Chemistry and Biology of DNA in the Age of Personalized Medicines

Dr. Ishtiaq Ahmad Khan

Assistant Professor

Dr. Panjwani Center for Molecular Medicine and Drug ResearchInternational Center for Chemical and Biological Sciences, University of

Karachi.

DNA in every organism

DNA – The molecule of Life

The building blocks of DNA are nucleotides.each nucleotide composed of:

– a nitrogenous base(adenine, thymine, guanine, cytosine abbreviated as A, T, G, C)

– a 5-carbon sugar called deoxyribose– a phosphate group (PO4)

Nucleotides

Nitrogenous base(adenine)

5-carbonRibose sugar

Phosphategroup

esterlinkage

DNA StructureNucleotides are connected to each other by

phosphodiester bonds to form a long chain

Double helical Structure of DNA– 2 sugar-phosphate backbones– nitrogenous bases toward the interior of the

molecule– bases form hydrogen bonds with complementary

bases on the opposite sugar-phosphate backbone• A pairs with T (2 H bonds)• C pairs with G (3 H Bonds)

Noble Prizes in DNA Chemistry

Watson, Crick, and Wilkins (1962): Discovery of structure of DNAH. Gobind Khorana (1973)Chemical synthesis of oligonucleotide Berg, Gilbert, and Sanger (1980): The determination of base sequences in nucleic acidsMullis and Smith (1993): Contributions to the developments of methods within DNA-based chemistry. Invention of PCR

Sequencing the DNAIn the 1970’s, Sanger’s group discovered a method of 'reading' the linear DNA sequence using special nucleotide bases called chain terminators or di-deoxy nucleotides.

This method is still in use today.

Died on November 19, 2013Frederick Sanger

Dideoxy Nucleotide

Next Generation DNA Sequencing

Complete genome copies

Massively parallel sequencing, Shotgun Genome Sequencing:for sequencing the whole genome and whole exome

Fragmented genome chunks

NOT REALLY DONE BY DUCK HUNTERS !Hydroshearing, sonication, enzymatic

shearing

Next Generation DNA Sequencing

Major NGS Platforms • 454 FLX Genome Sequencer (Roche)Pyrosequencing method• Hiseq2000, Solexa Genome Analyzer (Illumina)Sequencing by seynthesis • SOLiD ( Applied Biosystems)Sequencing by ligation chemistry• Ion-torrent (Life technologies)An integrated semiconductor device enabling non-optical genome sequencing

• Heliscope (Heliscope Biosciences)Single molecule sequencing by synthesis

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ATTGTTCCCACAGACCGCGGCGAAGCATTGTTCC ACCGTGTTTTCCGACCG

TTTCCGACCGAAATGGCTTGTTCCCACAGACCGTGAGCTCGATGCCGGCGAAGATGCCGGCGAAGCATTGT

TAATGCGACCTCGATGCCACAGACCGTGTTTCCCGA

AAGCATTGTTCCCACAG TGTTTTCCGACCGAAATCCGACCGAAATGGCTCCTGCCGGCGAAGCCTTGT

Assembly of short reads

17 bp

66 bp

TAATGCGACCTCGATGCCGGCGAAGCATTGTTCCCACAGACCGTGTTTTCCGACCGAAATGGCTCC

Consensus sequence:

Overview of DNA to RNA to Protein

• A gene is expressed in two steps– Transcription: RNA synthesis– Translation: Protein synthesis

DNA: A long double-stranded string of nucleotides that encode for many genes.

Gene

The Central Dogma: DNARNAProtein

DNA: A long double-stranded string of nucleotides that encode for many genes.

Gene

RNA: A single-stranded copy of one gene.

RNA

The Central Dogma: DNARNAProtein

DNA: A long double-stranded string of nucleotides that encode for many genes.

Gene

RNA: A single-stranded copy of one gene.

The Central Dogma: DNARNAProtein

RNA

Protein: Proteins are composed amino acids. Amino acids are made from triplets of nucleotides called codons.

DNA: A long double-stranded string of nucleotides that encode for many genes.

Gene

Protein: Proteins are composed amino acids. Amino acids are made from triplets of nucleotides called codons.

RNA: A single-stranded copy of one gene.

The Central Dogma: DNARNAProtein

Codon 1

DNA: A long double-stranded string of nucleotides that encode for many genes.

Gene

Protein: Proteins are composed amino acids. Amino acids are made from triplets of nucleotides called codons.

RNA: A single-stranded copy of one gene.

The Central Dogma: DNARNAProtein

Codon 1 Codon 2

DNA: A long double-stranded string of nucleotides that encode for many genes.

Gene

Protein: Proteins are composed amino acids. Amino acids are made from triplets of nucleotides called codons.

Amino acid 1 Amino acid 2

RNA: A single-stranded copy of one gene.

The Central Dogma: DNARNAProtein

Codon 1 Codon 2

DNA: A long double-stranded string of nucleotides that encode for many genes.

Gene

Protein: Proteins are composed amino acids. Amino acids are made from triplets of nucleotides called codons.

Amino acid 1 Amino acid 2

Protein!

RNA: A single-stranded copy of one gene.

The Central Dogma: DNARNAProtein

Codon 1 Codon 2

A small change in the gene sequence can result in a very different protein

ATG GTG CTG TCT CCTDNA:

A small change in the gene sequence can result in a very different protein

ATG GTG CTG TCT CCT

Met

DNA:

Amino Acids/Protein:

A small change in the gene sequence can result in a very different protein

ATG GTG CTG TCT CCT

Met

DNA:

Amino Acids/Protein: Val

A small change in the gene sequence can result in a very different protein

ATG GTG CTG TCT CCT

Met Leu

DNA:

Amino Acids/Protein: Val

A small change in the gene sequence can result in a very different protein

ATG GTG CTG TCT CCT

Met Leu Ser

DNA:

Amino Acids/Protein: Val

A small change in the gene sequence can result in a very different protein

ATG GTG CTG TCT CCT

Met Leu Ser Pro

DNA:

Amino Acids/Protein: Val

A small change in the gene sequence can result in a very different protein

ATG GTG CTG TCT CCT

Met Leu Ser Pro

DNA:

Amino Acids/Protein: Val

A small change in the gene sequence can result in a very different protein

ATG GTG CTG TCT CCT

Met Leu Ser Pro

DNA:

Amino Acids/Protein: Val

ATG GTG CTG TCT ACTDNA:

A small change in the gene sequence can result in a very different protein

ATG GTG CTG TCT CCT

Met Leu Ser Pro

DNA:

Amino Acids/Protein: Val

ATG GTG CTG TCT ACT

Met Leu Ser Thr

DNA:

Amino Acids/Protein: Val

A small change in the gene sequence can result in a very different protein

ATG GTG CTG TCT CCT

Met Leu Ser Pro

DNA:

Amino Acids/Protein: Val

Words: Tom and Sam are bad

ATG GTG CTG TCT ACT

Met Leu Ser Thr

DNA:

Amino Acids/Protein: Val

A small change in the gene sequence can result in a very different protein

ATG GTG CTG TCT CCT

Met Leu Ser Pro

DNA:

Amino Acids/Protein: Val

Words: Tom and Sam are bad

ATG GTG CTG TCT ACT

Met Leu Ser Thr

DNA:

Amino Acids/Protein: Val

Tom and Sam are sadWords:

A small change in the gene sequence can result in a very different protein

ATG GTG CTG TCT CCT

Met Leu Ser Pro

DNA:

Amino Acids/Protein: Val

Words: Tom and Sam are bad

ATG GTG CTG TCT ACT

Met Leu Ser Thr

DNA:

Amino Acids/Protein: Val

Tom and Sam are sadWords:

Changes in DNA are called variations or mutations

Variations in the DNA (genotype) can cause observable changes (phenotype) in individuals

Human Genome Research

• Human Genome Project in 2003•Finishing the euchromatic sequence of the human genome.

•Nature 2004; 431 (7011): 931-945.

• Phase I HapMap project in 2005•A haplotype map of the human genome.

•Nature 2005: 437(7063):1299-1320

• Encyclopedia of DNA Elements (ENCODE) project in 2007•Identification and analysis of functional elements in 1%

•of the human genome by the ENCODE pilot project.•Nature 2007; 447(7146):799-816

• 1000 Genomes Project in 2008•DNA sequences. A plan to capture human diversity in 1000 genomes.

•Science 2008; 319(5863):395

Genotypes and Human Disease

Do all humans have the same DNA?• Single nucleotide polymorphisms or SNPs.

• We can associate SNPs with medical histories of individuals and achieve statistically significant correlations.

• Pharmacogenetics (PGx) is the science of how an individual’s genotype affects their body’s response to drugs.

Variationsin our DNA

make usUNIQUE!

Genomics in Drug Discovery

Personalized MedicinesPersonalized medicine is the use of

information from a patient's genotype to:

• Initiate a preventative measure against the development of a disease or condition,

or

• Select the most appropriate therapy for a disease or condition that is particularly suited to that patient.

Why does it matter?

In treating all people with a certain lung cancer without having a

genetic test , 10 % of people might respond.

In treating people who have a genetic test and are found to have

a tumour mutation , 85% of people treated for that mutation

might respond.

The best drug for a specific disease in a

particular person.

Is Personalized medicine only for sick people?

Definitely not. Because an individual's genome influences his or her likelihood of developing (or not developing) a broad range of medical conditions, personalized medicine focuses strongly on wellness and disease prevention.

If a person's genomic information indicates a higher-than-average risk of developing diabetes or a particular form of cancer, that person may choose a lifestyle, or sometimes be prescribed medications.

Examples of SNPsLinked to Drug Response

Case Study: Warfarin

• Most widely prescribed oral anticoagulant for preventing thrombolytic events, despite its narrow therapeutic range.

• Problematic dosing due to patient’s diet, age, and other medications.

•CYP2D9/VKORC1 genes analysis predicts its prescription.

(Mol Interv. 2006, 6(4): 223-277)

Case Study: Irinotecan

• Irinotecan is used as chemotherapeutic agent for the treatment of metastatic colorectal cancer.

• It produces adverse drug reactions in some patients.• genotyping assay is carried out to mutations in UGT1A1 gene for irinotecan prescribing.

(Personalized Medicine 2006, 3(4): 415-419)

Case Study: Abacavir

• Abacavir is a nucleoside analog reverse transcriptase inhibitor used to treat human immunodeficiency virus (HIV) .

• Its main side effect is hypersensitivity reaction (HSR).• HSR is associated with ethnicity. A significantly increased risk of abacavir-induced HSR in human leukocyte antigen (HLA)-B*57:01-carrying patients.

Sci China Life Sci. 2013, 56(2):119-24

Interferon Therapy

• Standard approved therapy for Hepatitis C• Differential response• Interleukin 28B gene (IL28B) variants which

are associated with decreased HCV clearance• Interleukin 28B gene (IL28B) variants are

considered as key players in deferential therapeutic responses.

Malignant Melanoma 2007

Melanoma 2013

Targeting treatment to a specific variant in the Melanoma gene.

Structure of Vemurafenib (marketed as Zelboraf)

Beta-thalassemias (β-thalassemias) are a group of inherited blood disorders caused by problems in the

production of hemoglobin, the oxygen-carrying protein in red blood cells.Cause is the mutations in beta-chain, 200 SNPs and several deletion

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Hummmm……

Genomics

at

International Center for Chemical and Biological

Current Research Projects• Five human genome project• Integrated analysis of HCV genome and Exome

of Hepatitis C patients to Study genetics of differential response to interferon therapy

• Assessment of genetic factors for Ventricular Septal Defect

• Genomics of Diabetic patients

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Memorable Moments

Red Fort (Lal Qila) D

elhi India

Education complex of Islam

ic era at Q

utab complex D

elhi

Qutab M

inar Delhi India