Bio413 Cell Signaling

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					Cell Signaling 2008
Syllabus
Instructor: Yinsheng Wan, Ph. D. Associate Professor, Dept of Biology, Providence College, E-mail: yswan@providence.edu Textbook: No such books are available, but materials to be covered will be provided prior to each class. Relevant Web Sites: www.signaling-gateway.org and www.skte.org.

Brief Course Description: The physiological systems in human beings are tightly regulated and if unchallenged maintain homeostatic. Deviation from homeostasis however causes human diseases including various types of cancer. For the past two decades, modern cell/molecular biology techniques have been applied to unravel those regulatory mechanisms. The complicated process from stimulation such as hormones or environmental insults to gene expression is now termed cell signal transduction, namely information flow from cell surface receptor activation to kinase cascade activation to transcription factor activation to gene expression. This course, which will explore the convoluted cellular activities upon stimulation, is designed to provide coverage across a broad spectrum of disciplines including genetics, developmental biology, neurobiology, immunology, physiology, and cell biology. Molecular targets for drug development will be also discussed. Class discussion and presentation will focus on reading and comprehension from most recent scientific literatures and experimental design/methods. Prerequisites: BIO 200, CHM 201-202. CHM 309 is also highly recommended. Note: due to the progress made daily in cell signaling field, the lectures will be modified accordingly. Expectations: At the end of the semester, students are required 1) to remember the terminology associated with cell signaling, 2) to remember major cell signaling pathways, 3) to read and comprehend research papers in cell signaling filed and to be able to draw possible cell signaling pathways, 4) to write research proposal in certain areas, and 5) to work with others to execute experimentations in cell signaling research. Course Grade Distribution: Class discussion, 10%, two exams, 80%, one Project presentation, 10%. Class discussion is important for understanding the materials/concepts provided. Your involvement is mandatory. Since no book is available, please take notes. Two written exams will be based on the papers, my lectures, our discussion and your notes. To

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ensure that you understand the basic concepts and principles of cell signal transduction, before final exam, a project presentation after reading/digestion of at least 5 review articles on particular topic is imposed for this course. Your classmates will have a chance to give you a grade of presentation (1-10). The topics of the presentation and the rules will be given in the mid-semester. The topics to be covered in the course include but not limited to the following: I. The importance of the matrix in signal transduction Cell surface receptors as reception of extra-cellular signals Response to extra-cellular stimuli based upon the theory of Yin/Yang balance Amplification of signal during transmission---a quantitative study Tyrosine kinase and tyrosine phosphatase Cell membrane components and adapter proteins required for signal transmission Upstream and downstream Signal transduction without cell surface receptor activation G-protein coupled signaling The secondary messengers in signal transduction pathways CAMP, Ca2+, ROS, II. Various signal transduction pathways from cell surface to nucleus MAP kinase pathway SAP/JNK pathway p38 pathway ERK pathway NFkB pathway Cell survival pathway Wnt signaling pathway Jak/Stat pathway Smad pathway III. Cross-talks in signal transduction Cross talk among cell surface receptors, Crosstalks among cytoplasmic components Translocation of signal components during signal transmission From cytoplasm to cell membrane From cytoplasm to nucleus IV. The end point of signal transduction--- gene transcription Nuclear receptors and transcription factors From simple pathway to complex pathway From single gene expression to multiple gene expression: Superarray as a tool for the study of multiple gene transcription Practical application of the signal transduction research

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Tentative Lecture Schedule
Chapters Chapter 1 Chapter 2 Chapter 3 Chapter 4 Chapter 5 Chapter 6 Date Jan 18 Jan 25 Feb 1, No class Feb 8 Feb 15 Feb 22 March 7 Chapter 7 Chapter 8 Chapter 9 Chapter 10 Chapter 11 March 14 March 28 April 4 April 11 April 18 April 25 May 14 Chapter 14 Chapter 15 Chapter 16 Chapter 17 Chapter 18 Chapter 19 Chapter 20 Cell Cycle And Its Signaling TGF  Signaling EGFR And Its Signaling Cytoskeleton And Cell Signaling Carbohydrate Recognition Signaling MMPs And Cell Signaling G- Protein Signaling or Ca++ Signaling RNA Interference And Cell Signaling Senescence and Its Signaling Pathways Caveolins and Cell Signaling, reading Chromatin Remodeling And Gene Regulation NO Signaling And Neuronal Diseases Project Presentation Final Exam April 5-9, EB 2008 Lecture Introduction to Cell Signaling Apoptosis Signaling Transduction Pathway Reactive Oxygen Species and Hypoxia Signaling, reading NF-B Signaling Pathway and Inflammation PI3K/AKT Cell Survival Pathway MAP Kinase Signaling Pathways Mid-term exam Remarks

AAD, Feb 1-5

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Chapter 1 Introduction to Cell Signaling
Cell Signaling emerges as an important discipline in the interface between current biology and medicine. Breakthroughs are being made annually if not daily. This chapter will cover the emergence of Cell Signaling and its unparalleled importance in understanding the complicated biological system and fighting various diseases including cancer.

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Chapter 2. Apoptosis Signaling Transduction Pathway
Apoptosis, or programmed cell death, remains an important event in maintaining cellular homeostasis. Understanding the mechanisms of apoptosis would help cure or prevent from various neuronal diseases and cancer. Apoptosis remains a versatile pathway for therapeutic development. Apoptosis, or programmed cell death, has been a key area of focus at many pharmaceutical companies. Although the body has several apoptotic pathways designed to eliminate malignant cells, the mutations that occur in cancer cells frequently render them ineffective. Thus, therapies that may induce apoptosis in cancer cells have potential for treating a variety of cancer cells. Scientists have made important contributions to the understanding of multiple apoptotic pathways.

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Chapter 3. Reactive Oxygen Species and Hypoxia Signaling
Optimum concentration of ROS possesses cell signal functions such as activation of kinase activities and yet unregulated elevation of ROS could result in deleterious effects on cellular activities associated with damages of proteins, nucleic acids and lipids. Low oxygen tension, or hypoxia, occurring in solid tumors, is critical for induction of a transcription factor, or HIF that facilitates transcription of genes such as VEGF, an important factor for angiogenesis. HIF is thus considered as a valid target for cancer treatment.

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Chapter 4. NF-B Signaling Pathway and Inflammation
NF-B transcription factors play an important role in the regulation of immune response, embryo and cell lineage development, cell apoptosis, inflammation, cell-cycle progression, oncogenesis, viral replication, and various autoimmune diseases. The activation of NF-B is thought to be part of a stress response as it is activated by a variety of stimuli that include growth factors, cytokines, lymphokines, UV, pharmacological agents, and other stresses. In its inactive form NF-B is sequestered in the cytoplasm, bound by members of the IB family of inhibitor proteins. The various stimuli that activate NF-B cause phosphorylation of IB, which is followed by its ubiquitination and subsequent degradation.

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Chapter 5. PI3K/AKT Cell Survival Pathway
Since its discovery as a proto-oncogene nearly ten years ago, the serine/threonine kinase AKT, also known as protein kinase B (PKB), has become a major focus of attention because of its critical regulatory role in diverse cellular processes, including cancer progression. The AKT cascade is activated by receptor tyrosine kinases, integrins, B- and T-cell receptors, cytokine receptors, G-protein coupled receptors, and other stimuli that induce the accumulation of phosphatidylinositol 3,4,5 triphosphates, (PtdIns(3,4,5)P3), by the phosphoinositide 3-kinase (PI3K). The three AKT isoforms (Akt1, Akt2 and Akt3) thus mediate many of the downstream events regulated by PI3K. For instance, AKT is a major regulator of insulin signaling and glucose metabolism. Akt controls cell growth through its effects on the mTOR and p70 S6 kinase pathways, as well as the cell cycle and cell proliferation through its direct action on the CDK inhibitors, p21 and p27, and indirectly by affecting the levels of cyclin D1 and p53. AKT is also major mediator of cell survival by directly inhibiting different pro-apoptotic signals such as Bad and the Forkhead family of transcription factors, or indirectly by modulating two central regulators of cell death such as p53 and NF-B. AKT signaling in endothelial cells plays also critical roles in the regulation of vascular homeostasis and angiogenesis. These findings have turned AKT/PKB into important therapeutic target for the treatment of cancer, diabetes and stroke.

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Chapter 6. MAP Kinase Signaling Pathways
Mitogen-Activated Protein Kinases include, ERK, JNK and p38 protein kinases, activated by growth factors, cytokines and environmental stress. MAP kinase pathways are involved in gene expression, cell growth and differentiation, cytoskeleton activity.

Overall Cell regulation

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Chapter 7. RNA Interference And Cell Signaling
Small RNAs make big splash, becoming “BREAKTHROUGH OF THE YEAR of 2002”. Short stretches of RNA ranging in length from 21 to 28 nucleotides are called small RNAs. Their role had gone unnoticed until recently, in part because researchers, focused on the familiar larger RNA molecules, tossed out the crucial small ones. RNA has long been viewed primarily as an essential but rather dull molecule that ferries the genetic code from the nucleus to the ribosomes, and helps assemble amino acids during protein synthesis. Signs that RNA might be more versatile came in the early 1990s, when biologists determined that some small RNAs could quash the expression of various genes in plant and, later, animal cells. But they didn't appreciate the molecules' true powers until 1998. Andrew Fire of the Carnegie Institution of Washington in Baltimore, Maryland, Craig Mello of the University of Massachusetts Medical School in Worcester, and their colleagues injected stretches of double-stranded RNA into worms. Doublestranded RNA forms when a familiar single strand kinks back in a hairpin bend, putting two complementary sequences alongside each other. To the researchers' surprise, doublestranded RNA dramatically inhibited genes that had helped generate the RNA in the first place. This inhibition, which was later seen in flies and other organisms, came to be known as RNA interference (RNAi). It helped prove that RNA molecules were behind some gene silencing. Another crucial step came in 2001, when Gregory Hannon of Cold Spring Harbor Laboratory identified an enzyme, appropriately dubbed Dicer, that generates the small RNA molecules by chopping double-stranded RNA into little pieces. These bits belong to one of two small RNA classes produced by different types of genes: microRNAs (miRNAs) and small interfering RNAs (siRNAs). SiRNAs are considered to be the main players in RNAi, although miRNAs, which inhibit translation of RNA into protein, were recently implicated in this machinery as well. To bring about RNAi, small RNAs degrade the messenger RNA that transports a DNA sequence to the ribosome. Exactly how this degradation occurs isn't known, but scientists believe that Dicer delivers small RNAs to an enzyme complex called RISC, which uses the sequence in the small RNAs to identify and degrade messenger RNAs with a complementary sequence. Such degradation ratchets down the expression of the gene into a protein. Although quashing expression might not sound particularly useful, biologists now believe that in plants, RNAi acts like a genome "immune system," protecting against harmful DNA or viruses that could disrupt the genome. Developing RNAi-based therapeutics is under way for several disease areas including: ocular diseases, infectious diseases, oncology, metabolic disorders, inflammatory disease, central nervous system disease.

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Chapter 8. Senescence and Its Signaling Pathways
The study of human senescence has been fraught with controversy, conflicting theories, and puzzling data. Indeed, "pure" senescence is often difficult to distinguish from diseases of old age. Medical science has cataloged many signs of senescence. It manifests as dozens of changes in cells, tissues, and organs during aging. Human life is supported by a complex network of biochemical substances and reactions which affect the physical state and vitality of the body and mind. Senescent changes can be seen in the rate and outcome of many of these reactions. However, many of these changes are secondary effects of senescence, rather than primary causes. Senescence is becoming an attended issue in cancer research similar to apoptosis.

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Chapter 9. Caveolins and Cell Signaling
Caveolae were initially described some 50 years ago. The identification of a molecular marker for these domains, caveolin, combined with the possibility to isolate such cholesterol- and sphingolipid-rich regions as detergent-insoluble membrane complexes paved the way to more rigorous characterization of composition, regulation, and function. Experiments with knock-out mice for the caveolin genes clearly demonstrate the importance of caveolin-1 and -3 in formation of caveolae. Nonetheless, detergentinsoluble domains are also found in cells lacking caveolin expression and are referred to here as lipid rafts. Caveolae and lipid rafts were shown to represent membrane compartments enriched in a large number of signaling molecules whose structural integrity is essential for many signaling processes. Caveolin-1 is an essential structural component of cell surface caveolae, important for regulating trafficking and mobility of these vesicles. In addition, caveolin-1 is found at many other intracellular locations. Variations in subcellular localization are paralleled by a plethora of ascribed functions for this protein.

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Chapter 10. Chromatin Remodeling And Gene Regulation
DNA is wound around nucleosomes, which consist of Histones H2A, H2B, H3 and H4. These proteins all contain positively charged lysine-rich regions that form strong noncovalent bonds with the phospho-sugar backbone of the DNA double helix. In the nucleosome-bound state, it is difficult for RNA polymerase to transcribe messages. Therefore, one of the factors recruited to the proximal promoter by specific transcription factors is Histone Acetyltransferase (HAT), which acetylates and neutralizes those lysine residues on the histone core. This DNA/histone binding is much more conducive to transcription. However, other factors such as the dead box family of SWI ATPases help push nucleosomes out of the way to further ease transcription. Histone-modifying enzymes and chromatin remodeling complexes work in concert to condense and recondense stretches of chromatin. Modification by acetylation to the histone tail is necessary to decondense the chromatin in the promoter regions but histone acetylation and modification alone cannot disrupt the structure of the core particle of the nucleosome. Additional factors are needed to “remodel” the nucleosome cores to permit removal or repositioning. Chromatin remodeling is recognized to be an important event in gene regulation that may hold keys for cancer treatment.

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Chapter 11. NO Signaling And Neuronal Diseases
Researchers believed that amino acid arginine was responsible for smooth muscle relaxation that is endothelial cell dependent. In 1987, nitric oxide (NO) was discovered to be molecule responsible for that effect. More functions of NO have been uncovered for the past decade and NO signaling pathways have been unraveled.

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Chapter 12. Cell Adhesion And Its Importance In Cell Signaling And Cell Migration
The role of cell adhesion molecules such as cadherin and integrins in tumor progression and metastases has been recently implicated in the past ten years. Because of these cell adhesion proteins role in signaling from the outside to the inside of a cell, the way in which tumor cells survive and interact with their environment is closely tied to the expression and/or over-expression of these adhesion molecules. Integrins interact with the actin cytoskeleton and protein kinases such as FAK, ILK, Src and PKC. This leads to expression of MAPK and Erk pathways. This can cause up-regulation of MMPs. Integrins also can be positive mediators of angiogenesis. Cadherin, especially ECadherin, down-regulation has been shown to have metastatic effects. Also, a switch of E and P-Cadherins to N-Cadherins has been implicated in increased tumor progression.

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Chapter 13. Phosphatases And Regulation of Cell Signaling
Protein phosphatases play important parts in cell signaling, both activating and inactivating certain pathways. There is great diversity among phosphatases, making them important in all aspects of signaling and physiology. Phosphatases are potential targets for cancer therapy by either inhibiting them or activating them to attenuate cell cycle progression. Research is underway to determine whether targeting phosphatases will be an effective treatment for cancer.

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Chapter 14. Cell Cycle And Its Signaling
Regulation of the cell cycle is important because errors can lead to cancer. During most of the cell cycle, the cell does not require any extra-cellular signals. However, during the G1 phase, the cell does require these signals up to the restriction point (R) to tell the cell if it should proceed through R and continue with the rest of the cell cycle. R is near the end of the G1 phase, just prior to entry into S phase, when DNA is replicated. This serves as one of the main control points of the cell cycle.

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Chapter 15. TGF  Signaling

TGF signaling is involved in various cellular processes in a variety of cell types. The convoluted signaling pathways have been discovered recently and inhibitors are being developed to target the signaling pathways and eventually to alter the cellular responses in both normal and cancer cells.

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Chapter 16. EGFR And Its Signaling
Epidermal Growth Factor (EGF) is a protein that stimulates the growth and division of epidermal cells and many other cell types. EGF-receptor (EGFR) is a transmembrane glycoprotein found primarily on cells of epithelial origin. EGFR is involved in maturation of epithelial tissues during embryogenesis. In adults, EGFR plays a role in organ repair and wound healing and cell proliferation. More and more data indicate an unavoidable role of EGFR in cancer development and metastasis. EGFR is considered as a very important target for cancer treatment.

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Chapter 17. Cytoskeleton And Cell Signaling
Cytoskeleton has long been considered important in cell division. Not until recently has its cell signaling functions have been uncovered. Targeting cytoskeleton is becoming a valid approach for cancer treatment.

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Chapter 18. Carbohydrate Recognition Signaling
Carbohydrates have been discovered to play important roles in cellular activities such as Inflammation, immunology-immune cell transmigration and response. Carbohydrates are also involved in cell adhesion, tumorigenesis, metastasis, cell growth, differentiation and embryogenesis.

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Chapter 19. MMPs And Cell Signaling
MMPs serve to degrade the extracellular matrix which is important for many cellular responses. Abnormal development and pathological conditions are the result of MMPs not being regulated. MMP inhibitors have the ability to inhibit angiogenesis which is a promising avenue in cancer research.

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