Matrix Linear Models for connecting metabolite composition to individual characteristics

High-throughput metabolomics data provide a detailed molecular window into biological processes. We consider the problem of assessing how the association of metabolite levels with individual (sample) characteristics such as sex or treatment may depend on metabolite characteristics such as pathway. Typically this is one in a two-step process: In the first step we assess the association of each metabolite with individual characteristics. In the second step an enrichment analysis is performed by metabolite characteristics among significant associations. We combine the two steps using a bilinear model based on the matrix linear model (MLM) framework we have previously developed for high-throughput genetic screens. Our framework can estimate relationships in metabolites sharing known characteristics, whether categorical (such as type of lipid or pathway) or numerical (such as number of double bonds in triglycerides). We demonstrate how MLM offers flexibility and interpretability by applying our method to three metabolomic studies. We show that our approach can separate the contribution of the overlapping triglycerides characteristics, such as the number of double bonds and the number of carbon atoms. The proposed method have been implemented in the open-source Julia package, MatrixLM. Data analysis scripts with example data analyses are also available.

Abstract 4297: OFFONOME: a new notion of genes’ on/off

Background: RNA-seq is now the most widely used technique for gene expression profiling, which generates nucleotide level genome coverage as well as summary gene expression values. In general, low-expressed genes are excluded in the data processing due to their low signal-to-noise ratio. Nonetheless, it has been shown that low-expressed genes can provide crucial information such as presence of rare cells in bulk tissue samples. To optimize signal to noise in low-expressed genes, we applied a novel approach in which we transform low-expressed genes to a robust dichotomized state of being either “on” or “off”.

Methods: To determine the status of genes, we use the shape of base-level read coverage which is expected to be homogeneous across the samples if they are “on”, whereas appear to be random noise if they are “off”. We model base-resolution RNA-seq data as vectors in high dimensional data space and measure their level of shape similarity (LSS) using angles between samples with lower angles indicating higher similarity which is more likely to be “on” status. Applying this approach to 3 human cancer samples (head and neck squamous cell carcinoma (HNSC), lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC)) from the Cancer Genome Atlas (TCGA), we identified lists of genes, the OFFONOME, that were either always or sometimes “off”. Differential OFFONOME genes were queried to address supervised and unsupervised analyses.

Results: Using our technique, we characterized the OFFONOME of HNSC (5851 genes), a set which would typically have been filtering for removal because of low expression. In the HNSC OFFONOME, we observed five gene clusters, each of which was strongly associated with specific gene ontology. One of the clusters identified a rare population of normal myocytes infiltrating otherwise invasive tumors. For the OFFONOME of LUAD (5435 genes) and LUSC (5292 genes), we found clusters enriched with cilia and keratinization-related genes. In the result of integrated analysis, we observed that squamous cell carcinoma (SCC) tumor types shared “on” status for keratinization-related genes known for the cause of SCC. By comparison, LUAD had “on” status genes related to microtubule-based movement related with cilia structure. Strikingly, clustering the OFFONOME with the LSS distinguished 3 tumor types with almost perfect separation, outperforming several competing gene expression measures.

Conclusion: In this study, we applied a new notion of gene expression. This approach enables a robust characterization of “on” and “off” status which can be especially effective for the genes expressed at low level. The OFFONOME from 3 cancer types revealed not only the tissue-specific genes but also the genes shared in similar tumor types. Collectively, OFFONOME can provide new insights into genes expressed at vanishingly low levels, such as from minor cell populations within bulk tumor analysis.

Citation Format: Wonyoung Choi, Hyo Young Choi, Daivd Neil Hayes. OFFONOME: a new notion of genes’ on/off. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4297.

Abstract 6062: Viral genome structure correlates with patterns of somatic alteration in human papillomavirus associated head and neck squamous cell carcinoma

Integration of viral DNA into the host genome has been implicated in human papillomavirus (HPV) associated tumorigenesis, and studies in HPV associated head and neck squamous cell carcinoma (HNSCC) attempting to classify viral integration status have reported associations among HPV status, viral load, and overall survival. However, few genomic studies have correlated HPV structure with commonly occurring somatic mutations in HNSCC. Here, we conducted hybrid-capture DNA sequencing using a panel of over 800 cancer related genomic targets, as well as probes specific for the full HPV16 and HPV18 genomes, in a novel cohort of 525 HNSCC cases. Paired reads were aligned to a human reference containing complete viral genomes, including all high-risk HPV types, which allowed for robust identification of HPV(+) tumors and specific HPV type. Variant calling and filtering, followed by pathway analysis of significantly mutated genes, defined the catalog of somatic driver alterations in HNSCC. Viral genome structure, integration status, and viral load were determined via initial copy number analysis of HPV-specific reads, followed by identification of viral/human breakpoints and indels with variant calling algorithms. Manual review was required in some cases due to variability in read coverage and alignment to HPV genome. We identified 252 HPV(+) tumors, the majority of which were HPV16 (n=228, 90%). Analysis of HPV16(+) tumors revealed five classes with variable viral loads: pure episome (EPI, n=54), episomal rearranged (EPI-R, n=51), episomal chimeric (EPI-C, n=22), integrated (INT, n=92), and integrated deleted (INT-A, n=12). Integrated tumors had at least one integration event (INT) and a few exhibited recurrent deletions in the viral genome (INT-A). Episomal samples had either complete HPV genomes (EPI), circular genomes with one or more indels (EPI-R), or circular genomes with HPV and human DNA (EPI-C). Interestingly, PIK3CA, the most frequently mutated gene in HPV(+) HNSCC, was mutated at a higher frequency in all integrated samples compared to all episomal types (44% vs 23%, p=0.005). We also noticed more deleterious mutations in innate immunity genes (HLA-A/B, B2M, TRAF3, BIRC3) in the episomal samples (16% vs 8%), which may allow cells with intact HPV genomes to evade anti-viral immune responses. Additionally, mutations in oxidative stress response genes that lead to the constitutive activation of NRF2 (NFE2L2, CUL3, KEAP1) were more frequent in integrated samples (11% vs 4%), which could confer radiotherapy resistance and a worse prognosis. Overall, using DNA sequencing and integrative genomic analysis in the largest cohort of HPV(+) HNSCC to date, we developed a novel classification method based on viral genome structure which associates with host somatic alterations that may contribute to variable outcomes in HNSCCs.

Citation Format: Jeremiah Ray Holt, Xiaobei Zhao, Hyo Young Choi, Paul Little, Angela L. Mazul, Benjamin Wahle, Vonn Walter, Jose P. Zevallos, David Neil Hayes. Viral genome structure correlates with patterns of somatic alteration in human papillomavirus associated head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6062.

Abstract 2076: Novel framework for systematically detecting alternative transcript initiation by integrating ATAC-seq and RNA-seq

Background: Alternative transcription initiation (ATI) has been frequently observed in cancer suggesting that it contributes to the malignant transformation of the cells. However, ATI remains largely unexplored mainly due to the lack of tools for detecting ATI. We propose a computational method for integrating bulk ATAC-seq and bulk RNA-seq to identify ATI and understand their differential usage between tissues. We hypothesize that differential ATAC-seq intensity can be used as a guide for looking for differential promoter usage, which might enable the identification of novel ATI events in a transcript-agnostic way.

Methods: We recently published methods for RNA-seq base-level analysis for identifying structural variations in transcripts. Building on this, we developed a supervised sparse non-negative matrix factorization approach that integrates base-level RNA-seq and ATAC-seq, which aims to identify ATIs as well as characterize the latent structure of the underlying isoforms. This method equips many unique features that can be useful for the identification of novel ATIs. Because the method scans an entire collection of DNA accessible regions provided by ATAC-seq, it enables a comprehensive screening of novel ATI candidates that are not limited to the known promoters. Additionally, the uncompressed view of base-level RNA-seq allows us to infer the structure of individual isoforms independently of known gene annotation. The predicted isoforms can be further used to deconvolute base-level RNA-seq of individual cases into the isoforms and thus infer expression levels of each isoform.

Results: We applied this method to a sub-cohort (N=350) of TCGA pan-cancer samples in which both ATAC-seq and RNA-seq are available. Empiric comparison to existing methods confirmed known true positive ATIs including important cancer genes such as CDKN2A and ALK. In particular, the method successfully identified the ATIs including some challenging cases such as ATIs located at internal introns or at constitutive exons in other transcripts. The deconvolution analysis applied to the extended cohort to all available ~10,000 TCGA pan-caner samples across 32 tissue types revealed that ATIs were predominantly differentiated across tissue types. By applying the method to a set of transcription regulator genes, we identified ~1% of the genes had ATIs including the novel cancer-specific genes with known ATIs that had not been previously reported as relevant to cancer. Additionally, we provide examples in which the isoform’s function relative to cancer appears mechanistically interesting.

Conclusion: We propose a multi-omics integration method that is independent of known gene annotation, enabling a robust identification of ATIs. Our results strongly demonstrate our ability to pick up known as well as novel ATIs that are otherwise difficult to identify by existing methods.

Citation Format: Hyo Young Choi, Won-Young Choi, David N. Hayes. Novel framework for systematically detecting alternative transcript initiation by integrating ATAC-seq and RNA-seq [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2076.

Abstract 2071: Detecting somatic DNA copy number differences with DiNAMIC.Duo

Somatic DNA copy number alterations (CNAs) arise in tumor tissue because of underlying genomic instability. Recurrent CNAs that occur in the same genomic region across multiple independent samples are of interest to researchers because they may contain genes that contribute to the cancer phenotype. However, differences in copy number states between cancers are also commonly of interest, for example when comparing tumors with distinct morphologies in the same anatomic location. Current methodologies are limited by their inability to perform direct comparisons of CNAs between tumor cohorts, and thus they cannot formally assess the statistical significance of observed copy number differences or identify regions of the genome where these differences occur. We introduce the DiNAMIC.Duo R package that can be used to identify recurrent CNAs in a single cohort or recurrent copy number differences between two cohorts, including when neither cohort is copy neutral. The TCGA studies of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) identified statistically significant CNAs in many known cancer-related genes, including gains of EGFR and losses of CDKN2A in each tumor type separately. By directly comparing the two cohorts, DiNAMIC.Duo detects statistically significant copy number differences for CDKN2A, thus suggesting that losses are more pronounced in LUSC; in contrast, differences for EGFR are not statistically significant, which suggests similar levels of gain. Existing methods that detect recurrent CNAs in a single cohort cannot make this distinction. Recent studies have leveraged TCGA data to find known cancer genes in chr3q, chr14q13, and chr20q11 that are differentially expressed in LUAD vs. LUSC. DiNAMIC.Duo identifies statistically significant copy number differences in these regions, which suggests that the observed expression changes may be driven by underlying differences in copy number.

Citation Format: Vonn Walter, Hyo Young Choi, Xiaobei Zhao, Yan Gao, Jeremiah Holt, D. Neil Hayes. Detecting somatic DNA copy number differences with DiNAMIC.Duo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2071.

DiNAMIC.Duo: detecting somatic DNA copy number differences without a normal reference

MOTIVATION

Somatic DNA copy number alterations (CNAs) arise in tumor tissue because of underlying genomic instability. Recurrent CNAs that occur in the same genomic region across multiple independent samples are of interest to researchers because they may contain genes that contribute to the cancer phenotype. However, differences in copy number states between cancers are also commonly of interest, for example when comparing tumors with distinct morphologies in the same anatomic location. Current methodologies are limited by their inability to perform direct comparisons of CNAs between tumor cohorts, and thus they cannot formally assess the statistical significance of observed copy number differences or identify regions of the genome where these differences occur.

RESULTS

We introduce the DiNAMIC.Duo R package that can be used to identify recurrent CNAs in a single cohort or recurrent copy number differences between two cohorts, including when neither cohort is copy neutral. The package utilizes Python scripts for computational efficiency and provides functionality for producing figures and summary output files.

AVAILABILITY AND IMPLEMENTATION

The DiNAMIC.Duo R package is available from CRAN at https://cran.r-project.org/web/packages/DiNAMIC.Duo/index.html. This article uses publicly available data from the Broad Institute TCGA Genome Data Analysis Center, https://doi.org/10.7908/C11G0KM9.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Abstract 49: Integrative genomic analysis of human papillomavirus associated head and neck squamous cell carcinoma reveals selective pressure for somatic alteration of E6 and E7 targets

Purpose: Previous studies implicated viral oncoproteins E6 and E7, of which targets include but are not limited to tumor suppressors p53 and pRb, in human papillomavirus (HPV) associated tumorigenesis. However, HPV-associated tumors must accumulate additional genomic alterations as HPV oncoproteins alone are insufficient for tumor formation in vivo.

Experimental Design: Targeted sequencing was conducted with a panel of over 800 cancer related genomic regions and genes in a novel cohort of 525 head and neck squamous cell carcinoma (HNSCC) patients, including 252 HPV(+) and 273 HPV(-) tumors. Variant calling and filtering, followed by analysis with computational tools such as MutSig for somatic mutations and DiNAMIC.Duo for recurrent copy number alterations (CNAs), defined the catalog of driver alterations that are specific to HPV(+) and HPV(-) tumors. Pathway analysis was then used to elucidate the functional role of somatic alterations in the context of previously described HNSCC perturbations and HPV pathophysiology.

Results: Integrative genomic analysis in one of the largest HPV(+) HNSCC cohorts to date revealed differential patterns of somatic mutations and CNAs in E6/E7 targets between HPV(+) and HPV(-) tumors. Specifically, EP300, an activator of p53 and target of E6, and retinoblastoma (RB) family members RB1 (pRb) and RBL2 (p130), which are known targets of E7 mediated degradation, were selected as significantly mutated by MutSig in HPV(+) samples only (EP300 & RB1 P<0.001, RBL2 P=0.01), while RBL1 (p107) was significant for both HPV(+) and HPV(-) samples (P<0.001, P=0.02 respectively). Higher fractions of mutations in HPV(+) vs. HPV(-) tumors were observed for EP300 (13% vs 6%, Fisher’s exact test P=0.006), RB1 (7% vs 3%, P=0.07), RBL2 (3% vs 1%, P=0.09), and FOXM1 (4% vs 1%, P=0.02), another cell cycle pathway target of E7, but not for RBL1 (4% vs. 3%, P=1). Lower copy numbers were detected in HPV(+) tumors compared to HPV(-) for chromosome regions containing RB1 (P=0.03), RBL1 (P=0.08), RBL2 (P<0.001), and for another inhibitory target of E6, FADD (P<0.001), which is an activator of the proapoptotic protein caspase-8. Additionally, significant copy number gains were detected in HPV(+) vs. HPV(-) tumors within the genomic region containing E2F1 (P<0.001), the transcription factor whose inhibition by RB family proteins is abrogated in the presence of E7, thus leading to abnormal cell cycle progression and proliferation.

Conclusions: Previous studies suggest HPV-associated tumors lack significant levels of somatic alterations in canonical tumor suppressor genes that are known targets of viral oncoproteins. Here, we show additional selective pressure exists for somatic alteration of E6/E7 target genes in at least a subset of HPV(+) HNSCCs, which further deregulate cell cycle and apoptosis pathways in these tumors.

Citation Format: Jeremiah Holt, Heejoon Jo, Xiaobei Zhao, Hyo Young Choi, Vonn Walter, Paul Little, Benjamin Wahle, Angela Mazul, Jose P. Zevallos, David Neil Hayes. Integrative genomic analysis of human papillomavirus associated head and neck squamous cell carcinoma reveals selective pressure for somatic alteration of E6 and E7 targets [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 49.

Abstract 3355: The Offonome: Methods for characterizing gene expression of rare cell populations from whole tumor profiling data

Background: Tumors are composed of diverse cell types. While several approaches have been proposed to dissect the cellular heterogeneity using profiling data such as gene expression or methylation, it remains challenging to discover rare cell types from high-throughput sequencing data. To address this need, we apply a novel approach in which we hypothesize that rare cell subpopulations might be detected based on the expression of differential sets of transcripts, generally expressed at low levels proportional to the infiltrating cell percentage. In this case, the challenge is the precise measurement of gene expression at low levels or the detection of genes specifically attributable to those cell populations as being “off” or “on”.

Methods: We propose a novel computational approach for measuring the “offonome”, defined as a gene’s dichotomized state of being “on” or “off”. To accurately determine on/off status of a gene, we compare single nucleotide-level RNA-seq data modeled as vectors in high dimensional data space using the angles between samples. In this framework, sample vectors determined to have low angles can be defined as sharing an “on” gene versus sample vectors with high angle defining a state of “off”. We apply this approach to more than 5,000 human cancer samples drawn from the Cancer Genome Atlas (TCGA) to identify minor cell populations. Additionally, we compare this approach to the alternative gene abundance strategy in which on/off is defined by read-counts-based gene expression estimates from the same dataset.

Results: Using the overall and sub-populations, we identified minor cell populations across the TCGA dataset including in a sub-cohort of 522 TCGA head and neck squamous cell carcinoma (HNSCC). The Offonome approach applied genome-wide in HNSCC identified 5802 genes that were either always or sometimes “off” defined by angle-based statistics. Turning our attention to genes that were sometime, but not always off, we applied unsupervised learning to characterize clusters of genes within HNSCC tumors. At least five gene clusters were clearly observed, each of which was strongly associated with specific signaling pathways. For example, one cluster identified infiltrating myocytes, defined by infiltrating normal muscle cells, found only in tumors of the oral tongue. In addition to clustering analysis, we utilized the approach to identify high expression of genes found in outliers, or even a single sample such as those associated with salivary origin such as olfactory receptors.

Conclusions: We conclude that on/off status of a gene provides new insights into gene expression deconvolution, thereby characterizing interesting gene clusters. These results offer strong evidence that our approach can be useful for picking up rare transcripts from individual samples such as leukocyte transcripts and stromal transcripts.

Citation Format: Hyo Young Choi, David N. Hayes. The Offonome: Methods for characterizing gene expression of rare cell populations from whole tumor profiling data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3355.

Social Disparities of Pain and Pain Intensity Among Women Diagnosed With Early Stage Breast Cancer

Background

Breast cancer is one of the most commonly diagnosed cancers among women in the United States and pain is the most common side effect of breast cancer and its treatment. Yet, the relationships between social determinants of pain and pain experience/intensity remain under-investigated. We examined the associations between social determinants of pain both at the individual level and the neighborhood level to understand how social conditions are associated with pain perception among early stage breast cancer patients.

Methods

We conducted integrated statistical analysis of 1,191 women with early stage breast cancer treated at a large cancer center in Memphis, Tennessee. Combining electronic health records, patient-reported data and census data regarding residential address at the time of first diagnosis, we evaluated the relationships between social determinants and pain perception. Pain responses were self-reported by a patient as a numerical rating scale score at the patient’s initial diagnosis and follow-up clinical visits. We implemented two sets of statistical analyses of the zero-inflated Poisson model and estimated the associations between neighborhood poverty prevalence and breast cancer pain intensity. After adjustment for demographic characteristics, cancer stage, and chemotherapy, pain perception was significantly associated with poverty and blight level of the neighborhood.

Results

Among women living in the highest-poverty areas, the odds of reporting pain were 2.48 times higher than those in the lowest-poverty area. Women living in the highest-blight area had 5.43 times higher odds of reporting pain than those in the lowest-blight area. Neighborhood-level social determinants were significantly associated with pain intensity among women diagnosed with early-stage breast cancer.

Conclusions

Distressed neighborhood conditions are significantly associated with higher pain perception. Breast cancer patients living in socio-economically disadvantaged neighborhoods and in poor environmental conditions reported higher pain severity compared to patients from less distressed neighborhoods. Therefore, post-diagnosis pain treatment design needs to be tailored to the social determinants of the breast cancer patients.

Muscle insulin-like growth factor-I modulates murine craniofacial bone growth

Insulin-like growth factor I (IGF-I) is essential for muscle and bone development and a primary mediator of growth hormone (GH) actions. While studies have elucidated the importance of IGF-I specifically in muscle or bone development, few studies to date have evaluated the relationship between muscle and bone modulated by IGF-I in vivo, during post-natal growth. Mice with muscle-specific IGF-I overexpression (mIgf1+/+) were utilised to determine IGF-I- and muscle-mass-dependent effects on craniofacial skeleton development during post-natal growth. mIgf1+/+ mice displayed accelerated craniofacial bone growth when compared to wild-type animals. Virus-mediated expression of IGF-I targeting the masseter was performed to determine if post-natal modulation of IGF-I altered mandibular structures. Increased IGF-I in the masseter affected the mandibular base plane angle in a lateral manner, increasing the width of the mandible. At the cellular level, increased muscle IGF-I also accelerated cartilage thickness in the mandibular condyle. Importantly, mandibular length changes associated with increased IGF-I were not present in mice with genetic inhibition of muscle IGF-I receptor activity. These results demonstrated that muscle IGF-I could indirectly affect craniofacial growth through IGF-I-dependent increases in muscle hypertrophy. These findings have clinical implications when considering IGF-I as a therapeutic strategy for craniofacial disorders.

Immune checkpoint blockade reprograms systemic immune landscape and tumor microenvironment in obesity-associated breast cancer

Immune checkpoint blockade (ICB) has improved outcomes in some cancers. A major limitation of ICB is that most patients fail to respond, which is partly attributable to immunosuppression. Obesity appears to improve immune checkpoint therapies in some cancers, but impacts on breast cancer (BC) remain unknown. In lean and obese mice, tumor progression and immune reprogramming were quantified in BC tumors treated with anti-programmed death-1 (PD-1) or control. Obesity augments tumor incidence and progression. Anti-PD-1 induces regression in lean mice and potently abrogates progression in obese mice. BC primes systemic immunity to be highly responsive to obesity, leading to greater immunosuppression, which may explain greater anti-PD-1 efficacy. Anti-PD-1 significantly reinvigorates antitumor immunity despite persistent obesity. Laminin subunit beta-2 (Lamb2), downregulated by anti-PD-1, significantly predicts patient survival. Lastly, a microbial signature associated with anti-PD-1 efficacy is identified. Thus, anti-PD-1 is highly efficacious in obese mice by reinvigorating durable antitumor immunity. VIDEO ABSTRACT.

The anatomy of COVID-19 comorbidity networks among hospitalized Korean patients

OBJECTIVES

We aimed to examine how comorbidities were associated with outcomes (illness severity or death) among hospitalized patients with coronavirus disease 2019 (COVID-19).

METHODS

Data were provided by the National Medical Center of the Korea Disease Control and Prevention Agency. These data included the clinical and epidemiological information of all patients hospitalized with COVID-19 who were discharged on or before April 30, 2020 in Korea. We conducted comorbidity network and multinomial logistic regression analyses to identify risk factors associated with COVID-19 disease severity and mortality. The outcome variable was the clinical severity score (CSS), categorized as mild (oxygen treatment not needed), severe (oxygen treatment needed), or death.

RESULTS

In total, 5,771 patients were included. In the fully adjusted model, chronic kidney disease (CKD) (odds ratio [OR], 2.58; 95% confidence interval [CI], 1.19 to 5.61) and chronic obstructive pulmonary disease (COPD) (OR, 3.19; 95% CI, 1.35 to 7.52) were significantly associated with disease severity. CKD (OR, 5.35; 95% CI, 2.00 to 14.31), heart failure (HF) (OR, 3.15; 95% CI, 1.22 to 8.15), malignancy (OR, 3.38; 95% CI, 1.59 to 7.17), dementia (OR, 2.62; 95% CI, 1.45 to 4.72), and diabetes mellitus (OR, 2.26; 95% CI, 1.46 to 3.49) were associated with an increased risk of death. Asthma and hypertension showed statistically insignificant associations with an increased risk of death.

CONCLUSIONS

Underlying diseases contribute differently to the severity of COVID-19. To efficiently allocate limited medical resources, underlying comorbidities should be closely monitored, particularly CKD, COPD, and HF.

Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway

RTK/RAS/RAF pathway alterations (RPAs) are a hallmark of lung adenocarcinoma (LUAD). In this study, we use whole-genome sequencing (WGS) of 85 cases found to be RPA(-) by previous studies from The Cancer Genome Atlas (TCGA) to characterize the minority of LUADs lacking apparent alterations in this pathway. We show that WGS analysis uncovers RPA(+) in 28 (33%) of the 85 samples. Among the remaining 57 cases, we observe focal deletions targeting the promoter or transcription start site of STK11 (n = 7) or KEAP1 (n = 3), and promoter mutations associated with the increased expression of ILF2 (n = 6). We also identify complex structural variations associated with high-level copy number amplifications. Moreover, an enrichment of focal deletions is found in TP53 mutant cases. Our results indicate that RPA(-) cases demonstrate tumor suppressor deletions and genome instability, but lack unique or recurrent genetic lesions compensating for the lack of RPAs. Larger WGS studies of RPA(-) cases are required to understand this important LUAD subset.

SCISSOR: a framework for identifying structural changes in RNA transcripts

High-throughput sequencing protocols such as RNA-seq have made it possible to interrogate the sequence, structure and abundance of RNA transcripts at higher resolution than previous microarray and other molecular techniques. While many computational tools have been proposed for identifying mRNA variation through differential splicing/alternative exon usage, challenges in its analysis remain. Here, we propose a framework for unbiased and robust discovery of aberrant RNA transcript structures using short read sequencing data based on shape changes in an RNA-seq coverage profile. Shape changes in selecting sample outliers in RNA-seq, SCISSOR, is a series of procedures for transforming and normalizing base-level RNA sequencing coverage data in a transcript independent manner, followed by a statistical framework for its analysis ( https://github.com/hyochoi/SCISSOR ). The resulting high dimensional object is amenable to unsupervised screening of structural alterations across RNA-seq cohorts with nearly no assumption on the mutational mechanisms underlying abnormalities. This enables SCISSOR to independently recapture known variants such as splice site mutations in tumor suppressor genes as well as novel variants that are previously unrecognized or difficult to identify by any existing methods including recurrent alternate transcription start sites and recurrent complex deletions in 3' UTRs.

Integrative Analysis of miRNAs Identifies Clinically Relevant Epithelial and Stromal Subtypes of Head and Neck Squamous Cell Carcinoma

PURPOSE

The objective of this study is to characterize the role of miRNAs in the classification of head and neck squamous cell carcinoma (HNSCC).

EXPERIMENTAL DESIGN

Here, we analyzed 562 HNSCC samples, 88 from a novel cohort and 474 from The Cancer Genome Atlas, using miRNA microarray and miRNA sequencing, respectively. Using an integrative correlations method followed by miRNA expression-based hierarchical clustering, we validated miRNA clusters across cohorts. Evaluation of clusters by logistic regression and gene ontology approaches revealed subtype-based clinical and biological characteristics.

RESULTS

We identified two independently validated and statistically significant (P < 0.01) tumor subtypes and named them "epithelial" and "stromal" based on associations with functional target gene ontology relating to differing stages of epithelial cell differentiation. miRNA-based subtypes were correlated with individual gene expression targets based on miRNA seed sequences, as well as with miRNA families and clusters including the miR-17 and miR-200 families. These correlated genes defined pathways relevant to normal squamous cell function and pathophysiology. miRNA clusters statistically associated with differential mutation patterns including higher proportions of TP53 mutations in the stromal class and higher NSD1 and HRAS mutation frequencies in the epithelial class. miRNA classes correlated with previously reported gene expression subtypes, clinical characteristics, and clinical outcomes in a multivariate Cox proportional hazards model with stromal patients demonstrating worse prognoses (HR, 1.5646; P = 0.006).

CONCLUSIONS

We report a reproducible classification of HNSCC based on miRNA that associates with known pathologically altered pathways and mutations of squamous tumors and is clinically relevant.

Vertebral fracture is associated with myocardial infarction in incident hemodialysis patients: a Korean nationwide population-based study

Chronic kidney disease (CKD)-mineral and bone disorder suggests that fragile bone and vascular disorder might be connected closely in CKD patients. In this study, fracture event was significantly associated with myocardial infarction (MI) in end-stage renal disease patients on hemodialysis (HD), especially for vertebral fractures.

INTRODUCTION

CKD-mineral and bone disorder is characterized by biochemical abnormalities, bone disorders, and vascular calcification. We aimed to verify the association between fracture and MI in CKD patients.

METHODS

Records for incident CKD stage 3 to 5 patients and patients who initiated HD between July 2014 and June 2018 were retrieved from the Korean Health Insurance Review & Assessment Service Database. Fractures were defined using diagnostic codes and were classified into vertebral, femoral, and other site fractures. MI was defined using a combination of MI diagnostic codes and related procedure codes. Multiple logistic regressions and 1:1 propensity score matching analysis were conducted.

RESULTS

A total of 38,935 patients (HD, 11,379; pre-dialysis CKD, 27,556) were included in this study. A total of 5,057 (13.0%) patients experienced fracture, and 1,431 (3.7%) patients had MI. Multiple logistic regression analysis showed that fracture was significantly associated with MI in the HD group (odds ratio (OR) 1.34, P = 0.024), but not in the pre-dialysis CKD group (OR 1.04, P = 0.701). After propensity score matching for age, gender, and diabetes mellitus between patients with and without fracture, fracture still significantly correlated with MI in HD patients (OR 1.47, P = 0.034) but not in patients with pre-dialysis CKD (OR 1.04, P = 0.751). Subgroup analysis by fracture site found that vertebral fracture was associated with MI in HD patients (OR 2.11, P = 0.024), but femoral or other site fractures were not.

CONCLUSION

In HD patients, fracture was significantly associated with MI, especially for vertebral fractures patients.

Abstract 5460: Detecting somatic DNA copy number differences with cyclic shift testing

The most basic differential expression analysis involves the identification of genes that exhibit distinct expression patterns in two cohorts. Surprisingly, even though there are numerous computational methods for detecting and assessing the statistical significance of somatic DNA copy number (CN) gains and losses in a single cohort, there are no tools for detecting and assessing the statistical significance of CN differences between two cohorts. Instead, typically each cohort is analyzed separately and distinct findings are presented as evidence of CN differences.

Cyclic shift testing was originally introduced as a method to identify and assess the statistical significance of recurrent somatic CN gains and losses. Subsequent work explored theoretical statistical underpinnings of cyclic shift testing. Here we extend the previous results by showing that cyclic shift testing can be applied to detect and assess the statistical significance of CN differences between two cohorts.

Human papilloma virus (HPV) infection is a risk factor for head and neck squamous cell carcinoma (HNSC), and it is known that HPV+ and HPV- HNSC have distinct mutational and gene expression profiles. We apply cyclic shift testing to detect and assess the statistical significance of CN differences between HPV+ and HPV- HNSC using data from The Cancer Genome Atlas HNSC cohort. Our approach detects statistically significant CN differences in regions that are known to contain HNSC drivers (7p, 9p21, 11q13, 11q14-qter), as well as regions of chr14, chr16, and others that are less well characterized.

Citation Format: Vonn Walter, Hyo Young Choi, Xiaobei Zhao, Jose Zevallos, D. Neil Hayes. Detecting somatic DNA copy number differences with cyclic shift testing [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5460.

Abstract 5895: Whole-genome characterization of lung adenocarcinomas lacking alterations in RTK/RAS/RAF/MAPK pathway

Lung adenocarcinomas (LUAD) are typically characterized by genetic activation of the receptor tyrosine kinase (RTK)/RAS/RAF/MAP kinase (MAPK) pathway. A minority of LUAD cases (20-25%) lack apparent genetic alterations in this pathway, and thus are ineligible for most targeted therapies. These candidate “oncogene negative” LUADs may harbor novel classes of oncogenic drivers or represent a biologically distinct class of tumors. To characterize the genomic landscape of oncogene-negative LUADs, we nominated 98 cases that were found to lack an activating RTK/RAS/RAF/MAPK pathway alteration in a TCGA study utilizing whole exome sequencing, microarray, and transcriptome data. We profiled these tumors with high-depth whole genome sequencing (WGS), with the goal of identifying noncoding and structural variant driver DNA alterations in both known and novel loci. Of the 98 cases, 20 harbored somatic KRAS mutations that had been missed in the prior WES and transcriptome studies because of insufficient coverage, including 8 cases with the recently targetable p.G12C mutation. 16 samples harbored oncogenic or loss-of-function structural variants in FGFR1, MAPK1, EGFR, NF1, RASA1, ARAF, NTRK2 and NRG1. 5 other samples with SNV or indels in EGFR, ERBB2 and SOS1 were reclassified as oncogene positive. Thus via comprehensive genomic analysis, we confirmed that 57 of the 98 WGS cases did not harbor any detectable alterations in genes encoding any known RTK/RAS/RAF/MAPK members, representing 13% cases chosen as “lung adenocarcinomas” for the TCGA study. Among the 57 confirmed oncogene-negative LUADs, we identified focal deletions targeting the promoter and transcription start site of tumor suppressor genes STK11, KEAP1 and SMARCA4 in 10 samples. Expression and methylation profiling suggested an enrichment of the TP53-deficient phenotype, including cell cycle and FOXM1 deregulation, among the oncogene-negative samples. Moreover, novel promoter mutations associated with increased expression were identified in ILF2, which regulates DNA damage response pathways. Finally, a subset of confirmed oncogene-negative LUADs harbored increased expression of neuroendocrine markers, suggesting that these oncogene-negative samples may either be mis-diagnosed as LUAD or represent LUAD with mixed features of other subtypes of lung cancer; indeed, 14 of the 57 confirmed oncogene-negative cases show histological features of large cell neuroendocrine lung carcinoma. This would suggest that 10% of the cases in this study are both lung adenocarcinoma and “oncogene-negative” to date. Our results provide some of the first comprehensive genomic characterization of oncogene-negative LUADs, implicating TP53 and structural variants in the pathogenesis of this common and difficult to treat entity.

Citation Format: Jian Carrot-Zhang, Siddhartha Devarakonda, Nicolas Robine, Xiaotong Yao, Tiago C. Silva, Jeff Damrauer, Aditya Deshpande, Ming-Sound Tsao, Christina Yao, Chris Wong, Lisui Bao, Hyo Young Choi, Ina Felau, Jean C. Zenklusen, Gordon Robertson, Tuan Trieua, Wei-Wei Liang, Meng Zhou, Esther Rheinbay, Neil Hayes, Ekta Khurana, Li Ding, Peter Laird, Olivier Elemento, John Weinstein, David Kwiatkowski, Chris Benz, Josh Stuart, Lixing Yang, Mauro Castro, William Travis, Katherine Hoadley, Ben Berman, TCGA Analysis Network, Matthew Meyerson, Ramaswamy Govindan, Marcin Imielinski. Whole-genome characterization of lung adenocarcinomas lacking alterations in RTK/RAS/RAF/MAPK pathway [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5895.

Abstract 4273: Identification of RNA-seq shape abnormality

A substantial proportion of human genes differ in function through different forms of shape changes in read coverage of RNA-seq. For example, tumor-suppressor genes lose their function through various changes in expression such as aberrant splicing, frameshift indel, large deletions, or overexpression of noncoding RNAs. Although previous studies have examined mutational effect on such shape changes, it has been observed that a large fraction of shape aberration occurs in the absence of mutations. We hypothesize that read coverage shapes would show rich information on various forms of abnormality in RNA-seq data, which may have been missed in current mutation callers. We have developed a statistical method to systematically detect abnormal RNA-seq samples using read coverage data alone independently of mutational analysis. We model the underlying mechanism possibly generating aberrant shapes by multiple unknown mixture distributions, recasting the problem as high-dimensional latent variables framework. Based on this underlying mechanism, we normalize the read coverage to adjust different library sizes, extract the latent information in a robust way, and determine the cases that are strongly involved in abnormality. This approach allows us to detect not only local changes in expression such as alternative splicing events and frameshift indel but also landscape changes such as fusion and a wide range of deletions. This methodology can be applied genome-widely to detect key genes with strong shape aberrations, prioritizing genes for further investigation. We analyzed 522 TCGA head and neck squamous cell carcinomas RNA-seq tumor samples. At several known tumor-suppressor genes, we identified the cases with novel structural changes including alternative splicing, intragenic deletion, and fusion with/without mutations reported as well as the cases with no evidence of changes despite presence of mutations known for altering shapes. Notably, some of the identified shape changes in TP53 and CDKN2A were confirmed as being the outcomes of missing genetic variants near splice sites (exon-intron junctions). The genome-wide study with carefully chosen significance level provided a set of key genes with strong evidence of shape abnormality including TP53, CDKN2A, and FAT1 that are known for the most alternative splicing events. We also analyzed how often such shape changes arise with or without certain mutations in genome-wide scans. To conclude, our results provide a new statistical framework for various forms of RNA-seq shape changes and a tool for systematic discovery of such abnormal samples, and give insights into mutational effect on shape aberration.

Citation Format: Hyo Young Choi, David N. Hayes, James S. Marron. Identification of RNA-seq shape abnormality [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4273.

Risk of diabetes in viral hepatitis B or C patients compared to that in noninfected individuals in Korea, 2002-2013: A population-based cohort study

While the association between hepatitis C virus (HCV) infection and diabetes has been established, the relationship between hepatitis B virus (HBV) infection and diabetes remains unclear. Therefore, we compared the association between diabetes development in HBV, HCV and co-infected (HBV/HCV) patients to that in noninfected participants using population-based cohort data. We used the National Health Insurance Service-National Sample Cohort, which consists of 514 791 randomly selected persons among those who underwent health check-ups from 2002 to 2003 aged 40-79 years. Adults found to have HBV or HCV infection from 2002 to 2003, without a prior history of diabetes, were selected as subjects. Competing risk regression models were used to estimate cumulative incidence and hazards ratios (HRs) of diabetes development. The cumulative incidences, incidence densities and HRs of diabetes were highest in the co-infected group, followed by those in the HCV-, HBV- and noninfected groups. The 12-year cumulative incidences were as follows: 42.0% in HBV/HCV-, 32.9% in HCV-, 23.9% in HBV- and 18.3% in the noninfected groups. The incidence density per 1000 person-years was 55.0, 51.5, 38.2 and 28.2 for the HBV/HCV-, HCV-, HBV- and noninfected groups, respectively. The adjusted HRs for diabetes were 1.90, 1.68 and 1.41 for the HBV/HCV-, HCV- and HBV-infected groups, respectively. Our findings suggest that both HCV and HBV infections are associated with the development of diabetes; therefore, prevention of, screening for, and treatment of both may reduce the risk of diabetes in these patients.

Comparison of 3D and 2D shear-wave elastography for differentiating benign and malignant breast masses: focus on the diagnostic performance

AIM

To evaluate the diagnostic performance of three-dimensional (3D) image shear-wave elastography (SWE) for differentiating benign from malignant breast masses compared to two-dimensional (2D) SWE and B-mode ultrasound (US).

MATERIALS AND METHODS

This study consisted of 205 breast lesions from 199 patients who underwent B-mode US and SWE before biopsy from January 2014 to March 2016. Quantitative elasticity values (maximum and mean elasticity, Emax and Emean) obtained from 2D and 3D SWE (axial, sagittal, and coronal images) were reviewed retrospectively, in addition to the histopathological findings including immunohistochemistry profiles (luminal A, luminal B, human epidermal growth factor receptor 2 (HER2)-enriched, and triple-negative breast cancer) in cases of malignancy. Histopathological findings were regarded as the reference standard. The diagnostic performance of each data set was evaluated using the area under the receiver operating characteristic (ROC) curve (AUC) analysis to compare sensitivity and specificity.

RESULTS

Among 205 lesions, 105 (51.22%) were malignant and 100 (48.78%) were benign. Compared to benign masses, malignant masses had higher values of Emax and Emean on both 2D and 3D SWE, the differences of which were statistically significant (p<0.001). The AUCs of 2D, 3D axial, and sagittal SWE were significantly higher than that of 3D coronal SWE (p<0.05). In addition, the sensitivities of axial, sagittal, and coronal 3D SWE were all higher than that of 2D SWE for Emean (81.9%, 87.6%, and 89.5% versus 70.5%, respectively, p<0.05). Conversely, the specificity of 2D and 3D axial SWE was higher than that of 3D sagittal and coronal SWE (Emax, 84%, 83% versus 76%, 73%; Emean, 85%, 81% versus 68%, 50%, respectively, p<0.05). We also assessed changes in Breast Imaging-Reporting and Data System (BI-RADS) category 3 and category 4a lesions by adding each of the parameters for 2D and 3D SWE in B-mode US. The specificity, PPV, and accuracy of combined 2D or combined 3D SWE with B-mode US was statistically higher than that of B-mode US alone for differentiating benign and malignant lesions (p<0.05).

CONCLUSIONS

Among SWE images, 2D SWE, and 3D SWE axial and sagittal images exhibited superior diagnostic performance compared to 3D coronal images. Addition of 3D SWE images to B-mode US improved the diagnostic performance for distinguishing benign from malignant masses.

A Study on CYP2C19 and CYP2D6 Polymorphic Effects on Pharmacokinetics and Pharmacodynamics of Amitriptyline in Healthy Koreans

We performed a double-blinded, genotype-based stratification study to explore the pharmacokinetics and pharmacodynamics of amitriptyline according to CYP2C19 and CYP2D6 genotype in Korean subjects. Twenty-four healthy adults were grouped by genotype of CYP2C19 and CYP2D6. After a single dose of 25 mg of amitriptyline, blood samples were collected and anticholinergic effects were measured. The extent of N-demethylation of amitriptyline significantly decreased in subjects carrying two nonfunctional alleles of CYP2C19. The extent of hydroxylation of amitriptyline or nortriptyline was significantly reduced in subjects carrying two CYP2D6 decreased functional alleles compared with those with no or one decreased functional allele. The overall metabolic pathway of amitriptyline was more likely to be dominated by CYP2C19 than CYP2D6. The gene variations of CYP2C19 and CYP2D6 did not change the pharmacodynamic effect. The findings of this study will provide useful information on individualized drug treatment with amitriptyline considering both CYP2D6 and CYP2C19 gene variations.

Compensatory structural and functional adaptation after radical nephrectomy for renal cell carcinoma according to preoperative stage of chronic kidney disease. Choi DK, Jung SB, Park BH, Jeong BC, Seo SI, Jeon SS, Lee HM, Choi HY, Jeon HG.J Urol. 2015 Oct;194(4):910-5. [Epub 2015 Apr 28]. doi: 10.1016/j.juro.2015.04.093

PURPOSE

We investigated structural hypertrophy and functional hyperfiltration as compensatory adaptations after radical nephrectomy in patients with renal cell carcinoma according to the preoperative chronic kidney disease stage.

MATERIALS AND METHODS

We retrospectively identified 543 patients who underwent radical nephrectomy for renal cell carcinoma between 1997 and 2012. Patients were classified according to preoperative glomerular filtration rate as no chronic kidney disease-glomerular filtration rate 90ml/min/1.73m² or greater (230, 42.4%), chronic kidney disease stage II-glomerular filtration rate 60 to less than 90ml/min/1.73m² (227, 41.8%), and chronic kidney disease stage III-glomerular filtration rate 30 to less than 60ml/min/1.73m² (86, 15.8%). Computerized tomography performed within 2 months before surgery and 1 year after surgery was used to assess functional renal volume for measuring the degree of hypertrophy of the remnant kidney, and the preoperative and postoperative glomerular filtration rate per unit volume of functional renal volume was used to calculate the degree of hyperfiltration.

RESULTS

Among all patients (mean age = 56.0y) mean preoperative glomerular filtration rate, functional renal volume, and glomerular filtration rate/functional renal volume were 83.2ml/min/1.73m², 340.6cm³, and 0.25ml/min/1.73m²/cm³, respectively. The percent reduction in glomerular filtration rate was statistically significant according to chronic kidney disease stage (no chronic kidney disease 31.2% vs. stage II 26.5% vs. stage III 12.8%, P<0.001). However, the degree of hypertrophic functional renal volume in the remnant kidney was not statistically significant (no chronic kidney disease 18.5% vs. stage II 17.3% vs. stage III 16.5%, P = 0.250). The change in glomerular filtration rate/functional renal volume was statistically significant (no chronic kidney disease 18.5% vs. stage II 20.1% vs. stage III 45.9%, P<0.001). Factors that increased glomerular filtration rate/functional renal volume above the mean value were body mass index (P = 0.012), diabetes mellitus (P = 0.023), hypertension (P = 0.015), and chronic kidney disease stage (P<0.001).

CONCLUSIONS

Patients with a lower preoperative glomerular filtration rate had a smaller reduction in postoperative renal function than those with a higher preoperative glomerular filtration rate due to greater degrees of functional hyperfiltration.

KRT19 directly interacts with β-catenin/RAC1 complex to regulate NUMB-dependent NOTCH signaling pathway and breast cancer properties

Studies have reported that interactions between keratins (KRTs) and other proteins initiate signaling cascades that regulate cell migration, invasion, and metastasis. In the current study, we found that expression of KRT19 was specifically high in breast cancers and significantly correlated with their invasiveness. Moreover, knockdown of KRT19 led to increased proliferation, migration, invasion, drug resistance, and sphere formation in breast cancer cells via an upregulated NOTCH signaling pathway. This was owing to reduced expression of NUMB, an inhibitory protein of the NOTCH signaling pathway. In addition, we found that KRT19 interacts with β-catenin/RAC1 complex and enhances the nuclear translocation of β-catenin. Concordantly, knockdown of KRT19 suppressed the nuclear translocation of β-catenin as well as β-catenin-mediated NUMB expression. Furthermore, modulation of KRT19-mediated regulation of NUMB and NOTCH1 expression led to the repression of the cancer stem cell properties of breast cancer patient-derived CD133high/CXCR4high/ALDH1high cancer stem-like cells (CSLCs), which showed very low KRT19 and high NOTCH1 expression. Taken together, our study suggests a novel function for KRT19 in the regulation of nuclear import of the β-catenin/RAC1 complex, thus modulating the NUMB-dependent NOTCH signaling pathway in breast cancers and CSLCs, which might bear potential clinical implications for cancer or CSLC treatment.

Population Pharmacokinetic and Pharmacodynamic Modeling Analysis of GCC-4401C, a Novel Direct Factor Xa Inhibitor, in Healthy Volunteers

GCC‐4401C, an orally active direct factor Xa inhibitor that is similar to rivaroxaban, is currently under development for venous thromboembolic disease (VTE). The purpose of this study was to characterize the pharmacokinetics (PKs) and pharmacodynamics (PDs) of GCC‐4401C by population modeling analysis and to predict proper dosage regimens compared to rivaroxaban using data from two phase I clinical studies. Plasma GCC‐4401C concentrations over time were best described by a two‐compartment linear model and body weight was associated with central volume of distribution. Relevant PD markers generally changed in a dose‐dependent manner and were described well with sigmoid, simple maximum effect, or linear models. GCC‐4401C was absorbed more rapidly than rivaroxaban. Comparisons based on simulations of PD marker changes over time suggest that 20 mg and 40 mg of GCC‐4401C administered under fasted status are comparable to 10 mg and 20 mg of rivaroxaban under fed status.

On-scene factors that predict severe injury of patients involved in frontal crashes of passenger cars

PURPOSE

We sought to determine on-scene factors that predict severe injury to the occupants of passenger cars involved in frontal crashes.

METHODS

From January 2011 to December 2014, we collected data from patients who were taken to two emergency centres following a frontal motor vehicle crash. Binomial logistic regression was used to model the effects of occupant characteristics (sex, age, body mass index), vehicle damage (according to the collision deformation classification code), and safety devices on severe injuries (injury severity score >15).

RESULTS

Of 344 subjects, 75 (21.8 %) had severe injuries. Sex, seat belt status, extent of vertical crash, intrusion, and deformation extent (DE) were significantly different between severe and non-severe injuries. After adjusting for confounders, non-use of seat belt tripled the odds of severe injury [odds ratio (OR) 2.7, 95 % confidence interval (CI) 1.461-5.105]. DE ≥4 and intrusion increased the risk of severe injury (OR 2.4, 95 % CI 1.120-5.204 and OR 5.2, 95 % CI 2.525-10.780, respectively). A combination model to predict severe injury using intrusion, seat belt use, and DE ≥4 demonstrated 56.0 % sensitivity, 88.9 % specificity, and 58.4 % positive predictive value (AUC = 0.781, 95 % CI 0.734-0.824).

CONCLUSIONS

For passenger cars involved in a frontal crash, intrusion, unbelted status, and DE ≥4 are good predictors of severe injury. Sequential criteria using vehicle DE, seat belt use, and intrusion can be used by first responders to triage patients involved in a frontal collision.

Metal allergy in eyelid dermatitis and the evaluation of metal contents in eye shadows

BACKGROUND

Allergic contact dermatitis is a common diagnosis in eyelid dermatitis. Sensitization to metals is prevalent in eyelid dermatitis and colour cosmetic products are frequently suspected as the source of metal exposure.

OBJECTIVE

To investigate the contact allergens for eyelid dermatitis and to assess metal contents in eye shadow products.

METHODS

Data were collected in the department of dermatology of Ewha Womans University hospital from December 1998 to February 2014. A total of 983 patients were patch tested during the period and 67 patients had eyelid dermatitis among them. To examine metal elements in colour cosmetic products for eyes, randomly selected 10 eye shadows were analysed.

RESULTS

Frequent allergens were metals, thiomersal and phenylenediamine in patients with eyelid dermatitis. The sensitization rates of individual allergens were not significantly different between patients with eyelid dermatitis and without eyelid dermatitis. All 10 eye shadow products contained more than 5 ppm of at least one element, nickel, cobalt or chromium.

CONCLUSION

Metals were top-rank allergens in patients with eyelid dermatitis as in the remaining patients patch tested. The eye shadow products contained significant amount of nickel, cobalt or chromium to elicit allergic reactions.

Population-based epidemiology of primary biliary cirrhosis in South Korea

BACKGROUND

As a rare disease, only a few population-based epidemiology studies of primary biliary cirrhosis (PBC) have been reported.

AIMS

To elucidate the nationwide prevalence, incidence, complications, fatality and direct medical costs of PBC in South Korea.

METHODS

The nationwide Health Insurance Review and Assessment Service claims data and Rare Intractable Disease registration data on PBC, identified with the International Classification of Diseases (ICD) 10 code of K74.3, were obtained from 2009 to 2013. Age- and gender-specific prevalence and incidence rates of PBC were calculated, and data on complications, comorbidities, prescribed drugs, therapeutic procedures and direct medical costs were analysed.

RESULTS

A total of 2824 patients over 20 years old with PBC were identified in 2009-2013 (female-to-male ratio 6.2, median age 57 years old). The average age- and sex-adjusted incidence from 2011 to 2013 was 8.57 per million per year, and the average age- and sex-adjusted prevalence from 2009 to 2013 was 47.50 per million population. About 10% of patients presented with complications such as ascites (10.3%), variceal bleeding (5.8%) and/or hepatocellular carcinoma (HCC) (1.3%). Liver transplantation was undertaken in 71 patients (2.5%) for 5 years. Case fatality was 2.2% and the transplantation-free survival was 95.4% for 5 years.

CONCLUSIONS

This is the first report on the nationwide epidemiology of primary biliary cirrhosis in South Korea, demonstrating lower incidence and prevalence rates than those of Western countries, but a considerable disease burden, representing at least 10% were complicated with decompensated cirrhosis or hepatocellular carcinoma requiring liver transplantation.

Investigation of the magnetic properties in double perovskite R2CoMnO6 single crystals (R = rare earth: La to Lu)

We have successfully synthesized the series of the double-perovskite R2CoMnO6 (R  =  rare earth: La to Lu) single crystals and have investigated their magnetic properties. The ferromagnetic order of Co(2+)/Mn(4+) spins emerges mainly along the c axis. Upon decreasing the size of rare earth ion, the magnetic transition temperature decreases linearly from 204 K for La2CoMnO6 to 48 K for Lu2CoMnO6, along with the enhancement of monoclinic distortion. The temperature and magnetic-field dependences of magnetization reveal the various magnetic characteristics such as the metamagnetic transition in R  =  Eu, the isotropic nature of rare earth moment in R  =  Gd, and the reversal of magnetic anisotropy in R  =  Tb and Dy. Our results offer comprehensive information for understanding the roles of mixed-valent magnetic ions and rare earth magnetic moments on the magnetic properties.

Nodular Fasciitis of the Breast: A Case and Literature Review

Nodular fasciitis is a benign fibroblastic proliferation in soft tissue that is most commonly found in the upper extremities, trunk, head, and neck region. Its occurrence in the breast has been rarely reported. The most characteristic features are the sudden appearance and rapid growth of a palpable lesion. Nodular fasciitis can clinically, radiologically, and histopathologically mimic a breast carcinoma. We present a case of nodular fasciitis of the breast and a review of the relevant literature.

Association of glypican-4 with body fat distribution, insulin resistance, and nonalcoholic fatty liver disease

CONTEXT AND OBJECTIVE

Glypican-4 was identified as a novel adipokine capable of enhancing insulin signaling and modulating adipocyte differentiation. We investigated associations between glypican-4 and body composition, insulin resistance, arterial stiffness, and nonalcoholic fatty liver disease (NAFLD) in nondiabetic Asian subjects.

DESIGN AND PARTICIPANTS

We analyzed baseline cross-sectional data from the Korean Sarcopenic Obesity Study, an ongoing prospective cohort study. NAFLD was diagnosed by unenhanced computed tomography using the liver attenuation index. We also examined the effects of a 3-month combined aerobic and resistance exercise program on glypican-4 levels and cardiometabolic risk factors.

RESULTS

Circulating glypican-4 levels were higher in men than in women (1.83 [1.19, 2.78] ng/mL vs 1.17 [0.66, 2.00] ng/mL, P < .001) and had a significant positive relationship with the waist-to-hip ratio (WHR) (r = 0.20, P = .014) and the ratio of visceral to sc fat area (r = 0.30, P < .001). Furthermore, glypican-4 levels in women were correlated with cardiometabolic risk factors, including insulin resistance and arterial stiffness, and were independently associated with NAFLD by multiple logistic regression analysis (P = .017, R² = 0.33). The 3-month combined exercise training program significantly improved several cardiometabolic parameters and reduced retinol binding protein-4 levels. Changes in glypican-4 levels after the exercise program were significantly different between subjects with an increased WHR compared with those with a decreased WHR (P = .034).

CONCLUSION

A gender-based difference in circulating glypican-4 levels was apparent as these were increased in women with NAFLD and related to body fat distribution, insulin resistance, and arterial stiffness.

Change in cytokines in patients with warts after contact immunotherapy with squaric acid dibutylester

BACKGROUND

A wart is a skin lesion caused by infection with human papillomavirus (HPV). Contact immunotherapy is one of the many therapeutic options that have been used to treat warts; however, the effectiveness of contact immunotherapy differs from patient to patient, and the cause of this variation in clinical response is unclear.

AIM

To assess cytokine changes in patients after contact immunotherapy with squaric acid dibutylester (SADBE).

METHODS

In total, 21 patients with warts and 9 healthy control subjects were enrolled in the study. The frequencies of CD3+ T cells expressing interleukin (IL)-4, IL-10, IL-12, tumour necrosis factor-α and interferon-γ were measured by flow cytometry analysis of peripheral blood at baseline in both patients and controls, and after SADBE treatment in patients.

RESULTS

Lower expression of IL-4 and higher expression of IL-12 in CD3+ T cells were found in patients compared with controls. The percentage of CD3+/IL-4+ T cells significantly increased after contact immunotherapy in all responders, but was significantly higher in those with an excellent response, who also had a significantly higher percentage of CD3+/IL-10+ T cells. The patients with an excellent response also had a significant decrease in the percentage of CD3+/IL-12+ T cells, and the percentage of CD3+/IL-4+ T cells normalized.

CONCLUSIONS

Response to contact immunotherapy can vary depending on the types of cytokine changes produced by treatment. An excessive shift to a Th2 pattern and increased IL-10 production after contact immunotherapy may hinder clearance of HPV.

Erythrocyte sedimentation rate and anaemia are independent predictors of survival in patients with clear cell renal cell carcinoma

Background:

The 1997 international consensus conference on renal cell cancer (RCC) prognosis suggested erythrocyte sedimentation rate (ESR), alkaline phosphatase (ALP), and anaemia as prognostic biomarkers, but most studies reviewed were limited by small sample sizes.

Methods:

The Cox proportional hazards model was used to evaluate whether ESR, ALP, haemoglobin (Hb), and haematocrit (Hct) could predict survival outcomes in 1307 patients with clear cell RCC (ccRCC) who underwent nephrectomy during 1994–2008.

Results:

During a median follow-up of 43 months, we found that the patients with preoperative high levels of ESR, had a 2.10-fold (95% confidence interval (CI): 1.21–3.67) greater risk of dying from RCC compared with patients with low levels (normal range). Patients with preoperative anaemia, assessed by Hb and Hct, had a 3.11-fold (95% CI: 1.17–8.25) and 6.20-fold (95% CI: 2.30–16.72) greater risk of dying from other illnesses, respectively, compared with patients without anaemia. ALP levels were not associated with ccRCC patients' survival. These associations for ESR and anaemia were more pronounced in patients with body mass index (BMI) <25 compared with patients with BMI ⩾25 kg m⁻².

Conclusion:

Preoperative high ESR, but not ALP, was a significant predictor for cancer-specific survival among ccRCC patients. Anaemia increases the risk of death from other illness.

Efficacy of vasectomy reversal according to patency for the surgical treatment of postvasectomy pain syndrome

This study was conducted to assess outcomes (according to patency) of vasectomy reversal (VR) in qualified patients with postvasectomy pain syndrome (PVPS). A total of 32 patients with PVPS undergoing VR between January 2000 and May 2010 were examined retrospectively. Of these, 68.8% (22/32) completed a study questionnaire, either onsite at the outpatient clinic or via telephone interview. Preoperative clinical findings, preoperative and postoperative visual analogue scale (VAS) pain scores, patency and pregnancy rate and overall patient satisfaction were analyzed. For the latter, a four-point rating of (1) cure, (2) improvement, (3) no change or (4) recurrence was used. The mean age was 45.09±4.42 years and the mean period of follow-up was 3.22 years (0.74-7.41). Patency rates were 68.2% (15/22) and pregnancy rates were 36.4% (8/22). The mean VAS was 6.64±1.00 preoperatively and 1.14±0.71 postoperatively (P<0.001). The difference in the mean preoperative and postoperative VAS was 6.00±1.25 (4-8) in the patency group and 4.43±0.98 (3-6) in the no patency group (P=0.011). A significant difference in procedural satisfaction with surgical outcome was observed between patency and no patency groups (P=0.014). In conclusion, in PVPS patients requiring VR, a significant difference was observed between the patency and no patency groups in terms of pain reduction and the degree of patient procedural satisfaction.

Contrast-enhanced MR cholangiography: comparison of Gd-EOB-DTPA and Mn-DPDP in healthy volunteers

OBJECTIVE

The purpose of this study was to compare the biliary enhancement dynamics of gadolinium-ethoxybenzyl-diethylenetriamine-pentaacetic-acid (Gd-EOB-DTPA) and mangafodipir trisodium (Mn-DPDP) for contrast-enhanced MR cholangiography (MRC) in healthy subjects.

METHODS

15 healthy volunteers underwent MRI at 1.5 T with volumetric interpolated breath-hold examination sequence. Each volunteer was scanned once for each contrast agent. The signal-to-noise ratio (SNR) of the liver parenchyma and common hepatic duct (CHD) and the contrast-to-noise ratio (CNR) of CHD to liver parenchyma were evaluated and compared before and at several time points (5, 15, 30, 45, 60, 90, and 120 min) after injection of each agent.

RESULTS

SNR was significantly higher for Gd-EOB-DTPA than for Mn-DPDP in liver parenchyma after 5 min and in CHD after 15 min (p<0.05). CNR of CHD to liver parenchyma using Gd-EOB-DTPA showed an initial decrease at 5 min post-injection followed by a steep increase to a peak at 15 min post-injection. CNR using Mn-DPDP showed a steady increase to a peak at 15 min post-injection without an initial decrease. At 15 min, the value of CNR was significantly higher for Gd-EOB-DTPA than for Mn-DPDP (p<0.05).

CONCLUSION

For both contrast agents, CNR reached a peak at 15 min after contrast injection. At this time point, CNR of Gd-EOB-DTPA was significantly higher than that of Mn-DPDP. Therefore, Gd-EOB-DTPA may provide better contrast-enhanced MRC than Mn-DPDP at 15 min after contrast administration.

Serum selenoprotein P levels in patients with type 2 diabetes and prediabetes: implications for insulin resistance, inflammation, and atherosclerosis

CONTEXT AND OBJECTIVE

The dysregulation of hepatokines may be associated with the pathogenesis of insulin resistance and type 2 diabetes. A recent study has suggested that selenoprotein P (SeP), a novel hepatokine, may play a role in the regulation of glucose metabolism and insulin sensitivity. We examined the relationship between circulating SeP levels and clinical parameters associated with insulin resistance in humans.

PARTICIPANTS AND METHODS

We compared serum SeP concentrations in 100 subjects with diverse glucose tolerance statuses. Furthermore, we evaluated the relationship between SeP and cardiometabolic risk factors including insulin resistance, high-sensitivity C-reactive protein, and carotid intima-media thickness.

RESULTS

Serum SeP concentrations were significantly higher in patients with type 2 diabetes or prediabetes than those with normal glucose tolerance (all P < 0.01) and decreased in a stepwise manner [1032.4 (495.9-2149.4) vs. 867.3 (516.3-1582.7) vs. 362.0 (252.5-694.5), P = 0.004]. In addition, overweight and obese subjects had significantly increased SeP levels compared with lean subjects (P = 0.002). Spearman's partial correlation analysis adjusted for age and gender showed a significant relationship between SeP and cardiometabolic factors including body mass index, waist circumference, systolic blood pressure, triglycerides, glucose, hemoglobin A1c, aspartate aminotransferase, and insulin resistance. Furthermore, in multiple regression analyses, SeP showed an independent association with carotid intima-media thickness as well as high-sensitivity C-reactive protein, even after adjustment for other confounding factors.

CONCLUSIONS

Circulating SeP concentrations were elevated in patients with glucose metabolism dysregulation and were related to various cardiometabolic parameters including insulin resistance, inflammation, and atherosclerosis.

Effect of warfarin withdrawal on thrombolytic treatment in patients with ischaemic stroke

BACKGROUND AND PURPOSE

  Abruptly discontinuing warfarin may induce a rebound prothrombotic state. Thrombolytic agents may also paradoxically induce prothrombotic conditions, which include platelet activation and thrombin generation. Therefore, prothrombotic states may be enhanced by withdrawing warfarin in patients under thrombolytic treatment. This study was aimed to determine whether patients with warfarin withdrawal have different clinical outcomes from those without warfarin use after thrombolytic treatment.

METHODS

  A total of 148 consecutive patients with atrial fibrillation who were not on anticoagulants at admission and who received thrombolysis were included in this study. We compared the outcomes between a warfarin withdrawal group and a no-warfarin group.

RESULTS

  Fourteen patients (9.5%) were included in the warfarin withdrawal group. Although baseline National Institute of Health Stroke Scale (NIHSS) scores, recanalization rates, and hemorrhage frequencies did not differ between the groups, the warfarin withdrawal group showed poorer outcomes. Increased NIHSS scores during the first 7days were more frequent in the warfarin withdrawal group (57.1% vs. 26.9%, P=0.029). The median percent improvement in NIHSS scores at 24h after thrombolysis was also lower in the warfarin withdrawal group. After adjusting for covariates, warfarin withdrawal was a strong predictor of poor functional outcome at 3months (modified Rankin score≥3) (odds ratio, 17.067, 95% CI 2.703-107.748).

CONCLUSIONS

  Discontinuing warfarin was associated with early neurologic deterioration and poor long-term outcomes after thrombolytic treatment.

Curcumin interrupts the interaction between the androgen receptor and Wnt/β-catenin signaling pathway in LNCaP prostate cancer cells

Recently, studies have investigated the significance of the Wnt/β-catenin pathway in prostate cancer. The transcriptional activity of the androgen receptor (AR) is modulated by interaction with coregulators, one of which is β-catenin. Curcumin, a dietary yellow pigment of Curcuma longa, has emerged as having a chemopreventive role. Although curcumin has been shown to inhibit AR expression, its molecular mechanism has not been fully elucidated. In this study, whether curcumin mediates the Wnt/β-catenin signaling pathway with regard to AR/β-catenin interactions was studied. Curcumin was shown to induce significant inhibition of AR expression in a dose-dependent manner. Marked curcumin-induced suppression of β-catenin was shown in the nuclear and cytoplasmic extracts as well as whole cell lysates. Further analysis revealed that phosphorylation of Akt and glycogen synthase kinase-3β were attenuated, but phosphorylated β-catenin was increased after curcumin treatment. Finally, cyclin D1 and c-myc, the target gene of the β-catenin/T-cell factor transcriptional complex, were also decreased. These findings suggest that curcumin modulates the Wnt/β-catenin signaling pathway and might have a significant role in mediating inhibitory effects on LNCaP prostate cancer cells.

Optical performance monitoring technique using asynchronous amplitude and phase histograms

We report a new optical performance monitoring technique based on the amplitude and phase histograms of the optical signal. The amplitude and phase histograms are obtained by using an intradyne receiver and the asynchronous delay-tap sampling method. From these histograms, we can evaluate the amplitude and phase Q-factors of the optical signal regardless of its modulation format. In addition, by using these Q-factors, we can estimate the bit-error rate (BER) of the monitoring signal.

Electronic Raman scattering of two-band superconductors: a time-dependent Landau-Ginzburg theory approach

Electronic Raman scattering of two-band superconductors is studied based on the time-dependent Landau-Ginzburg theory. The focus is on the possible features of the π phase shift between the two superconducting order parameters which may be realized in the Fe-pnictides. The Raman response was computed up to the Gaussian fluctuations in the functional integral formalism including the long range Coulomb interaction with the four channels of symmetric and antisymmetric combinations of the phases and amplitudes of the two order parameters. The Raman spectra is found to be composed of the quasiparticle and the phase collective mode contributions without mixing between them. The contributions from the quasiparticle and the symmetric phase collective mode (the Anderson-Bogolyubov mode) are similar to the two-band superconductors without the π phase shift. The antisymmetric phase mode (the Leggett mode) originates from the fluctuations of the relative phase of the two order parameters. It lies between twice the smaller gap and twice the larger gap and is damped by the quasiparticles. However, this mode is eliminated by the long range Coulomb interaction in the zero-wavenumber limit.

Transmission of 108-Gb/s PDM 16ADPSK signal on 25-GHz grid using non-coherent receivers

We demonstrate the transmission of 108-Gb/s polarization-division-multiplexed (PDM) 16-ary amplitude- and differential phase-shift-keying (16ADPSK) signal by using a non-coherent receiver. We generate the 16ADPSK signal by using a differential 8-ary phase-shift-keying (D8PSK) modulator and a phase-distortion-free amplitude-shift-keying (ASK) modulator. On the other hand, the receiver is implemented by using a delay interferometer based on a 3x3 fiber coupler and the data-aided phase-noise estimation (DAPNE) algorithm. By using these transmitter and receiver, we achieve a nearly quantum-limited receiver sensitivity in the back-to-back condition. In addition, we examine the possibility of transmitting 108-Gb/s signals on a 25-GHz grid without using the coherent detection technology. The results show that we can secure a sufficient optical-signal-to-noise (OSNR) margin after the transmission of 80-km long dispersion managed link. The achieved spectral efficiency is 4.0 bit/s/Hz.

Neurosurgical aspects of sedimentation levels in acute intracerebral haematoma

We describe the neurosurgical aspects of sedimentation levels that are rarely found in acute intracerebral haematomas (ICH). We had four patients with acute ICH whose cerebral computed tomography revealed sedimentation levels. Two patients had received thrombolytic therapy for ischaemic heart disease and one for ischaemic stroke. Another patient, who was diagnosed later as having a coagulation disorder, did not have any medical history on admission. All patients had emergency ICH drainage under local anaesthesia. In the immediate postoperative period, we observed dramatic improvement in all the patients, without surgical complications. The sedimentation level in an ICH should be identified as a specific indicator of a coagulation defect and a thorough search for possible underlying coagulopathy is warranted. We believe that simple ICH drainage should be performed as the haematoma is in a liquid form.

Thrombus volume comparison between patients with and without hyperattenuated artery sign on CT

BACKGROUND AND PURPOSE

Although the hyperattenuated middle cerebral artery sign is known to be related to acute infarction, the volume of clot associated with it is not known. We investigated whether the presence or absence of hyperattenuated artery sign (HAS) on noncontrast CT (NCCT) can predict the thrombus volume.

MATERIALS AND METHODS

We enrolled 90 consecutive patients with acute infarction who underwent both 5- and 1.25-mm NCCT and CT angiography (CTA). HAS was determined on 5-mm NCCT retrospectively. According to the location of thrombi, the patients were classified into ICA (ICA terminus/ICA and others), M1 (M1/both M1 and M2), and M2 (M2) groups. Thrombus volumes were measured by 1.25-mm NCCT and were compared between patients with and without HAS.

RESULTS

Occlusion of major arteries was seen on CTA in 78 patients. HAS was found in 46 patients (59.0%). The mean thrombus volume was significantly larger in patients with HAS than in those without except for the M2 group (ICA group: [n = 14], 188.7 +/- 122.5 mm(3) versus 39.4 +/- 12.1 mm(3) [P = .022]; M1 group: [n = 42], 128.1 +/- 119.2 versus 56.8 +/- 32.5 [P = .005]; M2 group: [n = 22], 34.7 +/- 32.2 versus 20.0 +/- 20.0 [P = .18]). Thrombus volumes determined by receiver operating characteristic curve analysis were 52.36 mm(3) in the ICA group (sensitivity, 90.9%; specificity, 100%) and 53.96 mm(3) in the M1 group (sensitivity, 88.0%; specificity, 58.8%).

CONCLUSION

Thrombus volumes were significantly larger in patients with HAS than in those without in ICA and M1 occlusions. The detection of HAS may provide an idea concerning rapid and dichotomized estimation of thrombus volume, which may be helpful for treatment decisions in potential candidates for thrombolysis.

Podocyte biology in diabetic nephropathy

Glomerular visceral epithelial cells, namely podocytes, are highly specialized cells and give rise to primary processes, secondary processes, and finally foot processes. The foot processes of neighboring podocytes interdigitate, leaving between them filtration slits. These are bridged by an extracellular substance, known as the slit diaphragm, which plays a major role in establishing size-selective barrier to protein loss. Furthermore, podocytes are known to synthesize matrix molecules to the glomerular basement membrane (GBM), including type IV collagen, laminin, entactin, and agrin. Because diabetic nephropathy is clinically characterized by proteinuria and pathologically by glomerular hypertrophy and GBM thickening with foot process effacement, podocytes have been the focus in the field of research on diabetic nephropathy. As a result, many investigations have demonstrated that the diabetic milieu per se, hemodynamic changes, and local growth factors such as transforming growth factor-beta and angiotensin II, which are considered mediators in the pathogenesis of diabetic nephropathy, induce directly and/or indirectly hypertrophy, apoptosis, and structural changes, and increase type IV collagen synthesis in podocytes. This review explores some of the structural and functional changes of podocytes under diabetic conditions and their role in the development and progression of diabetic nephropathy.

Simultaneous monitoring technique for ASE and MPI noises in distributed Raman Amplified Systems

We develop a new technique for simultaneously monitoring the amplified spontaneous emission (ASE) and multi-path interference (MPI) noises in distributed Raman amplified (DRA) systems. This technique utilizes the facts that the degree-of polarization (DOP) of the MPI noise is 1/9, while the ASE noise is unpolarized. The results show that the proposed technique can accurately monitor both of these noises regardless of the bit rates, modulation formats, and optical signal-to-noise ratio (OSNR) levels of the signals.