Genomics In Premature Infants: A Non-Invasive Strategy To Obtain High-Quality DNA

Said, Mariam; Cappiello, Clint D.; Devaney, Joseph M.; Podini, Daniele; Beres, Alana L.; Vukmanović, Stanislav; Rais-Bahrami, Khodayar; Luban, Naomi L.C.; Sandler, Anthony D.; Tatari-Calderone, Zohreh

doi:10.1038/srep04286

Cited by 13 publications

(16 citation statements)

References 19 publications

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“…First, the swab, lasting seconds, is much less stressful than a painful needle prick to obtain peripheral blood, and this stress might influence methylation in itself. Second, this approach provides a more direct comparison with human studies where ethical reasons preclude needle pain, although buccal swabs are routinely implemented (20, 21). Finally, several studies found that DNA methylation profiles in buccal swab cells are more similar to patterns from several brain regions than methylation profiles in WBCs (21, 22, 23, 24).…”

Section: Resultsmentioning

confidence: 99%

Intra-individual methylomics detects the impact of early-life adversity

et al. 2019

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Genetic and environmental factors interact during sensitive periods early in life to influence mental health and disease via epigenetic processes such as DNA methylation. However, it is not known if DNA methylation changes outside the brain provide an “epigenetic signature” of early-life experiences. Here, we used a novel intra-individual approach by testing DNA methylation from buccal cells of individual rats before and immediately after exposure to one week of typical or adverse life experience. We find that whereas inter-individual changes in DNA methylation reflect the effect of age, DNA methylation changes within paired DNA samples from the same individual reflect the impact of diverse neonatal experiences. Genes coding for critical cellular metabolic enzymes, ion channels, and receptors were more methylated in pups exposed to the adverse environment, predictive of their repression. In contrast, the adverse experience was associated with less methylation on genes involved in pathways of death and inflammation as well as cell-fate–related transcription factors, indicating their potential up-regulation. Thus, intra-individual methylome signatures indicate large-scale transcription-driven alterations of cellular fate, growth, and function.

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Section: Resultsmentioning

confidence: 99%

Intra-individual methylomics detects the impact of early-life adversity

et al. 2019

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“…Cytological brushes were used to swab the buccal mucosa and obtain neonatal DNA using methodology previously validated by our group 27 . Enrolled subjects were nil per os (NPO) at the time of buccal swab collection.…”

Section: Methodsmentioning

confidence: 99%

“…DNA was extracted from buccal swab specimens using Qiagen Buccal Cell Kit (Qiagen Sciences, Germantown, MD). The buccal cell extraction kit was modified for a cell lysate volume of 900μl 27 . After cell lysis, genomic DNA was extracted with 5 μl proteinase k and isopropanol/ethanol precipitation.…”

Section: Methodsmentioning

confidence: 99%

Are Immune Modulating Single Nucleotide Polymorphisms Associated with Necrotizing Enterocolitis?

Franklin

Said

Cappiello

et al. 2015

Sci Rep

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Necrotizing enterocolitis (NEC) is a devastating gastrointestinal emergency. The purpose of this study is to determine if functional single nucleotide polymorphisms (SNPs) in immune-modulating genes pre-dispose infants to NEC. After Institutional Review Board approval and parental consent, buccal swabs were collected for DNA extraction. TaqMan allelic discrimination assays and BglII endonuclease digestion were used to genotype specific inflammatory cytokines and TRIM21. Statistical analysis was completed using logistic regression. 184 neonates were analyzed in the study. Caucasian neonates with IL-6 (rs1800795) were over 6 times more likely to have NEC (p = 0.013; OR = 6.61, 95% CI 1.48–29.39), and over 7 times more likely to have Stage III disease (p = 0.011; OR = 7.13, (95% CI 1.56–32.52). Neonates with TGFβ-1 (rs2241712) had a decreased incidence of NEC-related perforation (p = 0.044; OR = 0.28, 95% CI: 0.08–0.97) and an increased incidence of mortality (p = 0.049; OR = 2.99, 95% CI: 1.01 – 8.86). TRIM21 (rs660) was associated with NEC-related intestinal perforation (p = 0.038; OR = 4.65, 95% CI 1.09–19.78). In premature Caucasian neonates, the functional SNP IL-6 (rs1800795) is associated with both the development and increased severity of NEC. TRIM21 (rs660) and TGFβ-1 (rs2241712) were associated with NEC- related perforation in all neonates in the cohort. These findings suggest a possible genetic role in the development of NEC.

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“…Our study has demonstrated that HRM genotyping of DNA material derived from buccal swab yielded satisfactory and reliable results. A study which also employed buccal swab sampling indicated that buccal epithelial cells provided a reliable source of DNA and promising results were obtained from genetic analysis such as short tandem repeat analysis, Taqman allelic discrimination assay, PCR-restriction fragment length polymorphism (PCR-RFLP) and whole exome sequencing (Said et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

High resolution melting analysis of the NR1I3 genetic variants: Is there an association with neonatal hyperbilirubinemia?

Cheung

Rostenberghe

Ismail

et al. 2015

Gene

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Constitutive androstane receptor (CAR) encoded by the nuclear receptor subfamily 1, group I, member 3 (NR1I3) gene regulates the elimination of bilirubin through activating the components of the bilirubin clearance pathway. Hence, NR1I3 genetic variants may affect bilirubin metabolism and result in neonatal hyperbilirubinemia. Thus far, research which investigates the association between NR1I3 variants and neonatal hyperbilirubinemia has not been undertaken in any population. The present study aimed to evaluate the influence of MPJ6_1I3008 (rs10157822), IVS8+116T>G (rs4073054) and 540A>G (rs2307424) on neonatal hyperbilirubinemia development in the Malay population. Buccal swabs were collected from 232 hyperbilirubinemia and 277 control term newborns with gestational age ≥37weeks and birth weight ≥2500g. The NR1I3 variants were genotyped by using high resolution melting (HRM) assays and verified by DNA sequencing. Gender, mode of delivery and birth weight did not differ between hyperbilirubinemia and control groups. The genotypic and allelic frequencies of MPJ6_1I3008, IVS8+116T>G and 540A>G were not significantly different between the groups. However, stratification by gender revealed a significant inverse association between homozygous variant genotype of MPJ6_1I3008 and risk of neonatal hyperbilirubinemia in the females (OR, 0.44; 95% CI, 0.20-0.95; p=0.034). This study demonstrates that the homozygous variant genotype of MPJ6_1I3008 was associated with a significant reduced risk of neonatal hyperbilirubinemia in the females.

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Genomics In Premature Infants: A Non-Invasive Strategy To Obtain High-Quality DNA

Cited by 13 publications

References 19 publications

Intra-individual methylomics detects the impact of early-life adversity

Intra-individual methylomics detects the impact of early-life adversity

Are Immune Modulating Single Nucleotide Polymorphisms Associated with Necrotizing Enterocolitis?

High resolution melting analysis of the NR1I3 genetic variants: Is there an association with neonatal hyperbilirubinemia?

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