Erasmus MC : Toolbox

Resources

1. Breast tumor tissue, DNA, RNA, protein, and serum banks

• 14,000 fresh frozen breast tumor tissue samples and corresponding cytosol preparations stored in liquid nitrogen.
• 4,000 genomic DNA and 1,500 total RNA samples of tumor specimen extracted using quality controlled SOPs.
• Global gene-expression array data from >750 tumors.
• 1,500 formalin-fixed paraffin-embedded (FFPE) breast tumor tissues as separate blocks and grouped in tissue microarrays (TMA).
• 166 FFPE breast tumor tissues in dedicated TMA, representing the major pathological subtypes of breast cancer
• 10,000 longitudinally collected serum samples from metastatic breast cancer patients during therapy.
  

From all the above, computerized clinical follow-up information is available for studying the endpoints prognosis in primary breast cancer, and response to first-line endocrine- or chemotherapy in recurrent disease.

2. Familial breast cancer, blood-derived DNA, FFPE and fresh frozen tumor tissues

• 1,500 families with breast cancer, with extensive documentation of breast cancers and other cancers.
• Blood-derived DNA samples available of at average 2.5 affected and 3.5 unaffected members per family
• All families have been screened for germline mutations in BRCA1 and BRCA2, as well as various breast cancer risk alleles such as CHEK2 1100delC and low-risk breast cancer SNPs.
• Global gene-expression array data from 155 fresh-frozen familial tumors.
• FFPE breast tumor tissues as separate blocks and in TMAs for BRCA1, BRCA2, CHEK2 1100delC mutant tumors as well as tumors without mutations in these genes.
• Blood-derived DNA samples available of 800 matched controls from the same hospital.
  

3. Ovarian tumor tissue, DNA, RNA, protein and serum banks

• 300 fresh frozen ovarian tissues (180 tumor, 80 borderline, 20 benign, 20 normal).
• DNA and RNA from 150 ovarian tumor tissues (full clinical follow-up is available from 110 patients).
  

4. Human breast cancer cell lines

A collection of 41 breast cancer cell lines is extremely well characterized, and was found to have retained most molecular characteristics that are typical for clinical breast cancers. The collection consists of 20 luminal cell lines, 15 basal and normal-like cell lines and one unclassified cell line, together including 13 ERBB2-overexpressing cell lines and 17 triple-negative cell lines. We have identified 140 oncogenic driver mutations among 26 well-known cancer genes. The collection provides an engineerable preclinical model system for breast cancer that allows detailed in vitro or in vivo (mice) biological and chemical analysis.

• All cell lines are unique and monoclonal, determined with >150 polymorphic markers.
• DNA, RNA, and protein isolates are available (with QC), as well as a microarray of the cell lines embedded in paraffin.
• Growth and morphology characteristics of the cell lines have been documented.
• Gene expression data are available for Affymetrix U133A arrays and for Affymetrix exon 1.0 ST arrays. Other microarray data are being generated, including SNP, methylation and kinase profiles.
• Protein expression data by immunohistochemistry and/or western blotting are available for over 30 proteins known to be relevant for breast cancer.
• Gene mutation data by sequencing are available for 26 well-known cancer genes.
  

5. Human ovarian cancer cell lines

A collection of 40 ovarian cancer cell lines is extremely well characterized. Molecular subtypes identified in clinical samples are being evaluated in these cell lines. Clinically validated response prediction models are being generated based on miRNA and gene expression signatures developed in these cell lines.  The collection provides an engineerable preclinical model system for ovarian cancer that allows detailed in vitro or in vivo (mice) biological and chemical analysis.

• All cell lines are unique and monoclonal, determined with The PowerPlex® 16 System (Promega) including 16 polymorphic markers.
• DNA and total RNA isolates are available (with QC).
• Growth and morphology characteristics of the cell lines have been documented.
• Gene expression data are available (Affymetrix exon 1.0 ST arrays, 22.000 genes).
• miRNA expression data is available (TaqMan microRNA ArraySet, 400 miRNAs, Applied Biosystems).
• Drug response curves for drugs used in first and second line therapy of ovarian cancer patients are available.
• Gene mutation data by sequencing is being generated for 2000 well-known cancer genes.

Expertise and available tools

1. Genome-wide gene-expression analysis including U133a, U133plus2, and exon-arrays, using the Affymetrix platform, and miRNA profiling using RT-PCR (ABI) and microarrays (Exiqon).
2. Uni- and multiplex qRT-PCR on RNA isolated from fresh frozen and FFPE samples, and circulating tumor cells.
3. IHC and ISH on tissue sections (fresh frozen and FFPE)
4. Bioinformatics, including SAM, PAM, GSEA, and global testing.
5. Comprehensive medical statistics, including uni- and multivariate Cox and logistic regression analysis.
6. Tissue culture facility for in vitro studies, including drug sensitivity screening, invasion and migration assays, and various luciferase-based reporter assays.
7. Stable silencing using Lentiviral vectors or transient silencing using transfection of targets using siRNA or miRNAs.
8. Animal facility to study breast cancer xenografts in mice, and metastatic tumor models in rats, including orthotopic BN-472 breast cancer (metastasizes to lungs and lymph nodes), transplantable EnDA endometrial cancer (metastasizes to lungs and lymph nodes), transplantable CC-531 colon carcinoma (metastasizes to lungs and lymph nodes), transplantable CA-20948 pancreatic adenocarcinoma (metastasizes to liver and lymph nodes).
9. Equipment: Access to and experience with e.g., laser capture microdissection (PALM), mass spectrometry devices, such as MALDI-TOF/TOF (Bruker), MALDI-FTICR MS (Bruker), Ion trap (Bruker), Triple quadrupole (MDS Sciex), Orbitrap (Thermo), nLC (Dionex), peptide microarrays (PamGene), Affymetrix workstations for gene-expression, exon-array and SNP-array analysis, and ABI 3100 and whole genome sequencers.