Influence of Tyrosine Kinase Inhibition on Organic Anion Transporting Polypeptide 1B3-Mediated Uptake.

The organic anion transporting polypeptide family member (OATP) 1B3 is a hepatic uptake transporter that has a broad substrate recognition and plays a significant role in regulating elimination of endogenous biomolecules or xenobiotics. OATP1B3 works in tandem with OATP1B1, with which it shares approximately 80% sequence homology and a high degree of substrate overlap. Despite some substrates being recognized solely by OATP1B3, its ability to compensate for loss of OATP1B1-mediated elimination and recognition by regulatory agencies, little is known about OATP1B3 regulatory factors and how they are involved with drug-drug interaction. It was recently discovered that OATP1B1 function is mediated by the activity of a particular tyrosine kinase that is sensitive to a variety of tyrosine kinase inhibitors (TKIs). This study reports that OATP1B3 is similarly regulated, as at least 50% of its activity is reduced by 20 US Food and Drug Administration -approved TKIs. Nilotinib was assessed as the most potent OATP1B3 inhibitor among the investigated TKIs, which can occur at clinically relevant concentrations and acted predominantly through noncompetitive inhibition without impacting membrane expression. Finally, OATP1B3 function was determined to be sensitive to the knockdown of the Lck/Yes novel tyrosine kinase that is sensitive to nilotinib and has been previously implicated in mediating OATP1B1 activity. Collectively, our findings identify tyrosine kinase activity as a major regulator of OATP1B3 function which is sensitive to kinase inhibition. Given that OATP1B1 is similarly regulated, simultaneous disruption of these transporters can have drastic effects on systemic drug concentrations, which would promote adverse events. SIGNIFICANCE STATEMENT: The organic anion transporting polypeptide family member (OATP) 1B3 is a facilitator of hepatic drug elimination, although much is unknown of how OATP1B3 activity is mediated, or how such regulators contribute to drug-drug interactions. This study reports that OATP1B3 activity is dependent on the Lck/Yes novel tyrosine kinase, which is sensitive to numerous tyrosine kinase inhibitors. These findings provide insight into the occurrence of many clinical drug-drug interactions, and a rationale for future study of tyrosine kinases regulating drug disposition.

MOSCATO: a supervised approach for analyzing multi-Omic single-Cell data.

BACKGROUND: Advancements in genomic sequencing continually improve personalized medicine, and recent breakthroughs generate multimodal data on a cellular level. We introduce MOSCATO, a technique for selecting features across multimodal single-cell datasets that relate to clinical outcomes. We summarize the single-cell data using tensors and perform regularized tensor regression to return clinically-associated variable sets for each 'omic' type. RESULTS: Robustness was assessed over simulations based on available single-cell simulation methods, and applicability was assessed through an example using CITE-seq data to detect genes associated with leukemia. We find that MOSCATO performs favorably in selecting network features while also shown to be applicable to real multimodal single-cell data. CONCLUSIONS: MOSCATO is a useful analytical technique for supervised feature selection in multimodal single-cell data. The flexibility of our approach enables future extensions on distributional assumptions and covariate adjustments.

Gene-set integrative analysis of multi-omics data using tensor-based association test.

MOTIVATION: Facilitated by technological advances and the decrease in costs, it is feasible to gather subject data from several omics platforms. Each platform assesses different molecular events, and the challenge lies in efficiently analyzing these data to discover novel disease genes or mechanisms. A common strategy is to regress the outcomes on all omics variables in a gene set. However, this approach suffers from problems associated with high-dimensional inference. RESULTS: We introduce a tensor-based framework for variable-wise inference in multi-omics analysis. By accounting for the matrix structure of an individual's multi-omics data, the proposed tensor methods incorporate the relationship among omics effects, reduce the number of parameters, and boost the modeling efficiency. We derive the variable-specific tensor test and enhance computational efficiency of tensor modeling. Using simulations and data applications on the Cancer Cell Line Encyclopedia (CCLE), we demonstrate our method performs favorably over baseline methods and will be useful for gaining biological insights in multi-omics analysis. AVAILABILITY AND IMPLEMENTATION: R function and instruction are available from the authors' website: https://www4.stat.ncsu.edu/~jytzeng/Software/TR.omics/TRinstruction.pdf. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Automated Computational Detection of Interstitial Fibrosis, Tubular Atrophy, and Glomerulosclerosis.

BACKGROUND: Interstitial fibrosis, tubular atrophy (IFTA), and glomerulosclerosis are indicators of irrecoverable kidney injury. Modern machine learning (ML) tools have enabled robust, automated identification of image structures that can be comparable with analysis by human experts. ML algorithms were developed and tested for the ability to replicate the detection and quantification of IFTA and glomerulosclerosis that renal pathologists perform. METHODS: A renal pathologist annotated renal biopsy specimens from 116 whole-slide images (WSIs) for IFTA and glomerulosclerosis. A total of 79 WSIs were used for training different configurations of a convolutional neural network (CNN), and 17 and 20 WSIs were used as internal and external testing cases, respectively. The best model was compared against the input of four renal pathologists on 20 new testing slides. Further, for 87 testing biopsy specimens, IFTA and glomerulosclerosis measurements made by pathologists and the CNN were correlated to patient outcome using classic statistical tools. RESULTS: The best average performance across all image classes came from a DeepLab version 2 network trained at 40× magnification. IFTA and glomerulosclerosis percentages derived from this CNN achieved high levels of agreement with four renal pathologists. The pathologist- and CNN-based analyses of IFTA and glomerulosclerosis showed statistically significant and equivalent correlation with all patient-outcome variables. CONCLUSIONS: ML algorithms can be trained to replicate the IFTA and glomerulosclerosis assessment performed by renal pathologists. This suggests computational methods may be able to provide a standardized approach to evaluate the extent of chronic kidney injury in situations in which renal-pathologist time is restricted or unavailable.

Identification of supervised and sparse functional genomic pathways.

Functional pathways involve a series of biological alterations that may result in the occurrence of many diseases including cancer. With the availability of various "omics" technologies it becomes feasible to integrate information from a hierarchy of biological layers to provide a more comprehensive understanding to the disease. In many diseases, it is believed that only a small number of networks, each relatively small in size, drive the disease. Our goal in this study is to develop methods to discover these functional networks across biological layers correlated with the phenotype. We derive a novel Network Summary Matrix (NSM) that highlights potential pathways conforming to least squares regression relationships. An algorithm called Decomposition of Network Summary Matrix via Instability (DNSMI) involving decomposition of NSM using instability regularization is proposed. Simulations and real data analysis from The Cancer Genome Atlas (TCGA) program will be shown to demonstrate the performance of the algorithm.

Symptoms upon postural change and orthostatic hypotension in adolescents with concussion.

Objective: Concussion is associated with dysautonomia, altered blood pressure (BP) control, and may cause Orthostatic Hypotension (OH). We measured prevalence of OH using the 1-minute supine-to-standing OH Test in adolescents with concussion and controls.Participants: Adolescents within 10 days of injury (Concussion Group, n = 297, 15.0 ± 1.7 years, 59% male) were compared with controls (Control Group, n = 214, 15.0 ± 1.5 years, 58% male).Methods: BP, heart rate (HR), and complaints of lightheadedness/dizziness were measured after 2-minute supine and 1-minute standing. Control Group was assessed once. Concussion Group was assessed twice; (1) initial visit (mean 6.0 ± 3 days-since-injury) and (2) after clinical recovery (mean 46.3 ± 42 days-since-injury).Results: Initial visit; Concussion Group reported feeling lightheaded/dizzy on postural change more often than the Control Group (37% vs 4%, p < .001) but did not differ in meeting standard OH criteria (3% vs 5%, p = .32). Experiencing symptoms did not correlate with meeting OH criteria, but correlated with abnormal vestibulo-ocular reflex. After clinical recovery; Concussion Group did not differ in experiencing lightheaded/dizziness on postural change than controls (4%, p = .65).Conclusion: Adolescents commonly experience orthostatic intolerance after concussion without meeting the standard criteria for OH.

A Preliminary Study of Early-Onset Dementia of Former Professional Football and Hockey Players.

OBJECTIVE: To provide an overview of 3 studies of the same population of retired professional contact sport athletes compared with age-matched noncontact sport athlete controls on cognition, executive function, behavior, and advanced brain imaging. SETTING: University Concussion Management Clinic. PARTICIPANTS: Twenty-two retired professional hockey and football athletes (average age 56 years) and 21 age-matched noncontact sport athlete controls. DESIGN: Case control. MAIN MEASURES: Participants were assessed on a broad range of neuropsychological measures that are associated with identification of mild cognitive impairment and executive function. Athletes were also assessed using self-report measures of executive function and personality. Advanced structural and functional imaging techniques were utilized as well. RESULTS: The former National Football League and National Hockey League athletes perceived themselves to have impaired executive function, but this was not confirmed by objective neurocognitive assessment. No significant differences were found when comparing contact-sport athletes with controls on the presence of mild cognitive impairment or brain structural and functional tissue injury. Contact sport athletes were more anxious and more likely to report unusual beliefs and experiences. CONCLUSION: None of the retired contact sport athletes qualified as having early-onset dementia consistent with chronic traumatic encephalopathy. There were no remarkable differences in imaging, cognition, behavior, or executive function from noncontact sport athletes. The results underscore an apparent disconnect between public perceptions and evidence-based conclusions about the inevitability of chronic traumatic encephalopathy and the potential neurodegenerative effect on former athletes from contact sports.

A systematic review of criteria used to define recovery from sport-related concussion in youth athletes.

OBJECTIVE: The Concussion in Sport Group guidelines recommend a multifaceted approach to help clinicians make return to sport decisions. The purpose of this study was to identify the most common multifaceted measures used to define clinical recovery from sport-related concussion in young athletes (high school and/or college level) and to summarise existing knowledge of criteria used to make return to sport decisions. DESIGN: Systematic review. DATA SOURCES: The PubMed (MEDLINE), SPORTDiscus and Embase electronic databases were searched from 1 January 2000 to 1 March 2017 by three independent reviewers. ELIGIBILITY CRITERIA: Inclusion criteria: elementary, high school and college age groups, and a specific definition of clinical recovery that required two or more measures. EXCLUSION CRITERIA: review articles, articles using the same sample population, case studies, non-English language and those that used one measure only or did not specify the recovery measures used. STUDY QUALITY: Study quality was assessed using the Downs and Black Criteria. RESULTS: Of 2023 publications, 43 met inclusion criteria. Included articles reported the following measures of recovery: somatic symptom resolution or return to baseline (100%), cognitive recovery or return to baseline (86%), no exacerbation of symptoms on physical exertion (49%), normalisation of balance (30%), normal special physical examination (12%), successful return to school (5%), no exacerbation of symptoms with cognitive exertion (2%) and normalisation of cerebral blood flow (2%). Follow-up to validate the return to sport decision was reported in eight (19%) articles. Most studies were case-control or cohort (level of evidence 4) and had significant risk of bias. CONCLUSION: All studies of sport-related concussion use symptom reports to define recovery. A minority of studies used multiple measures of outcome or had clearly defined recovery criteria, the most common being a combination of a self-reported symptom checklist and a computerised neurocognitive test. Future studies ideally should define recovery a priori using objective physiological measures in addition to symptom reports.

Identification of consistent functional genetic modules.

It is often of scientific interest to find a set of genes that may represent an independent functional module or network, such as a functional gene expression module causing a biological response, a transcription regulatory network, or a constellation of mutations jointly causing a disease. In this paper we are specifically interested in identifying modules that control a particular outcome variable such as a disease biomarker. We discuss the statistical properties that functional networks should possess and introduce the concept of network consistency which should be satisfied by real functional networks of cooperating genes, and directly use the concept in the pathway discovery method we present. Our method gives superior performance for all but the simplest functional networks.

Dynamics of the Streptococcus gordonii Transcriptome in Response to Medium, Salivary α-Amylase, and Starch.

Streptococcus gordonii, a primary colonizer of the tooth surface, interacts with salivary α-amylase via amylase-binding protein A (AbpA). This enzyme hydrolyzes starch to glucose, maltose, and maltodextrins that can be utilized by various oral bacteria for nutrition. Microarray studies demonstrated that AbpA modulates gene expression in response to amylase, suggesting that the amylase-streptococcal interaction may function in ways other than nutrition. The goal of this study was to explore the role of AbpA in gene regulation through comparative transcriptional profiling of wild-type KS1 and AbpA(-) mutant KS1ΩabpA under various environmental conditions. A portion of the total RNA isolated from mid-log-phase cells grown in 5% CO2 in (i) complex medium with or without amylase, (ii) defined medium (DM) containing 0.8% glucose with/without amylase, and (iii) DM containing 0.2% glucose and amylase with or without starch was reverse transcribed to cDNA and the rest used for RNA sequencing. Changes in the expression of selected genes were validated by quantitative reverse transcription-PCR. Maltodextrin-associated genes, fatty acid synthesis genes and competence genes were differentially expressed in a medium-dependent manner. Genes in another cluster containing a putative histidine kinase/response regulator, peptide methionine sulfoxide reductase, thioredoxin protein, lipoprotein, and cytochrome c-type protein were downregulated in KS1ΩabpA under all of the environmental conditions tested. Thus, AbpA appears to modulate genes associated with maltodextrin utilization/transport and fatty acid synthesis. Importantly, in all growth conditions AbpA was associated with increased expression of a potential two-component signaling system associated with genes involved in reducing oxidative stress, suggesting a role in signal transduction and stress tolerance.

A novel characterization of the generalized family wise error rate using empirical null distributions.

We present a novel characterization of the generalized family wise error rate: kFWER. The interpretation allows researchers to view kFWER as a function of the test statistics rather than current methods based on p-values. Using this interpretation we present several theorems and methods (parametric and non-parametric) for estimating kFWER in various data settings. With this version of kFWER, researchers will have an estimate of kFWER in addition to knowing what tests are significant at the estimated kFWER. Additionally, we present methods that use empirical null distributions in place of parametric distributions in standard p-value kFWER controlling schemes. These advancements represent an improvement over common kFWER methods which are based on parametric assumptions and merely report the tests that are significant under a given value for kFWER.

Evaluation of the Zurich Guidelines and exercise testing for return to play in adolescents following concussion.

OBJECTIVE: To evaluate return to play (RTP) and return to classroom outcomes when the Zurich guidelines are combined with a standardized exercise treadmill test [Buffalo Concussion Treadmill Test (BCTT)] and computerized neuropsychological (cNP) testing in adolescent athletes after concussion. DESIGN: Retrospective chart review and follow-up. SETTING: University Sports Medicine Concussion Clinic. PARTICIPANTS: One hundred seventeen athletes (75% male) with sport concussion ages 13 to 19 years and telephone follow-up of 91 (77.8%) athletes and their parents. INTERVENTIONS: Concussed athletes who were asymptomatic at rest completed Automated Neuropsychological Assessment Metrics or Immediate Post-concussion Assessment and Cognitive Test cNP testing followed by the BCTT on the same day. Athletes then followed the Zurich consensus guidelines for RTP. MAIN OUTCOME MEASURES: The primary outcome measure was the degree of success in RTP, that is, RTP with or without return of concussive symptoms. Secondary outcome measure was return to school with or without symptoms. RESULTS: All athletes returned to sport without exacerbation of symptoms. Telephone follow-up revealed that 38.5% experienced new issues upon return to the classroom. Forty-eight percent of athletes had 1 or more cNP subtests below average (

TLR7 activation of age-associated B cells mediates disease in a mouse model of primary Sjögren's disease.

Primary Sjögren's disease (pSD) (also referred to as Sjögren's syndrome) is an autoimmune disease that primarily occurs in women. In addition to exocrine gland dysfunction, pSD patients exhibit B cell hyperactivity. B cell-intrinsic TLR7 activation is integral to the pathogenesis of systemic lupus erythematosus, a disease that shares similarities with pSD. The role of TLR7-mediated B cell activation in pSD, however, remains poorly understood. We hypothesized that age-associated B cells (ABCs) were expanded in pSD and that TLR7-stimulated ABCs exhibited pathogenic features characteristic of disease. Our data revealed that ABC expansion and TLR7 expression were enhanced in a pSD mouse model in a Myd88-dependent manner. Splenocytes from pSD mice showed enhanced sensitivity to TLR7 agonism as compared with those derived from control animals. Sort-purified marginal zone B cells and ABCs from pSD mice showed enhanced inflammatory cytokine secretion and were enriched for antinuclear autoantibodies following TLR7 agonism. Finally, IgG from pSD patient sera showed elevated antinuclear autoantibodies, many of which were secreted preferentially by TLR7-stimulated murine marginal zone B cells and ABCs. These data indicate that pSD B cells are hyperresponsive to TLR7 agonism and that TLR7-activated B cells contribute to pSD through cytokine and autoantibody production. Thus, therapeutics that target TLR7 signaling cascades in B cells may have utility in pSD patients.

Parents of 5-to-12-year-old children with food allergies report more frequent use of structure-based food parenting practices.

Objectives: Food parenting practices (FPP) can have effects on children's eating behaviors. Over 8 million children in the US have food allergies, however, little is known about FPP for those who have children with food allergies. The objective of this study was to describe FPP among children with food allergies. Methods: Recruited across the United States using ResearchMatch in February and March 2021, parents of children ages 5-12 years (n = 346; n = 77 with food allergies) completed a single, online survey which measured health history, demographics, and FPP. Linear regressions were used to examine associations between FPP of children with and without food allergies, and associations between food allergy factors and FPP. Results: Parents of children with food allergies reported greater use of limit exposure than parents of children without food allergies (B = 0.131; [CI], 0.021-0.293; P = 0.024), with no differences in other types of FPP. Conclusions: Parents of children with food allergies reported more frequent structure-based FPP than parents of children without food allergies. More work is needed to explore mechanisms that promote positive food parenting among this population.

FUSIM: a software tool for simulating fusion transcripts.

BACKGROUND: Gene fusions are the result of chromosomal aberrations and encode chimeric RNA (fusion transcripts) that play an important role in cancer genesis. Recent advances in high throughput transcriptome sequencing have given rise to computational methods for new fusion discovery. The ability to simulate fusion transcripts is essential for testing and improving those tools. RESULTS: To facilitate this need, we developed FUSIM (FUsion SIMulator), a software tool for simulating fusion transcripts. The simulation of events known to create fusion genes and their resulting chimeric proteins is supported, including inter-chromosome translocation, trans-splicing, complex chromosomal rearrangements, and transcriptional read through events. CONCLUSIONS: FUSIM provides the ability to assemble a dataset of fusion transcripts useful for testing and benchmarking applications in fusion gene discovery.

Sensitivity and Specificity of Exercise Intolerance on Graded Exertion Testing for Diagnosing Sport-Related Concussion: A Systematic Review and Exploratory Meta-Analysis.

Abstract There is no single gold standard test to diagnose sport-related concussion (SRC). Concussion-related exercise intolerance, that is, inability to exercise to the individual's appropriate level due to exacerbation of concussion-like symptoms, is a frequent finding in athletes early after SRC that has not been systematically evaluated as a diagnostic test of SRC. We performed a systematic review and proportional meta-analysis of studies that evaluated graded exertion testing in athletes after SRC. We also included studies of exertion testing in healthy athletic participants without SRC to assess specificity. Pubmed and Embase were searched in January 2022 for articles published since 2000. Eligible studies included those that performed graded exercise tolerance tests in symptomatic concussed participants (> 90% of subjects had an SRC, seen within 14 days of injury), at the time of clinical recovery from SRC, in healthy athletes, or both. Study quality was assessed using the Newcastle-Ottawa Scale. Twelve articles met inclusion criteria, most of which were of poor methodological quality. The pooled estimate of incidence of exercise intolerance in participants with SRC equated to an estimated sensitivity of 94.4% (95% confidence interval [CI]: 90.8, 97.2). The pooled estimate of incidence of exercise intolerance in participants without SRC equated to an estimated specificity of 94.6% (95% CI: 91.1, 97.3). The results suggest that exercise intolerance measured on systematic testing within 2 weeks of SRC may have excellent sensitivity for helping to rule in the diagnosis of SRC and excellent specificity for helping to rule out SRC. A prospective validation study to determine the sensitivity and specificity of exercise intolerance on graded exertion testing for diagnosing SRC after head injury as the source of symptoms is warranted.

A wholly defined Agilent microarray spike-in dataset.

MOTIVATION: Spike-in datasets provide a valuable resource for assessing and comparing among competing microarray analysis strategies. Our previous wholly defined spike-in datasets, the Golden and Platinum Spikes, have provided insights for the analysis of Affymetrix GeneChips. However, a similar dataset, in which all cRNA identities and relative levels are known prospectively, has not been available for two-color platforms. RESULTS: We have generated a wholly defined spike-in dataset for Agilent microarrays consisting of 12 arrays with more than 2000 differentially expressed, and approximately 3600 background, cRNAs. The composition of this 'Ag Spike' dataset is identical to that of our previous Platinum Spike dataset and therefore allows direct cross-platform comparison. We demonstrate here the utility of the Ag Spike dataset for evaluating different analysis methods designed for two-color arrays. Comparison between the Ag Spike and Platinum Spike studies shows high agreement between results obtained using the Affymetrix and Agilent platforms. AVAILABILITY: The Ag Spike raw data can be accessed at http://www.ccr.buffalo.edu/halfon/spike/index.html and through NCBI's Gene Expression Omnibus (GEO; accession GSE24866).

High precision implementation of Steck's recursion method for use in goodness-of-fit tests.

Classical continuous goodness-of-fit (GOF) testing is employed for examining whether the data come from an assumed parametric model. In many cases, GOF tests assume a uniform null distribution and examine extreme values of the order statistics of the samples. Many of these statistics can be expressed by a function of the order statistics and the p-values amount to a joint probability statement based on the uniform order statistics. In this paper, we utilize Steck's recursion method and propose two high precision computing algorithms to compute the p-values for these GOF statistics. The numerical difficulties in implementing Steck's method are discussed and compared with solutions provided in high precision libraries.

TLR7 agonism accelerates disease in a mouse model of primary Sjögren's syndrome and drives expansion of T-bet+ B cells.

Primary Sjögren's syndrome (pSS) is a systemic autoimmune disease characterized by chronic inflammation of exocrine tissue, resulting in loss of tears and saliva. Patients also experience many extra-glandular disease manifestations. Treatment for pSS is palliative, and there are currently no treatments available that target disease etiology. Previous studies in our lab demonstrated that MyD88 is crucial for pSS pathogenesis in the NOD.B10Sn-H2b (NOD.B10) pSS mouse model, although the way in which MyD88-dependent pathways become activated in disease remains unknown. Based on its importance in other autoimmune diseases, we hypothesized that TLR7 activation accelerates pSS pathogenesis. We administered the TLR7 agonist Imiquimod (Imq) or sham treatment to pre-disease NOD.B10 females for 6 weeks. Parallel experiments were performed in age and sex-matched C57BL/10 controls. Imq-treated pSS animals exhibited cervical lymphadenopathy, splenomegaly, and expansion of TLR7-expressing B cells. Robust lymphocytic infiltration of exocrine tissues, kidney and lung was observed in pSS mice following treatment with Imq. TLR7 agonism also induced salivary hypofunction in pSS mice, which is a hallmark of disease. Anti-nuclear autoantibodies, including Ro (SSA) and La (SSB) were increased in pSS mice following Imq administration. Cervical lymph nodes from Imq-treated NOD.B10 animals demonstrated an increase in the percentage of activated/memory CD4+ T cells. Finally, T-bet+ B cells were expanded in the spleens of Imq-treated pSS mice. Thus, activation of TLR7 accelerates local and systemic disease and promotes expansion of T-bet-expressing B cells in pSS.

A new normalizing algorithm for BAC CGH arrays with quality control metrics.

The main focus in pin-tip (or print-tip) microarray analysis is determining which probes, genes, or oligonucleotides are differentially expressed. Specifically in array comparative genomic hybridization (aCGH) experiments, researchers search for chromosomal imbalances in the genome. To model this data, scientists apply statistical methods to the structure of the experiment and assume that the data consist of the signal plus random noise. In this paper we propose "SmoothArray", a new method to preprocess comparative genomic hybridization (CGH) bacterial artificial chromosome (BAC) arrays and we show the effects on a cancer dataset. As part of our R software package "aCGHplus," this freely available algorithm removes the variation due to the intensity effects, pin/print-tip, the spatial location on the microarray chip, and the relative location from the well plate. removal of this variation improves the downstream analysis and subsequent inferences made on the data. Further, we present measures to evaluate the quality of the dataset according to the arrayer pins, 384-well plates, plate rows, and plate columns. We compare our method against competing methods using several metrics to measure the biological signal. With this novel normalization algorithm and quality control measures, the user can improve their inferences on datasets and pinpoint problems that may arise in their BAC aCGH technology.