Browsing by Author "Rots, Dmitrijs"
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Item Alanyl-tRNA synthetase 1 gene variants in hereditary neuropathy genotype and phenotype overview(2022-10-05) Setlere, Signe; Jurcenko, Marija; Gailite, Linda; Rots, Dmitrijs; Kenina, Viktorija; Department of Doctoral Studies; Scientific Laboratory of Molecular Genetics; Department of Biology and MicrobiologyBackground and Objectives Our objective was to report 2 novel variants and to reclassify previously reported alanyl-tRNA synthetase 1 (AARS1) variants associated with hereditary neuropathy and to summarize the clinical features of a previously published cohort of patients. Methods We performed detailed neurologic and electrophysiologic assessments and segregation analysis of 2 unrelated families with Charcot-Marie-Tooth (CMT) disease with novel variants in the AARS1 gene. Via literature search, we found studies that included neuropathy cases with AARS1 variants; we then reviewed and reclassified these variants. Results We identified 2 CMT families harboring previously unreported likely pathogenic AARS1 variants: c.1823C>A p.(Thr608Lys) and c.1815C>G p.(His605Gln). In addition, we reinterpreted a total of 35 different AARS1 variants reported in cases with neuropathy from the literature: 9 variants fulfilled the current criteria for being (likely) pathogenic. We compiled and summarized standardized clinical and genotypic information for 90 affected individuals from 32 families with (likely) pathogenic AARS1 variants. Most experienced motor weakness and sensory loss in the lower limbs. Discussion In total, 11 AARS1 variants can currently be classified as pathogenic or likely pathogenic and are associated with sensorimotor axonal or intermediate, slowly progressive polyneuropathy with common asymmetry and variable age of symptom onset with no apparent involvement of other organ systems.Item Analysis of possible genetic risk factors contributing to development of childhood acute lymphoblastic leukaemia in the Latvian population(2016) Kreile, Madara; Piekuse, Linda; Rots, Dmitrijs; Dobele, Zane; Kovalova, Zhanna; Lace, Baiba; Scientific Laboratory of Molecular Genetics; Onkoloģijas institūtsIntroduction: Childhood acute lymphoblastic leukaemia (ALL) is a complex disease caused by a combination of genetic susceptibility and environmental exposure. Previous genome-wide association studies have reported several single nucleotide polymorphisms (SNPs) associated with the incidence of ALL. Several variations in genes encoding enzymes involved in carcinogenesis are suggested as being associated with an increased risk of ALL development. Material and methods: We enrolled 77 paediatric ALL patients and 122 healthy controls, and in addition parental DNA was also available for 45 probands. SNPs rs10821936 (ARID5B), rs4132601(IKZF1), rs2239633 (CEBPE), rs3731217 (CDKN2A) and rs1800566 (NQO1) and the presence of GSTT1 and GSTM1 null variants were detected. For statistical analysis the hybrid method of two designs 'Haplin' was used as well as linkage disequilibrium for family-based association studies. Results: We identified the SNP rs10821936 in the ARID5B gene as being statistically significantly associated with childhood ALL, especially if the C allele is in a homozygous state, relative risk (RR) 4.65, 95% CI: 2.03-10.6, p = 0.0006. Statistically significant differences were not found in other SNPs. We found risk combinations including all five variations, the strongest association being found in a combination where all five genetic variants are in a homozygous state, CCTTTTTTCC, p = 0.032. Conclusions: The identified SNP rs10821936 could serve as a potential risk marker for childhood ALL development. Further studies in an independent population are needed for verification.Item The association of FMR1 gene (CGG)n variation with idiopathic female infertility(2021) Grasmane, Adele; Rots, Dmitrijs; Vītiņa, Zane; Magomedova, Valerija; Gailīte, Linda; Rīga Stradiņš UniversityIntroduction: The FMR1 gene plays an important role in brain development and in the regulation of ovarian function. The FMR1 gene contains CGG repeat variation and the expansion of the repeats is associated with various phenotypes e.g. fragile X syndrome, premature ovarian failure, etc. Repeats ranging < 55 CGG are considered normal, however recent studies suggest that high-normal (35-54 CGG) and low-normal ([removed] 0.05). In addition, the analysis of low-normal allele and genotype frequencies did not present a difference between primary, secondary infertility and the control group (p > 0.05). Conclusions: In our study, the FMR1 gene high-normal alleles were associated with secondary infertility. However, to address the controversies related to the role of FMR1 genes in the development of diminished ovarian reserve, further studies on the subject are required.Item Association of in-vitro fertilization twin pregnancy with maternal and perinatal complications(2018) Grasmane, Adele; Purina-Liberte, Katrina; Rots, Dmitrijs; Miltiņa, Ināra; Rezeberga, Dace; Faculty of Medicine; Scientific Laboratory of Molecular Genetics; Department of Obstetrics and GynaecologyObjective: To analyze maternal and perinatal complication rates in in-vitro fertilization (IVF) twins and spontaneous twin pregnancies. Methods: The information on obstetric and perinatal outcomes and complications covering 95 IVF twins and 165 spontaneous twin pregnancies was collected from the medical records of Riga Maternity Hospital. Statistical analysis and adjustment for confounders was performed using the SPSS v24.0 software. The continuous data were compared using the t-test and Mann-Whitney U test for parametrical and non-parametrical data accordingly. The nominal data were analyzed using Pearson's Chi-square test and Fisher's exact test. Results: The preterm labor risk, intrauterine growth restriction, fetus weight between IVF and spontaneous twins were not statistically significant (P>0.005). At the same time our study revealed a statistically significant association of gestational diabetes and pregnancy induced hypertension with IVF twin pregnancies (P=0.025 and P=0.003, respectively). Moreover, IVF twins had higher odds to be delivered by cesarean section (P=0.001). Conclusions: IVF twin pregnancies are associated with a higher risk of development of gestational diabetes and gestational hypertension than spontaneous twin pregnancies.Item Case report : Multiple UGT1A1 gene variants in a patient with Crigler-Najjar syndrome(2018-10-03) Gailite, Linda; Rots, Dmitrijs; Pukite, Ieva; Cernevska, Gunta; Kreile, Madara; Scientific Laboratory of Molecular GeneticsBackground: Inherited unconjugated hyperbilirubinemia is caused by variants in the gene UGT1A1 leading to Gilbert's syndrome and Crigler-Najjar syndrome types I and II. These syndromes are differentiated on the basis of UGT1A1 residual enzymatic activity and its affected bilirubin levels and responsiveness to phenobarbital treatment. Case presentation: In this report, we present a boy with Crigler-Najjar syndrome type II with high unconjugated bilirubin levels that decreased after phenobarbital treatment but increased in adolescence. Four different UGT1A1 gene variants have been identified for this patient, of which one is novel (g.11895-11898del) most likely confirming diagnose molecularly. Conclusions: The presented case highlights the challenges encountered with the interpretation of molecular data upon identification of multiple variants in one gene that are causing different degree reducing effect on enzyme activity leading to several clinical conditions.Item Clinical Phenotyping and Biomarkers in Spinal and Bulbar Muscular Atrophy(2021-01-20) Millere, Elīna; Rots, Dmitrijs; Glāzere, Ieva; Tauriņa, Gita; Kurjāne, Nataļja; Priedīte, Viktorija; Gailīte, Linda; Blennov, Kaj; Zetterberg, Henrik; Ķēniņa, Viktorija; Department of Doctoral Studies; Scientific Laboratory of Molecular Genetics; Department of Biology and MicrobiologyBackground: Spinal and bulbar muscular atrophy (SBMA) or Kennedy disease [OMIM: 313200] is a rare X-linked neuromuscular disease. Patients commonly present with muscle cramps, tremors, leg weakness, dysarthria and dysphagia. Methods: We deeply phenotyped and evaluated the possible extent of affected systems in all patients with SBMA in Latvia (n = 5). In addition, neurophysiological studies and blood analyses were used to perform a molecular diagnosis and evaluate biochemical values. We analyzed neurofilament light (NfL) as a possible biomarker. Results: Neurological examination revealed typical SBMA clinical manifestations; all patients had small or large nerve fiber neuropathy. Three of five patients had increased neurofilament light levels. Conclusion: The study confirms the systemic involvement in patients suffering from SBMA. Increased NfL concentration was associated with either peripheral neuropathy or decreased body mass index. The complex phenotype of the disease should be kept in mind, as it could help to diagnose patients with SBMA.Item Exploring disease-specific metabolite signatures in hereditary angioedema patients(2024) Kaņepa, Adīne; Fan, Jingzhi; Rots, Dmitrijs; Vaska, Annija; Ansone, Laura; Briviba, Monta; Klovins, Janis; Kurjāne, Nataļja; Kļaviņš, Kristaps; Rīga Stradiņš UniversityIntroduction: Hereditary angioedema (HAE) is a rare, life-threatening autosomal dominant genetic disorder caused by a deficient and/or dysfunctional C1 esterase inhibitor (C1-INH) (type 1 and type 2) leading to recurrent episodes of edema. This study aims to explore HAE patients' metabolomic profiles and identify novel potential diagnostic biomarkers for HAE. The study also examined distinguishing HAE from idiopathic angioedema (AE). Methods: Blood plasma samples from 10 HAE (types 1/2) patients, 15 patients with idiopathic AE, and 20 healthy controls were collected in Latvia and analyzed using LC-MS based targeted metabolomics workflow. T-test and fold change calculation were used to identify metabolites with significant differences between diseases and control groups. ROC analysis was performed to evaluate metabolite based classification model. Results: A total of 33 metabolites were detected and quantified. The results showed that isovalerylcarnitine, cystine, and hydroxyproline were the most significantly altered metabolites between the disease and control groups. Aspartic acid was identified as a significant metabolite that could differentiate between HAE and idiopathic AE. The mathematical combination of metabolites (hydroxyproline * cystine)/(creatinine * isovalerylcarnitine) was identified as the diagnosis signature for HAE. Furthermore, glycine/asparagine ratio could differentiate between HAE and idiopathic AE. Conclusion: Our study identified isovalerylcarnitine, cystine, and hydroxyproline as potential biomarkers for HAE diagnosis. Identifying new biomarkers may offer enhanced prospects for accurate, timely, and economical diagnosis of HAE, as well as tailored treatment selection for optimal patient care.Item Genetic Basis of Early Onset Atrial Fibrillation in Patients without Risk Factors(2023-03) Rudaka, Irina; Vilne, Baiba; Isakova, Jekaterina; Kalejs, Oskars; Gailite, Linda; Rots, Dmitrijs; Scientific Laboratory of Molecular Genetics; Bioinformatics GroupBackground: Atrial fibrillation (AF) is the most common arrhythmia and typically occurs in elderly patients with other cardiovascular and extracardiac diseases. However, up to 15% of AF develops without any related risk factors. Recently, the role of genetic factors has been highlighted in this particular form of AF. Aims: The aims of this study were to determine the prevalence of pathogenic variants in early-onset AF in patients without known disease-related risk factors and to identify any structural cardiac abnormalities in these patients. Materials and Methods: We conducted exome sequencing and interpretation in 54 risk factor-free early-onset AF patients and further validated our findings in a similar AF patient cohort from the UK Biobank. Results: Pathogenic/likely pathogenic variants were found in 13/54 (24%) patients. The variants were identified in cardiomyopathy-related and not arrhythmia-related genes. The majority of the identified variants were TTN gene truncating variants (TTNtvs) (9/13 (69%) patients). We also observed two TTNtvs founder variants in the analysed population—c.13696C>T p.(Gln4566Ter) and c.82240C>T p.(Arg27414Ter). Pathogenic/likely pathogenic variants were found in 9/107 (8%) individuals from an independent similar AF patient cohort from the UK Biobank. In correspondence with our Latvian patients, only variants in cardiomyopathy-associated genes were identified. In five (38%) of the thirteen Latvian patients with pathogenic/likely pathogenic variants, dilation of one or both ventricles was identified on a follow-up cardiac magnetic resonance scan. Conclusions: We observed a high prevalence of pathogenic/likely pathogenic variants in cardiomyopathy-associated genes in patients with risk factor-free early-onset AF. Moreover, our follow-up imaging data indicate that these types of patients are at risk of developing ventricular dilation. Furthermore, we identified two TTNtvs founder variants in our Latvian study population.Item Hereditary or acquired? Comprehensive genetic testing assists in stratifying angioedema patients(2024-03-30) Rozevska, Marija; Kaņepa, Adīne; Puriņa, Signe; Gailīte, Linda; Nartiša, Inga; Farkas, Henriette; Rots, Dmitrijs; Kurjāne, Nataļja; Rīga Stradiņš UniversityHereditary angioedema (HAE) poses diagnostic challenges due to its episodic, non-specific symptoms and overlapping conditions. This study focuses on the genetic basis of HAE, particularly focusing on unresolved cases and those with normal C1-inhibitor levels (nC1-INH HAE). This study reveals that conventional testing identified pathogenic variants in only 10 patients (n = 32), emphasizing the necessity for an integrative approach using genome, exome, and transcriptome sequencing. Despite extensive genetic analyses, the diagnostic yield for nC1-INH HAE remains low in our study, the pathogenic variant for nC1-INH HAE was identified in only 1 patient (n = 21). Investigation into candidate genes yielded no pathogenic variants, prompting a re-evaluation of patients’ diagnoses. This study advocates for a nuanced approach to genetic testing, recognizing its limitations and emphasizing the need for continuous clinical assessment. The complex genetic landscape of nC1-INH HAE necessitates further research for a more comprehensive understanding. In conclusion, this study contributes valuable insights into the genetic intricacies of HAE, highlighting the challenges in diagnosis and the evolving nature of the disease. The findings underscore the importance of advanced sequencing techniques and an integrated diagnostic strategy in unravelling the complexities of HAE, particularly in nС1-INH HAE cases.Item A higher polygenic risk score is associated with a higher recurrence rate of atrial fibrillation in direct current cardioversion-treated patients(2021) Vogel, Simon; Rudaka, Irina; Rots, Dmitrijs; Isakova, Jekaterīna; Kalējs, Oskars; Vīksne, Kristīne; Gailīte, Linda; Scientific Laboratory of Molecular GeneticsItem Lack of association between polymorphisms in genes MTHFR and MDR1 with risk of childhood acute lymphoblastic leukemia(2014) Kreile, Madara; Rots, Dmitrijs; Piekuse, Linda; Cebura, Elizabete; Grutupa, Marika; Kovalova, Zhanna; Lace, Baiba; Rīga Stradiņš UniversityBackground: Acute lymphoblastic leukemia (ALL) is a complex disease caused by interactions between hazardous exogenous or/and endogenous agents and many mild effect inherited susceptibility mutations. Some of them are known, but their functional roles still requireinvestigation. Age is a recognized risk factor; children with disease onset after the age of ten have worse prognosis, presumably also triggered by inherited factors. Materials and Methods: The MDR1 gene polymorphisms rs1045642, rs2032582 and MTHFR gene polymorphisms rs1801131 and rs1801133 were genotyped in 68 ALL patients in remission and 102 age and gender matched controls; parental DNA samples were also available for 42 probands. Results: No case control association was found between analyzed polymorphisms and a risk of childhood ALL development. Linkage disequilibrium was not observed in a family-based association study either. Only marginal association was observed between genetic marker rs2032582A and later disease onset (p=0.04). Conclusions: Our data suggest that late age of ALL onset could be triggered by mild effect common alleles.Item Long-Term Immunological Memory of SARS-CoV-2 Is Present in Patients with Primary Antibody Deficiencies for up to a Year after Vaccination(2023-02-03) Lucane, Zane; Slisere, Baiba; Ozola, Lota; Rots, Dmitrijs; Papirte, Sindija; Vilne, Baiba; Gailite, Linda; Kurjane, Natalja; Rīga Stradiņš UniversitySome studies have found increased coronavirus disease-19 (COVID-19)-related morbidity and mortality in patients with primary antibody deficiencies. Immunization against COVID-19 may, therefore, be particularly important in these patients. However, the durability of the immune response remains unclear in such patients. In this study, we evaluated the cellular and humoral response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigens in a cross-sectional study of 32 patients with primary antibody deficiency (n = 17 with common variable immunodeficiency (CVID) and n = 15 with selective IgA deficiency) and 15 healthy controls. Serological and cellular responses were determined using enzyme-linked immunosorbent assay and interferon-gamma release assays. The subsets of B and T lymphocytes were measured using flow cytometry. Of the 32 patients, 28 had completed the vaccination regimen with a median time after vaccination of 173 days (IQR = 142): 27 patients showed a positive spike-peptide-specific antibody response, and 26 patients showed a positive spike-peptide-specific T-cell response. The median level of antibody response in CVID patients (5.47 ratio (IQR = 4.08)) was lower compared to healthy controls (9.43 ratio (IQR = 2.13)). No difference in anti-spike T-cell response was found between the groups. The results of this study indicate that markers of the sustained SARS-CoV-2 spike-specific immune response are detectable several months after vaccination in patients with primary antibody deficiencies comparable to controls.Item The most common European HINT1 neuropathy variant phenotype and its case studies(2023) Rozevska, Marija; Rots, Dmitrijs; Gailite, Linda; Linde, Ronalds; Mironovs, Stanislavs; Timcenko, Maksims; Linovs, Viktors; Locmele, Dzintra; Micule, Ieva; Lace, Baiba; Kenina, Viktorija; Scientific Laboratory of Molecular GeneticsHINT1 is an ubiquitous homodimeric purine phosphoramidase belonging to the histidine-triad superfamily. In neurons, HINT1 stabilizes the interaction of different receptors and regulates the effects of their signaling disturbances. Changes in HINT1 gene are associated with autosomal recessive axonal neuropathy with neuromyotonia. Aim of the study was detailed description of patients' phenotype with HINT1 homozygous NM_005340.7: c.110G>C (p.Arg37Pro) variant. Seven homozygous and three compound heterozygous patients were recruited and evaluated using standardized tests for CMT patients, in four patients' nerve ultrasonography was performed. The median age of symptom onset was 10 years (range 1–20), with initial complaints being distal lower limb weakness with gait impairment, combined with muscle stiffness, more pronounced in the hands than in the legs and worsened by cold. Arm muscles became involved later, presenting with distal weakness and hypotrophy. Neuromyotonia was present in all reported patients and is thus a diagnostic hallmark. Electrophysiological studies demonstrated axonal polyneuropathy. Impaired mental performance was observed in six out of ten cases. In all patients with HINT1 neuropathy, ultrasound examination showed significantly reduced muscle volume as well as spontaneous fasciculations and fibrillations. The nerve cross-sectional areas of the median and ulnar nerves were closer to the lower limits of the normal values. None of the investigated nerves had structural changes. Our findings broaden the phenotype of HINT1-neuropathy and have implications for diagnostics and ultrasonographic evaluation of HINT1-neuropathy patients.Item National survey on clinical and genetic characteristics of patients with hereditary angioedema in Latvia(2023-04-08) Kanepa, Adine; Nartisa, Inga; Rots, Dmitrijs; Gailite, Linda; Farkas, Henriette; Kurjane, Natalja; Rīga Stradiņš UniversityBackground: Hereditary angioedema (HAE) is a rare and life-threatening inborn error of immunity. HAE is mostly caused by pathogenic variations in the serine protease inhibitor gene 1 (SERPING1), leading to deficient or dysfunctional C1-inhibitor (C1-INH), overproduction of bradykinin, and development of recurrent subcutaneous and/or submucosal oedema. The prevalence of HAE is 1 in 50,000 − 100000 people worldwide. We aimed to describe the clinical features and genetic spectrum of hereditary angioedema with C1-INH deficiency (C1-INH-HAE) in Latvia. Methods: All patients from Latvia diagnosed with HAE (types I/II) from 2006 to March 2022 were included in the study. Laboratory tests and clinical data were analysed, and genetic tests with Sanger sequencing and whole genome sequencing were performed. Results: The study identified 10 C1-INH-HAE patients (nine females, one male) from eight families. The point prevalence of HAE in Latvia is 0.53 per 100 000 inhabitants. Of all patients, seven (70%) had HAE type I and three (30%) had HAE type II. The median age of patients was 54 years and the median age at onset of symptoms was 15 years. A significant delay (median 20.5 years) until diagnosis was observed, and 60% of patients had a positive family history of angioedema. All HAE patients have been hospitalised a median two times during their lifetime. Skin (100%), abdominal (80%), and airway (80%) oedema were the most frequent symptoms. Triggering factors (60%) and prodromal symptoms (90%) were referred. Attacks were severe in 50% of patients, moderate in 10%, and mild in 40%. Pathogenic variations of SERPING1 were identified in eight patients (six families), confirming the diagnosis molecularly. In two patients (two families), no pathogenic variations in the genes were found even after whole genome sequencing. Conclusions: Current data shows a significant delay and clear underdiagnosis of HAE in Latvia. Higher awareness and better information and communication between doctors would improve the diagnosis and management of HAE; as would screening of family members, patients with recurrent angioedema unresponsive to antihistamines and glucocorticoids, and patients with recurrent episodes of severe, unexplained abdominal pain.Item Novel variant of the androgen receptor gene in a patient with complete androgen insensitivity syndrome and polyorchidism(2019) Konrade, Ilze; Zavorikina, Julija; Fridvalde, Aija; Rots, Dmitrijs; Kalere, Ieva; Strumfa, Ilze; Dambrova, Maija; Gailite, Linda; Department of Internal Diseases; Scientific Laboratory of Molecular Genetics; Faculty of Pharmacy; Department of Pathology; Department of Human Physiology and BiochemistryIntroduction: Complete androgen insensitivity (CAIS) in 65–95% cases is caused by pathogenic allelic variants (mutations) in the gene encoding androgen receptor (AR gene) and is characterized by female phenotype development with a male karyotype (46, XY). Patients are usually diagnosed during puberty and undergo gonadectomy due to increased testicular germ cell tumor risk. Only a few outcomes have been reported in older individuals with postponed gonadectomy. Case presentation: A 48-year-old CAIS patient presented with polyorchidism (four testes) without gonadal malignancies. Genetic testing identified a novel allelic variant in the AR gene [c.2141T>G (p.Phe805Cys)] causing the clinical symptoms. Conclusion: We have described a unique patient with CAIS and polyorchidism without malignancies in her late 40's bearing a novel likely pathogenic variant in the AR gene.Item Unravelling the genetic landscape of cervical insufficiency : Insights into connective tissue dysfunction and hormonal pathways(2024-09) Voložonoka, Ludmila; Bārdiņa, Līvija; Kornete, Anna; Krūmiņa, Zita; Rots, Dmitrijs; Minkauskienė, Meilė; Rota, Adele; Strelcoviene, Zita; Vilne, Baiba; Kempa, Inga; Miskova, Anna; Gailīte, Linda; Rezeberga, Dace; Rīga Stradiņš UniversityBACKGROUND: The intricate molecular pathways and genetic factors that underlie the pathophysiology of cervical insufficiency (CI) remain largely unknown and understudied. METHODS: We sequenced exomes from 114 patients in Latvia and Lithuania, diagnosed with a short cervix, CI, or a history of CI in previous pregnancies. To probe the well-known link between CI and connective tissue dysfunction, we introduced a connective tissue dysfunction assessment questionnaire, incorporating Beighton and Brighton scores. The phenotypic data obtained from the questionnaire was correlated with the number of rare damaging variants identified in genes associated with connective tissue disorders (in silico NGS panel). SKAT, SKAT-O, and burden tests were performed to identify genes associated with CI without a priori hypotheses. Pathway enrichment analysis was conducted using both targeted and genome-wide approaches. RESULTS: No patient could be assigned monogenic connective tissue disorder neither genetically, neither clinically upon clinical geneticist evaluation. Expanding our exploration to a genome-wide perspective, pathway enrichment analysis replicated the significance of extracellular matrix-related pathways as important contributors to CI's development. A genome-wide burden analysis unveiled a statistically significant prevalence of rare damaging variants in genes and pathways associated with steroids (p-adj = 5.37E-06). Rare damaging variants, absent in controls (internal database, n = 588), in the progesterone receptor (PGR) (six patients) and glucocorticoid receptor (NR3C1) (two patients) genes were identified within key functional domains, potentially disrupting the receptors' affinity for DNA or ligands. CONCLUSION: Cervical insufficiency in non-syndromic patients is not attributed to a single connective tissue gene variant in a Mendelian fashion but rather to the cumulative effect of multiple inherited gene variants highlighting the significance of the connective tissue pathway in the multifactorial nature of CI. PGR or NR3C1 variants may contribute to the pathophysiology of CI and/or preterm birth through the impaired progesterone action pathways, opening new perspectives for targeted interventions and enhanced clinical management strategies of this condition.