Estimating prevalence of rare genetic disease diagnoses using electronic health records in a children's hospital.

Rare genetic diseases (RGDs) affect a significant number of individuals, particularly in pediatric populations. This study investigates the efficacy of identifying RGD diagnoses through electronic health records (EHRs) and natural language processing (NLP) tools, and analyzes the prevalence of identified RGDs for potential underdiagnosis at Cincinnati Children's Hospital Medical Center (CCHMC). EHR data from 659,139 pediatric patients at CCHMC were utilized. Diagnoses corresponding to RGDs in Orphanet were identified using rule-based and machine learning-based NLP methods. Manual evaluation assessed the precision of the NLP strategies, with 100 diagnosis descriptions reviewed for each method. The rule-based method achieved a precision of 97.5% (95% CI: 91.5%, 99.4%), while the machine-learning-based method had a precision of 73.5% (95% CI: 63.6%, 81.6%). A manual chart review of 70 randomly selected patients with RGD diagnoses confirmed the diagnoses in 90.3% (95% CI: 82.0%, 95.2%) of cases. A total of 37,326 pediatric patients were identified with 977 RGD diagnoses based on the rule-based method, resulting in a prevalence of 5.66% in this population. While a majority of the disorders showed a higher prevalence at CCHMC compared with Orphanet, some diseases, such as 1p36 deletion syndrome, indicated potential underdiagnosis. Analyses further uncovered disparities in RGD prevalence and age of diagnosis across gender and racial groups. This study demonstrates the utility of employing EHR data with NLP tools to systematically investigate RGD diagnoses in large cohorts. The identified disparities underscore the need for enhanced approaches to guarantee timely and accurate diagnosis and management of pediatric RGDs.

An IQ Consortium Perspective on Best Practices for Bioanalytical and Immunogenicity Assessment Aspects of CAR-T and TCR-T Cellular Therapies Development.

CAR-T therapies have shown remarkable efficacy against hematological malignancies in the clinic over the last decade and new studies indicate that progress is being made to use these novel therapies to target solid tumors as well as treat autoimmune disease. Innovation in the field, including TCR-T, allogeneic or "off the shelf" CAR-T, and autoantigen/armored CAR-Ts are likely to increase the efficacy and applications of these therapies. The unique aspects of these cell-based therapeutics; patient-derived cells, intracellular expression, in vivo expansion, and phenotypic changes provide unique bioanalytical challenges to develop pharmacokinetic and immunogenicity assessments. The International Consortium for Innovation and Quality in Pharmaceutical Development (IQ) Translational and ADME Sciences Leadership Group (TALG) has brought together a group of industry experts to discuss and consider these challenges. In this white paper, we present the IQ consortium perspective on the best practices and considerations for bioanalytical and immunogenicity aspects toward the optimal development of CAR-T and TCR-T cell therapies.

Quantitative polymerase chain reaction in the bioanalytical laboratory and technical and scientific considerations for nonclinical and clinical assay characterization, validation and sample analysis.

In this manuscript, the European Bioanalysis Forum reports back on their discussions on practical and scientific considerations related to bioanalytical applications of quantitative polymerase chain reaction. This publication follows an earlier publication in which the European Bioanalysis Forum recommends to consider principles of context of use when defining assay acceptance criteria for method validation criteria and sample analysis.

Applying context of use to quantitative polymerase chain reaction method validation and analysis: a recommendation from the European Bioanalysis Forum.

Polymerase chain reaction (PCR) is widely used in various fields of laboratory testing, ranging from forensic, molecular biology, medical and diagnostic applications to a wide array of basic research purposes. COVID-19 infection testing has brought the three-letter PCR abbreviation into the vocabulary of billions of people, making it likely the most well-known laboratory test worldwide. With new modalities and translational medicine gaining importance in pharmaceutical research and development, PCR or more specifically, quantitative PCR (qPCR) is now becoming a standard tool in the (regulated) bioanalytical laboratory, driving the bioanalytical community to define best practices for method development, characterization and validation. In absence of specific guidance from health authorities, qPCR may be vulnerable to scope creep from pharmacokinetics (PK) assay validation as defined in bioanalytical method validation guidance/guidelines. In this manuscript, the European Bioanalysis Forum builds a rationale for applying context of use principles when defining requirements for qPCR assay performance and validation criteria.

Increased tongue use enhances 5-HT2C receptor immunostaining in hypoglossal motor nucleus.

Hypoglossal (XII) motoneurons are activated by type 2 receptors for serotonin (5-HT). This activation is especially strong during wakefulness which facilitates diverse motor functions of the tongue, including the maintenance of upper airway patency in obstructive sleep apnea (OSA) patients. We tested whether 5-HT2 receptor levels in the XII nucleus vary with intensity of tongue use. Three groups of rats were housed overnight under conditions of increasing oromotor activity: W-water available ad lib; S-sweetened water to stimulate drinking; S + O-sweetened water + oil applied on fur to increase grooming. After the exposures, immunostaining for 5-HT2C, but not 5-HT2A, receptors was higher in the XII nucleus in S + O than in W rats (65 ± 1.8 (SE) vs. 60 ± 2.0 arbitrary units; p = 0.008). In the medullary raphé obscurus region, the percentage of c-Fos-positive 5-HT cells was 13% higher (p = 0.03) in S + O than in W rats. The positive feedback between tongue use and 5-HT2C receptor immunostaining reveals a novel mechanism potentially relevant for OSA and neuromuscular disorders.

Modulation of Motoneuronal Activity With Sleep-Wake States and Motoneuronal Gene Expression Vary With Circadian Rest-Activity Cycle.

In both nocturnal and diurnal mammals, sleep and wake states differentially aggregate during the rest and active phases of circadian cycle. Closely associated with this rhythm are prominent changes in motor activity. Here, we quantified the magnitudes of electromyographic activity (EMG) measured separately during different sleep-wake states across the rest-activity cycle, thereby separating amplitude measurements from the known dependance of the timing of wake and sleep on the phase of circadian rest-activity cycle. In seven rats chronically instrumented for electroencephalogram and EMG monitoring, nuchal and lingual muscle EMGs were measured as a commonly used postural output in behavioral sleep studies and as a cranial motor output with potential clinical relevance in obstructive sleep apnea (OSA) syndrome, respectively. We found that, for both motor outputs, EMG measured during wake episodes was significantly higher during the active phase, than during the rest phase, of circadian cycle. The corresponding patterns observed during slow-wave sleep (SWS) and rapid eye movement sleep (REMS) were different. During SWS, lingual EMG was very low and did not differ between the rest and active phase, whereas nuchal EMG had pattern similar to that during wakefulness. During REMS, lingual EMG was, paradoxically, higher during the rest phase due to increased twitching activity, whereas nuchal EMG was very low throughout the rest and active periods (postural atonia). In the follow-up comparison of differences in transcript levels in tissue samples obtained from the medullary hypoglossal motor nucleus and inferior olive (IO) at rest onset and active period onset conducted using microarrays, we identified significant differences for multiple transcripts representing the core members of the molecular circadian clock and other genes important for the regulation of cell metabolism and activity (up to n = 130 at p < 0.001). Collectively, our data indicate that activity of motoneurons is regulated to optimally align it with the rest-activity cycle, with the process possibly involving transcriptional mechanisms at the motoneuronal level. Our data also suggest that OSA patients may be relatively better protected against sleep-related upper airway obstructions during REMS episodes generated during the rest phase, than during active phase, of the circadian cycle.

Evidence that adrenergic ventrolateral medullary cells are activated whereas precerebellar lateral reticular nucleus neurons are suppressed during REM sleep.

Rapid eye movement sleep (REMS) is generated in the brainstem by a distributed network of neurochemically distinct neurons. In the pons, the main subtypes are cholinergic and glutamatergic REMS-on cells and aminergic REMS-off cells. Pontine REMS-on cells send axons to the ventrolateral medulla (VLM), but little is known about REMS-related activity of VLM cells. In urethane-anesthetized rats, dorsomedial pontine injections of carbachol trigger REMS-like episodes that include cortical and hippocampal activation and suppression of motoneuronal activity; the episodes last 4-8 min and can be elicited repeatedly. We used this model to determine whether VLM catecholaminergic cells are silenced during REMS, as is typical of most aminergic neurons studied to date, and to investigate other REMS-related cells in this region. In 18 anesthetized, paralyzed and artificially ventilated rats, we obtained extracellular recordings from VLM cells when REMS-like episodes were elicited by pontine carbachol injections (10 mM, 10 nl). One major group were the cells that were activated during the episodes (n = 10). Their baseline firing rate of 3.7±2.1 (SD) Hz increased to 9.7±2.1 Hz. Most were found in the adrenergic C1 region and at sites located less than 50 µm from dopamine ß-hydroxylase-positive (DBH(+)) neurons. Another major group were the silenced or suppressed cells (n = 35). Most were localized in the lateral reticular nucleus (LRN) and distantly from any DBH(+) cells. Their baseline firing rates were 6.8±4.4 Hz and 15.8±7.1 Hz, respectively, with the activity of the latter reduced to 7.4±3.8 Hz. We conclude that, in contrast to the pontine noradrenergic cells that are silenced during REMS, medullary adrenergic C1 neurons, many of which drive the sympathetic output, are activated. Our data also show that afferent input transmitted to the cerebellum through the LRN is attenuated during REMS. This may distort the spatial representation of body position during REMS.

Reduced c-Fos expression in medullary catecholaminergic neurons in rats 20 h after exposure to chronic intermittent hypoxia.

Persons affected by obstructive sleep apnea (OSA) have increased arterial blood pressure and elevated activity in upper airway muscles. Many cardiorespiratory features of OSA have been reproduced in rodents subjected to chronic-intermittent hypoxia (CIH). We previously reported that, following exposure to CIH, rats have increased noradrenergic terminal density in brain stem sensory and motor nuclei and upregulated expression of the excitatory α(1)-adrenergic receptors in the hypoglossal motor nucleus. This suggested that CIH may enhance central catecholaminergic transmission. We now quantified c-Fos expression in different groups of pontomedullary catecholaminergic neurons as an indirect way of assessing their baseline activity in rats subjected to CIH or sham treatment (7 AM-5 PM daily for 35 days). One day after the last CIH exposure, the rats were gently kept awake for 2.5 h and then were anesthetized and perfused, and their pontomedullary brain sections were subjected to dopamine ß-hydroxylase (DBH) and c-Fos immunohistochemistry. DBH-positive cells were counted in the A1/C1, A2/C2, A5, subcoeruleus (sub-C) and A7 groups of catecholaminergic neurons, and the percentages of those expressing c-Fos were determined. We found that fewer DBH cells expressed c-Fos in CIH- than in sham-treated rats in the medulla (significant in the A1 group). In the pons (rostral A5, sub-C, and A7), c-Fos expression did not differ between the CIH- and sham-treated animals. We suggest that, when measured 20 h after the last CIH exposure, catecholaminergic transmission is enhanced through terminal sprouting and receptor upregulation rather than through increased baseline activity in pontomedullary catecholaminergic neurons.