Is the extraction by Whatman FTA filter matrix technology and sequencing of large ribosomal subunit D1-D2 region sufficient for identification of clinical fungi?

Although conventional identification of pathogenic fungi is based on the combination of tests evaluating their morphological and biochemical characteristics, they can fail to identify the less common species or the differentiation of closely related species. In addition these tests are time consuming, labour-intensive and require experienced personnel. We evaluated the feasibility and sufficiency of DNA extraction by Whatman FTA filter matrix technology and DNA sequencing of D1-D2 region of the large ribosomal subunit gene for identification of clinical isolates of 21 yeast and 160 moulds in our clinical mycology laboratory. While the yeast isolates were identified at species level with 100% homology, 102 (63.75%) clinically important mould isolates were identified at species level, 56 (35%) isolates at genus level against fungal sequences existing in DNA databases and two (1.25%) isolates could not be identified. Consequently, Whatman FTA filter matrix technology was a useful method for extraction of fungal DNA; extremely rapid, practical and successful. Sequence analysis strategy of D1-D2 region of the large ribosomal subunit gene was found considerably sufficient in identification to genus level for the most clinical fungi. However, the identification to species level and especially discrimination of closely related species may require additional analysis.

The usefulness of DNA sequencing after extraction by Whatman FTA filter matrix technology and phenotypic tests for differentiation of Candida albicans and Candida dubliniensis.

Since C. dubliniensis is similar to C. albicans phenotypically, it can be misidentified as C. albicans. We aimed to investigate the prevalence of C. dubliniensis among isolates previously identified as C. albicans in our stocks and to compare the phenotypic methods and DNA sequencing of D1/D2 region on the ribosomal large subunit (rLSU) gene. A total of 850 isolates included in this study. Phenotypic identification was performed based on germ tube formation, chlamydospore production, colony colors on chromogenic agar, inability of growth at 45 °C and growth on hypertonic Sabouraud dextrose agar. Eighty isolates compatible with C. dubliniensis by at least one phenotypic test were included in the sequence analysis. Nested PCR amplification of D1/D2 region of the rLSU gene was performed after the fungal DNA extraction by Whatman FTA filter paper technology. The sequencing analysis of PCR products carried out by an automated capillary gel electrophoresis device. The rate of C. dubliniensis was 2.35 % (n = 20) among isolates previously described as C. albicans. Consequently, none of the phenotypic tests provided satisfactory performance alone in our study, and molecular methods required special equipment and high cost. Thus, at least two phenotypic methods can be used for identification of C. dubliniensis, and molecular methods can be used for confirmation.

Angiotensin-converting enzyme gene insertion/deletion polymorphism frequency in normotensive children with a positive family history of essential hypertension.

AIM: To evaluate the possible relationship between blood pressure (BP) and angiotensin-converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism in normotensive children with a positive family history of essential hypertension (EHT). MATERIAL AND METHODS: Three hundred seventy-six randomly selected normotensive schoolchildren (147 boys, 229 girls) between the ages of seven and 17 years were enrolled. Children were subdivided into a 'first-degree relative group' and a 'second-degree relative group' according to the presence of EHT in parents or grandparents, respectively. BP was measured twice from the right arm and the systolic BP, diastolic BP and mean BP were recorded. ACE gene I/D polymorphism was performed from all studied children and frequency od DD, ID and ID allele were analysed in each study group. RESULTS: Allelic frequencies of the DD genotype of the ACE gene were higher in children with a positive history in the first- (36.2%) and second-degree (38.3%) relatives for EHT than the controls (30.7%) (P < 0.05 for both). Children with a positive family history of EHT and a DD genotype, had significantly higher SBP, DBP and MBP levels (P < 0.05) than the children with ID or II genotypes. CONCLUSION: We found that the ACE gene DD genotype was common and that BP levels were higher in Turkish children with a positive family history of EHT and DD genotype. Because the presence of DD allele might be the one of the potential contributor of EHT pathogenesis, further studies needed in large cohort for long term follow-up for EHT in children with DD allele.

A missense mutation in the M1S1 gene found in a turkish patient with gelatinous droplike corneal dystrophy.

PURPOSE: To report a missense mutation in the M1S1 gene found in a Turkish patient with gelatinous droplike corneal dystrophy (GDLD). METHODS: A Turkish patient with GDLD was examined. Keratoplasty was performed and a diagnosis of GDLD was made by histopathologic and electron microscopic studies. Genomic DNA was extracted from peripheral blood and the paraffin-embedded tissue of the corneal button. A 248-bp DNA fragment of the M1S1 gene was amplified, and sequencing reactions were analyzed. The results were compared with those of 30 healthy, nonrelated individuals. RESULTS: On light microscopic examination, sheets of amorphous amyloid deposits were observed in subepithelial regions and in the anterior and midcorneal stroma. Electron microscopy revealed dense collagen fibrils and entrapped filamentous amyloid fibrils in the corneal stroma. A substitution of T-->C at nucleotide 557 was found in the peripheral blood DNA sequence analysis, which resulted in an amino acid substitution of L-->P (L186P). Results were confirmed by direct DNA sequencing analysis of the paraffin-embedded corneal button. The patient with GDLD was homozygous for the mutation, resulting in amino acid substitution L186P. CONCLUSIONS: This is the first report, to our knowledge, of a homozygous mutation (L186P) in the M1S1 gene found in a Turkish patient. The clinical examination may be insufficient in sporadic cases, and histopathologic examination and molecular genetic analysis can accelerate and improve the accuracy of diagnosis in patients with GDLD.

Plasma total homocysteine levels in children with type 1 diabetes: relationship with vitamin status, methylene tetrahydrofolate reductase genotype, disease parameters and coronary risk factors.

The objectives of this study were: to determine plasma total homocysteine tHcy levels and the prevalence of hyperhomocysteinemia in children with type 1 diabetes, to determine correlates of plasma tHcy levels with nutritional factor such as serum folic acid and vitamin B12 levels, genetic factors as methylenetetrahydrofolate reductase MTHFR gene polymorphism (C677T and A1298C), to attempt to identify possible dependencies between tHcy and the degree of metabolic control, the duration of the disease and presence of complications, and also to determine the relationship between other coronary risk factors. Plasma tHcy levels and other related parameters performed in 32 children with type 1 diabetes and 23 age-sex matched healthy children. Median tHcy level was higher in the patient group (11.38, 3.28 to 66.01 micromol/l) than the control group (8.78, 1.06 to 13.66 mol/l) (p < 0.05). A 28.1 per cent (n = 9) of the diabetic patients had hyperhomocysteinemia, four case with mild and five case with moderate. Plasma tHcy levels were positively correlated with disease duration and C-reactive protein CRP levels and negatively correlated with disease onset age. The hyperhomocysteinemic group had higher CRP levels, longer disease duration and early onset of disease than non-hyperhomocysteinemic group (p < 0.05 in both), respectively. The hyperhomocysteinemic group had significantly higher CRP, total cholesterol, triglyceride, apolipoprotein B, systolic blood pressure, blood urea nitrogen and creatinine levels and lower folate, apolipoprotein A1 levels and glomerular filtration rate values than the control group. Plasma tHcy levels were higher in diabetic children with poor metabolic control. Because of hyperhomocysteinemia is common in diabetic children and plasma tHcy levels correlated with early onset of the disease and disease duration, we recommend the usage of plasma tHcy levels as a risk indicator parameter with other coronary risk factor for detecting and preventing cardiovascular disease in diabetic children.

Genetic imbalances in endometrial hyperplasia and endometrioid carcinoma detected by comparative genomic hybridization.

OBJECTIVE: To evaluate the sequential genomic copy alterations related to the development of precursor lesions and endometrioid-type endometrial carcinomas, and its association with cellular atypia. STUDY DESIGN: Paraffin-embedded tissue specimens from 32 cases of endometrial hyperplasia, 15 of endometrial carcinoma, and 20 of normal endometrial tissue were retrospectively evaluated by the comparative genomic hybridization (CGH) technique. The average number of copy alterations (ANCA) index was used to define the incidence of genomic imbalances in each tissue group. Identified sequential genetic abnormalities were compared with the final histopathological diagnosis and the cellular atypia. RESULTS: Detectable and consistent chromosomal imbalances were found in 13 hyperplasia and 9 carcinoma specimens. There was a significant correlation between ANCA value and degree of cellular atypia and tumor grade. While 1p36-pter, 20q deletions, and 4q overrepresentation were the most prevalent imbalances detected in both complex hyperplasia and complex atypical hyperplasia, 17q22-qter deletion and amplification of 2p34 were only seen in hyperplasia with atypical cells. Overrepresentations of chromosomes 8q, 1q, and 3q are the most frequent aberrations in endometrial carcinomas, but were absent from all the precursor lesions except one. Underrepresentations of chromosomes 1p36-pter and 10q are the other commonly seen aberrations in carcinomas, the latter being more frequent in moderately differentiated than in poorly differentiated lesions. CONCLUSIONS: Different patterns of chromosomal aberrations are seen in precursor lesions than in endometrial carcinomas, except for the loss of 1p36-pter. The presence of 1p deletion in both endometrial hyperplasia and cancer specimens suggests that this is an early event in the development of carcinoma. These results support a stepwise mode of tumorigenesis with accumulation of a series of genomic copy alterations in endometrial carcinogenesis.

The importance of genomic copy number changes in the prognosis of glioblastoma multiforme.

Glial tumors are the most common tumors of the nervous system, affecting individuals at any age. Since understanding of the molecular pathologies underlying human gliomas is still very poor, the treatment and therefore prognosis of this malignancy could not yet be improved. In order to determine whether different glioblastoma-associated genomic aberrations may serve as prognostic markers in combination with histopathological findings, 20 primary glioblastoma multiforme tumors were screened by comparative genomic hybridization, and the results were compared with histopathological and clinical features. All tumors showed genomic copy aberrations detected by comparative genomic hybridization. Regional and numerical increases in chromosome 7 copy number were the most frequently seen abnormality (10/20 tumors), followed by loss of chromosome 10 (8/20). Both of these aberrations were associated with shorter surveillance time. Chromosome 12q amplification was detected in seven tumors. Loss of 17p, 1p, and 19q in combination was seen in three cases. One of them was a giant cell GBM, whereas the remaining two cases were still alive. Combination of chromosome 1p and 19q deletions was also seen in a case with long surveillance. According to the preliminary findings of this study, in addition to the EGFR gene, amplification of other genes on chromosome 7 and the deletion of PTEN gene and other cancer-related genes on chromosome 10 appeared important to the development of glioblastoma multiforme and were associated with poor prognosis, whereas the combination of chromosome 1p and 19q deletions seems to be an informative molecular marker for better prognosis. The clinical features and genetic alterations of primary and secondary glioblastoma multiforme should be compared in large series to clarify the effective prognostic markers; and further molecular analyses focused on chromosomes 7 and 10 will be very helpful for understanding the molecular mechanisms underlying the progression of glioblastoma.

Detection of chromosomal imbalances in spinal meningiomas by comparative genomic hybridization.

Little is known about genetic mutations during the malignant progression of spinal meningiomas. This study investigated genomic changes across the entire genome in spinal meningioma samples to determine possible mechanism(s) of tumorigenesis. Paraffin-embedded tissue sections of 16 spinal meningiomas were analyzed by the comparative genomic hybridization (CGH) technique. Lymphocytes of the patients were evaluated as controls. Genomic change was detected in 11 samples. Complete or partial loss of chromosome 22 was the most commonly seen abnormality in eight cases. Chromosome losses on 1p, 9p, and 10q and gains on 5p and 17q were the other abnormalities. These changes are all frequently seen in meningiomas, but are mostly specific to atypical and anaplastic meningiomas. However, in the present study, copy number changes on chromosomes 9p (3 samples), 17q (2 samples), and 1p (2 samples) were seen even in the benign tumors. Our results suggest that in addition to the neurofibromatosis type 2 tumor suppressor gene, other cancer-related genes located on 1p, 9p, 10q, and 17q might be involved in the etiology of spinal meningiomas.

Comparative genomic hybridization analysis of genomic alterations in benign, atypical and anaplastic meningiomas.

BACKGROUND: Meningiomas are common tumors of the central nervous system. Although most are benign tumors, approximately 10% show a histologic progression to a higher malignancy grade similar to atypical (GII) and anaplastic (GIII) meningiomas. Monosomy 22q12 is the most frequent genetic alteration detected in these tumors, but failure of detection of 22q mutations in about 40% of tumors which are indistinguishable from meningiomas with 22q deletions with respect to clinical and histopathologic features, makes it apparent that an alternative mechanism is responsible for the initiation of meningioma. Moreover, little is known about genetic alterations during malignant progression of meningioma. PURPOSE: In order to determine the genetic pathways underlying the development of meningioma, 15 benign (WHO grade I), 7 atypical (WHO grade II) and 3 anaplastic (WHO grade III), sporadic meningiomas were screened by Comparative Genomic Hybridization (CGH). RESULTS: Statistical analysis revealed a significant correlation between the number of chromosomal imbalances and the tumor grade; the numbers of total alterations detected per tumor were 2.20 (2.24 for GI, 10.00 (1.17 for GII and 14.66 (1.15 for GIII. The most frequent abnormality seen in benign tumors was loss on 22q (47%). The second alteration was 1p deletion (33%) and this abnormality was also the common aberration in three tumors without CGH detected 22q deletion. In GII, aberrations most commonly identified were losses on 1p (6/7 cases), 22q (5/7 cases), 10q (4/7 cases), 14q and 18q (3/7 cases) as well as gains on 15q and 17q (3/7 cases). In GIII, genomic loss on 1p was the most commonly observed abnormality (3/3). Losses on 9p, 10q, 14q, 15q, 18q and 22q as well as gains on 12q, 15q and 18p were the other genomic alterations detected by CGH. Combined 1p/14q deletions were encountered in 2/15 benign, 3/7 atypical and 2/3 anaplastic meningiomas. By CGH, DNA sequences on 17q21-qter were seen to be amplified in 1/7 GII and 2/3 GIII, whereas highly amplified DNA sequences on 12q13-qter, 20q and 22q11-q12 were seen in one GII, two GII/one GIII, and one GIII, respectively. CONCLUSION: It was concluded that chromosomal deletion from 1p could play a major role in the initiation and progression of meningiomas and that 1p/14q deletions could be a primary focus of further detailed assessment of tumour genesis.