Evaluation of extraction methods for methylated cell-free fetal DNA from maternal plasma

Advances in biomarker discovery using circulating cell-free DNA for early detection of hepatocellular carcinoma

The past several decades have witnessed unprecedented progress in basic and clinical cancer research, and our understanding of the molecular mechanisms and pathogenesis of cancers have been greatly improved. More recently, with the availability of high-throughput sequencing and profiling platforms as well as sophisticated analytical tools and high-performance computing capacity, there have been tremendous advances in the development of diagnostic approaches in clinical oncology, especially the discovery of novel biomarkers for cancer early detection. Although tissue biopsy-based pathology has been the "gold standard" for cancer diagnosis, notable limitations such as the risk due to invasiveness and the bias due to intra-tumoral heterogeneity have limited its broader applications in oncology (e.g., screening, regular disease monitoring). Liquid biopsy analysis that exploits the genetic and epigenetic information contained in DNA/RNA materials from body fluids, particularly circulating cell-free DNA (cfDNA) in the blood, has been an intriguing alternative approach because of advantageous features such as sampling convenience and minimal invasiveness. Taking advantage of innovative enabling technologies, cfDNA has been demonstrated for its clinical potential in cancer early detection, including hepatocellular carcinoma (HCC), the most common liver cancer that causes serious healthcare burden globally. Hereby, we reviewed the current advances in cfDNA-based approaches for cancer biomarker discovery, with a focus on recent findings of cfDNA-based early detection of HCC. Future clinical investigations and trials are warranted to further validate these approaches for early detection of HCC, which will contribute to more effective prevention, control, and intervention strategies with the ultimate goal of reducing HCC-associated mortality. This article is categorized under: Cancer > Genetics/Genomics/Epigenetics.

Appraisal on the Wound Healing Potential of Deverra tortuosa DC. and Deverra triradiata Hochst Essential Oil Nanoemulsion Topical Preparation

Deverra tortuosa (Desf.) DC. and Deverra. triradiata Hochst. ex Bioss are perennial desert shrubs widely used traditionally for many purposes and they are characteristic for their essential oil. The objective of the present study was to investigate the in vivo wound healing activity of the essential oil (EO) of D. tortuosa and D. triradiata through their encapsulation into nanoemulsion. EO nanoemulsion was prepared using an aqueous phase titration method, and nanoemulsion zones were identified through the construction of phase diagrams. The EO was prepared by hydrodistillation (HD), microwave-assisted hydrodistillation (MAHD), and supercritical fluid extraction (SFE) and analyzed using GC/MS. D. tortuosa oil is rich in the non-oxygenated compound, representing 74.54, 73.02, and 41.19% in HD, MADH, and SFE, respectively, and sabinene represents the major monoterpene hydrocarbons. Moreover, D. triradiata is rich in oxygenated compounds being 69.77, 52.87, and 61.69% in HD, MADH, and SFE, respectively, with elemicin and myristicin as major phenylpropanoids. Topical application of the nanoemulsion of D. tortuosa and D. triradiata (1% or 2%) exhibited nearly 100% wound contraction and complete healing at day 16. Moreover, they exhibit significant antioxidant and anti-inflammatory effects and a significant increase in growth factors and hydroxyproline levels. Histopathological examination exhibited complete re-epithelialization accompanied by activated hair follicles and abundant collagen fibers, especially at a concentration of 2%. Therefore, the incorporation of the two Deverra species into nanoemulsion could professionally endorse different stages of wound healing.

Lipid Metabolism Affects Fetal Fraction and Screen Failures in Non-invasive Prenatal Testing

Objective: To assess the association between lipid metabolism and fetal fraction, which is a critical factor in ensuring a highly accurate non-invasive prenatal testing (NIPT), and on the rate of screen failures or “no calls” in NIPT.

Methods: A total of 4,514 pregnant women at 12–26 weeks of gestation underwent NIPT sequencing and serum lipid measurements. Univariate analysis and multivariate regression models were used to evaluate the associations of serum lipid concentrations with the fetal fraction and the rate of screen failures.

Results: The fetal fraction decreased with increased low-density lipoprotein cholesterol and triglyceride (TG) levels, which were significant factors (standardized coefficient: −0.11). Conversely, high-density lipoprotein cholesterol and the interval between the two tests were positively correlated with the fetal fraction. The median fetal fraction was 10.88% (interquartile range, 8.28–13.89%) and this decreased with TG from 11.56% at ≤1.10 mmol/L to 9.51% at >2.30 mmol/L. Meanwhile, multivariate logistic regression analysis revealed that increased TG levels were independently associated with the risk of screen failures. The rate of screen failures showed an increase with TG levels from 1.20% at ≤1.70 mmol/L to 2.41% at >2.30 mmol/L.

Conclusions: The fetal fraction and the rate of screen failures in NIPT are affected by TG levels. Meanwhile, in pregnant women with high TG levels, delaying the time between NIPT blood collections can significantly increase the fetal fraction.

Comparison of indications and results of prenatal invasive diagnostic tests before and after the implementation of the use of cell-free fetal DNA: a tertiary referral center experience

PURPOSE

In this study, we aimed to compare the changes in the number, yield, and the percentage of karyotyping indications of the invasive prenatal diagnostic tests between the periods before and after cell-free fetal DNA was introduced to clinical use.

METHOD

The number of invasive prenatal diagnostic procedures such as amniocentesis and chorionic villus sampling, indication percentages and karyotype results in the periods before (January 1, 2009-December 31, 2010), (n = 1412) and after (January 1, 2016-December 31, 2017), and (n = 593) the introduction of cell-free fetal DNA was retrospectively evaluated.

RESULTS

When compared with the period before cell-free fetal DNA came into clinical use, the number of invasive prenatal diagnostic tests decreased by 58% while their yield was found to have increased (4.4% vs. 10.3%) in the period after cell-free DNA began to be used (p < 0.001). While there was a decrease in the indications due to advanced maternal age, an increase was found in ultrasonography indications for structural anomaly and the risk of a single-gene disorder (p < 0.001). Amniocentesis rate was found to have decreased in invasive prenatal diagnostic procedure types, while an increase was reported in CVS rates (p < 0.001).

CONCLUSIONS

Invasive prenatal diagnosis gradually decreases over the years, but the yield of invasive prenatal diagnostic tests increases. In parallel with the rapid development of modern molecular technologies and cheaper and easier access to the tests, we think that the number of invasive prenatal diagnostic tests will experience a more dramatic decrease in the following years.

Potential of Next-Generation Sequencing in Noninvasive Fetal Molecular Blood Group Genotyping

Hemolytic disease of the fetus and newborn and fetal and neonatal alloimmune thrombocytopenia are caused by maternal antibodies against fetal alloantigens on red blood cells or platelets that are inherited from the father. After transplacental transport to the fetal circulation, antibodies of the IgG class may cause severe fetal anemia or bleeding complications. The indication for noninvasive fetal blood group genotyping is given if a clinically relevant antibody is detected in a pregnant woman and if the father is heterozygous (or unknown) for the implicated blood group allele. This mini-review will focus on the advantages and current limitations of next-generation sequencing (NGS) for noninvasive diagnosis of fetal blood groups which is, in contrast to fetal aneuploidy screening, proposed only by some research groups. Targeted massively parallel sequencing of short DNA fragments from maternal cell-free plasma samples enables counting of fetal alleles for many single nucleotide polymorphisms in parallel. This information can be utilized for estimation of the fetal fraction of cell-free DNA (cfDNA) as well as detection of the paternal blood group allele in question. Adherence to a cut-off of ≥4% fetal fraction for reporting conclusive results is recommended to avoid false-negative results due to low fetal fraction. For screening purposes of fetal RHD in RhD-negative pregnant women, real-time PCR methods are very well established. However, for diagnostic purposes, the targeted amplicon-based NGS approach has the inherent capability to estimate the fetal fraction of cfDNA. In the future, improving the accuracy of NGS by consensus sequencing of single cfDNA molecules may enable reliable fetal blood group genotyping already in the first trimester of pregnancy.

Sequencing of short cfDNA fragments in NIPT improves fetal fraction with higher maternal BMI and early gestational age

Low fetal DNA fraction (< 4%) samples obtained during noninvasive prenatal testing (NIPT) are responsible for 0.5%-3% of "no calls". Maternal characteristics such as body mass index (BMI) and gestational age (GA) are the main factors that influence fetal fraction. Here, we improved fetal fraction by performing semiconductor sequencing of shorter fragments (107-145 bp) of cfDNA (traditional NIPT fragment is 160 bp). Multivariable linear regression modeling was used to evaluate the association between fetal fraction and maternal characteristics including BMI and GA. Among the 1495 shorter cfDNA sequencing samples, BMI and GA were negatively and positively correlated with fetal fraction, respectively. Compared with underweight pregnant women, sequencing of shorter fragments decreased the mean fetal fraction differences between BMI groups, especially in the obese women (~15%). We also showed that the average fetal fraction was 22.2% and 96.3% fetal fraction more than 10% in the obese women with the average GA of 17 weeks. Size selection slightly decreased the mean fetal fraction differences between different GA groups, and sequencing shorter cfDNA can yield a fetal fraction at an earlier GA. Collectively, our results support the strategy of sequencing shorter to improve fetal fraction in subjects with a high maternal BMI and earlier GA.

Evaluation and statistical optimization of a method for methylated cell-free fetal DNA extraction from maternal plasma

PURPOSE

Methylated cell-free fetal DNA (cffDNA) in maternal plasma can potentially be used as a biomarker for accurate noninvasive prenatal testing (NIPT) of fetal disorders. Recovery and purification of cffDNA are key steps for downstream applications. In this study, we aimed to developed and evaluated different aspects of an optimized method and compared its efficiency with common methods used for extraction of methylated cffDNA.

METHODS

Single factor experiments, Plackett-Burman (PB) design, and response surface methodology (RSM) were conducted for conventional Triton/Heat/Phenol (cTHP) method optimization. The total cell-free DNA (cfDNA) was extracted from pooled maternal plasma using the optimized method called the Triton/Heat/Phenol/Glycogen (THPG), cTHP method, a column-based kit, and a magnetic bead-based kit. In the next step, methylated cfDNA from the extracted total cfDNA was enriched using a methylated DNA immunoprecipitation (MeDIP) kit. Real-time quantitative polymerase chain reaction was performed on the RASSF1 gene and hyper region to determine the genomic equivalents per milliliter (GEq/ml) values of the methylated cfDNA and cffDNA, respectively.

RESULTS

The optimum values of the significant factors affecting cfDNA extraction from 200 μl of plasma were 3% SDS, 1% Triton X-100, 0.9 μg/μl glycogen, and 0.3 M sodium acetate. The GEq/ml values of methylated cffDNA extracted using the THPG method were significantly higher than for the tested extraction methods (p < 0.001).

CONCLUSIONS

Our results indicate that the THPG method is more efficient than the other tested methods for extraction of low copy number methylated cffDNA from a small volume of maternal plasma.