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Miluna-Meldere S, Rostoka D, Broks R, Viksne K, Ciematnieks R, Skadins I, Kroica J. The Effects of Nicotine Pouches and E-Cigarettes on Oral Microbes: A Pilot Study. Microorganisms 2024; 12:1514. [PMID: 39203357 PMCID: PMC11356086 DOI: 10.3390/microorganisms12081514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/19/2024] [Accepted: 07/22/2024] [Indexed: 09/03/2024] Open
Abstract
It remains uncertain whether nicotine pouches and electronic cigarettes alter the oral environment and result in a high presence of periodontopathogenic bacteria in saliva, compared to that among cigarette users or non-tobacco users. In this study, saliva samples were collected from respondents using nicotine pouches, electronic cigarettes, and conventional cigarettes, alongside a control group of non-tobacco users. Polymerase chain reaction was used to identify clinical isolates of the following periodontal bacteria: Porphyromonas gingivalis, Tannerella forsythia, Prevotella intermedia, Fusobacterium nucleatum, Fusobacterium periodonticum, Porphyromonas endodontalis, and Rothia mucilaginosa. The presence of some periodontal pathogens was detected in the saliva samples from users of nicotine pouches, electronic cigarettes, and conventional cigarettes but not in samples taken from the control group. Therefore, the initial results of this pilot study suggest that the presence of periodontopathogenic bacteria in the saliva of nicotine pouch and electronic cigarette users could alter the oral microbiome, leading to periodontal diseases. However, further quantitative investigation is needed.
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Affiliation(s)
| | - Dagnija Rostoka
- Department of Biology and Microbiology, Riga Stradins University, LV-1007 Riga, Latvia; (R.B.); (I.S.); (J.K.)
| | - Renars Broks
- Department of Biology and Microbiology, Riga Stradins University, LV-1007 Riga, Latvia; (R.B.); (I.S.); (J.K.)
| | - Kristine Viksne
- Institute on Oncology and Molecular Genetics, Riga Stradins University, LV-1007 Riga, Latvia; (K.V.); (R.C.)
| | - Rolands Ciematnieks
- Institute on Oncology and Molecular Genetics, Riga Stradins University, LV-1007 Riga, Latvia; (K.V.); (R.C.)
| | - Ingus Skadins
- Department of Biology and Microbiology, Riga Stradins University, LV-1007 Riga, Latvia; (R.B.); (I.S.); (J.K.)
| | - Juta Kroica
- Department of Biology and Microbiology, Riga Stradins University, LV-1007 Riga, Latvia; (R.B.); (I.S.); (J.K.)
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Svikle Z, Paramonova N, Siliņš E, Pahirko L, Zariņa L, Baumane K, Petrovski G, Sokolovska J. DNA Methylation Profiles of PSMA6, PSMB5, KEAP1, and HIF1A Genes in Patients with Type 1 Diabetes and Diabetic Retinopathy. Biomedicines 2024; 12:1354. [PMID: 38927561 PMCID: PMC11202151 DOI: 10.3390/biomedicines12061354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
We explored differences in the DNA methylation statuses of PSMA6, PSMB5, HIF1A, and KEAP1 gene promoter regions in patients with type 1 diabetes and different diabetic retinopathy (DR) stages. Study subjects included individuals with no DR (NDR, n = 41), those with non-proliferative DR (NPDR, n = 27), and individuals with proliferative DR or those who underwent laser photocoagulation (PDR/LPC, n = 46). DNA methylation was determined by Zymo OneStep qMethyl technique. The methylation of PSMA6 (NDR 5.9 (3.9-8.7) %, NPDR 4.5 (3.8-5.7) %, PDR/LPC 6.6 (4.7-10.7) %, p = 0.003) and PSMB5 (NDR 2.2 (1.9-3.7) %, NPDR 2.2 (1.9-3.0) %, PDR/LPC 3.2 (2.5-7.1) %, p < 0.01) differed across the groups. Consistent correlations were observed between the methylation levels of HIF1A and PSMA6 in all study groups. DNA methylation levels of PSMA6, PSMB5, and HIF1A genes were positively correlated with the duration of diabetes, HbA1c, and albuminuria in certain study groups. Univariate regression models revealed a significant association between the methylation level z-scores of PSMA6, PSMB5, and HIF1A and severe DR (PSMA6: OR = 1.96 (1.15; 3.33), p = 0.013; PSMB5: OR = 1.90 (1.14; 3.16), p = 0.013; HIF1A: OR = 3.19 (1.26; 8.06), p = 0.014). PSMB5 remained significantly associated with DR in multivariate analysis. Our findings suggest significant associations between the severity of DR and the DNA methylation levels of the genes PSMA6, PSMB5, and HIF1A, but not KEAP1 gene.
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Affiliation(s)
- Zane Svikle
- Faculty of Medicine, University of Latvia, Jelgavas Street 3, LV 1004 Riga, Latvia; (Z.S.); (L.Z.); (K.B.)
| | - Natalia Paramonova
- Institute of Biology, University of Latvia, Jelgavas Street 1, LV 1004 Riga, Latvia;
| | - Emīls Siliņš
- Faculty of Physics, Mathematics and Optometry, University of Latvia, Jelgavas Street 3, LV 1004 Riga, Latvia; (E.S.); (L.P.)
| | - Leonora Pahirko
- Faculty of Physics, Mathematics and Optometry, University of Latvia, Jelgavas Street 3, LV 1004 Riga, Latvia; (E.S.); (L.P.)
| | - Līga Zariņa
- Faculty of Medicine, University of Latvia, Jelgavas Street 3, LV 1004 Riga, Latvia; (Z.S.); (L.Z.); (K.B.)
- Ophthalmology Department, Riga East University Hospital, Hipokrata Street 2, LV 1038 Riga, Latvia
| | - Kristīne Baumane
- Faculty of Medicine, University of Latvia, Jelgavas Street 3, LV 1004 Riga, Latvia; (Z.S.); (L.Z.); (K.B.)
- Ophthalmology Department, Riga East University Hospital, Hipokrata Street 2, LV 1038 Riga, Latvia
| | - Goran Petrovski
- Center of Eye Research and Innovative Diagnostics, Department of Ophthalmology, Oslo University Hospital, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway;
| | - Jelizaveta Sokolovska
- Faculty of Medicine, University of Latvia, Jelgavas Street 3, LV 1004 Riga, Latvia; (Z.S.); (L.Z.); (K.B.)
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Gudra D, Valdovska A, Kairisa D, Galina D, Jonkus D, Ustinova M, Viksne K, Kalnina I, Fridmanis D. Genomic diversity of the locally developed Latvian Darkheaded sheep breed. Heliyon 2024; 10:e31455. [PMID: 38807890 PMCID: PMC11130721 DOI: 10.1016/j.heliyon.2024.e31455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024] Open
Abstract
The Latvian Darkheaded is the only locally developed sheep breed. The breed was formed at the beginning of the 20th century by crossing local coarse-wooled sheep with the British Shropshire and Oxfordshire breeds. The breed was later improved by adding Ile-de-France, Texel, German blackheads, and Finnsheep to achieve higher prolificacy and better meat quality. Previous studies have reported the Latvian Darkheaded sheep to be closely related to Estonian and Lithuanian Blackface breeds, according to microsatellite data. To expand our knowledge of the genetic resources of the Latvian Darkheaded breed, we conducted a whole-genome resequencing analysis on 40 native sheep. The investigation showed that local sheep harbor genetic diversity levels similar to those observed among other improved breeds of European origin, including Charollais and Suffolk. Genome-wide nucleotide diversity (π) in Latvian Darkheaded sheep was 3.91 × 10-3, whereas the average observed heterozygosity among the 40 animals was 0.267 and 0.438 within the subsample of unrelated individuals. The Ne has rapidly decreased to 200 ten generations ago with a recent drop to Ne 73 four generations ago. However, inbreeding levels based on runs of homozygosity were, on average, low, with FROH ranging between 0.016 and 0.059. The analysis of the genomic composition of the breed confirmed shared ancestry with sheep of British origin, reflecting the history of the breed. Nevertheless, Latvian Darkheaded sheep were genetically separable. The contemporary Latvian Darkheaded sheep population is genetically diverse with a low inbreeding rate. However, further development of breed management programs is necessary to prevent an increase in inbreeding, loss of genetic diversity, and depletion of breed-specific genetic resources, ensuring the preservation of the native Latvian Darkheaded sheep.
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Affiliation(s)
- Dita Gudra
- Latvian Biomedical Research and Study Centre, Riga, LV, 1067, Latvia
| | - Anda Valdovska
- Latvia University of Life Sciences and Technologies, Jelgava, LV, 3001, Latvia
| | - Daina Kairisa
- Latvia University of Life Sciences and Technologies, Jelgava, LV, 3001, Latvia
| | - Daiga Galina
- Latvia University of Life Sciences and Technologies, Jelgava, LV, 3001, Latvia
| | - Daina Jonkus
- Latvia University of Life Sciences and Technologies, Jelgava, LV, 3001, Latvia
| | - Maija Ustinova
- Latvian Biomedical Research and Study Centre, Riga, LV, 1067, Latvia
| | - Kristine Viksne
- Latvian Biomedical Research and Study Centre, Riga, LV, 1067, Latvia
| | - Ineta Kalnina
- Latvian Biomedical Research and Study Centre, Riga, LV, 1067, Latvia
| | - Davids Fridmanis
- Latvian Biomedical Research and Study Centre, Riga, LV, 1067, Latvia
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4
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Gudra D, Valdovska A, Jonkus D, Kairisa D, Galina D, Ustinova M, Viksne K, Fridmanis D, Kalnina I. Genetic characterization of the Latvian local goat breed and genetic traits associated with somatic cell count. Animal 2024; 18:101154. [PMID: 38703755 DOI: 10.1016/j.animal.2024.101154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 05/06/2024] Open
Abstract
The Latvian local goat (LVK) breed represents the only native domestic goat breed in Latvia, but its limited population places it within the endangered category. However, the LVK breed has not yet undergone a comprehensive genetic characterization. Therefore, we completed whole genome sequencing to reveal the genetic foundation of the LVK breed while identifying genetic traits linked to the somatic cell count (SCC) levels. The study included 40 genomes of LVK goats sequenced to acquire at least 35x or 10x coverage. A Principal component analysis, a genetic distance tree, and an admixture analysis showed LVK's similarity to some European breeds, such as Finnish Landrace, Alpine, and Saanen, which aligns with the breed's history. An analysis of genome-wide heterozygosity, nucleotide diversity, and LD analysis indicated that the LVK population exhibits substantial levels of genetic diversity. LVK genome was dominated by short runs of homozygosity (ROHs, ≤ 500 kb) with a median length of 25 kb. With FROH 2.49%, average inbreeding levels were low; however, FROH ranged broadly from 0.13 to 12.2%. With the exception of one pure-blood breeding buck exhibiting FROH of 9.3% and FSNP of 8.5%, animals with at least 66% LVK ancestry showed moderate or no inbreeding. Overall, this study demonstrated that the LVK goats can be differentiated from imported breeds, although the population has a complex genetic structure. We were able to identify potential genetic traits associated with SCC levels, although the kinship of the animals and the heterogenic substructure of the population might have largely influenced the association analysis. We identified 26 genetic variants associated with SCC levels, which included the potentially relevant SNP rs662053371 in the OSBPL8 gene, indicating a potential signal linked to lipid metabolism in goats. To conclude, these findings present valuable insight into the genetic structure of the LVK breed for the conservation of local genetic resources.
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Affiliation(s)
- D Gudra
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - A Valdovska
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, Helmana iela 8 K, LV-3004 Jelgava, Latvia; Scientific Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia.
| | - D Jonkus
- Faculty of Agriculture, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia
| | - D Kairisa
- Faculty of Agriculture, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia
| | - D Galina
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, Helmana iela 8 K, LV-3004 Jelgava, Latvia; Scientific Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia
| | - M Ustinova
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - K Viksne
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - D Fridmanis
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - I Kalnina
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
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Upmale-Engela S, Vaivode I, Peculis R, Litvina H, Zake T, Skesters A, Gogins D, Rovite V, Konrade I. Genetic and Environmental Factors in Autoimmune Thyroid Disease: Exploring Associations with Selenium Levels and Novel Loci in a Latvian Cohort. Curr Issues Mol Biol 2024; 46:2553-2565. [PMID: 38534778 DOI: 10.3390/cimb46030162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/03/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024] Open
Abstract
The interplay of genetic, immune and environmental factors strongly contributes to the development of autoimmune thyroid disease (AITD), which can be classified as Graves' disease (GD) or Hashimoto thyroiditis (HT). One of the most studied exogenous factors in the pathogenesis of AITD is selenium, which, in the form of selenoproteins, strengthens the antioxidative defence system of thyroid cells against superoxide production. Furthermore, it modulates inflammatory cytokine release and autoantibody production. The aim of this study was to assess the associations of genetic factors with selenium levels in a cohort of adults with HT and GD and healthy controls from Latvia. A total of 148 GD patients, 102 HT patients and 2442 control participants were included in the study. The genotypes were determined using genome-wide genotyping; imputation was carried out using the TOPMed r2 imputation panel; and association analysis was performed with PLINK v1.90b7. We found three loci associated with GD (LSAMP, HNRNPA3P5, and NTN1) and one locus associated with HT (VAT1L); furthermore, one locus was associated with a serum selenium concentration > 80 µg/L (LINC01544/RNF152/PIGN). The detected associations could be attributed to population-specific effects or unknown stratification in our cohort, and further assessment of these results is required to explain the relationships of genetic traits with AITD and other phenotypes.
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Affiliation(s)
| | - Ieva Vaivode
- Department of Internal Medicine, Riga Stradins University, LV-1007 Riga, Latvia
| | - Raitis Peculis
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1-k1, LV-1067 Riga, Latvia
| | - Helena Litvina
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1-k1, LV-1067 Riga, Latvia
| | - Tatjana Zake
- Department of Internal Medicine, Riga Stradins University, LV-1007 Riga, Latvia
| | - Andrejs Skesters
- Laboratory of Biochemistry, Riga Stradins University, LV-1007 Riga, Latvia
| | - Deniss Gogins
- Department of Internal Medicine, Riga Stradins University, LV-1007 Riga, Latvia
| | - Vita Rovite
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1-k1, LV-1067 Riga, Latvia
| | - Ilze Konrade
- Department of Internal Medicine, Riga Stradins University, LV-1007 Riga, Latvia
- Department of Endocrinology, Riga East Clinical Hospital, Hipokrata Str. 2, LV-1038 Riga, Latvia
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6
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Brīvība M, Atava I, Pečulis R, Elbere I, Ansone L, Rozenberga M, Silamiķelis I, Kloviņš J. Evaluating the Efficacy of Type 2 Diabetes Polygenic Risk Scores in an Independent European Population. Int J Mol Sci 2024; 25:1151. [PMID: 38256224 PMCID: PMC10817091 DOI: 10.3390/ijms25021151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Numerous type 2 diabetes (T2D) polygenic risk scores (PGSs) have been developed to predict individuals' predisposition to the disease. An independent assessment and verification of the best-performing PGS are warranted to allow for a rapid application of developed models. To date, only 3% of T2D PGSs have been evaluated. In this study, we assessed all (n = 102) presently published T2D PGSs in an independent cohort of 3718 individuals, which has not been included in the construction or fine-tuning of any T2D PGS so far. We further chose the best-performing PGS, assessed its performance across major population principal component analysis (PCA) clusters, and compared it with newly developed population-specific T2D PGS. Our findings revealed that 88% of the published PGSs were significantly associated with T2D; however, their performance was lower than what had been previously reported. We found a positive association of PGS improvement over the years (p-value = 8.01 × 10-4 with PGS002771 currently showing the best discriminatory power (area under the receiver operating characteristic (AUROC) = 0.669) and PGS003443 exhibiting the strongest association PGS003443 (odds ratio (OR) = 1.899). Further investigation revealed no difference in PGS performance across major population PCA clusters and when compared with newly developed population-specific PGS. Our findings revealed a positive trend in T2D PGS performance, consistently identifying high-T2D-risk individuals in an independent European population.
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Affiliation(s)
- Monta Brīvība
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (I.A.); (I.E.); (L.A.); (J.K.)
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7
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Brīvība M, Silamiķele L, Birzniece L, Ansone L, Megnis K, Silamiķelis I, Pelcmane L, Borisova D, Rozenberga M, Jagare L, Elbere I, Kloviņš J. Gut Microbiome Composition and Dynamics in Hospitalized COVID-19 Patients and Patients with Post-Acute COVID-19 Syndrome. Int J Mol Sci 2024; 25:567. [PMID: 38203738 PMCID: PMC10779053 DOI: 10.3390/ijms25010567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/18/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
The gut microbiome plays a pivotal role in the modulation of host responses during viral infections, and recent studies have underscored its significance in the context of coronavirus disease 2019 (COVID-19). We aimed to investigate the dynamics and compositional changes in the gut microbiome of COVID-19 patients, addressing both the acute phase and the recovery process, with a particular focus on the emergence of post-COVID-19 conditions. Involving 146 COVID-19 patients and 110 healthy controls, this study employed a shotgun metagenomics approach for cross-sectional and longitudinal analyses with one- and three-month follow-ups. We observed a decline in taxonomic diversity among hospitalized COVID-19 patients compared to healthy controls, while a subsequent increase in alpha diversity was shown during the recovery process. A notable contribution of Enterococcus faecium was identified in the acute phase of the infection, accompanied by an increasing abundance of butyrate-producing bacteria (e.g., Roseburia, Lachnospiraceae_unclassified) during the recovery period. We highlighted a protective role of the Prevotella genus in the long-term recovery process and suggested a potential significance of population-specificity in the early gut microbiome markers of post-acute COVID-19 syndrome. Our study represents distinctive gut microbiome signatures in COVID-19, with potential diagnostic and prognostic implications, pinpointing potential modulators of the disease progression.
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Affiliation(s)
- Monta Brīvība
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (L.S.); (L.B.); (L.A.); (K.M.); (I.S.); (L.P.); (D.B.); (I.E.); (J.K.)
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8
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Elbere I, Orlovskis Z, Ansone L, Silamikelis I, Jagare L, Birzniece L, Megnis K, Leskovskis K, Vaska A, Turks M, Klavins K, Pirags V, Briviba M, Klovins J. Gut microbiome encoded purine and amino acid pathways present prospective biomarkers for predicting metformin therapy efficacy in newly diagnosed T2D patients. Gut Microbes 2024; 16:2361491. [PMID: 38868903 PMCID: PMC11178274 DOI: 10.1080/19490976.2024.2361491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/24/2024] [Indexed: 06/14/2024] Open
Abstract
Metformin is widely used for treating type 2 diabetes mellitus (T2D). However, the efficacy of metformin monotherapy is highly variable within the human population. Understanding the potential indirect or synergistic effects of metformin on gut microbiota composition and encoded functions could potentially offer new insights into predicting treatment efficacy and designing more personalized treatments in the future. We combined targeted metabolomics and metagenomic profiling of gut microbiomes in newly diagnosed T2D patients before and after metformin therapy to identify potential pre-treatment biomarkers and functional signatures for metformin efficacy and induced changes in metformin therapy responders. Our sequencing data were largely corroborated by our metabolic profiling and identified that pre-treatment enrichment of gut microbial functions encoding purine degradation and glutamate biosynthesis was associated with good therapy response. Furthermore, we identified changes in glutamine-associated amino acid (arginine, ornithine, putrescine) metabolism that characterize differences in metformin efficacy before and after the therapy. Moreover, metformin Responders' microbiota displayed a shifted balance between bacterial lipidA synthesis and degradation as well as alterations in glutamate-dependent metabolism of N-acetyl-galactosamine and its derivatives (e.g. CMP-pseudaminate) which suggest potential modulation of bacterial cell walls and human gut barrier, thus mediating changes in microbiome composition. Together, our data suggest that glutamine and associated amino acid metabolism as well as purine degradation products may potentially condition metformin activity via its multiple effects on microbiome functional composition and therefore serve as important biomarkers for predicting metformin efficacy.
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Affiliation(s)
- Ilze Elbere
- Translational Omics Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Zigmunds Orlovskis
- Translational Omics Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Laura Ansone
- Translational Omics Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ivars Silamikelis
- Translational Omics Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Lauma Jagare
- Translational Omics Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Liga Birzniece
- Translational Omics Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Kaspars Megnis
- Translational Omics Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Kristaps Leskovskis
- Faculty of Natural Sciences and Technology, Riga Technical University, Riga, Latvia
| | - Annija Vaska
- Institute of Biomaterials and Bioengineering, Faculty of Natural Sciences and Technology, Riga Technical University, Riga, Latvia
- Baltic Biomaterials Centre of Excellence, Headquarters at Riga Technical University, Riga, Latvia
| | - Maris Turks
- Faculty of Natural Sciences and Technology, Riga Technical University, Riga, Latvia
| | - Kristaps Klavins
- Institute of Biomaterials and Bioengineering, Faculty of Natural Sciences and Technology, Riga Technical University, Riga, Latvia
- Baltic Biomaterials Centre of Excellence, Headquarters at Riga Technical University, Riga, Latvia
| | - Valdis Pirags
- Translational Omics Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Monta Briviba
- Translational Omics Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Janis Klovins
- Translational Omics Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
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Fedulovs A, Pahirko L, Jekabsons K, Kunrade L, Valeinis J, Riekstina U, Pīrāgs V, Sokolovska J. Association of Endotoxemia with Low-Grade Inflammation, Metabolic Syndrome and Distinct Response to Lipopolysaccharide in Type 1 Diabetes. Biomedicines 2023; 11:3269. [PMID: 38137490 PMCID: PMC10740930 DOI: 10.3390/biomedicines11123269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 12/24/2023] Open
Abstract
The association of endotoxemia with metabolic syndrome (MS) and low-grade inflammation in type 1 diabetes (T1D) is little-studied. We investigated the levels of lipopolysaccharide (LPS), lipopolysaccharide-binding protein (LBP), endogenous anti-endotoxin core antibodies (EndoCAb IgG and IgM) and high-sensitivity C-reactive protein (hsCRP) in 74 T1D patients with different MS statuses and 33 control subjects. Within the T1D group, 31 patients had MS. These subjects had higher levels of LPS compared to patients without MS (MS 0.42 (0.35-0.56) or no MS 0.34 (0.3-0.4), p = 0.009). MS was associated with LPS/HDL (OR = 6.5 (2.1; 20.0), p = 0.036) and EndoCAb IgM (OR = 0.32 (0.11; 0.93), p = 0.036) in patients with T1D. LBP (β = 0.30 (0.09; 0.51), p = 0.005), EndoCAb IgG (β = 0.29 (0.07; 0.51), p = 0.008) and the LPS/HDL ratio (β = 0.19 (0.03; 0.41, p = 0.084) were significantly associated with log-transformed hsCRP in T1D. Higher levels of hsCRP and EndoCAb IgG were observed in T1D compared to the control (p = 0.002 and p = 0.091, respectively). In contrast to the situation in the control group, LPS did not correlate with LBP, EndoCAb, leukocytes or HDL in T1D. To conclude, endotoxemia is associated with low-grade inflammation, MS and a distinct response to LPS in T1D.
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Affiliation(s)
- Aleksejs Fedulovs
- Faculty of Medicine, University of Latvia, LV-1004 Riga, Latvia; (A.F.); (K.J.); (L.K.); (U.R.); (V.P.)
| | - Leonora Pahirko
- Faculty of Physics, Mathematics and Optometry, University of Latvia, LV-1004 Riga, Latvia; (L.P.); (J.V.)
| | - Kaspars Jekabsons
- Faculty of Medicine, University of Latvia, LV-1004 Riga, Latvia; (A.F.); (K.J.); (L.K.); (U.R.); (V.P.)
| | - Liga Kunrade
- Faculty of Medicine, University of Latvia, LV-1004 Riga, Latvia; (A.F.); (K.J.); (L.K.); (U.R.); (V.P.)
| | - Jānis Valeinis
- Faculty of Physics, Mathematics and Optometry, University of Latvia, LV-1004 Riga, Latvia; (L.P.); (J.V.)
| | - Una Riekstina
- Faculty of Medicine, University of Latvia, LV-1004 Riga, Latvia; (A.F.); (K.J.); (L.K.); (U.R.); (V.P.)
| | - Valdis Pīrāgs
- Faculty of Medicine, University of Latvia, LV-1004 Riga, Latvia; (A.F.); (K.J.); (L.K.); (U.R.); (V.P.)
- Pauls Stradins Clinical University Hospital, LV-1002 Riga, Latvia
| | - Jelizaveta Sokolovska
- Faculty of Medicine, University of Latvia, LV-1004 Riga, Latvia; (A.F.); (K.J.); (L.K.); (U.R.); (V.P.)
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10
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Kalnina I, Gudra D, Silamikelis I, Viksne K, Roga A, Skinderskis E, Fridmanis D, Klovins J. Variations in the Relative Abundance of Gut Bacteria Correlate with Lipid Profiles in Healthy Adults. Microorganisms 2023; 11:2656. [PMID: 38004667 PMCID: PMC10673050 DOI: 10.3390/microorganisms11112656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/04/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
The gut microbiome is a versatile system regulating numerous aspects of host metabolism. Among other traits, variations in the composition of gut microbial communities are related to blood lipid patterns and hyperlipidaemia, yet inconsistent association patterns exist. This study aims to assess the relationships between the composition of the gut microbiome and variations in lipid profiles among healthy adults. This study used data and samples from 23 adult participants of a previously conducted dietary intervention study. Circulating lipid measurements and whole-metagenome sequences of the gut microbiome were derived from 180 blood and faecal samples collected from eight visits distributed across an 11-week study. Lipid-related variables explained approximately 4.5% of the variation in gut microbiome compositions, with higher effects observed for total cholesterol and high-density lipoproteins. Species from the genera Odoribacter, Anaerostipes, and Parabacteroides correlated with increased serum lipid levels, whereas probiotic species like Akkermansia muciniphila were more abundant among participants with healthier blood lipid profiles. An inverse correlation with serum cholesterol was also observed for Massilistercora timonensis, a player in regulating lipid turnover. The observed correlation patterns add to the growing evidence supporting the role of the gut microbiome as an essential regulator of host lipid metabolism.
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Affiliation(s)
- Ineta Kalnina
- Latvian Biomedical Research and Study Centre 1, LV-1067 Riga, Latvia
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11
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Reščenko R, Brīvība M, Atava I, Rovīte V, Pečulis R, Silamiķelis I, Ansone L, Megnis K, Birzniece L, Leja M, Xu L, Shi X, Zhou Y, Slaitas A, Hou Y, Kloviņš J. Whole-Genome Sequencing of 502 Individuals from Latvia: The First Step towards a Population-Specific Reference of Genetic Variation. Int J Mol Sci 2023; 24:15345. [PMID: 37895026 PMCID: PMC10607061 DOI: 10.3390/ijms242015345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Despite rapid improvements in the accessibility of whole-genome sequencing (WGS), understanding the extent of human genetic variation is limited by the scarce availability of genome sequences from underrepresented populations. Developing the population-scale reference database of Latvian genetic variation may fill the gap in European genomes and improve human genomics research. In this study, we analysed a high-coverage WGS dataset comprising 502 individuals selected from the Genome Database of the Latvian Population. An assessment of variant type, location in the genome, function, medical relevance, and novelty was performed, and a population-specific imputation reference panel (IRP) was developed. We identified more than 18.2 million variants in total, of which 3.3% so far are not represented in gnomAD and dbSNP databases. Moreover, we observed a notable though distinct clustering of the Latvian cohort within the European subpopulations. Finally, our findings demonstrate the improved performance of imputation of variants using the Latvian population-specific reference panel in the Latvian population compared to established IRPs. In summary, our study provides the first WGS data for a regional reference genome that will serve as a resource for the development of precision medicine and complement the global genome dataset, improving the understanding of human genetic variation.
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Affiliation(s)
- Raimonds Reščenko
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Monta Brīvība
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Ivanna Atava
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Vita Rovīte
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Raitis Pečulis
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Ivars Silamiķelis
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Laura Ansone
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Kaspars Megnis
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Līga Birzniece
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Mārcis Leja
- Faculty of Medicine, University of Latvia, LV-1004 Riga, Latvia;
- Institute of Clinical and Preventive Medicine, University of Latvia, LV-1079 Riga, Latvia
| | - Liqin Xu
- Latvia MGI Tech, LV-2167 Mārupe, Latvia; (L.X.); (X.S.); (Y.Z.); (A.S.); (Y.H.)
| | - Xulian Shi
- Latvia MGI Tech, LV-2167 Mārupe, Latvia; (L.X.); (X.S.); (Y.Z.); (A.S.); (Y.H.)
| | - Yan Zhou
- Latvia MGI Tech, LV-2167 Mārupe, Latvia; (L.X.); (X.S.); (Y.Z.); (A.S.); (Y.H.)
| | - Andis Slaitas
- Latvia MGI Tech, LV-2167 Mārupe, Latvia; (L.X.); (X.S.); (Y.Z.); (A.S.); (Y.H.)
| | - Yong Hou
- Latvia MGI Tech, LV-2167 Mārupe, Latvia; (L.X.); (X.S.); (Y.Z.); (A.S.); (Y.H.)
| | - Jānis Kloviņš
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
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12
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Fedulovs A, Tzivian L, Zalizko P, Ivanova S, Bumane R, Janeviča J, Krūzmane L, Krustins E, Sokolovska J. Progression of Diabetic Kidney Disease and Gastrointestinal Symptoms in Patients with Type I Diabetes. Biomedicines 2023; 11:2679. [PMID: 37893052 PMCID: PMC10604159 DOI: 10.3390/biomedicines11102679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
(1) Background: Little research is conducted on the link between diabetic kidney disease (DKD) progression and diabetic gastroenteropathy in type 1 diabetes (T1D). (2) Methods. We performed a cross-sectional study with 100 T1D patients; 27 of them had progressive DKD, defined as an estimated glomerular filtration rate (eGFR) decline ≥3 mL/min/year or increased albuminuria stage, over a mean follow-up time of 5.89 ± 1.73 years. A newly developed score with 17 questions on gastrointestinal (GI) symptoms was used. Faecal calprotectin was measured by ELISA. Lower GI endoscopies were performed in 21 patients. (3) Results: The gastrointestinal symptom score demonstrated high reliability (Cronbach's α = 0.78). Patients with progressive DKD had higher GI symptom scores compared to those with stable DKD (p = 0.019). The former group demonstrated more frequent bowel movement disorders (p < 0.01). The scores correlated negatively with eGFR (r = -0.335; p = 0.001), positively with albuminuria (r = 0.245; p = 0.015), Hba1c (r = 0.305; p = 0.002), and diabetes duration (r = 0.251; p = 0.012). Faecal calprotectin levels did not differ between DKD groups significantly. The most commonly reported histopathological findings of enteric mucosa were infiltration with eosinophils, lymphocytes, plasmacytes, the presence of lymphoid follicles, and lymphoid aggregates. Conclusion: The progression of DKD is positively correlated with gastrointestinal symptoms; however, more research is needed to clarify the causal relationships of the gut-kidney axis in T1D.
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Affiliation(s)
- Aleksejs Fedulovs
- Faculty of Medicine, University of Latvia, Jelgavas Street 3, LV 1004 Riga, Latvia; (A.F.); (L.T.); (P.Z.); (S.I.); (R.B.); (J.J.); (L.K.)
| | - Lilian Tzivian
- Faculty of Medicine, University of Latvia, Jelgavas Street 3, LV 1004 Riga, Latvia; (A.F.); (L.T.); (P.Z.); (S.I.); (R.B.); (J.J.); (L.K.)
| | - Polina Zalizko
- Faculty of Medicine, University of Latvia, Jelgavas Street 3, LV 1004 Riga, Latvia; (A.F.); (L.T.); (P.Z.); (S.I.); (R.B.); (J.J.); (L.K.)
- Pauls Stradins Clinical University Hospital, Pilsoņu Street 13, LV 1002 Riga, Latvia;
| | - Santa Ivanova
- Faculty of Medicine, University of Latvia, Jelgavas Street 3, LV 1004 Riga, Latvia; (A.F.); (L.T.); (P.Z.); (S.I.); (R.B.); (J.J.); (L.K.)
| | - Renāte Bumane
- Faculty of Medicine, University of Latvia, Jelgavas Street 3, LV 1004 Riga, Latvia; (A.F.); (L.T.); (P.Z.); (S.I.); (R.B.); (J.J.); (L.K.)
| | - Jana Janeviča
- Faculty of Medicine, University of Latvia, Jelgavas Street 3, LV 1004 Riga, Latvia; (A.F.); (L.T.); (P.Z.); (S.I.); (R.B.); (J.J.); (L.K.)
- Pauls Stradins Clinical University Hospital, Pilsoņu Street 13, LV 1002 Riga, Latvia;
| | - Lelde Krūzmane
- Faculty of Medicine, University of Latvia, Jelgavas Street 3, LV 1004 Riga, Latvia; (A.F.); (L.T.); (P.Z.); (S.I.); (R.B.); (J.J.); (L.K.)
| | - Eduards Krustins
- Pauls Stradins Clinical University Hospital, Pilsoņu Street 13, LV 1002 Riga, Latvia;
| | - Jelizaveta Sokolovska
- Faculty of Medicine, University of Latvia, Jelgavas Street 3, LV 1004 Riga, Latvia; (A.F.); (L.T.); (P.Z.); (S.I.); (R.B.); (J.J.); (L.K.)
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13
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Gudra D, Valdovska A, Jonkus D, Galina D, Kairisa D, Ustinova M, Viksne K, Fridmanis D, Kalnina I. Genomic Characterization and Initial Insight into Mastitis-Associated SNP Profiles of Local Latvian Bos taurus Breeds. Animals (Basel) 2023; 13:2776. [PMID: 37685039 PMCID: PMC10487150 DOI: 10.3390/ani13172776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Latvia has two local Bos taurus breeds-Latvian Brown (LBG) and Latvian Blue (LZG)-characterized by a good adaptation to the local climate, longevity, and high fat and protein contents in milk. Since these are desired traits in the dairy industry, this study investigated the genetic background of the LBG and LZG breeds and identified the genetic factors associated with mastitis. Blood and semen samples were acquired, and whole genome sequencing was then performed to acquire a genomic sequence with at least 35× or 10× coverage. The heterozygosity, nucleotide diversity, and LD analysis indicated that LBG and LZG cows have similar levels of genetic diversity compared to those of other breeds. An analysis of the population structure revealed that each breed clustered together, but the overall differentiation between the breeds was small. The highest genetic variance was observed in the LZG breed compared with the LBG breed. Our results show that SNP rs721295390 is associated with mastitis in the LBG breed, and SNPs rs383806754, chr29:43998719CG>C, and rs462030680 are associated with mastitis in the LZG breed. This study shows that local Latvian LBG and LZG breeds have a pronounced genetic differentiation, with each one suggesting its own mastitis-associated SNP profile.
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Affiliation(s)
- Dita Gudra
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (D.G.); (M.U.); (K.V.); (D.F.)
| | - Anda Valdovska
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, LV-3001 Jelgava, Latvia
- Scientific Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, LV-3001 Jelgava, Latvia
| | - Daina Jonkus
- Faculty of Agriculture, Latvia University of Life Sciences and Technologies, LV-3001 Jelgava, Latvia (D.K.)
| | - Daiga Galina
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, LV-3001 Jelgava, Latvia
- Scientific Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, LV-3001 Jelgava, Latvia
| | - Daina Kairisa
- Faculty of Agriculture, Latvia University of Life Sciences and Technologies, LV-3001 Jelgava, Latvia (D.K.)
| | - Maija Ustinova
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (D.G.); (M.U.); (K.V.); (D.F.)
| | - Kristine Viksne
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (D.G.); (M.U.); (K.V.); (D.F.)
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, LV-1007 Riga, Latvia
| | - Davids Fridmanis
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (D.G.); (M.U.); (K.V.); (D.F.)
| | - Ineta Kalnina
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (D.G.); (M.U.); (K.V.); (D.F.)
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14
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Latkovskis G, Rescenko-Krums R, Nesterovics G, Briviba M, Saripo V, Gilis D, Terauda E, Meiere R, Skudrina G, Erglis A, Chora JR, Bourbon M, Klovins J. Genetic Characteristics of Latvian Patients with Familial Hypercholesterolemia: The First Analysis from Genome-Wide Sequencing. J Clin Med 2023; 12:5160. [PMID: 37568561 PMCID: PMC10419451 DOI: 10.3390/jcm12155160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/14/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND There is limited data on the genetic characteristics of patients with familial hypercholesterolemia (FH) in Latvia. We aim to describe monogenic variants in patients from the Latvian Registry of FH (LRFH). METHODS Whole genome sequencing with 30× coverage was performed in unrelated index cases from the LRFH and the Genome Database of Latvian Population. LDLR, APOB, PCSK9, LDLRAP1, ABCG5, ABCG8, LIPA, LPA, CYP27A1, and APOE genes were analyzed. Only variants annotated as pathogenic (P) or likely pathogenic (LP) using the FH Variant Curation Expert Panel guidelines for LDLR and adaptations for APOB and PCSK9 were reported. RESULTS Among 163 patients, the mean highest documented LDL-cholesterol level was 7.47 ± 1.60 mmol/L, and 79.1% of patients had LDL-cholesterol ≥6.50 mmol/L. A total of 15 P/LP variants were found in 34 patients (diagnostic yield: 20.9%): 14 in the LDLR gene and 1 in the APOB gene. Additionally, 24, 54, and 13 VUS were detected in LDLR, APOB, and PCSK9, respectively. No P/LP variants were identified in the other tested genes. CONCLUSIONS Despite the high clinical likelihood of FH, confirmed P/LP variants were detected in only 20.9% of patients in the Latvian cohort when assessed with genome-wide next generation sequencing.
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Affiliation(s)
- Gustavs Latkovskis
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV-1004 Riga, Latvia (V.S.); (E.T.)
- Latvian Center of Cardiology, Pauls Stradins Clinical University Hospital, LV-1002 Riga, Latvia
- Faculty of Medicine, University of Latvia, LV-1004 Riga, Latvia
| | | | - Georgijs Nesterovics
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV-1004 Riga, Latvia (V.S.); (E.T.)
- Latvian Center of Cardiology, Pauls Stradins Clinical University Hospital, LV-1002 Riga, Latvia
- Faculty of Medicine, University of Latvia, LV-1004 Riga, Latvia
| | - Monta Briviba
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia
| | - Vita Saripo
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV-1004 Riga, Latvia (V.S.); (E.T.)
- Latvian Center of Cardiology, Pauls Stradins Clinical University Hospital, LV-1002 Riga, Latvia
| | - Dainus Gilis
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV-1004 Riga, Latvia (V.S.); (E.T.)
- Latvian Center of Cardiology, Pauls Stradins Clinical University Hospital, LV-1002 Riga, Latvia
- Faculty of Medicine, University of Latvia, LV-1004 Riga, Latvia
| | - Elizabete Terauda
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV-1004 Riga, Latvia (V.S.); (E.T.)
- Latvian Center of Cardiology, Pauls Stradins Clinical University Hospital, LV-1002 Riga, Latvia
- Faculty of Medicine, University of Latvia, LV-1004 Riga, Latvia
| | - Ruta Meiere
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV-1004 Riga, Latvia (V.S.); (E.T.)
- Latvian Center of Cardiology, Pauls Stradins Clinical University Hospital, LV-1002 Riga, Latvia
| | - Gunda Skudrina
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV-1004 Riga, Latvia (V.S.); (E.T.)
- Latvian Center of Cardiology, Pauls Stradins Clinical University Hospital, LV-1002 Riga, Latvia
| | - Andrejs Erglis
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV-1004 Riga, Latvia (V.S.); (E.T.)
- Latvian Center of Cardiology, Pauls Stradins Clinical University Hospital, LV-1002 Riga, Latvia
- Faculty of Medicine, University of Latvia, LV-1004 Riga, Latvia
| | - Joana Rita Chora
- Department of Health Promotion and Prevention of Noncommunicable Diseases, National Institute of Health Dr. Ricardo Jorge, 164-9016 Lisbon, Portugal
- Department of Chemistry and Biochemistry, BioISI—BioSystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1649-004 Lisbon, Portugal
| | - Mafalda Bourbon
- Department of Health Promotion and Prevention of Noncommunicable Diseases, National Institute of Health Dr. Ricardo Jorge, 164-9016 Lisbon, Portugal
- Department of Chemistry and Biochemistry, BioISI—BioSystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1649-004 Lisbon, Portugal
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia
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15
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Niedra H, Konrade I, Peculis R, Isajevs S, Saksis R, Skapars R, Sivins A, Daukste BE, Mezaka D, Rovite V. Solitary fibrous tumor with IGF-II-induced non-islet cell tumor hypoglycemia: a case report and molecular characterization by next-generation sequencing. Front Oncol 2023; 13:1188579. [PMID: 37469410 PMCID: PMC10352493 DOI: 10.3389/fonc.2023.1188579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/19/2023] [Indexed: 07/21/2023] Open
Abstract
Background Non-islet cell tumor-induced hypoglycemia (NICTH) is a rare, life-threatening medical condition caused by excessive insulin-like growth factor II (IGF-II) secretion from tumors of most commonly mesenchymal origin. Using next-generation sequencing, we have characterized the genome and transcriptome of the resected IGF-II-secreting solitary fibrous tumor from a patient with severe hypoglycemia accompanied by hypoglycemia unawareness. Case presentation A 69-year-old male patient presenting with abdominal discomfort was examined using computer tomography, revealing a large lesion at the lesser pelvis extending above the umbilicus. As no bone and lymph node metastases were detected, the patient was scheduled for laparotomy. Before surgery, the patient presented with symptoms of severe hypoglycemia. Suppressed C-peptide levels and subsequent hypokalemia indicated a possible case of NICTH. The patient was treated with methylprednisolone (8 mg) to assess hypoglycemia. After the surgery, mild hypoglycemia was present for the postoperative period, and no radiological recurrences were observed 3 and 12 months after discharge. Histopathological examination results were consistent with the diagnosis of malignant solitary fibrous tumor (SFT). Overexpression of IGF-II was confirmed by both immunohistochemistry and RNA sequencing. Further NGS analysis revealed an SFT characteristic alteration-NAB2-STAT6 fusion. Additionally, three deleterious missense variants were detected in oncogenes BIRC6, KIT, and POLQ, and one homozygous in-frame deletion in the RBM10 tumor suppressor gene. Conclusion While the NAB2-STAT6 fusions are well characterized, the mutational landscape of SFTs remains understudied. This study reports the importance of NGS to characterize SFTs as we detected four coding variants in genes (BIRC6, KIT, POLQ, and RBM10) associated with tumorigenesis that could potentially contribute to the overall pathogenesis of SFT.
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Affiliation(s)
- Helvijs Niedra
- Department of Molecular and Functional Genomics, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ilze Konrade
- RigaEast Clinical University Hospital, Riga, Latvia
- Department of Internal Diseases, Riga Stradins University, Riga, Latvia
| | - Raitis Peculis
- Department of Molecular and Functional Genomics, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Rihards Saksis
- Department of Molecular and Functional Genomics, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | | | | - Dace Mezaka
- RigaEast Clinical University Hospital, Riga, Latvia
| | - Vita Rovite
- Department of Molecular and Functional Genomics, Latvian Biomedical Research and Study Centre, Riga, Latvia
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16
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Jagare L, Rozenberga M, Silamikelis I, Ansone L, Elbere I, Briviba M, Megnis K, Konrade I, Birka I, Straume Z, Klovins J. Metatranscriptome analysis of blood in healthy individuals and irritable bowel syndrome patients. J Med Microbiol 2023; 72. [PMID: 37335601 DOI: 10.1099/jmm.0.001719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Introduction. Although the presence of micro-organisms in the blood of healthy humans is a relatively new concept, there is a growing amount of evidence that blood might have its own microbiome.Gap Statement. Previous research has targeted the taxonomic composition of the blood microbiome using DNA-based sequencing methods, while little information is known about the presence of microbial transcripts obtained from the blood and their relation to conditions connected with increased gut permeability.Aim. To detect potentially alive and active micro-organisms and investigate differences in taxonomic composition between healthy people and patients with irritable bowel syndrome (IBS), we used the metatranscriptomics approach.Methodology. We collected blood samples from 23 IBS patients and 26 volunteers from the general population, and performed RNAseq on the isolated RNA. Reads corresponding to microbial genomes were identified with Kraken 2's standard plus protozoa and fungi database, and re-estimated at genus level with Bracken 2.7. We looked for trends in the taxonomic composition, making a comparison between the IBS and control groups, accounting for other different factors.Results. The dominant genera in the blood microbiome were found to be Cutibacterium, Bradyrhizobium, Escherichia, Pseudomonas, Micrococcus, Delftia, Mediterraneibacter, Staphylococcus, Stutzerimonas and Ralstonia. Some of these are typical environmental bacteria and could partially represent contamination. However, analysis of sequences from the negative controls suggested that some genera which are characteristic of the gut microbiome (Mediterraneibacter, Blautia, Collinsella, Klebsiella, Coprococcus, Dysosmobacter, Anaerostipes, Faecalibacterium, Dorea, Simiaoa, Bifidobacterium, Alistipes, Prevotella, Ruminococcus) are less likely to be a result of contamination. Differential analysis of microbes between groups showed that some taxa associated with the gut microbiome (Blautia, Faecalibacterium, Dorea, Bifidobacterium, Clostridium, Christensenella) are more prevalent in IBS patients compared to the general population. No significant correlations with any other factors were identified.Conclusion. Our findings support the existence of the blood microbiome and suggest the gut and possibly the oral microbiome as its origin, while the skin microbiome is a possible but less certain source. The blood microbiome is likely influenced by states of increased gut permeability such as IBS.
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Affiliation(s)
- Lauma Jagare
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Maija Rozenberga
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Ivars Silamikelis
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Laura Ansone
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Ilze Elbere
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Monta Briviba
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Kaspars Megnis
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
| | - Ilze Konrade
- Riga Stradins University, Dzirciema iela 16, Riga, LV-1007, Latvia
| | - Ilze Birka
- Pauls Stradins Clinical University Hospital, Pilsonu iela 13, Riga, LV-1002, Latvia
| | - Zane Straume
- Ogre Regional Hospital, Slimnicas iela 2, Ogre, LV-5001, Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Human Genetics and Disease Mechanisms Group, Ratsupites iela 1, Riga, LV-1067, Latvia
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17
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Abola I, Gudra D, Ustinova M, Fridmanis D, Emulina DE, Skadins I, Brinkmane A, Lauga-Tunina U, Gailite L, Auzenbaha M. Oral Microbiome Traits of Type 1 Diabetes and Phenylketonuria Patients in Latvia. Microorganisms 2023; 11:1471. [PMID: 37374973 DOI: 10.3390/microorganisms11061471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Some metabolic disorder treatments require patients to follow a specific diet or to consume supplements that, over time, can lead to oral microbiome alterations. Well-known disorders requiring such treatment are phenylketonuria (PKU), an inborn error of amino acid metabolism, and type 1 diabetes (T1D), a metabolic disorder that requires a specific diet regimen. Therefore, the aim of this study was to investigate the oral health and microbiome characteristics that might contribute to caries activity and periodontal disease risk in PKU and T1D patients. In this cross-sectional study, 45 PKU patients, 24 T1D patients, and 61 healthy individuals between the ages of 12 and 53 years were examined. Their anamnestic data and dental status were assessed by one dentist. Microbial communities were detected from saliva-isolated DNA using 16S rRNA gene V3-V4 sequencing on Illumina MiSeq sequencing platform. Results revealed that the PKU patient group displayed the highest number of extracted teeth (on average 1.34), carious teeth (on average 4.95), and carious activity (44.44% of individuals) compared to the T1D and CTRL groups. The lowest numbers of filled teeth (on average 5.33) and extracted teeth (on average 0.63) per individual were observed in T1D patients. Gingivitis appeared more often in the T1D group; however, possible risk of periodontal disease was seen in both the T1D and PKU patient groups. The highest number of differentially abundant genera was detected in the PKU group (n = 20), with enrichment of Actinomyces (padj = 4.17 × 10-22), Capnocytophaga (padj = 8.53 × 10-8), and Porphyromonas (padj = 1.18 × 10-5) compared to the CTRL group. In conclusion, the dental and periodontal health of PKU patients was found to be significantly inferior compared to T1D patients and healthy controls. T1D patients showed early signs of periodontal disease. Several genera that correlate with periodontal disease development were found in both groups, thus suggesting that T1D and PKU patients should seek early and regular dental advice and be educated about proper oral hygiene practices.
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Affiliation(s)
- Iveta Abola
- Scientific Laboratory of Molecular Genetics, Rīga Stradiņš University, LV-1007 Riga, Latvia
- Department of Conservative Dentistry and Oral Health, Rīga Stradiņš University, LV-1007 Riga, Latvia
| | - Dita Gudra
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia
| | - Maija Ustinova
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia
| | - Davids Fridmanis
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia
| | | | - Ingus Skadins
- Scientific Laboratory of Molecular Genetics, Rīga Stradiņš University, LV-1007 Riga, Latvia
- Department of Biology and Microbiology, Rīga Stradiņš University, LV-1007 Riga, Latvia
| | - Anda Brinkmane
- Department of Conservative Dentistry and Oral Health, Rīga Stradiņš University, LV-1007 Riga, Latvia
| | - Una Lauga-Tunina
- Department of Endocrinology, Children's Clinical University Hospital, LV-1004 Riga, Latvia
| | - Linda Gailite
- Scientific Laboratory of Molecular Genetics, Rīga Stradiņš University, LV-1007 Riga, Latvia
| | - Madara Auzenbaha
- Scientific Laboratory of Molecular Genetics, Rīga Stradiņš University, LV-1007 Riga, Latvia
- Department of Biology and Microbiology, Rīga Stradiņš University, LV-1007 Riga, Latvia
- Clinic of Medical Genetics and Prenatal Diagnostics, Children's Clinical University Hospital, LV-1004 Riga, Latvia
- European Reference Network for Hereditary Metabolic Disorders, Children's Clinical University Hospital, LV-1004 Riga, Latvia
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18
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Berga-Švītiņa E, Maksimenko J, Miklaševičs E, Fischer K, Vilne B, Mägi R. Polygenic Risk Score Predicts Modified Risk in BRCA1 Pathogenic Variant c.4035del and c.5266dup Carriers in Breast Cancer Patients. Cancers (Basel) 2023; 15:cancers15112957. [PMID: 37296919 DOI: 10.3390/cancers15112957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
The aim of this study was to assess the power of the polygenic risk score (PRS) in estimating the overall genetic risk of women carrying germline BRCA1 pathogenic variants (PVs) c.4035del or c.5266dup to develop breast (BC) or ovarian cancer (OC) due to additional genetic variations. In this study, PRSs previously developed from two joint models using summary statistics of age-at-onset (BayesW model) and case-control data (BayesRR-RC model) from a genome-wide association analysis (GWAS) were applied to 406 germline BRCA1 PV (c.4035del or c.5266dup) carriers affected by BC or OC, compared with unaffected individuals. A binomial logistic regression model was used to assess the association of PRS with BC or OC development risk. We observed that the best-fitting BayesW PRS model effectively predicted the individual's BC risk (OR = 1.37; 95% CI = 1.03-1.81, p = 0.02905 with AUC = 0.759). However, none of the applied PRS models was a good predictor of OC risk. The best-fitted PRS model (BayesW) contributed to assessing the risk of developing BC for germline BRCA1 PV (c.4035del or c.5266dup) carriers and may facilitate more precise and timely patient stratification and decision-making to improve the current BC treatment or even prevention strategies.
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Affiliation(s)
- Egija Berga-Švītiņa
- Bioinformatics Lab, Rīga Stradiņš University, Dzirciema Street 16, LV-1007 Riga, Latvia
- Institute of Oncology, Rīga Stradiņš University, Pilsoņu Street 13, Block 13, LV-1002 Riga, Latvia
| | - Jeļena Maksimenko
- Institute of Oncology, Rīga Stradiņš University, Pilsoņu Street 13, Block 13, LV-1002 Riga, Latvia
- Pauls Stradiņš Clinical University Hospital, Pilsoņu Street 13, LV-1002 Riga, Latvia
| | - Edvīns Miklaševičs
- Institute of Oncology, Rīga Stradiņš University, Pilsoņu Street 13, Block 13, LV-1002 Riga, Latvia
- Department of Biology and Microbiology, Rīga Stradiņš University, LV-1007 Riga, Latvia
| | - Krista Fischer
- Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia
- Institute of Mathematics and Statistics, University of Tartu, Narva mnt 18, 51009 Tartu, Estonia
| | - Baiba Vilne
- Bioinformatics Lab, Rīga Stradiņš University, Dzirciema Street 16, LV-1007 Riga, Latvia
| | - Reedik Mägi
- Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia
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19
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Bajo-Santos C, Priedols M, Kaukis P, Paidere G, Gerulis-Bergmanis R, Mozolevskis G, Abols A, Rimsa R. Extracellular Vesicles Isolation from Large Volume Samples Using a Polydimethylsiloxane-Free Microfluidic Device. Int J Mol Sci 2023; 24:7971. [PMID: 37175677 PMCID: PMC10178709 DOI: 10.3390/ijms24097971] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Extracellular vesicles (EV) have many attributes important for biomedicine; however, current EV isolation methods require long multi-step protocols that generally involve bulky equipment that cannot be easily translated to clinics. Our aim was to design a new cyclic olefin copolymer-off-stoichiometry thiol-ene (COC-OSTE) asymmetric flow field fractionation microfluidic device that could isolate EV from high-volume samples in a simple and efficient manner. We tested the device with large volumes of urine and conditioned cell media samples, and compared it with the two most commonly used EV isolation methods. Our device was able to separate particles by size and buoyancy, and the attained size distribution was significantly smaller than other methods. This would allow for targeting EV size fractions of interest in the future. However, the results were sample dependent, with some samples showing significant improvement over the current EV separation methods. We present a novel design for a COC-OSTE microfluidic device, based on bifurcating asymmetric flow field-flow fractionation (A4F) technology, which is able to isolate EV from large volume samples in a simple, continuous-flow manner. Its potential to be mass-manufactured increases the chances of implementing EV isolation in a clinical or industry-friendly setting, which requires high repeatability and throughput.
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Affiliation(s)
- Cristina Bajo-Santos
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia
| | - Miks Priedols
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia
| | - Pauls Kaukis
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia
| | - Gunita Paidere
- Institute of Solid-State Physics, University of Latvia, 8 Kengaraga Str., LV-1063 Riga, Latvia
| | | | - Gatis Mozolevskis
- Institute of Solid-State Physics, University of Latvia, 8 Kengaraga Str., LV-1063 Riga, Latvia
| | - Arturs Abols
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k-1, LV-1067 Riga, Latvia
| | - Roberts Rimsa
- Institute of Solid-State Physics, University of Latvia, 8 Kengaraga Str., LV-1063 Riga, Latvia
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20
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Nartisa I, Kirsteina R, Neiburga KD, Zigure S, Ozola L, Grantina I, Micule I, Murmane D, Slisere B, Gailite L, Vilne B, Rots D, Taurina G, Kurjane N. Clinical and genetic characterization of Netherton syndrome due to SPINK5 founder variant in Latvian population. Pediatr Allergy Immunol 2023; 34:e13937. [PMID: 37102386 DOI: 10.1111/pai.13937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 04/28/2023]
Abstract
OBJECTIVE Netherton syndrome (NS) (OMIM:256500) is a very rare autosomal recessive multisystem disorder mostly affecting ectodermal derivatives (skin and hair) and immune system. It is caused by biallelic loss-of-function variants in the SPINK5 gene, encoding the protease inhibitor lymphoepithelial Kazal-type-related inhibitor (LEKTI). MATERIAL, METHODS AND RESULTS Here, we describe NS clinical and genetic features of homogenous patient group: 9 individuals from 7 families with similar ethnic background and who have the same SPINK5 variant (NM_006846.4: c.1048C > T, p.(Arg350*)) in homozygous or compound heterozygous states, suggesting that it is a common founder variant in Latvian population. Indeed, we were able to show that the variant is common in general Latvian population, and it shares the same haplotype among the NS individual. It is estimated that the variant arose >1000 years ago. Clinically, all nine patients exhibited typical NS skin changes (scaly erythroderma, ichthyosis linearis circumflexa, itchy skin), except for one patient who has a different skin manifestation-epidermodysplasia. Additionally, we show that developmental delay, previously underrecognized in NS, is a common feature among these patients. CONCLUSIONS This study shows that the phenotype of NS individuals with the same genotype is highly homogeneous.
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Affiliation(s)
- Inga Nartisa
- Riga Stradins University, Riga, Latvia
- Children's Clinical University Hospital, Riga, Latvia
| | - Rasa Kirsteina
- Clinic for Medical Genetics and Prenatal Diagnosis, Children's Clinical University Hospital, Riga, Latvia
| | | | - Sanita Zigure
- Riga Stradins University, Riga, Latvia
- Children's Clinical University Hospital, Riga, Latvia
| | - Lota Ozola
- Children's Clinical University Hospital, Riga, Latvia
| | | | - Ieva Micule
- Clinic for Medical Genetics and Prenatal Diagnosis, Children's Clinical University Hospital, Riga, Latvia
| | - Daiga Murmane
- Clinic for Medical Genetics and Prenatal Diagnosis, Children's Clinical University Hospital, Riga, Latvia
| | - Baiba Slisere
- Riga Stradins University, Riga, Latvia
- Pauls Stradins Clinical University Hospital, Riga, Latvia
| | | | | | - Dmitrijs Rots
- Riga Stradins University, Riga, Latvia
- Children's Clinical University Hospital, Riga, Latvia
- Radboudumc, Nijmegen, The Netherlands
| | - Gita Taurina
- Clinic for Medical Genetics and Prenatal Diagnosis, Children's Clinical University Hospital, Riga, Latvia
| | - Natalja Kurjane
- Riga Stradins University, Riga, Latvia
- Clinic for Medical Genetics and Prenatal Diagnosis, Children's Clinical University Hospital, Riga, Latvia
- Pauls Stradins Clinical University Hospital, Riga, Latvia
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21
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Freimane L, Barkāne L, Kivrane A, Sadovska D, Ulanova V, Ranka R. Assessment of Amikacin- and Capreomycin-Related Adverse Drug Reactions in Patients with Multidrug-Resistant Tuberculosis and Exploring the Role of Genetic Factors. J Pers Med 2023; 13:jpm13040599. [PMID: 37108985 PMCID: PMC10145258 DOI: 10.3390/jpm13040599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/24/2023] [Accepted: 03/25/2023] [Indexed: 03/31/2023] Open
Abstract
Following the introduction of all-oral treatment regimens for patients with drug-resistant tuberculosis (TB), second-line injectable drug applications have been reduced in the last few years. However, they are still important for anti-TB therapy. This study aims to analyze the occurrence of amikacin- and capreomycin-related adverse drug reactions (ADR) in patients with multidrug-resistant tuberculosis (MDR-TB) and evaluate the role of multiple patient-, disease-, and therapy-related factors on the frequency of the observed adverse events. In addition, the possible role of genetic risk factors was studied by full-length mitochondrial DNA sequencing. Toward this aim, we retrospectively evaluated 47 patients with MDR-TB who received amikacin and/or capreomycin. In total, 16 (34.0%) patients developed ototoxicity and 13 (27.7%) developed nephrotoxicity, including 3 (6.4%) patients who experienced both adverse events. Ototoxicity development was more common in patients who received amikacin. No other factors showed a significant impact. Nephrotoxicity was likely associated with previous renal health impairment. Full mitochondrial genome sequencing did not reveal any specific ADR-associated variants, and results showed no differences in adverse event occurrence for any specific variants, mutation count, or mitochondrial haplogroup. The absence of the previously reported ototoxicity-related mtDNA variants in our patients with ototoxicity and nephrotoxicity highlighted the complex nature of the ADR occurrence.
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22
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Saksis R, Rogoza O, Niedra H, Megnis K, Mandrika I, Balcere I, Steina L, Stukens J, Breiksa A, Nazarovs J, Sokolovska J, Konrade I, Peculis R, Rovite V. Transcriptome of GH-producing pituitary neuroendocrine tumours and models are significantly affected by somatostatin analogues. Cancer Cell Int 2023; 23:25. [PMID: 36774501 PMCID: PMC9922463 DOI: 10.1186/s12935-023-02863-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/01/2023] [Indexed: 02/13/2023] Open
Abstract
Pituitary neuroendocrine tumours (PitNETs) are neoplasms of the pituitary that overproduce hormones or cause unspecific symptoms due to mass effect. Growth hormone overproducing GH-producing PitNETs cause acromegaly leading to connective tissue, metabolic or oncologic disorders. The medical treatment of acromegaly is somatostatin analogues (SSA) in specific cases combined with dopamine agonists (DA), but almost half of patients display partial or full SSA resistance and potential causes of this are unknown. In this study we investigated transcriptomic landscape of GH-producing PitNETs on several levels and functional models-tumour tissue of patients with and without SSA preoperative treatment, tumour derived pituispheres and GH3 cell line incubated with SSA to study effect of medication on gene expression. MGI sequencing platform was used to sequence total RNA from PitNET tissue, pituispheres, mesenchymal stromal stem-like cells (MSC), and GH3 cell cultures, and data were analysed with Salmon-DeSeq2 pipeline. We observed that the GH-producing PitNETs have distinct changes in growth hormone related pathways related to its functional status alongside inner cell signalling, ion transport, cell adhesion and extracellular matrix characteristic patterns. In pituispheres model, treatment regimens (octreotide and cabergoline) affect specific cell proliferation (MKI67) and core functionality pathways (RYR2, COL8A2, HLA-G, ARFGAP1, TGFBR2). In GH3 cells we observed that medication did not have transcriptomic effects similar to preoperative treatment in PitNET tissue or pituisphere model. This study highlights the importance of correct model system selection for cell transcriptomic profiling and data interpretation that could be achieved in future by incorporating NGS methods and detailed cell omics profiling in PitNET model research.
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Affiliation(s)
- Rihards Saksis
- grid.419210.f0000 0004 4648 9892Latvian Biomedical Research and Study Centre, Ratsupites Str 1-k1, Riga, 1067 Latvia
| | - Olesja Rogoza
- grid.419210.f0000 0004 4648 9892Latvian Biomedical Research and Study Centre, Ratsupites Str 1-k1, Riga, 1067 Latvia
| | - Helvijs Niedra
- grid.419210.f0000 0004 4648 9892Latvian Biomedical Research and Study Centre, Ratsupites Str 1-k1, Riga, 1067 Latvia
| | - Kaspars Megnis
- grid.419210.f0000 0004 4648 9892Latvian Biomedical Research and Study Centre, Ratsupites Str 1-k1, Riga, 1067 Latvia
| | - Ilona Mandrika
- grid.419210.f0000 0004 4648 9892Latvian Biomedical Research and Study Centre, Ratsupites Str 1-k1, Riga, 1067 Latvia
| | - Inga Balcere
- grid.488518.80000 0004 0375 2558Riga East Clinical University Hospital, Hipokrata Str 2, Riga, 1038 Latvia ,grid.17330.360000 0001 2173 9398Riga Stradins University, Dzirciema Str. 16, Riga, 1007 Latvia
| | - Liva Steina
- grid.419210.f0000 0004 4648 9892Latvian Biomedical Research and Study Centre, Ratsupites Str 1-k1, Riga, 1067 Latvia ,grid.477807.b0000 0000 8673 8997Pauls Stradins Clinical University Hospital, Pilsonu Str 13, Riga, 1002 Latvia
| | - Janis Stukens
- grid.477807.b0000 0000 8673 8997Pauls Stradins Clinical University Hospital, Pilsonu Str 13, Riga, 1002 Latvia
| | - Austra Breiksa
- grid.477807.b0000 0000 8673 8997Pauls Stradins Clinical University Hospital, Pilsonu Str 13, Riga, 1002 Latvia
| | - Jurijs Nazarovs
- grid.477807.b0000 0000 8673 8997Pauls Stradins Clinical University Hospital, Pilsonu Str 13, Riga, 1002 Latvia
| | - Jelizaveta Sokolovska
- grid.9845.00000 0001 0775 3222Faculty of Medicine, University of Latvia, Raina Blvd 19, Riga, 1586 Latvia
| | - Ilze Konrade
- grid.488518.80000 0004 0375 2558Riga East Clinical University Hospital, Hipokrata Str 2, Riga, 1038 Latvia ,grid.17330.360000 0001 2173 9398Riga Stradins University, Dzirciema Str. 16, Riga, 1007 Latvia
| | - Raitis Peculis
- grid.419210.f0000 0004 4648 9892Latvian Biomedical Research and Study Centre, Ratsupites Str 1-k1, Riga, 1067 Latvia
| | - Vita Rovite
- Latvian Biomedical Research and Study Centre, Ratsupites Str 1-k1, Riga, 1067, Latvia.
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23
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Igumnova V, Kivrane A, Viksna A, Norvaisa I, Ranka R. Next-Generation Sequencing and Bioinformatics-Based Protocol for the Full-Length CYP2E1 Gene Polymorphism Analysis. Pharmgenomics Pers Med 2022; 15:959-965. [DOI: 10.2147/pgpm.s371709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/07/2022] [Indexed: 11/09/2022] Open
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24
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Peculis R, Rovite V, Megnis K, Balcere I, Breiksa A, Nazarovs J, Stukens J, Konrade I, Sokolovska J, Pirags V, Klovins J. Whole exome sequencing reveals novel risk genes of pituitary neuroendocrine tumors. PLoS One 2022; 17:e0265306. [PMID: 36026497 PMCID: PMC9417189 DOI: 10.1371/journal.pone.0265306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 03/01/2022] [Indexed: 11/21/2022] Open
Abstract
Somatic genetic alterations in pituitary neuroendocrine tumors (PitNET) tissues have been identified in several studies, but detection of overlapping somatic PitNET candidate genes is rare. We sequenced and by employing multiple data analysis methods studied the exomes of 15 PitNET patients to improve discovery of novel factors involved in PitNET development. PitNET patients were recruited to the study before PitNET removal surgery. For each patient, two samples for DNA extraction were acquired: venous blood and PitNET tissue. Exome sequencing was performed using Illumina NexSeq 500 sequencer and data analyzed using two separate workflows and variant calling algorithms: GATK and Strelka2. A combination of two data analysis pipelines discovered 144 PitNET specific somatic variants (mean = 9.6, range 0–19 per PitNET) of which all were SNVs. Also, we detected previously known GNAS PitNET mutation and identified somatic variants in 11 genes, which have contained somatic variants in previous WES and WGS studies of PitNETs. Noteworthy, this is the third study detecting somatic variants in gene RYR1 in the exomes of PitNETs. In conclusion, we have identified two novel PitNET candidate genes (AC002519.6 and AHNAK) with recurrent somatic variants in our PitNET cohort and found 13 genes overlapping from previous PitNET studies that contain somatic variants. Our study demonstrated that the use of multiple sequencing data analysis pipelines can provide more accurate identification of somatic variants in PitNETs.
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Affiliation(s)
- Raitis Peculis
- Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
- * E-mail:
| | - Vita Rovite
- Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Kaspars Megnis
- Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Inga Balcere
- Department of Internal Medicine, Riga Stradins University, Riga, Latvia
| | - Austra Breiksa
- Institute of Pathology, Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Jurijs Nazarovs
- Institute of Pathology, Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Janis Stukens
- Department of Neurosurgery, Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Ilze Konrade
- Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
- Department of Internal Medicine, Riga Stradins University, Riga, Latvia
| | | | - Valdis Pirags
- Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
- Department of Endocrinology, Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Janis Klovins
- Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
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25
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Lace B, Micule I, Kenina V, Setlere S, Strautmanis J, Kazaine I, Taurina G, Murmane D, Grinfelde I, Kornejeva L, Krumina Z, Sterna O, Radovica-Spalvina I, Vasiljeva I, Gailite L, Stavusis J, Livcane D, Kidere D, Malniece I, Inashkina I. Overview of Neuromuscular Disorder Molecular Diagnostic Experience for the Population of Latvia. NEUROLOGY GENETICS 2022; 8:e685. [DOI: 10.1212/nxg.0000000000000685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/30/2022] [Indexed: 11/15/2022]
Abstract
Background and ObjectivesGenetic testing has become an integral part of health care, allowing the confirmation of thousands of hereditary diseases, including neuromuscular disorders (NMDs). The reported average prevalence of individual inherited NMDs is 3.7–4.99 per 10,000. This number varies greatly in the selected populations after applying population-wide studies. The aim of this study was to evaluate the effect of genetic analysis as the first-tier test in patients with NMD and to calculate the disease prevalence and allelic frequencies for reoccurring genetic variants.MethodsPatients with NMD from Latvia with molecular tests confirming their diagnosis in 2008–2020 were included in this retrospective study.ResultsDiagnosis was confirmed in 153 unique cases of all persons tested. Next-generation sequencing resulted in a detection rate of 37%. Two of the most common childhood-onset NMDs in our population were spinal muscular atrophy and dystrophinopathies, with a birth prevalence of 1.01 per 10,000 newborns and 2.08 per 10,000 (male newborn population), respectively. The calculated point prevalence was 0.079 per 10,000 for facioscapulohumeral muscular dystrophy type 1, 0.078 per 10,000 for limb-girdle muscular dystrophy, 0.073 per 10,000 for nondystrophic congenital myotonia, 0.052 per 10,000 for spinobulbar muscular atrophy, and 0.047 per 10,000 for type 1 myotonic dystrophy.DiscussionDNA diagnostics is a successful approach. The carrier frequencies of the common CAPN3, FKRP, SPG11, and HINT1 gene variants as well as that of the SMN1 gene exon 7 deletion in the population of Latvia are comparable with data from Europe. The carrier frequency of the CLCN1 gene variant c.2680C>T p.(Arg894Ter) is 2.11%, and consequently, congenital myotonia is the most frequent NMD in our population.
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26
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Telomere Lengths and Serum Proteasome Concentrations in Patients with Type 1 Diabetes and Different Severities of Diabetic Retinopathy in Latvia and Lithuania. J Clin Med 2022; 11:jcm11102768. [PMID: 35628895 PMCID: PMC9146024 DOI: 10.3390/jcm11102768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 02/01/2023] Open
Abstract
The aim of the study was to compare telomere lengths and circulating proteasome concentrations in patients with different stages of diabetic retinopathy and type 1 diabetes in Latvia and Lithuania. Methods. Patients with no diabetic retinopathy and with non-proliferative diabetic retinopathy were included in the NDR/NPDR group (n = 187). Patients with proliferative diabetic retinopathy and status post laser-photocoagulation were included int the PDR/LPC group (n = 119). Telomeres were evaluated by real-time quantitative polymerase chain reaction. Proteasome concentration was measured by ELISA. Results. Telomeres were longer in PDR/LPC (ΔCT 0.21 (0.12−0.28)) vs. NDR/NPDR (ΔCT 0.18 (0.1−0.28)), p = 0.036. In NDR/NPDR, telomeres were correlated negatively with age (R = −0.17, p = 0.019), BMI (R = −0.21, p = 0.004), waist/hip ratio (R = −0.21, p = 0.005), total cholesterol (R = −0.18, p = 0.021), and low-density cholesterol (R = −0.20, p = 0.010), and positively with estimated glomerular filtration rate (eGFR) (R = 0.28, p < 0.001). None of the above correlations were observed in PRD/LPC. Proteasome concentrations were lower in PDR/LPC (130 (90−210) ng/mL) vs. NDR/NPDR (150 (100−240) ng/mL), p = 0.024. This correlated negatively with eGFR (R = −0.17, p = 0.025) in the NDR/NPDR group and positively with age (R = 0.23, p = 0.014) and systolic blood pressure (R = 0.20, p = 0.032) in the PRD/LPC group. Telomere lengths did not correlate with proteasome concentrations. Conclusion. Longer telomeres and lower circulating proteasome concentrations are observed in patients with type 1 diabetes and advanced diabetic retinopathy.
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Niedra H, Peculis R, Konrade I, Balcere I, Romanovs M, Steina L, Stukens J, Sokolovska J, Klovins J, Rovite V. Case Report: Micro-RNAs in Plasma From Bilateral Inferior Petrosal Sinus Sampling and Peripheral Blood From Corticotroph Pituitary Neuroendocrine Tumors. Front Endocrinol (Lausanne) 2022; 13:748152. [PMID: 35528014 PMCID: PMC9072666 DOI: 10.3389/fendo.2022.748152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/17/2022] [Indexed: 01/15/2023] Open
Abstract
Objective Circulating miRNAs are found in bodily fluids including plasma and can serve as biomarkers for diseases. The aim of this study was to provide the first insight into the landscape of circulating miRNAs in close proximity to the adrenocorticotropic hormone (ACTH) secreting PitNET. To achieve this objective next-generation sequencing of miRNAs in plasma from bilateral inferior petrosal sinus sampling (BIPSS) - a gold standard in diagnosing ACTH-secreting PitNETs was carried out and selected miRNA candidates were further tested by RT-qPCR in independent patient cohorts. Methods Sinistral (left) and dextral (right) BIPSS blood samples of the patient were collected in three time points: before the administration of corticotropin-releasing hormone, 5 and 15 minutes after stimulation. In differential expression analysis, sinistral plasma was compared with dextral. The selected miRNA candidates were tested in plasma by RT-qPCR in two patient groups: 1) in five ACTH secreting PitNET patients with plasma samples taken before and 24 hours after surgery, 2) in 12 ACTH secreting PitNET patients vs. 9 non-functioning PitNET patients. Results BIPSS concluded that the highest amount of ACTH was released in the sinistral side at the 5th minute mark indicating a presence of a tumor. The highest amount of differentially expressed miRNAs was observed 5 minutes after stimulation (20 upregulated, 14 downregulated). At the 5th minute mark in sinistral plasma, two miRNAs were identified: hsa-miR-7-5p and hsa-miR-375-3p that were highly upregulated compared to other BIPSS samples and peripheral plasma samples. Further testing by qPCR revealed significant reduction of miR-7-5p in plasma 24 hours after surgery and upregulation in plasma of ACTH secreting PitNET patients compared to non-functioning PitNET patients (P =0.0013). Conclusions By stimulating the ACTH secreting PitNET with CRH a rapid increase of two miRNAs (hsa-mir-7-5p, hsa-mir-375-3p) and ACTH can be observed in sinistral inferior petrosal (tumor side). A decrease of miR-7-5p in plasma after surgery and upregulation in plasma of ACTH secreting PitNET patients was discovered implying that further studies of this miRNA as diagnostic marker is needed.
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Affiliation(s)
- Helvijs Niedra
- Department of Molecular and Functional Genomics, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Raitis Peculis
- Department of Molecular and Functional Genomics, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ilze Konrade
- Department of Endocrinology, Riga East Clinical University Hospital, Riga, Latvia
- Department of Internal Diseases, Riga Stradins University, Riga, Latvia
| | - Inga Balcere
- Department of Endocrinology, Riga East Clinical University Hospital, Riga, Latvia
- Department of Internal Diseases, Riga Stradins University, Riga, Latvia
| | - Mihails Romanovs
- Department of Endocrinology, Riga East Clinical University Hospital, Riga, Latvia
- Department of Internal Diseases, Riga Stradins University, Riga, Latvia
| | - Liva Steina
- Department of Neurosurgery, Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Janis Stukens
- Department of Neurosurgery, Pauls Stradins Clinical University Hospital, Riga, Latvia
| | | | - Janis Klovins
- Department of Molecular and Functional Genomics, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Vita Rovite
- Department of Molecular and Functional Genomics, Latvian Biomedical Research and Study Centre, Riga, Latvia
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Smetana J, Brož P. National Genome Initiatives in Europe and the United Kingdom in the Era of Whole-Genome Sequencing: A Comprehensive Review. Genes (Basel) 2022; 13:556. [PMID: 35328109 PMCID: PMC8953625 DOI: 10.3390/genes13030556] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 12/04/2022] Open
Abstract
Identification of genomic variability in population plays an important role in the clinical diagnostics of human genetic diseases. Thanks to rapid technological development in the field of massive parallel sequencing technologies, also known as next-generation sequencing (NGS), complex genomic analyses are now easier and cheaper than ever before, which consequently leads to more effective utilization of these techniques in clinical practice. However, interpretation of data from NGS is still challenging due to several issues caused by natural variability of DNA sequences in human populations. Therefore, development and realization of projects focused on description of genetic variability of local population (often called "national or digital genome") with a NGS technique is one of the best approaches to address this problem. The next step of the process is to share such data via publicly available databases. Such databases are important for the interpretation of variants with unknown significance or (likely) pathogenic variants in rare diseases or cancer or generally for identification of pathological variants in a patient's genome. In this paper, we have compiled an overview of published results of local genome sequencing projects from United Kingdom and Europe together with future plans and perspectives for newly announced ones.
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Affiliation(s)
- Jan Smetana
- Institute of Food Science and Biotechnology, Faculty of Chemistry, Brno University of Technology, 61200 Brno, Czech Republic
| | - Petr Brož
- Department of Genetics and Molecular Biology, Institute of Experimental Biology, Faculty of Science, Masaryk University, 61137 Brno, Czech Republic;
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Salna I, Salna E, Pahirko L, Skrebinska S, Krikova R, Folkmane I, Pīrāgs V, Sokolovska J. Achievement of treatment targets predicts progression of vascular complications in type 1 diabetes. J Diabetes Complications 2021; 35:108072. [PMID: 34635403 DOI: 10.1016/j.jdiacomp.2021.108072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/16/2021] [Accepted: 10/02/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIM To study the association between achievement of guideline-defined treatment targets on HbA1c, low-density lipoproteins (LDL-C), and blood pressure with the progression of diabetic complications in patients with type 1 diabetes (T1D). METHODS The study included 355 patients at baseline and 114 patients with follow-up data after 3-5 years. Outcome variables were the progression of diabetic kidney disease, retinopathy, or cardiovascular disease (CVD). We used logistic regression and other machine learning algorithms (MLA) to model the association of achievement of treatment targets and probability of progression of complications. RESULTS Achievement of the target blood pressure was associated with 96% lower odds of a new CVD event (0.04 (95% CI 0.00, 0.53), p = 0.016), and 72% lower odds of progression of any complication (0.28 (95% CI 0.09, 0.89), p = 0.027. Achievement of HbA1c target was associated with lower odds of composite complication progression by 82% (0.18 (95% CI 0.04, 0.88), p = 0.034.) None of the patients who achieved HbA1c target progressed in CVD. MLA demonstrated good accuracy for the prediction of progression of CVD (AUC 0.824), and lower accuracy for other complications. CONCLUSION The achievement of blood pressure and HbA1c treatment targets is associated with lower odds of vascular complication of T1D in a real life study.
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Affiliation(s)
- Ilze Salna
- University of Latvia, Faculty of Medicine, Jelgavas iela 3, LV 1004 Riga, Latvia; Pauls Stradiņš Clinical University Hospital, Endocrinology Department, Pilsoņu iela 13, LV 1002 Riga, Latvia
| | - Edgars Salna
- University of Latvia, Faculty of Medicine, Jelgavas iela 3, LV 1004 Riga, Latvia
| | - Leonora Pahirko
- University of Latvia, Faculty of Physics, Mathematics and Optometry, Jelgavas iela 3, LV 1004 Riga, Latvia
| | - Sabīne Skrebinska
- Riga Stradiņš University, Faculty of Residency, Dzirciema iela 16, LV 1007 Riga, Latvia
| | - Regīna Krikova
- University of Latvia, Faculty of Medicine, Jelgavas iela 3, LV 1004 Riga, Latvia
| | - Inese Folkmane
- University of Latvia, Faculty of Medicine, Jelgavas iela 3, LV 1004 Riga, Latvia; Pauls Stradiņš Clinical University Hospital, Centre of Nephrology, Pilsoņu iela 13, LV 1002 Riga, Latvia
| | - Valdis Pīrāgs
- University of Latvia, Faculty of Medicine, Jelgavas iela 3, LV 1004 Riga, Latvia; Pauls Stradiņš Clinical University Hospital, Endocrinology Department, Pilsoņu iela 13, LV 1002 Riga, Latvia
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Freimane L, Barkane L, Igumnova V, Kivrane A, Zole E, Ranka R. Telomere length and mitochondrial DNA copy number in multidrug-resistant tuberculosis. Tuberculosis (Edinb) 2021; 131:102144. [PMID: 34781086 DOI: 10.1016/j.tube.2021.102144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/03/2021] [Accepted: 11/07/2021] [Indexed: 12/25/2022]
Abstract
Multidrug resistant tuberculosis (MDR-TB) is a severe disease that requires prolonged chemotherapy and is associated with an increased probability of treatment failure and death. MDR-TB is a state of heightened oxidative stress and inflammation, which could be related to the aging-related processes and immunosenescence. We, therefore, tested the hypothesis that MDR-TB is associated with alterations in aging biomarkers in peripheral blood cells. We investigated 51 MDR-TB patients and 57 healthy individuals and carried out an analysis of covariance to assess the possible impact of different variables on biomarker perturbations. The results showed that MDR-TB patients had significantly reduced telomere length (TL) and increased mitochondrial DNA copy number (mtDNA CN) (P < 0.05) in comparison to the controls, and MDR-TB infection was the main influencing factor. Male sex and extrapulmonary TB strongly influenced mtDNA CN increment, and MDR-TB patients with normal weight had longer telomeres than those who were underweight (P < 0.05). In conclusion, the evidence for shorter telomeres and higher mtDNA CN in the peripheral blood cells of MDR-TB patients was obtained indicating the connection between MDR-TB and aging biomarkers. The observed associations highlight a complicated interplay between MDR-TB and immunosenescence, thus further studies are required to achieve full understanding.
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Affiliation(s)
- Lauma Freimane
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, Riga, LV1067, Latvia; Riga Stradins University, Dzirciema Street 16, Riga, LV1007, Latvia
| | - Linda Barkane
- Riga Stradins University, Dzirciema Street 16, Riga, LV1007, Latvia; Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Stopini Region, Upeslejas, LV2118, Latvia
| | - Viktorija Igumnova
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, Riga, LV1067, Latvia
| | - Agnija Kivrane
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, Riga, LV1067, Latvia
| | - Egija Zole
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, Riga, LV1067, Latvia
| | - Renate Ranka
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, Riga, LV1067, Latvia; Riga Stradins University, Dzirciema Street 16, Riga, LV1007, Latvia.
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LC-MS/MS method for simultaneous quantification of the first-line anti-tuberculosis drugs and six primary metabolites in patient plasma: Implications for therapeutic drug monitoring. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1185:122986. [PMID: 34688197 DOI: 10.1016/j.jchromb.2021.122986] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/28/2021] [Accepted: 10/08/2021] [Indexed: 11/20/2022]
Abstract
The pharmacokinetic profiling of drug substances and corresponding metabolites in the biological matrix is one of the most informative tools for the treatment efficacy assessment. Therefore, to satisfy the need for comprehensive monitoring of anti-tuberculosis drugs in human plasma, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and validated for simultaneous quantification of first-line anti-tuberculosis drugs (ethambutol, isoniazid, pyrazinamide, and rifampicin) along with their six primary metabolites. Simple single-step protein precipitation with methanol was chosen as the most convenient sample pre-treatment method. Chromatographic separation of the ten analyte mixture was achieved within 10 minutes on a reverse-phase C8 column using mobile phase gradient mode. The multiple reaction monitoring mode (MRM) was used for analyte detection and quantification in patient samples. The chosen quantification ranges fully covered expected plasma concentrations. The method exhibited acceptable selectivity; the within- and between-run accuracy ranged from 87.2 to 113.6%, but within- and between-run precision was between 1.6 and 14.9% (at the LLOQ level CV < 20%). Although the response of the isonicotinic acid varied depending on the matrix source (CV 21.8%), validation results proved that such inconsistency does not affect the accuracy and precision of results. If stored at room temperature plasma samples should be processed within 4 h after collection, temporary storage at -20 °C up to 24 h is acceptable due to stability issues of analytes. The developed method was applied for the patient sample analysis (n = 34) receiving anti-tuberculosis treatment with the first-line drugs.
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Rescenko R, Peculis R, Briviba M, Ansone L, Terentjeva A, Litvina HD, Birzniece L, Megnis K, Kolesova O, Rozentale B, Viksna L, Rovite V, Klovins J. Replication of LZTFL1 Gene Region as a Susceptibility Locus for COVID-19 in Latvian Population. Virol Sin 2021; 36:1241-1244. [PMID: 34668132 PMCID: PMC8526276 DOI: 10.1007/s12250-021-00448-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/24/2021] [Indexed: 01/02/2023] Open
Affiliation(s)
| | - Raitis Peculis
- Latvian Biomedical Research and Study Centre, Riga, 1067, Latvia
| | - Monta Briviba
- Latvian Biomedical Research and Study Centre, Riga, 1067, Latvia
| | - Laura Ansone
- Latvian Biomedical Research and Study Centre, Riga, 1067, Latvia
| | | | | | - Liga Birzniece
- Latvian Biomedical Research and Study Centre, Riga, 1067, Latvia
| | - Kaspars Megnis
- Latvian Biomedical Research and Study Centre, Riga, 1067, Latvia
| | | | | | | | - Vita Rovite
- Latvian Biomedical Research and Study Centre, Riga, 1067, Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Riga, 1067, Latvia.
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Araja D, Berkis U, Lunga A, Murovska M. Shadow Burden of Undiagnosed Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) on Society: Retrospective and Prospective-In Light of COVID-19. J Clin Med 2021; 10:jcm10143017. [PMID: 34300183 PMCID: PMC8303374 DOI: 10.3390/jcm10143017] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
Background: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a poorly understood, complex, multisystem disorder, with severe fatigue not alleviated by rest, and other symptoms, which lead to substantial reductions in functional activity and quality of life. Due to the unclear aetiology, treatment of patients is complicated, but one of the initial problems is the insufficient diagnostic process. The increase in the number of undiagnosed ME/CFS patients became specifically relevant in the light of the COVID-19 pandemic. The aim of this research was to investigate the issues of undiagnosed potential ME/CFS patients, with a hypothetical forecast of the expansion of post-viral CFS as a consequence of COVID-19 and its burden on society. Methods: The theoretical research was founded on the estimation of classic factors presumably affecting the diagnostic scope of ME/CFS and their ascription to Latvian circumstances, as well as a literature review to assess the potential interaction between ME/CFS and COVID-19 as a new contributing agent. The empirical study design consisted of two parts: The first part was dedicated to a comparison of the self-reported data of ME/CFS patients with those of persons experiencing symptoms similar to ME/CFS, but without a diagnosis. This part envisaged the creation of an assumption of the ME/CFS shadow burden “status quo”, not addressing the impact of COVID-19. The second part aimed to investigate data from former COVID-19 patients’ surveys on the presence of ME/CFS symptoms, 6 months after being affected by COVID-19. Descriptive and analytical statistical methods were used to analyse the obtained data. Results: The received data assumed that the previously obtained data on the ME/CFS prevalence of 0.8% in the Latvian population are appropriate, and the literature review reports a prevalence of 0.2–1.0% in developed countries. Regarding the reciprocity of ME/CFS and COVID-19, the literature review showed a lack of research in this field. The empirical results show quite similar self-esteem among ME/CFS patients and undiagnosed patients with longstanding disease experience, while former COVID-19 patients show a significantly lower severity of these problems. Notably, “psychological distress (anxiety)” and “episodic fatigue” are significantly predominant symptoms reported by former COVID-19 patients in comparison with ME/CFS patients and undiagnosed patients prior to the COVID-19 pandemic. The results of our analysis predict that the total amount of direct medical costs for undiagnosed patients (out-of-pocket payments) is more than EUR 15 million p.a. (in Latvia), and this may increase by at least 15% due to the consequences of COVID-19. Conclusions: ME/CFS creates a significant shadow burden on society, even considering only the direct medical costs of undiagnosed patients—the number of whom in Latvia is probably at least five times higher than the number of discerned patients. Simultaneously, COVID-19 can induce long-lasting complications and chronic conditions, such as post-viral CFS, and increase this burden. The Latvian research data assume that ME/CFS patients are not a high-risk group for COVID-19; however, COVID-19 causes ME/CFS-relevant symptoms in patients. This increases the need for monitoring of patients for even longer after recovering from COVID-19′s symptoms, in order to prevent complications and the progression of chronic diseases. In the context of further epidemiological uncertainty, and the possibility of severe post-viral consequences, preventive measures are becoming significantly more important; an integrated diagnostic approach and appropriate treatment could reduce this burden in the future.
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Affiliation(s)
- Diana Araja
- Department of Dosage Form Technology, Faculty of Pharmacy, Riga Stradins University, 16 Dzirciema Str, LV-1007 Riga, Latvia
- Institute of Microbiology and Virology, Riga Stradins University, 5 Ratsupites Str, LV-1067 Riga, Latvia; (U.B.); (M.M.)
- Correspondence:
| | - Uldis Berkis
- Institute of Microbiology and Virology, Riga Stradins University, 5 Ratsupites Str, LV-1067 Riga, Latvia; (U.B.); (M.M.)
- Development and Project Department, Riga Stradins University, 16 Dzirciema Str, LV-1007 Riga, Latvia;
| | - Asja Lunga
- Development and Project Department, Riga Stradins University, 16 Dzirciema Str, LV-1007 Riga, Latvia;
| | - Modra Murovska
- Institute of Microbiology and Virology, Riga Stradins University, 5 Ratsupites Str, LV-1067 Riga, Latvia; (U.B.); (M.M.)
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Rostoka E, Salna I, Dekante A, Pahirko L, Borisovs V, Celma L, Valeinis J, Sjakste N, Sokolovska J. DNA damage in leukocytes and serum nitrite concentration are negatively associated in type 1 diabetes. Mutagenesis 2021; 36:213-222. [PMID: 34008029 DOI: 10.1093/mutage/geab015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/12/2021] [Indexed: 11/12/2022] Open
Abstract
Chronic hyperglycaemia leads to DNA damage in diabetes and might be associated with nitrosative stress. In this study, we aimed at assessing the level of DNA strand breaks in leukocytes, serum nitrite and nitrate in patients with type 1 diabetes and healthy controls and associations of these parameters with diabetes-related outcomes in a prospective study. The level of DNA damage was determined in 71 patients with type 1 diabetes and 57 healthy controls by comet assay and scored with arbitrary units (AU). The chemiluminescence method was used to measure nitrite and nitrate. Clinical information and data on consumption of alcohol, physical activity and smoking were collected. Progression of complications in patients with diabetes was assessed after a follow-up time of 4-5 years. We observed a higher level of DNA damage in leukocytes of patients with type 1 diabetes compared with healthy subjects [type 1 diabetes AU 50 (36-74.5); control AU 30 (24.1-43), P < 0.001]. According to regression, type 1 diabetes leads to a 2-fold increase in DNA damage. In the group of type 1 diabetes, DNA damage correlated positively with total cholesterol (R = 0.262, P = 0.028) and negatively with serum glucose level (R = -0.284; P = 0.018) and serum nitrite (R = -0.335; P = 0.008). DNA damage was not significantly associated with HbA1c, diabetes duration, complications and lifestyle factors. However, DNA damage > 57 AU was associated with statistically significantly lower serum nitrite and 1.52 higher risk of progression of complications of diabetes over the follow-up period. The latter result was not statistically significant due to insufficient study power [relative risk 1.52 (95% confidence interval = 0.68, 3.42, P = 0.31)]. Our results confirm that type 1 diabetes is associated with a higher level of DNA strand breaks in leukocytes when compared with the reference group and demonstrate the negative association between DNA damage and serum nitrite concentration.
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Affiliation(s)
- Evita Rostoka
- Faculty of Medicine, University of Latvia, Jelgavas Street 3, LV1004 Riga, Latvia
| | - Ilze Salna
- Residency Development Program, University of Latvia, Aspazijas Bvd. 5, LV1050 Riga, Latvia
| | - Alise Dekante
- Residency Development Program, University of Latvia, Aspazijas Bvd. 5, LV1050 Riga, Latvia
| | - Leonora Pahirko
- Faculty of Physics, Mathematics and Optometry, University of Latvia, Jelgavas Street 3, LV1004 Riga, Latvia
| | - Vitalijs Borisovs
- Faculty of Medicine, University of Latvia, Jelgavas Street 3, LV1004 Riga, Latvia
| | - Laura Celma
- Faculty of Medicine, University of Latvia, Jelgavas Street 3, LV1004 Riga, Latvia
| | - Jānis Valeinis
- Faculty of Physics, Mathematics and Optometry, University of Latvia, Jelgavas Street 3, LV1004 Riga, Latvia
| | - Nikolajs Sjakste
- Faculty of Medicine, University of Latvia, Jelgavas Street 3, LV1004 Riga, Latvia
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Kivrane A, Igumnova V, Kimsis J, Freimane L, Sadovska D, Viksna A, Pole I, Ranka R. Implementation of a next-generation sequencing-based targeted approach for full-length CYP3A4 gene sequencing. Pharmacogenomics 2021; 22:519-527. [PMID: 34003019 DOI: 10.2217/pgs-2020-0128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To evaluate the application of next-generation sequencing-based targeted protocol for full-length CYP3A4 gene sequencing analysis. Materials & methods: The developed sequencing protocol was applied to analyze human DNA samples (n = 7) obtained from tuberculosis patients admitted to the Riga East University Hospital, Center of Tuberculosis and Lung diseases. Results: The sequencing data quality was sufficient for the detection of already known genetic variants, as well as for identifying rare and novel variants dispersed throughout the CYP3A4 gene with a high degree of confidence. Conclusion: Developed protocol can be applied in subpopulation level association studies to determine whether specific genetic variants or variant combinations from multiple regions of the CYP3A4 gene are of clinical significance.
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Affiliation(s)
- Agnija Kivrane
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, Riga, LV1067, Latvia.,Riga Stradins University, Dzirciema Street 16, Riga, LV1007, Latvia
| | - Viktorija Igumnova
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, Riga, LV1067, Latvia.,Riga Stradins University, Dzirciema Street 16, Riga, LV1007, Latvia
| | - Janis Kimsis
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, Riga, LV1067, Latvia
| | - Lauma Freimane
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, Riga, LV1067, Latvia
| | - Darja Sadovska
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, Riga, LV1067, Latvia.,Riga Stradins University, Dzirciema Street 16, Riga, LV1007, Latvia
| | - Anda Viksna
- Riga Stradins University, Dzirciema Street 16, Riga, LV1007, Latvia.,Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Stopini region, Upeslejas, LV2118, Latvia
| | - Ilva Pole
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Stopini region, Upeslejas, LV2118, Latvia
| | - Renate Ranka
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, Riga, LV1067, Latvia.,Riga Stradins University, Dzirciema Street 16, Riga, LV1007, Latvia
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Kovanda A, Zimani AN, Peterlin B. How to design a national genomic project-a systematic review of active projects. Hum Genomics 2021; 15:20. [PMID: 33761998 PMCID: PMC7988644 DOI: 10.1186/s40246-021-00315-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/23/2021] [Indexed: 01/18/2023] Open
Abstract
An increasing number of countries are investing efforts to exploit the human genome, in order to improve genetic diagnostics and to pave the way for the integration of precision medicine into health systems. The expected benefits include improved understanding of normal and pathological genomic variation, shorter time-to-diagnosis, cost-effective diagnostics, targeted prevention and treatment, and research advances.We review the 41 currently active individual national projects concerning their aims and scope, the number and age structure of included subjects, funding, data sharing goals and methods, and linkage with biobanks, medical data, and non-medical data (exposome). The main aims of ongoing projects were to determine normal genomic variation (90%), determine pathological genomic variation (rare disease, complex diseases, cancer, etc.) (71%), improve infrastructure (59%), and enable personalized medicine (37%). Numbers of subjects to be sequenced ranges substantially, from a hundred to over a million, representing in some cases a significant portion of the population. Approximately half of the projects report public funding, with the rest having various mixed or private funding arrangements. 90% of projects report data sharing (public, academic, and/or commercial with various levels of access) and plan on linking genomic data and medical data (78%), existing biobanks (44%), and/or non-medical data (24%) as the basis for enabling personal/precision medicine in the future.Our results show substantial diversity in the analysed categories of 41 ongoing national projects. The overview of current designs will hopefully inform national initiatives in designing new genomic projects and contribute to standardisation and international collaboration.
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Affiliation(s)
- Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Slajmerjeva 4, Ljubljana, Slovenia
| | - Ana Nyasha Zimani
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Slajmerjeva 4, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Slajmerjeva 4, Ljubljana, Slovenia.
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Saksis R, Silamikelis I, Laksa P, Megnis K, Peculis R, Mandrika I, Rogoza O, Petrovska R, Balcere I, Konrade I, Steina L, Stukens J, Breiksa A, Nazarovs J, Sokolovska J, Pirags V, Klovins J, Rovite V. Medication for Acromegaly Reduces Expression of MUC16, MACC1 and GRHL2 in Pituitary Neuroendocrine Tumour Tissue. Front Oncol 2021; 10:593760. [PMID: 33680922 PMCID: PMC7928352 DOI: 10.3389/fonc.2020.593760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022] Open
Abstract
Acromegaly is a disease mainly caused by pituitary neuroendocrine tumor (PitNET) overproducing growth hormone. First-line medication for this condition is the use of somatostatin analogs (SSAs), that decrease tumor mass and induce antiproliferative effects on PitNET cells. Dopamine agonists (DAs) can also be used if SSA treatment is not effective. This study aimed to determine differences in transcriptome signatures induced by SSA/DA therapy in PitNET tissue. We selected tumor tissue from twelve patients with somatotropinomas, with half of the patients receiving SSA/DA treatment before surgery and the other half treatment naive. Transcriptome sequencing was then carried out to identify differentially expressed genes (DEGs) and their protein–protein interactions, using pathway analyses. We found 34 upregulated and six downregulated DEGs in patients with SSA/DA treatment. Three tumor development promoting factors MUC16, MACC1, and GRHL2, were significantly downregulated in therapy administered PitNET tissue; this finding was supported by functional studies in GH3 cells. Protein–protein interactions and pathway analyses revealed extracellular matrix involvement in the antiproliferative effects of this type of the drug treatment, with pronounced alterations in collagen regulation. Here, we have demonstrated that somatotropinomas can be distinguished based on their transcriptional profiles following SSA/DA therapy, and SSA/DA treatment does indeed cause changes in gene expression. Treatment with SSA/DA significantly downregulated several factors involved in tumorigenesis, including MUC16, MACC1, and GRHL2. Genes that were upregulated, however, did not have a direct influence on antiproliferative function in the PitNET cells. These findings suggested that SSA/DA treatment acted in a tumor suppressive manner and furthermore, collagen related interactions and pathways were enriched, implicating extracellular matrix involvement in this anti-tumor effect of drug treatment.
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Affiliation(s)
- Rihards Saksis
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Pola Laksa
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Kaspars Megnis
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Raitis Peculis
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ilona Mandrika
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Olesja Rogoza
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Inga Balcere
- Riga East Clinical University Hospital, Riga, Latvia.,Riga Stradins University, Riga, Latvia
| | - Ilze Konrade
- Riga East Clinical University Hospital, Riga, Latvia.,Riga Stradins University, Riga, Latvia
| | - Liva Steina
- Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Janis Stukens
- Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Austra Breiksa
- Pauls Stradins Clinical University Hospital, Riga, Latvia
| | | | | | - Valdis Pirags
- Pauls Stradins Clinical University Hospital, Riga, Latvia.,University of Latvia Faculty of Medicine, Riga, Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Vita Rovite
- Latvian Biomedical Research and Study Centre, Riga, Latvia
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Ustinova M, Peculis R, Rescenko R, Rovite V, Zaharenko L, Elbere I, Silamikele L, Konrade I, Sokolovska J, Pirags V, Klovins J. Novel susceptibility loci identified in a genome-wide association study of type 2 diabetes complications in population of Latvia. BMC Med Genomics 2021; 14:18. [PMID: 33430853 PMCID: PMC7802349 DOI: 10.1186/s12920-020-00860-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 12/20/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Type 2 diabetes complications cause a serious emotional and economical burden to patients and healthcare systems globally. Management of both acute and chronic complications of diabetes, which dramatically impair the quality of patients' life, is still an unsolved issue in diabetes care, suggesting a need for early identification of individuals with high risk for developing diabetes complications. METHODS We performed a genome-wide association study in 601 type 2 diabetes patients after stratifying them according to the presence or absence of four types of diabetes complications: diabetic neuropathy, diabetic nephropathy, macrovascular complications, and ophthalmic complications. RESULTS The analysis revealed ten novel associations showing genome-wide significance, including rs1132787 (GYPA, OR = 2.71; 95% CI = 2.02-3.64) and diabetic neuropathy, rs2477088 (PDE4DIP, OR = 2.50; 95% CI = 1.87-3.34), rs4852954 (NAT8, OR = 2.27; 95% CI = 2.71-3.01), rs6032 (F5, OR = 2.12; 95% CI = 1.63-2.77), rs6935464 (RPS6KA2, OR = 2.25; 95% CI = 6.69-3.01) and macrovascular complications, rs3095447 (CCDC146, OR = 2.18; 95% CI = 1.66-2.87) and ophthalmic complications. By applying the targeted approach of previously reported susceptibility loci we managed to replicate three associations: MAPK14 (rs3761980, rs80028505) and diabetic neuropathy, APOL1 (rs136161) and diabetic nephropathy. CONCLUSIONS Together these results provide further evidence for the implication of genetic factors in the development of type 2 diabetes complications and highlight several potential key loci, able to modify the risk of developing these conditions. Moreover, the candidate variant approach proves a strong and consistent effect for multiple variants across different populations.
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Affiliation(s)
- Monta Ustinova
- Latvian Biomedical Research and Study Centre, Ratsupites iela 1, Riga, 1067, Latvia
| | - Raitis Peculis
- Latvian Biomedical Research and Study Centre, Ratsupites iela 1, Riga, 1067, Latvia
| | - Raimonds Rescenko
- Latvian Biomedical Research and Study Centre, Ratsupites iela 1, Riga, 1067, Latvia
| | - Vita Rovite
- Latvian Biomedical Research and Study Centre, Ratsupites iela 1, Riga, 1067, Latvia
| | - Linda Zaharenko
- Latvian Biomedical Research and Study Centre, Ratsupites iela 1, Riga, 1067, Latvia
| | - Ilze Elbere
- Latvian Biomedical Research and Study Centre, Ratsupites iela 1, Riga, 1067, Latvia
| | - Laila Silamikele
- Latvian Biomedical Research and Study Centre, Ratsupites iela 1, Riga, 1067, Latvia
| | - Ilze Konrade
- Latvian Biomedical Research and Study Centre, Ratsupites iela 1, Riga, 1067, Latvia
- Faculty of Medicine, Riga Stradins University, Dzirciema iela 16, Riga, 1007, Latvia
| | | | - Valdis Pirags
- Latvian Biomedical Research and Study Centre, Ratsupites iela 1, Riga, 1067, Latvia
- Faculty of Medicine, University of Latvia, Jelgavas iela 3, Riga, 1004, Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Ratsupites iela 1, Riga, 1067, Latvia.
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Grasmane A, Rots D, Vitina Z, Magomedova V, Gailite L. The association of FMR1 gene (CGG)n variation with idiopathic female infertility. Arch Med Sci 2021; 17:1303-1307. [PMID: 34522259 PMCID: PMC8425234 DOI: 10.5114/aoms.2019.85154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 09/16/2018] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION 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 (< 26 CGG) alleles may also have an impact on female reproductive function. MATERIAL AND METHODS We have performed a case-control study to assess the impact of FMR1 gene CGG repeats on female infertility. The study comprised 161 women with primary and secondary idiopathic infertility and 12 females with diminished ovarian reserve. The control group consisted of 129 healthy women with children. The FMR1 gene trinucleotide CGG repeat variation was detected using a triplet repeat primed polymerase chain reaction with capillary electrophoresis. RESULTS The analysis of CGG repeats revealed that high-normal alleles are statistically significantly more common in the secondary infertility group than in controls (12% vs. 4.3%, p = 0.03, OR = 3.1, 95% CI: 1.1-8.3). The distribution of high-normal alleles and genotypes did not differ between patients with primary infertility and controls (p > 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.
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Elbere I, Silamikelis I, Dindune II, Kalnina I, Ustinova M, Zaharenko L, Silamikele L, Rovite V, Gudra D, Konrade I, Sokolovska J, Pirags V, Klovins J. Baseline gut microbiome composition predicts metformin therapy short-term efficacy in newly diagnosed type 2 diabetes patients. PLoS One 2020; 15:e0241338. [PMID: 33125401 PMCID: PMC7598494 DOI: 10.1371/journal.pone.0241338] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023] Open
Abstract
Background The study was conducted to investigate the effects of metformin treatment on the human gut microbiome’s taxonomic and functional profile in the Latvian population, and to evaluate the correlation of these changes with therapeutic efficacy and tolerance. Methods In this longitudinal observational study, stool samples for shotgun metagenomic sequencing-based analysis were collected in two cohorts. The first cohort included 35 healthy nondiabetic individuals (metformin dose 2x850mg/day) at three time-points during metformin administration. The second cohort was composed of 50 newly-diagnosed type 2 diabetes patients (metformin dose–determined by an endocrinologist) at two concordant times. Patients were defined as Responders if their HbA1c levels during three months of metformin therapy had decreased by ≥12.6 mmol/mol (1%), while in Non-responders HbA1c were decreased by <12.6 mmol/mol (1%). Results Metformin reduced the alpha diversity of microbiota in healthy controls (p = 0.02) but not in T2D patients. At the species level, reduction in the abundance of Clostridium bartlettii and Barnesiella intestinihominis, as well as an increase in the abundance of Parabacteroides distasonis and Oscillibacter unclassified overlapped between both study groups. A large number of group-specific changes in taxonomic and functional profiles was observed. We identified an increased abundance of Prevotella copri (FDR = 0.01) in the Non-Responders subgroup, and enrichment of Enterococcus faecium, Lactococcus lactis, Odoribacter, and Dialister at baseline in the Responders group. Various taxonomic units were associated with the observed incidence of side effects in both cohorts. Conclusions Metformin effects are different in T2D patients and healthy individuals. Therapy induced changes in the composition of gut microbiome revealed possible mediators of observed short-term therapeutic effects. The baseline composition of the gut microbiome may influence metformin therapy efficacy and tolerance in T2D patients and could be used as a powerful prediction tool.
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Affiliation(s)
- Ilze Elbere
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | | - Ineta Kalnina
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Monta Ustinova
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | | - Vita Rovite
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Dita Gudra
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ilze Konrade
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- Riga Stradins University, Riga, Latvia
| | | | - Valdis Pirags
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- * E-mail:
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41
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García-Calzón S, Perfilyev A, Martinell M, Ustinova M, Kalamajski S, Franks PW, Bacos K, Elbere I, Pihlajamäki J, Volkov P, Vaag A, Groop L, Maziarz M, Klovins J, Ahlqvist E, Ling C. Epigenetic markers associated with metformin response and intolerance in drug-naïve patients with type 2 diabetes. Sci Transl Med 2020; 12:12/561/eaaz1803. [DOI: 10.1126/scitranslmed.aaz1803] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/27/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022]
Abstract
Metformin is the first-line pharmacotherapy for managing type 2 diabetes (T2D). However, many patients with T2D do not respond to or tolerate metformin well. Currently, there are no phenotypes that successfully predict glycemic response to, or tolerance of, metformin. We explored whether blood-based epigenetic markers could discriminate metformin response and tolerance by analyzing genome-wide DNA methylation in drug-naïve patients with T2D at the time of their diagnosis. DNA methylation of 11 and 4 sites differed between glycemic responders/nonresponders and metformin-tolerant/intolerant patients, respectively, in discovery and replication cohorts. Greater methylation at these sites associated with a higher risk of not responding to or not tolerating metformin with odds ratios between 1.43 and 3.09 per 1-SD methylation increase. Methylation risk scores (MRSs) of the 11 identified sites differed between glycemic responders and nonresponders with areas under the curve (AUCs) of 0.80 to 0.98. MRSs of the 4 sites associated with future metformin intolerance generated AUCs of 0.85 to 0.93. Some of these blood-based methylation markers mirrored the epigenetic pattern in adipose tissue, a key tissue in diabetes pathogenesis, and genes to which these markers were annotated to had biological functions in hepatocytes that altered metformin-related phenotypes. Overall, we could discriminate between glycemic responders/nonresponders and participants tolerant/intolerant to metformin at diagnosis by measuring blood-based epigenetic markers in drug-naïve patients with T2D. This epigenetics-based tool may be further developed to help patients with T2D receive optimal therapy.
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Affiliation(s)
- Sonia García-Calzón
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
- Department of Nutrition, Food Science and Physiology, University of Navarra, 31008 Pamplona, Spain
| | - Alexander Perfilyev
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
| | - Mats Martinell
- Department of Public Health and Caring Sciences, Uppsala University, 751 22 Uppsala, Sweden
| | - Monta Ustinova
- Latvian Biomedical Research and Study Centre, Rātsupītes Street 1, k-1, Riga LV-1067, Latvia
| | - Sebastian Kalamajski
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, 214 28 Malmö, Sweden
| | - Paul W. Franks
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, 214 28 Malmö, Sweden
| | - Karl Bacos
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
| | - Ilze Elbere
- Latvian Biomedical Research and Study Centre, Rātsupītes Street 1, k-1, Riga LV-1067, Latvia
| | - Jussi Pihlajamäki
- Institute of Public Health and Clinical Nutrition, Internal Medicine, University of Eastern Finland, 70211 Kuopio, Finland
- Clinical Nutrition and Obesity Center, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Petr Volkov
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
| | - Allan Vaag
- Type 2 Diabetes Biology Research, Steno Diabetes Center, 2820 Gentofte, Denmark
| | - Leif Groop
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
| | - Marlena Maziarz
- Bioinformatics Unit, Department of Clinical Sciences, Lund University Diabetes Centre, 214 28 Malmö, Sweden
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Rātsupītes Street 1, k-1, Riga LV-1067, Latvia
- Faculty of Biology, University of Latvia, Riga LV-1004, Latvia
| | - Emma Ahlqvist
- Genomics, Diabetes and Endocrinology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Scania University Hospital, 214 28 Malmö, Sweden
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Vedmedovska N, Bokucava D, Kivite-Urtane A, Rovite V, Zake-Nikitina L, Klovins J, Fodina V, Donders GGG. The Correlation Between Abnormal Uterine Artery Flow in the First Trimester and Genetic Thrombophilic Alteration: A Prospective Case-Controlled Pilot Study. Diagnostics (Basel) 2020; 10:diagnostics10090654. [PMID: 32878173 PMCID: PMC7555473 DOI: 10.3390/diagnostics10090654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/23/2020] [Accepted: 08/28/2020] [Indexed: 11/16/2022] Open
Abstract
INTRODUCTION Evaluation of the first trimester uterine artery flow can predict the development of obstetrical complications. A genotype, making women prone to microthrombi. constitutes the main known susceptibility factor for anomalous development of placenta. Our aim was to study whether polymorphisms of 10 genes leading to blood clotting abnormalities are related to abnormal uterine artery blood flow in the first trimester, and may predict placenta-related diseases. MATERIAL AND METHODS In primary analyses we included 19 singleton pregnancies with abnormal blood flow in the uterine arteries during the first trimester of gestation, and 24 matched control with normal flow patterns. All patients were genotyped for sequence variations in F5, F2, F11, MTHFR, SERPINE-1, CYP4V2, SELE, GP6, angiotensinogen (AGT) and fibrinogen gamma (FGG) genes and followed up until delivery. RESULTS There were no differences between groups regarding selected sequence variations in any of these genes. The co-occurrence of several polymorphisms in the same patient was also not related to the blood flow patterns in the uterine arteries. CONCLUSIONS Although we found certain trends of genetic polymorphisms being related to preeclampsia and fetal growth, we failed to find an association between clotting gene polymorphisms, single or in combination, with the abnormal uterine flow in the first trimester.
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Affiliation(s)
- Natalija Vedmedovska
- Department of Obstetrics and Gynecology, Riga Stradins University, LV-1007 Riga, Latvia;
- Correspondence: ; Tel.: +371-29429704
| | - Diana Bokucava
- Department of Obstetrics and Gynecology, Riga Stradins University, LV-1007 Riga, Latvia;
| | - Anda Kivite-Urtane
- Department of Public Health and Epidemiology, Riga Stradins University, LV-1010 Riga, Latvia;
| | - Vita Rovite
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (V.R.); (L.Z.-N.); (J.K.)
| | - Liene Zake-Nikitina
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (V.R.); (L.Z.-N.); (J.K.)
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (V.R.); (L.Z.-N.); (J.K.)
- Department of Medicine, University of Latvia, LV-1050 Riga, Latvia
| | | | - Gilbert G. G. Donders
- Department of Obstetrics and Gynecology, University of Antwerp, 2550 Antwerp-Edegem, Belgium;
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Ustinova M, Ansone L, Silamikelis I, Rovite V, Elbere I, Silamikele L, Kalnina I, Fridmanis D, Sokolovska J, Konrade I, Pirags V, Klovins J. Whole-blood transcriptome profiling reveals signatures of metformin and its therapeutic response. PLoS One 2020; 15:e0237400. [PMID: 32780768 PMCID: PMC7418999 DOI: 10.1371/journal.pone.0237400] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/25/2020] [Indexed: 12/18/2022] Open
Abstract
Metformin, a biguanide agent, is the first-line treatment for type 2 diabetes mellitus due to its glucose-lowering effect. Despite its wide application in the treatment of multiple health conditions, the glycemic response to metformin is highly variable, emphasizing the need for reliable biomarkers. We chose the RNA-Seq-based comparative transcriptomics approach to evaluate the systemic effect of metformin and highlight potential predictive biomarkers of metformin response in drug-naïve volunteers with type 2 diabetes in vivo. The longitudinal blood-derived transcriptome analysis revealed metformin-induced differential expression of novel and previously described genes involved in cholesterol homeostasis (SLC46A1 and LRP1), cancer development (CYP1B1, STAB1, CCR2, TMEM176B), and immune responses (CD14, CD163) after administration of metformin for three months. We demonstrate for the first time a transcriptome-based molecular discrimination between metformin responders (delta HbA1c ≥ 1% or 12.6 mmol/mol) and non-responders (delta HbA1c < 1% or 12.6 mmol/mol), that is determined by expression levels of 56 genes, explaining 13.9% of the variance in the therapeutic efficacy of the drug. Moreover, we found a significant upregulation of IRS2 gene (log2FC 0.89) in responders compared to non-responders before the use of metformin. Finally, we provide evidence for the mitochondrial respiratory complex I as one of the factors related to the high variability of the therapeutic response to metformin in patients with type 2 diabetes mellitus.
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Affiliation(s)
- Monta Ustinova
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Laura Ansone
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Vita Rovite
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ilze Elbere
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Ineta Kalnina
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | | - Ilze Konrade
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- Faculty of Medicine, Riga Stradins University, Riga, Latvia
| | - Valdis Pirags
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- * E-mail:
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Zalizko P, Stefanovics J, Sokolovska J, Paramonova N, Klavina E, Erts R, Rovite V, Klovins J, Pukitis A. Thiopurine S-methyltransferase genetic polymorphisms in adult patients with inflammatory bowel diseases in the Latvian population. Therap Adv Gastroenterol 2020; 13:1756284820937426. [PMID: 32704308 PMCID: PMC7361485 DOI: 10.1177/1756284820937426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 05/29/2020] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Thiopurine methyltransferase (TPMT) plays a significant role in the metabolism of thiopurines, and, for patients with inflammatory bowel disease (IBD), it is useful to perform TPMT genotyping prior to azathioprine (AZA) treatment. In this study, we determined TPMT gene polymorphisms in a cohort of IBD patients in Latvia. METHODS DNA samples were obtained from 244 IBD patients, and qPCR was performed for detection of rs1800462, rs1800460, and rs1142345 single-nucleotide polymorphisms (SNPs). Three common, non-functional TPMT alleles (TPMT*2, *3B, and *3C) were identified (women, 51%; men, 49%). TPMT*2, *3A, *3B, and *3C allelic variants detected using qPCR were consistent with restriction fragment length polymorphism (RFLP) data. RESULTS Among patients, 78% had ulcerative colitis and 22% had Crohn's disease, with 93.9% of the former carrying a wild-type homozygous TPMT*1/*1 genotype and 6.1% carrying heterozygous genotypes. The most frequent polymorphisms were TPMT*1/*3A (5.3%: two variants: TPMT*3B and TPMT*3C), TPMT*1/*3C (0.4%), and TPMT*1/*2 (0.4%). None of the patients carried a TPMT*3B polymorphism and no patients were homozygous for any mutation. CONCLUSION This is the first study to identify TPMT gene polymorphisms in adult IBD patients in Latvia. The results indicate that the frequency of common TPMT alleles is similar to that of other European populations.
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Affiliation(s)
| | - Juris Stefanovics
- Pauls Stradins Clinical University Hospital, Riga, Latvia
- Faculty of Medicine, Laboratory of Personalized Medicine, University of Latvia, Riga, Latvia
| | - Jelizaveta Sokolovska
- Faculty of Medicine, Laboratory of Personalized Medicine, University of Latvia, Riga, Latvia
| | - Natalia Paramonova
- Genomics and Bioinformatics, Institute of Biology of the University of Latvia, Salaspils, Latvia
| | - Evija Klavina
- Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Renars Erts
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Vita Rovite
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Aldis Pukitis
- Pauls Stradins Clinical University Hospital, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
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45
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Sokolovska J, Ostrovska K, Pahirko L, Varblane G, Krilatiha K, Cirulnieks A, Folkmane I, Pirags V, Valeinis J, Klavina A, Selavo L. Impact of interval walking training managed through smart mobile devices on albuminuria and leptin/adiponectin ratio in patients with type 2 diabetes. Physiol Rep 2020; 8:e14506. [PMID: 32652863 PMCID: PMC7354089 DOI: 10.14814/phy2.14506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 12/13/2022] Open
Abstract
Background Interval walking training has demonstrated more pronounced positive effects on physical fitness and metabolism in type 2 diabetes (T2D), compared to continuous walking. One of the pathogenic mechanisms of T2D is associated with derangements in leptin/adiponectin axis, which might predispose affected individuals to vascular inflammation and albuminuria. The aim of this study was to investigate the effects of interval walking training delivered through smart mobile devices upon albuminuria and leptin/adiponectin ratio in patients with T2D. Methods Patients with T2D aged 35–75 were randomized into control (n = 26) and interval training (IT, n = 14) groups. Patients in IT group had to perform three 60‐min interval walking sessions (3 min intervals of slow and fast walking with the intensity of 40% and 70% of the peak energy expenditure) per week delivered by smartphone application for four months. The adherence to training was monitored remotely. Outcome measures were albuminuria, leptin/adiponectin ratio, obesity indicators, and glycaemic control. Leptin and adiponectin concentration was measured in serum samples by Luminex technology. Results In the IT group compared to control group, we observed a statistically significant decrease in albuminuria (p = .002) and leptin/adiponectin ratio (p = .01), as well as a decrease in HbA1c close to statistical significance (p = .09). In IT group, changes in leptin/adiponectin ratio correlated significantly with changes in hip circumference (p = .024). Conclusion Interval walking training is beneficial for vascular health in T2D via impact on albuminuria and leptin/adiponectin ratio.
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Affiliation(s)
| | | | - Leonora Pahirko
- Faculty of Physics, Mathematics and Optometry, University of Latvia, Riga, Latvia
| | | | | | | | - Inese Folkmane
- Faculty of Medicine, University of Latvia, Riga, Latvia.,Centre of Nephrology, Pauls Stradins University Hospital, Riga, Latvia
| | - Valdis Pirags
- Faculty of Medicine, University of Latvia, Riga, Latvia.,Department of Internal Medicine, Pauls Stradins University Hospital, Riga, Latvia
| | - Janis Valeinis
- Faculty of Physics, Mathematics and Optometry, University of Latvia, Riga, Latvia
| | - Aija Klavina
- Latvian Academy of Sport Education, Riga, Latvia
| | - Leo Selavo
- Faculty of Computing, University of Latvia, Riga, Latvia
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46
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Peculis R, Balcere I, Radovica-Spalvina I, Konrade I, Caune O, Megnis K, Rovite V, Stukens J, Nazarovs J, Breiksa A, Kiecis A, Silamikelis I, Pirags V, Klovins J. Case report: recurrent pituitary adenoma has increased load of somatic variants. BMC Endocr Disord 2020; 20:17. [PMID: 31996211 PMCID: PMC6988340 DOI: 10.1186/s12902-020-0493-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 01/16/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Pituitary adenomas (PA) have an increased potential for relapse in one to 5 years after resection. In this study, we investigated the genetic differences in genomic DNA of primary and rapidly recurrent tumours in the same patient to explain the causality mechanisms of PA recurrence. CASE PRESENTATION The patient was a 69-year-old female with non-functional pituitary macroadenoma with extension into the left cavernous sinus (Knosp grade 2) who underwent craniotomy and partial resection in August 2010. Two years later, the patient had prolonged tumour growth with an essential suprasellar extension (Knosp grade 2), and a second craniotomy with partial tumour resection was performed in September 2012. In both tumours, the KI-67 level was below 1.5%. Exome sequencing via semiconductor sequencing of patient germline DNA and somatic DNA from both tumours was performed. Tmap alignment and Platypus variant calling were performed followed by variant filtering and manual review with IGV software. We observed an increased load of missense variants in the recurrent PA tumour when compared to the original tumour. The number of detected variants increased from ten to 26 and potential clonal expansion of four variants was observed. Additionally, targeted SNP analysis revealed five rare missense SNPs with a potential impact on the function of the encoded proteins. CONCLUSIONS In this case study, an SNP located in HRAS is the most likely candidate inducing rapid PA progression. The relapsed PA tumour had a higher variation load and fast tumour recurrence in this patient could be caused by clonal expansion of the leftover tumour tissue.
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Affiliation(s)
- Raitis Peculis
- Latvian Biomedical Research and Study Centre, Ratsupites str. 1-k1, Riga, LV-1067 Latvia
| | - Inga Balcere
- Riga East Clinical University Hospital, Hipokrata str. 2, Riga, LV-1038 Latvia
- Riga Stradins University, Dzirciema str. 16, Riga, LV-1007 Latvia
| | - Ilze Radovica-Spalvina
- Latvian Biomedical Research and Study Centre, Ratsupites str. 1-k1, Riga, LV-1067 Latvia
| | - Ilze Konrade
- Riga East Clinical University Hospital, Hipokrata str. 2, Riga, LV-1038 Latvia
- Riga Stradins University, Dzirciema str. 16, Riga, LV-1007 Latvia
| | - Olivija Caune
- Riga East Clinical University Hospital, Hipokrata str. 2, Riga, LV-1038 Latvia
| | - Kaspars Megnis
- Latvian Biomedical Research and Study Centre, Ratsupites str. 1-k1, Riga, LV-1067 Latvia
| | - Vita Rovite
- Latvian Biomedical Research and Study Centre, Ratsupites str. 1-k1, Riga, LV-1067 Latvia
- University of Latvia, Raina blvd. 19, Riga, LV-1586 Latvia
| | - Janis Stukens
- Pauls Stradins Clinical University Hospital, Pilsonu str. 13, Riga, LV-1002 Latvia
| | - Jurijs Nazarovs
- Pauls Stradins Clinical University Hospital, Pilsonu str. 13, Riga, LV-1002 Latvia
| | - Austra Breiksa
- Pauls Stradins Clinical University Hospital, Pilsonu str. 13, Riga, LV-1002 Latvia
| | - Aigars Kiecis
- Riga East Clinical University Hospital, Hipokrata str. 2, Riga, LV-1038 Latvia
| | - Ivars Silamikelis
- Latvian Biomedical Research and Study Centre, Ratsupites str. 1-k1, Riga, LV-1067 Latvia
| | - Valdis Pirags
- University of Latvia, Raina blvd. 19, Riga, LV-1586 Latvia
- Pauls Stradins Clinical University Hospital, Pilsonu str. 13, Riga, LV-1002 Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Ratsupites str. 1-k1, Riga, LV-1067 Latvia
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47
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Peculis R, Mandrika I, Petrovska R, Dortane R, Megnis K, Nazarovs J, Balcere I, Stukens J, Konrade I, Pirags V, Klovins J, Rovite V. Pituispheres Contain Genetic Variants Characteristic to Pituitary Adenoma Tumor Tissue. Front Endocrinol (Lausanne) 2020; 11:313. [PMID: 32528411 PMCID: PMC7256168 DOI: 10.3389/fendo.2020.00313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/24/2020] [Indexed: 12/16/2022] Open
Abstract
The most common type of pituitary neoplasms is benign pituitary adenoma (PA). Clinically significant PAs affect around 0.1% of the population. Currently, there is no established human PA cell culture available and when PA tumor cells are cultured they form two distinct types depending on culturing conditions either free-floating aggregates also known as pituispheres or cells adhering to the surface of cell plates and displaying mesenchymal stem-like properties. The aim of this study was to trace the origin of sphere-forming and adherent pituitary cell cultures and characterize the potential use of these surgery derived cell lines as PA model. We carried out a paired-end exome sequencing of patients' tumor and germline DNA using Illumina NextSeq followed by characterization of corresponding PA cell cultures. Variation analysis revealed a low amount of somatic mutations (mean = 5.2, range 3-7) in exomes of PAs. Somatic mutations of the primary surgery material can be detected in the exomes of respective pituispheres, but not in exomes of respective mesenchymal stem-like cells. For the first time, we show that the genome of pituispheres represents genome of PA while mesenchymal stem cells derived from the PA tissue do not contain mutations characteristic to PA in their genome, therefore, most likely representing normal cells of pituitary or surrounding tissues. This finding indicates that pituispheres can be used as a human model of PA cells, but combination of cell culturing techniques and NGS needs to be employed to adjust for disability to propagate spheres in culturing conditions.
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Affiliation(s)
- Raitis Peculis
- Department of Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ilona Mandrika
- Department of Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ramona Petrovska
- Department of Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Rasma Dortane
- Department of Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Kaspars Megnis
- Department of Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Jurijs Nazarovs
- Department of Pathology, Pauls Stradiņš Clinical University Hospital, Riga, Latvia
| | - Inga Balcere
- Department of Endocrinology, Riga East Clinical University Hospital, Riga, Latvia
- Department of Internal Medicine, Riga Stradinņš University, Riga, Latvia
| | - Janis Stukens
- Department of Neurosurgery, Pauls Stradiņš Clinical University Hospital, Riga, Latvia
| | - Ilze Konrade
- Department of Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Valdis Pirags
- Clinic of Internal Medicine, Pauls Stradiņš Clinical University Hospital, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Janis Klovins
- Department of Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Vita Rovite
- Department of Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
- *Correspondence: Vita Rovite
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48
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Metformin strongly affects transcriptome of peripheral blood cells in healthy individuals. PLoS One 2019; 14:e0224835. [PMID: 31703101 PMCID: PMC6839856 DOI: 10.1371/journal.pone.0224835] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/22/2019] [Indexed: 01/22/2023] Open
Abstract
Metformin is a commonly used antihyperglycaemic agent for the treatment of type 2 diabetes mellitus. Nevertheless, the exact mechanisms of action, underlying the various therapeutic effects of metformin, remain elusive. The goal of this study was to evaluate the alterations in longitudinal whole-blood transcriptome profiles of healthy individuals after a one-week metformin intervention in order to identify the novel molecular targets and further prompt the discovery of predictive biomarkers of metformin response. Next generation sequencing-based transcriptome analysis revealed metformin-induced differential expression of genes involved in intestinal immune network for IgA production and cytokine-cytokine receptor interaction pathways. Significantly elevated faecal sIgA levels during administration of metformin, and its correlation with the expression of genes associated with immune response (CXCR4, HLA-DQA1, MAP3K14, TNFRSF21, CCL4, ACVR1B, PF4, EPOR, CXCL8) supports a novel hypothesis of strong association between metformin and intestinal immune system, and for the first time provide evidence for altered RNA expression as a contributing mechanism of metformin’s action. In addition to universal effects, 4 clusters of functionally related genes with a subject-specific differential expression were distinguished, including genes relevant to insulin production (HNF1B, HNF1A, HNF4A, GCK, INS, NEUROD1, PAX4, PDX1, ABCC8, KCNJ11) and cholesterol homeostasis (APOB, LDLR, PCSK9). This inter-individual variation of the metformin effect on the transcriptional regulation goes in line with well-known variability of the therapeutic response to the drug.
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49
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Ozola A, Ruklisa D, Pjanova D. The complementary effect of rs1042522 in TP53 and rs1805007 in MC1R is associated with an elevated risk of cutaneous melanoma in Latvian population. Oncol Lett 2019; 18:5225-5234. [PMID: 31612033 PMCID: PMC6781780 DOI: 10.3892/ol.2019.10906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/30/2019] [Indexed: 11/06/2022] Open
Abstract
Genetic factors serve important roles in melanoma susceptibility. Although much genetic variation has been associated with cutaneous melanoma (CM), little is known about the interactions between genetic variants. The current study investigated the joint effect of rs1042522 in the tumour protein 53 (TP53) gene, rs2279744 in the murine double minute-2 (MDM2) gene and several single nucleotide polymorphisms (SNPs) in the melanocortin 1 receptor (MC1R) gene. All of these genes are interconnected in a single signalling pathway that regulates pigmentation. The current study included 479 individuals, of which, 255 were patients with CM and 224 were controls from the Latvian population. Multifaceted analyses of potential interactions between SNPs were performed, whilst taking into account the pigmentation phenotypes of individuals and tumour characteristics (Breslow thickness and ulceration). Univariate analyses revealed a borderline significant association between rs1042522 in the TP53 gene and CM risk. The results also confirmed a known association with rs1805007 in the MC1R gene. The rs1042522 was also selected as a CM risk factor in multivariate models, suggesting an effect that is independent from and complementary to that of rs1805007. The results indicated that these SNPs need to be taken into account when determining melanoma risk. A strong association between CM and red hair was identified for rs1805007, and rs1805008 in the MC1R gene was mainly associated with red hair. An association was also determined between rs2279744 in the MDM2 gene and brown eye colour. No convincing associations were identified between the analysed SNPs and Breslow thickness of tumours or ulcerations.
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Affiliation(s)
- Aija Ozola
- Latvian Biomedical Research and Study Centre, Riga LV-1067, Latvia
| | - Dace Ruklisa
- Newnham College, University of Cambridge, Cambridge CB3 9DF, United Kingdom
| | - Dace Pjanova
- Latvian Biomedical Research and Study Centre, Riga LV-1067, Latvia
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50
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Megnis K, Peculis R, Rovite V, Laksa P, Niedra H, Balcere I, Caune O, Breiksa A, Nazarovs J, Stukens J, Konrade I, Pirags V, Klovins J. Evaluation of the Possibility to Detect Circulating Tumor DNA From Pituitary Adenoma. Front Endocrinol (Lausanne) 2019; 10:615. [PMID: 31620080 PMCID: PMC6759656 DOI: 10.3389/fendo.2019.00615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/23/2019] [Indexed: 02/01/2023] Open
Abstract
Objective: Circulating free DNA (cfDNA) in general and circulating tumor DNA (ctDNA) in particular is becoming an increasingly used form of liquid biopsy biomarkers. In this study, we are investigating the ability to detect ctDNA from the plasma of pituitary adenoma (PA) patients. Design: Tumor tissue samples were obtained from planed PA resections, before which blood plasma samples were taken. Somatic variants found in PA tissue samples were evaluated in related cfDNA, isolated from plasma samples. Methods: Sanger sequencing, as well as previously obtained whole-exome sequencing data, were used to evaluate somatic variants composition in tumor tissue samples. cfDNA was isolated from the same PA patients and competitive allele-specific TaqMan PCR and amplicon-based next-generation sequencing (NGS) approach were used for targeted detection of variants found in corresponding tumor tissue samples. Results: Using NGS-based analysis, we detected five out of 17 somatic variants in 40 to 60% of total reads, three variants in 0.50-5.00% of total read count, including GNAS c.601C>T, which was detected using ultra-deep NGS (1.78 million X) in 0.77% of amplicons reads. Nine variants were not detected. We also detected We were not able to detect variant found in PA tissue in cfDNA using cast-PCR, indicating that the portion of variant-containing ctDNA in total isolated cfDNA is too small to be detected with this method. Conclusions: For the first time, we demonstrate the possibility to detect somatic variants of PA in cfDNA isolated from patients' blood plasma. Whether the source of variant detected in cfDNA is PA should be further tested.
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Affiliation(s)
- Kaspars Megnis
- Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Raitis Peculis
- Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Vita Rovite
- Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Pola Laksa
- Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Helvijs Niedra
- Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Inga Balcere
- Department of Internal Medicine, Riga Stradins University, Riga, Latvia
| | - Olivija Caune
- Department of Internal Medicine, Riga Stradins University, Riga, Latvia
| | - Austra Breiksa
- Institute of Pathology, Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Jurijs Nazarovs
- Institute of Pathology, Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Janis Stukens
- Department of Neurosurgery, Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Ilze Konrade
- Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
- Department of Internal Medicine, Riga Stradins University, Riga, Latvia
| | - Valdis Pirags
- Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
- Department of Endocrinology, Pauls Stradins Clinical University Hospital, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Janis Klovins
- Human Genetics and Molecular Medicine, Latvian Biomedical Research and Study Centre, Riga, Latvia
- *Correspondence: Janis Klovins
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