PCA-Plus: Enhanced principal component analysis with illustrative applications to batch effects and their quantitation.

Background: Principal component analysis (PCA), a standard approach to analysis and visualization of large datasets, is commonly used in biomedical research for detecting similarities and differences among groups of samples. We initially used conventional PCA as a tool for critical quality control of batch and trend effects in multi-omic profiling data produced by The Cancer Genome Atlas (TCGA) project of the NCI. We found, however, that conventional PCA visualizations were often hard to interpret when inter-batch differences were moderate in comparison with intra-batch differences; it was also difficult to quantify batch effects objectively. We, therefore, sought enhancements to make the method more informative in those and analogous settings. Results: We have developed algorithms and a toolbox of enhancements to conventional PCA that improve the detection, diagnosis, and quantitation of differences between or among groups, e.g., groups of molecularly profiled biological samples. The enhancements include (i) computed group centroids; (ii) sample-dispersion rays; (iii) differential coloring of centroids, rays, and sample data points; (iii) trend trajectories; and (iv) a novel separation index (DSC) for quantitation of differences among groups. Conclusions: PCA-Plus has been our most useful single tool for analyzing, visualizing, and quantitating batch effects, trend effects, and class differences in molecular profiling data of many types: mRNA expression, microRNA expression, DNA methylation, and DNA copy number. An early version of PCA-Plus has been used as the central graphical visualization in our MBatch package for near-real-time surveillance of data for analysis working groups in more than 70 TCGA, PanCancer Atlas, PanCancer Analysis of Whole Genomes, and Genome Data Analysis Network projects of the NCI. The algorithms and software are generic, hence applicable more generally to other types of multivariate data as well. PCA-Plus is freely available in a down-loadable R package at our MBatch website.

SETD2 Loss and ATR Inhibition Synergize to Promote cGAS Signaling and Immunotherapy Response in Renal Cell Carcinoma.

PURPOSE: Immune checkpoint blockade (ICB) demonstrates durable clinical benefits in a minority of patients with renal cell carcinoma (RCC). We aimed to identify the molecular features that determine the response and develop approaches to enhance it. EXPERIMENTAL DESIGN: We investigated the effects of SET domain-containing protein 2 (SETD2) loss on the DNA damage response pathway, the cytosolic DNA-sensing pathway, the tumor immune microenvironment, and the response to ataxia telangiectasia and rad3-related (ATR) and checkpoint inhibition in RCC. RESULTS: ATR inhibition activated the cyclic GMP-AMP synthase (cGAS)-interferon regulatory factor 3 (IRF3)-dependent cytosolic DNA-sensing pathway, resulting in the concurrent expression of inflammatory cytokines and immune checkpoints. Among the common RCC genotypes, SETD2 loss is associated with preferential ATR activation and sensitizes cells to ATR inhibition. SETD2 knockdown promoted the cytosolic DNA-sensing pathway in response to ATR inhibition. Treatment with the ATR inhibitor VE822 concurrently upregulated immune cell infiltration and immune checkpoint expression in Setd2 knockdown Renca tumors, providing a rationale for ATR inhibition plus ICB combination therapy. Setd2-deficient Renca tumors demonstrated greater vulnerability to ICB monotherapy or combination therapy with VE822 than Setd2-proficient tumors. Moreover, SETD2 mutations were associated with a higher response rate and prolonged overall survival in patients with ICB-treated RCC but not in patients with non-ICB-treated RCC. CONCLUSIONS: SETD2 loss and ATR inhibition synergize to promote cGAS signaling and enhance immune cell infiltration, providing a mechanistic rationale for the combination of ATR and checkpoint inhibition in patients with RCC with SETD2 mutations.

RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data.

SUMMARY: Reverse-Phase Protein Array (RPPA) is a robust high-throughput, cost-effective platform for quantitatively measuring proteins in biological specimens. However, converting raw RPPA data into normalized, analysis-ready data remains a challenging task. Here, we present the RPPA SPACE (RPPA Superposition Analysis and Concentration Evaluation) R package, a substantially improved successor to SuperCurve, to meet that challenge. SuperCurve has been used to normalize over 170 000 samples to date. RPPA SPACE allows exclusion of poor-quality samples from the normalization process to improve the quality of the remaining samples. It also features a novel quality-control metric, 'noise', that estimates the level of random errors present in each RPPA slide. The noise metric can help to determine the quality and reliability of the data. In addition, RPPA SPACE has simpler input requirements and is more flexible than SuperCurve, it is much faster with greatly improved error reporting. AVAILABILITY AND IMPLEMENTATION: The standalone RPPA SPACE R package, tutorials and sample data are available via https://rppa.space/, CRAN (https://cran.r-project.org/web/packages/RPPASPACE/index.html) and GitHub (https://github.com/MD-Anderson-Bioinformatics/RPPASPACE). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

KLF5 governs sphingolipid metabolism and barrier function of the skin.

Stem cells are fundamental units of tissue remodeling whose functions are dictated by lineage-specific transcription factors. Home to epidermal stem cells and their upward-stratifying progenies, skin relies on its secretory functions to form the outermost protective barrier, of which a transcriptional orchestrator has been elusive. KLF5 is a Krüppel-like transcription factor broadly involved in development and regeneration whose lineage specificity, if any, remains unclear. Here we report KLF5 specifically marks the epidermis, and its deletion leads to skin barrier dysfunction in vivo. Lipid envelopes and secretory lamellar bodies are defective in KLF5-deficient skin, accompanied by preferential loss of complex sphingolipids. KLF5 binds to and transcriptionally regulates genes encoding rate-limiting sphingolipid metabolism enzymes. Remarkably, skin barrier defects elicited by KLF5 ablation can be rescued by dietary interventions. Finally, we found that KLF5 is widely suppressed in human diseases with disrupted epidermal secretion, and its regulation of sphingolipid metabolism is conserved in human skin. Altogether, we established KLF5 as a disease-relevant transcription factor governing sphingolipid metabolism and barrier function in the skin, likely representing a long-sought secretory lineage-defining factor across tissue types.

Consensus subtypes of hepatocellular carcinoma associated with clinical outcomes and genomic phenotypes.

BACKGROUND AND AIMS: Although many studies revealed transcriptomic subtypes of HCC, concordance of the subtypes are not fully examined. We aim to examine a consensus of transcriptomic subtypes and correlate them with clinical outcomes. APPROACH AND RESULTS: By integrating 16 previously established genomic signatures for HCC subtypes, we identified five clinically and molecularly distinct consensus subtypes. STM (STeM) is characterized by high stem cell features, vascular invasion, and poor prognosis. CIN (Chromosomal INstability) has moderate stem cell features, but high genomic instability and low immune activity. IMH (IMmune High) is characterized by high immune activity. BCM (Beta-Catenin with high Male predominance) is characterized by prominent ß-catenin activation, low miRNA expression, hypomethylation, and high sensitivity to sorafenib. DLP (Differentiated and Low Proliferation) is differentiated with high hepatocyte nuclear factor 4A activity. We also developed and validated a robust predictor of consensus subtype with 100 genes and demonstrated that five subtypes were well conserved in patient-derived xenograft models and cell lines. By analyzing serum proteomic data from the same patients, we further identified potential serum biomarkers that can stratify patients into subtypes. CONCLUSIONS: Five HCC subtypes are correlated with genomic phenotypes and clinical outcomes and highly conserved in preclinical models, providing a framework for selecting the most appropriate models for preclinical studies.

Caries Risk Documentation And Prevention: eMeasures For Dental Electronic Health Records.

BACKGROUND: Longitudinal patient level data available in the electronic health record (EHR) allows for the development, implementation, and validations of dental quality measures (eMeasures). OBJECTIVE: We report the feasibility and validity of implementing two eMeasures. The eMeasures determined the proportion of patients receiving a caries risk assessment (eCRA) and corresponding appropriate risk-based preventative treatments for patients at elevated risk of caries (appropriateness of care [eAoC]) in two academic institutions and one accountable care organization, in the 2019 reporting year. METHODS: Both eMeasures define the numerator and denominator beginning at the patient level, populations' specifications, and validated the automated queries. For eCRA, patients who completed a comprehensive or periodic oral evaluation formed the denominator, and patients of any age who received a CRA formed the numerator. The eAoC evaluated the proportion of patients at elevated caries risk who received the corresponding appropriate risk-based preventative treatments. RESULTS: EHR automated queries identified in three sites 269,536 patients who met the inclusion criteria for receiving a CRA. The overall proportion of patients who received a CRA was 94.4% (eCRA). In eAoC, patients at elevated caries risk levels (moderate, high, or extreme) received fluoride preventive treatment ranging from 56 to 93.8%. For patients at high and extreme risk, antimicrobials were prescribed more frequently site 3 (80.6%) than sites 2 (16.7%) and 1 (2.9%). CONCLUSION: Patient-level data available in the EHRs can be used to implement process-of-care dental eCRA and AoC, eAoC measures identify gaps in clinical practice. EHR-based measures can be useful in improving delivery of evidence-based preventative treatments to reduce risk, prevent tooth decay, and improve oral health.

PGC1α is required for the renoprotective effect of lncRNA Tug1 in vivo and links Tug1 with urea cycle metabolites.

lncRNA taurine-upregulated gene 1 (Tug1) is a promising therapeutic target in the progression of diabetic nephropathy (DN), but the molecular basis of its protection remains poorly understood. Here, we generate a triple-mutant diabetic mouse model coupled with metabolomic profiling data to interrogate whether Tug1 interaction with peroxisome proliferator-activated receptor gamma coactivator 1α (PGC1α) is required for mitochondrial remodeling and progression of DN in vivo. We find that, compared with diabetic conditional deletion of Pgc1α in podocytes alone (db/db; Pgc1αPod-f/f), diabetic Pgc1α knockout combined with podocyte-specific Tug1 overexpression (db/db; TugPodTg; Pgc1αPod-f/f) reverses the protective phenotype of Tug1 overexpression, suggesting that PGC1α is required for the renoprotective effect of Tug1. Using unbiased metabolomic profiling, we find that altered urea cycle metabolites and mitochondrial arginase 2 play an important role in Tug1/PGC1α-induced mitochondrial remodeling. Our work identifies a functional role of the Tug1/PGC1α axis on mitochondrial metabolic homeostasis and urea cycle metabolites in experimental models of diabetes.

Assessing the completeness of periodontal disease documentation in the EHR: a first step in measuring the quality of care.

BACKGROUND: Our objective was to measure the proportion of patients for which comprehensive periodontal charting, periodontal disease risk factors (diabetes status, tobacco use, and oral home care compliance), and periodontal diagnoses were documented in the electronic health record (EHR). We developed an EHR-based quality measure to assess how well four dental institutions documented periodontal disease-related information. An automated database script was developed and implemented in the EHR at each institution. The measure was validated by comparing the findings from the measure with a manual review of charts. RESULTS: The overall measure scores varied significantly across the four institutions (institution 1 = 20.47%, institution 2 = 0.97%, institution 3 = 22.27% institution 4 = 99.49%, p-value < 0.0001). The largest gaps in documentation were related to periodontal diagnoses and capturing oral homecare compliance. A random sample of 1224 charts were manually reviewed and showed excellent validity when compared with the data generated from the EHR-based measure (Sensitivity, Specificity, PPV, and NPV > 80%). CONCLUSION: Our results demonstrate the feasibility of developing automated data extraction scripts using structured data from EHRs, and successfully implementing these to identify and measure the periodontal documentation completeness within and across different dental institutions.

Large-Scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines.

Perturbation biology is a powerful approach to modeling quantitative cellular behaviors and understanding detailed disease mechanisms. However, large-scale protein response resources of cancer cell lines to perturbations are not available, resulting in a critical knowledge gap. Here we generated and compiled perturbed expression profiles of ∼210 clinically relevant proteins in >12,000 cancer cell line samples in response to ∼170 drug compounds using reverse-phase protein arrays. We show that integrating perturbed protein response signals provides mechanistic insights into drug resistance, increases the predictive power for drug sensitivity, and helps identify effective drug combinations. We build a systematic map of "protein-drug" connectivity and develop a user-friendly data portal for community use. Our study provides a rich resource to investigate the behaviors of cancer cells and the dependencies of treatment responses, thereby enabling a broad range of biomedical applications.

Measuring sealant placement in children at the dental practice level.

BACKGROUND: Although sealants are an established and recommended caries-preventive treatment, many children still fail to receive them. In addition, research has shown that existing measures underestimate care by overlooking the sealable potential of teeth before evaluating care. To address this, the authors designed and evaluated 3 novel dental electronic health record-based clinical quality measures that evaluate sealant care only after assessing the sealable potential of teeth. METHODS: Measure I recorded the proportion of patients with sealable teeth who received sealants. Measure II recorded the proportion of patients who had at least 1 of their sealable teeth sealed. Measure III recorded the proportion of patients who received sealant on all of their sealable teeth. RESULTS: On average, 48.1% of 6- through 9-year-old children received 1 or more sealants compared with 32.4% of 10- through 14-year-olds (measure I). The average measure score decreased for patients who received sealants for at least 1 of their sealable teeth (measure II) (43.2% for 6- through 9-year-olds and 28.4% for 10- through 14-year-olds). Fewer children received sealants on all eligible teeth (measure III) (35.5% of 6- through 9-year-olds and 21% of 10- through 14-year-olds received sealant on all eligible teeth). Among the 48.5% who were at elevated caries risk, the sealant rates were higher across all 3 measures. CONCLUSIONS: A valid and actionable practice-based sealant electronic measure that evaluates sealant treatment among the eligible population, both at the patient level and the tooth level, has been developed. PRACTICAL IMPLICATIONS: The measure developed in this work provides practices with patient-centered and actionable sealant quality measures that aim to improve oral health outcomes.

Developing and Testing Electronic Health Record-Derived Caries Indices.

Caries indices, the basis of epidemiologic caries measures, are not easily obtained in clinical settings. This study's objective was to design, test, and validate an automated program (Valid Electronic Health Record Dental Caries Indices Calculator Tool [VERDICT]) to calculate caries indices from an electronic health record (EHR). Synthetic use case scenarios and actual patient cases of primary, mixed, and permanent dentition, including decayed, missing, and filled teeth (DMFT/dmft) and tooth surfaces (DMFS/dmfs) were entered into the EHR. VERDICT measures were compared to a previously validated clinical electronic data capture (EDC) system and statistical program to calculate caries indices. Four university clinician-researchers abstracted EHR caries exam data for 45 synthetic use cases into the EDC and post-processed with SAS software creating a gold standard to compare the -VERDICT-derived caries indices. Then, 2 senior researchers abstracted EHR caries exam data and calculated caries indices for 24 patients, allowing further comparisons to VERDICT indices. Agreement statistics were computed among abstractors, and discrepancies were resolved by consensus. Agreement statistics between the 2 final-phase abstractors and the VERDICT measures showed extremely high concordance: Lin's concordance coefficients (LCCs) >0.99 for dmfs, dmft, DS, ds, DT, dt, ms, mt, FS, fs, FT, and ft; LCCs >0.95 for DMFS and DMFT; and LCCs of 0.92-0.93 for MS and MT. Caries indices, essential to developing primary health outcome measures for research, can be reliably derived from an EHR using VERDICT. Using these indices will enable population oral health management approaches and inform quality improvement efforts.

Number of Pregnant Women at Four Dental Clinics and the Care They Received: A Dental Quality eMeasure Evaluation.

Process-of-care quality measure research can be used to identify gaps in the delivery of dental services to pregnant patients. The aim of this study was to evaluate the types of dental services that pregnant patients received in four dental clinics over five years as documented in the electronic health record (EHR). To accomplish this objective, the authors modified and validated a previously published claims-based dental quality measure for EHR use. After the electronic dental quality measure specifications were defined, the number of pregnant patients was calculated at three academic dental institutions and one large accountable care organization, and the types of dental care services they received over a five-year period (2013-17) were determined. Calibrated reviewers at each institution independently reviewed a sub-sample of patient charts to validate the information obtained from EHR queries, and the concordance between manual chart reviews and EHR query reports was analyzed. Of the 335,078 women aged 15-44 years who received care at the four clinics for the five reporting years, 3.9% (n=13,026) were pregnant. Among these pregnant patients, 48.9% (n=6,366) received a periodic dental examination; 30.0% (n=3,909) received a comprehensive dental exam; and 21.5% (n=2,799) received additional dental services, irrespective of comprehensive or periodic oral evaluations. Overall, the mean proportion of pregnant patients seeking care in these academic dental and group practice clinics was low, but 78.9% of them received either a periodic or comprehensive oral evaluation. Given the importance of oral health care during pregnancy, these findings suggest a need for curriculum development to incorporate prenatal oral health education in the training of dental students.

Assessing the validity of existing dental sealant quality measures.

BACKGROUND: Although sealants are highly effective in preventing caries in children, placement rates continue to be low. The authors' goals were to implement and assess the performance of 2 existing sealant quality measures against a manual audit of charts at 4 dental institutions and to identify measurement gaps that may be filled by using data from electronic health records. METHODS: The authors evaluated the performance of 2 quality measures designed for claims-based data: the Dental Quality Alliance (DQA) sealant measure, which includes patients at risk of developing elevated caries, and the Oregon Health Authority (OHA) sealant measure (irrespective of caries risk). The authors adapted and validated these measures at 4 sites: 3 dental schools and 1 large dental accountable care organization. RESULTS: The overall modified DQA and modified OHA measure scores in the 6- through 9-year-old age group were 37.0% and 31.6% and in the 10- through 14-year-old age group were 15.8% and 6.6%, respectively. Results from the manual review of charts showed that 67.6% of children who did not receive sealants did not have any teeth to seal because their molars had not yet erupted, had been extracted, had been sealed previously, or had existing caries or restorations. CONCLUSIONS: Both the DQA and OHA measures, which rely mainly on Current Dental Terminology procedure codes, led to underestimation of the care delivered from a practice perspective. Future sealant quality measures should exclude patients whose teeth cannot be sealed. PRACTICAL IMPLICATIONS: This study's results support the suitability of using electronic health record data for assessing the quality of oral health care, particularly for measuring sealant placement in children.

Maternal Residential Proximity to Major Roadways and Pediatric Embryonal Tumors in Offspring.

The environmental determinants of pediatric embryonal tumors remain unclear. Because of the growing concern over the impact of exposures to traffic-related air pollution on pediatric cancer, we conducted a population-based study evaluating the impact of maternal residential proximity to major roadways on the risk of pediatric embryonal tumors in offspring. We identified children diagnosed with neuroblastoma, Wilms tumor, retinoblastoma, or hepatoblastoma at <5 years of age from the Texas Cancer Registry and selected unaffected controls from birth certificates. Two residential proximity measures were used: (1) distance to the nearest major roadway, and (2) within 500 m of a major roadway. Logistic regression was used to estimate the adjusted odds ratio (aOR) and 95% confidence interval (CI) for each proximity measure on pediatric embryonal tumors. The odds of an embryonal tumor were increased in children born to mothers living within 500 m of a major roadway (aOR = 1.24, 95% CI: 1.00, 1.54). This was consistent for most tumor subtypes, with the strongest associations observed for unilateral retinoblastoma (aOR = 2.57, 95% CI: 1.28, 5.15, for every kilometer closer the mother lived to the nearest major roadway). These findings contribute to the growing evidence that traffic-related air pollution may increase risk for certain pediatric tumors.

Podoplanin--a novel marker in oral carcinogenesis.

Podoplanin, a transmembrane sialoglycoprotein, is a specific marker for lymphatic endothelial cells which in recent years has gained prominent notoriety for its role in tumor progression and metastasis. It is an extensively studied biomarker for predictive assessment of malignant transformation as well as biologic behavior in both human precancer and cancer, respectively. This review summarizes the association of podoplanin overexpression in oral potentially malignant disorders and oral cancer with special emphasis on its putative role in carcinogenesis as well as its prospective use in targeted therapy.

Primary fibrosarcoma of maxilla in an 8-year-old child: A rare entity.

Fibrosarcoma (FS) is a malignant mesenchymal neoplasm of the fibroblasts that is uncommon in the head and neck and constitutes less than 1% of malignancies and approximately 6% of the soft tissue sarcomas. FSs rarely occur before the third decade except infantile type. This condition primarily affects long bones, and its occurrence in the cranium is rare (15%), with the mandible being the most commonly involved cranial site. Here a case of primary FS in anterior maxilla of an 8-year-old male child is reported. This article is presented to document the rarity of FSs in the jaws of children with review of literature.