Subject: [Beg-sysbiol] is this something we can help with?
From: Yves Van de Peer <[email-masked]>
To: [email-masked]
Date: Sun, 20 Jul 2008 11:27:41 +0200
List-Id: beg-sysbiol.psb.ugent.be

-------- Original Message --------
Subject: 	FW: Systems Biology for PNS disease?
Date: 	Fri, 4 Jul 2008 16:07:03 +0200
From: 	Timmerman Vincent <[email-masked]>
To: 	<[email-masked]>

__________________________________________
*From:* Timmerman Vincent
*Sent:* Friday, July 04, 2008 4:03 PM
*To:* Yves Van de Peer ([email-masked])
_*_Cc_* <mailto:[email-masked]%29Cc>*:* Leonardo de Almeida 
Souza ; sophie janssens
*Subject:* Systems Biology for PNS disease?

Dear Yves,

As I enjoyed your presentation on “Systems Biology” at the VIB DC 
meeting in June, I would like to come back at our discussion we had. As 
you know we are studying the molecular genetics and cell biology of the 
peripheral nervous system (PNS). In particular we study the inherited 
forms of PNS disease, resulting in peripheral nerve degeneration. Up to 
date we have 40 genes and more than 800 mutations in these genes causing 
various types of peripheral neuropathies. For many of these genes, their 
protein function is “unknown” or it remains a mystery why mutations in 
these proteins are associated with neurodegeneration. As an example we 
identified mutations in small heat shock protein genes (HSPB1 and HSPB8) 
causing motor neuropathies, mutations in amino-acyl-tRNA synthetases 
(YARS, GARS) causing variants of Charcot-Marie-Tooth (CMT) neuropathies, 
mutations in small GTP-ases and GEF proteins causing other variants of 
CMT, etc. Other genes make sense since these are implicated in 
Schwann-cell biology and myelination, or axonal transport. You can find 
on this link (_http://www.molgen.ua.ac.be/CMTMutations/_) a database 
that we developed over the years showing the genes involved and the 
mutations identified so far in peripheral neuropathies.

It would be very interesting and timely to run one of your 
bio-informatic platforms to compare the wild type protein-protein 
interaction networks between these 40 known genes, with the mutant 
protein-protein interactions. This is of interest since we are currently 
hunting for differential interacting molecular partners (wild type 
versus mutant) for some of the genes we are currently focusing on in one 
of our research projects (through TAP purification and 
mass-spectrometry). The identification of small (or major: although 
unlikely) differences between wild type and patient/mutation specific 
protein interaction networks would provide novel insights into which 
“novel” proteins or genes could explain the neuronal specificity.

Would it be possible to meet with you and your colleagues this summer or 
in September to see what is feasible at the bio-informatics level with 
the hope to detect some interacting genes that could be relevant for 
neuropathies. FYI: I will be on holiday in August (1-23).

With my best and friendly greetings,

Vincent

Prof. Dr. Vincent Timmerman, PhD

VIB - Department of Molecular Genetics

Peripheral Neuropathy Group

University of Antwerp - CDE

Parking P4, Building V, Room 1.30

Universiteitsplein 1

BE-2610 Antwerpen

Belgium

Tel: +32-3-265.10.24

Tel: +32-3-265.10.02 (Secretary VIB8: Mrs. Gisèle Smeyers)

Fax: +32-3-265.10.12

E-mail: [email-masked] <mailto:[email-masked]>

_http://www.molgen.ua.ac.be/_

_http://www.molgen.ua.ac.be/CMTMutations/_

-- 
Yves Van de Peer, PhD.

Professor in Bioinformatics and Genome Biology
Group Leader Bioinformatics and Evolutionary Genomics
VIB Department of Plant Systems Biology, UGent
Ghent University
Technologiepark 927
B-9052 Ghent
Belgium

Phone: +32 (0)9 331 3807
Cell Phone: +32 (0)476 560 091
Fax: +32 (0)9 331 3809
email: [email-masked]

http://bioinformatics.psb.ugent.be/

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