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Sialuria: new observation of a rare inborn error of metabolism
Sialuria is an extremely rare disease with autosomal dominant inheritance from the group of inborn disorder of sialic acid metabolism. The most characteristic clinical manifestations of sialuria are mildly coarse facial features, moderate develomental retardation and massive urinary excretion of free sialic (N-acetylneuraminic) acid. The cause of the disease are pathogenic missense variants in GNE gene resulted in failed feedback inhibition of uridinediphosphate-N-acetylglucosamine (UDP-GlcNAc) 2-epimerase with overproduction of sialic acid. This study presents a new case of sialuria caused by the pathogenic variant NM_005476.7 (GNE): c.797G>A, p.Arg266Gln, rs121908622 and the first experience of quantitative determination of N-acetylneuraminic acid in dried capillary blood samples by tandem mass spectrometry for the diagnosis of this disease.
Clinical, biochemical and molecular-genetic features of selective screening of Russian patients with Niemann-Pick disease types A, B and A/B. Results of the selective screening program
Background. Niemann-Pick disease, types A, B and A/B (NPD) is a rare autosomal recessive disorder from the group of lysosomal disorders caused by deficiency of the enzyme acid sphingomyelinase. The average incidence of the disease is 0.4 – 0.6 cases per 100,000 live births. Aim: to describe the clinical, biochemical and molecular genetic features of 20 Russian patients with NPD, types A, B and A/B, and to describe the experience of selective screening for NPD types A, B and A/B. Methods. The activity of acid sphingomyelinase was analyzed in samples of 4498 patients admitted for examination to the Medical Genomics Laboratory of the Medical Genetics Center of the Federal State Autonomous Institution «National Medical Research Center of Children’s Health» of the Ministry of Health of the Russian Federation from 2013 to 2024 as part of various selective screening programs. Molecular genetic diagnostics in patients with reduced sphingomyelinase activity was performed using Sanger sequencing. Results. For the first time in Russia, the results of twelve years of experience in selective screening of a rare hereditary Niemann-Pick disease types A, B and A/B are presented, including clinical and anamnestic manifestations, biochemical and molecular genetic research methods. 24 different variants of the SMPD1 gene were identified in 20 Russian patients.
Profiling of differential gene expression in leomyoma and myometrium in primary and recurrent uterine fibroids
Background. The lack of clarity regarding the mechanisms underlying the pathogenesis of leiomyomas and their recurrence presents a significant challenge in developing a personalized approach to effective treatment, particularly for women in their reproductive years. Aim: to investigate the differential gene expression patterns in leiomyomas and unaltered myometrium, with the goal of developing a personalized strategy for predicting the progression and treatment of leiomyomas. Methods. The research material comprised samples of leiomyomas, myometrial tissue, and peripheral blood obtained from 32 patients diagnosed with primary or recurrent uterine fibroids, with 22 and 10 cases, respectively. Blood and leiomyomas samples were subjected to analysis for mutations in the MED12 gene employing the Sanger sequencing technique. Expression profiles of 18 potential genes were evaluated through reverse transcription and polymerase chain reaction on tissue samples obtained from leiomyomas and unaltered myometria. Results. The findings suggest that in both primary and recurrent leiomyoma nodules with somatic MED12 mutations, there is an upregulation of the expression of GRPR, TYMS, RANKL and MMP11 genes compared to their counterparts in morphologically normal myometrium. Conversely, in recurrent leiomyomas without MED12 somatic mutations, there is an increase in the expression of the GRPR and RANKL genes. Meanwhile, in primary leiomyomas, there is a decrease in the expression of these same genes when compared to the corresponding myometrial tissue. Conclusion. The genes GRPR, TUMS, RANKL and WMP11 represent promising targets for the development of a personalised approach to the prediction of the course and management of uterine fibroids.
Hereditary copy number variations of BRCA1/2 in breast and ovarian cancers
Testing of hereditary pathogenic variants in the BRCA1/2 genes is standard component of the evaluation of patients with breast cancer and ovarian cancer. Routine DNA testing is limited to the identification of point mutations and microdeletions/insertions, and practically does not take into account other types of aberrations. CNV analysis based on data from a targeted NGS study of DNA samples from patients with breast cancer (n = 3925) and breast cancer (n = 1175) was performed with the gCNV GATK tool. The subsequent verification of bioinformatically predicted CNV of BRCA1/2 exons was carried out by digital droplet PCR. We detected 35/5149 (0.7%) cases with hereditary large rearrangements in the BRCA1 (n = 31) and BRCA2 (n = 4). The most frequent CNV was BRCA1 exon 1-2 del (n = 11). The young age of diagnosis significantly increases the probability of detecting CNV mutations (breast cancer: 21/2294 (0.9 %) vs 6/1631 (0.4 %) p = 0.0247; ovarian cancer: 6/328 (1.8 %) vs 2/847 (0.2 %) p = 0.0062), similarly micromutations in these genes. CNVs account for approximately 5.6 % of all pathogenic variants in the BRCA1 and BRCA2 genes. This indicates the need for integrating CNV analysis into routine diagnosis of hereditary cancer syndromes.
New nucleotide sequence variant of the OCRL gene in a newborn with Lowe syndrome
Oculo-cerebro-renal syndrome (Lowe’s syndrome) belongs to rare X-linked diseases with recessive type of inheritance. We present a clinical observation of a newborn child with the debut of the disease and verification of the diagnosis in the neonatal period. The clinical picture was defined by the syndrome of muscular hypotonia, congenital ventriculomegaly, congenital cataract of both eyes, nephropathy with proteinuria. Based on the combined pathology, the diagnosis of the newborn was suspected: E72.03 Oculo-cerebro-renal Lowe syndrome. The diagnosis was confirmed by genetic testing using full-exome sequencing. A new nucleotide sequence variant (deletion of two nucleotides) in exon 16 of the OCRL gene in hemizygous state leading to a nonsense substitution (c.1638_1639del: p.Phe547Ter) was detected in the patient. This made it possible to timely determine the stages of specialized care for the patient and to plan medical and genetic counseling of the family.
Molecular-genetic and clinical diagnosis in a patient with complex eye dysgenesis, which included optic nerve coloboma and slight iris structure abnormalities
Associations of missense variants in the PAX6 gene with complex ocular phenotypes are in focus of the Genetic Epidemiology Laboratory. The report discusses the results of the molecular diagnosis of a unique clinical case of a combination of subnormal iris and severe optic nerve coloboma, as well as the details of the patient’s phenotype. The patient, a young woman of 29 y.o., with a referring diagnosis of congenital eye pathology and optic nerves partial atrophy was examined ophthalmologically and genetically. PAX6 gene Sanger sequencing, MLPA analysis of the 11p13 chromosome, and whole-exome sequencing (WES) were performed. Targeted sequencing revealed a missense variant in the PAX6 gene NM_000280.4(PAX6):c.341A>G p.(Asn114Ser) in a heterogenous state, qualified as a variant of undefined clinical significance. The variant was detected in a healthy mother. Later, the patient was found to have a missense variant in the MAB21L2 gene: NM_006439.5:c.134T>A p.(Val45Glu) in the heterozygous state. The variant was not present in a control cohort, pathogenicity prediction programs considered the variant as damaging. Heterozygous pathogenic variants of the MAB21L2 gene were described in patients with bilateral eye coloboma combined with skeletal anomalies or without them with an autosomal dominant type of inheritance. The variant was not detected in a healthy mother. Analysis of WES allowed a decision on the causality of the missense variant in the PAX6 gene in a complex case of an aniridia-like phenotype. In the diagnostic solution of complex PAX6-associated phenotypes, it is necessary to rely on additional data obtained from at least the variant segregation and exome analyses. Eventually the patient was diagnosed with colobomatous microphthalmia.
Study of genetic stability of induced pluripotent stem cells intended for modeling hereditary diseases
Background. Genetic stability of model cell cultures is a fundamental prerequisite for ensuring the validity and reproducibility of experimental results. Induced pluripotent stem cells (iPSCs) are inherently prone to developing spontaneous genetic abnormalities. Thus, monitoring the genetic stability of iPSCs every 5–10 passages during culture expansion is essential. Optimizing methods for routine analysis of iPSC genetic stability requires an in-depth investigation of the spectrum of abnormalities characteristic of these cells, along with their structural features and potential functional implications. Aim: to identify and analyze genomic anomalies in iPSC cultures derived from Russian laboratories. Methods. iPSC lines (n = 66), derived in five laboratories from biological material sourced from six healthy donors and 27 patients diagnosed with genetic diseases (15 nosologies), were analyzed using karyotyping techniques. Identified karyotype anomalies were validated through fluorescent in situ hybridization, spectral karyotyping, and SNP microarray analysis. Results. Karyotype abnormalities were observed in 23.6 % of the samples, including trisomy of chromosomes 20 and 8, isochromosome 20q, and structural rearrangements involving chromosomes 1, 2, 8, 15, and 18. Recurrent gains of chromosome segments 1q and 20q accounted for 69 % of the detected aberrations. Conclusions. The structure and frequency of karyotype abnormalities in iPSC lines derived from Russian laboratories are consistent with previously reported data from studies of iPSC lines in international collections. The high prevalence of recurrent aberrations highlights the potential for implementing targeted analysis of genetic stability of cell lines.
Relationship of pharmacoresistance, dose of antipsychotics and polymorphic gene loci CYP2D6, CYP1A2, MDR1, SLC6A4 in patients with schizophrenia
The pharmacogenetic characteristics of the patient may determine his individual therapeutic concentration, at which the drug provides effective clinical treatment without significant side effects. A relationship was found between the occurrence of polymorphic alleles A-/rs3892097; A-/rs762551;T-/rs1045642; S-/5-HTTLPR, antipsychotic dose, and pharmacoresistance in patients with schizophrenia. The effectiveness of antipsychotic therapy in some cases is based on an individual choice of medication and dose, taking into account the results of genetic testing.
The LZTFL1 gene polymorphic variant rs73064425 correlation with clinical and laboratory parameters in patients with novel coronavirus infection
Assessment of clinical and laboratory parameters plays an important role in predicting the severity of COVID-19. At the same time, the genetic markers identification will allow for the earliest stratification of patients by severe infection risk groups. We have genotyped 118 patients with moderate and severe forms of novel coronavirus infection by rs73064425 of the LZTFL1 gene associated with the COVID-19 severity. Based on the data obtained, a replicative analysis of the polymorphic variant rs73064425 association with the developing severe COVID-19 risk in the Russian population was performed. The correlation of this marker with clinical and laboratory parameters was also analyzed. Statistically significant differences were found between groups of patients with varying degrees of severity in the T allele. CT genotype was statistically significantly associated with thrombocytopenia, decreased white blood cell count and decreased blood saturation.
Cytokines levels as an inflammation markers in autoinflammatory diseases
Familial Mediterranean fever (FMF) is an autoinflammatory disease manifested by recurrent fever with signs of systemic inflammation caused by MEFV gene pathogenic variants that lead to inflammasome hyperactivation and hyperproduction of IL-1b and IL-18. FMF is a disorder with variable expressivity and penetrance. The study included 1336 samples, 1271 samples were positive for pathogenic variants in MEFV gene. 160 samples divided into 3 groups: 95 patients (FMF) with different MEFV genotypes (5 subgroups), 49 patients with systemic lupus erythematosus (SLE) and 16 samples as a group of healthy donors (HD). Concentrations of CRP, IL-6, IL-8 and IL-18 were measured for all samples. Concentrations of CRP, IL-6 and IL-18 in FMF group was significantly higher than in HD and SLE groups (р < 0.0001). Concentration of IL-18 was significantly higher in all FMF genotypes subgroups than in HD. Comparing IL-18 levels between different pathogenic MEFV variants samples with «aggressive» variants (p.Met694Val and p.Met680Ile) characterized by increased concentration of IL-18 (р = 0.0411).
Investigation of the sensitivity of CFTR variants to Ivacaftor/Lumacaftor in intestinal organoids model
Study of sensitivity of CFTR variants to targeted drugs allows to increase the number of patients with cystic fibrosis (CF) who can be prescribed effective therapy improving their quality and duration of life. Objective: to study the effect of the targeted drug Ivacaftor/Lumacaftor (I/L) on restoration of CFTR function on intestinal organoid (IO), derived from patients with different CFTR genotypes. Materials and methods: I/L effect was assessed using forskolin-induced swelling assay of IO. Results: IO cultures were obtained from 32 patients with 23 CFTR genotypes. I/L efficacy was assessed for 24 CFTR variants. Conclusion: for 11 CFTR gene variants, I/L targeted drug efficacy was demonstrated for the first time on the IO model.
Genetic landscape of Kabuki syndrome in Russian patients: spectrum of variants in KMT2D and KDM6A genes
Introduction. Kabuki syndrome (KS) is a rare hereditary disorder characterized by developmental delay, hypotonia, and a distinctive facial phenotype resembling the makeup of actors in Japanese Kabuki theater. KS is associated with variants in the KMT2D and KDM6A genes, which are critical for histone modification and embryonic development. Despite numerous international studies, the genetic landscape of KS in Russian patients remains unexplored. Objective: to identify and characterize the spectrum of molecular causes of KS in a Russian cohort of patients. Methods. Next-generation sequencing (NGS) was performed on 37 Russian patients with a clinical diagnosis of KS, including clinical exome sequencing, whole-exome sequencing (WES), and whole-genome sequencing (WGS). Results. Pathogenic or likely pathogenic variants were identified in 22 patients. Seven patients were found to have alternative molecular diagnoses. In KMT2D, 10 frameshift deletions, 4 nonsense variants, 2 in-frame deletions, and 4 missense variants were detected, consistent with global databases. In the KDM6A gene, WES revealed a deletion of exons 3–4, while WGS identified a novel translocation between the X chromosome and chromosome 1 with a breakpoint in intron 28 of KDM6A. Conclusions. The results confirm the previously described spectrum of variants in KMT2D and highlight the predisposition of KDM6A to copy number variations (CNVs) and structural variants. This study enhances the understanding of the molecular etiology of KS and underscores the importance of advanced genomic diagnostic methods.
Chromosome damage in miners with occupational lung diseases
Introduction. The article presents the results of a study of the level of chromosomal damage in blood lymphocytes of miners, patients with lung diseases, healthy miners and control donors. Aim: to analyze the structural damage of chromosomes in Kuzbass miners. Methods. 825 people were examined. Of these, 254 donors were included in the group of miners with lung diseases (chronic dust bronchitis, anthracosilicosis), 310 people were in the group of conditionally healthy miners and 261 people who do not work in production (control group). Results. The level of chromosomal damage in miners with lung diseases and in healthy miners was significantly different (4.91 ± 2.16 % and 4.08 ± 2.47 %, respectively) and was higher than in the control group – 1.80 ± 1.25 % (p < 0.00001). Age, work experience, and smoking did not significantly affect cytogenetic parameters in the studied groups. Conclusions. The development of occupational lung diseases in miners is accompanied by the accumulation of damage to the structure of chromosomes in blood cells.
Family case of type 2 agammaglobulinemia identified during expanded neonatal screening
A family case of type 2 agammaglobulinemia was described, identified during expanded neonatal screening (ENS) in the Krasnodar region. Molecular genetic testing allowed for the diagnosis to be made not only for the newborn but also for the brother of the proband. Timely medical genetic counseling will help prevent the birth of affected children with this condition in this family.
Сlinical manifestations and molecular genetic characterization of heterotaxy syndrome in patients from the Republic of Belarus
Clinical manifestations of heterotaxy syndrome are described. Congenital heart defects are diagnosed in 96-100 % of cases. In most cases, this is a functionally single ventricle of the heart with atresia/stenosis of the extreme degree of the pulmonary trunk. Mutations in genes involved in the formation (functioning) of cilia were identified in the genome of probands, which allows us to classify the presented cases as ciliopathies with an autosomal recessive (CFAP300: c.198_200delinsCC homozygote, LRRCC1: c.2686dup, c.2650C>A, BBS7: c.1967_1968delinsC, c.454T>C) or sex-linked (ZIC3: c.842_843del) type of inheritance. Heterotaxy syndrome has been described for the first time as part of Bardet-Biedl syndrome.
Clinical cytogenomics: advances and horizons
The upcoming cytogenomic era of clinical cytogenetics brings new opportunities for diagnosis, prevention and even the description of new chromosomal syndromes. Current advances in clinical cytogenomics, as well as outstanding challenges and horizons, are discussed.
Body composition in children with cystic fibrosis and its association with polymorphic variants of energy metabolism genes
Aim: to conduct an associative search for variants of ACE, PPARGC1A, ACTN3, PPARA genes with nutritional status and body composition of children with cystic fibrosis (CF). Methods: patients with CF (F508del/F508del) (n = 425) 0 to 18 years old (11,8 ± 3,8 лет) We studied: BMI, and body composition (for children over 5 years old) before and after 1 year of targeted therapy. Was study the percentage ratio (%) of active cellular body mass (ACM), skeletal muscle mass (SMM) and fat mass (FM) by Z-score. Single nucleotide polymorphisms (SNPs) of the ACE gene (rs1799752), of the PPARGC1A gene (rs8192678), of the ACTN3 gene (rs1815739), of the PPARA gene (rs4253778) were tested by PCR and RFLP analysis. Results: Dynamics after a 1 year of targeted therapy, body weight in boys significant increased by 5.3 (±2.5) kg, height by 5.7 (±1.7) cm (p < 0,01), in girls by 4.5 (±1.9) kg, height by 4.8 (±1.3) cm (p < 0,01). In boys showed an increase in FM (%) from -0.23 to 0.13 SD (p = 0.04). In girls, the FM (%) increased from -0.15 to 0.08 SD (p = 0.02) and the % SMM decreased from 0.79 to 0.6 SD (p = 0.04). The GA genotype of the PPARGC1A gene tended to have decreased % ACM (-1.1-2 SD) (p=0.071) and very low % ACM (<-2.1 SD) (p = 0.062). Conclusion: An analysis of body composition in children with CF showed an increase in the proportion of fat mass after 1 year of taking the targeted drug.
Rare nucleotide sequence variants of pyroptosis-related genes in premature infants with bronchopulmonary dysplasia
Bronchopulmonary dysplasia (BPD) is a common respiratory disease in preterm infants caused by multifactorial etiology. Rare variants (MAF<0.005) of pyroptosis-related genes (CHMP7, NLRC4, NLRP1, NLRP2, NLRP3, NLRP6, NLRP7, NLRP9, NLRP10, NLRP12) were identified in 36 premature infants with BPD and 32 premature infants without BPD using the whole exome sequencing. Two previously undescribed in ClinVar missense variants of the NLRP7 (chr19-54939647-G-T) and NLRP2 (chr19-54981629-C-A) genes were found in the newborns with BPD. According to Data Interpretation Guidelines, the NLRP7 gene variant is assessed to be of uncertain significance, and the NLRP2 gene variant is likely to be benign.
Characteristics of a cohort of Russian patients with sceletal ciliopathys
The study presents clinical and genetic groups within a cohort of 45 Russian patients. We show six clinical groups with identified nucleotide sequence variants in 12 genes: DYNC2H1, DYNC2I2, IFT122, IFT80, IFT140, WDR19, WDR35, EVC, EVC2, CFAP410, OFD1, and CPLANE1. It is noted that 40 % of the cases belong to four types of thoracic dysplasia with short ribs, with or without polydactyly. Within this group, 61.1 % represent type 3, which is associated with the DYNC2H1 gene. Ultra-rare variants of skeletal ciliopathies have been identified.
Study of neurofibromatosis type 1 in the Republic of Bashkortostan – results and prospects
Introduction. Neurofibromatosis type 1 (NF1) is one of the most common hereditary tumor syndromes caused by NF1 gene mutations. For differential diagnostics and reliable diagnosis of NF1, finding NF1 gene mutation is crucial, which will allow for primary preimplantation and secondary prevention of NF1. Objective: to determine clinical, epidemiological and molecular features of NF1 in the Republic of Bashkortostan. Methods. Retrospective analysis of NF1 from the Republic of Bashkortostan, describing NF1 clinical manifestations. Blood was taken to isolate DNA samples. Results. NF1 prevalence in the republic was 13.5 per 100,000. The frequency of registration of neurofibromas (58 %), Lisch nodules (1 %), plexiform neurofibromas (7 %), optic nerve gliomas (6 %), and intellectual disability (14 %) is significantly lower than the global average for NF1. The molecular genetic analysis of DNA samples from patients revealed 14 different mutations in NF1 gene in 20 patients from 17 families. Conclusions. The frequency of registration of NF1 specific signs in patients from the republic is significantly lower than the world average, which indicates the need for dynamic examination of patients, the whole body MRI, consultations with psychologists and psychiatrists. It is promising to search for mutations in the NF1 gene in all patients.
Identification of a novel pathogenic variant in the BBS9 gene in three family members with Bardet-Biedl syndrome
Bardet-Biedl syndrome (BBS) is a rare genetic disorder from the group of ciliopathies, characterized by multi-organ involvement. This study presents the clinical and genetic characteristics of a family with BBS caused by a novel pathogenic variant in the BBS9 gene. A previously undescribed variant c.288del (p.Val97CysfsTer27) in the BBS9 gene was identified in homozygous state in three siblings with clinical manifestations of BBS and in heterozygous state in their parents. The main symptoms included retinitis pigmentosa, renal anomalies, obesity, delayed speech development and polydactyly. The results confirm the important role of the BBS9 gene in the pathogenesis of this syndrome.
Progressive familial intrahepatic cholestasis: сlinicalе features and genetic heterogeneity
Introduction. Progressive familial intrahepatic cholestasis (PFIC) is a genetically heterogeneous liver disease leading to cirrhosis and liver failure. Early diagnosis and a personalized treatment approach are essential. Methods. A total of 25 probands with PFIC were examined. A clinical and genetic analysis was performed, including targeted gene panel sequencing and whole-exome sequencing. Results. The most common form of the disease was PFIC type 2. The median age of disease onset was 1.5 months. The most frequent symptoms included cholestasis, hepatomegaly, pruritus, and hemorrhagic syndrome. A total of 19 pathogenic and 6 likely pathogenic variants were identified, including novel mutations in the ABCB11, USP53, MYO5B, ABCB4, and ATP8B1 genes. Conclusions. Genetic variant verification enables personalized therapy selection, including bile acid transporter inhibitors, and facilitates decision-making regarding liver transplantation timing.
Features of steroidogenesis gene variants in female patients with a burdened obstetric and gynecological history
In women with a complex obstetric and gynecological history, miscarriage is a predominant concern. Steroidogenesis plays a crucial role in female reproductive health. Different genes involved in this process, the polymorphism of which may be associated with the risk of pregnancy loss. We analyzed CYP21A2, HSD3B2, CYP17A1, STAR, CYP11A1, POR genes using NGS, PCR-RFLP and MLPA methods in 30 women with a history of miscarriage and 46 individuals in the control group. A total of 142 nucleotide sequence variants were identified in both coding and non-coding regions of these genes, with different clinical significance. Pathogenic variants in the CYP21A2 gene were detected in 30 % of women with miscarriage compared to 6.5 % in the control group. One missense variant (rs17853284) with a potential pathogenic effect was identified in the POR gene. These findings suggest that heterozygous carriage in steroidogenesis-related genes, particularly CYP21A2, requares further investigation as potential predictors of possible obstetric complications.
An Exhaustive Analysis of a Rare Case of Paternal Uniparental Isodisomy of Chromosome 16
Uniparental disomies (UPDs) are among the causes of imprinting disorders. Here, we describe the case of a patient, who presented syndromic phenotype, where anomalies in the methylation of the ZNF597 gene were detected by ONT sequencing. Our case demonstrates syndromic phenotype of a patient with paternal uniparental disomy of chromosome 16 as opposed to the previously described cases with a normal phenotype or with abnormal phenotypes caused by acquired homozygosity of pathogenic variants at autosomal recessive genes located on chromosome 16. Reporting such observations will help systematize data on the phenotypes of imprinting disorders in insufficiently studied imprinted regions, which include chromosome 16.
Analysis of the patterns of combinations of polymorphic variants in redox homeostasis genes associated with aging and longevity
The aim of the study was to identify associations with aging and longevity of combinations of polymorphic DNA loci in genes regulating cellular redox balance. It was found that combinations of alleles and genotypes of SOD2 (rs4880), GPX4 (rs713041), GSTP1 (rs1695) and KEAP1 (rs1048290) are associated with old age in men, while combinations of SOD2, KEAP1, NFE2L2 (rs6721961) and AKT1 (rs3803304) are associated with reduced chances of longevity.
The role of aphidicolin-sensitive fragile sites in iPSCs genetic instability
Introduction. One of the causes of genetic instability in iPSCs is replication stress (RS). RS leads to the formation of chromatid breaks and gaps in regions of constitutive fragile sites (cFS), which are «hotspots» for chromosomal rearrangements. The process of mitotic DNA synthesis (MiDAS) serves to restore genome integrity under RS and acts as a marker of cFS. Objective: mapping chromosomal breaks and MiDAS sites in iPSCs. Methods. RS was induced using aphidicolin and caffeine. MiDAS regions were detected by EdU incorporation at early mitotic stages. Differential staining was performed using DAPI and actinomycin D. Results. Three iPSC lines (P1L5, P12L3, P16L1) were analyzed. Among 800 mapped chromosomal breaks, 33 cFS were identified. Both previously described and iPSC-specific cFS were characterized. cFS co-localized with breakpoints of recurrent karyotypic abnormalities in iPSCs were identified. Conclusions. For the first time, a repertoire of cFS in iPSCs and their associations with recurrent rearrangements has been described.
Rare variants in the LEPR gene identified in three patients with severe early-onset obesity and hyperphagia
Congenital leptin receptor deficiency (LEPR) is a rare monogenic form of severe early-onset obesity. This study presents new pathogenic variants in the LEPR gene identified in Russian patients with early-onset severe obesity. Two rare variants were discovered: c.133_136dup in a homozygous state in two patients and a variant in a compound heterozygous state with a novel variant c.2590_2591del in a third patient. Both variants cause the synthesis of non-functional leptin receptors, which is characteristic of autosomal recessive LEPR deficiency. The results expand the spectrum of known LEPR variants and emphasize the importance of genetic testing when monogenic forms of obesity are suspected.
Hereditaty spastic paraplegias: new findings and rare phenotypes
Hereditary spastic paraplegias are characterized by prominent clinical and genetic heterogeneity. The number of forms with established genes (SPG numbered in the order of genes discovering) came up to 94; few more have individual titles based on gene name or phenotype. SPG scientific research and practical diagnostics are performed in RCMG using modern methods of DNA analysis, MPS panel in particular. In 2023, we set up a new panel including 179 genes: SPGs and numerous genocopies. By now, our SPG group counts 278 families with 36 different forms. More than half of 254 pathogenic variants detected in 36 genes were novel. Several cases found out in the last 4 years (period after Russian Society of Medical Genetics previous congress) are presented, recently discovered forms and atypical phenotypes among them.
Identification of hereditary forms of morbid obesity in children
Given the important role of obesity in the development of metabolic disorders, identifying pathogenic gene variants in children with severe obesity is a key task of endocrinology. Whole exome sequencing (WES) was performed in 59 children with morbid obesity and 30 variants were found in 16 genes that were clinically significant in 23 children, which amounted to 38.9% of the total sample, more than half of them were identified for the first time. The results of the study expand the understanding of the genetic structure of obesity in the Russian population.
Study of the effect of methylene blue on DNA breaks in Esсherichia coli cells using gel electrophoresis method
The method of gel electrophoresis of DNA was used to assess the extent of DNA damage in bacteria exposed to methylene blue (MB). Gel electrophoretic analysis of DNA integrity in Escherichia coli cells revealed that MB induces DNA breaks, with the level of fragmentation depending on its concentration.
Association study of polymorphisms of the glutathione s-transferase alpha 4 (GSTA4) gene and the risk of psoriasis: a pilot study
The aim of this pilot study was to investigate the associations between polymorphic variants of the GSTA4 gene and the risk of psoriasis. The study involved 474 patients with psoriasis and 470 controls, whose DNA samples were genotyped for the variants rs7496, rs17614871, rs12524274, rs316133, and rs2274760 of the GSTA4 gene using the MassArray-4 system. No statistically significant associations were found between these variants and the predisposition to the disease, either when comparing the overall groups or when stratifying by sex (p > 0.05). However, the GSTA4 CACCG haplotype was identified, which was associated with a decreased risk of psoriasis in men (pperm = 0.004). Although the studied variants of the GSTA4 gene do not exhibit individual effects on the risk of developing psoriasis, the relatively rare CACCG haplotype demonstrated a protective effect against the disease.
A study on the association between the single nucleotide polymorphisms rs17293632 and rs2033784 of the SMAD3 gene and the risk of bronchial asthma in children from the Kursk region
Various smooth muscle-specific genes and proteins, including SMAD3, play a crucial role in airway remodeling associated with bronchial asthma (BA), significantly impacting the pathogenesis of this condition. Our study revealed that both single nucleotide polymorphisms (SNPs) in the general population were linked to an increased risk of developing BA. Specifically, rs17293632 was associated with a p-value of 6.0 × 10-4, and rs2033784 had a p-value of 0.0019. Additionally, we identified an association between the rs17293632 polymorphism and the risk of developing BA in girls, with a p-value of 2.0 × 10-4. The influence of the rs2033784 polymorphism on the increased risk of developing BA in girls was also confirmed, with a p-value of 6.0 × 10-4.
Comorbidity of autosomal recessive diseases with developmental delay: а clinical case
Genetic diseases combined in a single patient can cause unusual and complex clinical manifestations that may have overlapping symptoms or different composite phenotypes. This article reviews a clinical case of comorbidity of two autosomal recessive diseases in a patient born in a consanguineous marriage. Full-exome sequencing revealed variants with unknown clinical significance – c.3585+1G>A (p.?) in the KIDINS220 associated with autosomal recessive ventriculomegaly and arthrogryposis, and the c.275A>C (p.Gln92Pro) in the CA2 associated with autosomal recessive type 3 osteopetrosis with renal tubular acidosis. Due to the overlapping symptoms described for these conditions (ventriculomegaly, hepatosplenomegaly, anemia, retinopathy, growth and developmental delay), Proband and his parents have been assigned to Sanger sequencing. We provide reasons for the reclassification of one of these genetic variants with increasing pathogenicity class.
Assessment of senior students’ satisfaction with teaching medical and clinical genetics at Kursk State Medical University
The article presents the results of a survey of students of the medical and pediatric faculties regarding the quality of the educational process. A survey of students was conducted after studying the components of Medical Genetics and Clinical Genetics within the discipline «Genetics, Medical Ecology» at the medical faculty, as well as the «Clinical Genetics at the pediatric faculty. The results indicated a high level of student satisfaction with the teaching of genetic disciplines at the Department of Biology, Medical Genetics, and Ecology of KSMU. This assessment provides valuable insights for enhancing the educational process.
Role of AID/APOBEC cytidine deaminases in genome destabilization in cancer: insights from a yeast test system
Uncontrolled expression of AID/APOBEC family cytidine deaminases is an important factor in genome destabilization during carcinogenesis. In normal cells, these enzymes deaminate cytosine to uracil in RNA or DNA during mRNA editing, defense against viruses, and immunoglobulin affinity maturation. Misregulation of AID/APOBEC gene expression results in non-specific deamination of genomic DNA and, consequently, increased mutagenesis. Somatic mutations induced by AID/APOBEC can trigger the process of carcinogenesis and contribute to the development of cancer cell resistance to therapy and increased tumor aggressiveness. A convenient approach to studying the mechanisms of AID/APOBEC cytidine deaminase-dependent mutagenesis is using of a heterologous expression system in yeast strains Saccharomyces cerevisiae carrying human cytidine deaminase genes. In this work, we constructed S. cerevisiae strains expressing the human APOBEC3A, APOBEC3B, and AID genes and the PmCDA gene from the sea lamprey Petromyzon marinus as a positive control. Using these strains, we identified specific amino acid substitutions that enhance or attenuate deaminase activity and demonstrated that recombination repair and base excision repair significantly affect the mutagenic activity of cytosine deaminases in the heterologous expression system. Our results confirm the efficiency of the developed model and open the way to study factors that can modify the activity of AID/APOBEC, which is of great importance for finding therapeutic and diagnostic methods for treating cancer and infectious diseases.
Cytogenetic monitoring using the buccal micronucleus cytome assay (BMCA)
The results of cytogenetic monitoring of the personnel of two enterprises of the Rosatom State Corporation and the child population using the buccal micronucleus cytome assay (BMCA) in our modification are presented. Its essence is in the quantitative analysis of the «quality» of epithelial cells of the buccal mucosa and determination of the index of accumulation of cytogenetic damage. The indicative standard values (INV) were adjusted when analyzing the cytogenetic status of 620 people. Methodological recommendations were published. The average values of the cytogenetic status end points of the personnel of both enterprises working under conditions of compliance with hygienic standards do not exceed the INV, but this excess was noted in individual employees in each of the examined groups. At both enterprises, in groups working under conditions of combined action of low-intensity radiation and chemicals a deterioration of the end points was noted; the index of accumulation of cytogenetic damage is 1.2-2.2 higher than in the comparison groups; there is also a higher proportion of people with excess of the IVB for a number of end points. Four-fold examination of the personnel confirmed the initial conclusion about the «territory of trouble», which indicates a stable impact of a set of production factors of the enterprise. In general, in the impact groups, the risk level of cytogenetic damage is determined as moderate. In children living near the examined enterprise, the frequency of cells with micronuclei does not exceed the established control of 1.1 %. The level of cytogenetic stress is determined as acceptable.
CETP gene polymorphism in Siberian populations
The present study was carried out within the framework of an actual direction, the task of which is to study the peculiarities of the population-genetic structure of the indigenous peoples of Siberia in genogeographical and biomedical aspects. The aim was to identify ethnic peculiarities in the distribution of polymorphic variants of the CETP gene (G1264A, rs5882) in Siberian populations. Using realtime PCR, the frequencies of the CETP 1264G allele associated with favorable blood lipid parameters were determined in samples of Yakuts, Dolgans, Nganasans, Tuvinians, Kazakhs of Altai, and Russians of Siberia. The increased frequency of the CETP 1264G allele in Tuvinians (48.5 %) compared to Caucasians was shown to be close to that in East Asian populations, while in Dolgans it was statistically significantly lowest (21.5 %) compared to the majority of the studied ethnic groups. The other samples do not have significant differences from the groups of Europeans described in the literature; however, Yakuts (27.3 % and 31.8 %), Nganasans (35.6 %), Kazakhs (31.4 %), and Russians (30.7 %) are statistically significantly separated from populations in China and Japan by lower CETP 1264G frequency values. In general, indigenous Siberian populations are intermediate between Caucasoid groups and East Asian populations in terms of CETP 1264G allele frequency. A high frequency of the CETP 1264G allele in Tuvinians was shown, while in the Dolgan population it is the lowest, which may indicate an increased risk of atherosclerosis.
Gene pool of Altai Kazakhs by Y-chromosome haplogroups
The gene pool of Kazakhs of the Altai Mountains living in the Kosh-Agach district was studied. Altai Kazakhs are distinguished by the frequency of haplogroups C2a1a, O2a2b1a2a1a1b1b2a1 and J2a2a1a1a. They fully correspond to the data of these haplogroups in the Naimans. The obtained results of their gene pool confirm the process of their formation on the basis of migrants from the territory of eastern Kazakhstan and Western Mongolia.
Two faces of DNMT3A-associated pathology
The syndromic disorders of neuropsychiatric development associated with DNMT3A mutations have been described relatively recently. Interestingly, two dissimilar phenotypes are associated with DNMT3A defects: Tatton-Brown-Rahman syndrome (with macrocephaly and tall stature) and an extremely rare Hein-Sproul-Jackson syndrome (with microcephaly and short stature). We have identified two patients corresponding to the clinical signs of these syndromes. Whole-exome sequencing revealed rare variants of the DNMT3A gene. Patient with Hein-Sproul-Jackson syndrome demonstrated previously undescribed clinical features.
Analysis of single nucleotide polymorphism of genes of the blood coagulation system FV (G1691A), ITGA2 (C807T) in patients with miscarriage
The article reports findings from a molecular genetic analysis conducted on women experiencing habitual miscarriage. The study evaluated the frequency of single nucleotide polymorphisms in the FV (G1691A) and ITGA2 (C807T) genes within the sample population. The results indicated that the heterozygous variant of the ITGA2 (C807T) gene was the most prevalent among the participants, whereas the heterozygous variant of the FV (G1691A) gene was observed less frequently. Notably, the occurrence of mutant homozygotes was not identified in this cohort.
Do we know everything about the KRAS gene?
The mutation status of MAPK-kinase signaling pathway genes plays an important role in anti-EGFR therapy. However not all tumors after diagnostics of RAS/BRAF genes have answered to anti-EGFR therapy. To search predictive markers for anti-EGFR therapy, 341 patients with colorectal cancer were examined. Frequent mutations in the KRAS, NRAS, and BRAF genes were detected in 200 (58.6 %) people. In addition, 4 rare mutations were detected. Also, it was found that the number of copies of the KRAS gene ≥ 9 is a predictive marker of resistance to anti-EGFR therapy.
On the 60th anniversary of the birth of Academician of the Russian Academy of Sciences Sergei Ivanovich Kutsev