gene mapping clonning of disease gene

1. ABIPER
TOPIC “GENE MAPPING, CLONING OF
DISEASE GENE, GENETIC VARIATION
IN DRUG TRANSPORTERS”
PREPARED BY:
RAJESH YADAV
DEPARTMENT OF PHARMACOLOGY
CELLULAR & MOLECULAR PHARMACOLOGY

2. Introduction: Gene Mapping
 The technique of genetic mapping was first described by Thomas Hunt
Morgan in 1911. It is also called linkage mapping.
 Gene mapping describes the methods used to identify the location of
a gene and the relative distances between genes on the
chromosomes.
 It studies the relation of genotypes and phenotypes.

3. Genome Map
 A genome map is one-dimensional, linear, like the DNA molecules that
make up the genome itself.
 They are usually made of combinations of letters and numbers that
stand for genes or other features—for example, D14S72, GATA-P7042,
and so on.
Importance of Gene Mapping:
 it can help us determine which genes are responsible for which
trait(s).That greatly simplifies scientific investigations of all sorts :
 For instance:

4.  Using gene mapping, scientists were able to determine that the same
genes were responsible for all of the different bill shapes that are found
in the different species of finches.
 The different bill shapes are made possible by the differences in timing
and intensity of the expression of these genes.

5. Types of Gene Mapping:
 1) Genetic Mapping
 2) Physical Mapping
 Genetic mapping looks at how genetic information is
passed between chromosomes or between different regions
in the same chromosome during meiosis
 Physical mapping looks at the physical distance between
known DNA sequences by working out the number of base
pairs between them.

7. GENETIC MARKERS
 A genetic marker is a gene or DNA sequence with a known location on a
chromosome that can be used to identify individuals or species.
 Genes and markers are located close to each other on chromosomes

8. 5 MAJOR DNA MARKERS FOR
GENETIC MAPPING
1. RFLP ( Restriction Fragment Length Polymorphism)
2. AFLP (Amplified Fragment Length Polymorphism)
3. RAPD (Random Amplification of Polymorphic DNA)
4. SNP (Single Nucleotide Polymorphism)
5. VNTR (Variable Number Tandem Repeat)

9. RFLP ( Restriction Fragment Length Polymorphism)
 RFLP refers to a difference between samples of homologous
DNA molecules from differing locations of restriction enzyme
sites, and to a related laboratory technique by which these
segments can be distinguished.
 A restriction enzyme cuts the DNA molecules at every
occurrence of restriction site into million restriction fragments.
Eg. EcoR1 enzyme cuts at GAATTC or CTTAG.

10.  Any mutation of a single nucleotide may destroy or create the
restriction and alter the length of the corresponding fragment.
RFLP
Single locus probe(SLP) Multi locus probe(MLP)
 RFLP is an important tool in genome mapping.

11. ANALYSIS TECHNIQUE
 The basic technique for detecting RFLPs involves fragmenting a
sample of DNA by a restriction enzyme, which can recognize and cut
DNA wherever a specific short sequence occurs, in a process known
as a restriction digestion.
• The resulting DNA fragments are then separated by length through a
process known as agarose gel electrophoresis.
• Then transferred to a membrane via the Southern blot procedure
• Hybridization of the membrane to a labeled DNA probe then
determines the length of the fragments which are complementary to
the probe.
• Each fragment length is considered an allele, and can be used in
genetic analysis.

13. PHYSICAL MAPPING
•Physical map consists of continuous overlapping fragments of cloned DNA that has
the same linear order as found on the chromosome from which they were derived

16. 2) Restriction fragment fingerprinting
 Individual clones are digested with
different restriction enzymes.
 The digested DNA is labeled with
radioactive or fluorescent dye and
run on a sequencing gel
 The fingerprint data is collected and
analyzed for contig assembly

17. 3)Sequence Tagged Sites (STSs)
 STSs is a short (200 to 500 basepair) DNA sequence that has a
single occurrence in the genome and whose location and base
sequence are known.
 STSs can be easily detected by the (PCR) using specific primers.
 They serve as landmarks on the developing physical map of a
genome.

18. Application of gene mapping
 Identify genes which are responsible for disease.
 Heritable disease
 Cancer
 Identify genes which are responsible for traits.
 Plant or animals
 Disease resistance
 Meat or milk Production.

19. Cloning of Disease Genes
 Cloning is to duplicate a cell or an organism, Usually asexually
which is genetically an exact replica of the other cell or
organism.
 The first disease gene to be cloned was
the Duchenne muscular dystrophy gene in 1987.
 Many disorders exist which can be diagnosed clinically, but its
gene is not identified or the pathogenesis of the disease is
not understood.
Cloning genes that cause specific disorders
should lead to better diagnosis, the ability to
understand the disease process and ultimately to better
treatments.
 Genes for disorders, e.g. metabolic disorders, can
be cloned by a biochemical approach. Genes for disorders
where the function is not known can be cloned if their
chromosomal position is known (positional cloning).

20. Cloning a Disease Gene of Known Function
 The first step is to isolate the protein.
 Protein isolation requires an assay for the protein, such as an
enzyme activity assay where a product can be measured.
 One needs to know the function of the protein in order to purify
it.
 Once the protein is purified, small pieces of the protein
are sequenced, i.e. the amino acid order is determined.
 Based on the protein sequence,
a synthetic oligonucleotide DNA probe is
generated using the genetic code. This probe is used to search
a cDNA library.
 Examples of genes of known function that have been
cloned : phenylalanine hydroxylase (phenylketonuria),
hexosaminidase A (TaySachs disease)

21. Cloning a Disease Gene of Unknown Function
 It is also called “Reverse Genetics” or “Positional Cloning”.
 In Positional Cloning one identifies the disease gene based on DNA
sequence differences between affected and unaffected individuals,
and NOT based on its function
 To find a disease causative gene, the goal is to locate and identify
sequence differences, which may be a single base
pair change between an affected versus an unaffected individual.
 There are 4 steps to cloning a gene based on its position:
 Step 1 Narrow the location of the disease to a specific chromosomal
region using linkage analysis, with polymorphic genetic markers.
This is called identifying the gene critical region.

22.  Step 2 – Usually a gene critical region has several genes
located in this region, all of which need to be identified, from
which one needs to narrow down a single disease causing
gene.
 Step 3 Evaluate and prioritize the group of genes in a given
region to determine which is the best candidate that might
cause the disease.
 Step 4 Search for disease causing mutations in
candidate genes.

23. Possible Positive Consequences
 Early and more stringent screening can be performed in individuals
with higher risk for developing a specific disorder.
 The physician may be able to recommend preventative measures
to avert disease occurrence.
 Pharmacogenetics or personalized medication.
 Give Physicians the ability to predict which diseases an individual
may acquire during their lifetime.

24. Possible Negative Consequences.
 In complex disorders, it is difficult to determine which individuals may
actually become symptomatic.
 An individual may react negatively if they know they
have a high chance of developing a disorder.
 Privacy of such genetic information must be guarded.
 An individual may lose their health insurance if they
are deemed to have a “preexisting” condition.

25. Genetic Variation in Drug Transport
 Transporters are those proteins that carry either endogenous compounds or
xenobiotics across biological membranes.
 They play an important role in regulating the absorption, distribution and
excretion of many drugs.
 They can be classified into efflux and uptake proteins, depending on the
direction of transport.
 Efflux pumps on a cell membrane can remove drugs from the cell, even
before they can act.
 Transport proteins that are responsible for the influx of ions and nutrients
such as glucose can promote growth of tumor cells if overexpressed.
 There are two families of transport proteins:
1. ATP-binding cassette (ABC)
2. Solute-carrier proteins (SLC)
Transporters

26. ABC Transporters:
 They are among the most extensively studied transporters involved in
drug disposition and effects.
 They often transport substances against a concentration gradient by
using the hydrolysis of ATP.
 There are at least 49 ABC transporter genes, which are divided into
seven different families
 Three of these seven gene families are particularly important for drug
transport. i.e.
1. ABCB1 gene (P-glycoprotein/ MDR1)
2. ABCG2 gene (breast cancer resistance protein);
3. ABCC family (ABCC1 through ABCC6) or multidrug resistance
proteins (MRP).

27. Structure of ABC transporter

28. Mechanism of ABC Transporters

29. ABCB1 Transporters: P-glycoprotein
 The protein is commonly referred to as P-glycoprotein(P-gp),
PGY1, or multidrug resistance protein-1 (MDR1).
 The ABCB1 gene codes for a glycosylated membrane protein.
It was originally detected in cells that had developed resistance
to cancer chemotherapy agents.
 It is known as a multidrug resistance protein because its
expression in a cell may lead to resistance to multiple classes
of drugs.

30.  A principle function of P-glycoprotein is energy dependent
efflux of substances like bilrubin, anti cancer drugs, cardiac
glycosides, immunosuppressive agents and many other
medications.
 Besides being expressed in cancer cells, P-glycoprotein is
expressed in multiple normal tissues with protective function
including intestine, kidney, liver, blood-brain barrier, spinal
cord, testes and placenta.
 P-gp serves as a barrier against entry of xenobiotics into the
body and tissues.

31. Genetic Polymorphism/ mutation
 Mutations are inheritable changes produced in the genetic
information stored in the DNA of living cells.
 Mutation/ Polymorphism/ Genetic Variation is a difference in
DNA sequence among individual, groups or populations.
 It may occur because of SNPs, sequence repeats, insertions,
deletions and recombination.

32. Single Nucleotide Polymorphism (SNP)
 DNA sequence variation that occurs when a single
nucleotide in the genome sequence is altered.
 …CTAGATACGAACTGCATC…
 …CTAGATACGGACTGCATC…
Consequence of Polymorphism
•May result in formation of different amino acid
•May result in a change in protein formation and quantity

33. Genetic polymorphism of drug transporters
1. Polymorphism of ABCB1(P-
glycoprotein)
The effect of ABCB1 variation
on P-glycoprotein in various
tissues (e.g. the liver, gut and
heart) appears to be small.
It leads to alterations in drug
disposition and drug response,
including adverse events with
various ABCB1 substrates in
different ethnic populations.

34.  2. Polymorphism of ABCG2 gene
 It influences the PK and therapeutic effect of Rosuvastatin.
 Causes reduced biliary excretion, reduction in LDL cholesterol level in a
gene-dose-dependent manner.
 It influences the uric acid levels and makes the person susceptible for
gouts.

35. Solute Carrier Proteins:
 They are important in transport of ions and organic
substances across
biological membranes in the maintenance of homeostasis.
• Examples steroid hormones, thyroid hormones, Leukotriene,
and prostaglandins.
 It includes the transporters like OATs (organic anion
transporters), the OATPs (organic anion transporting
polypeptides, OCTs (organic cation transporters), and PepTs
(peptide transport proteins).
 SLCs are expressed in a variety of tissues such as liver,
kidney, brain, and intestine.