View Project Scheck-3U24NS043571-01S1

Project Summary
Status:	Public
Publications:	1 Published
Project Detail		Data Detail
Platform:	Affymetrix	MIAME Areas	Compliance
Species:	Human	Array Design Detail	true
Organ/Tissue Type:	brain	Experiment Detail	true
Organ Region:	unknown	Sample Detail	false
Cell Type:	pia-arachnoid	Hybridization Detail	false
Study Type:	subclassification	Measurement Detail	false
Disease/Condition:	Meningioma
Replicates:	3
Expected Samples:

Available Actions

Investigator Contact Detail
Name	Adrienne C Scheck
Street Address:	Neuro-Oncology Research, Barrow Neurological Institute
	350 W Thomas Rd.
City, State/Province:	Phoenix , AZ
Zip/Postal Code:	85013
Country:	United States
Work Phone:	602 406-3647
Fax:	603 406-7172
E-mail:	adrienne.scheck@chw.edu

Proposal Detail

Grant:

3U24NS043571-01S1

Status:

Public

Service Type:

Start to Finish Profiling

IRB:

94BN098

IRB date:

2003-11-10

Study Relevance:

Meningiomas are typically considered a benign tumor that can be cured by complete surgical resection; however, a percentage of patients have recurrent disease, even after apparently complete resections. These patients require additional surgeries, radiation therapy, chemotherapy, or a combination of all three. The ability to recognize these patients prior to recurrence would promote earlier use of adjuvant therapy, thus improving overall patient outcome. Unfortunately, identification of meningiomas with this more aggressive phenotype is difficult, and standard histopathological techniques rarely suffice. The identification of genetic and molecular parameters that can help to define these more aggressive tumors would improve prognostication and treatment planning for patients with meningiomas.

Hypothesis:

Our overall hypothesis is that there are molecular and biochemical changes that can be used to identify meningiomas that will have a more aggressive clinical course.

Specific Aim:

1. Establish gene profiles for benign (grade 1) and aggressive (grades 2 and 3) meningiomas. 2. Determine if there are particular expression profiles that can help differentiate between benign and aggressive meningiomas. 3. Determine if there is/are specific gene(s) whose expression is/are altered in benign vs aggressive tumors. 4. Determine if there is a correlation between specific genetic abnormalities in these tumors (as analyzed by fluorescent in situ hybridization; FISH) and gene expression profiles.

Experimental Procedure and Design:

Specific Aims 1 and 2: RNA from flash frozen or RNA-later preserved tissue (from all three grades of meningiomas) has been used for RNA isolation using standard protocols. RNA quantity has been determined using a RiboGreen RNA quantitation Kit (Molecular Probes), and RNA quality has been demonstrated using standard formaldehyde gels. These samples will be sent to the NINDS/NIMH microarray consortium for Affymetrix microarray analyses. Data analysis will be done using GeneSpring software (Silicon Genetics, Inc.) with assistance from consortium personnel. Specific Aim 3: Differentially expressed genes identified through microarray analyses will be analyzed using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Real time qRT-PCR is a standard technique used in our laboratory for gene expression analysis. Specific Aim 4: FISH analyses of paraffin-embedded tissue has been completed for 77 tumors. We have frozen tissue from a number of these patients. RNA from these samples will be used for microarray analyses (Specific Aims 1-3). The results of Speicifc Aims 1 and 2 will affect how we perform our correlation analyses. This will be done with the assistance of contracted statistical personnel.

Experimental Factors:

Conditions that are tested in the experiment. At least one is required. Experimental factors are the independent variables in the experiment.

Factor Name	Description	Factor Category
Cells vs. Tissue	Cell behavior compared to the origina...	cell_type

Project Samples

Samples associated with this project.

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Name	Description	Bio-Source	Extracts
00ZP	Meningioma Primary Grade 1 ...	BioSource3	1
03BE	Meningioma Primary Grade 1 ...	BioSource4	1
03AM	Meningioma Primary Grade 1 ...	BioSource5	1
04IC	Primary Grade 1 Tissue/Cells	Biosource 6	1
03GK	Primary Grade 1 Tissue/Cells	Biosource 7	1
04IC(5)	Primary Grade 1 Cells	Biosource 8	1
04IC(10)	Primary Grade 1 Cells	Biosource 8	1
03GK(5)	Primary Grade 1 Cells	Biosource 7	0
03GK(10)	Primary Grade 1 Cells	Biosource 7	1
03BE(5)	Meningioma Primary Grade 1 ...	BioSource4	1
03BE(10)	Meningioma Primary Grade 1 ...	BioSource4	1
03AM(5)	Meningioma Primary Grade 1 ...	BioSource5	1
03AM(10)	Meningioma Primary Grade 1 ...	BioSource5	1
00ZP(5)	Meningioma Primary Grade 1 ...	BioSource3	1
00ZP(10)	Meningioma Primary Grade 1 ...	BioSource3	1
00FA(5)	Meningioma Primary Grade 1 ...	BioSource 8	1
00FA(10)	Meningioma Primary Grade 1 ...	BioSource 8	1
00FA	Meningioma Primary Grade 1 ...	BioSource 8	1
04LZR	recurrent Grade 3 surgical ...	BioSource12	1
04SA	Primary Grade 3 surgical sa...	BioSource10	1
04MR	Primary Grade 2 surgical sa...	BioSource11	1
04NU	Primary Grade 2 - surgical ...	BioSource12	1
05KT	Primary Grade 2 - surgical ...	BioSource11	1
05MI	Primary Grade 2 surgical sa...	BioSource12	1
05LT	Primary Grade 2	BioSource11	1
05LO	Primary Grade 2	BioSource11	1
05KF	Primary Grade 2	BioSource12	1
05LZ	Primary Grade 2	BioSource9	1
05LE	Primary Grade 2	BioSource12	1
05KY	Primary Grade 2	BioSource12	1
04RG	Primary grade 2	BioSource11	1
05HO	Recurrent - grade not known	BioSource11	1
03CUR	Meningioma ecurrent grade 2...	BioSource11	1
03BHR	Meningioma - recurrent (03B...	BioSource11	1
03BH	Meningioma - primary - recu...	BioSource11	1
05MA	Meningioma - primary -grade...	Biosource 13	1
04RO	Meningioma - primary grade 3	BioSource12	1
06BR	meningioma grade 2 - surgic...	BioSource12	1
06BS	meningioma grade 2 - surgic...	BioSource12	1
03CS	meningioma grade 2 invasive...	BioSource12	1
05DJ	Meningioma - primary grade 2	BioSource12	1

Project Hybridizations

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Project Reference Files

File Name	Size
SignalValues121406.TXT	13.06 Mb

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