Recombinant Proteins Flashcards

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1
Q

What are recombinant proteins?

A

Splicing of; 2 pieces of DNA stitched together (bringing together genetic material from multiple sources)

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2
Q

Why use recombinant proteins as therapeutics?

A
  • Protein perform complex and highly specific functions; nor easily mimicked by chemical drugs
  • Humans proteins can be produced from non-human sources via recombinant techniques
  • Relatively cost effective and limitless supply
  • Facilitates protein engineering to improve stability, yield, ADME properties
  • Reduced possibility of pathogen contamination (e.g. prions, HIV)
  • Reduced possibility of immune rejection/allergic reactions due to species differences or contaminants
  • Circumvents religious objections to animal products e.g. porcine insulin
  • More rapid clinical development and regulatory approval compared to small molecules
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3
Q

What are some clinical uses of recombinant proteins/biologicals?

A
  • Replacing missing or defective protein e.g. in endocrine, metabolic disorders (insulin, growth hormone, clotting factors, metabolic enzymes)
  • Enhance/augment existing pathways (interferons; MS, cytokines, erythropoietin; anaemia, HRT)
  • Interfere with harmful molecules or proteins produced by the body (inhibitors of growth hormone receptors; acromegaly, TNFalpha blockers; psoriasis/RA, DNAse; cystic fibrosis, anti-clotting agents.
  • Delivery of other proteins or drugs to a specific site/tissue (antibodies linked to cytocidal compounds selectively targeting cancer cells)
  • Antiinfectives - antibiotics, antivirals (interferon α and γ, monoclonal Abs, vaccines)
  • Eliminating other harmful foreign substances (anti-venoms, anti-toxins)
  • Treat autoimmune diseases, inflammation, transplant rejection (anti-TNF-α; psoriasis, anti-rhesus immunoglobulin, interferon β; MS)
  • Anti-cancer therapies (avastin, herceptin; breast cancer, rituximab; B-cell lymphoma)
  • Promote tissues repair, regeneration (bone morphogenic proteins)
  • Diagnostics/biomarkers of disease, infection, cancer, metabolic disorders (HIV, HPV, TB, PSA, GHRH, TSH, Glucagon)
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4
Q

How has insulin progressed to recombinant human insulin?

A

1922 - Porcine insulin used to treat DM
> But animal derived insulins (cow, horse, pig) caused allergic reactions; low purity
1978 - Human insulin produced in E. coli
1982 - Eli Lilly markets ‘humulin’

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5
Q

How are fast-acting insulins e.g. lispro/glulisine/aspart modified for their therapeutic use?

A
  • They exist as monomeric forms; unable to form hexamers (when insulin binds zinc and clumps with other insulins)
  • Alterations at C-terminus of B-chain (swap AAs)
  • Lispro; Lys-Pro-Thr
  • Glulisine; Pro-Glu-Thr
  • OG Humulin; Pro-Lys-Thr
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6
Q

How does the long-acting insulin glargine have such an effect?

A
  • Modified A and B chains
  • Form microcrystals/other aggregates
  • Slow rate of monomer release
  • Arg-Arg added onto OG Pro-Lys-Thr
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7
Q

What is Gaucher’s disease and how is it treated?

A
  • Rare congenital disorder of lipid metabolism
  • Deficiency in β-glucocerebrosidase enzyme
  • Lipids build up in macrophages
    Symptoms: hepatomegaly, splenomegaly, bone lesions

Treatment: enzyme replacement therapy; infusion of the enzyme extracted from human placentas.

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8
Q

How did recombinant proteins change how Gaucher’s disease was treated? What does this result in?

A
  • Initially required 50,000 placentas to treat ONE patient for a year
  • Production of recombinant form Cerezyme made treatment feasible
  • Arginine 495 is changed to histidine
  • This results in addition of mannose sugar
  • Mannose recognised by cell surface receptors enhancing uptake in macrophages
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9
Q

What is erythropoietin (EPO) and what can it be used to treat?

A
  • Growth factor, stimulating erythrocyte (RBC) production

- Treats anaemia in CKD, and in IBD

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10
Q

How can EPO be modified and what advantages does this bring?

A
  • Change of two AAs introduces 2 additional N-glycosylation sites
  • Half-life normally 5 hours; becomes 3-fold longer
  • This meant fewer injections were required
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11
Q

What can contribute to growth failures disorders that result in the under production/resistance to growth hormone (GH)?

How is it treated?

A
  • CKD, growth hormone deficiency, Prader-Willi Syndrome, Turner syndrome

Treated with recombinant human growth hormone (GH) and insulin-like growth factor (IGF-1); daily injections.

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12
Q

How does GHRH affect GH etc. to lead to growth?

A
  • Hypothalamus releases GHRH (Growth Hormone Releasing Hormone)
  • This stimulates the pituitary, which then releases GH
  • GH acts at the liver causing the production of IGF-1 (insulin-like growth factor)
  • This stimulates long bone growth, encouraging processes such as metabolism of fats and CHO = cell growth
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13
Q

What is gigantism and how is it characterised?

A
  • Symmetrical enlargement of the body; overgrowth of long bones, connective tissues, visceral organs
  • Caused by excess GH/IGF-1 caused by benign pituitary tumours (adenomas)
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14
Q

What is the difference between gigantism and acromegaly?

A
  • Gigantism = excess GH/IGF-1 in early life

- Acromegaly = excess secretion of GH/IGF-1 after the body has stopped growing

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15
Q

What characterises acromegaly and how can it be treated?

A
  • Enlargement of bones in hands, feet, face

- Treated with somatostatin analogues, blocking GF production

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16
Q

What areas of biomedical research use recombinant proteins?

A
  • Protein structure/function studies
  • Antibody production
  • Drug discovery
  • Recombinant DNA techniques
  • Stem cell technology
  • Gene therapy
  • Bioimaging
  • Disease biomarkers
  • Translational research
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17
Q

Define: Recombinant DNA.

A
  • Fragments of DNA (or copy DNA) recombined to generate a synthetic molecule
  • DNA from different species can be recombined
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18
Q

Define: Host/vector systems

A
  • DNA of interest inserted into plasmid or viral vector
  • Vector introduced into host cell/organism
  • Vector contains a gene promoter functional in host organism
  • Expression of recombinant proteins for medical use/reseach
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19
Q

Define: Recombinant proteins

A
  • Proteins generated from recombinant DNA vectors
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20
Q

Define: Transgene

A
  • Recombinant DNA that is introduced into the genome of another organism
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21
Q

Define: Genetic engineering

A
  • Alteration of DNA sequences to change gene function or expression
  • In vitro/in vivo methods to combine DNA sequences from different organisms
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22
Q

What is a GMO?

A

Genetically modified organism

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23
Q

What is DNA and how is it transcribed to RNA?

A
  • Pair of antiparallel chains
  • ATGC
  • Adenine
  • Thymine
  • Guanine
  • Cytosine
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24
Q

What is transcription?

A

The process of making a copy of the anti-sense DNA strand into a sense RNA strand

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25
Q

How are proteins made from RNA?

A
  • Via tRNA in ribosomes

- Translation of RNA to protein

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26
Q

What are prokaryotes and what is their gene structure?

A
  • Bacteria

DNA:

  • PROMOTER; transcription start site for RNA polymerase to start synthesising RNA at
  • AUG start codon for translation in ribosomes
  • Open Reading Frame (ORF); (the Cistron/gene)
  • Stop codon for translation in ribosomes
  • TERMINATOR; transcription stop site for RNA polymerase

mRNA:

  • Random regulatory region not translated e.g. attracting ribosomes (bit between Promoter and ORF from DNA?)
  • ORF (Cistron)
  • Random regulatory region

Protein:

  • Linear sequence
  • Displayed from N to C terminus
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27
Q

Describe mammalian gene structure.

A

dsDNA (double-stranded):

  • Transcription Start Site (TSS)
  • Introns (non-coding parts)
  • Exons (protein coding parts)
  • Transcription Termination
pre mRNA (primary transcript):
- Whole gene transcribed inc. non-coding introns

mRNA (processed; capped and spliced):

  • pre mRNA is processed down to much smaller size
  • Introns removed by spliceosome
  • 5’ end capped w/7-methyl Guanylate cap
  • 3’ end cleaved and PolyA tail (adenine nucleotides) added (increases stability/prevents degradation)
  • Untranslated regions at either end
  • CDS/coding sequence in middle
  • Primary transcript now processed to mRNA
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28
Q

What techniques can genetic engineers employ?

A
  • Restriction/modification enzymes
  • DNA ligase (stitching DNA together)
  • Reverse transcriptase (make DNA copy from RNA)
  • PCR
  • DNA sequencing
  • Plasmid/viral vectors
  • Controlled expression systems
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29
Q

What are restriction enzymes?

A
  • Bacterial endonucleases
  • Restrict growth of viruses infecting bacteria
  • Cleave/cut specific DNA sequences
  • Often recognise palindromic sequences (reads same backwards/flipped)
  • Evolved as a defence against bacteriophage infection (killing viral infection in bacteria)
  • Co-evolve with modification system to protect self (self-immunity)
30
Q

What is the difference between endonucleases and exonucleases?

A

Endonucleases: cleaves DNA in middle etc from recognising sequence

Exonucleases: doesn’t look for specific sequence; only the end of the molecule and chops it uo

31
Q

How do restriction enzymes e.g. EcoR1 modify itself to prevent self-cleave?

A
  • Modification entails adding methyl group to relevant palindromic sequence that is potentially shared with foreign/invading virus
  • Methylation protects own genome from endonucleases
32
Q

How do restriction enzymes e.g. EcoR1 cleave DNA and what can happen to the products?

A
  • Non-uniformly, like sideways Z
  • Generates cleavage products with a 5’ overhang
  • Single-stranded AATT followed by dsDNA
  • Products complementary to each other; can be annealed by DNA ligase in the presence of ATP
33
Q

How do blunt ends differ from cohesive ends (from restriction enzyme cleavage)?

A
  • Blunt ends; cleaving both chains at same position
  • Thus any 2 blunt ends can be ligated together with DNA ligase (+ ATP); they are not sequence specific
  • However cohesive ends require sequence compatibility (if they have complementary base pairs) e.g. EcoR1 will only ligate with another EcoR1
34
Q

What host-vector systems are available for recombinant proteins?

A
  • Bacterial cells (E.coli, Corynebacterium spp., Bacillus spp.)
  • Yeast cells (Pichia, Saccharomyces cerevisiae, S. pombe)
  • Cultured mammalian cells
  • Transgenic plants and animals (pharming)
  • In vitro systems

> DNA of interest is introduced into cell/organism so that RNA can be generated to make the protein

35
Q

What is a cloning vector?

A

A piece of DNA that is selectable that can carry your gene of interest, and make sure it’s expressed in the host cell system.

36
Q

What are examples of cloning vectors?

A
  • Bacterial plasmid DNA
  • Bacterial viruses (bacteriophage DNA)
  • Yeast plasmids
  • Animal viruses (retrovirus, lentivirus, adenovirus)

> Process referred to as ‘DNA Cloning’; generation of many identical copies of a gene or piece of DNA

37
Q

What barriers are present in making recombinant proteins from inserting human DNA into bacteria?

A
  • Human genes contain introns and exons
  • Bacteria cannot process introns (can’t splice them out)
  • Bacterial RNA polymerase cannot recognise mammalian promoter sequences (that drive expression of genes)
38
Q

What solutions are available to overcome the issues of making recombinant proteins from human DNA in bacteria?

A
  • Remove intron sequences
  • Or use cDNA (copy DNA instead of cloning genomic DNA); a copy of the processed mRNA
  • Insert into a vector behind a bacterial promoter
39
Q

What does cDNA/transcript cloning entail?

A
  • processed mRNA transcribed from dsDNA (full human gene), undergone splicing to remove introns etc
  • From mRNA transcript a DNA copy (cDNA) is made
  • cDNA ligated into vector

> Only transcript is taken instead of whole gene
‘Transcript cloning’ more accurate than ‘gene cloning

40
Q

What enzyme is used to make cDNA from mRNA?

A
  • Via reverse transcriptase enzyme
  • Enzyme found in animal RNA viruses (retroviruses; unusual viruses that have their genome as RNA instead of DNA
  • When they affect a mammalian cell they have to convert their RNA genome back into DNA so it can be expressed by human host
  • Thus reverse transcriptase enzyme taken from animal viral cells and used in vivo to generate DNA from RNA
41
Q

How is cDNA made from processed mRNA?

A
  • mRNA tales all have PolyA tales
  • Add in short sequence poly dT primer (or other specific primer), hybridises and anneals to PolyA tail; allows reverse transcriptase to synthesise DNA from mRNA template
  • Reverse transcriptase makes a copy of the mRNA (cDNA)
  • Want to rid of mRNA now; degrade it by adding NaOH to leave single-stranded DNA
  • Add random primers (short 6 base pair oligonucleotides) binding randomly to ssDNA
  • Allows DNA polymerase to make a copy of cDNA, resulting in dscDNA (double-stranded)
42
Q

What is the basis of PCR?

A
  • Thermostable DNA polymerase (thermus aquaticus; likes heat and water, happy at 70-80 degrees etc)
  • Amplification (multiple copies) of a specific DNA sequence
  • Temperature cycling
  • PCR makes multiple copies exponentially, can use the enzyme again and again
43
Q

What is a primer?

A
  • Every DNA polymerase needs a primer
  • It is a short DNA (oligonucleotide) sequence usually 15-30 base pairs long
  • Complementary to the strand you’re copying
  • Primer annealing/hybridisation (base pairing) to its complementary sequence
44
Q

What are the steps of PCR?

A
  • Start off with PCR Reaction Mix: Template, Primers, dNTPs (nucleotide triphosphates containing deoxyribose), Taq Polymerase Enzyme
  • Temperature denaturation at 94 degrees; dsDNA denatures
  • Cooling down to 37 degrees quickly; double strands don’t come back together because too long
  • But primers will anneal to complementary system to each chain
  • Bring temperature back up to 72 degrees; optimal temperature for Taq Pol Enzyme, synthesises DNA
  • Leaves you with 2 strands of DNA instead of the starting 1
  • 30 second process
  • Second cycle start with 2 strands of dsDNA; denature/anneal/synthesise and end up with double number of copies
  • Repeat for 35 cycles (thermal cycling; 94/37/72 degrees)
45
Q

What other uses do PCR Primers have?

A
  • Can be used to insert Restriction Enzyme sites e.g. annealing/hybridisation of EcoR1 into a sequence, engineering changes
  • Can be used to mutagenesis/introduce sequence mutation, e.g. to swap AAs in insulin lispro; mismatch primer (but w/enough annealing to stick) generating a sequence change
46
Q

What is bacterial plasmid DNA/does it get passed on to daughter cells?

A
  • Extrachromosomal DNA
  • Very small ‘mini-chromosomes’; 1kb to several Mb in size (kilo-base)
  • Autonomously replicating bacteria
  • Circular double stranded DNA molecules
  • Behave independently from OG genome
  • Daughter cells of replicating DNA get full genome each and plasmid DNA too
47
Q

What are the typical genes that plasmids carry?

A
  • Antibiotic resistance genes
  • Virulence factors (bad shit e.g. endotoxin)
  • Metabolic enzymes
  • Plasmid transfer
48
Q

What is the significance of horizontal gene transfer (F plasmid)?

A
  • Bacteria can share plasmids
  • Even cross-species
  • Leads to antibiotic resistance etc
49
Q

How are plasmid vectors modified in genetic engineering?

A
  • Adding a Promoter region (for bacteria, yeast, mammals)
  • Adding restriction enzyme sites; allows insertion of different bits of DNA
  • Antibiotic resistance e.g. Amp, Tep, Kan for resistance
50
Q

What does DNA cloning entail?

A
  • Insertion of DNA fragment into plasmid DNA
  • DNA fragment (usually from PCR) is digested and treated with restriction enzymes
  • Plasmid DNA also cut with the same restriction enzyme
  • Then ligation can occur via DNA ligase (complementary as cut with same restriction enzyme)
  • Plasmid DNA expresses gene behind bacterial promoter
51
Q

What does blunt end ligation require?

A
  • All PCRs have blunt ends; thus restriction enzymes not required for DNA cloning
  • But will consequently require plasmid DNA to be cut with blunt-end generating restriction enzyme
  • PCR fragment can be inserted in either rotations, but the wrong rotation won’t be read as the promoter will be on the wrong side
  • Thus directionality is important
52
Q

How does cohesive/sticky end ligation differ from blunt end ligation?

A
  • Instead of 50/50 yield with one half having the promoter at the wrong end, 100% yield can be achieved
  • Via cutting ends of PCR fragment/plasmid DNA with a different restriction enzyme each e.g. EcoR1 and BamH1
  • Forces direction to give single desirable product, ensuring correct orientation
  • Two different restriction enzymes required as using just one means both ends are complementary = wrong rotation
53
Q

What does Sanger Sequencing/the Chain Termination method entail?

What is used now?

A
  • Spike mixture with dideoxy NTPs which are modified NTPs which can no longer form chain elongation
  • Results in chain termination
  • 100:1 ratio
  • Denature and separate daughter strands by electrophoresis
  • Runs through acrylamide gel according to molecular weight
  • Fluorescent automated system now in place
54
Q

How do we get the treated plasmid vector into the host?

A

Bacterial transformation:

  • Treatment with CaCl/MgCl2 forms holes in the bacterial cell wall
  • Heating to 42 degrees makes plasmid DNA enter bacterial cell
  • Cells recover and then express the genes carried by the plasmid
  • Antibiotic resistance gene included to find which cells have taken up the plasmid
  • All cells that didn’t take up the plasmid die, and the one’s that did (desirable) grow because resistant
55
Q

How do bacterial expression vectors differ from mammalian expression vectors?

A

Both can:

  • employ different selective markers (e.g. antibiotic resistance)
  • Have multiple different restriction enzyme sites e.g. lacZ’ in bacterial; allows for insertion of whatever DNA code etc with ease
  • Can be tagged with epitope/affinity tags to monitor expression
  • Have different inducible promoter systems; thus gene might only be expressed in the mammalian cell and remains dormant in bacterial due to mammalian cell promoter
56
Q

How can LacZ be used to our advantage to increase efficiency/yield of recombinant DNA production?

A

Detection of cloned inserted DNA:

  • LacZ comes from E.coli, codes for β-galactosidase activity
  • LacZ engineered to generate multiple cloning sites without compromising protein function
  • DNA fragment treated with EcoR1 as well as host plasmid
  • Ligation; plasmid can ligate back together without taking in DNA fragment = LacZ gene not compromised and xCAL gel turns white
  • But if DNA fragment taken up; disrupts LacZ gene reading, xCAL colonies remain white instead
  • Indication that white colonies have taken up the DNA fragment/insert; ones of interest
57
Q

What are the reasons behind controlling plasmid gene expression in a host cell?

A
  • Maximise yield and solubility

- Minimise toxicity to host cell; keeping expression silent if toxic

58
Q

What are inducible expression vectors and how do they work?

A
  • Plasmid inert without the addition of an inducer; is repressed at promoter
  • Upon activation with a small molecule, the repressor is removed and the gene is expressed e.g in presence of TPTG/doxicycline only
  • Controls where/when the recombinant protein is made
59
Q

How do we identify and detect recombinant proteins in vitro? What other role does it serve?

A

Immunopurification:

  • Western Blotting: use antibody specific to the protein to detect it
  • Or add epitope tag which fuses to protein of interest where a specific antibody immobilised on a matrix detects the tag instead
  • Purifies ‘soup’ of bacterial enzymes and shit from E.coli etc too with highly specific antibody capturing protein of interest
60
Q

What are the steps of Western Blotting?

A
  1. ) Electrophoresis via SDS PAGE
  2. ) Proteins transferred to nitrocellulose sheet in blotting tank; covalently bond to sheet holding OG positions of electrophoresis by MW
  3. ) Add/incubate with first antibody that recognises the desired protein, washing excess
  4. ) Incubate with enzyme-linked second antibody which has fluorescent tag or something that recognises first antibody
  5. ) React with substrate for second antibody; showing fluoro tags etc.
61
Q

When are epitope tags added in the instances of a protein not having a corresponding antibody for detection?

A

Epitope tag sequences added in the primer by PCR

62
Q

What are the common problems/challenges with generating recombinant proteins?

A
  • Differences in codon usage reduces translation efficiency (bacteria & mammals have different preference for tRNA codons; might have to engineer human sequences to more resemble bacteria e.g. CGA to CGG)
  • Yield limited by toxicity of product to the host cell (thus control expression)
  • Incorrect folding - poor solubility/aggregation
  • Proteolytic degradation
  • Absence of disulfide bonds
  • Contamination; bacterial proteins, other molecules copurify
  • Modified proteins may be immunogenic (evoking immune response)
63
Q

Choosing the right/vector expression system; what is insulin/HGH grown in?

A

Insulin in bacterial cells,

HGH in mammalian cells

64
Q

What are the advantages of bacterial expression systems?

A
  • Rapid growth in relatively inexpensive culture media
  • Scale up easily in large fermenter
  • Well defined genetic tractability (know how to manipulate them)
  • Absence of contamination by animal/human viruses; very safe (for clinical use)
65
Q

What are the disadvantages of bacterial expression systems?

A
  • May lack posttranslational modifications

- Correct folding/tertiary structure may be difficult to acieve

66
Q

What are the steps used in generating a recombinant protein?

A
  • Human tissue
  • Isolate mRNA transcript of interest (not the gene)
  • Generate cDNA using reverse transcriptase
  • PCR amplification (and modify w/restriction enzyme sites)
  • Subclone in Expression vector
  • Transform E.coli or other host cell (getting plasmid in)
  • Induce protein expression/production
  • Optimise harvesting/protein purification
  • Scale up Fermentation
  • QA (quality assurance) and validation
  • Preclinical trials
67
Q

What is the pathway from idea of drug to patient?

A
  • Preliminary research; investigate idea or hypothesis, if successful formal project established. May also buy in idea or technology from universities/research institutes/SMEs
  • Research; develop production method; validation in closest animal models, experimenting with mutations
  • Industrial manufacture; optimisation of production under increasing quality requirements, development of analytical methods to assess quality/activity
  • Preclinical trials; toxicity studies in all organ systems (animal models)
  • Clinical trials; phase 1, 2, 3
  • Product registration; 12-18 months
  • Launch
  • Phase 4 trials; surveillance of long term side effects, treatment experience

> 7 - 10 years

68
Q

What are the potential risks with recombinant protein therapeutics?

A
  • Unintended (off target) effects in the body e.g. cancer promoting, toxic effects
  • Allergenicity, toxicity
  • Extensive preclinical testing of products in animals is mandatory before clinical trials in patients
  • But problems may only arise during clinical use
69
Q

What are the risks from industrial scale recombinant protein production?

A
  • Large scale production of GMOs; could result in accidental environmental release? Damage to environment, animals, man?
  • Inadvertent transfer of genes to other species e.g. pathogens
  • Mutation of the GMO into a harmful organism
70
Q

How are risks reduced in industrial scale recombinant protein production?

A
  • Bacteria and yeast GMOs are engineered to be inviable in the environment (can’t grow; essential genes removed so unable to survive outside the lab)
  • E.coli strains used are unable to persist in human gut
  • Engineered to have reduced capability for DNA transfer or mutation
  • Product may be produced in an inert or inactive form
  • High standards of containment, inactivation of waste products
71
Q

What is the HSE?

A
  • Health and Safety Executive; oversees all GMO generation/use with strict legislation for industrial production/research
  • Risk assessed and subject to appropriate containment
  • Level 1 = negligible/no risk
  • Level 4 = high risk