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BISC 005 Biochemistry of Life

From Human Genomics to Proteomics (II)

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Human Genomic Project has changed Medicine: (2) Gene Therapy

• Many scientists and physicians think that many medical benefits could flow fromknowing the location and sequences of all the genes

• Such knowledge would facilitate locating genes that are associated with diseasesor disease susceptibility

• This make possible the development of “Gene Therapy”

What is “Gene Therapy” ?

To introduce a normal gene, via genetically engineered cell, into individuals who do not possess a functional copy of this gene, for therapeutic purposes.

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Gene Therapy for SCIDS

Gene therapy has been successfully used to treat Severe Combined ImmuneDeficiency Syndrome (SCID)

• Fatal disease in which a child is born without a functional immune system• Unable to fight infections• These children die from the slight infection unless they are lived in total isolation: “Boy/Girl in a bubble” Treatment

• Enzyme that control SCID• adenosine deaminase (ADA)• its gene located on chromosome 20

Deficiency of ADA will cause SCID, while gene therapy can transfer gene for ADA into immune cells of patients.

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Gene Therapy for SCIDS

LASN virus is chosen as vector to transfer the gene into the desired human cells.

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Gene Therapy for SCIDS

The genetically engineered lymphocytes are injected into the patient, where they are expected to outgrow the genetically defective lymphocytes because the ADA-deficient cells do not divideas fast as cells with the ADA enzymes.

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Technical Limitations in Gene Therapy

The enzyme (ADA) controls the symptoms of the disease, but it is NOT a curebecause the underlying disease is still present.

• the genetically engineered cells are matured lymphocytes, which have onlya limited life span, repeated injection of genetically engineered cells are needed

• people questioned the term “Gene Therapy” as what have been done so far is notdesigned to cure any condition, only to alleviate the symptoms

Hope of a MORE LASTING cure

• Italian researchers have tried using genetically engineered bone marrow stem cells• Stem cells can develop into different type of blood cells• After the repaired lymphocytes die off, stem cells with repaired DNA could divide to

• provide new, ADA functional lymphocytes• for the lifetime of the individual

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Questions of SafetyMight the virus (used as vector) cause a disease of its own ?

Might random insertion of DNA into the host DNA destroy some other genes?

One case in US

In 1999, an 18-year old boy died after receiving a viral factor for gene therapyfor a metabolic disease, then

• Gene therapy clinical trail were halted in US• The boy’s father has testified at a US Senate hearing that the boyand his family were not fully informed of the dangers of the experiment

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Questions of Ethics

New recombinant DNA procedures for gene therapy is very expensive to develop,this raises issues of fairness:

• Will the benefits of gene therapy be available only to those who can affordthem ?

• Should government hospitals provide this kind of treatment by using taxpayer’smoney ?

• Should insurance cover their use ?• How can society’s health care resources best be distributed ?

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Unexplored Potentials of Gene Therapy

Insertion of the functional gene for insulin into pancreatic cells of patients with diabetes might cure them of the disease,

but they would still pass on the defective traits to their children.“The effects of gene therapy would last as much as lifetime, but NO LONGER…..”

Germ Cell Gene TherapyIf successful gene therapy is performed on GERM CELL, then the genetic defect

will be cured in the future generations derived from those germ cells !

However, most people advise caution and waiting in the case of germ cell gene therapy until human have more experience with gene therapy on somatic cells.

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The “Other” Genomes

The human genome project also funded the sequencing of the genomes ofmany other species.

Yeast Worm Fruit Fly Mouse

Genome projects of these so-called “model organisms” are attractive todrug hunters as comparatively these simple organisms are harnessed tofind new drugs for human.

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Bioinformatics Gold RushBioinformatics is the combination of molecular biology and computer scienceto navigate through the tremendous amounts of data produced by genomeprojects of different species (human, yeast, worm…..).

“The race and competition will be who can mine [the data] best.There will be such a wealth of riches.”

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Bioinformatics is doing what ?Within bioinformatics, people are programming computers to scan the sequencedata to locate genes (meaning sequences that code for proteins).

The rule is:• Start codon: “ATG”; Stop codon: “TAA, TAG or TGA”• Computer can scan the sequences that follow any ATG and find those areas where next stop codon occurs a few hundred bases further along

Gene scanning is much more difficult in human as human genome has long, non-coding regions dispersed among much shorter regions of coding regions. This requires massive computer power.

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Using Bioinformatics to Find Drug Targets

By looking for the genes in model organism that are similar to given human genes, researcherscan learn about the protein the human gene encodes and search for drugs to block it.The MLH1 gene, which is associated with colon cancer in humans, is used in this example.

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Using Bioinformatics to Find Drug Targets

“A 300-million industry has emerged around turning raw genome data intoknowledge for making new drugs.”

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Beyond the Human Genome…..!The DNA sequence tells only a small fraction of the story about what a specific cell is doing.

• With all the DNA that codes for a human in hand, researchers begins a morechallenging tasks: Proteomics

Proteomics is biotech’s “new new thing”.

It is a business of human genome, which holds the keys to multibillion-dollar

biotech industries of the future.

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Proteomics is doing what ?• The complete protein content of an organism is its proteome• Proteomics is the cataloging and analysis of every protein in the human body and to figure out how they “network” with one another

“Network of proteins pervade all cells.”

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Proteomics leads to more and better drugs

Knowing the DNA sequence (from study of human genome)

Discovery of amino acid sequence of proteins

Computer programs uses the known energies and bond angles ofchemical bond to generate graphics for 3-D shape of protein model

Based on the computer graphics, designing new drugs

Synthesis and testing of new drugs by biochemists

New drugs(More specific, less side-effects)

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Proteomics leads to more and better drugs

Unfortunately, the PROTEOME is muchMORE COMPLICATED than the genome.

• Investors have poured hundreds of millions of dollars into companies that are devoted to producing proteomic equipment

• Determining the 3-dimensional structure of proteins allows researchers tofind sites where proteins are most vulnerable to drugs

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Proteomics Equipment: 2-Dimensional Gel Identifying Unknown Protein

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Proteomics Equipment: Mass Spectrometer Identifying Unknown Protein

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Proteomics Equipment: Robotic Workstation

ROBOTIC WORKSTATION in a proteomics facility borrows technology from the assembly lines of the automative industry.This one is configured to automate repetitive tasks such as pipetting and changing the growth medium – steps involved ingrowing cell cultures, a prerequisite for proteomics studies.

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Proteomics Equipment: X-Ray Crystallography

X-RAY CRYSTALLOGRAPHY requires growing a pure crystal (inset) of the protein under study. Here a crystal of CD4, theprotein that serves as a gateway for the AIDS virus to infect immune cells, is held in a tiny tube sealed with a ball of wax. Thetube will be bombarded with x-rays to yield a pattern that scientists can interpret to determine the 3-dimensional structure of an individual molecule of protein.

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How Proteomics can help drug development FINDING NEW DRUG TARGETS(Here, devising a drug to kill the skin cancer melanoma)

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How Proteomics can help drug development AVOIDING DRUGS WITH SIDE EFFECTS(Here, determining whether an investigational drug prompts production of possibly harmful protein)