Naveen prakash master project report combined_final

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Glioma Pathways Thesis_Analysis_M.Sc Project

Transcript of Naveen prakash master project report combined_final

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    BS 592 M.Sc. Project Dissertation

    DEVELOPMENT OF GLIOMA GENOME

    AND PROTEOME DATABASE FOR

    PATHWAY ANALYSIS

    Project dissertation submitted by

    NAVEEN PRAKASH BOKOLIA

    09530022

    In partial fulfillment of the requirements for the award of the

    degree of Master of Science (Biotechnology)

    Guide: Dr. Sanjeeva Srivastava

    Department of Biosciences and Bioengineering

    INDIAN INSTITUTE OF TECHNOLOGY, BOMBAY

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    ACKNOWLEDGEMENT

    I would like to express my sincere gratitude towards my supervisor Dr.

    Sanjeeva Srivastava and for giving me an opportunity to work in their labs and

    for guiding me throughout my project.

    I would specially want to thank Dr. G. Subharmanyam and Dr. Ashutosh

    Kumar for their kind support and guidance.

    I would like to thank my lab mates Karthik, Shipra, Meghna and Renissa, for

    helping me out throughout the project and also for making my stay in the lab

    memorable.

    I would also like to convey my regards to my batchmates Komal and Kishore

    for making my stay at IITB a memorable one.

    Finally, I express my sincere gratitude to my parents, my sisters and my friends

    for their everlasting support.

    NAME: Naveen Prakash Bokolia

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    I. CONTENTS

    1. INTRODUCTION

    1.1 Glioma 10-11

    1.1.1 Classification of Glioma or Tumor Grading 11-14

    1.1.2 Genetic Alterations in the Glioma 14-15

    1.2 Proteomics and Glioma 15

    1.3 Databases

    1.3.1 Need of Databases 15

    1.3.2 Disease Database - Oncomine Database 15-16

    1.3.3 Protein Interaction Database HPRD 16

    1.3.4 Need of Glioma Database 16

    1.4 Pathway Analysis 16-17

    1.5 Ingenuity Pathway Analysis Software 17

    2. OBJECTIVES

    2.1 Glioma Genome and Proteome Databse 17

    2.2 Pathway Analysis/ Analysis of Database Containing Proteins and Genes 17-18

    3. GLIOMA DATABASE

    3.1 Davelopment Stages of the Glioma Database 18-19

    3.2 Important features of the Glioma Database 19-21

    4. MATERIALS AND METHODS FOR PATHWAY ANALYSIS

    4.1 INGENUITY PATHWAY ANALYSIS SOFTWARE 21

    4.2 DAVID Bioinformatics Resource 6.7 21

    4.3 PANTHER (Protein ANalysis THrough Evolutionary Relationships) 21

    4.4 Input Files 22

    4.5 Software and Websites 22

    5. OUTPUTS AS THE RESULTS FROM THE IPA: 23-24

    6. RESULTS FROM THE IPA FOR EACH DATASET FILE:

    6.1 Results for the High Grade 1 24-34

    6.2 Results for the High Grade 2 35-37

    6.3 Results for the Glioblastoma 37-39

    6.4 Results for Astrocytoma 39-42

    6.5 Results for Low Grade 42-43

    6.6 Results for Validated High Grade 43-45

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    7. ANALYSIS AND DISCUSSION PART - WITH THE HELP OF RESEARCH

    ARTICLES:

    7.1 Criteria for Analyzing Pathways with the Help of Research Articles 45-46

    7.2 Pathways Already Well Established in the Glioma 46-54

    7.3 Novel Information for Signaling Pathways Involved in the Glioma 54-68

    7.4 New findings and New Correlations of Canonical Pathways with the Glioma 68-76

    8. CONCLUSION 76-77

    9. REFERENCES 77-86

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    LIST OF FIGURES

    Figure 1: Immunohistochemical Image of the Anaplastic Astrocytoma

    Figure 2: Immunohistochemical Image of the Glioblastoma Tumor

    Figure 3: Excel Image of the Glioma Genome and Proteome-Manual Curation Part

    Figure 4: Pathways Categories

    Figure 5: Canonical Pathways for the High Grade1

    Figure 6: Canonical Pathways for the High Grade2

    Figure 7: Canonical Pathways for the Glioblastoma

    Figure 8: Canonical Pathways for the Astrocytoma

    Figure 9: Canonical Pathways for the Low Grade

    Figure 10: Canonical Pathways for the Validated High Grade

    Figure 11: GBM Signaling

    Figure 12: GBM Signaling from the Literature

    Figure 13: PTEN Signaling

    Figure 14: PI3K-AKT signaling

    Figure 15: p53 Signaling

    Figure 16: Glioma Signaling

    Figure 17: Glioma Invasiveness Signaling

    Figure 18: Integrin Signaling

    Figure 19: Axonal Guidance Signaling

    Figure 20: Semaphorins signaling in Neurons

    Figure 21: IL-8 Signaling

    Figure 22: IL-6 Signaling

    Figure 23: HIF-1 Alpha Signaling

    Figure 24: Feedback Regulation of PHD

    Figure 25: Wnt-beta catenin signaling

    Figure 26: Glucocorticoid Signaling

    Figure 27: Newly Suggested role of Glucocorticoid Signaling in Glioma

    Figure 28: Arachidonic Acid Metabolism

    Figure 29: Newly Suggested Role of Upregulated Arachidonic Acid metabolism in

    Glioma

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    Figure 30: Role of NANOG in Embryonic cell Pluripotency

    Figure 31: Sonic HEDGHOG Signaling

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    Gliomas are the most common primary brain tumors that originate from the cancerous glial cells.

    These glial cells are the mainly astrocytes, oligodendrocytes and Schwann cells. When the

    genetic alterations occur in these types of cells they become cancerous. The degree of genetic

    alterations varies from low grade to high grade or less malignant stage to the higher malignant

    stage of glioma. The major objective of this project is to understand the various possible

    molecular mechanisms and signaling pathways that leads to the glioma. Therefore the first part

    of this project focused on manual curation of glioma data from the literatures to identify

    candidate genes/proteins based on the genomics and proteomics studies. By manually curating

    the data we extracted scientifically important information: genes, proteins, fold change values

    techniques etc. After completion of this manual curation part we documented all the genes and

    proteins information related to glioma and made a master table for further analysis. We obtained

    the entire gene IDs and organized the data for further analysis by using various softwares. We

    used Ingenuity Pathway Analysis (IPA), DAVID and PANTHER software to obtain the various

    possible pathways from our genome and proteome dataset. The results obtained from this

    analysis revealed that many signaling pathways are possible to build from our input genes and

    proteins information. These pathways are ranked according to their p-values so that we can

    obtain information for their significance. We further looked at the relevance of these signaling

    pathways in the context of glioma and other diseases. For example, our results demonstrated

    integrin and wnt-catenin signaling could be involved in glioma but we dont know which type of

    integrin or wnt plays role in the glioma. Furthermore, we modified few pathways by adding new

    information from the research papers. Few pathways obtained in our study such as glioma

    signaling, GBM Signaling and PTEN Signaling validated that our findings are similar to

    published studies in literature but we did not perform further investigation about these pathways

    since these are known targets. Our analysis and discussion is more focused on new potential

    signaling pathways in glioma in the possible short time period. Finally, this study enabled us to

    provide an overview of various pathways involved in glioma, find out new correlations and

    connections as well as possible new roles of various signaling pathways in glioma.

    1. INTRODUCTION

    1.1 Glioma: Gliomas are the most common primary brain tumor which develops from the

    cancerous glial cells, therefore called gliomas. There are several different kinds of glial

    cells: astrocytes, oligodendrocytes and ependymal cells. Primary brain tumors are 1.4%

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    among all the cancer types; and 2.4% deaths are only due to this type of cancer in the

    United States. Where approximately 20,500 newly diagnosed cases come and 12,500

    deaths are accounted every year due to the primary malignant tumor [Gladson et al.,

    2010].

    Unlike other cancers, glioma tumors grow in the defined space inside the head. So they

    grow by pushing healthy cells and due to space limitation they kill healthy cells also. To

    kill healthy nerve cells, glioma tumors release large quantities of the neurotransmitter

    glutamate [Takano et al., 2001]. Large amount of glutamate is very toxic to neurons and

    causes seizures in most of the people. Depending on the size of the tumor and location,

    other symptoms also found like paralysis, behavior changes and dizziness. One major

    difference between other cancer and glioma is that metastasis term is not used for the

    glioma because malignant form does not affect or spread to the other organs in the body.

    1.1.1 Classification of Glioma or Tumor Grading: Tumors are mainly graded based on

    their microscopic appearances. The grade indicates the level of malignancy. Tumors

    are graded based on their mitotic index (growth rate), vascularity (blood supply),

    presence of a necrotic center, invasive potential (border distinctness) and the extent of

    similarity to normal cells. Glioma tumors are histologically divided into four grades,

    according to the World Health Organization (WHO) criteria [Gladson et al., 2010].

    Grade I: These tumors typically having a good prognosis and are least malignant

    form of the tumor. These tumors g