Abstract 1980: Integrating common and rare genetic variants to predict cancer risks in diverse populations

Inherited germline genetic factors contribute substantially to cancer risk. Large-scale DNA-Sequencing (DNA-Seq) studies have identified rare pathogenic variants in 5~10% of adult cancer cases, while genome-wide association studies (GWAS) have revealed hundreds of common variants that require aggregation using polygenic risk scores (PRS). However, rare and common genetic variants are often assessed separately and prohibit accurate risk assessments. Here, we developed methods to combine common and rare variants for improved cancer risk predictions using the diverse Mount Sinai BioMe population cohort of 49,854 individuals, including 22% African Americans, 1.9% Asian, 34% Latinx/Hispanic, 32% Europeans, and 11% of Other self-reported ancestries. By linking and analyzing EHR data, we identified over 4,000 cancer cases and another 815 individuals with family history, and analyzed 14 solid tumor types with at least 50 cases with pass-QC whole-exome sequencing (WES) data. The landscape of pathogenic variants differs across ancestries and highlighted multiple founder variants, while PRSs predict cancer risks in major cancer types across different ancestries. Notably, we detect significant interactions of common and rare genetic variants contributing to risks of selected cancer types. Machine learning models that combine both common and rare variants show higher predictive accuracy than using common or rare variants alone. Overall, our study underscores the importance of jointly considering common and rare genetic factors to provide accurate cancer risk assessment for diverse individuals.

Citation Format: Abdulkadir Elmas, Hannah Kittrell, Kuan-lin Huang. Integrating common and rare genetic variants to predict cancer risks in diverse populations [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 1980.

Abstract 6540: Multiscale protein networks: de novo aberrant protein interactions and oncogenic regulators in seven cancer types

We conducted integrative proteomic network analyses of 687 cases across 7 cancer types including breast cancer (115 tumor samples), clear cell renal carcinoma (100 tumor samples), colorectal cancer (91 tumor samples), hepatocellular carcinoma (101 tumor samples), lung adenocarcinoma (104 tumor samples), stomach adenocarcinoma (80 tumor samples), and uterine corpus endometrial carcinoma (96 tumor samples). Using Multi-scale embedded gene co-expression network analysis (MEGENA), we constructed co-expression protein network for each cancer type, and interrogated the network topology and co-expressed protein modules. For each cancer type, we identified disease-associated pathways as co-expressed protein modules enriched for differentially expressed proteins in tumor. Comparing with respective cancer transcriptome network models, this systematically revealed proteome-specific cancer subnetworks associated with heme metabolism, DNA repair, spliceosome, oxidative phosphorylation and KRAS oncogenic signaling pahways in several cancer types. Cross-cancer comparison identified highly preserved protein modules showing robust pan-cancer interactions and identified endoplasmic reticulum-associated degradation (ERAD) and N-acetyltransferase activity as the central functional axes. Then, we utilized these network models to predict pan-cancer protein network regulators in the up-stream of disease-associated pathways. The predicted pan-cancer regulators were experimentally validated by loss-of-function to confer anti-tumor effects in diverse cancer types: lung (H847), colon (HCT116), fetal kidney (HEK293T) and breast (MDA-MB-231) cancer cells. Overall, the study was designed to provide tractable network models of cancer proteome, and unlock the further potentials to understand oncogenic regulators and mechanisms in different cancer types.

Citation Format: Won Min Song, Abdulkadir Elmas, Richard Farias, Peng Xu, Xianxiao Zhou, Benjamin Hopkins, Kuan-lin Huang, Bin Zhang. Multiscale protein networks: de novo aberrant protein interactions and oncogenic regulators in seven cancer types [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 6540.

Abstract A47: Characterization of immune cell composition across cancer types in pan-cancer genomic cohorts

Introduction: Identifying immune cell signatures in individual tumors can help guide treatment selection for patients. Numerous deconvolution methods have been developed to estimate immune cell fractions from bulk gene expression data, but they have yet to be systematically applied and cross-validated in pan-cancer genomic cohorts. We undertook this study to cross-validate immune cell quantification methods across 25 cancer types spanning 11,011 samples and provide a public immuno-oncology resource. Methods: Using gene expression data from both The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), we employed and compared six methods to estimate immune cell fractions in each cancer type (CIBERSORT, quanTIseq, EPIC, TIMER, MCP-counter, xCell; immunedeconv R package). We mapped these results to a common vocabulary of five broad cell categories for comparison: T cells, B cells, natural killer cells (NK cells), macrophages/monocytes, and myeloid dendritic cells (mDCs). In parallel, we computed immune cell proportions for seven cancer types using single-cell RNA-seq (scRNA-seq) data from a single-cell tumor immune atlas of 217 patients. We correlated the median immune cell fractions estimated from bulk deconvolution with scRNA-seq proportions for each cancer type. To demonstrate the application of this resource, we compared the immune cell fractions (1) in adjacent normal versus tumor tissues, and (2) in head and neck squamous cell carcinoma (HNSC) and colorectal adenocarcinoma (COAD) tumor subtypes using multivariable linear regression adjusted for age and sex. Results: Overall, 9,689 TCGA samples and 1,322 ICGC samples were analyzed, and correlations across six deconvolution tools were performed. Two well-performing cell estimation methods, EPIC and quanTIseq, demonstrated good correlation between median deconvoluted T cell enrichment score and single-cell cytotoxic CD8+ T cell populations (spearman coefficient; EPIC = 0.71, quanTIseq = 0.43). However, cross-cancer type correlations between scRNA-seq and bulk estimated fractions were not statistically significant for most cancer types. In multivariable regression comparing immune cell estimates across cancer subtypes, we found increased T cell (EPIC: OR=1.65, 95% CI = 1.23-2.21, quanTIseq: OR = 1.30, 95% CI = 1.20-1.40) and B cell (EPIC: OR = 2.92, 95% CI = 2.05-4.15, quanTIseq: OR = 1.48, 95% CI = 1.37-1.60) enrichment in HPV-positive compared to HPV-negative HNSC. In COAD, we found increased T cell enrichment in the microsatellite instability (MSI) subtype compared to the genome stable subtype (OR = 1.16, 95% CI = 1.01-1.33). Conclusion: Overall, our study provides a public resource of immune cell annotations for two widely used, pan-cancer genomics cohorts and can facilitate future studies that aim to characterize the tumor immune microenvironment. Furthermore, we validated the use of this resource by demonstrating enrichment of specific immune cell subsets in HNSC and COAD subtypes, consistent with prior reports of these well-characterized cancers.

Citation Format: Makda Getachew Zewde, Daniel Fulop, Alexander Tsankov, Kuan-lin Huang. Characterization of immune cell composition across cancer types in pan-cancer genomic cohorts [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy; 2022 Oct 21-24; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2022;10(12 Suppl):Abstract nr A47.

Analysis of germline-driven ancestry-associated gene expression in cancers

Differential mRNA expression between ancestry groups can be explained by both genetic and environmental factors. We outline a computational workflow to determine the extent to which germline genetic variation explains cancer-specific molecular differences across ancestry groups. Using multi-omics datasets from The Cancer Genome Atlas (TCGA), we enumerate ancestry-informative markers colocalized with cancer-type-specific expression quantitative trait loci (e-QTLs) at ancestry-associated genes. This approach is generalizable to other settings with paired germline genotyping and mRNA expression data for a multi-ethnic cohort.

For complete details on the use and execution of this protocol, please refer to Carrot-Zhang et al. (2020), Robertson et al. (2021), and Sayaman et al. (2021).

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Protocol for obtaining controlled access TCGA datasets

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Protocols for quality control analysis and genotype imputation of TCGA germline data

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Statistical analysis for determining ancestry-associated SNPs

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Determination of ancestry-associated germline genetic variation driving mRNA expression

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Multiethnic Investigation of Risk and Immune Determinants of COVID-19 Outcomes

Background

Disparate COVID-19 outcomes have been observed between Hispanic, non-Hispanic Black, and White patients. The underlying causes for these disparities are not fully understood.

Methods

This was a retrospective study utilizing electronic medical record data from five hospitals within a single academic health system based in New York City. Multivariable logistic regression models were used to identify demographic, clinical, and lab values associated with in-hospital mortality.

Results

A total of 3,086 adult patients with self-reported race/ethnicity information presenting to the emergency department and hospitalized with COVID-19 up to April 13, 2020, were included in this study. While older age (multivariable odds ratio (OR) 1.06, 95% CI 1.05–1.07) and baseline hypoxia (multivariable OR 2.71, 95% CI 2.17–3.36) were associated with increased mortality overall and across all races/ethnicities, non-Hispanic Black (median age 67, interquartile range (IQR) 58–76) and Hispanic (median age 63, IQR 50–74) patients were younger and had different comorbidity profiles as compared to non-Hispanic White patients (median age 73, IQR 62–84; p < 0.05 for both comparisons). Among inflammatory markers associated with COVID-19 mortality, there was a significant interaction between the non-Hispanic Black population and interleukin-1-beta (interaction p-value 0.04).

Conclusions

This analysis of a multiethnic cohort highlights the need for inclusion and consideration of diverse populations in ongoing COVID-19 trials targeting inflammatory cytokines.

Abstract 5692: Tissue specificity of chromosome aneuploidy correlates with BRCA-associated cancer risk

Pathogenic germline variants of BRCA1 and BRCA2 disproportionally elevated the risk of specific cancer types (ex. breast [BRCA] and ovarian [OV] cancer) compared to tumors arising from other tissues. The reason underlying the strong tissue-specificity for BRCA-associated cancer risk remains largely unknown. Under the two-hit hypothesis, BRCA-mediated oncogenesis is thought to originate from a cell where the germline BRCA1/2 variant underwent loss of heterozygosity (LOH) of the wildtype BRCA allele, resulting in homologous recombination DNA repair deficiencies. Notably, tumor aneuploidy and loss of chromosome arms also show strong tissue specificity across cancer types. The apparent tissue specificities of BRCA-associated cancer risk and chromosome aneuploidy, together with deletion-induced LOH underlying the two-hit hypothesis, pose an intriguing possibility that they may be linked. Using genomic data from the TCGA PanCanAtlas and ICGC PCAWG projects, we calculated the frequencies of deletions of the chromosomal arms where the BRCA1/2 genes are located (17q for BRCA1; 13q for BRCA2) across different cancer types in tumors with no whole-genome doublings (WGD). Among TCGA cases, OV and BRCA showed significantly higher frequencies of 17q deletion (32.75% and 8.05%, respectively) than other cancer types (ranked 2/30 and 5/30, permutation p-value = 0.030 and 0.024), and relatively higher frequencies of 13q deletion (32.75% and 21.92%, respectively) compared to other cancers (ranked 5/32 and 8/32, p-value = 0.101 and 0.078). As expected, cancer types showing high fractions of BRCA1/2 deletions overlap with those showing 17q/13q deletions and often include BRCA and OV. Subsequently, we determined how often BRCA1/2 deletion co-occurred and thus may be caused by the corresponding 17q/13q deletions, showing that BRCA1 deletion carriers who also had chr17q deletion accounted for 40.76% in OV and 25.93% in BRCA patients, compared to 33.33% in all other cancer types while BRCA2 deletion carriers who also had chr13q deletion accounted for OV (53.97%) and BRCA (58.60%) patients, compared to 49.83% in all other cancer types. In addition, we validated our findings in non-overlapping cases of the ICGC PCAWG projects. Consistent with TCGA results, OV and BRCA showed higher frequencies of 17q and 13q deletion compared to other cancer types. To conclude, we identified a correlation between cross-cancer difference in arm-level and focal chromosome aneuploidy affecting BRCA1/2 and BRCA-associated cancer risk, and how chromosome aneuploid may give rise to tissue-specific risks of cancer remain to be investigated.

Citation Format: Xinfeng Wang, Tomi Jun, Nan Sun, Jie He, Kuan-lin Huang. Tissue specificity of chromosome aneuploidy correlates with BRCA-associated cancer risk [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 5692.

Proteomic Analyses Identify Therapeutic Targets in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is the fourth cause of cancer-related mortality worldwide. While many targeted therapies have been developed, the majority of HCC tumors do not harbor clinically actionable mutations. Protein-level aberrations, especially those not evident at the genomic level, present therapeutic opportunities but have rarely been systematically characterized in HCC. In this study, we performed proteogenomic analyses of 260 primary tumors from two HBV-related HCC patient cohorts with global mass-spectrometry (MS) proteomics data. Combining tumor-normal and inter-tumor analyses, we identified overexpressed targets including PDGFRB, FGFR4, ERBB2/3, CDK6 kinases and MFAP5, HMCN1, and Hsp proteins in HCC, many of which showed low frequencies of genomic and/or transcriptomic aberrations. Protein expression of FGFR4 kinase and Hsp proteins were significantly associated with response to their corresponding inhibitors. Our results provide a catalog of protein targets in HCC and demonstrate the potential of proteomics approaches in advancing precision medicine in cancer types lacking druggable mutations.

Multi-ethnic Investigation of Risk and Immune Determinants of COVID-19 Outcomes.. [PMID: 35350196 PMCID: PMC8963691 DOI: 10.21203/rs.3.rs-1055587/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Background:

Disparate COVID-19 outcomes have been observed between Hispanic, Non-Hispanic Black, and White patients. The underlying causes for these disparities are not fully understood.

Methods:

This was a retrospective study utilizing electronic medical record data from five hospitals within a single academic health system based in New York City. Multivariable logistic regression models were used to identify demographic, clinical, and lab values associated with in-hospital mortality.

Results:

3,086 adult patients with self-reported race/ethnicity information presenting to the emergency department and hospitalized with COVID-19 up to April 13, 2020 were included in this study. While older age (multivariable OR 1.06, 95% CI 1.05-1.07) and baseline hypoxia (multivariable OR 2.71, 95% CI 2.17-3.36) were associated with increased mortality overall and across all races/ethnicities, Non-Hispanic Black (median age 67, IQR 58-76) and Hispanic (median age 63, IQR 50-74) patients were younger and had different comorbidity profiles compared to Non-Hispanic White patients (median age 73, IQR 62-84; p<0.05 for both comparisons). Among inflammatory markers associated with COVID-19 mortality, there was a significant interaction between the Non-Hispanic Black population and interleukin-1-beta (interaction p-value 0.04).

Conclusions:

This analysis of a multi-ethnic cohort highlights the need for inclusion and consideration of diverse popualtions in ongoing COVID-19 trials targeting inflammatory cytokines.

[Interpretation of the American Association for Thoracic Surgery expert consensus document: coronary artery bypass grafting in patients with ischemic cardiomyopathy and heart failure in 2021]

An expert consensus on coronary artery bypass grafting (CABG) in patients with ischemic cardiomyopathy (ICM) was released by the American Association for Thoracic Surgery in May 2021, which contains a vast array of perioperative recommendations. During preoperative period, a comprehensive assessment on ICM including myocardial viability and valve function by a multi-disciplinary team (MDT) approach should be performed. In terms of intraoperative period, multiple arterial conduits and on-pump CABG using cold blood cardioplegia should be considered, meanwhile, other aspects involving concomitant management of mitral valve regurgitation and arrythmia, as well as active use of mechanical cardiac assist devices (e.g., intra-aortic balloon pump) should also be achieved. Finally, a range of postoperative interventions which includes standardized MDT management in intensive care unit (ICU), continuous use of cardiac assist devices, cardiac pacing, close follow-up within 90 days and drug treatment strictly guided by the guidelines after discharge from hospital should be conducted. The above-mentioned perioperative bundled care might reduce perioperative complications and operative mortality, and thus improve the prognosis of the patients with ICM.

Phenome-wide and expression quantitative trait locus associations of coronavirus disease 2019 genetic risk loci

While several genes and clinical traits have been associated with higher risk of severe coronavirus disease 2019 (COVID-19), how host genetic variants may interact with these parameters and contribute to severe disease is still unclear. Herein, we performed phenome-wide association study, tissue and immune-cell-specific expression quantitative trait locus (eQTL)/splicing quantitative trait locus, and colocalization analyses for genetic risk loci suggestively associated with severe COVID-19 with respiratory failure. Thirteen phenotypes/traits were associated with the severe COVID-19-associated loci at the genome-wide significance threshold, including monocyte counts, fat metabolism traits, and fibrotic idiopathic interstitial pneumonia. In addition, we identified tissue and immune subtype-specific eQTL associations affecting 48 genes, including several ones that may directly impact host immune responses, colocalized with the severe COVID-19 genome-wide association study associations, and showed altered expression in single-cell transcriptomes. Collectively, our work demonstrates that host genetic variations associated with multiple genes and traits show genetic pleiotropy with severe COVID-19 and may inform disease etiology.

[Survey of Oncomelania hupensis in national schistosomiasis surveillance sites of Guangxi Zhuang Autonomous Region from 2015 to 2019]

OBJECTIVE

To investigate the distribution characteristics of Oncomelania hupensis in Guangxi Zhuang Autonomous Region, so as to provide insights into the assessment of the risk of schistosomiasis transmission and the scientific formulation of the schistosomiasis surveillance strategy.

METHODS

From 2015 to 2019, a total of 19 national schistosomiasis surveillance sites were assigned in Guangxi Zhuang Autonomous Region, including 4 fixed sites and 15 mobile sites. Snail survey was performed by means of systematic sampling in combination with environmental sampling, and the infection of Schistosoma japonicum was detected by the crushing method combined with loop-mediated isothermal amplification (LAMP) assay.

RESULTS

From 2015 to 2019, snail habitats were detected at areas of 17 040 to 39 527 m², including 6 214 m² emerging snail habitats and 16 563 m² re-emerging snail habitats. The overall mean density of living snails was 0.019 2 snails/0.1 m² and the occurrence of frames with snails was 1.11% in the national schistosomiasis surveillance sites; however, no S. japonicum infection was identified in snails. The area of snail habitats increased by 121.46% in the national surveillance sites in 2019 as compared to that in 2015; however, 50.34% (Z = -0.422, P > 0.05) and 42.85% (χ² = 130.41, P < 0.01) reductions were seen in the overall means density of living snails and the occurrence of frames with snails. All snail habitats were distributed in the 4 fixed surveillance sites, and were mainly found in ditches, paddy fields and dry lands, with weeds as the primary vegetation type.

CONCLUSIONS

There are still risk factors leading to re-emergent transmission of schistosomiasis in Guangxi Zhuang Autonomous Region, such as local snail spread, and the monitoring of schistosomiasis remains to be reinforced to further consolidate the achievements of schistosomiasis elimination in the region.

AeQTL: eQTL analysis using region-based aggregation of rare genomic variants

Concurrently available genomic and transcriptomic data from large cohorts provide opportunities to discover expression quantitative trait loci (eQTLs)-genetic variants associated with gene expression changes. However, the statistical power of detecting rare variant eQTLs is often limited and most existing eQTL tools are not compatible with sequence variant file formats. We have developed AeQTL (Aggregated eQTL), a software tool that performs eQTL analysis on variants aggregated according to user-specified regions and is designed to accommodate standard genomic files. AeQTL consistently yielded similar or higher powers for identifying rare variant eQTLs than single-variant tests. Using AeQTL, we discovered that aggregated rare germline truncations in cis exomic regions are significantly associated with the expression of BRCA1 and SLC25A39 in breast tumors. In a somatic mutation pan-cancer analysis, aggregated mutations of those predicted to be missense versus truncations were differentially associated with gene expressions of cancer drivers, and somatic truncation eQTLs were further identified as a new multi-omic classifier of oncogenes versus tumor-suppressor genes. AeQTL is easy to use and customize, allowing a broad application for discovering rare variants, including coding and noncoding variants, associated with gene expression. AeQTL is implemented in Python and the source code is freely available at https://github.com/Huan-glab/AeQTL under the MIT license.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

Mannose Phosphate Isomerase and Mannose Regulate Hepatic Stellate Cell Activation and Fibrosis in Zebrafish and Humans

The growing burden of liver fibrosis and lack of effective antifibrotic therapies highlight the need for identification of pathways and complementary model systems of hepatic fibrosis. A rare, monogenic disorder in which children with mutations in mannose phosphate isomerase (MPI) develop liver fibrosis led us to explore the function of MPI and mannose metabolism in liver development and adult liver diseases. Herein, analyses of transcriptomic data from three human liver cohorts demonstrate that MPI gene expression is down-regulated proportionate to fibrosis in chronic liver diseases, including nonalcoholic fatty liver disease and hepatitis B virus. Depletion of MPI in zebrafish liver in vivo and in human hepatic stellate cell (HSC) lines in culture activates fibrotic responses, indicating that loss of MPI promotes HSC activation. We further demonstrate that mannose supplementation can attenuate HSC activation, leading to reduced fibrogenic activation in zebrafish, culture-activated HSCs, and in ethanol-activated HSCs. Conclusion: These data indicate the prospect that modulation of mannose metabolism pathways could reduce HSC activation and improve hepatic fibrosis.

[Mid-term multi-center outcomes of bilateral radial artery as conduits in coronary artery bypass grafting]

Objective: To evaluate the mid-term outcomes of bilateral radial artery (BRA) grafts in coronary artery bypass grafting (CABG). Methods: All perioperative medical records and follow-up results of CABG with BRA grafts in multi-centers of China were analyzed retrospectively. Results: A total of 211 patients (170 males and 41 females) underwent CABG grafting with BRA conduits between August 2013 and September 2018, with a mean age of (56.5±9.7) years old (rang 41 to 73 years). There were 161 cases of triple-vessel disease and 50 cases of two-vessel disease. Ninety patients had diabetes mellitus (DM), 35 patients with peripheral vascular disease, 4 patients with chronic obstructive pulmonary disease and 11 with heart valve disease. Two patients underwent off-pump CABG and 209 patients accepted on-pump CABG with commitment valve surgery. There were 210 cases of total arterial revascularization and 161 cases using left thoracic artery conduits, with a graft number of 2-4 (2.7±0.9). No operation-related death occurred, atrial fibrillation happened in 12 patients, hemothorax in 7 cases, and forearm hematoma in one case, hypoxemia in 13 cases and pneumonia in one case. The duration of mechanical ventilation was (8.3±4.7) hours and the mean hospital length of stay was (7.1±2.9) days. Follow-up was completed in 191 patients (90.52%) with a duration of 3-59 (35.5±9.3) months. The mean left ventricular ejection fraction at 3 months after operation was significantly improved, compared to that of the pre-operation (61.0%±7.2% vs 47.1%±5.3%, P=0.017). All patients survived, except that one died from brain injury. No major cardiac events occurred, with a cumulative survival rate of 100% at 1 year and 99.53% at 3 year after operation, respectively. It was showed in coronary CT angiography (CTA) examination that all grafts in 132 patients were patent at the mean follow-up duration of (21.5±6.4) months. Conclusions: BRA grafts as arterial conduit in CABG are proved to be safe, easy for total arterial revascularization and have good mid-term clinical results.

Pan-cancer methylation and expression profiling of adenocarcinomas revealed epigenetic silencing in the WNT signaling pathway

Adenocarcinomas are tumors of glandular characteristics. While tissues of common origins have been known to undergo similar epigenetic changes, it is unclear whether adenocarcinomas of different cancer types would exhibit similar DNA methylation and epigenetic regulation profiles. Herein, we studied global methylation and mRNA expression levels in 1214 lung, prostate, colon, and rectal cancer samples from The Cancer Genome Atlas (TCGA). We identified 602 candidate epigenetically silenced genes shared across these cancer types, and 835 associated CpG sites. The shared candidate genes are enriched in developmental processes. Specifically, 15 of these genes were found in the WNT signaling pathway (enrichment test p-value=1.53x10-6). Notably, the subset of silenced WNT pathway genes in each sample may be different, and both WNT activating or inhibiting genes could be suppressed. Clustering analysis showed that each tumor type contained a similar hyper-methylated subset of samples showing strong epigenetic silencing in the WNT pathway genes, and other fractions of samples expressing subset of the genes. Overall, our results showed that aberration in epigenetic regulation of the WNT signaling pathway is a common signature in adenocarcinomas.

Abstract 5359: Regulatory germline variants in 10,389 adult cancers

Previous studies of rare germline variants in cancer has largely been limited to the coding regions of known predisposition genes. The TCGA PanCanAtlas Germline Working Group is analyzing germline predisposing variants of 10,389 cases in 33 cancer types. We deployed more than 121,000 virtual machines running for over 600,000 hours on the ISB Cancer Genome Cloud to conduct massively parallel variant calling and analyses, and the resulting data are shared with scientists across institutions worldwide. Carriers of the functional regulatory variants add on to the 8.9% of cases carrying known pathogenic variants. Burden analyses reveal enrichment of rare variants in the 3'UTR region of NHP2 and POLH. Further, we observed variants aggregating in conserved regions of selected microRNA families that are also affected by somatic mutations, including mir-17 and mir-29. We nominate regulatory variants by using GWAVA and FunSeq2 corroborated with their enrichment in cancer. The prioritized variants are then further evaluated by further co-occurrence of two-hit events and expression changes in their respective tumor samples. Finally, we examine ancestries, familial history and age at onset for carriers of these variants. Overall, we aim to discover and establish the role of regulatory germline variants in oncogenesis.

Citation Format: Kuan-lin Huang, Amila Weerasinghe, Yige Wu, Wen-wei Liang, R. Jay Mashl, Sheila Reynolds, Kathleen E. Houlahan, Ninad Oak, The Cancer Genome Atlas, Alexander J. Lazar, Michael C. Wendel, Ekta Khurana, Sharon Plon, Feng Chen, Mark Gerstein, Ilya Shmulevich, Li Ding. Regulatory germline variants in 10,389 adult cancers [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 5359.

A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease

A genome-wide survival analysis of 14,406 Alzheimer's disease (AD) cases and 25,849 controls identified eight previously reported AD risk loci and 14 novel loci associated with age at onset. Linkage disequilibrium score regression of 220 cell types implicated the regulation of myeloid gene expression in AD risk. The minor allele of rs1057233 (G), within the previously reported CELF1 AD risk locus, showed association with delayed AD onset and lower expression of SPI1 in monocytes and macrophages. SPI1 encodes PU.1, a transcription factor critical for myeloid cell development and function. AD heritability was enriched within the PU.1 cistrome, implicating a myeloid PU.1 target gene network in AD. Finally, experimentally altered PU.1 levels affected the expression of mouse orthologs of many AD risk genes and the phagocytic activity of mouse microglial cells. Our results suggest that lower SPI1 expression reduces AD risk by regulating myeloid gene expression and cell function.

Abstract LB-267: The proteomic landscape of patient-derived breast cancer xenografts reveals tumor-specific differences in the breast tumor microenvironment

Crosstalk between the tumor and surrounding microenvironment has emerged as an important regulator of tumor growth, metastasis and drug response. Patient-derived breast xenografts (PDXs) closely mimic the tumor microenvironment including the tumor architecture and interactions among cancer cells and stromal cells. PDXs provide a unique opportunity to study tumor-stroma interactions and the regulation of protein expression in the tumor microenvironment since species-specific amino acid sequences of the tumor (human) can be distinguished from the stroma (mouse) by LC-MS. However, quantitative proteomics workflows usually do not report species-specific peptides. We therefore developed a proteomics workflow based on 10-plex isobaric tagging to quantitatively profile the protein expression of PDXs and their associated microenvironment. Three biological replicates of seven breast cancer PDXs, representing three breast cancer subtypes, were profiled. Selecting only gene- and species-specific peptides for quantification of protein expression, we identified 8,113 human proteins (4,867 genes) and 2,251 mouse proteins (1,763 genes). Surprisingly, hierarchical clustering by mouse protein expression tightly clustered 4 of the 7 PDXs, with each of the 3 biological replicates next to one another. Notably, the 4 tightly clustered PDXs were from tumors with claudin-low, Her2-E and luminal B subtypes, whereas the biological replicates of three basal subtypes in the dataset were not tightly clustered. Gene set enrichment analysis of the stromal protein expression revealed upregulation of MTORC1 signaling, EMT, and interferon gamma response signaling with false discovery rates below 5%. We further investigated expression of signaling proteins in the tumor microenvironment by enriching active kinases with multiplexed kinase inhibitor beads. 152 mouse kinases were identified in the tumor microenvironment many tumor-specific differences in kinase levels. Taken together, our results imply that individual patient-derived breast tumors can actively and consistently orchestrate unique alterations in the proteins expressed in their microenvironment. Furthermore, we demonstrate the utility of our proteomic analysis workflow to delineate tumor-stroma signaling networks in PDXs.

Citation Format: Xuya Wang, Petra Erdmann-Gilmore, Rosa Viner, Matthew Meyer, Tim Stuhlmiller, Sherri Davies, Shunqiang Li, Qiang Zhang, Arshag Mooradian, Kuan-lin Huang, Ryan Bomgarden, Li Ding, Matthew Ellis, John Rogers, Gary Johnson, Reid Townsend, David Fenyo, Jason M. Held. The proteomic landscape of patient-derived breast cancer xenografts reveals tumor-specific differences in the breast tumor microenvironment. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-267.

Proteogenomics connects somatic mutations to signalling in breast cancer

Somatic mutations have been extensively characterized in breast cancer, but the effects of these genetic alterations on the proteomic landscape remain poorly understood. We describe quantitative mass spectrometry-based proteomic and phosphoproteomic analyses of 105 genomically annotated breast cancers of which 77 provided high-quality data. Integrated analyses allowed insights into the somatic cancer genome including the consequences of chromosomal loss, such as the 5q deletion characteristic of basal-like breast cancer. The 5q trans effects were interrogated against the Library of Integrated Network-based Cellular Signatures, thereby connecting CETN3 and SKP1 loss to elevated expression of EGFR, and SKP1 loss also to increased SRC. Global proteomic data confirmed a stromal-enriched group in addition to basal and luminal clusters and pathway analysis of the phosphoproteome identified a G Protein-coupled receptor cluster that was not readily identified at the mRNA level. Besides ERBB2, other amplicon-associated, highly phosphorylated kinases were identified, including CDK12, PAK1, PTK2, RIPK2 and TLK2. We demonstrate that proteogenomic analysis of breast cancer elucidates functional consequences of somatic mutations, narrows candidate nominations for driver genes within large deletions and amplified regions, and identifies therapeutic targets.

Abstract IA29: Proteogenomic and phosphoproteomic analysis of breast cancer

The genetic landscape of human breast cancer has been well defined in The Cancer Genome Atlas (TCGA) project. Mass spectrometry (MS)-based global proteome and phosphoproteome analyses provide a complementary, orthogonal approach to genomic studies to further improve the molecular taxonomy and biological understanding of breast cancer. We analyzed human breast cancer samples that had previously undergone comprehensive genomic and reversed phase protein array (RPPA) characterization by TCGA. Tumor samples were analyzed by global shotgun proteomics and phosphoproteomics at an unprecedented coverage of &gt;11,000 quantified proteins and &gt;27,000 phosphorylation sites for each tumor. We verified the translation of hundreds of genomically characterized single nucleotide and splice junction variants at the protein level. The correlation of mRNA to protein abundance was significant for 6,135 out of 9,302 protein/mRNA pairs, but differed amongst protein classes. Genes that did not correlate on the protein/mRNA level included components of basic cellular machineries such as the ribosome, RNA polymerase and spliceosome, as well as those involved in processes regulated by proteolysis. Hierarchical clustering yielded three major clusters in both the proteome and the phosphoproteome data: basal-enriched, luminal-enriched and stroma-enriched groups, the last also enriched for what have been previously designated “reactive-type” tumors by RPPA. Our deep proteome analysis promoted new insights including the consequences of chromosomal loss, such as the 5q deletion characteristic of basal-like breast cancer. The 5q trans effects were interrogated using the Library of Integrated Network-based Cellular Signatures. Theses analyses connected the 5q genes CETN3 and SKP1 to elevated expression of EGFR, and SKP1 also to SRC. Differential phosphopeptide analyses, integrated with activity maps derived from knock-in mutated cell lines, identified multiple novel downstream effects of PIK3CA and TP53 mutation. Besides ERBB2, other amplicon-associated, highly phosphorylated kinases were identified, including CDK12, PAK1, PTK2, RIPK2 and TLK2. These and other examples demonstrate that proteogenomic analysis of breast cancer elucidates functional consequences of somatic mutations, narrows candidate nominations for driver genes within large deletions and amplified regions, and identifies potential therapeutic targets.

Citation Format: Philipp Mertins, DR Mani, Kelly Ruggles, Michael Gillette, Karl Clauser, Pei Wang, Xianlong Wang, Jana Qiao, Song Cao, Francesca Petralia, Filip Mundt, Zhidong Tu, Jonathan Lei, Michael Gatza, Matthew Wilkerson, Charles Perou, Venkata Yellapantula, Kuan-lin Huang, Chenwei Lin, Michael McLellan, Ping Yan, Sherri Davies, Reid Townsend, Steven Skates, Jing Wang, Bing Zhang, Christopher Kinsinger, Mehdi Mesri, Henry Rodriguez, Li Ding, Amanda Paulovich, David Fenyo, Matthew Ellis, Steven Carr, NCI CPTAC. Proteogenomic and phosphoproteomic analysis of breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr IA29.

Abstract 1939: Discovery and proteogenomic investigation of genetic variants in human cancers

A significant fraction of cancers have a heritable component, and require an interplay between somatic and germline variants. Common and rare germline variants have been investigated by previous GWAS and family based studies. However, a comprehensive analysis of both somatic and germline variants in cancer using high throughput sequencing data to discover genetic variants of functional relevance is lacking. Herein, we investigated the potential role of somatic and germline variants from over 20 major cancer types from large-scale studies such as TCGA and ICGC and discovered thousands of somatic and germline variants in cancer genomes. To link these genetic variants to cancer phenotypes, we analyzed the proteomics data in breast, ovarian and colorectal cancers generated by the Clinical Proteomic Tumour Analysis Consortium (CPTAC) using a PepScan pipeline that can detect whether a genomic variant is observed at the peptide level. The pipeline incorporated QUILTS to construct patient-specific protein database and MS-GF+ to identify peptide sequences in the database from MS spectra. Our analysis validated roughly 2% of non-synonymous genetic variants in peptides with matched spectra. We correlated the effect of genetic mutations on proteomic subtypes based on global protein expression levels. Additionally, we assessed the role of genetic variations in kinase genes using phosphoproteome profiles, and identified downstream markers that may be candidate targets for diagnosis or treatment. This analysis also helped us prioritize kinase variants that are likely functional candidates for experimental validation. In conclusion, the comprehensive study of genetic variants utilizing an integrated proteogenomic approach revealed genetic variants with potential functional impacts in cancer.

Citation Format: Kuan-lin Huang, Jaiyin Wang, Song Cao, Mingchao Xie, Reyka Jayasinghe, Jie Ning, Michael McLellan, Michael Wendl, Adam Scott, Kimberly Johnson, Sherri Davies, David Fenyö, Reid Townsend, Feng Chen, Jeffrey Parvin, Matthew Ellis, Li Ding. Discovery and proteogenomic investigation of genetic variants in human cancers. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1939. doi:10.1158/1538-7445.AM2015-1939

Abstract 1929: Pan-Cancer analysis of the effects of splice-altering variants on mRNA splicing and stability

Sequences surrounding splice junctions function to recruit splicing elements to promote and suppress the inclusion of an adjacent exon. Mutations disrupting motifs around splice regions and the creation of de novo splice sites have not been functionally characterized genome-wide. Furthermore, many variants that alter the mRNA isoform have been shown to introduce splicing defects, such as premature termination codons (PTCs), which are degraded via nonsense-mediated decay (NMD). Using cancer samples across multiple cancer types, we have the unique opportunity to study the effects of somatic and germline events introduced throughout the genome and with the large dataset provided by The Cancer Genome Atlas (TCGA), we have the power to identify significant events that are influencing mRNA splicing and stability.

In this study we aim to characterize splice altering variants (SAVs) and nonsense mutations that directly effect exon inclusion and mRNA degradation, respectively, utilizing the TCGA dataset consisting of both DNA-Seq (whole genome and/or exome sequencing) and RNA-seq from approximately 8,000 tumors representing 24 major cancer types. We have identified 23,615 somatic splice site mutations and 71,009 somatic nonsense mutations in 24 cancer types. For each variant, we have collected the following expression data derived from the RNA-seq: exon, splice junction, isoform, and gene; defining the expression signature of each variant. Expression signatures of known SAVs will facilitate the identification of novel and mis-classified missense and silent mutations affecting splicing. Exploring the distribution of mutations and their correlation with the aforementioned expression data will allow us to establish commonalities and differences that may be indicative of cancer type, molecular subtype, or clinical characteristics. Furthermore our position dependent analysis of nonsense mutations and their correlation with degradation will enhance our ability to determine significant sites influencing mRNA isoform presence. We hypothesize that some intronic/exonic variants outside the canonical splice site will influence exon inclusion and alter the ratio of mRNA isoforms present.

Our analysis has identified a number of SAVs, including variants that were mis-classified as missense mutations such as c.190 in BRCA1. The germline coding mutation was found to strengthen a cryptic splice site and discovered to have a higher variant allele fraction in the tumor relative to the normal tissue in two ovarian samples. In conclusion our findings and the continued development of our project will contribute to improving current annotation methods and broaden our understanding of variants that affect splicing and their biological contribution to mRNA isoforms selection in the cell.

Citation Format: Reyka G. Jayasinghe, Kuan-lin Huang, Jie Ning, Matthew Wyczalkowski, Charles Lu, Mingchao Xie, Michael Wendl, Michael McLellan, Kai Ye, Li Ding. Pan-Cancer analysis of the effects of splice-altering variants on mRNA splicing and stability. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1929. doi:10.1158/1538-7445.AM2015-1929

An isolated intracranial mucocoele herniated from the frontal sinus

Mucocoeles are chronic mucosa-lined retention cysts that occur due to sinus ostium obstruction and expand along the path of least resistance, most commonly involving the frontal sinus. A frontal mucocoele typically appears as a smooth and rounded expansile enlargement of a completely opacified frontal sinus, with or without thinning of the bony wall of the sinus. Here we report a rare case of isolated intracranial mucocoele that presented with posterior herniation to the anterior cranial fossa through a small bony defect on the posterior table of the frontal sinus. The findings upon imaging could easily be confused with intracranial abscess, potentially leading to craniotomy drainage. In the present case of mucocoele, the frontal intracranial lesion was completely resolved following endoscopic frontal sinusotomy.

Yeast Tdh3 (glyceraldehyde 3-phosphate dehydrogenase) is a Sir2-interacting factor that regulates transcriptional silencing and rDNA recombination

Sir2 is an NAD(+)-dependent histone deacetylase required to mediate transcriptional silencing and suppress rDNA recombination in budding yeast. We previously identified Tdh3, a glyceraldehyde 3-phosphate dehydrogenase (GAPDH), as a high expression suppressor of the lethality caused by Sir2 overexpression in yeast cells. Here we show that Tdh3 interacts with Sir2, localizes to silent chromatin in a Sir2-dependent manner, and promotes normal silencing at the telomere and rDNA. Characterization of specific TDH3 alleles suggests that Tdh3's influence on silencing requires nuclear localization but does not correlate with its catalytic activity. Interestingly, a genetic assay suggests that Tdh3, an NAD(+)-binding protein, influences nuclear NAD(+) levels; we speculate that Tdh3 links nuclear Sir2 with NAD(+) from the cytoplasm.

Hyperbaric oxygen ameliorates delayed neuropsychiatric syndrome of carbon monoxide poisoning

OBJECTIVES

Delayed neuropsychiatric syndrome (DNS) is characterized by mental impairment, motor dysfunction, dementia, or psychosis that develops between a few days and weeks after acute carbon monoxide (CO) poisoning. One possible mechanism responsible for CO-mediated encephalopathy involves oxidative stress, such as lipid peroxidation, caused by the cellular uptake of CO and which leads to an inflammatory cascade. There is no current effective treatment for DNS. We applied 8-40 sessions of hyperbaric oxygen therapy (HBO2) to patients with DNS and evaluated its effectiveness.

METHODS

After admission, all patients were administered piracetam or bromocriptine, or both, and received HBO2. Neuropsychiatric tests included EEG, mini-mental status examination (MMSE), brain MRI, event-related potential (ERP), and brain perfusion scan (brain SPECT). Results of these tests were compared before and after HBO2, and the clinical features were monitored during this period.

RESULTS

The symptoms of DNS for all patients improved significantly after HBOT. Although white matter changes remained evident in the brain MRI scans, other examinations such as EEG, MMSE, ERP, and 99mTc-ECD brain SPECT were nearly normal after HBOT.

CONCLUSION

Our results suggest that HBO2 decreases the severity of impairment in patients with DNS. Although a large randomized trial is required to address the efficacy of this therapy, therapeutic application of HBO2 may be recommended in patients with DNS after CO poisoning.

A high yield robotic synthesis of 9-(4-[18F]-fluoro-3-hydroxymethylbutyl)guanine ([18F]FHBG) and 9-[3-[18F]fluoro-1-hydroxy-2-propoxy)methyl]guanine([18F] FHPG) for gene expression imaging

The aim of this study was to develop an automated synthesis of 9-(4-[(18)F]-fluoro-3-hydroxymethylbutyl)guanine ([(18)F]FHBG) and 9-[(3-[(18)F]fluoro-1-hydroxy-2-propoxy)methyl]guanine ([(18)F]FHPG) using a Scanditronix Anatech RB III robotic system. [(18)F]HF was produced via (18)O(p, n)(18)F using a Scanditronix MC17F cyclotron. On average, a typical run produced [(18)F]FHBG and [(18)F]FHPG with an uncorrected radiochemical yield of 19% and 16%, respectively, at end of synthesis (EOS) from irradiation of 95% enriched [(18)O]water. The total synthesis time was 80 min. The retention time of [(18)F]FHBG and [(18)F]FHPG (the radio-peak) was 3.9 and 4.0 min, respectively, which was consistent with the [(19)F]FHBG and [(19)F]FHPG ultraviolet peak. The radiochemical purity was greater than 97%. A robotic, automated method for [(18)F]FHBG and [(18)F]FHPG radiosynthesis is therefore feasible. The radiation burden for the operator can be reduced as much as possible. Sufficient radioactivities of [(18)F]FHBG and [(18)F]FHPG could be obtained for non-invasive monitoring the expression of transfected gene in vivo with positron emission tomography (PET).

Pulmonary inflammation caused by chitosan microparticles

Chitosan is a cationic biopolymer derived from chitin with potential therapeutic applications such as controlled drug delivery to mucosal-epithelial surfaces in the body. Inhaled chitosan microparticles (CM), for example, are of potential interest in pulmonary pharmacotherapy. In this context, we examine some basic reactions of lung tissue to CM. Inhaled CM (2-10 mg/kg of particles) induce dose-dependent proinflammatory effects in rat lungs; these effects are documented in increases in bronchoalveolar lavage fluid protein (BALF-P) and lactate dehydrogenase activity (BALF-LDH) and increases in lung tissue myeloperoxidase (MPO) activity and leukocyte migration. Overall, the biochemical parameters (i.e., average of BALF-P, BALF-DH, and MPO) indicate that the inflammation response is 1.8-fold greater than controls without CM; the same inflammation parameters, however, are 1.9-fold lower with CM compared with the proinflammatory effects of lipopolysaccharide (LPS). Cytological examination of BALF shows a large infiltration of polymorphonuclear neutrophils to lung tissue: more than a sixfold increase in this population of inflammatory cells, after inhalation of CM relative to air inhalation controls. Thus, the results indicate that inhaled CM can have significant proinflammatory effects on lung tissues; these effects are mild relative to LPS but need to be considered in the context of therapeutic applications via pulmonary delivery if such concentrations of CM are used.

The use of air fuel cell cathodes to remove contaminants from spent chromium plating solutions

Results from experiments using an impregnation-reduction (I-R) Pt / Nafion membrane electrode assembly (MEA) in an air fuel cell cathode to remove contaminants (Cu(II), Ni(II), and Fe(III)) from spent chromium electroplating baths are presented in this study. A platinum-carbon (Pt-C) / Nafion MEA and a Pb planar cathode were also used for comparison. The average removal rates of Cu(II) and Ni(II) were almost the same (0.39 and 0.40 mM hr(-1) (or 0.117 and 0.12 mmol hr(-1)), respectively) but higher than that of Fe(III) (0.16 mM hr(-1), or 0.048 mmol hr(-1)) in accordance with the Nernst-Planck flux equation. The removal rates for the same cation were independent of the cathode used. The average removal rate of each impurity was approximately proportional to the product of its initial concentration and separator area/anolyte volume ratio using Pb cathodes. Under constant current conditions the system using the Pt-C / Nafion cathode needed the highest cell voltage, about 3 V more than needed for the system with the Pt / Nafion cathode. The cell voltage required using the Pt / Nafion cathode was similar to that using the conventional planar Pb cathode. Analyses of cathode deposits by SEM/EDS and XPS techniques indicated they were minimal on the Pb and Pt / Nafion cathode and more apparent on the Pt-C / Nafion cathode. The primary deposits on the Pb cathode were chromium oxides (e.g., Cr2O3) with minor amount of lead chromate (lead dichromate or lead trichromate) and other chromium solids (Cr black). As expected, the dominant deposit on the lead anode surface was PbO2.

Hyperbaric oxygen increases the lung's susceptibility to inhaled lipopolysaccharide in mice

Hyperbaric oxygen (HBO2) has been shown to inhibit the adhesion function of beta(2)-integrin, which is important in mediating cell-to-cell adhesion and extravasation of inflammatory cells. In the present study, we examined the effects of HBO2 exposure on neutrophil infiltration and tissue injury in a model of acute lung inflammation induced by lipopolysaccharide (LPS) inhalation. Male C57BL/6 mice of 8 weeks old were exposed to 3 atmosphere absolute (ATA) 100% HBO2, 3 ATA hyperbaric air (HBA), or room air for 90 min. After exposure, they were exposed to aerosolized LPS solution (1 mg/ml) or saline in a plexiglass chamber for 10 min. Four hours after inhalation, bronchoalveolar lavage (BAL) was performed to determine protein concentration, LDH activity, total cells, and differential cell counts in the lavage fluid (BALF). Myeloperoxidase (MPO) content, lung histopathology, and plasma nitric oxide (NO) metabolite concentrations were also determined in separate sets of animals. We observed that LPS inhalation increased neutrophil number in the BALF, which was significantly inhibited by HBO2 but not HBA pre-exposure. However, MPO content in the lung was prominently increased by HBO2 pre-exposure, which correlated with increased PMN infiltration in lung tissues. Further, HBO2 plus LPS, but not saline inhalation caused a significant increase in the BALF protein level and LDH activity compared with that of LPS inhalation alone. LPS exposure induced significant increase in plasma NO metabolites, which was not potentiated by HBO2 pre-exposure. The inducible nitric oxide synthase inhibitor, aminoguanidine, significantly attenuated the increases in plasma NO metabolites and tissue MPO content as well as lung injuries. In summary, our data suggest that HBO2 pre-exposure increases the lung's susceptibility to inhaled LPS, which may be related to increased tissue neutrophil infiltration and dependent on interaction(s) between HBO2 exposure with LPS-induced nitric oxide production.

Biogeography and origin of Lilium longiflorum and L. formosanum (Liliaceae) endemic to the Ryukyu Archipelago and Taiwan as determined by allozyme diversity

Allozyme diversity on 13 isozyme loci was investigated for two bulbous species, Lilium longiflorum and L. formosanum, endemic to the subtropical archipelago of continental origin located in East Asia. Degrees of allozyme variability and divergence for L. longiflorum were very high for insular endemic species, indicating relatively longtime persistence of the present widespread distribution across many islands in this phenotypically little-changed species. Lilium formosanum exhibited rather lower variability and divergence than did L. longiflorum and was genetically close to the southern peripheral populations of L. longiflorum with 0.978 as its highest genetic identity value. Combined with other biological and insular geohistorical information, our results suggest that L. longiflorum was established around the end of the Pliocene when the current distribution area was still a continuous part of the ancient Asian continent, and L. formosanum was derived from southern populations of L. longiflorum around the late Pleistocene when the mainland of Taiwan was completely separated from the adjacent islands and the main continent. Depauperization of allozyme variability in some L. longiflorum populations was found on islands with lower altitudes. This reflects bottleneck effects after the complete or almost complete submergence of such low islands during the archipelago's development.

Endoscopic stenting in the treatment of bile leakage after laparoscopic cholecystectomy

BACKGROUND

Bile leakage is one of the most common complications after laparoscopic cholecystectomy surgery, and biliary decompression is a key factor in treatment. We retrospectively investigated 6 patients with bile leakage after laparoscopic cholecystectomy who were treated with endoscopic stent.

METHODS

From March 1995 to May 1999, six patients (4 men and 2 women) aged 30-64 years (mean, 51 years) with bile leakage after laparoscopic cholecystectomy were enrolled. Biliary stent (10 French, 6-10 cm) placement with (n = 4) or without (n = 2) sphincterotomy was attempted. The symptoms, results and outcomes were reviewed.

RESULTS

The interval from operation to presentation of bile leakage ranged from 1 to 10 days. Bile leakage was detected from cystic duct stump in 5 patients (83%) and from right IHD in 1 patient (17%). Plastic stent placement was successfully in all patients. Endoscopic stenting healed bile leakage successfully in 5 cases (83%). One patient required surgical correction due to persistent bile leakage. The mean duration between stent placement and cessation of bile leakage was 6.8 days (range 1 to 24 days).

CONCLUSIONS

Endoscopic stenting is a safe, rapid and effective treatment for bile leakage after laparoscopic cholecystectomy.

Temporal trends and molecular epidemiology of HIV-1 infection in Taiwan from 1988 to 1998

Eight hundred and seventy-nine HIV-1-infected patients (comprising 46% of reported HIV-1/AIDS cases in Taiwan) were recruited for this study of the molecular epidemiology of HIV-1 in Taiwan from 1988 to 1998. HIV-1 subtypes were determined using a modified peptide-enzyme immunoassay complemented with DNA sequencing and phylogenetic analysis. Of the 807 HIV-1 infected men, 68.2% were infected with HIV-1B, 29.5% with HIV-1 circulating recombinant form (CRF)01_AE and 2.3% with other subtypes. Of the 72 HIV-1-infected women, 72.2% were infected with HIV-1 CRF01_AE, 13.9% with HIV-1B, and 13.9% with other subtypes. All of 8 foreign-born, Southeast Asian women and 6 of 7 (85.7%) Taiwan-native female commercial sex workers were infected with HIV-1 CRF01_AE. Fourteen of the 33 (42.4%) heterosexual married men with CRF01_AE had transmitted HIV-1 to their wives, whereas only 1 of 17 (5.9%) men with HIV-1 B had transmitted HIV-1 to their spouses (p < .01). Of 18 heterosexual male injecting drug users, 1 of 12 (8.5%) with HIV-1B and 5 of 6 (83.3%) with HIV-1 CRF01_AE had had sexual contact with female commercial sex workers (p < .01). Therefore, in this population, CRF01_AE was preferentially associated with heterosexual risk groups, a finding compatible with differences in transmission capability between B and non-B subtypes.

Prolonged exposure to hyperbaric oxygen induces neuronal damage in primary rat cortical cultures

While seizure attack is one of the serious complications during the hyperbaric oxygen (HBO) therapy, there is still no direct evidence showing that HBO can induce neuronal damage in the brain. The objective of this study was first to investigate whether HBO would lead to neurotoxicity in the primary rat cortical culture. Second, since alterations in neurotransmitters have been suggested in the pathophysiology of central nervous system (CNS) oxygen toxicity, the protective effects of the N-methyl-D-aspartate (NMDA) receptor antagonism and nitric oxide (NO) synthase inhibition on the HBO-induced neuronal damage were examined. The results showed that HBO exposure to 6 atmosphere absolute pressure (ATA) for 30, 60, and 90 min increased the lactate dehydrogenase (LDH) activity in the culture medium in a time-dependent manner. Accordingly, the cell survival, measured by the 3,(4,5-dimethyl-2-thiazolyl)2, 5-diphenyl-tetrazolium bromide (MTT) assay, was decreased after HBO exposure. Pretreatment with the NMDA antagonist MK-801 protected the cells against the HBO-induced damage. The protective effect was also noted in the cells pretreated with L-N(G)-nitro-arginine methyl ester, an NO synthase inhibitor. Thus, our results suggest that activation of NMDA receptors and production of NO play a role in the neurotoxicity produced by hyperbaric oxygen exposure.

Systemic administration of d-amphetamine induces long-lasting oxidative stress in the rat striatum

The long-term effect of d-amphetamine (AMPH) on the induction of oxidative stress was examined in vivo in the rat brain. In this study, 2,3-dihydroxybenzoic acid (2,3-DHBA) and malonaldehyde (MDA) were used as the index of the hydroxyl radical and lipid peroxidation, respectively. The levels of 2,3-DHBA, MDA and dopamine (DA) in striatal homogenates were examined 7 days following injection of a single large dose of AMPH (7.5 mg/kg, i.p.) in rats pretreated with desipramine (10 mg/kg, i.p.), an agent that inhibits the metabolism of AMPH. Our results showed that 2,3-DHBA and MDA levels were significantly increased by AMPH, whereas DA and its metabolites, DOPAC and HVA were depleted in the striatum. Pretreatment with the glutamate NMDA receptor subtype antagonist MK-801 (1 mg/kg, i.p.) attenuated the increases of 2,3-DHBA and MDA, and provided partial protection against the long-lasting loss of DA produced by AMPH. Overall, the results demonstrate that AMPH could induce sustained production of free radical and oxidative damage, and lead to DA terminal degeneration in the striatum of the rat.

Tuberculosis of skeletal muscle in a case of polymyositis

We describe a patient with polymyositis receiving corticosteroid therapy, who presented with persistent fever and mass lesion at the left thigh. Surgical exploration and mycobacterial culture proved to be Mycobacterium Tuberculosis infection involving the semitendinous muscle of the left thigh. Suitable surgical debridement, anti-TB medications, and sufficient corticosteroid administration resulted in a good control of both polymyositis and the tuberculous infection.

Diving pattern and work schedule of construction well divers in Taiwan

Construction well divers in Taiwan reportedly suffer a high prevalence of dysbaric osteonecrosis. We studied five divers working at the same construction site. We recorded their diving methods, diving depths, bottom times, work patterns, water temperatures, and heart rates. We also monitored gas bubbles in the subclavian vein in selected dives. A crude but effective hot-water system protected divers against hypothermia and allowed them to work in 24 degrees-27 degrees C water. Divers worked approximately 6.6 h a day and progressed approximately 3.0 m a day while excavating an average of 148 buckets of sand and rock each weighing 49.5 kg. The divers sustained a heart rate increase of 49%. Sixty percent of their equivalent single dive bottom times exceeded the U.S. Navy's no-decompression limits. Two cases of venous bubbles were detected, and one of these divers showed symptoms of decompression sickness. The prolonged bottom time and lack of a decompression schedule probably contributed to a risk of decompression sickness and dysbaric osteonecrosis.

Dibutyryl cAMP prevents increased vascular permeability caused by air embolism in isolated rat lungs

BACKGROUND AND HYPOTHESIS

Venous gas bubbles are routinely detected in astronauts undergoing extravehicular activities at lower suit pressure. Venous air embolism increases the pulmonary arterial pressure and the vascular permeability leading to acute lung injury. In the present study we evaluated the protective effect of dibutyryl cAMP, aminophylline, and pentoxifylline on the pulmonary vasculatures after air embolism.

METHOD

In isolated and perfused rat lungs, we induced air embolism by introducing air bubbles into the pulmonary artery. We measured the pulmonary arterial pressures and capillary pressure. Vascular permeability was determined by measuring the filtration coefficient (Kf) and the protein concentration in the lung lavage fluid.

RESULTS

Air infusion caused pulmonary hypertension and increased vascular permeability, resulting in pulmonary edema. The Kf (in g.min-1.cm H2O-1.100 g-1) increased from 0.44 +/- 0.05 at baseline to 2.98 +/- 0.47 after air infusion. Pretreatment with DBcAMP prevented the increase in Kf (0.63 +/- 0.09) caused by air embolism without altering the hemodynamics. Aminophylline and pentoxifylline did not prevent lung injury induced by air embolism. Although aminophylline did not alter the response of pulmonary arterial pressure to air infusion, it elevated the capillary pressure to 5.1 +/- 0.4 mmHg, which was significantly greater than that in the lung receiving air infusion alone.

CONCLUSION

Our results suggest that DBcAMP prevents the increase in vascular permeability caused air embolism. The ineffectiveness of aminophylline and pentoxifylline on the prevention of air embolism-induced lung injury remains for further investigation.

Activation of complement and neutrophils increases vascular permeability during air embolism

Pulmonary air embolism occurs in diving and aviation during acute pressure reductions and in clinical complications. Undoubtedly physical obstructions play a role, but bubbles in blood can produce a number of indirect effects leading to tissue injury. In the present study, we investigated the involvement of the complement system and polymorphonuclear leukocytes (PMN) in altering segmental vascular resistance, lung weight gain, and filtration coefficient (Kf), by using isolated and perfused rat lungs. After establishing ventilation with air and 5% CO2, the lung was removed en bloc and suspended in a humidified chamber at 37 degrees C. Lung weight and arterial and venous pressures were monitored continuously. The buffered salt perfusate contains 4% Ficoll for osmotic balance. We used four series of perfusates containing 20% of: a) normal plasma; b) decomplemented plasma (from donor rats pretreated with a cobra venom factor); c) normal plasma and PMN at 2 x 10(6).ml-1; and d) decomplemented plasma and PMN at 2 x 10(6).ml-1. Pulmonary air embolism, air bubbles introduced through the pulmonary artery, increased pulmonary arterial resistance and pulmonary arterial blood pressure. The lung weight and lung water content were greater than those in the control groups. Air embolism increased vascular permeability, which was shown by an elevated Kf after air infusion. After air embolism, Kf was 0.63 +/- 0.05 g.min-1.cm H2O-1.100 g-1 in lungs perfused with both PMN and plasma, which was significantly greater than those in lungs perfused with either plasma (0.49 +/- 0.04), decomplemented plasma (0.44 +/- 0.03), or PMN and decomplemented plasma (0.47 +/- 0.03). These results demonstrated that air embolism increases vascular permeability of the lung by pulmonary hypertension, activation of the complement, and activation of PMN.

The GST T1 and CYP2E1 genotypes are possible factors causing vinyl chloride induced abnormal liver function

Vinyl chloride monomer (VCM) is hepatotoxic as well as carcinogenic in humans. There are reports that exposure to VCM seems to induce abnormal liver function, liver fibrosis, cirrhosis, portal hypertension, and angiosarcoma of the liver. In vivo, VCM is metabolized by cytochrome P450 2E1 (CYP2E1) to form the electrophilic metabolites, chloroethylene oxide (CEO) and chloroacetaldehyde (CAA), which may either cause cell damage or be further metabolized and detoxified by glutathione S-transferases (GSTs). This study investigated whether or not the genotypes CYP2E1, glutathione S-transferase theta (GST T1) and mu (GST M1) correlated with abnormal liver function found in vinyl chloride exposed workers. For this study, 251 workers from five polyvinyl chloride plants were enrolled. The workers were classified into two exposure groups (high and low) and the degree of exposure was determined based on their job titles and airborne VCM concentration. The activity of serum alanine aminotransferase (ALT) was used as the parameter of liver function. The genotypes CYP2E1, GST T1 and GST M1 were determined by polymerase chain reaction and restriction fragment length polymorphism on peripheral white blood cell DNA. Other potential risk factors were also ascertained and the confounding effect was adjusted accordingly. Stratified analyses were used to explore the correlation between the alteration of liver function and the genotypes CYP2E1, GST T1 and GST M1 among the workers exposed to different levels of VCM. The following results were obtained (1) at low VCM exposure, the odds ratio (OR) of positive GST T1 on abnormal ALT was 3.8 (95% CI 1.2-14.5) but the CYP2E1 genotype was not associated with abnormal ALT. (2) At high VCM exposure, a c2c2 CYP2E1 genotype was associated with increased OR on abnormal ALT (OR 5.4, 95% CI 0.7-35.1) and positive GST T1 was significantly associated with decreased OR on abnormal ALT (OR 0.3, 95% CI 0.1-0.9). (3) Multiple linear and logistic regression also showed strong interactions of the VCM exposure to CYP2E1 as well as to the GST T1 genotype. These observations suggest that the two genotypes, CYP2E1 and GST T1, may play important roles in the biotransformation of VCM, the effect of which leads to liver damage.

Pharmacologic modulation of pulmonary vascular permeability during air embolism

Pulmonary air embolism induces the generation of vasoactive and cytotoxic substances leading to lung injury. In the present study we investigated, in isolated and perfused rat lungs, the involvement of arachidonic acid metabolites in the alterations of vascular pressure, lung water content, and the filtration coefficient (Kf). We also tested the effects of a beta-agonist, a calcium channel blocker, and a cyclo-oxygenase inhibitor on the hemodynamic and the permeability changes following pulmonary air embolism. The artificially ventilated rat lungs were removed en bloc and suspended in a humidified chamber at 37 degrees C. The salt and buffered perfusate contained 4% Ficoll as albumin substitute for osmotic balance. We introduced air bubbles through the pulmonary artery. Air embolism increased pulmonary arterial resistance and caused pulmonary hypertension. Lungs receiving air infusion contained 88.6 +/- 0.6% water, which was significantly greater than the lung water content in the control groups (81.9 +/- 0.4%). Air embolism increased Kf by 145 +/- 19% from the baseline value. Pretreatment with indomethacin, isoproterenol, or nifedipine significantly reduced post-air-embolism lung water content to 85.8 +/- 0.5%, 84.1 +/- 0.4%, and 86.5 +/- 04%, respectively, and reduced the Kf increase to 17 +/- 8%, 1 +/- 9%, and 72 +/- 8%, respectively. These interventions did not alter the hemodynamic responses, except for the isoproterenol infusion, which shortened the half-time (T1/2) for pressure recovery after ending air infusion compared to the group with air embolism alone. Our results showed that indomethacin prevented vascular permeability increase and reduced pulmonary edema, suggesting that the cyclo-oxygenase products partially mediate the lung injury following air embolism. Furthermore, isoproterenol and nifedipine prevented or reduced the permeability increase, suggesting that alterations of the intracellular cAMP and cytosolic Ca2+ level play an important role in the pathophysiology of pulmonary air embolism.

Effects of lead on systolic and diastolic cardiac functions

In this paper, both systolic and diastolic cardiac functions were evaluated in 54 lead exposed and 24 non-exposed workers by Doppler echocardiography. With regard to systolic cardiac function, the results suggested that cardiac systolic function increased in exposed groups as a compensatory response for the effect of lead on myocardium. To study left ventricular diastolic function, 2.5 MHz pulsed Doppler analyses of transmitral flow velocity were performed from apical four-chamber view. The results showed that time-related parameters were comparable among all groups, but blood flow velocity through the mitral valve and Doppler area fractions changed significantly in lead-exposed groups as evidenced by increased value A, decreased value E and E/A ratio. The decrease of diastolic cardiac function was more significant in lead intoxication group. It was also observed in this study that the activity in serum of the MB isoenzyme of creatine phosphokinase (CPK-MB), one of the indices of myocardial damage, was significantly higher in exposed group than that in control (P < 0.05), and a positive correlation was found between CPK-MB activity and Pb-B. It denoted that the increasing of lead burden leads to more release of CPK-MB from the myocardial cells and suggested the existence of slight myocardial damage, which, conceivably, might cause harm to diastolic cardiac function.

Diving pattern of fishermen in the Pescadores

Professional diving fishermen in the Pescadores Archipelago (119.30 degrees W, 23.30 degrees N) dive with a simple hookah system. Although they use modern equipment, such as wet suit, face mask, mouth piece with demand valve, spear gun, weight belt, and fins, their lack of knowledge of diving medicine is apparent. On the average, 180 cases of decompression sickness (DCS) per year were reported to occur in the Pescadores. We conducted studies in 1990 and 1992 on three islands of the Archipelago. At the time of our study, an estimated 140 diving fishermen resided on these three islands. Of the 62 fishermen interviewed, 14 volunteered for the recording of dive profiles using a diver-carried data logger. In the summer of 1990, a group of eight fishermen dived, on the average, to a depth of 17.8 +/- 5.3 m (mean +/- SD; range, 8-27 m) for 26.9 +/- 19.7 min (5-66 min). Although the diving depth was similar to that of the average recollections of 43 divers, 20.1 +/- 4.4 m (15-30 m), the actual diving time was far shorter than that of their recollections, 426 +/- 138 min (240-630 min). The post-typhoon sea floor conditions may have shortened their diving time. In the summer of 1992, a group of six fishermen dived to 20.5 +/- 3.8 m (15-26 m) for 56.4 +/- 21.2 min (18-84 min). Again, the diving depth matched that of their recollection well, 22.2 +/- 2.5 m (20-26 m), but their bottom time was far shorter than they believed, 270 +/- 108 min (120-480 min). They used no decompression procedures, regardless of the bottom time and diving depth. In the 1990 group, 5 out of 10 equivalent single dive bottom times (ESDBT) exceeded U.S. Navy no-decompression (No-D) air dive limits; whereas in the 1992 group, 7 out of 9 ESDBTs exceeded No-D limits. Eight of the 38 discrete dives exceeded the No-D limits, even if we underestimate their decompression stress by disregarding their repetitive dive history. However, no symptoms of DCS were observed in either the 1990 or 1992 groups of 14 divers, despite 63% of the ESDBTs and 21% of discrete dives having exceeded the No-D limits. Adaptation to diving work may have allowed them to exceed the established No-D limits. The existing records of incidence of DCS from this region suggest that previously they must have dived longer or deeper or both during times of abundant resources.

Application of conservation principle in estimating body volume in rats

Obesity is a risk factor in diving and aviation during acute reduction of pressure, because N2 is five times more soluble in fat than in water. In addition to concerns of decompression applications, body fat content (BFC) bears importance in the disposition of drugs, the evaluation of dietary regimens and exercise programs, and in long-term health status. Most of the currently available methods for quantifying BFC are impractical for small animals. We devised a method that does not require the cooperation of the animal. Our method uses a simple gas-dilution technique to measure the body volume. The body density was determined as the ratio of body weight (g) to body volume (ml). After the whole body density was determined, the fraction of body fat was calculated according to established formulas. Calibration with aluminum blocks showed a high correlation (r = 0.99) between measured volumes and the known block volumes. Furthermore, comparing body volumes of shaved and unshaved rats showed that the volume of air between hairs did not affect the measurement of body volume with the dilution method. In four groups, each consisting of 10 male Wistar rats [body wt 81 +/- 1 (SE), 152 +/- 3,297 +/- 5, and 496 +/- 4 g], BFC was 7.0 +/- 2.8, 14.6 +/- 1.9, 22.0 +/- 1.8, and 32.3 +/- 1.3%, respectively. These values compared favorably with chemically determined BFC values for rats in the literature. Our results suggest that the gas-dilution technique is a feasible and simple method for the determination of BFC in small animals.