Characterisation of the promoter region of the SLC40A1 gene implicated in iron metabolism

Vervalle, Jessica (2010-12)

Thesis (MSc)--Stellenbosch University, 2010.

Thesis

ENGLISH ABSTRACT: Oesophageal cancer (OC) is a disease characterised by development of malignant tumours in the cell lining of the oesophagus. The disease is divided into two subtypes, which shows marked ethinic variation, with adenocarcinoma (ADC) being more prevalent in Caucasians and squamous cell carcinoma (SCC) more prevalent in the Black population. There are several factors that have been associated with OC development, including oesophageal injury and inflammation, as well as excess iron, which contributes to increased tumour growth. Investigation into OC development is essential due to the rapidly increasing incidence rates and the poor survival rate of this complex disease. The present study aimed to investigate nucleotide variation in the promoter region of SLC40A1, a gene implicated in iron metabolism, in a Black South African OC population. The patient group encompassed 80 (41 males and 39 females) unrelated patients presenting with SCC of the oesophagus. The control group consisted of 71 unrelated, healthy population-matched control individuals. The techniques applied for mutation detection in this study included polymerase chain reaction (PCR) amplification, heteroduplex single stranded conformation polymorphism (HEXSSCP) analysis, restriction fragment length polymorphism (RFLP) analysis and hybridisation probe analysis. Identified variants were confirmed by bi-directional semi-automated DNA sequencing analysis. Statistical analysis was performed to determine associations between identified variants and disease incidence, as well as between identified variants and various iron parameters. Mutation analysis of the promoter region of SLC40A1 resulted in the identification of nine previously described (-1470C/T, -1461T/C, -1399G/A, -1355G/C, -1098G/A, -750G/A, -501T/C, - 23A/G and -8C/G) and three novel, (-1087G/C, -663C/T and -637G/A) variants as well as a previously described trinucleotide repeat. Statistical analyses revealed statistically significant association between -501T/C and OC in this population (P = 0.004). Statistical investigation of the effect of the variants on iron parameters revealed various statistically significant associations. The survival rate of OC remains poor due to absence of early symptoms and therefore late diagnosis of the disease, after which treatment is highly ineffective. Treatment of OC would significantly improve with earlier detection and treatment. This can be achieved by establishing a screening programme in the populations of high risk areas, such as the Transkei area in Southern Africa. Therefore investigation into nucleotide variation of potential modifier genes is of great importance to improved diagnosis, treatment and counselling to individuals presenting with OC. To our knowledge, this is the first study investigating the promoter region of SLC40A1 and possible associations with iron dysregulation in the Black South African population with OC.

AFRIKAANSE OPSOMMING: Oesofageale kanker is ‘n siekte wat gekenmerk word deur die ontwikkeling van kwaadaardige gewasse in the selvoering van die oesofagus. Die siekte word verdeel in twee subtipes wat opvallende etniese variasie toon, met adenokarsinoom wat meer algemeen in die Kaukasiese populasie voorkom en plaveisel selkarsinoom wat meer algemeen in die Swart populasie is. Daar is verskeie faktore wat verbind word met die ontwikkeling van oesofageale kanker, insluitend oesofageale besering en ontsteking, asook ‘n oormaat yster wat bydra tot verhoogde gewasgroei. Ondersoek met betrekking tot die ontwikkeling van oesofageale kanker is noodsaaklik as gevolg van die verhoogde voorkoms-tempo en die swak oorlewingsyfers van hierdie komplekse siekte. Die huidige studie het beoog om die nukleotied variasie in die promoter area van SLC40A1, ‘n geen betrokke in yster metabolisme, in ‘n Swart Suid-Afrikaanse oesofageale kanker populasie te ondersoek. Die pasiënt-groep het bestaan uit 80 (41 mans en 39 vrouens) onverwante pasiënte by wie plaveisel selkarsinoom van die oesofagus voorgekom het. Die kontrole groep het bestaan uit 71 onverwante, gesonde bevolkings-soortgelyke individue. Die tegnieke wat gebruik is vir mutasie opsporing in hierdie studie sluit in: polimerase kettingreaksie amplifikasie, heterodupleks enkelstring konformasie polimorfisme (HEX-SSCP) analise, restriksie fragment lengte polimorfisme (RFLP) analise en hibridisasie peiler analise. Geïdentifiseerde variante is bevestig deur tweerigting semi-geoutomatiseerde DNS volgorde-bepalingsanalise. Statistiese analise is uitgevoer om moontlike assosiasies tussen geïdentifiseerde variante en siekte voorkoms, sowel as tussen geïdentifiseerde variante en verskeie yster parameters te bepaal. Mutasie analise van die promoter area van SLC40A1 het gelei tot die identifikasie van nege voorheen bekende (-1470C/T, -1461T/C, -1399G/A, -1355G/C, -1098G/A, -750G/A, -501T/C, - 23A/G and -8C/G) en drie nuwe (-1087G/C, -663C/T and -637G/A) variante, sowel as ‘n bekende trinukleotied herhaling. Statistiese analise het getoon dat daar ‘n statistiese betekenisvolle assosiasie tussen -501T/C en oesofageale kanker in hierdie populasie voorkom (P = 0.004). Statistiese ondersoek van die effek van die geïdentifiseerde variante op yster parameters het verskeie statisties betekenisvolle assosiasies getoon. Die oorlewingsyfers van oesofageale kanker bly laag as gevolg van die afwesigheid van vroeë simptome en dus word die siekte eers op ‘n laat stadium gediagnoseer, waarna behandeling hoogs oneffektief is. Behandeling van oesofageale kanker sou betekenisvol verbeter met vroegtydige identifikasie en behandeling. Dit is bereikbaar deur die vestiging van ‘n siftingsprogram vir die populasies van hoë risiko areas, soos die Transkei area in Suidelike Afrika. Ondersoeke na die nukleotied variasie van potensiële modifiserende gene kan daarom van groot belang wees vir verbeterde diagnose, behandeling en berading van individue met oesofageale kanker. Sover as wat ons kennis strek, is hierdie die eerste studie wat die promoter area van die SLC40A1 geen en die moontlike effek op yster disregulasie in ‘n Swart Suid-Afrikaanse populasie met oesofageale kanker ondersoek.

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