An EMR-Based Approach to Determine Frequency, Prescribing Pattern, and Characteristics of Patients Receiving Drugs with Pharmacogenomic Guidelines.

(1) Background: This retrospective analysis utilizing electronic medical record (EMR) data from a tertiary integrated health system sought to identify patients and prescribers who would benefit from pharmacogenomic (PGx) testing based on Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines. (2) Methods: EMR data from a clinical research data warehouse were analyzed from 845,518 patients that had an encounter between 2015 and 2019 at an academic medical center. Data were collected for 42 commercially available drugs with 52 evidence-based PGx guidelines from CPIC. Provider data were obtained through the EMR linked by specialty via national provider identification (NPI) number. (3) Results: A total of 845,518 patients had an encounter in the extraction period with 590,526 medication orders processed. A total of 335,849 (56.9%) patients had medication orders represented by CPIC drugs prescribed by 2803 providers, representing 239 distinct medications. (4) Conclusions: The results from this study show that over half of patients were prescribed a CPIC actionable medication from a variety of prescriber specialties. Understanding the magnitude of patients that may benefit from PGx testing, will enable the development of preemptive testing processes, physician support strategies, and pharmacist workflows to optimize outcomes should a PGx service be implemented.

Factors Associated With Receipt of Molecular Testing and its Impact on Time to Initial Systemic Therapy in Metastatic Non-Small Cell Lung Cancer.

BACKGROUND: Despite recommendations for molecular testing irrespective of patient characteristics, differences exist in receipt of molecular testing for oncogenic drivers amongst metastatic non-small cell lung cancer (mNSCLC) patients. Exploration into these differences and their effects on treatment is needed to identify opportunities for improvement. PATIENTS AND METHODS: We conducted a retrospective cohort study of adult patients diagnosed with mNSCLC between 2011 and 2018 using PCORnet's Rapid Cycle Research Project dataset (n = 3600). Log-binomial, Cox proportional hazards (PH), and time-varying Cox regression models were used to ascertain whether molecular testing was received, and time from diagnosis to molecular testing and/or initial systemic treatment in the context of patient age, sex, race/ethnicity, and multiple comorbidities status. RESULTS: The majority of patients in this cohort were ≤ 65 years of age (median [25th, 75th]: 64 [57, 71]), male (54.3%), non-Hispanic white individuals (81.6%), with > 2 comorbidities in addition to mNSCLC (54.1%). About half the cohort received molecular testing (49.9%). Patients who received molecular testing had a 59% higher probability of initial systemic treatment than patients who were yet to receive testing. Multiple comorbidity status was positively associated with receipt of molecular testing (RR, 1.27; 95% CI 1.08, 1.49). CONCLUSION: Receipt of molecular testing in academic centers was associated with earlier initiation of systemic treatment. This finding underscores the need to increase molecular testing rates amongst mNSCLC patients during a clinically relevant period. Further studies to validate these findings in community centers are warranted.

The effect of number of healthcare visits on study sample selection in electronic health record data.

INTRODUCTION: Few studies have addressed how to select a study sample when using electronic health record (EHR) data. OBJECTIVE: To examine how changing criterion for number of visits in EHR data required for inclusion in a study sample would impact one basic epidemiologic measure: estimates of disease period prevalence. METHODS: Year 2016 EHR data from three Midwestern health systems (Northwestern Medicine in Illinois, University of Iowa Health Care, and Froedtert & the Medical College of Wisconsin, all regional tertiary health care systems including hospitals and clinics) was used to examine how alternate definitions of the study sample, based on number of healthcare visits in one year, affected measures of disease period prevalence. In 2016, each of these health systems saw between 160,000 and 420,000 unique patients. Curated collections of ICD-9, ICD-10, and SNOMED codes (from CMS-approved electronic clinical quality measures) were used to define three diseases: acute myocardial infarction, asthma, and diabetic nephropathy). RESULTS: Across all health systems, increasing the minimum required number of visits to be included in the study sample monotonically increased crude period prevalence estimates. The rate at which prevalence estimates increased with number of visits varied across sites and across diseases. CONCLUSIONS: In addition to providing thorough descriptions of case definitions, when using EHR data authors must carefully describe how a study sample is identified and report data for a range of sample definitions, including minimum number of visits, so that others can assess the sensitivity of reported results to sample definition in EHR data.

Host genetic modifiers of nonproductive angiogenesis inhibit breast cancer.

PURPOSE: Multiple aspects of the tumor microenvironment (TME) impact breast cancer, yet the genetic modifiers of the TME are largely unknown, including those that modify tumor vascular formation and function. METHODS: To discover host TME modifiers, we developed a system called the Consomic/Congenic Xenograft Model (CXM). In CXM, human breast cancer cells are orthotopically implanted into genetically engineered consomic xenograft host strains that are derived from two parental strains with different susceptibilities to breast cancer. Because the genetic backgrounds of the xenograft host strains differ, whereas the inoculated tumor cells are the same, any phenotypic variation is due to TME-specific modifier(s) on the substituted chromosome (consomic) or subchromosomal region (congenic). Here, we assessed TME modifiers of growth, angiogenesis, and vascular function of tumors implanted in the SSIL2Rγ and SS.BN3IL2Rγ CXM strains. RESULTS: Breast cancer xenografts implanted in SS.BN3IL2Rγ (consomic) had significant tumor growth inhibition compared with SSIL2Rγ (parental control), despite a paradoxical increase in the density of blood vessels in the SS.BN3IL2Rγ tumors. We hypothesized that decreased growth of SS.BN3IL2Rγ tumors might be due to nonproductive angiogenesis. To test this possibility, SSIL2Rγ and SS.BN3IL2Rγ tumor vascular function was examined by dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), micro-computed tomography (micro-CT), and ex vivo analysis of primary blood endothelial cells, all of which revealed altered vascular function in SS.BN3IL2Rγ tumors compared with SSIL2Rγ. Gene expression analysis also showed a dysregulated vascular signaling network in SS.BN3IL2Rγ tumors, among which DLL4 was differentially expressed and co-localized to a host TME modifier locus (Chr3: 95-131 Mb) that was identified by congenic mapping. CONCLUSIONS: Collectively, these data suggest that host genetic modifier(s) on RNO3 induce nonproductive angiogenesis that inhibits tumor growth through the DLL4 pathway.

Comprehensive Proteomic and Metabolomic Signatures of Nontypeable Haemophilus influenzae-Induced Acute Otitis Media Reveal Bacterial Aerobic Respiration in an Immunosuppressed Environment.

A thorough understanding of the molecular details of the interactions between bacteria and host are critical to ultimately prevent disease. Recent technological advances allow simultaneous analysis of host and bacterial protein and metabolic profiles from a single small tissue sample to provide insight into pathogenesis. We used the chinchilla model of human otitis media to determine, for the first time, the most expansive delineation of global changes in protein and metabolite profiles during an experimentally induced disease. After 48 h of infection with nontypeable Haemophilus influenzae, middle ear tissue lysates were analyzed by high-resolution quantitative two-dimensional liquid chromatography-tandem mass spectrometry. Dynamic changes in 105 chinchilla proteins and 66 metabolites define the early proteomic and metabolomic signature of otitis media. Our studies indicate that establishment of disease coincides with actin morphogenesis, suppression of inflammatory mediators, and bacterial aerobic respiration. We validated the observed increase in the actin-remodeling complex, Arp2/3, and experimentally showed a role for Arp2/3 in nontypeable Haemophilus influenzae invasion. Direct inhibition of actin branch morphology altered bacterial invasion into host epithelial cells, and is supportive of our efforts to use the information gathered to modify outcomes of disease. The twenty-eight nontypeable Haemophilus influenzae proteins identified participate in carbohydrate and amino acid metabolism, redox homeostasis, and include cell wall-associated metabolic proteins. Quantitative characterization of the molecular signatures of infection will redefine our understanding of host response driven developmental changes during pathogenesis. These data represent the first comprehensive study of host protein and metabolite profiles in vivo in response to infection and show the feasibility of extensive characterization of host protein profiles during disease. Identification of novel protein targets and metabolic biomarkers will advance development of therapeutic and diagnostic options for treatment of disease.

RNA expression profiling of human iPSC-derived cardiomyocytes in a cardiac hypertrophy model.

Cardiac hypertrophy is an independent risk factor for cardiovascular disease and heart failure. There is increasing evidence that microRNAs (miRNAs) play an important role in the regulation of messenger RNA (mRNA) and the pathogenesis of various cardiovascular diseases. However, the ability to comprehensively study cardiac hypertrophy on a gene regulatory level is impacted by the limited availability of human cardiomyocytes. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) offer the opportunity for disease modeling. Here we utilize a previously established in vitro model of cardiac hypertrophy to interrogate the regulatory mechanism associated with the cardiac disease process. We perform miRNA sequencing and mRNA expression analysis on endothelin 1 (ET-1) stimulated hiPSC-CMs to describe associated RNA expression profiles. MicroRNA sequencing revealed over 250 known and 34 predicted novel miRNAs to be differentially expressed between ET-1 stimulated and unstimulated control hiPSC-CMs. Messenger RNA expression analysis identified 731 probe sets with significant differential expression. Computational target prediction on significant differentially expressed miRNAs and mRNAs identified nearly 2000 target pairs. A principal component analysis approach comparing the in vitro data with human myocardial biopsies detected overlapping expression changes between the in vitro samples and myocardial biopsies with Left Ventricular Hypertrophy. These results provide further insights into the complex RNA regulatory mechanism associated with cardiac hypertrophy.

Bioavailability of antioxidants applied to stratified human corneal epithelial cells.

PURPOSE: Oxidative damage to the corneal epithelium may be involved in dry eye disease. The bioavailability and efficacy of antioxidants in human corneal limbal epithelial (HCLE) cells were measured to determine whether antioxidants might be beneficial constituents of lubricant eye drops. METHODS: The activity of antioxidants was evaluated using a cellular antioxidant activity assay in which, cells were loaded with the reactive oxygen species (ROS)-sensitive fluorescent indicator, 2',7'-dichlorofluorescin diacetate (DCFH-DA), and an antioxidant compound. ROS were then generated intracellularly using 2,2'-azobis(2-amidinopropane) dihydrochloride (ABAP) or extracellularly using xanthine oxidase, and the ability of an antioxidant to inhibit ROS-generated fluorescence was measured. RESULTS: When ROS were generated by ABAP, EC50 values for quercetin, epigallocatechin gallate (EGCG), n-propyl gallate, and gallic acid were 2.98, 3.41, 6.30, and 50.7 µM, respectively. When ROS were generated extracellularly by xanthine oxidase, EC50 values for quercetin, EGCG, n-propyl gallate, and gallic acid were 41.3, 56.5, 70.5, and 337.5 µM. These values were reduced significantly when an antioxidant was present both in the medium with the xanthine oxidase and within the cells. CONCLUSIONS: The antioxidants were effective at quenching ROS in HCLE cells, indicating that they are bioavailable and might be effective in protecting the corneal epithelium from oxidative damage if included in a lubricant eye drop.

Sequencing of the rat genome and databases.

The rat is an important system for modeling human disease. Four years ago, the rich 150-year history of rat research was transformed by the sequencing and annotation of the rat genome, ushering in an era of exceptional opportunity for identifying genes and pathways underlying disease phenotypes. With the genome sequence in place, there is the prospect of not only linking the extensive literature of mechanistic and pharmacological studies in the rat to its genome, but by using comparative genomics to other organisms as well. Genome-wide association studies (GWAS) in human populations have recently provided a direct approach for finding robust genetic associations in common diseases, but identifying the precise genes and their mechanisms of action remains challenging.The explosion of genomic tools and sequence over the last decade has created a wealth of data. Along with the data has arisen a need to manage it and to make it usable to scientists with a wide-range of research interests. This chapter is designed to overview the existing sequence and its utility, as well as provide a glimpse of some of the databases and bioinformatic tools available to the investigator.

The Rat Genome Database 2009: variation, ontologies and pathways.

The Rat Genome Database (RGD, http://rgd.mcw.edu) was developed to provide a core resource for rat researchers combining genetic, genomic, pathway, phenotype and strain information with a focus on disease. RGD users are provided with access to structured and curated data from the molecular level through to the level of the whole organism, including the variations associated with disease phenotypes. To fully support use of the rat as a translational model for biological systems and human disease, RGD continues to curate these datasets while enhancing and developing tools to allow efficient and effective access to the data in a variety of formats including linear genome viewers, pathway diagrams and biological ontologies. To support pathophysiological analysis of data, RGD Disease Portals provide an entryway to integrated gene, QTL and strain data specific to a particular disease. In addition to tool and content development and maintenance, RGD promotes rat research and provides user education by creating and disseminating tutorials on the curated datasets, submission processes, and tools available at RGD. By curating, storing, integrating, visualizing and promoting rat data, RGD ensures that the investment made into rat genomics and genetics can be leveraged by all interested investigators.

Hormone-induced protection against mammary tumorigenesis is conserved in multiple rat strains and identifies a core gene expression signature induced by pregnancy.

Women who have their first child early in life have a substantially lower lifetime risk of breast cancer. The mechanism for this is unknown. Similar to humans, rats exhibit parity-induced protection against mammary tumorigenesis. To explore the basis for this phenomenon, we identified persistent pregnancy-induced changes in mammary gene expression that are tightly associated with protection against tumorigenesis in multiple inbred rat strains. Four inbred rat strains that exhibit marked differences in their intrinsic susceptibilities to carcinogen-induced mammary tumorigenesis were each shown to display significant protection against methylnitrosourea-induced mammary tumorigenesis following treatment with pregnancy levels of estradiol and progesterone. Microarray expression profiling of parous and nulliparous mammary tissue from these four strains yielded a common 70-gene signature. Examination of the genes constituting this signature implicated alterations in transforming growth factor-beta signaling, the extracellular matrix, amphiregulin expression, and the growth hormone/insulin-like growth factor I axis in pregnancy-induced alterations in breast cancer risk. Notably, related molecular changes have been associated with decreased mammographic density, which itself is strongly associated with decreased breast cancer risk. Our findings show that hormone-induced protection against mammary tumorigenesis is widely conserved among divergent rat strains and define a gene expression signature that is tightly correlated with reduced mammary tumor susceptibility as a consequence of a normal developmental event. Given the conservation of this signature, these pathways may contribute to pregnancy-induced protection against breast cancer.

Genomic analysis of early murine mammary gland development using novel probe-level algorithms.

We describe a novel algorithm (ChipStat) for detecting gene-expression changes utilizing probe-level comparisons of replicate Affymetrix oligonucleotide microarray data. A combined detection approach is shown to yield greater sensitivity than a number of widely used methodologies including SAM, dChip and logit-T. Using this approach, we identify alterations in functional pathways during murine neonatal-pubertal mammary development that include the coordinate upregulation of major urinary proteins and the downregulation of loci exhibiting reciprocal imprinting.

A lysosomal tetraspanin associated with retinal degeneration identified via a genome-wide screen.

The Drosophila visual system has provided a model to study phototransduction and retinal degeneration. To identify new candidate proteins that contribute to these processes, we conducted a genome-wide screen for genes expressed predominately in the eye, using DNA microarrays. This screen appeared to be comprehensive as it led to the identification of all 22 eye-enriched genes previously shown to function in phototransduction or implicated in retinal degeneration. In addition, we identified 93 eye-enriched genes whose roles have not been previously defined. One of the eye-enriched genes encoded a member of a large family of transmembrane proteins, referred to as tetraspanins. We created a null mutation in the eye-enriched tetraspanin, Sunglasses (Sun), which resulted in light-induced retinal degeneration. We found that the Sun protein was distributed primarily in lysosomes, and functioned in a long-known but poorly understood phenomenon of light-induced degradation of rhodopsin. We propose that lysosomal tetraspanins in mammalian cells may also function in the downregulation of rhodopsin and other G-protein-coupled receptors, in response to intense or prolonged agonist stimulation.