A Mathematical Model for DNA Damage and Repair

In cells, DNA repair has to keep up with DNA damage to maintain the integrity of the genome and prevent mutagenesis and carcinogenesis. While the importance of both DNA damage and repair is clear, the impact of imbalances between both processes has not been studied. In this paper, we created a combined mathematical model for the formation of DNA adducts from oxidative estrogen metabolism followed by base excision repair (BER) of these adducts. The model encompasses a set of differential equations representing the sequence of enzymatic reactions in both damage and repair pathways. By combining both pathways, we can simulate the overall process by starting from a given time-dependent concentration of 17β-estradiol (E2) and 2′-deoxyguanosine, determine the extent of adduct formation and the correction by BER required to preserve the integrity of DNA. The model allows us to examine the effect of phenotypic and genotypic factors such as different concentrations of estrogen and variant enzyme haplotypes on the formation and repair of DNA adducts

Detection and Estimation Theory

Contains research objectives and summary of research.Joint Services Electronics Program (Contract DAAB07-71-C-0300)National Science Foundation (Grant GX-36331

Metabolic alteration of urinary steroids in pre- and post-menopausal women, and men with papillary thyroid carcinoma

<p>Abstract</p> <p>Background</p> <p>To evaluate the metabolic changes in urinary steroids in pre- and post-menopausal women and men with papillary thyroid carcinoma (PTC).</p> <p>Methods</p> <p>Quantitative steroid profiling combined with gas chromatography-mass spectrometry was used to measure the urinary concentrations of 84 steroids in both pre- (n = 21, age: 36.95 ± 7.19 yr) and post-menopausal female (n = 19, age: 52.79 ± 7.66 yr), and male (n = 16, age: 41.88 ± 8.48 yr) patients with PTC. After comparing the quantitative data of the patients with their corresponding controls (pre-menopause women: n = 24, age: 33.21 ± 10.48 yr, post-menopause women: n = 16, age: 49.67 ± 8.94 yr, male: n = 20, age: 42.75 ± 4.22 yr), the levels of steroids in the patients were normalized to the mean concentration of the controls to exclude gender and menopausal variations.</p> <p>Results</p> <p>Many urinary steroids were up-regulated in all PTC patients compared to the controls. Among them, the levels of three active androgens, androstenedione, androstenediol and 16α-hydroxy DHEA, were significantly higher in the pre-menopausal women and men with PTC. The corticoid levels were increased slightly in the PTC men, while progestins were not altered in the post-menopausal PTC women. Estrogens were up-regulated in all PTC patients but 2-hydroxyestrone and 2-hydroxy-17β-estradiol were remarkably changed in both pre-menopausal women and men with PTC. For both menopausal and gender differences, the 2-hydroxylation, 4-hydroxylation, 2-methoxylation, and 4-methoxylation of estrogens and 16α-hydroxylation of DHEA were differentiated between pre- and post-menopausal PTC women (<it>P </it>< 0.001). In particular, the metabolic ratio of 2-hydroxyestrone to 2-hydroxy-17β-estradiol, which could reveal the enzyme activity of 17β-hydroxysteroid dehydrogenase, showed gender differences in PTC patients (<it>P </it>< 1 × 10^-7).</p> <p>Conclusions</p> <p>These results are expected be helpful for better understanding the pathogenic differences in PTC according to gender and menopausal conditions.</p

Association of a Deletion of GSTT2B with an Altered Risk of Oesophageal Squamous Cell Carcinoma in a South African Population: A Case-Control Study

Polymorphisms in the Glutathione S-transferase genes are associated with altered risks in many cancers, but their role in oesophageal cancer is unclear. Recently a 37-kb deletion polymorphism of GSTT2B that reduces expression of GSTT2 has been described. We evaluated the influence of the GSTT1 and GSTT2B deletion polymorphisms, and the GSTP1 Ile105Val polymorphism (rs1695) on susceptibility to oesophageal squamous cell carcinoma (OSCC) in the Black and Mixed Ancestry populations of South Africa.The GSTT1, GSTT2B and GSTP1 variants were genotyped in 562 OSCC cases and 907 controls, and tested for association with OSCC and for interaction with smoking and alcohol consumption. Linkage disequilibrium (LD) between the deletions at GSTT1 and GSTT2B was determined, and the haplotypes tested for association with OSCC. Neither the GSTT1 deletion nor the GSTP1 Ile105Val polymorphism was associated with OSCC risk in the Black or Mixed Ancestry populations. The GSTT2B deletion was not associated with OSCC risk in the Black population, but was associated with reduced risk of OSCC in the Mixed Ancestry population (OR=0.71; 95% CI 0.57-0.90, p=0.004). Case-only analysis showed no interaction between the GST polymorphisms and smoking or alcohol consumption. LD between the neighboring GSTT1 and GSTT2B deletions was low in both populations (r(2)(Black)=0.04; r(2)(MxA)=0.07), thus these deletions should be assessed independently for effects on disease risk.Although there was no association between the GSTT1 deletion polymorphism or the GSTP1 Ile105Val polymorphism with OSCC, our results suggest that the presence of the recently described GSTT2B deletion may have a protective effect on the risk of OSCC in the Mixed Ancestry South African population. This is the first report of the contribution of the GSTT2B deletion to cancer risk

UDP-glucuronosyltransferase and sulfotransferase polymorphisms, sex hormone concentrations, and tumor receptor status in breast cancer patients

INTRODUCTION: UDP-glucuronosyltransferase (UGT) and sulfotransferase (SULT) enzymes are involved in removing sex hormones from circulation. Polymorphic variation in five UGT and SULT genes – UGT1A1 ((TA)(6)/(TA)(7)), UGT2B4 (Asp(458)Glu), UGT2B7 (His(268)Tyr), UGT2B15 (Asp(85)Tyr), and SULT1A1 (Arg(213)His) – may be associated with circulating sex hormone concentrations, or the risk of an estrogen receptor-negative (ER(-)) or progesterone receptor-negative (PR(-)) tumor. METHODS: Logistic regression analysis was used to estimate the odds ratios of an ER(- )or PR(- )tumor associated with polymorphisms in the genes listed above for 163 breast cancer patients from a population-based cohort study of women in western Washington. Adjusted geometric mean estradiol, estrone, and testosterone concentrations were calculated within each UGT and SULT genotype for a subpopulation of postmenopausal breast cancer patients not on hormone therapy 2–3 years after diagnosis (n = 89). RESULTS: The variant allele of UGT1A1 was associated with reduced risk of an ER(- )tumor (P for trend = 0.03), and variants of UGT2B15 and SULT1A1 were associated with non-statistically significant risk reductions. There was some indication that plasma estradiol and testosterone concentrations varied by UGT2B15 and SULT1A1 genotypes; women with the UGT2B15 Asp/Tyr and Tyr/Tyr genotypes had higher concentrations of estradiol than women with the Asp/Asp genotype (P = 0.004). Compared with women with the SULT1A1 Arg/Arg and Arg/His genotypes, women with the His/His genotype had elevated concentrations of testosterone (P = 0.003). CONCLUSIONS: The risk of ER(- )breast cancer tumors may vary by UGT or SULT genotype. Further, plasma estradiol and testosterone concentrations in breast cancer patients may differ depending on some UGT and SULT genotypes

Morphometrical malignancy grading is a valuable prognostic factor in invasive ductal breast cancer

The aim of the present study is to augment the prognostic power of breast cancer grading by elaboration of quantitative histopathological methods. We focus on the recently introduced morphometrical grading system in which the three grading sub-features of the WHO grading system are evaluated with the help of computerised nuclear morphometry, and quantitative methods for assessing mitotic activity and tubular differentiation. The prognostic value of the morphometrical grading system is now confirmed in a material of 159 cases of invasive ductal breast cancer. In the current material the morphometrical grading system very efficiently predicted the prognosis of breast cancer by dividing the patients into favourable (grade I), intermediate (grade II), and unfavourable (grade III) outcome (P<0.0001). The morphometrical grading system was especially efficient in identifying patients with the most unfavourable outcome. In our material the morphometrical grade III was associated with a 5.4-fold risk of breast cancer death. In light of the present results, the morphometrical grading can be applied to clinical use as an aid in treatment decisions of patients with invasive ductal breast cancer

Genome Instability and Bleomicin Sensitivity Test

Procjena individualne osjetljivosti na mutagene često je dio istraživanja u epidemiološkim studijama koje prate pojavnost zloćudnih bolesti u populacijama. Posljedica djelovanja mutagena u genomu izloženih osoba jest nastanak određene, manje ili veće, količine oštećenja, uvjetovane individualnim razlikama u osjetljivosti. Viša razina takve genomske nestabilnosti znači opasnost (rizik) od razvoja zloćudnih bolesti. Interindividualne razlike u odgovoru na mutagene obično se povezuju i s promijenjenom (većinom smanjenom) sposobnosti (kapacitetom) za popravak DNA. Citogenetičke studije su pokazale da je genom tumorskih stanica nestabilniji od normalnih, a time i skloniji akumuliranju oštećenja, bilo da je nestabilnost uzrokovana nasljeđem, izloženošću ili kombinacijom tih dvaju učinaka. U oboljelih ispitanika utvrđena je povećana učestalost kromatidnih i kromosomskih aberacija naspram normalne populacije te sklonost razvoju određenih vrsta neoplazija. U praćenju povezanosti promijenjenog odgovora i pojavnosti tumora služe nam različiti biomarkeri. Kao indirektni pokazatelji uspješnosti popravka DNA često se rabe testovi osjetljivosti na mutagene u kulturama limfocita periferne krvi. Jedan od takvih testova je i bleomicinski test. Radiomimetik i citostatik, a po strukturi glikopeptid, bleomicin se u stanici prevodi u aktivni oblik sposoban cijepati molekulu DNA što uzrokuje brojne jednolančane i dvolančane lomove. Kao jednostavna i jeftina metoda, zasniva se na utvrđivanju ukupnog broja jednolančanih lomova u kromosomima limfocita uzgajanih u staničnoj kulturi koji su u uvjetima in vitro tijekom kasne G2-faze staničnog ciklusa bili izloženi bleomicinu. Ovaj revijalni rad daje pregled utjecaja raznih faktora na rezultate samog testa i pokazuje njegovu široku primjenu u proučavanju genomske nestabilnosti koju najčešće uzrokuje kombinacija raznih faktora.Estimation of individual susceptibility to mutagens is often a part of epidemiological studies monitoring the appearance of malignant disease in different populations. Genome exposure to mutagens can lead to DNA damage. The rate of damage depends on individual differences in response, which are usually associated with differences in DNA repair capacity. Cytogenetic studies have shown that the genome of tumour cells is less stable than normal cells and therefore accumulates more damage. Tumour patients show a higher frequency of chromatid and chromosomal aberrations and a predisposition to certain types of tumours. One of the common biomarkers used in monitoring tumour appearance and changed response to DNA damage is the bleomycin test. In its active form, bleomycin (glycopeptid) is a radiomimetic cytostatic that can damage the DNA molecule and cause multiple single and double strands. The bleomycin test is simple and inexpensive, and is based on scoring chromatid breaks in lymphocytes in vitro exposed to bleomycin during the late G2 phase of the cell cycle. This review looks into different factors that may affect test results and discusses its wide implementation in studies of genome instability usually caused by a combination of factors

sj-xlsx-3-cix-10.1177_11769351221148592 – Supplemental material for Different Tumor Types Share a Common Nuclear Map of Chromosome Territories

Supplemental material, sj-xlsx-3-cix-10.1177_11769351221148592 for Different Tumor Types Share a Common Nuclear Map of Chromosome Territories by Fritz F Parl in Cancer Informatics</p