ............................................................ 30 Table 4.2: Datasets on Array Express used for PCB analysis ............................ 31 Table 4.3: Differentially expressed genes, including –up and down – regulate genes in Diffuse Large B cell lymphoma compared to normal cells .................. 33 Table 4.4: Differentially expressed genes, including up-and down – regulated genes activated by PCB compared to control group ........................................... 35 viii ABBRIVIATION ABC Activated B cell AML Acute myeloid leukemia ALL Acute lymphoblastic leukemia B-Cells B-lymphocytes B-NHL Non Hodgkin lymphoma DLBCL Diffuse large B cell lymphoma DMSO Dimethyl sulfoxide DEGS Differentially expressed genes analysis FL Follicular lymphoma FDR False discovery rate GEO (NCBI) Gene expression omnibus National center for Biotechnology information GO Gene Ontology HL Hodgkin lymphoma HIV Human immunodeficiency virus ID Identifier IARC International agency for research on cancer MIAME Minimum information about microarray experiment MAGE-ML Microarray and Gene Expression Markup Language NPL N-acetylneuraminate pyruvate lyase NHL Non Hodgkin lymphoma PCB Polychlorinated biphenyls RS Reed-Sternberg SNPs Single Nocleotide Polymorphisms T-Cells T-lymphocytes ix PART I: INTRODUCTION 1.1. Rationale Polychlorinated biphenyls, in short PCBs, are a group of man-made chemicals.PCBs have been used in many different products, including electrical equipment, surface coatings, inks, adhesives, flame-retardants, and paints. PCBs may be released into the environment, for instance when waste that contains PCBs is incinerated or stored in landfills(Morris, 2017).PCBs are probable human carcinogens and can also cause non-cancer health effects, such as reduced ability to fight infections, low birth weights, and learning problems. The risks and hazards associated with PCBs in the Hudson River are a function of the toxicity of PCBs and an individual's exposure(Hudson, 2016).The most commonly observed health effects in people exposed to large amounts of PCBs are skin conditions such as acne and rashes. Studies in exposed workers have shown changes in blood and urine that may indicate liver damage. PCB exposures in the general population are not likely to result in skin and liver effects. Most of the studies of health effects of PCBs in the general population examined children of mothers who were exposed to PCBs(Buford Hwy NE, 2014). Polychlorinated biphenyls (PCBs) were powerful carcinogens. A carcinogen is any substance or agent that tends to produce a cancer. Polychlorinated biphenyls are found in things such as asbestos and radon. However, we are also forced to consume it in our foods. There are exposed to many substances at any given time. This includes those we encounter at work, school, or home, in the food we eat and in the air we breathe(Jeni, 2011). 1 But it’s almost impossible anyone could know precisely what they’ve been exposed to. PCBs are toxic. They can provoke serious health effects that go beyond cancer. They can also play a role in hormone disruption, reduced ability to reproduce, skin toxicity, immune system disorders. Lymphoma is the most common blood cancer that develop in lymphatic system. The two main categories of lymphoma are Hodgkin lymphoma and non-Hodgkin lymphoma (NHL)(Ferlay, 2013). Lymphoma occurs when cells of the immune system called lymphocytes, a type of white blood cell, grow and multiply uncontrollably. Cancerous lymphocytes can travel to many parts of the body, including the lymph nodes, spleen, bone marrow, blood, or other organs, and form a mass called a tumor. The body has two main types of lymphocytes that can develop into lymphomas: Blymphocytes (B-cells) and T-lymphocytes (T-cells). Diffuse large cell lymphoma (DLBCL or DLBL) is a cancer of B cells, a type of white blood cell responsible for producing antibodies. It is the most common type of non-Hodgkin lymphoma among adults (Clinical, 1997), with an annual incidence of 7–8 cases per 100,000 people per year in the USA and the UK (Morton et al., 19922001). This cancer occurs primarily in older individuals, with a median age of diagnosis at approximately 70 years of age (Smith et al., 2011), though it can also occur in children and young adults in rare cases(Smith at el., 2010). DLBCL is an aggressive tumor which can arise in virtually any part of the body (Kumar et al., 2009),and the first sign of this illness is typically the observation of a rapidly growing mass, sometimes associated with B symptoms: fever, weight loss, and night sweats (Freeman et al, 2012). 2 1.2. Objectives • The aims of the study was tosummarize the health implications associated with exposure topolychlorinatedbiphenyls (PCBs). • To identify the potential pathway exposure to dioxin corresponding to DLBCL • To express the gene number that exposure to dioxin can induce DLBCL and PCBs • To evaluate diffuse large B-cell lymphoma (DLBCL) and construct regulatory networks of genes and miRNAs to gradually reveal the underlying mechanisms of DLBCL development. 3 PART II:LITERATURE REVIEW 2.1. Polychlorinated biphenyls (PCBs) Polychlorinated biphenyls (PCBs) is a group of organic compounds used in the manufacture of plastics, as lubricants, and dielectric fluids in transformers, in protective coating for wood, metal and concrete, and in adhesives, wire coating and so forth (New York, 2003). It can cause a number of different harmfuleffects. They are highly toxic to aquatic life and persist in the environment for long periods of time. They can accumulate in food chains and may produce harmful sideeffects at high concentrations. There are no known natural sources of PCBs in the environment. PCBs are either oilyliquids or solids and are colorless to light yellow. Some PCBs are volatile and may exist as avapor in air. They have no known smell or taste(Buford Hwy NE, 2014). PCBs enter the environment as mixturescontaining a variety of individual chlorinated biphenyl components, known as congeners, as wellas impurities. Because the health effects of environmental mixtures of PCBs are difficult toevaluate, most of the information in thistoxicological profile is about seven types of PCBmixtures that were commercially produced. These seven kinds of PCB mixtures include 35% ofall the PCBs commercially produced and 98% of PCBs sold in the United States since 1970.Some commercial PCB mixtures are known in the United States by their industrial trade name,Aroclor. For example, the name Aroclor 1254 means that the mixture contains approximately54% chlorine by weight, as indicated by the second two digits in the name. Because they do not burn easily and are good insulating materials, PCBs were used widely as coolants and lubricantsin transformers, capacitors, and other electrical equipment. The manufacture of PCBs stopped inthe 4 United States in August 1977 because there was evidence that PCBs build up in theenvironment and may cause harmful effects. Consumer products that may contain PCBs includeold fluorescent lighting fixtures, electrical devices or appliances containing PCB capacitors madebefore PCB use was stopped, old microscope oil, and old hydraulic oil. 2.1.1. Polychlorinated Biphenyls (PCBs) Toxicity Since PCBs are found throughout the environment, it is likely that everyone has been exposed to them. PCBs can enter the body by eating or drinking contaminated food, through the air we breathe, or by skin contact. PCBs are easily absorbed by the body and are stored in fatty tissue. PCBs are not eliminated well, so they can accumulate in the body (Gray et al.,2003; Thrasher and Crawley, 2009). Most people are exposed to PCBs by eating contaminated fish, meat, and dairy products. Catfish, buffalo fish, and carp usually have the highest PCB levels. Plants take up only small amounts of PCBs from the soil, so amounts in grazing animals and dairy products are generally lower than in fish. Dust contaminated with very small levels of PCBs may be found on the outer surfaces of fruits and vegetables PCBs do not dissolve well, so exposure to them from water is usually not a concern. Some private wells may use old submersible pumps that contain PCB oil. If the pump seal fails, PCBs can leak into the well and contaminate the drinking water older fluorescent lights found in schools, offices and homes may still contain transformers or ballasts that contain PCBs. If the ballasts fail, PCBs can leak out and contaminate exposed surfaces and the air. PCB levels measured in the air after a light ballast failure can be 5 significant. The workplace also may be a source of PCB exposure(Crago et al., 2003, Etzel, 2006). Figure 2.1: Diagram of Polychlorinated Biphenyls (PCBs)(Shoemaker, 2005) PCBs are chemicals formed by attaching one or more chlorine atoms (at the Xs in Figure 1 above) to a pair of connected benzene rings.Depending on the number and position of chlorine atoms attached to the biphenyl ring structure, 209 different PCB congeners can be formed. PCB congeners can be divided into the coplanar, the monoortho-substituted PCBs, and other non-dioxin-like PCBs. The significance of this designation is that coplanar and some of the mono-ortho-substituted PCBs have dioxin-like toxicological effects(Shoemaker, 2005). 2.1.2. The industrial production of PCB PCBs were used for many different industrial purposes, including the afore mentioned electrical industry and: Hydraulic fluids; casting wax; carbonless carbon paper; compressors; heat transfer systems; plasticizers; pigments; adhesives; liquid cooled electric motors; fluorescent light ballasts. There is little wonder that this group of chemicals was so readily accepted. One of the qualities that make PCBs so desirable is one of the characteristics that make PCBs so hazardous to the environment. The high thermal and chemical resistance of PCBs means that they do not readily break down when exposed to heat 6 orchemical treatment. This is a very desirable trait for lubricants. However, since PCBs do not break down they remain in the environment and continue to build up as more are introduced into the environment. Worms consume organic matter contaminated with PCBs, and small fishes eat the worms. Small fish are then eaten by larger fish, and perhaps the large fish are eaten by an eagle. Worms may only live for a short time, but eagles live for a long time. They continue to eat lots of large fish that ate lots of small fish that ate lots of contaminated worms. Over a lifetime, the PCB concentration in the fatty tissue of the eagle would continue to increase as it ate more and more contaminated fish. This accumulation of a chemical in animals at the top of the food chain is known as bioaccumulation. If the chemical happens to be toxic, the consequences become obvious. 2.1.3. PCBs and Environment Before 1977, PCBs entered the air, water, and soil during their manufacture and use in theUnited States. Wastes that contained PCBs were generated at that time, and these wastes wereoften placed in landfills. PCBs also entered the environment from accidental spills and leaksduring the transport of the chemicals, or from leaks or fires in transformers, capacitors, or otherproducts containing PCBs. Today, PCBs can still be released into the environment from poorlymaintained hazardous waste sites that contain PCBs; illegal or improper dumping of PCBwastes, such as old transformer fluids; leaks or releases from electrical transformers containingPCBs; and disposal of PCB-containing consumer products into municipal or other landfills notdesigned to handle hazardous waste. PCBs may be released into the environment by the burningof some wastes in municipal and industrial incinerators.Once in the environment, PCBs 7 do not readily break down and therefore may remain for verylong periods of time. They can easily cycle between air, water, and soil. For example, PCBs canenter the air by evaporation from both soil and water. In air, PCBs can be carried long distancesand have been found in snow and sea water in areas far away from where they were released intothe environment, such as in the arctic. As a consequence, PCBs are found all over the world. Ingeneral, the lighter the type of PCBs, the further they may be transported from the source ofcontamination. PCBs are present as solid particles or as a vapor in the atmosphere. They willeventually return to land and water by settling as dust or in rain and snow. In water, PCBs maybe transported by currents, attach to bottom sediment or particles in the water, and evaporate intoair. Heavy kinds of PCBs are more likely to settle into sediments while lighter PCBs are morelikely to evaporate to air. Sediments that contain PCBs can also release the PCBs into thesurrounding water. PCBs stick strongly to soil and will not usually be carried deep into the soilwith rainwater. They do not readily break down in soil and may stay in the soil for months oryears; generally, the more chlorine atoms that the PCBs contain, the more slowly they breakdown.Evaporation appears to be an important way by which the lighter PCBs leave soil. As agas, PCBs can accumulate in the leaves and above-ground parts of plants and food crops.PCBs are taken up into the bodies of small organisms and fish in water. They are also taken upby other animals that eat these aquatic animals as food. PCBs especially accumulate in fish andmarine mammals (such as seals and whales) reaching levels that may be many thousands oftimes higher than in water. PCB levels are highest in animals high up in the food chain. 8 Environmental contamination from PCBs has been caused by accidental releases, careless disposal practices, and leaks from industrial facilities or chemical waste-water disposal sites. PCBs degrade very slowly, are cycled and transported within the ecosystem, and bioaccumulate as they move up the food chain. Once released into the environment, PCBs adsorb strongly to soil and sediment. As a result, these compounds tend to persist in the environment, with half-lives for most congeners ranging from months to years. PCBs leach from soil slowly, particularly the more highly chlorinated congeners, and translocate to plants via soil insignificantly. Cycling of PCBs through the environment involves volatilization from land and water surfaces into the atmosphere, with subsequent removal from the atmosphere by wet or dry deposition, then revolatilization. In the general population, inhalation of these airborne PCBs is one route of exposure, in addition to the food source of exposure to PCBs. Once released into the environment, PCBs may undergo all of the volatilization from land and water surfaces into the atmospheres, biotransformation into more complex undefined mixtures, fast degradation within the ecosystem and strong adsorption to soil and sediment. 2.1.4. Health Effects of PCBs A growing number of studies have found serious health effects from exposure to PCBs. PCBs are likely to cause cancer and are classified as a “probable carcinogen” by the federal Environmental Protection Agency and the International Agency for Research on Cancer. In addition, a study found children’s risk of developing acute lymphocytic leukemia, increased by two-fold when PCBs were detected in the dust of 9 a room in which the child spent a significant amount of time(Ward M H, 2009). People with potentially high exposures to PCBs include: Recreational and subsistence fishers who typically consume larger quantities of locally caught fish than the general population, Children with in utero and lactational exposure to PCBs from mothers who eat large quantities of contaminated fish during pregnancy and while nursing,Certain farmers and their families who consume PCB-contaminated food via their own farmraised beef and dairy cattle, andpeople living near incinerators, other PCB-disposal facilities, or NPL hazardous waste sites where PCBs have been detected (Buford Hwy NE A. , 2016). PCBs can enter human cells and tissues when contaminated air is breathed in, when contaminated food enters the digestive system, or through contact with the skin. Tests on laboratory animals show that PCBs are readily absorbed through the digestive tract when swallowed, and to a lesser extent through the skin. The main PCB elimination routes are through the faeces, urine, and breast milk. Once in the gastrointestinal tract, ingested PCBs diffuse across cell membranes and enter blood vessels and the lymphatic system. PCBs, especially those that contain a greater number of chlorine atoms, are readily soluble in fats and thus tend to accumulate in fat-rich tissues such as the liver, brain and skin.In mothers, PCBs have also been found to pass into the placenta, umbilical cord blood, and breast milk. PCBs can undergo different transformations in the body and then either be stored in certain tissues or excreted. Transformations that lead to accumulation,PCBs can easily be transformed into persistent metabolites that are not readily excreted and that can accumulate in 10