A Study of Cystic Fibrosis Using Web-Based Tools

1
A Study of Cystic Fibrosis Using Web-Based Tools

• Anuradha Datta Murphy
• Graduate Student, Dept. of Molecular and
  Integrative Physiology,
• University of Illinois at Urbana-Champaign

2
Introduction

• We will use several medical and computational
  biology web sites to obtain information on cystic
  fibrosis, an inherited respiratory disorder.
• Outline of presentation
• What is cystic fibrosis (CF)?
• Gather information on cause and symptoms of CF
  from medical web sites
• Search for cystic fibrosis transmembrane
  receptor (CFTR) protein, locate CF-causing
  mutation, view CFTR structure using web-based
  tools
• Obtain information on other inherited disorders
  of interest

3
What is cystic fibrosis?

• Cystic fibrosis (CF) is an inherited genetic
  disease that affect cells producing sweat,
  saliva, mucus, and digestive fluids. Normally
  thin and slippery, in CF patients these
  secretions are sticky and block tubes and
  passageways. Most CF patients die of bacterial
  infections resulting from blocked airways in the
  lungs.
• Most children with CF have frequent coughing,
  wheezing, and respiratory infections.

4
Symptoms of CF, contd.

• CF also affects the pancreas, liver, and
  intestines, leading to poor absorption of
  nutrients and poor weight gain. CF patients have
  salt crystal formation on their skin when they
  sweat excessively.
• CF slide show available at http//www.healthcentr
  al.com/library/April_03/flash_content/hcplay.asp?i
  d110

5
What causes CF?

• A mutation in the gene coding for the CFTR
  (cystic fibrosis transmembrane receptor) protein
  causes CF.
• CF is caused when a child inherits two copies of
  this defective (mutated) gene, one from each
  parent.
• The CFTR protein is a Cl- channel located on the
  plasma membrane of epithelial cells of the lungs,
  pancreas, sweat glands, and other tissues.
• In non-CF individuals, Cl- transport from the
  cell is increased in the presence of ATP. In CF
  patients this transport malfunctions, causing
  salt and water imbalance in and around the cell.

6
The CFTR protein

• A single mutation in the CFTR gene results in
  cystic fibrosis.
• This mutation involves deletion of three
  basepairs of DNA, resulting in deletion of a
  phenylalanine residue (delta-F508 mutation) from
  a normal (wild type) CFTR sequence.
• Theory deletion of Phe508 prevents the CFTR
  protein from being properly delivered to the
  plasma membrane, thus causing Cl- transport
  malfunction.

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Properties of the CFTR protein

• The CFTR gene is located on chromosome 7 in the
  human genome
• This protein is made up of 1480 amino acids and
  contains two domains (1) membrane association,
  and (2) ATP-binding
• In CF patients, deletion of Phe 508 causes
  defective Cl- transport.

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Locating and viewing the CFTR protein

• In the Biology Student Workbench, search for the
  CFTR protein using the following
• search words cystic fibrosis homo sapiens
• search database Non-Redundant protein sequence
  database
• tool Ndjinn
• Select SDSCNR315424, Cystic Fibrosis
  Transmembrane Conductance Regulator , import
  sequence.
• View sequence, note accession number, P13569.
  Use other tools on BSW to learn about CF.

9
Using the NCBI web site

• The National Center for Biotechnology Center is
  available at the following url
  http//www.ncbi.nlm.nih.gov
• Many computational biology tools are available
  here, including PubMed (a database of biological
  literature), Entrez (a search engine for
  information on protein and nucleotide sequences
  across databases), BLAST (alignment search tool
  for protein and nucleotide sequences), OMIM
  (Online Mendelian Inheritance in Man, a directory
  of human genes and genetic disorders), and Cn3D
  (structure viewer).

10
Study of CFTR using tools on NCBI

• In the NCBI home page search Entrez for cystic
  fibrosis select Entrez, type human cystic
  fibrosis in the Search window, click on Go.
• In the results page note that our keyword search
  has yielded hits on multiple databases contained
  within NCBI.
• Since CF is an inherited genetic disorder, click
  on OMIM to view results within the Online
  Mendelian Inheritance in Man database.
• In the OMIM hits list page, click on the top hit,
  602421.

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Using OMIM

• Note the exhaustive information on CF available
  in OMIM, including cause and symptoms of the
  disease, molecular basis, summary of literature
  on CFTR mutation research, study of other related
  diseases generated by mutations on CFTR, etc.
• Click on Gene map locus 7q31.2 near the top of
  the page. This gives the CFTR gene location on
  the human genome. Click on Location in the
  following page to get more detailed information,
  including a figure of human chromosome 7 and
  other genes located in the vicinity.

12
Using OMIM

• Return to the OMIM results page. Scroll down the
  page to locate literature on F508 deletion (you
  can click on Edit in the toolbar header, click
  on Find on This Page and type delF508).
  Research indicates that this deletion causes CF.
  Click on (602421.0001). This is the mutated CFTR
  gene causing CF. In the displayed page, there is
  more literature on CFTR mutation research.

13
Using NCBI tools

• Return to the Entrez results page. Click on
  Protein to examine the CFTR protein sequence.
  In the hits page, click on P13569.
• Note presence of a phenylalanine residue (F) at
  position 508 in the CFTR sequence. There is also
  detailed information on various CFTR sequence
  mutations and their results.

14
Using Cn3D structure viewer

• Return to the Entrez results page. Click on
  Structure.
• Note presence of multiple CFTR structures based
  on Phe508 mutation.
• Click on 1CKZ, view structure of CFTR segment
  affected by Phe508 mutation using Cn3D.
• In the MMDB Structure Summary page, click on
  View 3D Structure button.
• Click on amino acid residues below to observe
  location on structure. Note absence of F
  residue.

15
Using NCBI tools

• Return to the OMIM page.
• On the left column, click on Search Morbid Map
• In the Search for window, type in keywords for
  any inherited disease of interest (ex., sickle
  cell anemia, muscular dystrophy, diabetes, etc.)
• Locate the affected gene on the human genome,
  view location on the chromosome, view structure
  of protein (if available) using Cn3D, and read up
  on literature of research (both clinical trials
  and gene mutations), all using tools on NCBI!

16
Closing Notes

• For more information on CF symptoms and
  treatment, see
• http//www.merck.com/mrkshared/CVMHighLight?file/
  mrkshared/mmanual_home2/sec04/ch053/ch053a.jsp3Fr
  egion3Dmerckcomwordcysticwordfibrosisdomain
  www.merck.comhl_anchor
• http//www.healthcentral.com/library/libraryconten
  t.cfm?id222
• http//www.healthcentral.com/library/libraryconten
  t.cfm?id222