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| Status |
Public on Dec 21, 2011 |
| Title |
Genomic aberrations in distant fields from oral potentially malignant lesions by high resolution DNA flow cytometry and array-CGH |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by genome tiling array
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| Summary |
The aim of the study was to address the concept of field cancerization in oral cancer. The presence of genomic aberrations, indicative of chromosomal instability (CIN), in oral distant fields (ODFs) of visually normal and non-dysplastic mucosa at the mirror image from concomitant oral potentially malignant lesions (OPMLs) was investigated.
This pilot study comprised 16 OPMLs (8 without dysplasia, nd-OPMLs; 8 with dysplasia, d-OPMLs) and 16 ODFs. DNA diploid (DNA Index, DI=1) and aneuploid (DI≠1) sublines were detected by high resolution DNA-flow cytometry (FCM) at (hr DNA-FCM) using DAPI stained nuclei suspensions. Nuclei with different DIs were FCM-sorted in order to enrich the epithelial component and to obtain genomic DNA for high resolution oligonucleotide array-Comparative Genomic Hybridization (a-CGH) analysis to provide a genome-wide measurement of DNA copy number aberrations (CNAs).
The frequencies of DNA aneuploidy in ODFs and OPMLs were 6.2% and 43.8%, respectively (p=0.037). ODFs and nd-OPMLs were all near-diploid (DI≠1 and DI≤1.4), while d-OPMLs were also high-aneuploid (DI>1.4). CNA averages were 2.3 in ODFs (1.5 for nd-OPMLs and 3.1 for d-OPMLs), and 7.325 in OPMLs (3.0 in nd-OPMLs; 11.6 in d-OPMLs). CNAs were present in the DNA diploid sublines and often the same CNAs were observed in both ODFs and corresponding OPMLs
DNA aneuploid sublines and CNAs in the present series of 16 ODFs are likely to represent early events of the natural history of oral carcinogenesis and to indicate an early onset of the field effect cancerization. Moreover, gains within 20q13.33-qter, 7p22.2-pter and 16p13.3-pter chromosomal regions in ODFs and in the relative OPMLs suggest that specific genes localized in these regions (RTEL1, MAD1L1 and TEL2) might contribute to the ODF/d-OPML transition.
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| Overall design |
We analyzed: 8 samples of oral potentially malignant lesions with dysplasia, 8 samples of oral potentially malignant lesions without dysplasia and for each patient a corresponding oral distant field of visually normal mucosa.
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| Contributor(s) |
Scaruffi P, Coco S, Tonini G, Maffei M, Donadini A, Giaretti W |
| Citation(s) |
22144094 |
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| Submission date |
Apr 28, 2011 |
| Last update date |
Mar 23, 2012 |
| Contact name |
PAOLA SCARUFFI |
| E-mail(s) |
[email protected]
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| Organization name |
"San Martino" Hospital
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| Lab |
Center of Physiopathology of Human Reproduction
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| Street address |
LARGO R. BENZI, 10
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| City |
Genova |
| State/province |
GE |
| ZIP/Postal code |
16132 |
| Country |
Italy |
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| Platforms (1) |
| GPL4093 |
Agilent-014698 Human Genome CGH Microarray 105A (G4412A) |
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| Samples (32)
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| GSM714701 |
Pt008A Leukoplakia_Gingiva-biopsy |
| GSM714705 |
Pt013A Leukoplakia_Buccal mucosa, cheek left-biopsy |
| GSM714707 |
Pt014A Leukoplakia_Buccal mucosa, cheek right-biopsy |
| GSM714711 |
Pt022B Leukoplakia_Buccal mucosa- curette |
| GSM714714 |
Pt024B Leukoplakia_Tongue- curette |
| GSM714715 |
Pt029A Leukoplakia_Buccal mucosa, cheek right-biopsy |
| GSM714718 |
Pt035A Leukoplakia_Buccal mucosa-biopsy_1 |
| GSM714722 |
Pt043A Leukoplakia_Buccal mucosa, cheek right-biopsy |
| GSM714726 |
Pt059A Leukoplakia_Buccal mucosa, cheek right- curette |
| GSM714727 |
Pt061A Leukoplakia_Buccal mucosa, retromolar trigone right- curette |
| GSM714728 |
Pt062A Leukoplakia_Hard palate- curette |
| GSM714731 |
Pt076A Leukoplakia_Tongue, border left- biopsy |
| GSM716369 |
Pt008A Distal mucosa_Gingiva, left |
| GSM716370 |
Pt013A Distal mucosa_Buccal mucosa, cheek right |
| GSM716371 |
Pt014A Distal mucosa_Buccal mucosa, cheek left |
| GSM716372 |
Pt022B Distal mucosa_Buccal mucosa |
| GSM716373 |
Pt024B Distal mucosa_Tongue |
| GSM716374 |
Pt029A Distal field_Buccal mucosa, cheek |
| GSM716375 |
Pt032B Distal mucosa_Tongue |
| GSM716376 |
Pt032B Leukoplakia_Tongue (Front lesion) |
| GSM716377 |
Pt035A Distal mucosa_Buccal mucosa, cheek |
| GSM716378 |
Pt041A Distal mucosa_Buccal mucosa, cheek right |
| GSM716379 |
Pt041A Leukoplakia_Tongue right |
| GSM716380 |
Pt042A Distal field_Buccal mucosa |
| GSM716381 |
Pt042A Leukoplakia_Buccal mucosa, cheek right |
| GSM716382 |
Pt043A Distal mucosa_Buccal mucosa, cheek |
| GSM716383 |
Pt059A Distal field_Buccal mucosa |
| GSM716384 |
Pt061A Distal mucosa_Buccal mucosa, retromolar trigone left |
| GSM716385 |
Pt062A Distal mucosa_Hard palate |
| GSM716386 |
Pt074B Distant field_Soft palate |
| GSM716387 |
Pt074B Leukoplakia_Soft palate |
| GSM716388 |
Pt076A Distal mucosa_Border tongue right |
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| Relations |
| BioProject |
PRJNA140669 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE28906_RAW.tar |
1010.7 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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