FMR1 linked haplotype analysis in a mentally retarded male population

Funding Information: The study was supported by Riga Stradins University ESF projects No. 2004/0005/VPD1/ ESF/PIAA/04/NP/3.2.3.1./0001/0004/0066 and No. 2009/0147/1DP/1.1.2.1.2/09/IPIA/VIAA/009. We are grateful to Dr. K. Eiklid, Ulleval University Hospital, Oslo, Norway, and Prof. R. A. Wevers and Dr. H. Yntema, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands for technical help and inspiration for this project.Fragile X syndrome is caused by dynamic mutation of FMR1 gene CpG island CGG repeats. The underlying mutational mechanism is not fully understood. Different microsatellite markers and SNP have previously been reported as markers associated with FMR1 CGG repeat instability. The aim of the present study was to identify specific haplotypes among Latvian FXS patients and the control group with respect to allelic stability. Eleven male FXS patients and 122 control male patients participated in the study. In total, 27 different DXS548-FRAXAC1-ATL1-FRAXAC2 haplotypes were found. The prevalent haplotype in the control group was 7-4-A-5+ (rel. frequency 0.327). The prevalent haplotype associated with the FXS group was 2-2-G-4 (rel. frequency 0.818; p < 0.0001). Grey zone alleles with a long uninterrupted CGG tract at the 3' end were significantly associated with the 2-2-G-4 haplotype (p = 0.0022). Our findings suggest that, for the Latvian population, the haplotype 2-2-G-4 is a marker of CGG tract instability. We conclude that a founder effect could not be an explanation for our findings on the basis of heterogeneity exhibited by the Latvian population and lack of studies throughout this geographical region. This data may provide evidence of different mutational pathways of expansion in the Baltic States region.publishersversionPeer reviewe

The fragile X syndrome13 years of experience

Funding Information: The study was approved by the Latvian Central Medical Ethics Committee and the Rîga Stradiòð University Medical Ethics Committee, and supported by ESF project No. 2009/ 0147/1DP/1.1.2.1.2/09/IPIA/VIAA/009.Fragile X syndrome (FXS; MIM #300624; FRAXA, Xq27.3) is well known and a common cause of X-linked mental retardation. The syndrome is caused by dynamic mutation of FMR1 gene CpG island CGG repeats. Clinically FXS patients demonstrate delayed developmental milestones, particularly speech, attention-deficit/hyperactivity disorder, autistic features, and psychomotor development delay. Dysmorphic face and macroorchidism are important features in the postpubertal age. We present our 13-year experience with FXS patients who were confirmed by molecular diagnostic. Phenotype-genotype evaluation was made for 12 male FXS patients. Genotype-phenotype analysis did not reveal significant correlation between clinical symptoms observed in FXS patients and genotypes obtained from leucocytes DNA analysis. The prevalence of the fragile X syndrome in the Latvian male population was estimated to be 1/6428 (95% CI 5538-7552) or 15.55/100 000 males (95% CI 13.24 - 18.05). The prevalence of the fragile X syndrome among mentally retarded male patients was estimated to be 2.67%. The low number of diagnosed patients with fragile X syndrome demonstrated in our study led to the conclusion that fragile X syndrome is generally clinically unrecognised.publishersversionPeer reviewe

Application of the UHPLC-DIA-HRMS Method for Determination of Cheese Peptides

Until now, cheese peptidomics approaches have been criticised for their lower throughput. Namely, analytical gradients that are most commonly used for mass spectrometric detection are usually over 60 or even 120 min. We developed a cheese peptide mapping method using nano ultra-high-performance chromatography data-independent acquisition high-resolution mass spectrometry (nanoUHPLC-DIA-HRMS) with a chromatographic gradient of 40 min. The 40 min gradient did not show any sign of compromise in milk protein coverage compared to 60 and 120 min methods, providing the next step towards achieving higher-throughput analysis. Top 150 most abundant peptides passing selection criteria across all samples were cross-referenced with work from other publications and a good correlation between the results was found. To achieve even faster sample turnaround enhanced DIA methods should be considered for future peptidomics applications.Peer reviewe

An effect of culture media on epithelial differentiation markers in breast cancer cell lines MCF7, MDA-MB-436 and SkBr3

Funding Information: Acknowledgments: This research was supported by the Latvian National Research Program “Biomedicine for Public Health (BIOMEDICINE)”, project No. 5.5 “Personalized cancer diagnostics and prediction of therapy efficacy”. Publisher Copyright: © 2018 by the authors. Licensee MDPI, Basel, Switzerland. Copyright: Copyright 2018 Elsevier B.V., All rights reserved.Background and objectives: Cell culture is one of the mainstays in the research of breast cancer biology, although the extent to which this approach allows to preserve the original characteristics of originating tumor and implications of cell culture findings to real life situations have been widely debated in the literature. The aim of this study was to determine the role of three cell culture media on transcriptional expression of breast cancer markers in three breast cancer reference cell lines (MCF7, SkBr3 and MDA-MB-436). Materials and methods: Cell lines were conditioned in three studied media (all containing 5% fetal bovine serum (FBS) + hormones/growth factors; different composition of basal media) for four passages. Population growth was characterized by cumulative population doubling levels, average generation time, cell yield and viability at the fourth passage. Transcriptional expression of breast cancer differentiation markers and regulatory transcriptional programs was measured by qPCR. Results: Differences in the composition of growth media significantly influenced the growth of studied cell lines and the expression of mammary lineage governing transcriptional programs and luminal/basal markers. Effects of media on transcriptional expression were more pronounced in luminal cell lines (MCF7, SkBr3), than in the basal cell line (MDA-MB-436). Changes in growth media in terms of supplementation and basal medium delayed growth of cells, but improved cell yields. Conclusions: The expression of breast cancer cell differentiation phenotypic markers depends on the composition of cell growth medium, therefore cell culture as a tool in phenotypic studies should be used considering this effect. The findings of such studies should always be interpreted with caution. The formulation of cell growth media has greater effect on the expression of phenotypic markers in luminal, rather than basal cell lines. Media containing mitogens and higher vitamin content improved efficacy of cell culture in terms of cell yields, although greatly increased growth times.publishersversionPeer reviewe

Allelic variants of breast cancer susceptibility genes PALB2 and RECQL in the Latvian population

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Pathogenic APC variants in latvian familial adenomatous polyposis patients

Funding Information: This research was funded by the state research program ?Biomedicine for Public Health (BIOMEDICINE)" project 5 ?Personalized cancer diagnostics and treatment effectiveness evaluation?. Publisher Copyright: © 2019 by the authors. Licensee MDPI, Basel, Switzerland. Copyright: Copyright 2019 Elsevier B.V., All rights reserved.Background and objectives: Familial adenomatous polyposis is one of the APC-associated polyposis conditions described as genetically predetermined colorectal polyposis syndrome with a variety of symptoms. The purpose of this study was to determine sequence variants of the APC gene in patients with familial adenomatous polyposis (FAP) phenotype and positive or negative family history. Materials and Methods: Eight families with defined criteria of adenomatous polyposis underwent molecular genetic testing. Coding regions and flanking intron regions of the APC gene were analyzed by Sanger sequencing. Results: Eight allelic variants of the APC gene coding sequence were detected. All allelic variants of the APC gene were predicted to be pathogenic based on criteria according to the “Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology” (2015), four of them c.1586_1587insAT, c.2336delT, c.3066_3067insGA, and c.4303_4304insC, were considered novel. Conclusions: The timely molecular genetic analysis of APC germline variants and standardized interpretation of the pathogenicity of novel allelic variants has a high impact on choice for treatment, cancer prevention, and family genetic counseling.Peer reviewe

Trauslās X hromosomas sindroms pacientiem ar garīgo atpalicību Latvijā. Promocijas darba kopsavilkums

Elaboration of the Study: Medical Genetics Clinic, University Children`s Hospital, Riga, Latvia. Defence: on 21st of December, 2011 at 14.00 o`clock in the Hippocratic lecture-hall of Riga Stradins University (RSU) Dzirciema Str.16.Mental retardation (MR) is a complex phenotype, affecting 2 - 3% of the general population. A quarter of cases are caused by genetic disorders. Mental retardation is the most frequent cause of severe handicap in children. We focussed our study on fragile X syndrome, which is both well known and a common cause of X-linked mental retardation. One of principle tasks in our study was to estimate the prevalence of fragile X syndrome (FXS) in the entire Latvian male population. In the prevalence study we analysed retrospective data of the male individuals with mental retardation and developmental disabilities, diagnosed in ten years time. The prevalence of fragile X syndrome in the Latvian male population was estimated to be 1/6428 (95% CI 5538 – 7552) or 15.55/100 000 males (95% CI 13.24 – 18.05). Fragile X syndrome is caused by an expanded CGG repeat (> 200 units, full mutation) at the 5' end of the FMR1 gene. In our study we characterised the distribution and structure of CGG repeats among X chromosomes with normal CGG repeat alleles and chromosomes with full mutation. We analysed elsewhere described FMR1 gene linked STR based markers FRAXAC1, FRAXAC2 and DXS548, and one SNP based marker ATL1, found within 150 kb of the FMR1 CGG repeat. STR and SNP marker haplotypes were combined as follows: DXS548-FRAXAC1-ATL1-FRAXAC2. DNA studies of X chromosomes with normal CGG repeats revealed high incidences of allele 30 (29.95%), allele 31 (13.10%) and allele 29 (12.83%). A statistically significant association with ATL1 SNP was found in following cases: allele 29 and G (p = 0.001); allele 30 and A (p < 0.0001) and allele 31 with A (p = 0.0013). Polymorphism G was found to be associated with grey-zone CGG alleles (p = 0.0271) and exclusively associated with all FXS alleles. A structure analysis of grey-zone alleles suggest haplotype 7-4-A-5+ as a “protective” haplotype for CGG tract stability. The case-control study results also imply that in the Latvian population, haplotype 2-2-G-4 is a marker of CGG tract instability. Results of AMOVA for haplotypes revealed distinct genetic background for FXS chromosomes. This is the first study regarding FMR1 linked haplotypes in the Baltic States region. Our results provide evidence of different mutational pathways of CGG repeat expansion in North-Eastern Europe.The work was supported by ESF Project “Support to doctor’s studies and acquiring an academic degree in Riga Stradins University” No. 2009/ 0147/1DP/ 1.1.2.1.2/ 09/ IPIA/ VIAA/ 00

Hypercalcemia and CYP24A1 Gene Mutation Diagnosed in the 2nd Trimester of a Twin Pregnancy : A Case Report

Publisher Copyright: © Am J Case Rep, 2021.Objective: Rare disease Background: Loss-of-function mutations of the CYP24A1 gene cause a deficiency of the CYP24A1 enzyme, which is involved in the catabolism of 1,25-dihydroxyvitamin D3. Patients who are CYP24A1 enzyme deficient are at increased risk of developing hypercalcemia during pregnancy and should avoid additional vitamin D supplementation. This case report provides additional information for managing and diagnosing patients with a CYP24A1 gene mutation. Case Report: A primipara woman with a twin pregnancy was admitted to our hospital for frequent hypertensive crises. She had no history of hypercalcemia-associated signs and symptoms except nephrocalcinosis, and reported no oth-er abnormalities or discomfort at presentation. Laboratory tests revealed that the parathyroid hormone level was suppressed and the serum calcium level was markedly increased. The 25-hydroxyvitamin D level was at the upper limit of the reference range while the 1,25-dihydroxyvitamin D3 level was elevated, suggesting a vitamin D catabolism disorder. A genetic test was performed and a homozygous likely pathogenic variant (based on the American College of Medical Genetics and Genomics guidelines) c.964G>A (p.Glu322Lys) was detected in the CYP24A1 gene (NM_000782.5). A cesarean section delivery was performed due to a single intrauterine demise at 33 weeks of gestation. The preterm newborn was diagnosed with transitional hypercalcemia and hyperphosphatemia; however, he was not treated, as he was asymptomatic. Conclusions: Patients with a CYP24A1 gene mutation are at increased risk of hypercalcemia and fetal demise; therefore, 25-hy-droxyvitamin D and calcium levels should be monitored in routine blood tests during pregnancy. Hypercalcemia in a newborn should be carefully evaluated and treated, as hypercalciuria can lead to nephrocalcinosis.Peer reviewe

X-Linked Lymphoproliferative Disease in Latvia: A Report of Two Clinically Distinct Cases

X-linked lymphoproliferative disease (XLP) is a rare primary immunodeficiency. Affected individuals usually present with the Epstein–Barr virus infection and have no apparent disease prior to presentation. The most common clinical manifestations are fulminant infectious mononucleosis, dysgammaglobulinaemia, and lymphoma (usually of B-cell origin). XLP is caused by mutations in the SH2D1A gene which encodes the intracellular adaptor molecule SAP (signalling lymphocyte activation molecule- (SLAM-) associated protein). SAP is predominantly expressed in T cells and NK cells and functions to regulate signal transduction pathways downstream of the SLAM family of surface receptors to control CD4+ T cell (and by extension B-cell), CD8+ T cell and NK cell function, and development of NKT cells. Thus, SAP mutations cause dysregulation of the immune system, with defects in both cellular and humoral immunity. Here we report two clinical cases of three patients who presented with different manifestations of XLP, namely, fulminant infectious mononucleosis, Burkitt lymphoma and hypogammaglobulinaemia