Saliva: a convenient source of DNA for analysis of bi-allelic polymorphisms of Fc gamma receptor IIA (CD32) and Fc gamma receptor IIIB (CD16)

Comprehensive Analysis of Differentially Expressed Genes in Clinically Diagnosed Irreversible Pulpitis by Multiplatform Data Integration Using a Robust Rank Aggregation Approach

INTRODUCTION

Molecular diagnosis may overcome the limitations of clinical and histologic diagnosis in pulpitis, thereby benefiting many treatment techniques, such as vital pulp therapies. In this study, integrated microarray data on pulpitis were used to obtain a list of normalized differentially expressed (DE) genes for analyzing the molecular mechanisms underlying pulpitis and identifying potential diagnostic biomarkers.

METHODS

A systematic search of public microarray and sequencing databases was performed to obtain expression data of pulpitis. Robust rank aggregation (RRA) was used to obtain DE gene lists (RRA_DEmRNAs and RRA_DElncRNAs) between inflamed pulp and normal samples. DE genes were evaluated by functional enrichment analyses, correlation analyses for inflammation-related RRA_DEmRNAs, and protein-protein interaction and competing endogenous RNA network construction. Quantitative real-time polymerase chain reaction validation was applied in snap-frozen pulp tissues.

RESULTS

Using the GSE77459 and GSE92681 data sets, 280 RRA_DEmRNAs and 90 RRA_DElncRNAs were identified. RRA_DEmRNAs were significantly enriched in inflammation-related biological processes and osteoclast differentiation and tumor necrosis factor, chemokine, and B-cell receptor signaling pathways. The molecular complex detection and cytoHubba methods identified 2 clusters and 10 hub genes in the protein-protein interaction network. The competing endogenous RNA network was composed of 2 long noncoding RNAs (ADAMTS9-AS2 and LINC00290), 2 microRNAs (hsa-miR-30a-5p and hsa-miR-128-3p), and 3 messenger RNAs (ABCA1, FBLN5, and SOCS3). The expression between most top inflammation-related RRA_DEmRNAs in pulpitis showed positive correlations. Quantitative real-time polymerase chain reacation validated the expression trends of selected genes, including ITGAX, TREM1, CD86, FCGR2A, ADAMTS9-AS2, LINC00290, hsa-miR-30a-5p, hsa-miR-128-3p, RASGRP3, IL3RA, CCDC178, CRISPLD1, LINC01857, AC007991.2, ARHGEF26-AS1, and AL021408.1.

CONCLUSIONS

The identified biomarkers provide insight into the pathology and may aid in the molecular diagnosis of pulpitis.

Biochemical analysis of oral fluids for disease detection

The field of diagnostics using invasive blood testing represents the majority of diagnostic tests used as part of routine health monitoring. The relatively recent introduction of salivary diagnostics has lead to a major paradigm shift in diagnostic analyses. Additionally, in this era of big data, oral fluid testing has shown promising outcomes in a number of fields, particularly the areas of genomics, microbiomics, proteomics, metabolomics, and transcriptomics. Despite the analytical challenges involved in the interpretation of large datasets generated from biochemical studies involving bodily fluids, including saliva, many studies have identified novel oral biomarkers for diagnosing oral and systemic diseases. In this regard, oral biofluids, including saliva, gingival crevicular fluid (GCF), peri-implant crevicular fluid (PICF), dentinal tubular fluid (DTF), are now attracting increasing attention due to their important attributes, such as noninvasive sampling, easy handling, low cost, and more accurate diagnosis of oral diseases. Recently, the utilization of salivary diagnostics to evaluate systemic diseases and monitor general health has increased in popularity among clinicians. Saliva contains a wide range of protein, DNA and RNA biomarkers, which assist in the diagnosis of multiple diseases and conditions, including cancer, cardiovascular diseases (CVD), auto-immune and degenerative diseases, respiratory infections, oral diseases, and microbial (viral, bacterial and fungal) diseases. Moreover, due to its noninvasive nature and ease-of-adoption by children, it is now being used in mass screening programs, oral health-related studies and clinical trials in support of the development of therapeutic agents. The recent advent of highly sensitive technologies, such as next-generation sequencing, mass spectrometry, highly sensitives ELISAs, and homogeneous immunoassays, suggests that even small quantities of salivary biomarkers are able to be assayed accurately, providing opportunities for the development of many future diagnostic applications (including emerging technologies, such as point-of-care and rapid molecular technologies). The present article explores the omics and biochemical compositions of various oral biofluids with important value in diagnostics and monitoring.

T-Cell Receptor Stimulation Enhances the Expansion and Function of CD19 Chimeric Antigen Receptor-Expressing T Cells

PURPOSE

Current protocols for CD19 chimeric antigen receptor-expressing T cells (CD19.CAR-T cells) require recipients to tolerate preinfusion cytoreductive chemotherapy, and the presence of sufficient target antigen on normal or malignant B cells.

PATIENTS AND METHODS

We investigated whether additional stimulation of CD19.CAR-T cells through their native receptors can substitute for cytoreductive chemotherapy, inducing expansion and functional persistence of CD19.CAR-T even in patients in remission of B-cell acute lymphocytic leukemia. We infused a low dose of CD19.CAR-modified virus-specific T cells (CD19.CAR-VST) without prior cytoreductive chemotherapy into 8 patients after allogeneic stem cell transplant.

RESULTS

Absent virus reactivation, we saw no CD19.CAR-VST expansion. In contrast, in patients with viral reactivation, up to 30,000-fold expansion of CD19.CAR-VSTs was observed, with depletion of CD19⁺ B cells. Five patients remain in remission at 42-60+ months.

CONCLUSIONS

Dual T-cell receptor and CAR stimulation can thus potentiate effector cell expansion and CAR-target cell killing, even when infusing low numbers of effector cells without cytoreduction.

Evaluation of salivary DNA obtained from dental prosthesis and its applicability in forensic investigations

AIM

This study evaluated the salivary DNA obtained from dental prosthesis after a period of storage and its applicability in human identification.

MATERIAL AND METHODS

In first phase, DNA was extracted after a span of 1 week and 1 month from the dental prosthesis dipped in whole saliva for 15 min. It was followed by PCR and electrophoresis. In second phase, from extracted DNA samples 15 STRs (short tandem repeats) of human genomic DNA were amplified via polymerase chain reaction.

RESULTS & CONCLUSION

DNA isolated from saliva stained dental prosthesis after a period of storage and the techniques employed are adequate for further forensic analysis.

Collection and extraction of saliva DNA for next generation sequencing

The preferred source of DNA in human genetics research is blood, or cell lines derived from blood, as these sources yield large quantities of high quality DNA. However, DNA extraction from saliva can yield high quality DNA with little to no degradation/fragmentation that is suitable for a variety of DNA assays without the expense of a phlebotomist and can even be acquired through the mail. However, at present, no saliva DNA collection/extraction protocols for next generation sequencing have been presented in the literature. This protocol optimizes parameters of saliva collection/storage and DNA extraction to be of sufficient quality and quantity for DNA assays with the highest standards, including microarray genotyping and next generation sequencing.

Evaluation of the long-term storage stability of saliva as a source of human DNA

OBJECTIVES

The objectives of this paper are to determine the storage stability of saliva at 37 °C over an 18-month period, and its influence on the DNA yield, purity, PCR protocols and genotyping efficacy.

MATERIALS AND METHODS

Of the 60 participants, blood samples were obtained from 10 and saliva from 50. Samples were subjected to different storage conditions: DNA extracted immediately; DNA extracted following storage at 37 °C for 1, 6, 12 and 18 months. Subsequently, DNA yield, OD(260/280) and OD(260/230) ratios were measured. The isolated DNA was used to amplify exons 0-7 of the RUNX2 gene and subsequently sequenced. Furthermore, 25 SNPs were genotyped.

RESULTS

The mean DNA yield, OD(260/280) and OD(260/230) ratios obtained from blood were 67.4 ng/μl, 1.8 ± 0.05 and 1.8 ± 0.4 respectively. DNA yield obtained from saliva was significantly higher than blood (p < 0.0001), ranging from 97.4 to 125.8 ng/μl while the OD(260/280) ratio ranged from 1.8 ± 0.13 to 1.9 ± 0.1. The success rates for the 25 SNPs ranged from 98 to 100 % for blood and 96-99 % for saliva samples with the genotype frequencies in Hardy-Weinberg equilibrium (>0.01).

CONCLUSIONS

Saliva can be stored at 37 °C for 18 months without compromising its quality and ability to endure genetic analyses.

CLINICAL RELEVANCE

Saliva is a viable source of human DNA to facilitate the feasibility of large-scale genetic studies.

Comparison of different collection procedures and two methods for DNA isolation from saliva

The non-invasive, flexible and easy sample collection makes saliva an interesting source of DNA for research and diagnostic purposes. The aim of our study was to find the most suitable collection method for biological material from the oral cavity and the most effective DNA isolation technique for further analytic applications.

DNA was isolated from swabs, Salivette saliva, whole saliva and samples collected with a commercial set for scraping of buccal cells. Phenol-chloroform extraction and isolation using a silica membrane based commercial kit were compared. Quantity of bacterial and human genomic DNA was estimated using real time PCR. The effects of storage conditions on DNA recovery were assessed.

Sample collection techniques significantly affected the quantity of DNA for both, silica membrane based and phenol-chloroform isolations. Whole saliva provided the largest number of bacterial and human genome copies after both extraction methods. Storage for 36 months at –20°C reduced recovery of human genomic DNA five times after silica membrane based extraction and 10 times after phenol-chloroform isolation.

Whole saliva was found to be the most suitable material for human and bacterial DNA isolation. Both compared methods are useful considering the quantity of extracted DNA.

Diagnosis of mediterranean visceral leishmaniasis by detection of leishmania antibodies and leishmania DNA in oral fluid samples collected using an Oracol device

Current methods for diagnosis of visceral leishmaniasis (VL) require invasive sampling procedures such as visceral aspiration and/or blood drawing. The use of diagnostic tests using oral fluid, which is easier to collect, would be more simple and practical for VL diagnosis, especially under field conditions. Oral fluids from 37 VL patients and 40 healthy controls were collected using Oracol devices. Blood samples and oral fluid specimens from both groups were analyzed by recombinant protein K39 (rK39) enzyme-linked immunosorbent assay and quantitative real-time PCR. Detection of antibodies in the oral fluid had a sensitivity of 100% and a specificity of 97.5%. Antibody levels measured in serum and oral fluid showed a significant positive correlation (ρ = 0.655 and P = 0.01). Detection of Leishmania DNA in oral fluid had a sensitivity of 94.6% and a specificity of 90%. The median parasite load estimated in blood was 133 parasites/ml (interquartile range [IR], 10 to 1,048), whereas that in oral fluid specimens was 3 parasites/ml (IR, 0.41 to 92). However, there was no significant linear relationship between parasite loads assessed in the two biological samples (ρ = 0.31 and P = 0.06). VL diagnosis based on specific antibody detection and Leishmania DNA identification using oral fluid samples was equivalent in accuracy to that using blood and therefore is promising for clinical use.

An application of salivary DNA in twin research of Chinese children

Since saliva collection is noninvasive, painless and inexpensive, it may become an alternative to obtain genomic DNA, which is critical to evaluate zygosity and the role of genetic factors in twin research. This study provided a rough description of salivary DNA in Chinese twin children, and presented the DNA yield and quality extracted from saliva in a large-scale children sample, which supplied an example for saliva sample using in genetic epidemiology. Three milliliters of saliva was collected from 356 twin children aged 6 to 15, and DNA was extracted by a commercial DNA isolation kit. The DNA yield and purity was determined by spectrophotometry at 260 nm and 280 nm. The zygosity determination of the same-sex twins and the assay of Polymerase Chain Reaction-Restriction Fragment Length Polymorphism indicated the quality of salivary DNA. The amount of extracted DNA from three milliliters of saliva was about 34.91 microg (2.20 approximately 122.04 microg), average OD(260/280) values was 1.84. Saliva DNA is a reliable sample for the determination of twins' zygosity. We conclude that saliva may be a feasible and reliable source of DNA for genetic epidemiology studies, especially for twin research.

Can we predict neuropathy risk before stavudine prescription in a resource-limited setting?

A toxic sensory neuropathy associated with exposure to inexpensive nucleoside analogue reverse transcriptase inhibitors (NRTIs) [particularly stavudine (d4T)] causes dilemmas in the management of patients with HIV, especially in resource-poor settings. Here patients (n = 96) attending Pokdisus AIDS Clinic at the Cipto Mangunkusumo Hospital, Jakarta who had been treated with d4T were screened for symptomatic neuropathy. Clinical, demographic, and genetic factors were considered as possible neuropathy risk factors. DNA from saliva was used to examine alleles of TNFA-308, BAT1 (intron 10), TNFA-1031, IL1A+4845, and IL12B (3' UTR). The prevalence of neuropathy (symptoms and signs) was 34%. On multivariate analysis, neuropathy following d4T exposure was associated with increasing age, increasing height, and TNFA-1031*2 (model p = 0.0009). Isoniazid exposure (present in 56% of patients) was not associated with neuropathy in this cohort, where all patients had received pyridoxine coadministration. These data suggest that a simple algorithm based on patient age, height, and TNF genotype could be used to predict the individual's risk of symptomatic neuropathy prior to prescription of d4T.

New saliva DNA collection method compared to buccal cell collection techniques for epidemiological studies

Epidemiological studies may require noninvasive methods for off-site DNA collection. We compared the DNA yield and quality obtained using a whole-saliva collection device (Oragene DNA collection kit) to those from three established noninvasive methods (cytobrush, foam swab, and oral rinse). Each method was tested on 17 adult volunteers from our center, using a random crossover collection design and analyzed using repeated-measures statistics. DNA yield and quality were assessed via gel electrophoresis, spectophotometry, and polymerase chain reaction (PCR) amplification rate. The whole-saliva method provided a significantly greater DNA yield (mean +/- SD = 154.9 +/- 103.05 microg, median = 181.88) than the other methods (oral rinse = 54.74 +/- 41.72 microg, 36.56; swab = 11.44 +/- 7.39 microg, 10.72; cytobrush = 12.66 +/- 6.19, 13.22 microg) (all pairwise P < 0.05). Oral-rinse and whole-saliva samples provided the best DNA quality, whereas cytobrush and swab samples provided poorer quality DNA, as shown by lower OD(260)/OD(280) and OD(260)/OD(230) ratios. We conclude that both a 10-ml oral-rinse sample and 2-ml whole-saliva sample provide sufficient DNA quantity and better quality DNA for genetic epidemiological studies than do the commonly used buccal swab and brush techniques.

Filaggrin repeat number polymorphism is associated with a dry skin phenotype

Profilaggrin is a key epidermal protein, critical for the generation and maintenance of the stratum corneum barrier. It is encoded by a gene located in the epidermal differentiation complex of Chromosome 1q21 and is composed of multiple filaggrin repeats connected by highly conserved linker peptides. Within the human population the number of filaggrin repeats encoded by this gene varies between 10, 11 or 12 repeats. Using a PCR-based approach we have determined individual profilaggrin allelotypes in a group of 113 subjects and identified preliminary evidence of an inverse association between the 12 repeat allele and self-perceived frequent dry skin (P=0.0293). This is the first demonstration of a potential association between a genetic marker and cosmetic skin condition and suggests that cosmetic skin dryness may in part be genetically determined and associated with specific profilaggrin allelotypes.

Human herpesvirus 6 in oral fluids from healthy individuals

BACKGROUND

Human herpesvirus 6 (HHV6) is the etiologic agent of exanthem subitum. The virus is latent in salivary glands and saliva is the main form of viral transmission. The objective of this study was to assess HHV6 incidence in the fluids from healthy individuals using a standardised technique for collecting and extracting viral DNA from gingival crevicular fluid, whole saliva and parotid gland saliva.

DESIGN

Samples of oral fluids and peripheral blood were collected from 28 blood donors and HHV6 was detected using PCR assay. Parotid gland saliva and gingival crevicular fluid were collected by endodontic paper cones in order to not contaminate these fluids with whole saliva.

RESULTS

Of the 28 donors, 20 (71.4%) presented positive results in at least one of the three oral fluids researched. Whole saliva was positive in 19 (67.8%) volunteers, while only four (14.2%) samples of gingival crevicular fluid and four of parotid gland saliva proved to be positive.

CONCLUSIONS

The results suggest that HHV6 is present in the saliva of a large proportion of the healthy adult population. The use of endodontic paper cones for oral fluid collection and viral extraction was efficient, simple, cheap and painless. In spite of, the small number of cases studied it was possible to demonstrate that neither gingival crevicular fluid nor parotid gland saliva were the principal source of HHV6 in whole saliva.

Detection of Helicobacter pylori DNA in feces and saliva by polymerase chain reaction: a review

The polymerase chain reaction (PCR), known for its high sensitivity and specificity, has been used for the detection of Helicobacter pylori DNA in bodily materials such as feces and saliva. Since fecal specimens contain PCR inhibitors, DNA before PCR amplification has been purified using various biochemical, immunological and physical pre-PCR steps. Several PCR protocols, differing from each other in the selection of genomic targets and primers, have produced varying degrees of specificity and sensitivity in detecting H. pylori DNA. PCR identified antimicrobial resistance of H. pylori in feces. It also detected virulence factor genes such as the cytotoxin-associated gene (cagA) and vacuolating cytotoxin gene (vacA) in feces and saliva. While the cagA gene was detected in 50-60% of fecal specimens, it was found in 25% of salivary specimens from patients. There was considerable variation in the detection rate of H. pylori DNA in salivary samples. The detection rate in saliva with the most effective primer pair was lower than that observed in feces, making saliva a less suitable specimen for the diagnosis of H. pylori infection. There is controversy regarding the permanent presence of H. pylori in saliva. Whether the salivary and gastric specimens of an individual harbor identical or different strains has not been resolved. PCR cannot distinguish between living and dead organisms. However, it can offer quick results on fecal and salivary specimens, which may contain fastidious and slow-growing H. pylori in low numbers.

Immune-mediated neutropenia in the neonate

Alloimmune neonatal neutropenia, neonatal autoimmune neutropenia and autoimmune neutropenia of infancy have remained nebulous entities with difficulties in both clinical and laboratory identification. These disorders are reviewed in this article.

Fc gamma receptor genes as risk markers for localized aggressive periodontitis in African-Americans

BACKGROUND

Receptors for the Fc fragment of immunoglobulin G (Fc gammaRs) play a crucial role in host defense against bacterial infection by linking humoral and cell-mediated immune responses. Allelic variants of certain Fc gammaRs have been shown to differ relative to their biologic activity. Thus, genes encoding allotypes with diminished activity have been suggested as potential risk factors for infectious diseases. The goal of this study was to determine whether specific Fc gammaRIIa, Fc gammaRIIIa, and Fc gammaRIIIb alleles and/or genotypes could be used to predict susceptibility to localized aggressive periodontitis (LAgP) in an African-American population.

METHODS

Whole blood or saliva was obtained from 48 LAgP and 67 periodontally-healthy African-American subjects. DNA was prepared from each sample. Fc gammaRIIa and Fc gammaRIIIa genotyping was analyzed by polymerase chain reaction (PCR) amplification of DNA with allele-specific primers followed by allele-specific restriction digestion of the products. Fc gammaRIIIb genotyping was done by allele-specific PCR.

RESULTS

There was a statistically significant over-representation of the Fc gammaRIIIb-NA2 allele in LAgP patients compared to controls (P = 0.024). Relative to the Fc gammaRIIIb-NA1/NA2 and homozygous NA1/NA1 genotypes, the prevalence of the Fc gammaRIIIb NA2/NA2 genotype was higher in the LAgP group relative to the control population. Individuals expressing this genotype appeared at greater risk for developing LAgP (odds ratio 2.271, 95% confidence interval: 1.005 to 5.132). There were no significant differences in the distribution of the Fc gammaRIIa H/R or Fc gammaRIIIa-158 F/V genotypes nor their allelic frequencies between the LAgP patients and controls.

CONCLUSIONS

These data suggest that the Fc gammaRIIIb NA2 allele and/or NA2/NA2 genotype may represent risk markers for susceptibility to LAgP in African-Americans.

Neutrophil disorders and their management

Neutrophil disorders are an uncommon yet important cause of morbidity and mortality in infants and children. This article is an overview of these conditions, with emphasis on clinical recognition, rational investigation, and treatment. A comprehensive list of references is provided for further reading.

Evaluation of human FcgammaRIIA (CD32) and FcgammaRIIIB (CD16) polymorphisms in Caucasians and African-Americans using salivary DNA

Two classes of low-affinity receptors for the Fc region of immunoglobulin G (IgG) (FcgammaR) are constitutively expressed on resting human neutrophils. These receptors, termed FcgammaRIIa (CD32) and FcgammaRIIIb (CD16), display biallelic polymorphisms which have functional consequences with respect to binding and/or ingestion of targets opsonized by human IgG subclass antibodies. The H131-R131 polymorphism of CD32 influences binding of human IgG2 and, to a lesser extent, human IgG3 to neutrophils. The neutrophil antigen (NA1-NA2) polymorphism of CD16 influences the efficiency of phagocytosis of bacteria opsonized by human IgG1 and IgG3. These polymorphisms may influence host susceptibility to certain infectious and/or autoimmune diseases, prompting interest in the development of facile methods for determination of CD32 and CD16 genotype in various clinical settings. We previously reported that genomic DNA from saliva is a suitable alternative to DNA from blood in PCR-based analyses of CD32 and CD16 polymorphisms. In the present study, we utilized for the first time this salivary DNA-based methodology to define CD32 and CD16 genotypes in 271 Caucasian and 118 African-American subjects and to investigate possible linkage disequilibrium between certain CD32 and CD16 genotypes in these two ethnic groups. H131 and R131 gene frequencies were 0.45 and 0.55, respectively, among Caucasians and 0.59 among African-Americans. NA1 and NA2 gene frequencies were 0.38 and 0.62 among Caucasians and 0. 39 and 0.61 among African-Americans. Since FcgammaRIIa and FcgammaRIIIb synergize in triggering neutrophils, we also assessed the frequency of different CD32 and CD16 genotype combinations in these two groups. In both groups, the R/R131-NA2/NA2 genotype combination was more common than the H/H131-NA1/NA1 combination (threefold for Caucasians versus sevenfold for African-Americans). Whether individuals with the combined R/R131-NA2/NA2 genotype are at greater risk for development of infectious and/or autoimmune diseases requires further investigation, which can be conveniently performed using DNA from saliva rather than blood.