A protein expression atlas on tissue samples and cell lines from cancer patients provides insights into tumor heterogeneity and dependencies.

The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE) are foundational resources in cancer research, providing extensive molecular and phenotypic data. However, large-scale proteomic data across various cancer types for these cohorts remain limited. Here, we expand upon our previous work to generate high-quality protein expression data for approximately 8,000 TCGA patient samples and around 900 CCLE cell line samples, covering 447 clinically relevant proteins, using reverse-phase protein arrays.

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.

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.

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.

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.

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.

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; Pgc1α), diabetic Pgc1α knockout combined with podocyte-specific Tug1 overexpression (db/db; Tug; Pgc1α) reverses the protective phenotype of Tug1 overexpression, suggesting that PGC1α is required for the renoprotective effect of Tug1.

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.

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.

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.

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.

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.

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).

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.

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.