Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine.

Precision medicine initiatives across the globe have led to a revolution of repositories linking large-scale genomic data with electronic health records, enabling genomic analyses across the entire phenome. Many of these initiatives focus solely on research insights, leading to limited direct benefit to patients. We describe the biobank at the Colorado Center for Personalized Medicine (CCPM Biobank) that was jointly developed by the University of Colorado Anschutz Medical Campus and UCHealth to serve as a unique, dual-purpose research and clinical resource accelerating personalized medicine. This living resource currently has more than 200,000 participants with ongoing recruitment. We highlight the clinical, laboratory, regulatory, and HIPAA-compliant informatics infrastructure along with our stakeholder engagement, consent, recontact, and participant engagement strategies. We characterize aspects of genetic and geographic diversity unique to the Rocky Mountain region, the primary catchment area for CCPM Biobank participants. We leverage linked health and demographic information of the CCPM Biobank participant population to demonstrate the utility of the CCPM Biobank to replicate complex trait associations in the first 33,674 genotyped individuals across multiple disease domains. Finally, we describe our current efforts toward return of clinical genetic test results, including high-impact pathogenic variants and pharmacogenetic information, and our broader goals as the CCPM Biobank continues to grow. Bringing clinical and research interests together fosters unique clinical and translational questions that can be addressed from the large EHR-linked CCPM Biobank resource within a HIPAA- and CLIA-certified environment.

Unique molecular characteristics of NAFLD-associated liver cancer accentuate ß-catenin/TNFRSF19-mediated immune evasion.

BACKGROUND & AIMS: The hepatic manifestation of the metabolic syndrome, non-alcoholic fatty liver disease (NAFLD), can lead to the development of hepatocellular carcinoma (HCC). Despite a strong causative link, NAFLD-HCC is often underrepresented in systematic genome explorations. METHODS: Herein, tumor-normal pairs from 100 patients diagnosed with NAFLD-HCC were subject to next-generation sequencing. Bioinformatic analyses were performed to identify key genomic, epigenomic and transcriptomic events associated with the pathogenesis of NAFLD-HCC. Establishment of primary patient-derived NAFLD-HCC culture was used as a representative human model for downstream in vitro investigations of the underlying CTNNB1 S45P driver mutation. A syngeneic immunocompetent mouse model was used to further test the involvement of CTNNB1mutand TNFRSF19 in reshaping the tumor microenvironment. RESULTS: Mutational processes operative in the livers of patients with NAFLD inferred susceptibility to tumor formation through defective DNA repair pathways. Dense promoter mutations and dysregulated transcription factors accentuated activated transcriptional regulation in NAFLD-HCC, in particular the enrichment of MAZ-MYC activities. Somatic events common in HCCs arising from NAFLD and viral hepatitis B infection underscore similar driver pathways, although an incidence shift highlights CTNNB1mut dominance in NAFLD-HCC (33%). Immune exclusion correlated evidently with CTNNB1mut. Chromatin immunoprecipitation-sequencing integrated with transcriptome and immune profiling revealed a unique transcriptional axis, wherein CTNNB1mut leads to an upregulation of TNFRSF19 which subsequently represses senescence-associated secretory phenotype-like cytokines (including IL6 and CXCL8). This phenomenon could be reverted by the Wnt-modulator ICG001. CONCLUSIONS: The unique mutational processes in the livers of patients with NAFLD and NAFLD-HCC allude to a "field effect" involving a gain-of-function role of CTNNB1 mutations in immune exclusion. LAY SUMMARY: The increasing prevalence of metabolic syndrome in adult populations means that NAFLD is poised to be the major cause of liver cancer in the 21st century. We showed a strong "field effect" in the livers of patients with NAFLD, wherein activated ß-catenin was involved in reshaping the tumor-immune microenvironment.

Specialization in a Nitrogen-Fixing Symbiosis: Proteome Differences Between Sinorhizobium medicae Bacteria and Bacteroids.

Using tandem mass spectrometry (MS/MS), we analyzed the proteome of Sinorhizobium medicae WSM419 growing as free-living cells and in symbiosis with Medicago truncatula. In all, 3,215 proteins were identified, over half of the open reading frames predicted from the genomic sequence. The abundance of 1,361 proteins displayed strong lifestyle bias. In total, 1,131 proteins had similar levels in bacteroids and free-living cells, and the low levels of 723 proteins prevented statistically significant assignments. Nitrogenase subunits comprised approximately 12% of quantified bacteroid proteins. Other major bacteroid proteins included symbiosis-specific cytochromes and FixABCX, which transfer electrons to nitrogenase. Bacteroids had normal levels of proteins involved in amino acid biosynthesis, glycolysis or gluconeogenesis, and the pentose phosphate pathway; however, several amino acid degradation pathways were repressed. This suggests that bacteroids maintain a relatively independent anabolic metabolism. Tricarboxylic acid cycle proteins were highly expressed in bacteroids and no other catabolic pathway emerged as an obvious candidate to supply energy and reductant to nitrogen fixation. Bacterial stress response proteins were induced in bacteroids. Many WSM419 proteins that are not encoded in S. meliloti Rm1021 were detected, and understanding the functions of these proteins might clarify why S. medicae WSM419 forms a more effective symbiosis with M. truncatula than S. meliloti Rm1021.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Wild-type APC Is Associated with Poor Survival in Metastatic Microsatellite Stable Colorectal Cancer.

BACKGROUND: The prognostic implication of wild-type APC (APC-WT) in microsatellite stable (MSS) metastatic colorectal cancer (mCRC) is not well defined. MATERIALS AND METHODS: APC prognostic value was evaluated retrospectively in two independent cohorts of patient with MSS mCRC with a confirmatory analysis from a public data set from Memorial Sloan Kettering Cancer Center (MSKCC). RESULTS: In comparison with the APC-mutant (APC-MT) population (n = 255), APC-WT patients (n = 86) tended to be younger (59% of age < 40 vs. 26% of age > 50), right-sided (41.7% vs. 27%), BRAFV600E mutated (23.3% vs. 0.8%), and KRAS wild type (65.1% vs. 49.8%). Alternative WNT pathway alterations, RNF43 and CTNNB1, were over-represented in the APC-WT versus APC-MT population (7% vs. 0.4% and 4.7% vs. 0.4%, respectively). APC-WT patients had a worse overall survival (OS) than APC-MT patients (22.6 vs. 45.6 months, p < .0001). Using a multivariate model correcting for primary tumor location, RAS and BRAF status, APC-WT was predictive of poor survival (APC-MT vs. APC-WT, hazard ratio [HR], 0.62; 95% confidence interval [CI], 0.44-0.86, p = .0037). The prognostic implication of APC-WT on OS was confirmed further in a similar multivariate model of 934 stage IV patients from MSKCC public database (APC-MT vs. APC-WT, HR, 0.63, 95% CI, 0.49-0.81, p < .0001). CONCLUSION: APC-WT is associated with poor OS in MSS mCRC regardless of RAS and BRAF status. Compared with APC-MT mCRC tumors, APC-WT tumors were associated with other Wnt activating alterations, including RNF43 and CTNBB1. Our data suggest alternative therapy needs to be investigated in APC-WT patients. IMPLICATIONS FOR PRACTICE: Patients with microsatellite stable metastatic colorectal cancer with wild-type APC had a worse overall survival than patients with mutated APC regardless of RAS/RAF status. APC status should be considered as a stratification factor in prospective trials, and novel therapeutic strategies need to be developed for this subgroup of patients.

Sinorhizobium medicae WSM419 Genes That Improve Symbiosis between Sinorhizobium meliloti Rm1021 and Medicago truncatula Jemalong A17 and in Other Symbiosis Systems.

Some soil bacteria, called rhizobia, can interact symbiotically with legumes, in which they form nodules on the plant roots, where they can reduce atmospheric dinitrogen to ammonia, a form of nitrogen that can be used by growing plants. Rhizobium-plant combinations can differ in how successful this symbiosis is: for example, Sinorhizobium meliloti Rm1021 forms a relatively ineffective symbiosis with Medicago truncatula Jemalong A17, but Sinorhizobium medicae WSM419 is able to support more vigorous plant growth. Using proteomic data from free-living and symbiotic S. medicae WSM419, we previously identified a subset of proteins that were not closely related to any S. meliloti Rm1021 proteins and speculated that adding one or more of these proteins to S. meliloti Rm1021 would increase its effectiveness on M. truncatula A17. Three genes, Smed_3503, Smed_5985, and Smed_6456, were cloned into S. meliloti Rm1021 downstream of the E. coli lacZ promoter. Strains with these genes increased nodulation and improved plant growth, individually and in combination with one another. Smed_3503, renamed iseA (increased symbiotic effectiveness), had the largest impact, increasing M. truncatula biomass by 61%. iseA homologs were present in all currently sequenced S. medicae strains but were infrequent in other Sinorhizobium isolates. Rhizobium leguminosarum bv. viciae 3841 containing iseA led to more nodules on pea and lentil. Split-root experiments with M. truncatula A17 indicated that S. meliloti Rm1021 carrying the S. medicae iseA is less sensitive to plant-induced resistance to rhizobial infection, suggesting an interaction with the plant's regulation of nodule formation. IMPORTANCE Legume symbiosis with rhizobia is highly specific. Rhizobia that can nodulate and fix nitrogen on one legume species are often unable to associate with a different species. The interaction can be more subtle. Symbiotically enhanced growth of the host plant can differ substantially when nodules are formed by different rhizobial isolates of a species, much like disease severity can differ when conspecific isolates of pathogenic bacteria infect different cultivars. Much is known about bacterial genes essential for a productive symbiosis, but less is understood about genes that marginally improve performance. We used a proteomic strategy to identify Sinorhizobium genes that contribute to plant growth differences that are seen when two different strains nodulate M. truncatula A17. These genes could also alter the symbiosis between R. leguminosarum bv. viciae 3841 and pea or lentil, suggesting that this approach identifies new genes that may more generally contribute to symbiotic productivity.

Diabetic ketoacidosis at diagnosis among youth with type 1 and type 2 diabetes: Results from SEARCH (United States) and YDR (India) registries.

BACKGROUND: There is significant global variation in the prevalence of diabetic ketoacidosis (DKA) at diagnosis among youth with type 1 diabetes (T1D). However, data for youth with type 2 diabetes (T2D) are limited, even in developed countries. We compared the prevalence of DKA at diagnosis among individuals with T1D and T2D from the SEARCH for Diabetes in Youth (SEARCH) and the Registry of Youth Onset Diabetes in India (YDR) registries. METHODS: We harmonized the SEARCH and YDR registries to the structure and terminology in the Observational Medical Outcome Partnership Common Data Model. Data used were from youth with T1D and T2D diagnosed before 20 years and newly diagnosed between 2006 and 2012 in YDR and 2009 and 2012 in SEARCH. RESULTS: There were 5366 US youth (4078 with T1D, 1288 with T2D) and 2335 Indian youth (2108 with T1D, 227 with T2D). More than one third of T1D youth enrolled in SEARCH had DKA at diagnosis which was significantly higher than in YDR (35.3% vs 28.7%, P < .0001). The burden of DKA in youth with T1D was significantly higher among younger age groups; this relationship was similar across registries (P = .4). The prevalence of DKA among T2D in SEARCH and YDR were 5.5% and 6.6% respectively (P = .4). CONCLUSIONS: There is significant burden of DKA at diagnosis with T1D among youth from United States and India, especially among the younger age groups. The reasons for this high prevalence are largely unknown but are critical to developing interventions to prevent DKA at diagnosis.

Clinical profile at diagnosis with youth-onset type 1 and type 2 diabetes in two pediatric diabetes registries: SEARCH (United States) and YDR (India).

BACKGROUND: Over the last decades, diabetes in youth has increased in both India and the United States, along with the burden of long-term complications and healthcare costs. However, there are limited standardized population-based data in contemporary youth cohorts for comparison of clinical and demographic characteristics of diabetes for both type 1 (T1D) and type 2 (T2D). METHODS: In partnership, we harmonized demographic and clinical data from the SEARCH for Diabetes in Youth (SEARCH) registry in the United States and the Registry of People with Diabetes with Youth Age at Onset (YDR) in India to the structure and terminology of the Observational Medical Outcomes Partnership Common Data Model. Data were from youth with T1D and T2D, aged <20 years and newly diagnosed between 2006 and 2010. We compared key characteristics across registries using χ2 tests and t-tests. RESULTS: In total, there were 9650 youth with T1D and 2406 youth with T2D from 2006 to 2012. SEARCH youth were diagnosed at younger ages than YDR youth for T1D and T2D (10.0 vs 10.5 years, P < .001 and 14.7 vs 16.1 years, P < .001, respectively). For T2D, SEARCH had a higher proportion of females and significantly lower proportion of youth of high socioeconomic status compared to YDR. For T1D and T2D, SEARCH youth had higher BMI, lower blood pressure, and lower A1c compared to YDR youth. CONCLUSIONS: These data offer insights into the demographic and clinical characteristics of diabetes in youth across the two countries. Further research is needed to better understand why these differences exist.

Treatment regimens and glycosylated hemoglobin levels in youth with Type 1 and Type 2 diabetes: Data from SEARCH (United States) and YDR (India) registries.

OBJECTIVE: To compare treatment regimens and glycosylated hemoglobin (A1c) levels in Type 1 (T1D) and Type 2 diabetes (T2D) using diabetes registries from two countries-U.S. SEARCH for Diabetes in Youth (SEARCH) and Indian Registry of youth onset diabetes in India (YDR). METHODS: The SEARCH and YDR data were harmonized to the structure and terminology in the Observational Medical Outcomes Partnership Common Data Model. Data used were from T1D and T2D youth diagnosed <20 years between 2006-2012 for YDR, and 2006, 2008, and 2012 for SEARCH. We compared treatment regimens and A1c levels across the two registries. RESULTS: There were 4003 T1D (SEARCH = 1899; YDR = 2104) and 611 T2D (SEARCH = 384; YDR = 227) youth. The mean A1c was higher in YDR compared to SEARCH (T1D:11.0% ± 2.9% vs 7.8% ± 1.7%, P < .001; T2D:9.9% ± 2.8% vs 7.2% ± 2.1%, P < .001). Among T1D youth in SEARCH, 65.1% were on a basal/bolus regimen, whereas in YDR, 52.8% were on once/twice daily insulin regimen. Pumps were used by 16.2% of SEARCH and 1.5% of YDR youth with T1D. Among T2D youth, in SEARCH and YDR, a majority were on metformin only (43.0% vs 30.0%), followed by insulin + any oral hypoglycemic agents (26.3% vs 13.7%) and insulin only (12.8% vs 18.9%), respectively. CONCLUSION: We found significant differences between SEARCH and YDR in treatment patterns in T1D and T2D. A1c levels were higher in YDR than SEARCH youth, for both T1D and T2D, irrespective of the regimens used. Efforts to achieve better glycemic control for youth are urgently needed to reduce the risk of long-term complications.

Comparison of the incidence of diabetes in United States and Indian youth: An international harmonization of youth diabetes registries.

OBJECTIVE: Incidence of youth-onset diabetes in India has not been well described. Comparison of incidence, across diabetes registries, has the potential to inform hypotheses for risk factors. We sought to compare the incidence of diabetes in the U.S.-based registry of youth onset diabetes (SEARCH) to the Registry of Diabetes with Young Age at Onset (YDR-Chennai and New Delhi regions) in India. METHODS: We harmonized data from both SEARCH and YDR to the Observational Medical Outcomes Partnership (OMOP) Common Data Model. Data were from youth registered with incident diabetes (2006-2012). Denominators were from census and membership data. We calculated diabetes incidence by averaging the total cases across the entire follow-up period and dividing this by the estimated census population corresponding to the source population for case ascertainment. Incidence was calculated for each of the registries and compared by type and within age and sex categories using a 2-sided, skew-corrected inverted score test. RESULTS: Incidence of type 1 was higher in SEARCH (21.2 cases/100 000 [95% CI: 19.9, 22.5]) than YDR (4.9 cases/100 000 [95% CI: 4.3, 5.6]). Incidence of type 2 diabetes was also higher in SEARCH (5.9 cases/100 000 [95% CI: 5.3, 6.6] in SEARCH vs 0.5/cases/100 000 [95% CI: 0.3, 0.7] in YDR). The age distribution of incident type 1 diabetes cases was similar across registries, whereas type 2 diabetes incidence was higher at an earlier age in SEARCH. Sex differences existed in SEARCH only, with a higher rate of type 2 diabetes among females. CONCLUSION: The incidence of youth-onset type 1 and 2 diabetes was significantly different between registries. Additional data are needed to elucidate whether the differences observed represent diagnostic delay, differences in genetic susceptibility, or differences in distribution of risk factors.

High Incidence of Barotrauma in Patients With Severe Coronavirus Disease 2019.

OBJECTIVE.: To report the high incidence of barotrauma in critically ill patients admitted to the intensive care unit (ICU) with coronavirus disease 2019 (COVID-19) and to discuss its implications. DESIGN.: Retrospective cohort study. SETTING.: ICU of an academic county hospital in Los Angeles, CA admitted from March 15-June 20, 2020. PATIENTS.: 77 patients with COVID-19 pneumonia. 75 patients met inclusion criteria. RESULTS.: 21% of patients with severe COVID-19 sustained barotrauma (33% of patients receiving IMV, 8% of patients receiving (NIV). There were no differences between the barotrauma and non-barotrauma groups regarding demographics, illness severity, or medications received, nor tidal volume or average/peak airway pressures in those receiving IMV. In the barotrauma group there was a greater proportion of patients receiving therapeutic anticoagulation (81% vs. 47%, p = 0.023) and ventilated using airway pressure release ventilation mode (13% vs. 0%, p = 0.043). Barotrauma was associated with increased likelihood of receiving a tracheostomy (OR 2.58 [0.23-4.9], p = 0.018]), longer median ICU length of stay (17 days vs. 7 days, p = 0.03), and longer median length of hospitalization (26 days vs. 14 days, p < 0.001). There was also a trend toward prolonged median duration of IMV (12.5 days vs 7 days, p = 0.13) and higher average mortality (56% vs 37%, p = 0.25). CONCLUSIONS.: Barotrauma is seen in 5-12% of patients with ARDS receiving IMV and is exceedingly rare in patients receiving NIV. We report a high incidence of barotrauma observed in critically ill patients with COVID-19 requiring either NIV or IMV. While there was a trend toward increased mortality in patients with barotrauma, this did not reach statistical significance. The increased incidence of barotrauma with COVID-19 may be a product of the pathophysiology of this disease state and a heightened inflammatory response causing rampant acute lung injury. Evidence-based medicine and lung-protective ventilation should remain the mainstay of treatment.

Pharmacologically Targeting the WNT/ß-Catenin Signaling Cascade: Avoiding the Sword of Damocles.

WNT/ß-catenin signaling plays fundamental roles in numerous developmental processes and in adult tissue homeostasis and repair after injury, by controlling cellular self-renewal, activation, division, differentiation, movement, genetic stability, and apoptosis. As such, it comes as no surprise that dysregulation of WNT/ß-catenin signaling is associated with various diseases, including cancer, fibrosis, neurodegeneration, etc. Although multiple agents that specifically target the WNT/ß-catenin signaling pathway have been studied preclinically and a number have entered clinical trials, none has been approved by the FDA to date. In this chapter, we provide our insights as to the reason(s) it has been so difficult to safely pharmacologically target the WNT/ß-catenin signaling pathway and discuss the significant efforts undertaken towards this goal.

Predictors of one year chronic post-surgical pain trajectories following thoracic surgery.

PURPOSE: Chronic post-surgical pain (CPSP) is a highly prevalent complication following thoracic surgery. This is a prospective cohort study that aims to describe the pain trajectories of patients undergoing thoracic surgery beginning preoperatively and up to 1 year after surgery METHODS: Two hundred and seventy nine patients undergoing elective thoracic surgery were enrolled. Participants filled out a preoperative questionnaire containing questions about their sociodemographic information, comorbidities as well as several psychological and pain-related statuses. They were then followed-up during their immediate postoperative period and at the three, six and 12 month time-points to track their postoperative pain, complications and pain-related outcomes. Growth mixture modeling was used to construct pain trajectories. RESULTS: The first trajectory is characterized by 185 patients (78.1%) with mild pain intensity across the 12 month period. The second is characterized by 32 patients (7.5%) with moderate pain intensity immediately after surgery which decreases markedly by 3 months and remains low at the 12 month follow-up. The final trajectory is characterized by 20 patients (8.4%) with moderate pain intensity immediately after surgery which persists at 12 months. Patients with moderate to severe postoperative pain intensity were much more likely to develop CPSP compared to patients with mild pain intensity. Initial pain intensity levels immediately following surgery as well as levels of pain catastrophizing at baseline were predicting pain trajectory membership. None of the surgical or anesthetic-related variables were significantly associated with pain trajectory membership. CONCLUSION: Patients who undergo thoracic surgery can have postoperative pain that follows one of the three different types of trajectories. Higher levels of immediate postoperative pain and preoperative pain catastrophizing were associated with moderately severe CPSP.

Metal-Assisted Protein Quantitation (MAPq): Multiplex Analysis of Protein Expression Using Lanthanide-Modified Antibodies with Detection by Inductively Coupled Plasma Mass Spectrometry.

Understanding the complex relationships between genomics, transcriptomics, and proteomics requires the development of more sensitive and rapid methods of multiplexed protein analysis. This is necessary to understand the relationship between cellular responses to environmental stresses, disease progression, and/or drug treatment; however, most methods are limited by low sensitivity, nonspecificity, and minimal multiplexing capacity. To more fully explore the relationship between multiple cellular pathways, we have developed a novel antibody-based multiplex assay using inductively coupled plasma mass spectrometry (ICP-MS), which we term metal-assisted protein quantitation (MAPq). MAPq utilizes lanthanide-conjugated antibodies to simultaneously quantify up to 35 proteins with low pg/mL sensitivity. This method is especially advantageous for low-abundance proteins, a significant limitation of many multiplex MS methods. We observed a limit of detection of 0.5 pg/mL and a limit of quantitation of 5 pg/mL with virtually no background signal. We applied this method to both cultured cells and mouse tissues to investigate changes in low-abundance nuclear and cytoplasmic proteins following drug or environmental stresses. MAPq was found to be at least 10 times more sensitive than Western blots and could detect quantitative changes in protein expression not readily observed using conventional approaches.

Estimating the prevalence of congenital heart disease among adolescents and adults in Colorado adjusted for incomplete case ascertainment.

BACKGROUND: Congenital heart defects (CHDs), the most common type of birth defect in the United States, are increasing in prevalence in the general population. Though CHD prevalence at birth has been well described in the United States at about 1%, little is known about long-term survival and prevalence of CHDs beyond childhood. This study aimed to estimate the prevalence of CHDs among adolescents and adults in Colorado. METHODS: The prevalence of CHDs among adolescents and adults residing in Colorado during 2011 to 2013 was estimated using log-linear capture-recapture methods to account for incomplete case ascertainment. Five case-finding data sources were used for this analysis including electronic health record data from 4 major health systems and a state-legislated all payer claims database. RESULTS: Twelve thousand two hundred ninety-three unique individuals with CHDs (2481 adolescents and 9812 adults) were identified in one or more primary data sources. We estimated the crude prevalence of CHDs in adolescents and adults in Colorado to be 3.22 per 1000 individuals (95% CI 3.19-3.53). After accounting for incomplete case ascertainment, the final capture-recapture model yielded an estimated total adolescent and adult CHD population of 23,194 (95% CI 22,419-23,565) and an adjusted prevalence of 6.07 per 1000 individuals (95% CI 5.86-6.16), indicating 47% of the cases in the catchment area were not identified in the case-identifying data sources. CONCLUSION: This statewide study yielded new information on the prevalence of CHDs in adolescents and adults. These high prevalence rates underscore the need for additional specialized care facilities for this population with CHDs.

Population-level surveillance of congenital heart defects among adolescents and adults in Colorado: Implications of record linkage.

BACKGROUND: The objective was to describe the design of a population-level electronic health record (EHR) and insurance claims-based surveillance system of adolescents and adults with congenital heart defects (CHDs) in Colorado and to evaluate the bias introduced by duplicate cases across data sources. METHODS: The Colorado CHD Surveillance System ascertained individuals aged 11-64 years with a CHD based on International Classification of Diseases, Ninth Revision, Clinical Modification diagnostic coding between 2011 and 2013 from a diverse network of health care systems and an All Payer Claims Database (APCD). A probability-based identity reconciliation algorithm identified duplicate cases. Logistic regression was conducted to investigate bias introduced by duplicate cases on the relationship between CHD severity (severe compared to moderate/mild) and adverse outcomes including all-cause mortality, inpatient hospitalization, and major adverse cardiac events (myocardial infarction, congestive heart failure, or cerebrovascular event). Sensitivity analyses were conducted to investigate bias introduced by the sole use or exclusion of APCD data. RESULTS: A total of 12,293 unique cases were identified, of which 3,476 had a within or between data source duplicate. Duplicate cases were more likely to be in the youngest age group and have private health insurance, a severe heart defect, a CHD comorbidity, and higher health care utilization. We found that failure to resolve duplicate cases between data sources would inflate the relationship between CHD severity and both morbidity and mortality outcomes by ~15%. Sensitivity analyses indicate that scenarios in which APCD was excluded from case finding or relied upon as the sole source of case finding would also result in an overestimation of the relationship between a CHD severity and major adverse outcomes. DISCUSSION: Aggregated EHR- and claims-based surveillance systems of adolescents and adults with CHD that fail to account for duplicate records will introduce considerable bias into research findings. CONCLUSION: Population-level surveillance systems for rare chronic conditions, such as congenital heart disease, based on aggregation of EHR and claims data require sophisticated identity reconciliation methods to prevent bias introduced by duplicate cases.

Integrating the Practical Robust Implementation and Sustainability Model With Best Practices in Clinical Decision Support Design: Implementation Science Approach.

BACKGROUND: Clinical decision support (CDS) design best practices are intended to provide a narrative representation of factors that influence the success of CDS tools. However, they provide incomplete direction on evidence-based implementation principles. OBJECTIVE: This study aims to describe an integrated approach toward applying an existing implementation science (IS) framework with CDS design best practices to improve the effectiveness, sustainability, and reproducibility of CDS implementations. METHODS: We selected the Practical Robust Implementation and Sustainability Model (PRISM) IS framework. We identified areas where PRISM and CDS design best practices complemented each other and defined methods to address each. Lessons learned from applying these methods were then used to further refine the integrated approach. RESULTS: Our integrated approach to applying PRISM with CDS design best practices consists of 5 key phases that iteratively interact and inform each other: multilevel stakeholder engagement, designing the CDS, design and usability testing, thoughtful deployment, and performance evaluation and maintenance. The approach is led by a dedicated implementation team that includes clinical informatics and analyst builder expertise. CONCLUSIONS: Integrating PRISM with CDS design best practices extends user-centered design and accounts for the multilevel, interacting, and dynamic factors that influence CDS implementation in health care. Integrating PRISM with CDS design best practices synthesizes the many known contextual factors that can influence the success of CDS tools, thereby enhancing the reproducibility and sustainability of CDS implementations. Others can adapt this approach to their situation to maximize and sustain CDS implementation success.

Role of miR-96/EVI1/miR-449a Axis in the Nasopharyngeal Carcinoma Cell Migration and Tumor Sphere Formation.

The Wnt signaling pathway is one of the major signaling pathways used by cancer stem cells (CSC). Ecotropic Viral Integration Site 1 (EVI1) has recently been shown to regulate oncogenic development of tumor cells by interacting with multiple signaling pathways, including the Wnt signaling. In the present study, we found that the Wnt modulator ICG-001 could inhibit the expression of EVI1 in nasopharyngeal carcinoma (NPC) cells. Results from loss-of-function and gain-of-function studies revealed that EVI1 expression positively regulated both NPC cell migration and growth of CSC-enriched tumor spheres. Subsequent studies indicated ICG-001 inhibited EVI1 expression via upregulated expression of miR-96. Results from EVI1 3'UTR luciferase reporter assay confirmed that EVI1 is a direct target of miR-96. Further mechanistic studies revealed that ICG-001, overexpression of miR-96, or knockdown of EVI1 expression could restore the expression of miR-449a. The suppressive effect of miR-449a on the cell migration and tumor sphere formation was confirmed in NPC cells. Taken together, the miR-96/EVI1/miR-449a axis is a novel pathway involved in ICG-001-mediated inhibition of NPC cell migration and growth of the tumor spheres.

Characterization of the Sinorhizobium meliloti HslUV and ClpXP Protease Systems in Free-Living and Symbiotic States.

Symbiotic nitrogen fixation (SNF) in the interaction between the soil bacteria Sinorhizobium meliloti and legume plant Medicago sativa is carried out in specialized root organs called nodules. During nodule development, each symbiont must drastically alter their proteins, transcripts, and metabolites in order to support nitrogen fixation. Moreover, bacteria within the nodules are under stress, including challenges by plant antimicrobial peptides, low pH, limited oxygen availability, and strongly reducing conditions, all of which challenge proteome integrity. S. meliloti stress adaptation, proteome remodeling, and quality control are controlled in part by the large oligomeric protease complexes HslUV and ClpXP1. To improve understanding of the roles of S. meliloti HslUV and ClpXP1 under free-living conditions and in symbiosis with M. sativa, we generated ΔhslU, ΔhslV, ΔhslUV, and ΔclpP1 knockout mutants. The shoot dry weight of M. sativa plants inoculated with each deletion mutant was significantly reduced, suggesting a role in symbiosis. Further, slower free-living growth of the ΔhslUV and ΔclpP1 mutants suggests that HslUV and ClpP1 were involved in adapting to heat stress, the while ΔhslU and ΔclpP1 mutants were sensitive to kanamycin. All deletion mutants produced less exopolysaccharide and succinoglycan, as shown by replicate spot plating and calcofluor binding. We also generated endogenous C-terminal enhanced green fluorescent protein (eGFP) fusions to HslU, HslV, ClpX, and ClpP1 in S. meliloti Using anti-eGFP antibodies, native coimmunoprecipitation experiments with proteins from free-living and nodule tissues were performed and analyzed by mass spectrometry. The results suggest that HslUV and ClpXP were closely associated with ribosomal and proteome quality control proteins, and they identified several novel putative protein-protein interactions.IMPORTANCE Symbiotic nitrogen fixation (SNF) is the primary means by which biologically available nitrogen enters the biosphere, and it is therefore a critical component of the global nitrogen cycle and modern agriculture. SNF is the result of highly coordinated interactions between legume plants and soil bacteria collectively referred to as rhizobia, e.g., Medicago sativa and S. meliloti, respectively. Accomplishing SNF requires significant proteome changes in both organisms to create a microaerobic environment suitable for high-level bacterial nitrogenase activity. The bacterial protease systems HslUV and ClpXP are important in proteome quality control, in metabolic remodeling, and in adapting to stress. This work shows that S. meliloti HslUV and ClpXP are involved in SNF, in exopolysaccharide production, and in free-living stress adaptation.

Developing a Regional Distributed Data Network for Surveillance of Chronic Health Conditions: The Colorado Health Observation Regional Data Service.

Electronic health records (EHRs) provide an alternative to traditional public health surveillance surveys and administrative data for measuring the prevalence and impact of chronic health conditions in populations. As the infrastructure for secondary use of EHR data improves, many stakeholders are poised to benefit from data partnerships for regional access to information. Electronic health records can be transformed into a common data model that facilitates data sharing across multiple organizations and allows data to be used for surveillance. The Colorado Health Observation Regional Data Service, a regional distributed data network, has assembled diverse data partnerships, flexible infrastructure, and transparent governance practices to better understand the health of communities through EHR-based, public health surveillance. This article describes attributes of regional distributed data networks using EHR data and the history and design of Colorado Health Observation Regional Data Service as an emerging public health surveillance tool for chronic health conditions. Colorado Health Observation Regional Data Service and our experience may serve as a model for other regions interested in similar surveillance efforts. While benefits from EHR-based surveillance are described, a number of technology, partnership, and value proposition challenges remain.