Assessing the Impact of Novel BRCA1 Exon 11 Variants on Pre-mRNA Splicing.

Our study focused on assessing the effects of three newly identified BRCA1 exon 11 variants (c.1019T>C, c.2363T>G, and c.3192T>C) on breast cancer susceptibility. Using computational predictions and experimental splicing assays, we evaluated their potential as pathogenic mutations. Our in silico analyses suggested that the c.2363T>G and c.3192T>C variants could impact both splicing and protein function, resulting in the V340A and V788G mutations, respectively. We further examined their splicing effects using minigene assays in MCF7 and SKBR3 breast cancer cell lines. Interestingly, we found that the c.2363T>G variant significantly altered splicing patterns in MCF7 cells but not in SKBR3 cells. This finding suggests a potential influence of cellular context on the variant's effects. While attempts to correlate in silico predictions with RNA binding factors were inconclusive, this observation underscores the complexity of splicing regulation. Splicing is governed by various factors, including cellular contexts and protein interactions, making it challenging to predict outcomes accurately. Further research is needed to fully understand the functional consequences of the c.2363T>G variant in breast cancer pathogenesis. Integrating computational predictions with experimental data will provide valuable insights into the role of alternative splicing regulation in different breast cancer types and stages.

Identification of a variant associated with adult-type hypolactasia.

Adult-type hypolactasia, also known as lactase non-persistence (lactose intolerance), is a common autosomal recessive condition resulting from the physiological decline in activity of the lactase-phlorizin hydrolase (LPH) in intestinal cells after weaning. LPH hydrolyzes lactose into glucose and galactose. Sequence analyses of the coding and promoter regions of LCT, the gene encoding LPH, has revealed no DNA variations correlating with lactase non-persistence. An associated haplotype spanning LCT, as well as a distinct difference in the transcript levels of 'non-persistence' and 'persistence' alleles in heterozygotes, suggest that a cis-acting element contributes to the lactase non-persistence phenotype. Using linkage disequilibrium (LD) and haplotype analysis of nine extended Finnish families, we restricted the locus to a 47-kb interval on 2q21. Sequence analysis of the complete region and subsequent association analyses revealed that a DNA variant, C/T-13910, roughly 14 kb upstream from the LCT locus, completely associates with biochemically verified lactase non-persistence in Finnish families and a sample set of 236 individuals from four different populations. A second variant, G/A-22018, 8 kb telomeric to C/T-13910, is also associated with the trait in 229 of 236 cases. Prevalence of the C/T-13910 variant in 1,047 DNA samples is consistent with the reported prevalence of adult-type hypolactasia in four different populations. That the variant (C/T-13910) occurs in distantly related populations indicates that it is very old.

Screening of interleukin 17F gene polymorphisms and eight subgingival pathogens in chronic periodontitis in Libyan patients.

Background: Chronic periodontitis (CP) is triggered by periodontal pathogens influenced by genetic and environmental factors. Recent studies have suggested that anti-inflammatory cytokines such as interleukin 17 (IL-17) play a prominent role in the pathogenesis of CP.Aim: This study aimed to investigate the association between eight sub-gingival pathogens and interleukin 17F (IL-17F) gene single nucleotide polymorphisms with CP among Libyans.Materials and Methods: A case-control study was conducted on 100 individuals between the ages of 25-65 years. Species-specific 16S rRNA primers for each pathogen were used in a multiplex PCR reaction to detect sub-gingival pathogens from a paper point sample. DNA was also extracted from buccal swab samples and IL-17F polymorphisms were detected by Sanger sequencing.Results: A highly significant association between the seven sub-gingival pathogens and CP, (p-value 0.0001) and a high prevalence of P. intermedia (100%), T. forsythia (96%), T. denticola and E. corrodens (92%), P. gingivalis (82%), C. rectus (74%), P. nigrescens (72%), A. actinomvcetcmcomitans (40%) were found in the case group compared with control group. A novel variant in the c. *34 G>A in IL-17F gene caused a change in glutamic amino acid to lysine amino acid, position on chromosome number (6) in the third exon, mRNA/genomic position 597, found in 14.6% of CP patients (p-value = 0.010) while the IL-17F (rs763780) SNP showed no association with CP (p-value = 0.334).Conclusion: P. intermedia appear as keystone pathogen for CP in the Libyan population. A novel variant in the IL-7F gene may be related to the severity of CP.

Correlation between maternal and fetal umbilical cord blood lead concentrations in Libya.

Background: People are exposed to lead from car exhaust fumes (leaded petrol), lead-based paints, plumbing systems, cigarette smoking, contaminated soil and dust, foods grown in polluted areas, and water sources. Among the vulnerable subpopulations are pregnant women, fetuses and infants. Aims: To estimate and correlate maternal and neonatal blood lead levels and compare these between neonates and their mothers in Tripoli and Ghadames. Methods: In this cross-sectional study, blood was collected from 120 and 116 mothers and their neonates from Tripoli and Ghadames, respectively. Lead levels were determined using atomic absorption spectrophotometry. A simple questionnaire was filled by the participants using face-to face interview. Data were analysed using SPSS version 20.0 and Excel. Results: Mean blood and umbilical cord lead levels were 6.83 (standard deviation 4.96) and 6.05 (4.89) µg/dl in mothers and neonates from Tripoli, respectively, and 5.91 (4.02) and 4.54 (4.09) µg/dl from Ghadames. There was no significant difference in blood lead level between mothers from Tripoli and Ghadames. However, there was a significant correlation between maternal blood and umbilical cord blood in Tripoli and Ghadames. Linear regression revealed that neonatal umbilical cord blood lead levels reflected the levels in maternal blood. Blood lead in this study was higher than that reported in industrialized western countries. Conclusion: We detected moderate blood lead levels among pregnant women in Tripoli and Ghadames. It is important to detect the source of lead in the Libyan population to treat this problem effectively.

Independent introduction of two lactase-persistence alleles into human populations reflects different history of adaptation to milk culture.

The T(-13910) variant located in the enhancer element of the lactase (LCT) gene correlates perfectly with lactase persistence (LP) in Eurasian populations whereas the variant is almost nonexistent among Sub-Saharan African populations, showing high prevalence of LP. Here, we report identification of two new mutations among Saudis, also known for the high prevalence of LP. We confirmed the absence of the European T(-13910) and established two new mutations found as a compound allele: T/G(-13915) within the -13910 enhancer region and a synonymous SNP in the exon 17 of the MCM6 gene T/C(-3712), -3712 bp from the LCT gene. The compound allele is driven to a high prevalence among Middle East population(s). Our functional analyses in vitro showed that both SNPs of the compound allele, located 10 kb apart, are required for the enhancer effect, most probably mediated through the binding of the hepatic nuclear factor 1 alpha (HNF1 alpha). High selection coefficient (s) approximately 0.04 for LP phenotype was found for both T(-13910) and the compound allele. The European T(-13910) and the earlier identified East African G(-13907) LP allele share the same ancestral background and most likely the same history, probably related to the same cattle domestication event. In contrast, the compound Arab allele shows a different, highly divergent ancestral haplotype, suggesting that these two major global LP alleles have arisen independently, the latter perhaps in response to camel milk consumption. These results support the convergent evolution of the LP in diverse populations, most probably reflecting different histories of adaptation to milk culture.

Correlation of intestinal disaccharidase activities with the C/T-13910 variant and age.

AIM: To correlate the C/T(-13910) variant, associated with lactase persistence/non-persistence (adult-type hypolactasia) trait, with intestinal disaccharidase activities in different age groups of the adult population. METHODS: Intestinal biopsies were obtained from 222 adults aged 18 to 83 years undergoing upper gastrointestinal endoscopy because of unspecified abdominal complaints. The biopsies were assayed for lactase, sucrase and maltase activities and genotyped for the C/T(-13910) variant using PCR-minisequencing. RESULTS: There was a significant correlation between lactase activity and the C/T(-13910) variant (P < 0.00001). The mean level of lactase activity among subjects with C/C(-13910) genotype was 6.86 +/- 0.35 U/g, with C/T(-13910) genotype 37.8 +/- 1.4 U/g, and with T/T(-13910) genotype 57.6 +/- 2.4 U/g protein, showing a trimodal distribution of this enzyme activity. Significant differences were also observed in maltase activities among individuals with different C/T(-13910) genotypes (P = 0.005). In contrast, in sucrase activity, no significant differences emerged between the C/T(-13910) genotypes (P = 0.14). There were no statistical differences in lactase (P = 0.84), sucrase (P = 0.18), or maltase activity (P = 0.24) among different age groups. In the majority (> 84%) of the patients with the C/C(-13910) genotype associated with lactase non-persistence, the lactase activity was less than 10 U/g protein. CONCLUSION: Our study demonstrates a statistically significant correlation between the C/T(-13910) genotype and lactase activity and this correlation is not affected by age in adults but the cut-off value of 20 U/g protein used for the diagnosis of lactase non-persistence might be too high.

Genetic variant of lactase-persistent C/T-13910 is associated with bone fractures in very old age.

OBJECTIVES: To determine the relation between the C/T(-13910) single-nucleotide polymorphism residing 13,910 base pairs from the 5' end of the lactase gene associated with lactase persistence and the occurrence of bone fractures in elderly people. DESIGN: Population-based study. SETTING: Vantaa 85+ population-based study, including all 601 subjects born before April 1, 1906, who were living in the city of Vantaa, Finland, on April 1, 1991. PARTICIPANTS: Four hundred eighty-three people aged 85 and older (106 men and 377 women). MEASUREMENTS: Genotype determination was made using a polymerase chain reaction minisequencing technique. RESULTS: The frequency of the genotype C/C(-13910) associated with adult-type hypolactasia (low lactase enzyme activity or primary lactose malabsorption (LM)) was significantly greater in individuals with hip fractures, with an adjusted odds ratio (OR) of 3.7 (95% confidence interval (CI)=1.8-7.8), wrist fractures with an adjusted OR of 2.5 (95% CI=1.2-5.2), and hip and wrist fractures combined with an adjusted OR of 4.1 (95% CI=2.0-8.3). CONCLUSION: The C/C(-13910) genotype associated with primary LM could represent a genetic risk factor for bone fractures for elderly people.

Polymorphisms of the thiopurine S-methyltransferase gene among the Libyan population.

BACKGROUND: Thiopurine S-methyltransferase (TPMT) is a cytosolic enzyme that catalyses the S-methylation of 6-mercaptopurine and azathioprine. Low activity phenotypes are correlated with polymorphism in the TPMT gene. Patients with low or undetectable TMPT activity could develop severe myelosuppression when they are treated with standard doses of thiopurine drugs. Since ethnic differences in the TPMT gene polymorphism have been demonstrated worldwide, assessing it in the Libyan population is worthwhile. METHODS: We investigated TPMT gene polymorphism in a total of 246 Libyan healthy adult blood donors from three different Libyan regions (Tripoli, Yefren, and Tawargha) and 50 children with acute lymphoblastic leukaemia (ALL). We used polymerase chain reaction restriction length polymorphism (PCR-RFLP) and allele-specific PCR-based assays to analyse the TPMT gene for the variants *2 c.238 G>C, *3A (c.460 G>A and c.719 A>G), *3B (c.460 G>A), and *3C (c.719 A>G). RESULTS: Our results show that the TPMT variants associated with low enzymatic activity were detected in 3.25% (8 in 246) of adult Libyan individuals and the frequency of total mutant alleles was 1.63%. Heterozygous genotypes were TPMT*3A in three subjects (0.61%) and TPMT*3C in five subjects (1.02%). No TPMT*2 and TPMT*3B allelic variants and no homozygous or compound heterozygous mutant alleles were detected. The normal allele (wild-type) was found in 98.4% of the adult individuals studied. No mutant alleles were detected among the 50 children who had ALL. CONCLUSIONS: We report on the presence of the TPMT*3C and *3A mutant alleles in the Libyan population. Therefore, monitoring the patients to be treated with doses of thiopurine drugs for TPMT variants is worthwhile to avoid the development of severe myelosuppression.

Association between vitamin D receptor gene polymorphisms and chronic periodontitis among Libyans.

BACKGROUND: Chronic periodontitis (CP) is a common oral disease characterized by inflammation in the supporting tissue of the teeth 'the periodontium', periodontal attachment loss, and alveolar bone loss. The disease has a microbial etiology; however, recent findings suggest that the genetic factors, such as vitamin D receptor (VDR) gene polymorphisms, have also been included. AIM: Investigation of the relationship between VDR gene polymorphisms and CP among Libyans. MATERIALS AND METHODS: In this study, we examined 196 unrelated Libyans between the ages of 25 and 65 years, including 99 patients and 97 controls. An oral examination based on Ramfjord Index was performed at different dental clinics in Tripoli and information were collected using a self-reported questionnaire. DNA was extracted from buccal swabs; the VDR ApaI, BsmI, and FokI polymorphisms were genotyped using polymerase chain reaction and were sequenced using Sanger Method. RESULTS: A significant difference in the newly detected ApaI SNP C/T rs#731236 was found (p=0.022), whereas no significant differences were found in ApaI SNP G/T rs#7975232, BsmI SNP A/G rs#1544410, and FokI SNP A/G rs#2228570 between patients and controls (p=0.939, 0.466, 0.239), respectively. CONCLUSION: VDR ApaI SNP C/T rs#731236 may be related to the risk of CP in the Libyan population.

Evidence of still-ongoing convergence evolution of the lactase persistence T-13910 alleles in humans.

A single-nucleotide variant, C/T(-13910), located 14 kb upstream of the lactase gene (LCT), has been shown to be completely correlated with lactase persistence (LP) in northern Europeans. Here, we analyzed the background of the alleles carrying the critical variant in 1,611 DNA samples from 37 populations. Our data show that the T(-13910) variant is found on two different, highly divergent haplotype backgrounds in the global populations. The first is the most common LP haplotype (LP H98) present in all populations analyzed, whereas the others (LP H8-H12), which originate from the same ancestral allelic haplotype, are found in geographically restricted populations living west of the Urals and north of the Caucasus. The global distribution pattern of LP T(-13910) H98 supports the Caucasian origin of this allele. Age estimates based on different mathematical models show that the common LP T(-13910) H98 allele (approximately 5,000-12,000 years old) is relatively older than the other geographically restricted LP alleles (approximately 1,400-3,000 years old). Our data about global allelic haplotypes of the lactose-tolerance variant imply that the T(-13910) allele has been independently introduced more than once and that there is a still-ongoing process of convergent evolution of the LP alleles in humans.

Mutations in the translated region of the lactase gene (LCT) underlie congenital lactase deficiency.

Congenital lactase deficiency (CLD) is a severe gastrointestinal disorder characterized by watery diarrhea in infants fed with breast milk or other lactose-containing formulas. We initially assigned the CLD locus by linkage and linkage disequilibrium on 2q21 in 19 Finnish families. Here we report the molecular background of CLD via characterization of five distinct mutations in the coding region of the lactase (LCT) gene. Twenty-seven patients out of 32 (84%) were homozygous for a nonsense mutation, c.4170T-->A (Y1390X), designated "Fin(major)." Four rare mutations--two that result in a predicted frameshift and early truncation at S1666fsX1722 and S218fsX224 and two point mutations that result in substitutions Q268H and G1363S of the 1,927-aa polypeptide--confirmed the lactase mutations as causative for CLD. These findings facilitate genetic testing in clinical practice and enable genetic counseling for this severe disease. Further, our data demonstrate that, in contrast to common adult-type hypolactasia (lactose intolerance) caused by a variant of the regulatory element, the severe infancy form represents the outcome of mutations affecting the structure of the protein inactivating the enzyme.