needles in the migraine haystack, cerebrospinal fluid biomarkers
DESCRIPTION
Needles in the migraine haystack, cerebrospinal fluid biomarkers. Company: Huntington Medical Research Institutes Mentors: Alfred Fonteh Ph.D., Mike Harrington M.B. Ch.B., F.R.C.P. Intern: Samuel Wein Earlham College, IN. USA. Uncovering the protein changes brought about by migraine. - PowerPoint PPT PresentationTRANSCRIPT
Needles in the migraine haystack, cerebrospinal fluid biomarkers
Company: Huntington Medical Research InstitutesMentors:
Alfred Fonteh Ph.D., Mike Harrington M.B. Ch.B., F.R.C.P.
Intern: Samuel WeinEarlham College, IN. USA
Uncovering the protein changes brought about by migraine
Goal: To process MS/MS data to graph the levels of proteins from cerebrospinal fluid (CSF) during migraine and then combine these graphs with protein protein interaction data to create a map
of expressions.
Why do we care?
Chronic Migraine is a debilitating disorder affecting as many as 10% of people
Migraine has a direct medical cost of over $1 billion dollars
By understanding how the brain changes during migraine we come closer to finding better treatments
CSF is a likely pool for biomarkers as it is within the blood brain barrier
What is migraine?
A neurological disorder which manifests in severe headaches, photophobia, phonophobia, and nausea
Caused by over-excitation of various nerves
What is CSF?
Produced in the brain Pushed down spinal
column where it is absorbed
Physically protects the brain
Acts as a conduit for signals
What I am doing
Taking protein sequence data from CSF samples taken over a four day period
Using existing databases to find how the proteins interact
Mapping expression levels of each protein every day onto their interactions
Grouping proteins by expression profile over time
Grouping proteins by presence in specific pathways
Protein sequence data
Data was collected from a stent inserted
into the spinal column
CSF was harvested every four hours
Protein sequence was obtained using
liquid chromatography and mass spectrometry
Input:
MS/MS data
Proteins were digested with trypsin MS/MS data was interpreted using BioWorks
SEQUEST algorithm was used to determine protein composition as well as frequency of protein appearance
Protein abundance was measured by height of peaks
Raw Ms/MsData Parser
Return SeparatedList of Protein names
CSV file withProtein name
number of expressions
PICR List ofsynonyms
APID2Net& Cytoscape
Interactionsbetweenproteins
VANTED
Final Graph
Protein similarities
Python & Shell Scripts• Used to
convert between different formats
• Populate VANTED templates
• Creates a list of proteins
Raw Ms/MsData Parser
Return SeparatedList of Protein names
CSV file withProtein name
number of expressions
PICR List ofsynonyms
APID2Net& Cytoscape
Interactionsbetweenproteins
VANTED
Final Graph
Protein similarities
Cytoscape
Raw Ms/MsData Parser
Return SeparatedList of Protein names
CSV file withProtein name
number of expressions
PICR List ofsynonyms
APID2Net& Cytoscape
Interactionsbetweenproteins
VANTED
Final Graph
Protein similarities
Apid2NET
Proteins are tagged based upon what known pathways they participate in
Can also be tagged by structural homology
Apid2NET
Raw Ms/MsData Parser
Return SeparatedList of Protein names
CSV file withProtein name
number of expressions
PICR List ofsynonyms
APID2Net& Cytoscape
Interactionsbetweenproteins
VANTED
Final Graph
Protein similarities
PICR
Protein identifier cross-reference service Finds synonyms of protein names and uniprot
numbers
Raw Ms/MsData Parser
Return SeparatedList of Protein names
CSV file withProtein name
number of expressions
PICR List ofsynonyms
APID2Net& Cytoscape
Interactionsbetweenproteins
VANTED
Final Graph
Protein similarities
VANTED
Links represent known protein interactions
Colors represent similar expression profiles
Line graphs show the expression levels
VANTED
Raw Ms/MsData Parser
Return SeparatedList of Protein names
CSV file withProtein name
number of expressions
PICR List ofsynonyms
APID2Net& Cytoscape
Interactionsbetweenproteins
VANTED
Final Graph
A schematic procedure
Protein similarities
Conclusion
Automated generation of protein expression graphs
Automated ability to search protein functions
These tools will be invaluable in searching the migraine haystack
Thanks and acknowledgements
• Drs Fonteh and Harrington
• HMRI
• All of the SocalBSI staff
• All of my fellow students
• NSF and NIH