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GOD Cant Come in Person to Help or Trouble You.

He Will Send Some


One in the Form of Homosepian to Achieve it, Believe it. Good or Bad give it
Back as Twice, Even if it is Delayed.

COGNITIVE CONCEPT MAP ON CYSTIC FIBROSIS (CF)_SELF DIRECTED ON-LINE LEARNING RESOURCES
Problem Based Learning (PBL) for Large Groups Medical Students: e-Problem Solving Test: A Mutation Causing Cystic Fibrosis (CF)
*International Medical University (IMU),
ST Matthews School of Medicine (SMU),
AIMST-U, MSU, Vinayaka Missions Med School

Mother: The ONLY Visible GOD I Know.

Dr Kumar Ponnusamy & Dr Jegathambigai RN


*
International Medical School (IMS), Management & Science University (MSU), Malaysia
*

Acknowledgements: The Authors Gratefully Acknowledges All On-Line Resources Including Google.com, BRS, Kaplan, Slideshare, PubMed, Elsieviers Ltd, Scriibd.com., ect.,.

Cysti Fibrosis (CF): Incidence of CF: Cystic Fibrosis is one of the most common life threatening genetically inherited conditions affecting Caucasians. In the UK, the incidence is about 1/2,500 live births and about one in every 25 people is a carrier. It is uncommon in people from Asia or Africa in whom the prevalence of
CF may be as infrequent as 1/90,000. The high prevalence of the CF gene in certain populations has led to speculations that there may be some heterozygote (carrier) advantages . Clinical Features:Cystic fibrosis is a heterogeneous recessive genetic disorder with features that reflect mutations in the cystic fibrosis
transmembrane conductance regulator (CFTR) gene. Genotype and Phenotype: CF is caused by mutations in the CF transmembrane conductance regulator (CFTR) gene which encodes a protein expressed in the apical membrane of exocrine epithelial cells. This genotypic variation provides a rationale for
phenotypic effects of the specific mutations. The extent to which various CFTR alleles contribute to clinical variation in CF is evaluated by genotype-phenotype studies. The poor correlation between CFTR genotype and severity of lung disease strongly suggests an influence of environmental and secondary
genetic factors (CF modifiers). Several candidate genes related to innate and adaptive immune response have been implicated as pulmonary CF modifiers. In addition, the presence of a genetic CF modifier for meconium ileus has been demonstrated on human chromosome 19q13.2. The phenotypic spectrum
associated with mutations in the CFTR gene extends beyond the classically defined CF. Besides patients with atypical CF, there are large numbers of so-called monosymptomatic diseases such as various forms of obstructive azoospermia, idiopathic pancreatitis or disseminated bronchiectasis associated with
CFTR mutations uncharacteristic for CF. Classic CF is characterized by chronic bacterial infection of the airways and sinuses, fat maldigestion due to pancreatic exocrine insufficiency, infertility in males due to obstructive azoospermia, and elevated concentrations of chloride in sweat. Patients with
nonclassic cystic fibrosis have at least one copy of a mutant gene that confers partial function of the CFTR protein, and such patients usually have no overt signs of maldigestion because some pancreatic exocrine function is preserved. CFTR transports chloride ions (Cl-) ions across the membranes of cells in
the lungs, liver, pancreas, digestive tract, reproductive tract, and skin. Two membrane-spanning domains (MSD1 and MSD2) that form the chloride ion channel. Two nucleotide-binding domains (NBD1 and NBD2) that bind and hydrolyze ATP, and a regulatory (R) domain. Delta F508, the most common
CF-causing mutation, occurs in the DNA sequence that codes for the first nucleotide-binding domain (NBD1). Learning Outcomes: Clinical manifestations of CF. Clinical photographs and X-rays. Molecular genetic basis of CF, including the structure of the
CFTR gene, PCR and sequencing. Examples of pedigrees and explanation of risk calculation. CF Case scenario. Key Words: Cystic fibrosis, Autsomal Recessive (AR) Inheritance, Inherited disease. Outline: Affects 1 in 2,500 babies in
the UK (240 babies annually), Recessively inherited, Lifelong, life-limiting illness, Affects the lungs, digestive tract and pancreas by clogging them with thick, sticky mucus, Daily physiotherapy, dietary supplements and intensive
treatment for chest infections. CF Prevalence:Commonest AR-inherited disease amongst Northern European Caucasians, Incidence in UK Caucasian population 1 in 2,500 carrier risk 1 in 25. Incidence in UK Asian population 1 in
10,000 carrier risk 1 in 50. Pathophysiology: Gland secretions thicker or more viscous than normal. Small bowel: obstruction (meconium ileus in the newborn), Lungs : thick bronchial mucous, recurrent chest infections, progressive
lung damage, heart/lung transplantation. Pancreas: failure to secrete digestive enzymes causing malabsorption, failure of growth and late development, Men nearly always infertileabsence/atrophy of vas deferens, Lifelong
potentially fatal disease. Cystic Fibrosis Gene: Large gene encoding 1480 amino acids. Over 1,100 different mutations identified in the gene. Routinely test for 29 commonest mutations. If mutation/s not found in clinically affected
child - send DNA to laboratory to be tested for rarer mutations. The only way to cure CF would be to use gene therapy to replace the defective gene or to give the patient the normal form of the protein before symptoms cause permanent damage. The major goal in treating CF is to clear
the abnormal and excess secretions and control infections in the lungs, and to prevent obstruction in the intestines. For patients with advanced stages of the disease, a lung transplant operation may be necessary. Although treating the symptoms does not cure the disease, it can greatly improve the quality of
life for most patients and has, over the years, increased the average life span of CF patients to 30 years. Treatment: Major objectives, Promote clearance of secretions, Control lung infection Provide adequate nutrition, Prevent intestinal obstruction, Investigation into therapies to restore the processing of
misfolded CFTR protein. Lung: >95% of CF patients die from complications of lung infection. Breathing exercises. Flutter valves. Chest percussion. ? Hypertonic saline aerosols. Lung: Antibiotics: Early intervention, long course, high dose, Staphylococcus- Penicillin or cephalosporin Oral cipro for
pseudomonas: Rapid emergence of resistance, Intermittent treatment (2-3 weeks), not chronic, IV antibiotics for severe infections or infections resistant to orals.. Antibiotics: Pseudomonas treated with two drugs with different mechanisms to prevent resistance. e.g. cephalosporin + aminoglycoside Use of
aerosolized antibiotics. Increasing mucus clearance: N-acetylcysteine not clinically helpful. Long-term DNAse treatment increases time between pulmonary exacerbations.. Inhaled -adrenergic agonists to control airway constriction. No evidence of long-term benefit, Oral glucocoticoids for allergic
bronchopulmonary aspergillosis. Studying benefits of high dose NSAID therapy for chronic inflammatory changes.. Atelectasis Chest PT + antibiotics. Respiratory failure and cor pulmonale Vigorous medical management, Oxygen supplementation, Only effective treatment for respiratory failure is lung
transplantation , 2 year survival >60% with lung transplatation. Gastrointestinal: Pancreatic enzyme replacement, Replacement of fat-soluble vitamins- especially vitamin E & K. Insulin for hyperglycemia, Intestinal obstruction. Pancreatic enzymes + osmotically active agents, Distal- hypertonic
radiocontrast material via enema. Gastrointestinal: End-stage liver disease- transplantation, 2 year survival rate >50%, Hepatic and gallbladder complications treated as in patient without CF.
The Self-Directed PBL Process Overall (Day-1-Induction; Day -2 Presentation)
DAY 1: Induction of PBL on Cystic Fibrosis (CF)
1 Day 1-Step 1-Trigger 1: Release of the Digital Copy of Picture 1 Shows
the Presentation of Cystic Fibrosis.
2 Day 1-Step 2: Fig 2-Trigger 2: Display of Digital Copy of Chromosome 7 .
3 Day 1- Step 3:Trigger 3: Display of Pedigree Chart on CF. Figure 3: Genetic
Features of CF.
4 Day 1-Step 4: Research Component on CF-Review Article: URL:
http://www.wjgnet.com/1007-9327/pdf/v19/i46/8552.pdf
5 Day 1- Step 5: Matching and Fine Tuning of the Learning Outcomes Arrived by
the Team, Facilitated by Team Leader (Chair-Person of PBL Process).
Day 2: Presentation on Cystic Fibrosis (CF)
1 Day 2-Step 1: Presentations and Summarization on CF.
2 Day 2-Step 2: Display of Video Clip on CF.
URL: https://www.youtube.com/watch?v=LItSsVJPQEY
3 Day 2-Step 3: Construction of cognitive concept mapping. Model Map
on CF: URL: Dr Kumar Ponnusamy, Scribd
4 Day 2-Step 4: Spot Test on Matching Questions on CF.

Location of CF Gene Cytogenetics Presentation of CF


Cystic fibrosis Gene
Mutations

Commonest mutation Delta F508

Epidemiology
UK Caucasians - 75%
Prevalence of CF

UK Asians
- 29% .
Common mutation found in 1 in 10
UK Asians - Y569D (substitution G T)
Delta F508 and 28 others account
for 85% mutations in the Northern
European Caucasian population

The PBL Process: Day 1-Step 1-Trigger 1: Release of the Digital Copy of CF
Pathophysiology of Lungs & Chest X-Ray
Fig.1 Shows the Presentations of Cystic Fibrosis (CF) Pheno Type

Pathology

Mucous in the airways cannot be easily cleared from the lungs

Molecular Genetics & Gene Function

Locus: 7q31.2 - The CFTR gene is found in region q31.2 on the


long (q) arm of human chromosome 7.
Gene Structure: The normal allelic variant for this gene is about
250,000 bp long and contains 27 exons.
mRNA: The intron-free mRNA transcript for the CFTR gene is 6129
bp long.
Coding Sequence (CDS): 4443 bp within the mRNA code for the
amino acid sequence of the gene's protein product.
Protein Size: The CFTR protein is 1480 amino acids long and has a
molecular weight of 168,173 Da.
Protein Function: The normal CFTR protein product is a chloride
channel protein found in membranes of cells that line passageways of
the lungs, liver, pancreas, intestines, reproductive tract, and skin.
CFTR is also involved in the regulation of other transport pathways.
Associated Disorders: Defective versions of this protein, caused by
CFTR gene mutations, can lead to the development of cystic fibrosis
(CF) and congenital bilateral aplasia of the vas deferens (CBAVD).

Presentation of CF

Colon
Pancreas

Protein Function & Biochemistry

Pathophysiology of CF

Recessive Inheritance: A phenotype expressed only in homozygotes (for Xlinked, male hemizygotes) and not in heterozygotes. Most recessive disorders are
due to mutations that reduce or eliminate function of a gene (i.e., loss-of-function
mutations).

Molecular Biology
of CF

Sticky Mucus
Secretion

Lab Diagnosis of CF
Ducts are Filled with Sticky
Sweat Cl-test >70 mEq/L Pathology of CF
Mucus, Scaring of Tissue
:
Structure of the CFTR Gene: An alternative graphical display of Human
Genome Project data, as displayed by the ENSEMBL genome browser. Some
closely spaced exons appear as a single bar. The arrow shows the 53
direction of the sense strand.
Day 1-Step 2:Trigger-2:Fig.2: Display of Digital Copy of XP.
Day 1-Step 3:Trigger 3: Display of CF Inheritance

CF

GENETICS

AR
George
June
d 42 yrs 5.10.50
RTA

Robert
22.8.70

Diagnosis: DNA analysis not useful due to large variety of CF mutations. Sweat chloride test >70 mEq/L. 12% of patients with clinical. manifestations of CF have a normal sweat chloride test. Nasal transepithelial
potential difference. Criteria: One of the following: Presence of typical clinical features. History of CF in a
sibling.Positive newborn screening test.. Plus laboratory evidence for CFTR dysfunction: Two elevated sweat chloride
concentrations on two separate days. Identification of two CF mutations. Abnormal nasal potential difference measurement .
Genetic Counseling & Prenatal Diagnsis: As CF is an autosomal recessive disorder withAbnormal
100% CFTR
penetrance,
it isnon
function: When

A multiplex allele-specific PCR test


for 29 common CFTR mutations: The
same seven samples are amplified with
different cocktails of primers in the two
gels. No mutation is detected in lanes 3
or 4. Extra bands in the other lanes
define particular mutations by their
presence and size

functioning CFTR is produvced or when no


CFTR is produced the chloride ballance within
cells is altered dramatically. ENaC is released
from its inhibition and an increase in sodium
conductance is observed. This leads to
abnormal 'salty' cellular secretions which
promotes bacterial colonisation of the lungs
and ultimately to severe lung damage in CF
patients.

only possible to offer prenatal diagnostic

Molecular Biology

CFTR Controls Cl- ion Movement in & out of the Cell

BOARD QUESTIONS
1. Which of the following are multifactorial disorders?.
A) Marfan syndrome, neurofibromatosis
B) Klinefelter syndrome, Turner syndrome
C) diabetes, most cancers
D) cystic fibrosis, sick cell anemia.
2. Which of the following is the risk that an unaffected full sibling of a patient with cystic
fibrosis carries a mutated CF gene?
A) 1 in 2
Autosomal recessive: A genetic condition that appears only in individuals who have received two
copies of an autosomal gene, one copy from each parent. The gene is on an autosome, a nonsex
B) 1 in 4
chromosome. The parents are carriers who have only one copy of the gene and do not exhibit the
C) 3 in 4
trait because the gene is recessive to its normal counterpart gene.
D) 2 in 3
3. Which of the following are multifactorial disorders?
A) Marfan syndrome, neurofibromatosis
B) Klinefelter syndrome, Turner syndrome
C) diabetes, most cancers
D) cystic fibrosis, sick cell anemia. Explanation: Diabetes and most cancers have a number of
environmental and genetic components that are involved in their causation. Marfan and
neurofibromatosis are autosomal dominant. Klinefelter and Turner are caused by chromosomal
aneuploidy, cystic fibrosis and sickle cell anemia are AR.
4. Which of the following is the risk that an unaffected full sibling of a patient with cystic
fibrosis carries a mutated CF gene?
A) 1 in 2
B) 1 in 4
C) 3 in 4
D) 2 in 3. Explanation: If the full siblings status is unknown, he would have a 1 in 4 risk of being
unaffected and not carrying a CF mutation gene, a 2 in 4 risk of being unaffected but a carrier of a
CF mutation and a 1 in 4 risk of having CF. Because he is unaffected, there are 3 possible outcomes.
He now has a 1 in 3 chance of not carrying a mutated CF gene, but a 2 in 3 chance of being a carrier
of a CF mutation.

Note & Disclaimer: The content in this e-Cognitive Concept Map on BIO-GEN is based on the knowledge that
I acquired studying regular reference books and On-Line Learning Resources in Google, PUBMed ect., and
after years of teaching biochemistry-Genetics to Medical and Allied Health Science students in PBL Based
Integrated Med Curriculum. The sourvce of the figures, animation used in this Map is mentioned where ever
applicable, and they are used purely for teaching Biochemistry-Genetics to audience and no monetary benefit
intended out of it. If copyright owner of the figures used in this Map do not agree with this disclaimer, they are
welcome to contact me about it and, I will delete their content and source from my presentation. Thanking You!.

Preventive Medicine & Behavioural Issue:


Treatments : Prevention-Genetic Counseling & Gene therapy.

Treat ment /
Management

Ruth
18.1.72

Helen
1.5.74

Sally
James
6.4.79
9.6.76
adopted

Paul
15.2.81

Aaron
3.7.84

Sally (1999):

7 weeks pregnant, niece recently


diagnosed with Cystic Fibrosis. Emergency referral by
GP (by telephone).

Research Component on CF

DNA sequencer trace of part of the exon 14b PCR


product from Joanne Browns CFTR gene
At the arrowed position G and C nucleotides are both present, showing
that Joanne is heterozygous for a nucleotide substitution (remember
that the products of PCR and sequencing are normally a mix of the
products from the two alleles). Control samples show only the G. It is
usual to sequence both strands of the DNA separately to confirm any
change. In this case the sequence shown is of the reverse strand, so
in the sense strand the change in Joanne is C>G.

Pedigree of Joanne Browns family:

Note
the complete absence of any family history of cystic
fibrosis. Autosomal recessive conditions commonly
present as a single isolated case.

3D Image of Protein
When a CFTR protein with the delta F508
mutation reaches the ER, the quality-control
mechanism of this cellular component recognizes
that the protein is folded incorrectly and marks
the defective protein for degradation. As a result,
delta F508 never reaches the cell membrane.
People who are homozygous for delta F508
mutation tend to have the most severe symptoms
of cystic fibrosis due to critical loss of chloride
ion transport.
This upsets the sodium and chloride ion balance
needed to maintain the normal, thin mucus layer
that is easily removed by cilia lining the lungs
and other organs. The sodium and chloride ion
imbalance creates a thick, sticky mucus layer that
cannot be removed by cilia and traps bacteria,
resulting in chronic infections.

AR

Gene Therapy: Gene therapy is the use of


normal DNA to "correct" for the damaged
genes that cause disease.
In the case of CF, gene therapy involves
inhaling a spray that delivers normal DNA
to the lungs.
The goal is to replace the defective CF
gene in the lungs to cure CF or slow the
progression of the disease.

Cystic Fibrosis: a). The outlook for cystic fibrosis patients


has improved over the years but they still need frequent
hospital admissions, physiotherapy and constant
medications. b). Chest X-ray of lungs of cystic fibrosis
patient. c). Erect abdominal film of newborn with
meconium ileus showing multiple fluid levels. Photos (a)
and (b) courtesy of Dr Tim David, Royal Manchester
Gastrointestinal
Treatment: Modified diet: Due to pancreatic
Childrens Hospital.

disorders, children with CF


require a modified diet, including vitamin supplements (vitamins A, D, E, and K) and
pancreatic enzymes. Maintaining adequate nutrition is essential. The diet calls for a highcaloric content (twice what is considered normal for the child's age), which is typically
low in fat and high in protein. Patients or their caregivers should consult with their health
care providers to determine the most appropriate diet.
ETHICS: GENETIC COUNSELING , PRENATAL & POSTNATAL DIAGNOSIS OF
CF, REFERRAL TO SPECILITY CLINICS ON CF & SUPPORT GROUPS.

References: [1] . Jane C Davies, Eric W F W Alton, Andrew Bush. Cystic fibrosis. BMJ, 15 DEC 2007, VOL 335, 1255-1259.

Mother: The ONLY Visible GOD I Know.

GOD Cant Come in Person to Help You. He Will Send Some One in the
Form of Homosepian, Believe it. The Only Thing What You Are Going to
Take Away is Karma _Educate_Dr P Kumar, BIO-GEN.

COGNITIVE CONCEPT MAP ON XERODERMA PIGMENTOSUM (XP)


Problem Based Learning (PBL) for Large Groups Medical Students: e-Problem Solving Test: A Mutation Causing Retinoblastoma (Rb)
*International Medical University (IMU),
ST Matthews School of Medicine (SMU),
AIMST-U, MSU, Vinayaka Missions Med School

Dr Kumar Ponnusamy and Dr Jegathambigai Rameshwar Naidu


*
International Medical School (IMS), Management & Science University (MSU), Malaysia
*

Acknowledgements: The Authors Gratefully Acknowlwdges All On-Line Resources Including Google.com, PubMed, Elsieviers Ltd, Eye Cancer Network, Scriibd.com., ect.,.

Xeroderma Pigmentosum (XP): First discovered in late 1800s by Moritz Kaposi Severe lesions, tumors and skin deformations result from sun exposure. Autosomal recessive (AR)
hereditary disease, Incidence: 1 in 250,000 in Western world 1 in 40,000 in Japan, Disease caused by ineffective DNA repair. Median age to develop skin cancer is age 8, Incidence of skin
cancer is elevated 1000 fold under the age of 20. In 1960s, proved XP was due to defective NER. Phenotype can be caused by a mutation in a number of different genes. UV damage to
DNA: UV light causes nucleotide bases to form Thymine-Thymine dimers, disrupt DNA synthesis and lead to mutations. Nucleotide Excision Repair (NER): Responsible for repairing
everyday damage to genome. Scary fact: base damage estimated to occur in 25,000 bases per human cell genome per day ~ thats a lot of error to catch and correct!. A repair
mechanism that works by removing the altered base and allowing for resequencing, Discovery of pathway. Introduction Genomic DNA is highly susceptible to damage caused by its
intrinsic instability, endogenously produced reactive oxygen species and a wide variety of environmental agents such as radiations and chemicals. Some lesions, like double strand
breaks, can directly lead to chromosome aberrations (e.g. deletion, translocation, etc.), whereas structural changes in the bases often interfere with DNA replication in S-phase. When
replicating DNA polymerases are blocked by base lesions on the template strand, the replication forks may collapse, thereby resulting in double strand breaks. In addition, depending
on the type of lesions, certain DNA polymerases are capable of elongating DNA strands across damaged sites, and this translesion DNA synthesis (TLS) is frequently associated with
replication errors, giving rise to mutations. To cope with such deleterious effects of DNA damage promoting carcinogenesis, organisms are equipped with multiple DNA repair systems
(1,2).. Nucleotide excision repair (NER) is a versatile DNA repair system that eliminates a broad spectrum of base lesions generated on one strand, including ultraviolet light (UV)induced cyclobutane pyrimidine dimer (CPD) and pyrimidine (6-4) pyrimidone photoproduct (6-4PP), as well as other bulky base adducts that can be induced by numerous chemical
compounds (1,3). Although these lesions do not share common chemical structures, they are supposed to induce more or less distortion of the DNA helical structure (4). It is known that
defects in NER are associated with several human autosomal recessive hereditary disorders, such as Xeroderma pigmentosum (XP). Patients suffering from XP exhibit extreme
sensitivity to sun exposure and a marked predisposition to skin cancer. Classical complementation analyses using cell fusion have identified eight genetic complementation groups in XP,
for which the genes responsible are already cloned (5) (Table I). Seven of these groups, XP-A through XP-G, are associated with defective NER, while the remaining group, a variant
form of XP (XP-V), is proficient in NER but deficient in a specialized DNA polymerase g (pol g) involved in TLS. This article overviews how these XP gene products function in DNA
repair and prevent carcinogenesis.
The Self-Directed PBL Process Overall (Day-1-Induction; Day -2 Presentation)
DAY 1: Induction of PBL on Xeroderma Pigmentosum (XP)
1 Day 1-Step 1-Trigger 1: Release of the Digital Copy of Picture 1 Shows
the Presentations of Xeroderma Pigmentosum..
2 Day 1-Step 2: Fig 2-Trigger 2: Display of Digital Copy of Karyotype of XP.
3 Day 1- Step 3:Trigger 3: Display of Pedigree Chart on Rb. Figure 3: Genetic
Features of XP.
4 Day 1-Step 4: Research Component on XP-Review Article: URL:
http://www.ojrd.com/content/pdf/1750-1172-6-70.pdf
5 Day 1- Step 5: Matching and Fine Tuning of the Learning Outcomes Arrived by
the Team, Facilitated by Team Leader (Chair-Person of PBL Process).
Day 2: Presentation on Xeroderma Pigmentosum
1 Day 2-Step 1: Presentations and Summarization on XP.
2 Day 2-Step 2: Display of Video Clip on XP.
URL: https://www.youtube.com/watch?v=nDtZyUc1gB8
3 Day 2-Step 3: Construction of cognitive concept mapping. Model Map
on XP: URL: Dr Kumar Ponnusamy, Scribd
4 Day 2-Step 4: Spot Test on Matching Questions on XP.

In persons with XP who carry specific


mutations in the XPD gene. XPD gene
encodes a subunit of the TFII H
required for transcription initiation.
Mutations in XPD could lead to defect In
both DNA repair and transcription.

The PBL Process: Day 1-Step 1-Trigger 1: Release of the Digital Copy of
Fig.1 Shows the Presentations of Xeroderma Pigmentosum Pheno Type

Location of XP Gene Cytogenetics:

3
Molecular Biology
NER: XPC, XPA recognize base damage (mechanism not
understood). Triggers binding of several more proteins, including
XPG. Binding of ERCC1-XPF endonuclease; NER complex
complete. Cleavage and removal of damaged oligonucleotide
fragment. DNA polymerase resynthesizes missing sequence and
ligase reseals backbone. Figure from Friedberg paper

Recessive Inheritance: a phenotype expressed


only in homozygotes (for X-linked, male
hemizygotes) and not in heterozygotes. Most
recessive disorders are due to mutations that reduce
or eliminate function of a gene (i.e., loss-offunction mutations).

GENETICS

Day 1-Step 2:Trigger-2:Fig.2: Display of Digital Copy of XP.

What is the name of the DNA repair system in E. coli in which dual incisions are made
in the damaged part of the double helix, and a 12-13 base segment is removed and
replaced with new DNA?
A. Mismatch repair
B.Base excision repair
C.Nucleotide excision repair
D.AP site repair Answer .C. Nucleotide excision repair (NER) Explanation: Nucleotide

Day 1-Step 3:Trigger 3: Display of DNA Excision Repair Mechanism

excision repair is an almost universal repair mechanism in which a section of damaged DNA is
removed and replaced with new DNA by a DNA polymerase. It is used to repair photoproducts
caused by UV damage and bulky DNA lesions caused by a variety of mutagens.
Dignosis: Initially the diagnosis is predominantly clinical: a young child may be brought to the paediatric department with
bright, confluent erythema over all sun-exposed sites, or with lentigines at an unusually early age in sun-exposed areas. In the
former case, the clinician assessing the child may suspect a skin allergy, drug reaction or even in some cases sunburn caused by
parental neglect. After all differentials are excluded, the clinician would then request cellular tests to assess for defective DNA
repair. This requires a 4 mm punch biopsy of the skin taken from an unexposed site (e.g. buttock area). This specimen is used to
culture fibroblasts followed by UVR exposure and subsequent measurement of unscheduled DNA synthesis (UDS). UDS refers
to the newly synthesised DNA, which is formed when the damaged DNA is excised. UDS can be measured as incorporation of
nucleotides into DNA of the irradiated cells by autoradiography,64 liquid scintillation counting, or fluorescence assay. Typically
a reduced level of UDS confirms diagnosis of XP. Mutational analysis to assign complementation group and define pathogenic
mutation(s) in the affected gene(s) is then performed. Using next-generation sequencing techniques, a platform of DNA repair
genes can be used for rapid identification of both complementation group and mutation analysis. Diagnosis of XP-V is different
as XP-V cells have normal levels of UDS. However, UVR-exposed XP-V cells show an exquisite sensitivity to caffeine, which
impairs their survival. Therefore, if XP-V is suspected, cultured fibroblasts are incubated in caffeine for a few days and their
viability compared to that of normal cells. If UDS is normal and post-UV sensitivity to caffeine is detected, a diagnosis of XP-V
is confirmed. Of the eight genes implicated in XP, mutations in the XP-C gene count for a substantial proportion in most but not
all populations. Immunohistochemistry staining with an antibody for XP-C protein has recently been shown to be a new rapid
and cost-effective method for both diagnosis and potentially as a screening tool in suspected XP-C patients. UVR-protected,
tumour-free skin of XP-C patients will show negative expression of the XP-C protein compared to normal controls. In
principle, use of antibodies to other XP proteins can be used to also look at deficiencies in other XP complementation groups.
However, although this procedure is a rapid method of identifying reductions or absence of protein, as is the case for most XP-C
and XP-V patients, immunohistochemistry cannot be used as a diagnostic tool in many other complementation groups because
pathogenic missense mutations result in production of a defective XP protein present in normal quantity. All the diagnostic
procedures require specialised laboratories and technical skills and are therefore often not available in poorer countries, in
which there may be high incidences of XP.

Treatments & Studies:


Prevention.
Gene therapy.
Dimericine (T4N5 Liposome
Lotion).

Genetic Counseling & Prenatal Diagnsis: As XP is an autosomal recessive disorder with 100% penetrance, it is
only possible to offer prenatal diagnostic testing for XP in a family where parents already have an affected child.72
Counselling and psychological support is of paramount importance in families at reproductive risk. These families can
have prenatal diagnosis by mutational analysis or DNA repair testing on chorionic villus sampling at 10-12 weeks
gestation.73-76 In principle pre-implantation genetic diagnosis can also be carried out, if the pathogenic mutations are
known and the carrier status of both parents confirmed, although to our knowledge this has not yet been done for XP.

Q. Which of the following autosomal recessive disorder is associated with development of skin
malignancies?
Note & Disclaimer: The content in this e-Cognitive Concept Map on BIO-GEN is based on the knowledge that
I acquired studying regular reference books and On-Line Learning Resources in Google, PUBMed ect., and
A.Peutz Jeghers
after years of teaching biochemistry-Genetics to Medical and Allied Health Science students in PBL Based
B.Tuberous sclerosis
Integrated Med Curriculum. The sourvce of the figures, animation used in this Map is mentioned where ever
applicable, and they are used purely for teaching Biochemistry-Genetics to audience and no monetary benefit
C.Neurofibromatosis
intended out of it. If copyright owner of the figures used in this Map do not agree with this disclaimer, they are
D.Xeroderma pigmentosa
welcome to contact me about it and, I will delete their content and source from my presentation. Thanking You!.
E.Familial polyposis coli
Answer D: Xeroderma pigmentosa is an autosomal recessive (AR) condition in which the ability of DNA
to repair damaged caused by UV light is deficient 2. Even the slightest amount of sunlight can induce
skin cancer in this disorder 3. Multiple basal cell cancers and melanomas usually appear at a young age.
The disorder is most common in Japanese individuals 4. The defects is because of the defective
nucleotide excision repair enzymes.
Xeroderma pigmentosum is produced as a result of a defect in :
A. DNA polymerase III
B. DNA polymerase I
C. DNA exonuclease
D. DNA ligase
Answer:B. DNA polymerase I or D. DNA ligase.
Xeroderma pigmentosum is an autosomal recessive disease with defect in DNA repair. It is characterised
by extreme sensitivity to sunlight. The enzymes affected in this condition are:
1. UV specific endonuclease (most common)
2. DNA polymerase I
3. DNA ligase.

Research
Component
on XP

Which of the following is the name of the human


genetic disorder resulting from defects in nucleotide
excision repair?
A.Hereditary nonpolyposis colorectal cancer (HNPCC)
B.Xeroderma pigmentosum (XP)
C.Lynch syndrome
D.Diabetes
Answer B. Xeroderma pigmentosum (XP)
.Explanation.: People born with the disorder, xeroderma
pigmentosum, have a mutation in one of the genes coding
for nucleotide excision repair enzymes. Therefore they are
unable to carry out efficient repair on sunlight damage and
they are hypersensitive to sunlight. They have to protect
their skin from daylight or risk getting skin cancer.

5
What is XPF?: In the NER pathway, XPF forms a
heterodimeric endonuclease with ERCC1.
The ERCC1-XPF protein is responsible for splicing
the 5 end of the damaged sequence.

6
7

ETHICS: GENETIC COUNSELING & REFERRAL TO


SPECILITY CLINICS ON XP & SUPPORT GROUPS.

References: [1] . Lee J. Martin, DNA Damage and Repair: Relevance to Mechanisms of Neurodegeneration. J Neuropathol Exp
Neurol. 2008 May ; 67(5): 377387.