A systematic review and standardized clinical validity assessment of genes involved in female reproductive failure

Genetic testing is becoming increasingly required at almost every stage of failed female reproduction/infertility. Nonetheless, clinical evidence for the majority of identified gene-disease relationships is ill-defined, thus leading to difficult gene variant interpretation and poor translation of existing knowledge into clinics. We aimed to identify the genes that have ever been implicated in monogenic female reproductive failure in humans and to classify the identified gene-disease relationship pairs using a standardized clinical validity assessment. A PubMed search following PRISMA guidelines was conducted on 20 September 2021 aiming to identify studies pertaining to genetic causes of phenotypes of female reproductive failure. The clinical validity of identified gene-disease pairs was assessed using standardized criteria, counting whether sufficient genetic and experimental evidence has been accumulated to consider a single gene 'characterized' for a single Mendelian disease. In total, 1256 articles were selected for the data extraction; 183 unique gene-disease pairs were classified spanning the following phenotypes: hypogonadotropic hypogonadism, ovarian dysgenesis, premature ovarian failure/insufficiency, ovarian hyperstimulation syndrome, empty follicle syndrome, oocyte maturation defect, fertilization failure, early embryonic arrest, recurrent hydatidiform mole, adrenal disfunction and Mullerian aplasia. Twenty-four gene-disease pairs showed definitive evidence, 36 - strong, 19 - moderate, 81 - limited and 23 - showed no evidence. Here, we provide comprehensive, systematic and timely information on the genetic causes of female infertility. Our classification of genetic causes of female reproductive failure will facilitate the composition of up-to-date guidelines on genetic testing in female reproduction, the development of diagnostic gene panels and the advancement of reproductive decision-making.publishersversionPeer reviewe

Management of Pregnancy with Cervical Shortening: Real-Life Clinical Challenges

Funding Information: The study was funded by the Fundamental and Applied Research Projects grant of The Latvian Council of Science (Project No. 2020/1-0042 to DR). The funders had no role in the study design, data collection or analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: © 2023 by the authors.Background and Objectives: Preterm birth is the leading cause of neonatal mortality worldwide and may be responsible for lifelong morbidities in the survivors. Cervical shortening is one of the common pathways to preterm birth associated with its own diagnostic and management challenges. The preventive modalities that have been tested include progesterone supplementation and cervical cerclage and pessaries. The study aimed to assess the management strategies and outcomes in a group of patients with a short cervix during pregnancy or cervical insufficiency. Materials and Methods: Seventy patients from the Riga Maternity Hospital in Riga, Latvia, were included in the prospective longitudinal cohort study between 2017 and 2021. Patients were treated with progesterone, cerclage, and/or pessaries. The signs of intra-amniotic infection/inflammation were assessed, and antibacterial therapy was given when the signs were positive. Results: The rates of PTB were 43.6% (n = 17), 45.5% (n = 5), 61.1% (n = 11), and 50.0% (n = 1) in progesterone only, cerclage, pessary, and cerclage plus pesssary groups, respectively. The progesterone therapy was associated with a reduced preterm birth risk (x2(1) = 6.937, p = 0.008)), whereas positive signs of intra-amniotic infection/inflammation significantly predicted the risk of preterm birth (p = 0.005, OR = 3.82, 95% [CI 1.31–11.11]). Conclusions: A short cervix and bulging membranes, both indicators of intra-amniotic infection/inflammation, are the key risk factors in preterm birth risk predictions. Progesterone supplementation should remain at the forefront of preterm birth prevention. Among patients with a short cervix and especially complex anamnesis, the preterm rates remain high. The successful management of patients with cervical shortening lies between the consensus-based approach for screening, follow-up, and treatment on the one side and personalising medical therapy on the other.publishersversionPeer reviewe

Higher CTX-M, TEM, and SHV extended-spectrum beta-lactamase plasmid gene combination frequency in ESBL producing Klebsiella pneumoniae compared with ESBL producing Escherichia coli

publishersversionPeer reviewe

Association of BMP4 polymorphisms with non-syndromic cleft lip with or without cleft palate and isolated cleft palate in Latvian and Lithuanian populations

Cleft lip with or without cleft palate (CLP and CL, respectively) and isolated cleft palate (CP) represent one of the most common human birth defects, with a prevalence of approximately 1 in 300-2500 depending on the population. Formation of non-syndromic CL/CLP and CP arises from the interaction of environmental and genetic factors. The objective of this study was to investigate the association between the BMP4 gene (encoding bone morphogenetic protein 4) and non-syndromic CL/CLP and CP in order to clarify the role of this gene in the aetiology of the malformation in Latvian and Lithuanian populations. We genotyped three markers of the BMP4 gene (rs17563, rs2071047 and rs1957860) in order to perform single marker and haplotype association analyses for Latvian and Lithuanian non-syndromic CL/CLP and CP patients and controls. Transmission disequilibrium test was also conducted for Latvian and Lithuanian proband-parent trios. The case-control analysis revealed that SNP rs2071047 allele A was associated with a decreased risk of CL/CLP in the Latvian population, which was confirmed by the haplotype analysis. A modest association was detected between SNP rs1957860 and CP in the Lithuanian population, where allele C was associated with a decreased risk of this cleft phenotype, corroborating haplotype analysis data. Our findings support a role of the BMP4 gene in the aetiology of non-syndromic CL/CLP and CP in the studied populations.publishersversionPeer reviewe

Lack of Association between Rs2067474 Polymorphism in the Histamine Receptor H2 Gene and Gastric Cancer in Latvian Population

Funding Information: The study was partly supported by the Latvian Government Research Programme BIOMEDICINE 2014–2017 Project Nr. 4 “Study of gastric cancer mortality reduction capability in Latvia”. Publisher Copyright: © 2018 Georgijs Moisejevs et al.Histamine has an important role in the process of the gastric mucosa inflammation acting via histamine receptor H2 (encoded by the gene HRH2). Single nucleotide polymorphism of the enhancer element of HRH2 gene promoter rs2067474 (1018G>A)may be associated with changes of expression of the receptor. We attempted to clarify the association of this polymorphism with gastric cancer and/or atrophic gastritis in the Latvian (Caucasian) population. The study group consisted of 121 gastric cancer patients and 650 patients with no evidence of gastric neoplasia on upper gastrointestinal endoscopy. Genotyping for rs2067474 was performed with the TaqMan probe-based system using a commercially available probe for RT-PCR. The frequency of the A allele in the gastric cancer group was 0.41% and in the control group - 1.54% (p = 0.231). No significant differences were found comparing genotypes between gastric cancer versus control patients (OR = 0.236, CI95% = 0.030-1.896), patients with (n = 165) versus without (n = 485) gastric metaplastic lesions (OR = 0.854, CI95% = 0.288-2.540) and patients with (n = 297) and without (n = 353) gastric atrophic lesions (OR = 1.145, CI95% = 0.451-2.906). Our findings suggest that the HRH2 -1018G>A polymorphism (rs2067474) is neither associated with gastric cancer nor the grade of atrophic gastritis in the Latvian (Caucasian) population.Peer reviewe

Role of Single Nucleotide Variants in FSHR, GNRHR, ESR2 and LHCGR Genes in Adolescents with Polycystic Ovary Syndrome

Funding Information: Funding: The study was financially supported by a Riga Stradins University internal research grant. Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Background: Polycystic ovary syndrome (PCOS) is the most common endocrinopathy in women, affecting up to 16.6% of reproductive-age women. PCOS symptoms in adolescents comprise oligomenorrhoea/amenorrhoea and biochemical and/or clinical hyperandrogenism. Long-term health risks of PCOS patients include infertility, metabolic syndrome, type 2 diabetes and cardiovascular disease. Genetic factors have been proven to play a role in development of the syndrome and its symptoms. Objective: To investigate single nucleotide variants (SNVs) in the GNRHR, ESR2, LHCGR and FSHR genes in adolescent patients with PCOS and their association with PCOS symptoms. Methods: We conducted a cross-sectional study comprising of 152 adolescents: 63 patients with PCOS, 22 patients at risk of developing PCOS and 67 healthy controls. Participants were recruited from out-patients attending a gynaecologist at the Children’s Clinical University Hospital, Riga, Latvia, between January 2017 and December 2020. Genomic DNA was extracted from whole blood, and SNVs in the GNRHR, ESR2, LHCGR and FSHR genes were genotyped. The distributions of SNV genotypes were compared among the three groups and genotype-phenotype associations within the PCOS group were evaluated. Results: No statistically significant differences were found in the distributions of genotypes for GNRHR (rs104893837), ESR2 (rs4986938), LHCGR (rs2293275) and FSHR (rs6166, rs6165, rs2349415) among PCOS patients, risk patients and healthy controls. Within the PCOS group, ESR2 rs4986938 minor allele homozygous patients had a significantly higher level of total testosterone than major allele homozygous patients and heterozygous patients. A significantly higher total testosterone level was also observed in PCOS patients carrying the LHCGR rs2293275 minor allele compared with major allele homozygous patients. Conclusions: The SNVs ESR2 rs4986938 and LHCGR rs2293275 play a role in the phenotypic characteristics of PCOS. To fully uncover their influence on the development of PCOS and its symptoms, further studies of larger cohorts and a follow up of this study sample through to adulthood are required. Furthermore, studies of adolescent PCOS patients conducted prior to the latest European Society of Human Reproduction and Embryology (ESHRE) criteria (2018) should be re-evaluated as the study groups might include risk patients according to these updated criteria, thereby potentially significantly impacting the published results.publishersversionPeer reviewe

Performance comparison of two whole genome amplification techniques in frame of multifactor preimplantation genetic testing

Publisher Copyright: © 2018, The Author(s).Purpose: To compare multiple displacement amplification and OmniPlex whole genome amplification technique performance during array comparative genome hybridization (aCGH), Sanger sequencing, SNaPshot and fragment size analysis downstream applications in frame of multifactor embryo preimplantation genetic testing. Methods: Preclinical workup included linked short tandem repeat (STR) marker selection and primer design for loci of interest. It was followed by a family haplotyping, after which an in vitro fertilization preimplantation genetic testing (IVF-PGT) cycle was carried out. A total of 62 embryos were retrieved from nine couples with a confirmed single gene disorder being transmitted in their family with various inheritance traits—autosomal dominant (genes—ACTA2, HTT, KRT14), autosomal recessive (genes—ALOX12B, TPP1, GLB1) and X-linked (genes—MTM1, DMD). Whole genome amplification (WGA) for the day 5 embryo trophectoderm single biopsies was carried out by multiple displacement amplification (MDA) or polymerase chain reaction (PCR)-based technology OmniPlex and was used for direct (Sanger sequencing, fragment size analysis, SNaPshot) and indirect mutation assessment (STR marker haplotyping), and embryo aneuploidy testing by array comparative genome hybridization (aCGH). Results: Family haplotyping revealed informative/semi-informative microsatellite markers for all clinical cases for all types of inheritance. Indirect testing gave a persuasive conclusion for all embryos assessed, which was confirmed through direct testing. The overall allele dropout (ADO) rate was higher for PCR-based WGA, and MDA shows a better genomic recovery scale. Five euploid embryos were subjected to elective single embryo transfer (eSET), which resulted in four clinical pregnancies and birth of two healthy children, which proved free of disease causative variants running in the family postnataly. Conclusions: A developed multifactor PGT protocol can be adapted and applied to virtually any genetic condition and is capable of improving single gene disorder preimplantation genetic testing in a patient-tailored manner thus increasing pregnancy rates, saving costs and increasing patient reliability.publishersversionPeer reviewe

Interaction between IRF6 and TGFA Genes Contribute to the Risk of Nonsyndromic Cleft Lip/Palate

Previous evidence from tooth agenesis studies suggested IRF6 and TGFA interact. Since tooth agenesis is commonly found in individuals with cleft lip/palate (CL/P), we used four large cohorts to evaluate if IRF6 and TGFA interaction contributes to CL/P. Markers within and flanking IRF6 and TGFA genes were tested using Taqman or SYBR green chemistries for case-control analyses in 1,000 Brazilian individuals. We looked for evidence of gene-gene interaction between IRF6 and TGFA by testing if markers associated with CL/P were overtransmitted together in the case-control Brazilian dataset and in the additional family datasets. Genotypes for an additional 142 case-parent trios from South America drawn from the Latin American Collaborative Study of Congenital Malformations (ECLAMC), 154 cases from Latvia, and 8,717 individuals from several cohorts were available for replication of tests for interaction. Tgfa and Irf6 expression at critical stages during palatogenesis was analyzed in wild type and Irf6 knockout mice. Markers in and near IRF6 and TGFA were associated with CL/P in the Brazilian cohort (p<10-6). IRF6 was also associated with cleft palate (CP) with impaction of permanent teeth (p<10-6). Statistical evidence of interaction between IRF6 and TGFA was found in all data sets (p = 0.013 for Brazilians; p = 0.046 for ECLAMC; p = 10-6 for Latvians, and p = 0.003 for the 8,717 individuals). Tgfa was not expressed in the palatal tissues of Irf6 knockout mice. IRF6 and TGFA contribute to subsets of CL/P with specific dental anomalies. Moreover, this potential IRF6-TGFA interaction may account for as much as 1% to 10% of CL/P cases. The Irf6-knockout model further supports the evidence of IRF6-TGFA interaction found in humans. © 2012 Letra et al

Risk Factors that Determine Less Favourable Hospitalisation Course and Outcome in Patients with ESBL Producing Enterobacteriaceae Infection : Preliminary Results

Publisher Copyright: © 2016 by Vita Skuja. Copyright: Copyright 2016 Elsevier B.V., All rights reserved.Hospitalisation course and outcome for patients with extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae infection is less favourable due to extensive antibacterial resistance. This study was conducted to identify possible risk factors that could influence the hospitalisation course and outcome in these patients. The study protocol included demographic, clinical, hospitalisation, bacteriological and plasmid genetic data. The preliminary study results showed that hospitalisation course and outcome was less favourable for internal medicine profile patients with ESBL producing bacteria, TEM gene presence in the bacterial plasmid genome, patient age < 65 years and patients with infectious and musculoskeletal diseases. The study includes preliminary data only and further studies should be carried out to verify the suggested risk factors.publishersversionPeer reviewe

Identification of Candidate Genes Involved in the Etiology of Non-Syndromic Cleft Lip with or without Cleft Palate and Isolated Cleft Palate. Summary of the Doctoral Thesis

Promocijas darbs izstrādāts Latvijas Biomedicīnas pētījumu un studiju centrā, Rīga, Latvija un Molekulārās ģenētikas zinātniskā laboratorijā, Rīgas Stradiņa universitāte, Rīga, Latvija, sadarbībā ar Pitsburgas Universitāti, Pitsburga, ASV un Tartu Universitāti, Tartu, Igaunija. Aizstāvēšana: 2013. gada 29. aprīlī plkst. 15.00 Rīgas Stradiņa universitātes Teorētiskās medicīnas Promocijas padomes atklātā sēdē Rīgā, Dzirciema ielā 16, Hipokrāta auditorijā.Lūpas šķeltne ar/bez aukslēju šķeltnes un izolēta aukslēju šķeltne (LŠ/LŠ+AŠ/AŠ) ir viens no visbiežāk sastopamajiem iedzimtajiem defektiem visā pasaulē, ar prevalenci Eiropas populācijā aptuveni 1 no 700 jaundzimušajiem. Indivīdiem ar LŠ/LŠ+AŠ/AŠ nepieciešama multidisciplināra aprūpe visā dzīves laikā, arī pēc ķirurģiskas operācijas. Lūpas šķeltne ar/bez aukslēju šķeltnes un izolēta aukslēju šķeltne ir saistīta ne tikai ar personas runas, dzirdes traucējumiem, zobu attīstības, bet arī ar izskata un psiholoģiskām problēmām. Tiek uzskatīts, ka indivīdiem ar LŠ/LŠ+AŠ/AŠ, ir paaugstināts sirds-asinsvadu slimību un audzēju saslimstības un mirstības risks, salīdzinot ar veseliem indivīdiem. Neskatoties uz iespēju ķirurģiski labot šo defektu, mūsdienās LŠ/LŠ+AŠ/AŠ ir kļuvusi par vienu no svarīgām sabiedrības veselības problēmām visā pasaulē. LŠ/LŠ+AŠ/AŠ veidojas, mijiedarbojoties ārējās vides faktoriem un ģenētiskajiem faktoriem. Pēdējie pētījumi liecina, ka aptuveni 2-14 gēni varētu būt iesaistīti nesindromālo LŠ/LŠ+AŠ/AŠ veidošanā. Šajā pētījumā tika veikta gadījuma-kontroles analīze un ģimenes asociācijas tests, lai identificētu iespējamos kandidātgēnus, kuri varētu būt iesaistīti nesindromālo lūpas šķeltnes ar/bez aukslēju šķeltņu un izolētas aukslēju šķeltnes attīstībā Latvijas populācijā. Mūsu pētījumā iegūtie rezultāti atklāja ļoti augstu saistību starp FGFR1, WNT3, SKI, BMP4 un IRF6 gēniem un nesindromālajām LŠ/LŠ+AŠ un AŠ, kā arī norāda uz iespējamo saistību starp 19q13 lokusu un nesindromālajām LŠ/LŠ+AŠ. Šie rezultāti turpina apstiprināt minēto gēnu nozīmi nesindromālo lūpas ar/bez aukslēju šķeltņu un izolētas aukslēju šķeltnes attīstībā eiropiešiem. Šis ir pirmais tik liela mēroga pētījums, kas ir veltīts nesindromālo LŠ/LŠ+AŠ/AŠ kandidātgēnu analīzei Latvijā. Pētījumā iegūtie rezultāti ir vērā ņemams ieguldījums šīs sarežģītās patoloģijas izpratnē un iespējamo gēnu ietekmes izvērtēšanā slimības izraisīšanā.Promocijas darbs veikts ar Eiropas sociālā fonda projekta “Atbalsts doktorantiem studiju programmas apguvei un zinātniskā grāda ieguvei Rīgas Stradiņa universitātē” finansiālu atbalst