Optimal reference genes for RT-qPCR normalization in the newborn

Neonatal body composition, salivary feeding gene expression, and feeding outcomes in infants of diabetic mothers

Introduction

Infants of diabetic mothers (IDMs) may exhibit decreased oral intake, requiring nasogastric feedings and prolonged hospitalization. The objective of this study was to explore whether saliva serves as an informative biofluid for detecting expression of hunger signaling and energy homeostasis modulator genes and to perform exploratory analyses examining expression profiles, body composition, and feeding outcomes in late preterm and term IDMs and infants born to mothers with normoglycemia during pregnancy.

Methods

In this prospective cohort pilot study, infants born at ≥ 35 weeks' gestation to mothers with gestational or type II diabetes (IDM cohort) and normoglycemic mothers (control cohort) were recruited. The presence of known hunger signaling genes: 5'AMP-activated protein kinase (PRKAA2) and neuropeptide Y2 receptor (NPY2R); adipokines: leptin (LEP) and adiponectin (ADIPOQ); and energy homeostasis regulators: ghrelin (GHRL) and proopiomelanocortin (POMC) in neonatal saliva was determined with RT-qPCR and compared between cohorts. Body composition was assessed via skinfold measurements and compared between cohorts. Feeding outcomes were recorded. Exploratory analyses were performed examining associations between infant body composition, energy homeostasis and hunger signaling gene expression.

Results

Twenty-three infants in the IDM cohort and 22 infants in the control cohort were recruited. LEP and ADIPOQ were not reliably detected in neonatal saliva in either cohort. PRKAA2, GHRL and NPY2R were less likely to be detected in the IDM cohort, whereas POMC was more likely to be detected in the IDM cohort. Infants in the IDM cohort had greater adiposity compared to infants in the normoglycemia cohort. Only 3 IDMs had documented poor feeding; no infant in the control group struggled to feed. In exploring associations between hunger signaling gene expression with energy homeostasis gene expression and body composition, the odds of detecting salivary NPY2R expression decreased as fat mass increased, and the odds of detecting PRKAA2 expression increased in the presence of GHRL expression.

Discussion

Non-invasive assessment of hunger signaling and energy homeostasis gene expression is possible through neonatal salivary analysis. This pilot study lays the foundation for a larger scale study to further investigate the link between in utero exposure to diabetes with body composition and regulation of appetite.

A Strategy for the Selection of RT-qPCR Reference Genes Based on Publicly Available Transcriptomic Datasets

In the next-generation sequencing era, RT-qPCR is still widely employed to quantify levels of nucleic acids of interest due to its popularity, versatility, and limited costs. The measurement of transcriptional levels through RT-qPCR critically depends on reference genes used for normalization. Here, we devised a strategy to select appropriate reference genes for a specific clinical/experimental setting based on publicly available transcriptomic datasets and a pipeline for RT-qPCR assay design and validation. As a proof-of-principle, we applied this strategy to identify and validate reference genes for transcriptional studies of bone-marrow plasma cells from patients with AL amyloidosis. We performed a systematic review of published literature to compile a list of 163 candidate reference genes for RT-qPCR experiments employing human samples. Next, we interrogated the Gene Expression Omnibus to assess expression levels of these genes in published transcriptomic studies on bone-marrow plasma cells from patients with different plasma cell dyscrasias and identified the most stably expressed genes as candidate normalizing genes. Experimental validation on bone-marrow plasma cells showed the superiority of candidate reference genes identified through this strategy over commonly employed "housekeeping" genes. The strategy presented here may apply to other clinical and experimental settings for which publicly available transcriptomic datasets are available.

Age, sex, and frailty modify the expression of common reference genes in skeletal muscle from ageing mice

Changes in gene expression with age are typically normalised to constitutively expressed reference genes (RGs). However, RG expression may be affected by age or overall health and most studies use only male animals. We investigated whether expression of common RGs (Gapdh, Gusb, Rplp0, B2m, Tubb5, Rpl7l1, Hprt, Rer1) was affected by age, sex and/or overall health (frailty index) in skeletal muscle from young (4-mos) and aged (25-26-mos) mice. Standard RG selection programs recommended Gapdh (RefFinder/Genorm/NormFinder) or Rpl7l1 (BestKeeper) without considering age and sex. Analysis of raw Cq values showed only Rplp0 was stable in both sexes at both ages. When qPCR data were normalised to Rplp0, age affected RG expression, especially in females. For example, Hprt expression declined with age (Hprt=9.8 ×10-2 ± 4.7 ×10-2 vs. 6.5 ×10-3 ± 8.8 ×10-4; mean±SEM), while Gusb expression increased (6.0 ×10-4 ± 5.5 ×10-5 vs. 1.7 ×10-3 ± 3.1 ×10-4; n = 5/group; p < 0.05). These effects were not seen in males. Tubb5 and Gapdh were not affected by age or sex when normalised to Rplp0. Similar results were seen with normalisation by Gapdh or the Rplp0/Gapdh pair. Interestingly, RG expression was graded not only by age but by frailty. These data demonstrate that age, sex, and frailty of animals must be carefully considered when selecting RGs to normalise mRNA abundance data.

Sex-specific inflammatory and white matter effects of prenatal opioid exposure: a pilot study

BACKGROUND

Preclinical data demonstrate that opioids modulate brain reward signaling through an inflammatory cascade, but this relationship has yet to be studied in opioid-exposed neonates.

METHODS

Saliva samples of 54 opioid-exposed and sex- and age-matched non-exposed neonates underwent transcriptomic analysis of inflammatory and reward genes. A subset of 22 neonates underwent brain magnetic resonance imaging (MRI) to evaluate white matter injury commonly associated with inflammatory response. Gene expression and brain MRI were compared between opioid- and non-exposed neonates and further stratified by sex and pharmacotherapy need.

RESULTS

Opioid-exposed females regardless of pharmacotherapy need had higher expression of inflammatory genes than their male counterparts, with notable differences in the expression of CCL2 and CXCL1 in females requiring pharmacotherapy (p = 0.01 and 0.06, respectively). Opioid-exposed males requiring pharmacotherapy had higher expression of DRD2 than exposed females (p = 0.07), validating our prior research. Higher expression of IL1β, IL6, TNFα, and IL10 was seen in opioid-exposed neonates with T1 white matter hyperintensity (WMH) compared to exposed neonates without WMH (p < 0.05).

CONCLUSION

Prenatal opioid exposure may promote inflammation resulting in changes in reward signaling and white matter injury in the developing brain, with unique sex-specific effects. The actions of opioids through non-neuronal pathways need further investigation.

IMPACT

Opioid-exposed neonates are at risk for punctate T1 white matter hyperintensity (WMH). Females carry a greater propensity for WMH. Salivary transcriptomic data showed significantly higher expression of inflammatory genes in opioid-exposed neonates with WMH than those without WMH, irrespective of pharmacotherapy need. Adding to prior studies, our findings suggest that prenatal opioid exposure may modulate white matter injury and reward signaling through a pro-inflammatory process that is sex specific. This novel study highlights the short-term molecular and structural effects of prenatal opioids and the need to elucidate the long-term impact of prenatal opioid exposure.

Extracellular Vesicle-microRNAs as Diagnostic Biomarkers in Preterm Neonates

Neonates born prematurely (<37 weeks of gestation) are at a significantly increased risk of developing inflammatory conditions associated with high mortality rates, including necrotizing enterocolitis, bronchopulmonary dysplasia, and hypoxic-ischemic brain damage. Recently, research has focused on characterizing the content of extracellular vesicles (EVs), particularly microRNAs (miRNAs), for diagnostic use. Here, we describe the most recent work on EVs-miRNAs biomarkers discovery for conditions that commonly affect premature neonates.

Internal reference genes with the potential for normalizing quantitative PCR results for oral fluid specimens

In basic research, testing of oral fluid specimens by real-time quantitative polymerase chain reaction (qPCR) has been used to evaluate changes in gene expression levels following experimental treatments. In diagnostic medicine, qPCR has been used to detect DNA/RNA transcripts indicative of bacterial or viral infections. Normalization of qPCR using endogenous and exogenous reference genes is a well-established strategy for ensuring result comparability by controlling sample-to-sample variation introduced during sampling, storage, and qPCR testing. In this review, the majority of recent publications in human (n = 136) and veterinary (n = 179) medicine did not describe the use of internal reference genes in qPCRs for oral fluid specimens (52.9% animal studies; 57.0% human studies). However, the use of endogenous reference genes has not been fully explored or validated for oral fluid specimens. The lack of valid internal reference genes inherent to the oral fluid matrix will continue to hamper the reliability, reproducibility, and generalizability of oral fluid qPCR assays until this issue is addressed.

The Utility of Speech-Language Biomarkers to Predict Oral Feeding Outcomes in the Premature Newborn

Purpose Successful oral feeding and speech emergence are dependent upon the coordination of shared oral muscles and facial nerves. We aimed to determine if the speech-associated genes, forkhead box P2 (FOXP2), contactin-associated protein-like 2 (CNTNAP2), glutamate receptor, ionotropic, N-methyl D-aspartate 2A (GRIN2A), and neurexin 1, were detectable in neonatal saliva and could predict feeding outcomes in premature newborns. Method In this prospective, observational, preliminary study, saliva collected from 51 premature infants (gestational ages: 30-34 6/7 weeks) at different stages of oral feeding development underwent gene expression analysis. Binary (+/-) expression profiles were explored and examined in relation to days to achieve full oral feeds. Results GRIN2A and neurexin 1 rarely amplified in neonatal saliva and were not informative. Infants who amplified FOXP2 but not CNTNAP2 at the start of oral feeds achieved oral feeding success 3.20 (95% CI [-2.5, 8.9]) days sooner than other gene combinations. Conclusions FOXP2 and CNTNAP2 may be informative in predicting oral feeding outcomes in newborns. Salivary analysis at the start of oral feeding trials may inform feeding outcomes in this population and warrants further investigation.

Technical Considerations and Protocol Optimization for Neonatal Salivary Biomarker Discovery and Analysis

Non-invasive techniques to monitor and diagnose neonates, particularly those born prematurely, are a long-sought out goal of Newborn Medicine. In recent years, technical advances, combined with increased assay sensitivity, have permitted the high-throughput analysis of multiple biomarkers simultaneously from a single sample source. Multiplexed transcriptomic and proteomic platforms, along with more comprehensive assays such as RNASeq, allow for interrogation of ongoing physiology and pathology in unprecedented ways. In the fragile neonatal population, saliva is an ideal biofluid to assess clinical status serially and offers many advantages over more invasively obtained blood samples. Importantly, saliva samples are amenable to analysis on emerging proteomic and transcriptomic platforms, even at quantitatively limited volumes. However, biomarker targets are often degraded in human saliva, and as a mixed source biofluid containing both human and microbial targets, saliva presents unique challenges for the investigator. Here, we provide insight into technical considerations and protocol optimizations developed in our laboratory to quantify and discover neonatal salivary biomarkers with improved reproducibility and reliability. We will detail insights learned from years of experimentation on neonatal saliva within our laboratory ranging from salivary collection techniques to processing to downstream analyses, highlighting the need for consistency in approach and a global understanding of both the potential benefits and limitations of neonatal salivary biomarker analyses. Importantly, we will highlight the need for robust and stringent research in this population to provide the field with standardized approaches and workflows to impact neonatal care successfully.

The role and robustness of the Gini coefficient as an unbiased tool for the selection of Gini genes for normalising expression profiling data

We recently introduced the Gini coefficient (GC) for assessing the expression variation of a particular gene in a dataset, as a means of selecting improved reference genes over the cohort ('housekeeping genes') typically used for normalisation in expression profiling studies. Those genes (transcripts) that we determined to be useable as reference genes differed greatly from previous suggestions based on hypothesis-driven approaches. A limitation of this initial study is that a single (albeit large) dataset was employed for both tissues and cell lines. We here extend this analysis to encompass seven other large datasets. Although their absolute values differ a little, the Gini values and median expression levels of the various genes are well correlated with each other between the various cell line datasets, implying that our original choice of the more ubiquitously expressed low-Gini-coefficient genes was indeed sound. In tissues, the Gini values and median expression levels of genes showed a greater variation, with the GC of genes changing with the number and types of tissues in the data sets. In all data sets, regardless of whether this was derived from tissues or cell lines, we also show that the GC is a robust measure of gene expression stability. Using the GC as a measure of expression stability we illustrate its utility to find tissue- and cell line-optimised housekeeping genes without any prior bias, that again include only a small number of previously reported housekeeping genes. We also independently confirmed this experimentally using RT-qPCR with 40 candidate GC genes in a panel of 10 cell lines. These were termed the Gini Genes. In many cases, the variation in the expression levels of classical reference genes is really quite huge (e.g. 44 fold for GAPDH in one data set), suggesting that the cure (of using them as normalising genes) may in some cases be worse than the disease (of not doing so). We recommend the present data-driven approach for the selection of reference genes by using the easy-to-calculate and robust GC.

Sex-Dependent Gene Expression in Infants with Neonatal Opioid Withdrawal Syndrome

OBJECTIVES

To evaluate salivary biomarkers that elucidate the molecular mechanisms by which in utero opioid exposure exerts sex-specific effects on select hypothalamic and reward genes driving hyperphagia, a hallmark symptom of infants suffering from neonatal opioid withdrawal syndrome (NOWS).

STUDY DESIGN

We prospectively collected saliva from 50 newborns born at ≥34 weeks of gestational age with prenatal opioid exposure and 50 sex- and gestational age-matched infants without exposure. Saliva underwent transcriptomic analysis for 4 select genes involved in homeostatic and hedonic feeding regulation (neuropeptide Y2 receptor [NPY2R], proopiomelanocortin [POMC], leptin receptor [LEPR], dopamine type 2 receptor [DRD2]). Normalized gene expression data were stratified based on sex and correlated with feeding volume on day of life 7 and length of stay in infants with NOWS requiring pharmacotherapy.

RESULTS

Expression of DRD2, a hedonistic/reward regulator, was significantly higher in male newborns compared with female newborns with NOWS (Δ threshold cycle 10.8 ± 3.8 vs 13.9 ± 3.7, P = .01). In NOWS requiring pharmacotherapy expression of leptin receptor, an appetite suppressor, was higher in male subjects than female subjects (Δ threshold cycle 8.4 ± 2.5 vs 12.4 ± 5.1, P = .05), DRD2 expression significantly correlated with intake volume on day of life 7 (r = 0.58, P = .02), and expression of NPY2R, an appetite regulator, negatively correlated with length of stay (r = -0.24, P = .05).

CONCLUSIONS

Prenatal opioid exposure exerts sex-dependent effects on hypothalamic feeding regulatory genes with clinical correlations. Neonatal salivary gene expression analyses may predict hyperphagia, severity of withdrawal state, and length of stay in infants with NOWS.

The validation of Short Interspersed Nuclear Elements (SINEs) as a RT-qPCR normalization strategy in a rodent model for temporal lobe epilepsy

Background

In gene expression studies via RT-qPCR many conclusions are inferred by using reference genes. However, it is generally known that also reference genes could be differentially expressed between various tissue types, experimental conditions and animal models. An increasing amount of studies have been performed to validate the stability of reference genes. In this study, two rodent-specific Short Interspersed Nuclear Elements (SINEs), which are located throughout the transcriptome, were validated and assessed against nine reference genes in a model of Temporal Lobe Epilepsy (TLE). Two different brain regions (i.e. hippocampus and cortex) and two different disease stages (i.e. acute phase and chronic phase) of the systemic kainic acid rat model for TLE were analyzed by performing expression analyses with the geNorm and NormFinder algorithms. Finally, we performed a rank aggregation analysis and validated the reference genes and the rodent-specific SINEs (i.e. B elements) individually via Gfap gene expression.

Results

GeNorm ranked Hprt1, Pgk1 and Ywhaz as the most stable genes in the acute phase, while Gusb and B2m were ranked as the most unstable, being significantly upregulated. The two B elements were ranked as most stable for both brain regions in the chronic phase by geNorm. In contrast, NormFinder ranked the B1 element only once as second best in cortical tissue for the chronic phase. Interestingly, using only one of the two algorithms would have led to skewed conclusions. Finally, the rank aggregation method indicated the use of the B1 element as the best option to normalize target genes, independent of the disease progression and brain region. This result was supported by the expression profile of Gfap.

Conclusion

In this study, we demonstrate the potential of implementing SINEs -notably the B1 element- as a stable normalization factor in a rodent model of TLE, independent of brain region or disease progression.