Ph. D., Faculty of Health Sciences, University of the Witwatersrand, 2008. / The human chromosome complement contains nonrandom genomic regions that are
prone to breaks and recurrently altered in tumors. These chromosomal “hot spots” are
preferentially involved in early events of genomic instability and point to genes in
their vicinity that may participate to carcinogenesis. Amplicons and deletions are
frequently generated at “hot spots”, including common fragile sites (CFS), and are
thought to host cancer genes whose rearrangements drive cell proliferation and
promote the initiation and progression of cancer. Chromosomal “hot spots” in South
African cancer patients, were investigated in this study with a view to characterizing
underlying gene alterations.
A chromosome 12p amplicon was mapped and array comparative genomic
hybridization (aCGH) was pioneered to identify candidate genes in the amplicon.
Genes of the 12p stem cell gene cluster (NANOG, STELLAR and GDF3) were
involved in striking similarity to what has been reported in testicular germ cell tumors
and suggest that they may be more commonly involved in different types of cancer.
Two tumor suppressor genes, FHIT and WWOX, are located at the two most
commonly expressed fragile sites, FRA3B and FRA16D respectively. Alterations in
these fragile site associated genes have been reported in a variety of tumors including
lung, esophageal, gastric, breast and cervical cancers most frequently as a result of
submicroscopic deletions. Genomic deletions at CFS have been mostly investigated
using loss of heterozygosity assays that do not necessarily inform on gene exon
deletions. A new method was developed based on multiplex ligation-dependent probe
amplification (MLPA) that screens for exon deletions/amplifications of genes at CFS.
The assay was validated on five esophageal squamous carcinoma cell lines and
showed deletions in the FRA3B-associated gene FHIT in four of the cell lines.
Two geographically distinct South African cohorts of esophageal squamous cell
carcinoma were then screened for FHIT/WWOX exon deletions and a visual basic
(VBA) encoded program was written to automate MPLA products analysis. A high
frequency of intragenic deletions in FHIT and/or WWOX (73%) was observed in the
Eastern Cape cohort. FHIT deletions were seen in 27% of specimens from the
Gauteng cohort, which by contrast did not show WWOX deletions. This difference
may however reflect a difference in sampling collection.
The breakpoints of a translocation t(3;11)(p14;p15.1) present in an ovarian carcinoma
cell line was characterized using the above MLPA assay, aCGH and the polymerase
chain reaction. The translocation was found to interrupt the FHIT gene making it the
5th cancer associated translocation involving FHIT. The evaluation of gene relative
copy number by aCGH and MLPA were highly correlated further validating the
power of the MLPA assay in fresh tissue.
The involvement of critical genes at “hot spots” in SA cancer patients was high in the
context of this study raising questions about the possible role of environmental
exposure. The new MLPA assay may assist to expand the screening of critical genes at fragile sites in the future.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:wits/oai:wiredspace.wits.ac.za:10539/7352 |
| Date | 14 October 2009 |
| Creators | Willem-Belot, Pascale Sylvie |
| Source Sets | South African National ETD Portal |
| Language | English |
| Detected Language | English |
| Type | Thesis |
| Format | application/pdf |
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