Nw biotech fundamentals day 1 session 4 trends and techniques

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This presentation covers:
• Definition of life sciences
• The stages of a therapeutic drugs or vaccines R&D project
• The state of the art
• Regulatory nuances
• Pre-clinical and in the clinic issues
• Future trends
• Challenges and opportunities
• Case studies and examples

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Nw biotech fundamentals day 1 session 4 trends and techniques

  1. 1. Presenter: Viktoriia Hristova Melbourne, Brisbane, Sydney 28 May – 18 June, 2014 Biotech Boot Camp Session 4 – Trends and techniques
  2. 2. This session provides an overview of the scientific tools and techniques used in the various biotechnology laboratories Analysis includes key techniques pivotal to medicine, pharmaceuticals, life sciences, agriculture, and cleantech The session applies the techniques to specific examples while allowing a comparison of those techniques in other industries and in non-traditional applications Trends and techniques Agenda 2
  3. 3. • Basic overview of lab procedures • Research objectives of lab procedures • Trends and techniques in Australia and overseas • Case studies Session 4 Overview Trends and techniques 3
  4. 4. • Basic overview of lab procedures • Biotechnology • Molecular genetics • Immunology • Biochemistry • Research objectives of lab procedures • Trends and techniques in Australia and overseas • Case studies Session 4 Overview Trends and techniques 4
  5. 5. • Biotechnology: a group of diverse industries with the common link that they apply scientific knowledge to living organisms or the products from living organisms to benefit life on Earth • Biologics: means the products that are produced by means of biological processes involving DNA technology • Traditional biotechnology industries: adopts new approaches and modern techniques to improve the quality and productivity of their products . These industries include Molecular Genetics, Immunology, and Biochemistry laboratories Trends and techniques Basic overview of lab procedures 5
  6. 6. • All living things are made of cells • Organisms can be unicellular or multicellular • There are two types of cells • Eukaryotes • Prokaryotes Just as each tissue in the human body has a function, each cell type also has a function • Communicate • Grow and divide • Manufacture proteins Trends and techniques Back to basics - cells 6
  7. 7. Trends and techniques Cells 7
  8. 8. • In multicellular organisms cells communicate with other cells via signal transduction pathways, a type of chemical message • A target cell receives its message through proteins inserted into the cell membrane, known as receptors • When the signalling molecule binds to its receptor, it then transduces an inter cellular pathway, such as transcription • These receptor proteins, the pathways and processes they control and the production of these proteins are mechanisms central to biotechnology Trends and techniques Cellular communication 8
  9. 9. Trends and techniques Cellular communications Gene Expression Protein Production Signalling Molecule Receptor 9
  10. 10. • As cells grow, they produce more organelles such as mitochondria to increase the energy of the cell • Before a cell divides it must copy its entire genome sequence to transfer into the new cell • This process of cell growth and division is highly regulated and controlled, however cancer cells do not have this level of control and grow uncontrollably • Cells also have a well regulated cell death process called apoptosis. Some cancer mutations occur in these genes that control cell death Trends and techniques Cell division 10
  11. 11. Trends and techniques Cell division 11
  12. 12. Trends and techniques Cell death in healthy and cancerous cells 12 http://www.cancer.gov/cancertopics/understandingcancer/targetedtherapies/htmlcourse/page3
  13. 13. • Cells produce proteins • These proteins recognise hormones, antibodies, small molecules or other proteins • The proteins are encoded into the cells DNA • In order to understand the function of proteins science must understand the genome and be able to manipulate it Trends and techniques Cellular mechanisms and functions 13
  14. 14. • At the centre of all cellular mechanisms, communication and even cell division, is DNA • Often referred to as the blueprint for life • DNA is the molecule used by all organisms to store and transfer information • DNA is the molecule upon which the entire biotechnology industry is built • Particularly the understanding of how cells use DNA, and how to manipulate DNA Trends and techniques The role of DNA 14
  15. 15. • Recombinant DNA Separation, and Monoclonal Antibody Procedures • Gel Electrophoresis (acrylamide and agarose) • Immunocytochemistry • ELISA • Nucleic Acid Purification and Molecular Weight Determinations • Cell Separation Methods • Protein Separation and Quantitation • Liquid Scintillation (double label) Counting • Gene Expression • Oligonucleotide Synthesis • Autoradiography (cellular and gross) • Restriction Enzyme Mapping Trends and techniques Basic overview of biotechnology lab procedures 15
  16. 16. • Recombinant DNA Separation, and Monoclonal Antibody Procedures • Gel Electrophoresis (acrylamide and agarose) • Immunocytochemistry • ELISA • Nucleic Acid Purification and Molecular Weight Determinations • Cell Separation Methods • Protein Separation and Quantitation • Liquid Scintillation (double label) Counting • Gene Expression • Oligonucleotide Synthesis • Autoradiography (cellular and gross) • Restriction Enzyme Mapping Trends and techniques Basic overview of biotechnology lab procedures 16
  17. 17. • Recombinant DNA Separation, and Monoclonal Antibody Procedures • Gel Electrophoresis (acrylamide and agarose) • method for separation and analysis of macromolecules such as DNA, RNA and proteins, and their fragments, based on their size and charge • It involves applying an electric field to move the negatively charged molecules through a matrix of agarose gel or other substances • It is used in clinical chemistry to separate proteins by charge and/or size and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge Trends and techniques Basic overview of biotechnology lab procedures 17
  18. 18. • Recombinant DNA Separation, and Monoclonal Antibody Procedures • Gel Electrophoresis (acrylamide and agarose) • Immunocytochemistry • ELISA • Nucleic Acid Purification and Molecular Weight Determinations • Cell Separation Methods • Protein Separation and Quantitation • Liquid Scintillation (double label) Counting • Gene Expression • Oligonucleotide Synthesis • Autoradiography (cellular and gross) • Restriction Enzyme Mapping Trends and techniques Basic overview of biotechnology lab procedures 18
  19. 19. • Recombinant DNA Separation, and Monoclonal Antibody Procedures • Immunocytochemistry • A technique used to assess the presence of a specific protein or antigen in cells, by use of a specific antibody which binds to it, thereby allowing visualisation Trends and techniques Basic overview of biotechnology lab procedures 19
  20. 20. • Recombinant DNA Separation, and Monoclonal Antibody Procedures • Gel Electrophoresis (acrylamide and agarose) • Immunocytochemistry • ELISA • Nucleic Acid Purification and Molecular Weight Determinations • Cell Separation Methods • Protein Separation and Quantitation • Liquid Scintillation (double label) Counting • Gene Expression • Oligonucleotide Synthesis • Autoradiography (cellular and gross) • Restriction Enzyme Mapping Trends and techniques Basic overview of biotechnology lab procedures 20
  21. 21. • Recombinant DNA Separation, and Monoclonal Antibody Procedures • ELIZA • Enzyme-Linked ImmunoSorbant Assay is used to determine if a particular protein is present in a sample and if so, how much • There are two main variations on this method: • Measuring the amount of antibody in a sample • Or measuring how much protein is bound by an antibody • This technique is central to Immunology Trends and techniques Basic overview of biotechnology lab procedures 21
  22. 22. • Recombinant DNA Separation, and Monoclonal Antibody Procedures • Gel Electrophoresis (acrylamide and agarose) • Immunocytochemistry • ELISA • Nucleic Acid Purification and Molecular Weight Determinations • Cell Separation Methods • Protein Separation and Quantitation • Liquid Scintillation (double label) Counting • Gene Expression • Oligonucleotide Synthesis • Autoradiography (cellular and gross) • Restriction Enzyme Mapping Trends and techniques Basic overview of biotechnology lab procedures 22
  23. 23. • Recombinant DNA Separation, and Monoclonal Antibody Procedures • Protein Separation and Quantitation • (or quantitative proteomics) the aim of is to obtain quantitative information about all proteins in a sample • It yields information about differences between samples • For example, this approach can be used to compare samples from healthy and diseased patients, while a further Immunocytochemistry or ELIZA test will provide a qualitative result Trends and techniques Basic overview of biotechnology lab procedures 23
  24. 24. Trends and techniques Basic overview of recombinant DNA lab procedures Genetic Cloning with bacterial plasmids U.S. Department of Energy Genome Programs 24
  25. 25. Genetic cloning with bacterial plasmids • Plasmids are small circular segments of DNA that have only a small number of genes. Plasmids replicate separately from the bacterial chromosome • Foreign DNA is inserted into the plasmid, which results in a recombinant DNA molecule. The recombinant plasmid is inserted into the bacterium and the bacterium is allowed to replicate • The bacterial cell divides and replicates into a clone of cells all genetically identical to each other, and in the processes replicates the recombinant plasmid Trends and techniques Basic overview of biotechnology lab procedures 25
  26. 26. • Overcomes the problem of source availability • Allows the manufacture of any protein in whatever quantity it is required • Overcomes the problem of product safety and toxicity • Provides an alternative to direct extraction from inappropriate or dangerous source materials • Facilitates the generation of newly designed proteins Trends and techniques Basic overview of recombinant DNA lab procedures 26
  27. 27. • Basic overview of lab procedures • Biotechnology • Molecular genetics • Immunology • Biochemistry • Research objectives of lab procedures • Trends and techniques in Australia and overseas • Case studies Session 4 Overview Trends and techniques 27
  28. 28. Trends and techniques DNA (gene) RNA Protein Trait (or phenotype) Transcription Translation Basic overview of molecular genetics lab procedures Molecular Genetics is the branch of genetics concerned with the structure and activity of genetic material at the molecular level 28
  29. 29. • Basic overview of lab procedures • Biotechnology • Molecular genetics • Immunology • Biochemistry • Research objectives of lab procedures • Trends and techniques in Australia and overseas • Case studies Session 4 Overview Trends and techniques 29
  30. 30. The branch of biomedicine concerned with • the structure and function of the immune system, • innate and acquired immunity, and • laboratory techniques involving the interaction of antigens with antibodies ELISA uses the basic immunology concept of an antigen binding to its specific antibody. Trends and techniques Basic overview of immunology procedures used in labs Antigen Antigen Binding Site Antibody 30
  31. 31. Antigens can include: • proteins • peptides • hormones • antibody Trends and techniques Basic overview of immunology lab procedures Antigen Antigen Binding Site Antibody 31
  32. 32. Immunoassays Trends and techniques Wash Bind capture antibody Add Antigen Add detection AntibodyWells Basic overview of immunology lab procedures 32
  33. 33. Applications • presence of antigen • presence of antibody − HIV test or West Nile Virus • food allergens − milk, peanuts, walnuts, almonds, and eggs Trends and techniques Basic overview of immunology lab procedures 33
  34. 34. Trends and techniques Cells - Monoclonal antibodies at work 34 http://cisncancer.org/research/new_treatments/immunotherapy/how_it_works_002.html
  35. 35. Gardasil • The human papillomavirus (HPV) vaccine manufactured by Merck and approved for preventing cervical cancer, is produced by making a recombinant HPV protein called L1 • The recombinant L1 protein molecules reassemble to make virus-like particles which mimic real HPV and result in the immune system making antibodies against HPV Trends and techniques Cells at work – monoclonal antibodies 35
  36. 36. • Basic overview of lab procedures • Biotechnology • Molecular genetics • Immunology • Biochemistry • Research objectives of lab procedures • Trends and techniques in Australia and overseas • Case studies Session 4 Overview Trends and techniques 36
  37. 37. Trends and techniques Basic overview of biochemistry lab procedures 37
  38. 38. Biochemistry is the study of the chemical substances and vital processes occurring in living organisms; biological chemistry; physiological chemistry The production of ethanol via fermentation and anaerobic conversion is a biochemical process that occurs naturally in micro-organisms In recent times these organisms have become regarded as biochemical "factories" for the treatment and conversion of biological materials into usable energy Biochemical conversion involves use of enzymes, bacteria or other microorganisms to break down biomass into liquid fuels, and includes anaerobic digestion, and fermentation Trends and techniques Basic overview of biochemistry lab procedures 38
  39. 39. The unique physicochemical and functional characteristics of carbohydrates isolated from different sources such as corn, potato, rice and wheat are used in a variety of biomedical and pharmaceutical applications Carbohydrates have properties that mimic the mechanical behaviour and enzymatic digestibility of enzymes and proteins that control biochemical reaction in a cell Are used as carriers for the controlled release of drugs and other bioactive agents, and chemically modified starches with more reactive sites are used to carry biologically active compounds which can easily be metabolized in the human body Trends and techniques Basic overview of biochemistry lab procedures 39
  40. 40. Along with the techniques explained in previous slides, some further lab techniques specific to Biochemistry include: • Northern Blotting • Southern Blotting • Fusion Proteins • DNA microarray • Bioinformatics, and • Flow cytometry Trends and techniques Basic overview of biochemistry lab procedures 40
  41. 41. • Basic overview of lab procedures • Research objectives of lab procedures • Biotechnology • Molecular Genetics • Immunology • Trends and techniques in Australia and overseas • Case studies Session 4 Overview Trends and techniques 41
  42. 42. • Biotechnology: a group of diverse industries with the common link that they apply scientific knowledge to living organisms or the products from living organisms to benefit life on Earth • Protein engineering : Design of proteins/enzymes based on structural and mechanistic knowledge, molecular evolution, computational design • Synthetic biology : Creation of new biosystems (Cells and biomolecules): Systematic, hierarchical design of artificial, bio- inspired system using robust, standardised and well-characterised building block Trends and techniques Research objectives of lab procedures used in Biotechnology 42
  43. 43. Metabolic pathway engineering - design of more efficient metabolic pathways to produce high yield of target product but low by-products Production of biofuels from natural resources - Increase in the yield and alcohol tolerance • Redesign of pathway for the ethanol production in yeast to use raw materials : corn starch, cellulose, soybean, sugar cane • Elucidation of enzyme mechanisms • Redesign of pathway to increase the yield and to reduce by-products • Design of critical enzymes in the pathway • Process development (eg: fermentation process) • Separation and concentration Trends and techniques Research objectives of lab procedures used in Molecular Genetics 43
  44. 44. • Determine weak spots in viruses • Easy design of antibodies with high affinity for a target • Design tests and techniques with low immunogenicity and cytotoxicity • Development of new therapeutics with high efficacy and low side effect from non-antibody protein scaffold • Designer therapeutic proteins Trends and techniques Research objectives of lab procedures used in Immunology 44
  45. 45. • Basic Overview of lab procedures • Research objectives of procedures used in • Trends and techniques in Australia and overseas • Case Studies Session 4 Overview Trends and techniques 45
  46. 46. Targeted therapies to treat cancer − Roche, Genentech and ImmunoGen − The antibody-drug conjugate field uses targeted antibodies attached to anti-cancer toxins to home in on tumour cells − Roche has registered the latest win with data from a mid-stage trial that showed that T-DM1, an antibody linked to a toxin, outperformed the standard treatment of two separate drugs for an advanced form of breast cancer Trends and techniques Australia and Overseas 46
  47. 47. Small molecules to treat Alzheimers − NeuroPhage − a new molecule it's developing based on a platform it calls a general amyloid interaction motif, or GAIM. GAIM works by recognizing and seeking out a characteristic common to many toxic misfolded proteins and targeting key stages of misfolded protein assembly to convert toxic assemblies into nontoxic ones, blocking the spread of misfolded proteins within cells Trends and techniques Australia and Overseas 47
  48. 48. Health care / medical devices / diagnostics • Development of therapeutics: efficacy, toxicity • Diagnosis: early detection and prevention of diseases • Examples • Biofnatics¹ – biodegradable coronary stent valve • Encapsulate¹ – metal protein attenuating compound Agriculture: Crop production with high yield and quality • Examples in Australia • Hexima – disease resistant crop • New Natural¹ – crop fungicide Trends and techniques Australia and Overseas 1. AusIndustry R&D Tax Incentive Biotechnology Guidance product48
  49. 49. Bio-based process: Pollution, CO2 emission, global warming • Examples in Australia: • MBD Energy – bioremediation with algae • Licella – biofuels from plant waste • Biofiba – biodegradable packaging materials • Biomine¹ – bacteria for highly saline environments Alternative energy (Bio-energy) : • Depletion of fossil fuels • Use of renewable sources: Corn, sugar cane, cellulose • Example in Australia: • Microbiogen – fuel and feed from plant biomass • TimbaFuels¹ – wood-waste biofuels Trends and techniques Australia and Overseas 1. AusIndustry R&D Tax Incentive Biotechnology Guidance product49
  50. 50. • Basic Overview of lab procedures • Research objectives of lab procedures • Trends and techniques in Australia and overseas • Case studies Session 4 Overview Trends and techniques 50
  51. 51. Trends and techniques Case Studies and Examples R&D Tax Incentive Biotechnology Guidance example in context Encapsulate - Zinc metal protein attenuating powder for amyloid plaques* • 10 Feb 2014: Summer Street Analyst Bart Classen on Prana Biotechnology Limited (Nasdaq: PRAN) “We are not enthusiastic about the drug's proposed mechanism, allowing zinc and copper ions into the cell, because there is only a limited amount of ions that can enter the cell before they would precipitate and cause toxic deposits” • Sangamo Biosciences early stage data shows gene therapy approach slowed Alzheimer’s related deterioration in brain * Fictitious example from AusIndustry R&D Tax Incentive Biotechnology Guidance product, April 201351
  52. 52. Trends and techniques Case Studies and Examples R&D Tax Incentive Biotechnology Guidance example in context Encapsulate* Development of metal protein attenuating compounds as therapies for Parkinson’s disease • April 2013 - Sanofi announced it will not pursue clinical trials for Alzheimers indication until better understanding of the disease’s mechanism exists • March 2014 - Otsuka licenses Lundbeck’s Alzheimer’s disease drug for up to $825M • July 2013 - Biogen Idec in-licenses mouse model for demyelinating diseases, another approach to Alzheimer’s, from Myelin Research Foundation • Dec 2013 - Eisai, Lilly form dementia consortium with Alzheimer’s Research UK, MRC Technology * Fictitious example from AusIndustry R&D Tax Incentive Biotechnology Guidance product, April 201352
  53. 53. Trends and techniques Case Studies and Examples The UPS regulatory pathway Nurix, Inc¹ • Nurix, Inc. is a leader in discovering and developing therapies that modulate the ubiquitin proteasome system (UPS) • The UPS is the body's 24/7 cleaning service for the cell, degrading and cleaning up targeted proteins inside the cell, regulating cellular processes and maintaining protein homeostasis in a way that can have profound implications for a wide variety of diseases • Nurix has a particular interest in oncology and is doing R&D on the possibilities of both speeding up (enhancing) and slowing (inhibiting) the protein degradation process using the UPS regulatory pathway • Nurix has developed a high-resolution molecular understanding of the UPS ¹ Source: Fierce Biotech 201453
  54. 54. Trends and techniques Case Studies and Examples The UPS regulatory pathway Nurix, Inc¹ • able to engineer high selectivity small molecule drug candidates to modulate critical ligase-substrate (protein-protein) interactions in the UPS that drive serious diseases • therapeutic targets previously inaccessible to small molecule drug discovery • initial discovery work funded by VC fund Third Rock Ventures to get a coherent idea of the product potential and timelines involved in the drug development while recruiting some of the top researchers in the UPS field • VC partner is CEO ¹ Source: Fierce Biotech 201454
  55. 55. Trends and techniques Case Studies and Examples Microarray to determine cancer predisposition • An array of probes capable of simultaneously detecting multiple analytes in a sample • In this case short, repetitive DNA sequences but can be proteins • Each probe is printed as a spot on the membrane as a small spot, approximately 100 – 500 µm in diameter • These probes or microsatellites can also be used in forensics for paternity testing • 2 million microsatellites in human genome using 300,000 probes • In this case aim is to identify unique pattern of microsatellite variation in breast cancer http://www.ncbi.nlm.nih.gov/55

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