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Ciesielski TH, Zhang X, Tacconelli A, Lutsar I, de Cabre VM, Roilides E, Ciccacci C, Borgiani P, Scott WK, Williams SM, Sirugo G. Late-onset neonatal sepsis: genetic differences by sex and involvement of the NOTCH pathway. Pediatr Res 2023; 93:1085-1095. [PMID: 35835848 DOI: 10.1038/s41390-022-02114-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/10/2022] [Accepted: 04/27/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND Late-Onset Neonatal Sepsis (LOS) is a rare condition, involving widespread infection, immune disruption, organ dysfunction, and often death. Because exposure to pathogens is not completely preventable, identifying susceptibility factors is critical to characterizing the pathophysiology and developing interventions. Prior studies demonstrated both genetics and infant sex influence susceptibility. Our study was designed to identify LOS associated genetic variants. METHODS We performed an exploratory genome wide association study (GWAS) with 224 LOS cases and 273 controls from six European countries. LOS was defined as sepsis presenting from 3 to 90 days of age; diagnosis was established by clinical criteria consensus guidelines. We tested for association with both autosomal and X-chromosome variants in the total sample and in sex-stratified analyses. RESULTS In total, 71 SNPs associated with neonatal sepsis at p < 1 × 10-4 in at least one analysis. Most importantly, sex-stratified analyses revealed associations with multiple SNPs (28 in males and 16 in females), but no variants from single-sex analyses associated with sepsis in the other sex. Pathway analyses showed NOTCH signaling is over-represented among genes linked to these SNPS. CONCLUSION Our results indicate genetic susceptibility to LOS is sexually dimorphic and corroborate that NOTCH signaling plays a role in determining risk. IMPACT Genes associate with late onset neonatal sepsis. Notch pathway genes are overrepresented in associations with sepsis. Genes associating with sepsis do not overlap between males and females. Sexual dimorphism can lead to sex specific treatment of sepsis.
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Affiliation(s)
- Timothy H Ciesielski
- The Department of Population and Quantitative Health Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Mary Ann Swetland Center for Environmental Health at Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Xueyi Zhang
- The Department of Population and Quantitative Health Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | | | - Irja Lutsar
- Department of Microbiology, School of Medicine, University of Tartu, Tartu, Estonia
| | | | - Emmanuel Roilides
- Laboratory of Infectious Diseases, 3rd Department of Paediatrics, School of Medicine, Aristotle University, Thessaloniki, Greece
| | - Cinzia Ciccacci
- Dipartimento di Biomedicina e Prevenzione, Facolta' di Medicina e Chirurgia, Universita' di Tor Vergata, Rome, Italy
- Unicamillus, Saint Camillus International University of Health Sciences, Rome, Italy
| | - Paola Borgiani
- Dipartimento di Biomedicina e Prevenzione, Facolta' di Medicina e Chirurgia, Universita' di Tor Vergata, Rome, Italy
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | | | - Scott M Williams
- The Department of Population and Quantitative Health Sciences at Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA.
- 10900 Euclid Ave, Cleveland Institute for Computational Biology, Cleveland, USA.
| | - Giorgio Sirugo
- Institute of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
- Division of Translational Medicine and Human Genetics, Perelman SPerelman School of Medicine, University of Pennsylvaniachool of Medicine, University of Pennsylvania, Philadelphia, USA.
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Noro F, Santonastaso F, Marotta A, Bonaccio M, Orlandi S, Tirozzi A, Costanzo S, De Curtis A, Gianfagna F, Di Castelnuovo A, Brighenti F, Cerletti C, Donati MB, de Gaetano G, Iacoviello L, Gialluisi A, Izzi B, de Gaetano G, Donati MB, Bonaccio M, Bonanni A, Cerletti C, Costanzo S, De Curtis A, Di Castelnuovo A, Gialluisi A, Gianfagna F, Persichillo M, Di Prospero T, Vermylen J, Pegoraro R, Spagnolo A, Assanelli D, Rago L, Costanzo S, Olivieri M, Panzera T, Di Castelnuovo A, Bonaccio M, Costanzo S, Esposito S, Gialluisi A, Gianfagna F, Orlandi S, Ruggiero E, Tirozzi A, De Curtis A, Magnacca S, Noro F, Tirozzi A, Persichillo M, Bracone F, Panzera T, Bonanni A. Association of nutritional glycaemic indices with global DNA methylation patterns: results from the Moli-sani cohort. Clin Epigenetics 2022; 14:189. [PMID: 36578055 PMCID: PMC9798643 DOI: 10.1186/s13148-022-01407-3] [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: 07/04/2022] [Accepted: 12/13/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND High dietary glycaemic index (GI) and load (GL) have been associated with increased risk of various cardiometabolic conditions. Among the molecular potential mechanisms underlying this relationship, DNA methylation has been studied, but a direct link between high GI and/or GL of diet and global DNA methylation levels has not been proved yet. We analyzed the associations between GI and GL and global DNA methylation patterns within an Italian population. RESULTS Genomic DNA methylation (5mC) and hydroxymethylation (5hmC) levels were measured in 1080 buffy coat samples from participants of the Moli-sani study (mean(SD) = 54.9(11.5) years; 52% women) via ELISA. A 188-item Food Frequency Questionnaire was used to assess food intake and dietary GI and GL for each participant were calculated. Multiple linear regressions were used to investigate the associations between dietary GI and GL and global 5mC and 5hmC levels, as well as the proportion of effect explained by metabolic and inflammatory markers. We found negative associations of GI with both 5mC (β (SE) = - 0.073 (0.027), p = 0.007) and 5hmC (- 0.084 (0.030), p = 0.006), and of GL with 5mC (- 0.14 (0.060), p = 0.014). Circulating biomarkers did not explain the above-mentioned associations. Gender interaction analyses revealed a significant association of the gender-x-GL interaction with 5mC levels, with men showing an inverse association three times as negative as in women (interaction β (SE) = - 0.16 (0.06), p = 0.005). CONCLUSIONS Our findings suggest that global DNA methylation and hydroxymethylation patterns represent a biomarker of carbohydrate intake. Based on the differential association of GL with 5mC between men and women, further gender-based separate approaches are warranted.
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Affiliation(s)
- Fabrizia Noro
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Federica Santonastaso
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy ,grid.510779.d0000 0004 9414 6915Present Address: Human Technopole, Viale Rita Levi Montalcini 1, 20157 Milan, Italy ,grid.4708.b0000 0004 1757 2822Present Address: European School of Molecular Medicine, University of Milan, 20122 Milan, Italy
| | - Annalisa Marotta
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy ,grid.412451.70000 0001 2181 4941Present Address: Center of Predictive Molecular Medicine, Center for Excellence on Ageing and Translational Medicine (CAST), University of Chieti-Pescara, Chieti, Italy
| | - Marialaura Bonaccio
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Sabatino Orlandi
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Alfonsina Tirozzi
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Simona Costanzo
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Amalia De Curtis
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Francesco Gianfagna
- grid.18147.3b0000000121724807EPIMED Research Center, Department of Medicine and Surgery, University of Insubria, Varese, Italy ,grid.477084.80000 0004 1787 3414Mediterranea Cardiocentro, Naples, Italy
| | | | - Furio Brighenti
- grid.10383.390000 0004 1758 0937Department of Food and Drug, University of Parma, Parma, Italy
| | - Chiara Cerletti
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Maria Benedetta Donati
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Giovanni de Gaetano
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
| | - Licia Iacoviello
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy ,grid.18147.3b0000000121724807EPIMED Research Center, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Alessandro Gialluisi
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy ,grid.18147.3b0000000121724807EPIMED Research Center, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Benedetta Izzi
- grid.419543.e0000 0004 1760 3561Department of Epidemiology and Prevention, IRCCS Neuromed, Via Dell’Elettronica, 86077 Pozzilli, IS Italy
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Noro F, Marotta A, Bonaccio M, Costanzo S, Santonastaso F, Orlandi S, Tirozzi A, Parisi R, De Curtis A, Persichillo M, Gianfagna F, Di Castelnuovo A, Donati MB, Cerletti C, de Gaetano G, Iacoviello L, Gialluisi A, Izzi B. Fine-grained investigation of the relationship between human nutrition and global DNA methylation patterns. Eur J Nutr 2021; 61:1231-1243. [PMID: 34741648 DOI: 10.1007/s00394-021-02716-8] [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: 01/27/2021] [Accepted: 10/18/2021] [Indexed: 10/19/2022]
Abstract
PURPOSE Nutrition is an important, modifiable, environmental factor affecting human health by modulating epigenetic processes, including DNA methylation (5mC). Numerous studies investigated the association of nutrition with global and gene-specific DNA methylation and evidences on animal models highlighted a role in DNA hydroxymethylation (5hmC) regulation. However, a more comprehensive analysis of different layers of nutrition in association with global levels of 5mC and 5hmC is lacking. We investigated the association between global levels of 5mC and 5hmC and human nutrition, through the stratification and analysis of dietary patterns into different nutritional layers: adherence to Mediterranean diet (MD), main food groups, macronutrients and micronutrients intake. METHODS ELISA technique was used to measure global 5mC and 5hmC levels in 1080 subjects from the Moli-sani cohort. Food intake during the 12 months before enrolment was assessed using the semi-quantitative EPIC food frequency questionnaire. Complementary approaches involving both classical statistics and supervised machine learning analyses were used to investigate the associations between global 5mC and 5hmC levels and adherence to Mediterranean diet, main food groups, macronutrients and micronutrients intake. RESULTS We found that global DNA methylation, but not hydroxymethylation, was associated with daily intake of zinc and vitamin B3. Random Forests algorithms predicting 5mC and 5hmC through intakes of food groups, macronutrients and micronutrients revealed a significant contribution of zinc, while vitamin B3 was reported among the most influential features. CONCLUSION We found that nutrition may affect global DNA methylation, suggesting a contribution of micronutrients previously implicated as cofactors in methylation pathways.
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Affiliation(s)
- Fabrizia Noro
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Annalisa Marotta
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Marialaura Bonaccio
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Simona Costanzo
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Federica Santonastaso
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Sabatino Orlandi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Alfonsina Tirozzi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Roberta Parisi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Amalia De Curtis
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Mariarosaria Persichillo
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Francesco Gianfagna
- Mediterranea Cardiocentro, Naples, Italy.,Department of Medicine and Surgery, EPIMED Research Center, University of Insubria, Varese, Italy
| | | | - Maria Benedetta Donati
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Chiara Cerletti
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Giovanni de Gaetano
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Licia Iacoviello
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy. .,Department of Medicine and Surgery, EPIMED Research Center, University of Insubria, Varese, Italy.
| | - Alessandro Gialluisi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
| | - Benedetta Izzi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Via dell'Elettronica, 86077, Pozzilli, IS, Italy
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Kazartsev IA, Lednev GR. Distribution and Diversity of Beauveria in Boreal Forests of Northern European Russia. Microorganisms 2021; 9:1409. [PMID: 34210043 PMCID: PMC8308049 DOI: 10.3390/microorganisms9071409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 11/17/2022] Open
Abstract
The distribution and genetic diversity of 91 of Beauveria isolates collected during a long-term survey in boreal forests of northern European Russia was studied. Based on morphological and sequence analysis of TEF and Bloc loci, three Beauveria spp. were identified: B. pseudobassiana, B. bassiana, and B. caledonica, with abundance of 81, 11, and 8%, respectively. Through multilocus sequencing, four haplotypes of B. bassiana and two haplotypes of B. caledonica were detected. Twelve haplotypes of B. pseudobassiana with non-random distribution were identified. Two haplotypes of B. pseudobassiana were the most abundant and widespread occurring across the whole study area, whereas others tended to be more specific to either the north or south of the study area, indicating the presence of different subpopulations. For further analysis of these putative subpopulations, southern and northern areas were separated along the boundary of the Köppen-Geiger climate zones (dfb and dfc), and the genetic structure was examined by analysis of molecular variance and spatial autocorrelation. Molecular evidence of intraspecific recombination of B. pseudobassiana and B. bassiana across northern European Russia area was indicated.
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Affiliation(s)
- Igor A. Kazartsev
- Laboratory of Mycology and Phytopathology, Laboratory of Microbiological Plant Protection, All-Russian Institute of Plant Protection (FSBSI VIZR), Pushkin, 196608 St. Petersburg, Russia;
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Marotta A, Noro F, Parisi R, Gialluisi A, Tirozzi A, De Curtis A, Costanzo S, Di Castelnuovo A, Cerletti C, Donati MB, de Gaetano G, Iacoviello L, Izzi B, Gianfagna F. NMU DNA methylation in blood is associated with metabolic and inflammatory indices: results from the Moli-sani study. Epigenetics 2021; 16:1347-1360. [PMID: 33393847 DOI: 10.1080/15592294.2020.1864167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Neuromedin U (NMU) is a neuropeptide involved in gut-brain axis, energy balance and immune response. We aimed at analysing the association between NMU epigenetic variability and metabolic indices and the potential mediating role of low-grade inflammation in a general population of Italian adults.NMU Blood DNA methylation levels at two CpG islands (NMU76 and NMU32) were analysed using pyrosequencing in a randomly selected sub-cohort of 1,160 subjects from the Moli-sani study (≥35years; 49.20% men). Multivariable regressions adjusted for age, sex, smoking, alcohol and vegetable consumption were performed to estimate the associations between methylation and metabolic phenotypes (BMI, waist-to-hip ratio, blood pressure, glucose, HOMA-IR, lipids, lipoprotein(a) and apolipoproteins). Mediation analysis was performed to identify the influence of low-grade inflammation in the association using a composite index based on C reactive protein, granulocyte-to-lymphocyte ratio (GLR), platelet and white blood cell counts (INFLA-score).Using principal component analysis four methylation factors were identified: NMU76-F1, NMU76-F2, NMU32-F1 and NMU32-F2. NMU76-F1 was FDR significantly associated with total cholesterol (for 1 SD increase: β = 4.5 ± 1.4 mg/dL of, R2 = 10.8%, p = 0.001), ApoB (0.03 ± 0.01 g/L, 12.2%, p = 0.0004), with INFLA-score (1.05 ± 0.22, p = 2.7E-6) and GLR (-0.27 ± 0.03, 30.4%, p = 1.3E-20). GLR and lymphocyte numbers mediate the association of NMU76-F1 with cholesterol (24.0% of total effect, Sobel p = 0.013) and ApoB (42.6%, p = 9E-7), respectively.These findings suggest that NMU promoter methylation patterns could mark a pathway linking lipids with haematopoiesis and systemic inflammation.
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Affiliation(s)
- Annalisa Marotta
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, Italy
| | - Fabrizia Noro
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, Italy
| | - Roberta Parisi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, Italy
| | | | - Alfonsina Tirozzi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, Italy
| | - Amalia De Curtis
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, Italy
| | - Simona Costanzo
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, Italy
| | | | - Chiara Cerletti
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, Italy
| | | | | | - Licia Iacoviello
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, Italy.,EPIMED Research Center, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Benedetta Izzi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, Italy
| | - Francesco Gianfagna
- Mediterranea Cardiocentro, Napoli, Italy.,EPIMED Research Center, Department of Medicine and Surgery, University of Insubria, Varese, Italy
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Rhizobia Isolated from the Relict Legume Vavilovia formosa Represent a Genetically Specific Group within Rhizobium leguminosarum biovar viciae. Genes (Basel) 2019; 10:genes10120991. [PMID: 31805683 PMCID: PMC6947851 DOI: 10.3390/genes10120991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/20/2019] [Accepted: 11/27/2019] [Indexed: 01/09/2023] Open
Abstract
Twenty-two rhizobia strains isolated from three distinct populations (North Ossetia, Dagestan, and Armenia) of a relict legume Vavilovia formosa were analysed to determine their position within Rhizobium leguminosarum biovar viciae (Rlv). These bacteria are described as symbionts of four plant genera Pisum, Vicia, Lathyrus, and Lens from the Fabeae tribe, of which Vavilovia is considered to be closest to its last common ancestor (LCA). In contrast to biovar viciae, bacteria from Rhizobium leguminosarum biovar trifolii (Rlt) inoculate plants from the Trifolieae tribe. Comparison of house-keeping (hkg: 16S rRNA, glnII, gltA, and dnaK) and symbiotic (sym: nodA, nodC, nodD, and nifH) genes of the symbionts of V. formosa with those of other Rlv and Rlt strains reveals a significant group separation, which was most pronounced for sym genes. A remarkable feature of the strains isolated from V. formosa was the presence of the nodX gene, which was commonly found in Rlv strains isolated from Afghanistan pea genotypes. Tube testing of different strains on nine plant species, including all genera from the Fabeae tribe, demonstrated that the strains from V. formosa nodulated the same cross inoculation group as the other Rlv strains. Comparison of nucleotide similarity in sym genes suggested that their diversification within sym-biotypes of Rlv was elicited by host plants. Contrariwise, that of hkg genes could be caused by either local adaptation to soil niches or by genetic drift. Long-term ecological isolation, genetic separation, and the ancestral position of V. formosa suggested that symbionts of V. formosa could be responsible for preserving ancestral genotypes of the Rlv biovar.
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Noro F, Gianfagna F, Gialluisi A, De Curtis A, Di Castelnuovo A, Napoleone E, Cerletti C, Donati MB, de Gaetano G, Hoylaerts MF, Iacoviello L, Izzi B. ZBTB12 DNA methylation is associated with coagulation- and inflammation-related blood cell parameters: findings from the Moli-family cohort. Clin Epigenetics 2019; 11:74. [PMID: 31077224 PMCID: PMC6511189 DOI: 10.1186/s13148-019-0665-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/09/2019] [Indexed: 12/12/2022] Open
Abstract
Background Zinc finger and BTB domain-containing protein 12 (ZBTB12) is a predicted transcription factor with potential role in hematopoietic development. Recent evidence linked low methylation level of ZBTB12 exon1 to myocardial infarction (MI) risk. However, the role of ZBTB12 in the pathogenesis of MI and cardiovascular disease in general is not yet clarified. We investigated the relation between ZBTB12 methylation and several blood parameters related to cardio-cerebrovascular risk in an Italian family-based cohort. Results ZBTB12 methylation was analyzed on white blood cells from the Moli-family cohort using the Sequenom EpiTYPER MassARRAY (Agena). A total of 13 CpG Sequenom units were analyzed in the small CpG island located in the only translated ZBTB12 exon. Principal component analysis (PCA) was performed to identify groups of CpG units with similar methylation estimates. Linear mixed effect regressions showed a positive association between methylation of ZBTB12 Factor 2 (including CpG units 8, 9–10, 16, 21) and TNF-ɑ stimulated procoagulant activity, a measure of procoagulant and inflammatory potential of blood cells. In addition, we also found a negative association between methylation of ZBTB12 Factor 1 (mainly characterized by CpG units 1, 3–4, 5, 11, and 26) and white blood cell and granulocyte counts. An in silico prediction analysis identified granulopoiesis- and hematopoiesis-specific transcription factors to potentially bind DNA sequences encompassing CpG1, CpG3–4, and CpG11. Conclusions ZBTB12 hypomethylation is linked to shorter TNF-ɑ stimulated whole blood coagulation time and increased WBC and granulocyte counts, further elucidating the possible link between ZBTB12 methylation and cardiovascular disease risk. Electronic supplementary material The online version of this article (10.1186/s13148-019-0665-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fabrizia Noro
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, IS, Italy
| | - Francesco Gianfagna
- Department of Medicine and Surgery, University of Insubria, Varese, Italy.,Mediterranea Cardiocentro, Naples, Italy
| | | | - Amalia De Curtis
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, IS, Italy
| | | | | | - Chiara Cerletti
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, IS, Italy
| | | | - Giovanni de Gaetano
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, IS, Italy
| | - Marc F Hoylaerts
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Licia Iacoviello
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, IS, Italy. .,Department of Medicine and Surgery, University of Insubria, Varese, Italy.
| | - Benedetta Izzi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, IS, Italy
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8
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Mitina G, Kazartsev I, Vasileva A, Yli-Mattila T. Multilocus genotyping based species identification of entomopathogenic fungi of the genus Lecanicillium (=Verticillium lecanii s.l.). J Basic Microbiol 2017; 57:950-961. [PMID: 28787109 DOI: 10.1002/jobm.201700092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 07/04/2017] [Accepted: 07/07/2017] [Indexed: 11/06/2022]
Abstract
Mitochondrial gene NADH dehydrogenase subunit 1 (nad1), β-tubulin gene, and elongation factor 1-alpha (tef) were used to characterize and to identify 42 Lecanicillum spp. isolates (former complex species Verticillium lecanii Zimm. Viegas) and to study the phylogenetic relationships in this group. Within the isolates under investigation, Lecanicillium muscarium was the most common species (about 70% of all isolates, collected on the different hosts, predominantly on the insects from the order Hemiptera). Based on nad1 sequencing four main molecular haplotypes were revealed. All four haplotypes have Holarctic origin. Most of them were isolated in the Central part of Russia. One haplotype showed a specific association with the certain geographical area, limited to southwest Georgia and the Krasnodar Territory. For most strains their affiliation to species L. muscarium, L. longisporum, L. psalliotae, L. pissodes were confirmed by the phylogenetic tree, based on the combined sequences of nad1, β-tub, and tef genes. Only five strains of haplotype C and strain F-2643 could not be identified to any present Lecanicillium species and their position remains ambiguous. Thus, the use of multilocus molecular approach based on these genes was useful to identify the Lecanicillium species. Inter-simple sequence repeat (ISSR) study evaluated a high diversity among the L. muscarium strains. The topology of the NJ-tree based on the ISSR-PCR markers has shown the genetic relationships with the support values 62-91% between L. muscarium isolates.
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Affiliation(s)
- Galina Mitina
- All-Russian Institute of Plant Protection, St. Petersburg, Russia
| | - Igor Kazartsev
- All-Russian Institute of Plant Protection, St. Petersburg, Russia
| | - Aleksandra Vasileva
- All-Russian Institute of Plant Protection, St. Petersburg, Russia.,RASA Research Center, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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9
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Ali A, Gale RE, Shakoori AR. Detection of FLT3/TKD and IDH1 Mutations in Pakistani Acute Myeloid Leukemia Patients by Denaturing HPLC. J Cell Biochem 2017; 118:1174-1181. [PMID: 27735988 DOI: 10.1002/jcb.25761] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 10/10/2016] [Indexed: 11/05/2022]
Abstract
Acute myeloid leukemia (AML) is characterized by an increase in the number of myeloid cells in the marrow and an arrest in their maturation. Various genetic mutations are associated with AML. FMS-like tyrosine kinase 3 (FLT3), a member of the class III receptor tyrosine kinase family, plays an important role in stem cell survival, and the development of dendritic and natural killer cells. FLT3/TKD mutations are generally missense mutations or in-frame alterations of residues D835 and I836 within the activation loop of the FLT3 protein. D835 mutations have been reported to occur in ≈ 7% of AML patients. Mutations have also been reported in exon 4 of isocitrate dehydrogenase 1 (IDH1) in ≈9% of AML patients. Mutations in FLT3/TKD and IDH1 genes were studied in AML patients from Pakistan and correlated with the laboratory findings. FLT3/TKD mutations were found in 7%, while IDH1 mutations were found in 10% Pakistani AML patients. Neither of these mutations was significantly correlated with age and sex, although the incidence of these mutations was higher in female patients. These mutations were found to be positively associated with each other. IDH1 mutations were positively associated with FAB type M1 and negatively associated with FAB type M2. In conclusion, the overall incidence of all these mutations in Pakistani patients was within the globally reported ranges. J. Cell. Biochem. 118: 1174-1181, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Akbar Ali
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, 54590, Pakistan.,Faculty of Pharmacy, Northern Border University, Rafha, Kingdom of Saudi Arabia
| | - Rosemary E Gale
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Abdul Rauf Shakoori
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, 54590, Pakistan
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10
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Mellai M, Cattaneo M, Storaci AM, Annovazzi L, Cassoni P, Melcarne A, De Blasio P, Schiffer D, Biunno I. SEL1L SNP rs12435998, a predictor of glioblastoma survival and response to radio-chemotherapy. Oncotarget 2016; 6:12452-67. [PMID: 25948789 PMCID: PMC4494950 DOI: 10.18632/oncotarget.3611] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/14/2015] [Indexed: 12/18/2022] Open
Abstract
The suppressor of Lin-12-like (C. elegans) (SEL1L) is involved in the endoplasmic reticulum (ER)-associated degradation pathway, malignant transformation and stem cells. In 412 formalin-fixed and paraffin-embedded brain tumors and 39 Glioblastoma multiforme (GBM) cell lines, we determined the frequency of five SEL1L single nucleotide genetic variants with regulatory and coding functions by a SNaPShot™ assay. We tested their possible association with brain tumor risk, prognosis and therapy. We studied the in vitro cytotoxicity of valproic acid (VPA), temozolomide (TMZ), doxorubicin (DOX) and paclitaxel (PTX), alone or in combination, on 11 GBM cell lines, with respect to the SNP rs12435998 genotype. The SNP rs12435998 was prevalent in anaplastic and malignant gliomas, and in meningiomas of all histologic grades, but unrelated to brain tumor risks. In GBM patients, the SNP rs12435998 was associated with prolonged overall survival (OS) and better response to TMZ-based radio-chemotherapy. GBM stem cells with this SNP showed lower levels of SEL1L expression and enhanced sensitivity to VPA.
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Affiliation(s)
- Marta Mellai
- Neuro-Bio-Oncology Center/Policlinico di Monza Foundation, Vercelli 13100, Italy
| | - Monica Cattaneo
- Institute for Genetic and Biomedical Research, National Research Council, Milan 20138, Italy
| | | | - Laura Annovazzi
- Neuro-Bio-Oncology Center/Policlinico di Monza Foundation, Vercelli 13100, Italy
| | - Paola Cassoni
- Department of Medical Sciences, University of Turin/Città della Salute e della Scienza, Turin 10126, Italy
| | - Antonio Melcarne
- Department of Neurosurgery, CTO Hospital/Città della Salute e della Scienza, Turin 10126, Italy
| | | | - Davide Schiffer
- Neuro-Bio-Oncology Center/Policlinico di Monza Foundation, Vercelli 13100, Italy
| | - Ida Biunno
- Institute for Genetic and Biomedical Research, National Research Council, Milan 20138, Italy.,IRCCS-Multimedica, Milan 20138, Italy
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11
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Biunno I, Aceto G, Awadelkarim KD, Morgano A, Elhaj A, Eltayeb EA, Abuidris DO, Elwali NE, Spinelli C, De Blasio P, Rovida E, Mariani-Costantini R. BRCA1 point mutations in premenopausal breast cancer patients from Central Sudan. Fam Cancer 2015; 13:437-44. [PMID: 24729269 DOI: 10.1007/s10689-014-9717-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Premenopausal breast cancer (BC) is one of the most common cancers of women in rural Africa and part of the disease load may be related to hereditary predisposition, including mutations in the BRCA1 gene. However, the BRCA1 mutations associated with BC in Africa are scarcely characterized. We report here 33 BRCA1 point mutations, among which 2 novel missense variants, found in 59 Central Sudanese premenopausal BC patients. The high fractions of mutations with intercontinental and uniquely African distribution (17/33, 51.5 % and 14/33, 42.4 %, respectively) are in agreement with the high genetic diversity expected in an African population. Overall 24/33 variants (72.7 %) resulted neutral; 8/33 of unknown significance (24.3 %, including the 2 novel missense mutations); 1 (3.0 %) overtly deleterious. Notably, in silico studies predict that the novel C-terminal missense variant c.5090G>A (p.Cys1697Tyr) affects phosphopeptide recognition by the BRCA1 BRCT1 domain and may have a pathogenic impact. Genetic variation and frequency of unique or rare mutations of uncertain clinical relevance pose significant challenges to BRCA1 testing in Sudan, as it might happen in other low-resource rural African contexts.
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Affiliation(s)
- Ida Biunno
- Institute for Genetic and Biomedical Research, National Research Council, Via Fantoli 16/15, 20138, Milan, Italy
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12
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D'Urso DG, La Spada A, Tramonte T, Rainoldi B, De Blasio A. Evaluation of cross-sample contamination in tissue microarrays by polymerase chain reaction. Biopreserv Biobank 2015; 13:219-23. [PMID: 26035013 DOI: 10.1089/bio.2014.0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In the past decade, the popularity and power of Tissue Microarray (TMA) technology has increased since it provides a method to detect diagnostic and prognostic markers in an array of clinical tissue specimens collected for translational research. TMAs allow for rapid and cost-effective analysis of hundreds of molecular markers at the nucleic acid and protein levels. This technology is particularly useful in the realization of the Human Protein Atlas Project, since it aims to create a reference database of non-redundant human proteins. In this context, it is important to assure the lack of cross-sample contamination due to the repeated use of the same needle in consecutive coring. Here we show that carry-over contamination from one tissue core to another does not occur, reinforcing the accuracy of the TMA technology in the simultaneous testing of multiple bio-samples.
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13
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Cardano M, Diaferia GR, Falavigna M, Spinelli CC, Sessa F, DeBlasio P, Biunno I. Cell and tissue microarray technologies for protein and nucleic acid expression profiling. J Histochem Cytochem 2012; 61:116-24. [PMID: 23172795 DOI: 10.1369/0022155412470455] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Tissue microarray (TMA) and cell microarray (CMA) are two powerful techniques that allow for the immunophenotypical characterization of hundreds of samples simultaneously. In particular, the CMA approach is particularly useful for immunophenotyping new stem cell lines (e.g., cardiac, neural, mesenchymal) using conventional markers, as well as for testing the specificity and the efficacy of newly developed antibodies. We propose the use of a tissue arrayer not only to perform protein expression profiling by immunohistochemistry but also to carry out molecular genetics studies. In fact, starting with several tissues or cell lines, it is possible to obtain the complete signature of each sample, describing the protein, mRNA and microRNA expression, and DNA mutations, or eventually to analyze the epigenetic processes that control protein regulation. Here we show the results obtained using the Galileo CK4500 TMA platform.
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14
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Gao J, Hou RG, Zhang HQ, He JZ, Li SM, Su JL, Han B. A novel DNA extraction and duplex polymerase chain reaction assay for the rapid detection of Prototheca zopfii genotype 2 in milk. Lett Appl Microbiol 2011; 53:278-82. [DOI: 10.1111/j.1472-765x.2011.03102.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Andronov EE, Petrova SN, Chizhevskaya EP, Korostik EV, Akhtemova GA, Pinaev AG. Influence of introducing the genetically modified strain Sinorhizobium meliloti ACH-5 on the structure of the soil microbial community. Microbiology (Reading) 2009. [DOI: 10.1134/s0026261709040110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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16
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Staritz P, Kurz K, Stoll M, Giannitsis E, Katus HA, Ivandic BT. Platelet reactivity and clopidogrel resistance are associated with the H2 haplotype of the P2Y12-ADP receptor gene. Int J Cardiol 2008; 133:341-5. [PMID: 18485500 DOI: 10.1016/j.ijcard.2007.12.118] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Revised: 12/20/2007] [Accepted: 12/26/2007] [Indexed: 01/30/2023]
Abstract
BACKGROUND Platelet hyperreactivity was reported in clopidogrel-naiotave carriers of the H2 haplotype of the P2Y(12) platelet ADP receptor. Here, we studied the influence of this genetic variant on clopidogrel responsiveness. METHODS ADP-mediated (5 micromol/L) platelet aggregation was determined by impedance (Omega) aggregometry in 43 clopidogrel-naïve blood donors and 557 patients treated with aspirin and clopidogrel after percutaneous coronary stent implantation. A cut-off of 5 Omega was used to classify the aggregation response. Haplotype tagging single nucleotide polymorphism G52T was genotyped using a TaqMan assay. RESULTS The number of H2 alleles correlated with aggregation in clopidogrel-naïve subjects in healthy subjects (p=0.041): impedance results were 8.4+/-3.6, 10.5+/-1.6 and 12.5+/-2.1 Omega in carriers of the H1/H1 (n=30), H1/H2 (n=11) and H2/H2 (n=2) haplotypes, respectively. 87.1% (n=485) and 12.9% (n=72) of clopidogrel treated patients were responders and nonresponders, respectively. Women were more likely to be nonresponders (O.R. 3.90 [95% CI 2.34-6.50]). Carriers of a H2/H2 haplotype (n=14) exhibited stronger aggregation than patients with at least one H1 allele (6.3+/-7.5 vs. 1.8+/-3.3 Omega, p=0.0212) and were more frequently nonresponders (p=0.004). Consequently, the H2/H2 haplotype was associated with clopidogrel resistance (O.R. 5.42 [95% CI 1.82-16.11]). This risk factor was independent of the gender effect. CONCLUSIONS This is the first large study in clopidogrel treated patients suggesting that a homozygote H2 genotype contributes to clopidogrel resistance. The clinical significance of this finding remains to be demonstrated.
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Affiliation(s)
- Peter Staritz
- Department of Medicine III, University of Heidelberg, Germany
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17
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Biagiotti L, Proverbio MC, Bosio L, Gervasi F, Rovida E, Cerioni V, Bove M, Valin PS, Albarello L, Zamproni I, Grassi S, Doglioni C, Mora S, Chiumello G, Biunno I. Identification of two Novel Frameshift Mutations in the KCNJ11 gene in two Italian patients affected by Congenital Hyperinsulinism of Infancy. Exp Mol Pathol 2007; 83:59-64. [PMID: 17316607 DOI: 10.1016/j.yexmp.2006.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Revised: 11/02/2006] [Accepted: 11/02/2006] [Indexed: 11/21/2022]
Abstract
Congenital Hyperinsulinism of Infancy (CHI) is a genetically heterogeneous disorder characterized by profound hypoglycemia related to inappropriate insulin secretion. Two histopathologically and genetically distinct groups are recognized among patients with CHI due to ATP-sensitive potassium channel (KATP) defects: a diffuse type (Di-CHI), which involves the whole pancreas, and a focal form (Fo-CHI), which shows adenomatous islet-cell hyperplasia of a particular area within the normal pancreas. The beta-cell KATP channel consists of two essential subunits: Kir6.2 encoded by the KCNJ11 gene which is the pore-forming unit and belongs to the inwardly rectifying potassium channel family, and SUR1 (sulfonylurea receptor 1) encoded by the ABCC8 gene, which belongs to the ATP-binding cassette (ABC) transporter family. The KATP channel is an octameric complex of four Kir6.2 and four SUR1 subunits. More than one hundred mutations have been found in KATP channel genes ABCC8 and KCNJ11, but to date only twenty mutations have been identified in KCNJ11, most of them are missense mutations and only one is a single base deletion. The Fo-CHI has been demonstrated to arise in individuals who have a germline mutation in the paternal allele of ABCC8 or KCNJ11 in addition to a somatic loss of the maternally derived chromosome region 11p15 in adenomatous pancreatic beta-cells, while Di-CHI predominantly arises from the autosomal recessive inheritance of KATP channel gene mutations. Here we describe the molecular findings in nine children who presented, in the neonatal period, with signs and symptoms of hypoglycemia and diagnosed affected by CHI according to international diagnostic criteria. Direct sequencing of the complete coding exon and promoter region of KCNJ11 gene showed, in two Italian patients, two new heterozygous mutations which result in the appearance of premature translation termination codons resulting in the premature end of Kir6.2. Interestingly most of the CHI mutations detected in other population studies are situated in the ABCC8 gene.
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Affiliation(s)
- Laura Biagiotti
- Department of Sciences and Biomedical Technologies, University of Milan, Italy
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18
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Saltini G, Dominici R, Lovati C, Cattaneo M, Michelini S, Malferrari G, Caprera A, Milanesi L, Finazzi D, Bertora P, Scarpini E, Galimberti D, Venturelli E, Musicco M, Adorni F, Mariani C, Biunno I. A novel polymorphism in SEL1L confers susceptibility to Alzheimer's disease. Neurosci Lett 2006; 398:53-8. [PMID: 16412574 DOI: 10.1016/j.neulet.2005.12.038] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Revised: 12/13/2005] [Accepted: 12/14/2005] [Indexed: 01/16/2023]
Abstract
Alzheimer's disease (AD) is considered to be a conformational disease arising from the accumulation of misfolded and unfolded proteins in the endoplasmic reticulum (ER). SEL1L is a component of the ER stress degradation system, which serves to remove unfolded proteins by retrograde degradation using the ubiquitin-proteosome system. In order to identify genetic variations possibly involved in the disease, we analysed the entire SEL1L gene sequence in Italian sporadic AD patients. Here we report on the identification of a new polymorphism within the SEL1L intron 3 (IVS3-88 A>G), which contains potential binding sites for transcription factors involved in ER-induced stress. Our statistical analysis shows a possible role of the novel polymorphism as independent susceptibility factor of Alzheimer's dementia.
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Affiliation(s)
- Giuliana Saltini
- Department of Sciences and Biomedical Technologies, University of Milan Via F.lli Cervi 93, 20090 Segrate-Milan, Italy
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19
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Oliveri C, Frequin M, Malferrari G, Saltini G, Gramegna M, Tagliabue R, Blasio PD, Biunno I, Biagiotti L. A Simple Extraction Method Useful to Purify DNA from Difficult Biologic Sources. ACTA ACUST UNITED AC 2006. [DOI: 10.1089/cpt.2006.4.51] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Claudio Oliveri
- Department of Science and Biomedical Technologies, University of Milan, Italy
| | - Melissa Frequin
- Department of Science and Biomedical Technologies, University of Milan, Italy
| | - Giulia Malferrari
- Department of Science and Biomedical Technologies, University of Milan, Italy
| | - Giuliana Saltini
- Department of Science and Biomedical Technologies, University of Milan, Italy
| | | | | | | | - Ida Biunno
- BioRep S.r.l. Milan, Italy
- Institute for Biomedical Technologies-CNR, Milan, Italy
| | - Laura Biagiotti
- Department of Science and Biomedical Technologies, University of Milan, Italy
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20
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Cremonesi P, Castiglioni B, Malferrari G, Biunno I, Vimercati C, Moroni P, Morandi S, Luzzana M. Technical Note: Improved Method for Rapid DNA Extraction of Mastitis Pathogens Directly from Milk. J Dairy Sci 2006; 89:163-9. [PMID: 16357279 DOI: 10.3168/jds.s0022-0302(06)72080-x] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Efficient control against bovine mastitis requires sensitive, rapid, and specific tests to detect and identify the main bacteria that cause heavy losses to the dairy industry. Molecular detection of pathogenic microorganisms is based on DNA amplification of the target pathogen. Therefore, efficient extraction of DNA from pathogenic bacteria is a major step. In this study, we aimed to develop a specific, sensitive, and rapid method to extract DNA directly from the main gram-positive bacteria known to cause bovine mastitis (Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, and Streptococcus uberis) found in milk samples. The DNA extraction method is based on the lysing and nuclease-inactivating properties of the chaotropic agent, guanidinium thiocyanate, together with the nucleic acid-binding properties of the silica particles. An efficient protocol consisting of 6 basic steps (3 of which were done twice) was developed and applied directly to milk samples. Absence of PCR inhibitors and DNA quality were evaluated by PCR amplification of the species-specific DNA sequences of the target bacteria. The level of sensitivity achieved in our experiments is applicable to milk sample analysis without sample enrichment.
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Affiliation(s)
- P Cremonesi
- Department of Biomedical Sciences and Technologies, University of Milan, Segrate, Milan, Italy.
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21
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Poli M, Gatta LB, Dominici R, Lovati C, Mariani C, Albertini A, Finazzi D. DNA sequence variations in the prolyl isomerase Pin1 gene and Alzheimer's disease. Neurosci Lett 2005; 389:66-70. [PMID: 16095818 DOI: 10.1016/j.neulet.2005.07.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2005] [Accepted: 07/14/2005] [Indexed: 01/25/2023]
Abstract
Senile plaques and neurofibrillary tangles (NFT) are the prominent lesions in the brain of Alzheimer's disease (AD) patients. NFT are mainly composed of an abnormally phosphorylated form of tau protein, which has lost its function to bind microtubules and promote their assembly. Tau hyperphosphorylation critically decreases tau function and precedes neurodegeneration. The majority of tau phosphorylation sites are Ser/Thr-Pro motifs, which are known to exist in two distinct cis and trans conformations. The prolyl isomerase Pin1 catalyses the conversion of those conformations. Pin1 binds to tau specifically at the Thr231-Pro site and restores tau function, either by inducing conformational changes or facilitating dephosphorylation. It has been shown that Pin1 expression levels inversely correlate with the predicted vulnerability of different brain areas to neurodegeneration and soluble Pin1 is depleted in neurons from AD brains; furthermore, Pin1 knock-out mice develop signs and symptoms of tau-related pathologies late in life. It seems that Pin1 plays an important role in maintaining tau function, thereby preserving neuronal homeostasis and preventing age-dependent neurodegeneration. DNA sequence variations in Pin1 gene may affect its expression level or function and influence the individual risk for developing AD. We screened by denaturing high performance liquid chromatography the genomic DNA of 120 AD subjects and 134 age-matched controls and we found very few and rare sequence variations in the promoter region and in exons 2 and 3. We conclude that Pin1 is a very well conserved gene, whose rare nucleotide variations have no effect on the individual genetic risk for AD.
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Affiliation(s)
- Maura Poli
- Section of Biochemistry, Faculty of Medicine, University of Brescia, Viale Europe 11, 25123 Brescia, Italy
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22
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Poli M, Gatta LB, Dominici R, Lovati C, Mariani C, Albertini A, Finazzi D. Apolipoprotein E haplotyping by denaturing high-performance liquid chromatography. Clin Chem Lab Med 2005; 43:512-8. [PMID: 15899673 DOI: 10.1515/cclm.2005.090] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The apolipoprotein E ( APOE ) gene in humans contains two single-base polymorphisms in exon 4, which result in three common alleles, conventionally named epsilon2 , epsilon3 and epsilon4 . Numerous studies have shown an important association between the epsilon4 variant and an increased risk of Alzheimer's disease; other data suggest a possible linkage of APOE genetic heterogeneity with lipid profile and an increased risk of atherothrombotic stroke and coronary heart disease. APOE genotyping is therefore an increasingly common assay in laboratory medicine. The most widely used technique for APOE genotyping is based upon restriction isotyping, i.e., amplification of the fragment of exon 4 containing the most common sequence variations, followed by enzymatic digestion of the amplicon and fragments analysis by gel electrophoresis. We developed a novel, reliable and fast method that exploits the sensitivity and specificity of denaturing high-performance liquid chromatography in detecting single-nucleotide polymorphisms. We show that, in most cases, with a single chromatographic separation it is possible to correctly identify the six different APOE allelic patterns, without any manipulation after the polymerase chain reaction amplification. When compared to restriction isotyping, our method is much faster, less labor intensive and similarly inexpensive.
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Affiliation(s)
- Maura Poli
- Section of Chemistry, Faculty of Medicine, University of Brescia, Italy
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23
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Saltini G, Proverbio MC, Malferrari G, Biagiotti L, Boettcher P, Dominici R, Monferini E, Lorenzini E, Cattaneo M, Antonello D, Moore PS, Zamproni I, Viscardi M, Chiumello G, Biunno I. Identification of a novel polymorphism in the fibronectin type II domain of the SEL1L gene and possible relation to the persistent hyperinsulinemic hypoglycemia of infancy. Mutat Res 2004; 554:159-63. [PMID: 15450414 DOI: 10.1016/j.mrfmmm.2004.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2004] [Revised: 04/22/2004] [Accepted: 04/22/2004] [Indexed: 04/30/2023]
Abstract
SEL1L, a human gene located on chromosome 14q24.3-q31, is highly expressed in adult pancreas. It is proximal to D14S67 (IDDM11) a proposed type I diabetes susceptibility locus. Considering the organ specific expression of SEL1L, a fundamental role of SEL1L in pancreatic growth can be hypothesized. While screening for mutations in young diabetic patients, in children affected by persistent hyperinsulinemic hypoglycemia of infancy (PHHI), in patients with non-functional endocrine tumours and in over 100 control subjects, we identified a novel polymorphism (D162G) residing on the fourth exon of the gene. This exon encodes for the fibronectin type II domain and the nucleotide change involves a highly conserved amino acid. The D162G polymorphism induces a major change in the amino acid composition producing a possible disruptive role in collagen binding.
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Affiliation(s)
- G Saltini
- Centre for Bio-molecular Interdisciplinary Studies and Industrial applications, University of Milan, Italy
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