Exploring Optimal Biomarker Sources: A Comparative Analysis of Exosomes and Whole Plasma in Fasting and Non-Fasting Conditions for Liquid Biopsy Applications

The study of liquid biopsy with plasma samples is being conducted to identify biomarkers for clinical use. Exosomes, containing nucleic acids and metabolites, have emerged as possible sources for biomarkers. To evaluate the effectiveness of exosomes over plasma, we analyzed the small non-coding RNAs (sncRNAs) and metabolites extracted from exosomes in comparison to those directly extracted from whole plasma under both fasting and non-fasting conditions. We found that sncRNA profiles were not affected by fasting in either exosome or plasma samples. Our results showed that exosomal sncRNAs were found to have more consistent profiles. The plasma miRNA profiles contained high concentrations of cell-derived miRNAs that were likely due to hemolysis. We determined that certain metabolites in whole plasma exhibited noteworthy concentration shifts in relation to fasting status, while others did not. Here, we propose that (1) fasting is not required for a liquid biopsy study that involves both sncRNA and metabolomic profiling, as long as metabolites that are not influenced by fasting status are selected, and (2) the utilization of exosomal RNAs promotes robust and consistent findings in plasma samples, mitigating the impact of batch effects derived from hemolysis. These findings advance the optimization of liquid biopsy methodologies for clinical applications.

sRNAfrag: a pipeline and suite of tools to analyze fragmentation in small RNA sequencing data

Fragments derived from small RNAs such as small nucleolar RNAs are biologically relevant but remain poorly understood. To address this gap, we developed sRNAfrag, a modular and interoperable tool designed to standardize the quantification and analysis of small RNA fragmentation across various biotypes. The tool outputs a set of tables forming a relational database, allowing for an in-depth exploration of biologically complex events such as multi-mapping and RNA fragment stability across different cell types. In a benchmark test, sRNAfrag was able to identify established loci of mature microRNAs solely based on sequencing data. Furthermore, the 5' seed sequence could be rediscovered by utilizing a visualization approach primarily applied in multi-sequence-alignments. Utilizing the relational database outputs, we detected 1411 snoRNA fragment conservation events between two out of four eukaryotic species, providing an opportunity to explore motifs through evolutionary time and conserved fragmentation patterns. Additionally, the tool's interoperability with other bioinformatics tools like ViennaRNA amplifies its utility for customized analyses. We also introduce a novel loci-level variance-score which provides insights into the noise around peaks and demonstrates biological relevance by distinctly separating breast cancer and neuroblastoma cell lines after dimension reduction when applied to small nucleolar RNAs. Overall, sRNAfrag serves as a versatile foundation for advancing our understanding of small RNA fragments and offers a functional foundation to further small RNA research. Availability: https://github.com/kenminsoo/sRNAfrag.

sRNAfrag: A pipeline and suite of tools to analyze fragmentation in small RNA sequencing data

Fragments derived from small RNAs such as small nucleolar RNAs hold biological relevance. However, they remain poorly understood, calling for more comprehensive methods for analysis. We developed sRNAfrag, a standardized workflow and set of scripts to quantify and analyze sRNA fragmentation of any biotype. In a benchmark, it is able to detect loci of mature microRNAs fragmented from precursors and, utilizing multi-mapping events, the conserved 5' seed sequence of miRNAs which we believe may extraoplate to other small RNA fragments. The tool detected 1411 snoRNA fragment conservation events between 2/4 eukaryotic species, providing the opportunity to explore motifs and fragmentation patterns not only within species, but between. Availability: https://github.com/kenminsoo/sRNAfrag.

Circulating microRNA Biomarker for Detecting Breast Cancer in High-Risk Benign Breast Tumors

High-risk benign breast tumors are known to develop breast cancer at high rates. However, it is still controversial whether they should be removed during diagnosis or followed up until cancer development becomes evident. Therefore, this study sought to identify circulating microRNAs (miRNAs) that could serve as detection markers of cancers arising from high-risk benign tumors. Small RNA-seq was performed using plasma samples collected from patients with early-stage breast cancer (CA) and high-risk (HB), moderate-risk (MB), and no-risk (Be) benign breast tumors. Proteomic profiling of CA and HB plasma was performed to investigate the underlying functions of the identified miRNAs. Our findings revealed that four miRNAs, hsa-mir-128-3p, hsa-mir-421, hsa-mir-130b-5p, and hsa-mir-28-5p, were differentially expressed in CA vs. HB and had diagnostic power to discriminate CA from HB with AUC scores greater than 0.7. Enriched pathways based on the target genes of these miRNAs indicated their association with IGF-1. Furthermore, the Ingenuity Pathway Analysis performed on the proteomic data revealed that the IGF-1 signaling pathway was significantly enriched in CA vs. HB. In conclusion, these findings suggest that these miRNAs could potentially serve as biomarkers for detecting early-stage breast cancer from high-risk benign tumors by monitoring IGF signaling-induced malignant transformation.

Comprehensive landscape of tRNA-derived fragments in lung cancer

Transfer RNA (tRNA)-derived fragment (tRDF) is a novel small non-coding RNA that presents in different types of cancer. The comprehensive understanding of tRDFs in non-small cell lung cancer remains largely unknown. In this study, 1,550 patient samples of non-small cell lung cancer (NSCLC) were included, and 52 tRDFs with four subtypes were identified. Six tRDFs were picked as diagnostic signatures based on the tRDFs expression patterns, and area under the curve (AUC) in independent validations is up to 0.90. Two signatures were validated successfully in plasma samples, and six signatures confirmed the consistency of distinguished expression in NSCLC cell lines. Ten tRDFs along with independent risk scores can be used to predict survival outcomes by stages; 5a_tRF-Ile-AAT/GAT can be a prognosis biomarker for early stage. Association analysis of tRDFs-signatures-correlated mRNAs and microRNA (miRNA) were targeted to the cell cycle and oocyte meiosis signaling pathways. Five tRDFs were assessed to associate with PD-L1 immune checkpoint and correlated with the genes that target in PD-L1 checkpoint signaling pathway. Our study is the first to provide a comprehensive analysis of tRDFs in lung cancer, including four subtypes of tRDFs, investigating the diagnostic and prognostic values, and demonstrated their biological function and transcriptional role as well as potential immune therapeutic value.

Abstract 5865: Analysis of RNA sequencing data to advance our understanding of colorectal cancer health disparity in Native Hawaiians

Background Colorectal cancer (CRC) is the third deadliest cancer among Americans. Native Hawaiians (NH) as a unique ethnic group in the US, exhibit many disproportionate health issues. In particular, they suffer from both elevated CRC incidence and mortality rates. This study aimed to investigate if genetic differences could contribute to disparities observed between NH and White CRC patients by defining the association between unique NH-genetic differences and CRC outcomes.

Methods Paired tumor and adjacent normal biospecimens of NH CRC patients were collected from the Hawaii Tumor Registry (HTR), and gene expression and mutation were examined by RNA sequencing. Genomic data of CRC Whites was extracted from The Cancer Genome Atlas (TCGA) database as a comparative cohort. Differential expressed genes (DEGs) were identified for both NH and TCGA cohorts via DESeq2 with FDR q-value < 0.05 and a cutoff of 2-fold change. MutTecT2 and GATK were used to identify significant somatic mutations. Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression with 10-fold cross validation was performed to predict genetic risk factors for early detection, and Ingenuity Pathway Analysis (IPA) was processed for canonical pathways and network discovery. Univariate Cox proportional regression was performed to identify DEGs related to patient survival; multivariable Cox regression model with stepwise fitting generated a prognostic index (PI), and the prediction value was examined by the Area Under the Receiver Operating Characteristic Curve (AUC). A nomogram was developed by integrating PI and clinicopathologic factors; calibration curves were provided to internally validate the performance, and discriminative ability was appraised by concordance index.

Results In total, 2096 DEGs were identified between NH tumor and normal groups, 1740 transcripts and 78 carrying mutations were unique to NH compared to the TCGA Whites cohort. A set of 23 genes including 10 NH specific DEGs were identified as genetic risk factors for detecting NH with CRC, and the AUC was 99.8%. A 9 gene-signature prognostic model including 5 NH specific DEGs was built with high survival prediction capability (AUC=0.99), and Kaplan-Meier curve showed that the low PI group had a better survival than the high PI group in NH with CRC (Logrank P=3.6E-05). After adjustment by age, gender, and tumor grade, the prognostic 9 gene-signature was still significant (P=0.0059). By integrating the above signatures with prognostic clinicopathologic features, a nomogram was constructed to stratified patients with overall survival rates for 3, 10, and 20 years.

Conclusion This study demonstrated that CRC tumors from NH patients differ from White patients in their gene expression patterns and mutations, particularly those associated with clinical outcomes, which reinforced the necessity of NH race-specific biomedical research.

Citation Format: Yuanyuan Fu, Devin Takahashi, Vedbar Khadka, Masaki Nasu, Mayumi Jijiwa, Heather Borgard, Peiwen Fei, Youping Deng. Analysis of RNA sequencing data to advance our understanding of colorectal cancer health disparity in Native Hawaiians [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 5865.

Abstract 1241: Six potential biomarkers for non-small cell lung cancer diagnosis and prognosis

tRNA-derived fragment (tRDF) is novel small non-coding RNA that presences in different types of cancer tissue. More evidence has shown that tRDFs are associated with cancer progression through cell proliferation. In this study, we took advantage of public database and small RNA sequencing to investigate the diagnosis and prognosis potential of tRDFs as a biomarker for non-small cell lung cancer. We collected 1028 patient samples including adenocarcinoma from TCGA, GEO, and plasma. We gathered all fragments upstream sequences and 5’-tRF, to be categorized as 5’-tRDF and fragments 3’-tRF and downstream sequences, to be categorized as 3’-tRDF. 52 tRDFs were identified that were common in TCGA and GEO, and clustering results separated two GEO with TCGA as distinct expression pattern. 11 differentially expressed tRDFs were screened out from the GEO data and exhibited excellent diagnostic value. The AUC of two independent validations was up to 0.90. Six tRDFs, 5P_tRNA-Gly-TCC-1-1, 5a_tRF-Ile-AAT/GAT, 3P_tRNA-Arg-TCG-1-1, and 3P_tRNA-Arg-TCT-4-1, 5P_tRNA-Asn-GTT-2-3, 5a_tRF-Asp-GTC, were named as tRDF signatures and exhibited the same excellent diagnosis ability, and combination had better performance than individual tRDFs. Plasma data validated the diagnostic characteristics of two signatures, 3P_tRNA-Arg-TCG-1-1 and 5P_tRNA-Asn-GTT-2-3, that could serve as novel diagnostic biomarkers. We investigated the relationship between signatures and prognosis by stages and following-up times in TCGA-LUAD. 5a_tRF-Ile-AAT/GAT were identified to be a significant prognostic value with survival time on 36 months and 24 months among early stages patients. 3P_tRNA-Arg-TCT-4-1 was identified to associate with survival outcome within 12 and six months in early stages. We also assessed the role of tRDFs in transcriptional and post-transcriptional events. 3’-tRDFs showed more correlation with miRNA than 5’-tRDFs. A correlation analysis showed signatures, 5a_tRF-Asp-GTC, dominated the most correlation with miRNAs. Enrichment results of six tRDFs signatures presented PI3K-Akt, MAPK, and endocytosis signaling pathways are associated with tRDF target miRNAs. We also analyzed the signaling pathway characteristic of the six signatures tRDFs-target genes and found the tRDFs correlated genes are significantly activated in the cell cycle, oocyte meiosiss. Five signatures were assessed to associate with PD-L1 immune checkpoint and correlated with the genes that targets in PD-L1 checkpoint signaling pathway. Our study is the first to provide a comprehensive analysis of tRDFs as biomarkers in lung cancer, investigating the diagnostic and prognostic values of tRDFs, and demonstrated their biological function and transcriptional role as well as potential immune therapeutic value. This work highlights the potential clinical utility of tRDFs in lung cancer therapy and provides evidence of tRDF-target treatment in lung cancer.

Citation Format: Zitong Gao, Mayumi Jijiwa, Masaki Nasu, Heather Borgard, Jinwen Xu, Ting Gong, Shaoqiu Chen, Yuanyuan Fu, Youping Deng. Six potential biomarkers for non-small cell lung cancer diagnosis and prognosis [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 1241.

Abstract PO-167: Predictive genetic risk factors and prognostic nomogram for colorectal cancer in Native Hawaiian population

Background While Native Hawaiians (NH) comprise a small portion of the US population, their numbers are expected to increase. Concerningly, NH exhibit disproportionate health issues, and specifically those with colorectal cancer (CRC) present elevated incidence and mortality above the US population. This study aims to identify race-specific genetic factors for CRC early detection and prognosis in this unique population. Methods Paired tumor and adjacent normal biospecimens from NH patients with primary CRC were collected from the Hawaii Tumor Registry (HTR), and RNA sequencing on 41 paired samples were performed to establish the first genome-wide transcriptome profiling dataset specifically for NH with CRC. RNAseq data of 18 paired samples and additional 212 cancer samples were taken from The Cancer Genome Atlas (TCGA) white patients. Differential expressed genes (DEGs) were identified for both NH and TCGA cohorts via DESeq2 with FDR q-value < 0.05 and a cutoff of 2-fold change. A diagnostic model was built by Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression with 10-fold cross validation, and Ingenuity Pathway Analysis (IPA) was processed for canonical pathways and network discovery. Univariate Cox proportional regression was performed to identify DEGs related to NH patient survival; multivariable Cox regression model with stepwise fitting generated a prognostic index (PI): PI=Σbi × expGenei (where expGene defines the gene expression and b equals the regression coefficient), and the prediction value was examined by the Area Under the Receiver Operating Characteristic (ROC) Curve (AUC). A nomogram was developed by integrating PI and clinicopathologic factors; calibration curves were provided to internally validate the performance, and discriminative ability was appraised by concordance index. Results In total, 2096 DEGs were identified between tumor and normal groups, and 1740 transcripts were unique to NH compared to the TCGA Whites cohort. A set of 23 genes including 10 NH specific DEGs was identified as genetic risk factors for detecting NH with CRC, and the AUC was 99.8%. A 9 gene-signature prognostic model including 5 NH specific DEGs was built with high survival prediction capability (AUC=0.99), and Kaplan-Meier curve showed that the low PI group had a better survival than the high PI group in NH with CRC (Logrank P=3.6E-05). After adjustment by age, gender, and tumor grade, the prognostic 9 gene-signature was still significant (P=0.0059). By integrating the above signatures with prognostic clinicopathologic features, a nomogram was constructed to stratified patients with overall survival rates for 3, 10, and 20 years. Conclusion Divergent DEGs and consequential pathways between NH and TCGA cohort reinforced the necessity of NH race specific biomedical research. The prognostic gene signature offered evidence that genomic data provided independent and complementary prognostic information, and the nomogram incorporating genetic and clinicopathological factors refined the prognosis of CRC for this unique population.

Citation Format: Yuanyuan Fu, Devin Takahashi, Vedbar Khadka, Masaki Nasu, Mayumi Jijiwa, Yu Chen, Heather Borgard, Youping Deng. Predictive genetic risk factors and prognostic nomogram for colorectal cancer in Native Hawaiian population [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PO-167.

The SEQC2 epigenomics quality control (EpiQC) study

BACKGROUND

Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA's Epigenomics Quality Control Group.

RESULTS

Each sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms.

CONCLUSIONS

The data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.

The Function and Mechanism of Lipid Molecules and Their Roles in The Diagnosis and Prognosis of Breast Cancer

Lipids are essential components of cell structure and play important roles in signal transduction between cells and body metabolism. With the continuous development and innovation of lipidomics technology, many studies have shown that the relationship between lipids and cancer is steadily increasing, involving cancer occurrence, proliferation, migration, and apoptosis. Breast cancer has seriously affected the safety and quality of life of human beings worldwide and has become a significant public health problem in modern society, with an especially high incidence among women. Therefore, the issue has inspired scientific researchers to study the link between lipids and breast cancer. This article reviews the research progress of lipidomics, the biological characteristics of lipid molecules, and the relationship between some lipids and cancer drug resistance. Furthermore, this work summarizes the lipid molecules related to breast cancer diagnosis and prognosis, and then it clarifies their impact on the occurrence and development of breast cancer The discussion revolves around the current research hotspot long-chain non-coding RNAs (lncRNAs), summarizes and explains their impact on tumor lipid metabolism, and provides more scientific basis for future cancer research studies.

Identification of plasma lipid species as promising diagnostic markers for prostate cancer

BACKGROUND

Prostate cancer is a very common and highly fatal in men. Current non-invasive detection methods like serum biomarker are unsatisfactory. Biomarkers with high accuracy for diagnostic of prostate cancer are urgently needed. Many lipid species have been found related to various cancers. The purpose of our study is to explore the diagnostic value of lipids for prostate cancer.

RESULTS

Using triple quadruple liquid chromatography electrospray ionization tandem mass spectrometry, we performed lipidomics profiling of 367 lipids on a total 114 plasma samples from 30 patients with prostate cancer, 38 patients with benign prostatic hyperplasia (BPH), and 46 male healthy controls to evaluate the lipids as potential biomarkers in the diagnosis of prostate cancer. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database was used to construct the potential mechanism pathway. After statistical analysis, five lipids were identified as a panel of potential biomarkers for the detection of prostate cancer between prostate cancer group and the BPH group; the sensitivity, specificity, and area under curve (AUC) of the combination of these five lipids were 73.3, 81.6%, and 0.800, respectively. We also identified another panel of five lipids in distinguishing between prostate cancer group and the control group with predictive values of sensitivity at 76.7%, specificity at 80.4%, and AUC at 0.836, respectively. The glycerophospholipid metabolism pathway of the selected lipids was considered as the target pathway.

CONCLUSIONS

Our study indicated that the identified plasma lipid biomarkers have potential in the diagnosis of prostate cancer.

Optimal fluorescent-dye staining time for the real-time detection of microbes: a study of Saccharomyces cerevisiae

AIMS

To provide information on the time-dependent behaviour of microbe staining by fluorescent dyes in the order of seconds, which is important in terms of the recent rapid and online techniques for microbe measurements and/or environmental microbe analysis.

METHODS AND RESULTS

For combinations of yeast (Saccharomyces cerevisiae) and typical dyes, including DAPI (4',6-diamidino-2-phenylindole) and Auramine-O, a suspension of yeast cells in ultrapure water was injected into a dye solution in a micro cuvette placed inside a spectrofluorometer and the fluorescence intensity of the resulting solution was measured at 1 s intervals, starting immediately after the mixing and continued until the time for the maximum intensity using various concentrations of yeast and dyes. The relaxation time τ, which corresponds to ~63·2% of the maximum fluorescence intensity, was shown to decrease to below 1 s with increasing DAPI concentration, whereas it remained constant for 2-3 s with increasing Auramine-O concentration, for example at a yeast concentration of 100 µg ml^-1 .

CONCLUSIONS

For the conditions of yeast >10 µg ml^-1 , DAPI >1 µg ml^-1 and Auramine-O >0·1 µg ml^-1 , τ could be adjusted to below 5 s to achieve a rapid and stable staining.

SIGNIFICANCE AND IMPACT OF THE STUDY

Design and operating conditions for rapid and online measurements of microbes can be optimized.

A Subset of Mesotheliomas With Improved Survival Occurring in Carriers of BAP1 and Other Germline Mutations

PURPOSE

We hypothesized that four criteria could help identify malignant mesotheliomas (MMs) most likely linked to germline mutations of BAP1 or of other genes: family history of MM, BAP1-associated cancers, or multiple malignancies; or age younger than 50 years.

PATIENTS AND METHODS

Over the course of 7 years, 79 patients with MM met the four criteria; 22 of the 79 (28%) reported possible asbestos exposure. They were screened for germline BAP1 mutations by Sanger sequencing and by targeted next-generation sequencing (tNGS) for germline mutations in 55 additional cancer-linked genes. Deleterious mutations detected by tNGS were validated by Sanger sequencing.

RESULTS

Of the 79 patients, 43 (16 probands and 27 relatives) had deleterious germline BAP1 mutations. The median age at diagnosis was 54 years and median survival was 5 years. Among the remaining 36 patients with no BAP1 mutation, median age at diagnosis was 45 years, median survival was 9 years, and 12 had deleterious mutations of additional genes linked to cancer. When compared with patients with MMs in the SEER cohort, median age at diagnosis (72 years), median survival for all MM stages (8 months), and stage I (11 months) were significantly different from the 79 patients with MM in the current study ( P < .0001).

CONCLUSION

We provide criteria that help identify a subset of patients with MM who had significantly improved survival. Most of these patients were not aware of asbestos exposure and carried either pathogenic germline mutations of BAP1 or of additional genes linked to cancer, some of which may have targeted-therapy options. These patients and their relatives are susceptible to development of additional cancers; therefore, genetic counseling and cancer screening should be considered.

Heat Dissipation through the Blood Contacting Surface of a Thermally Driven LVAS

A heat exchanger for a totally implantable heat driven LVAD is an essential element in overall system thermal management. The heat exchange is accomplished by supplying cooling water from a pusher-plate driven water pump to the engine and then to the heat exchanger on the pump housing. The temperature of the interface between the blood and pump surface is of critical importance for clinically acceptable operation of the system. Temperatures were measured by instrumenting a pump housing with thermocouples and an electric heater on a mock circulatory loop. Flows were varied from 1 to 8 l/min and heat input was 20 watts. At 1.0 l/min pump flow the maximum inner surface temperature rise is 4.5°C. In vitro tests were conducted to examine the effect of elevated temperature on platelete function. Both platelet aggregation and adhesion were reduced at elevated temperatures of 42 and 478C indicating a potential benefit of reduced thrombogenesis on the heated housing surface.

Abstract 2553: High-density array-CGH with targeted NGS unmask multiple non-contiguous minute deletions on chromosome 3p21 in mesothelioma

We used a custom-made comparative genomic hybridization-array (aCGH; average probe interval 254 bp) to screen 33 malignant mesothelioma (MM) biopsies for somatic copy number loss throughout the 3p21 region (10.7 Mb) that harbors 251 genes, including BRCA1-associated protein 1 (BAP1), the most commonly mutated gene in MM. We identified frequent minute biallelic deletions (&lt;3 Kb) in 46/251 genes: four were cancer associated genes: SETD2 (7/33), BAP1 (8/33), PBRM1 (3/33) and SMARCC1 (2/33). These four genes were further investigated by targeted Next Generation Sequencing (tNGS), which revealed sequence-level mutations causing biallelic inactivation. Combined high-density aCGH and tNGS revealed biallelic gene inactivation in SETD2 (9/33, 27%), BAP1 (16/33, 48%), PBRM1 (5/33, 15%) and SMARCC1 (2/33, 6%). The incidence of genetic alterations detected is much higher than reported in the literature because minute deletions are not detected by NGS or commercial aCGH. Many of these minute deletions were not contiguous but rather they alternated with segments showing oscillating copy number changes along the 3p21 region. Functional assays revealed that SETD2, PBRM1 and SMARCC1 act as tumor suppressor in MM. In summary, we found that in MM: 1) multiple minute simultaneous biallelic deletions are frequent in chromosome 3p21, where they occur as distinct events involving multiple genes; 2) in addition to BAP1, mutations of SETD2, PBRM1 and SMARCC1 are frequent in MM; 3) our results suggest that high-density aCGH combined with tNGS provide a more precise estimate of the frequency and types of genes inactivated in human cancer, than approaches based exclusively on NGS strategy.

Citation Format: Michele Carbone, Yoshie Yoshikawa, Mitsuru Emi, Tomoko Hashimoto-Tamaoki, Masaki Ohmuraya, Ayuko Sato, Tohru Tsujimura, Seiki Hasegawa, Takashi Nakano, Masaki Nasu, Sandra Pastorino, Agata Szymiczek, Angela Bononi, Harvey I. Pass, Haining Yang. High-density array-CGH with targeted NGS unmask multiple non-contiguous minute deletions on chromosome 3p21 in mesothelioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2553. doi:10.1158/1538-7445.AM2017-2553

Combined Genetic and Genealogic Studies Uncover a Large BAP1 Cancer Syndrome Kindred Tracing Back Nine Generations to a Common Ancestor from the 1700s

We recently discovered an inherited cancer syndrome caused by BRCA1-Associated Protein 1 (BAP1) germline mutations, with high incidence of mesothelioma, uveal melanoma and other cancers and very high penetrance by age 55. To identify families with the BAP1 cancer syndrome, we screened patients with family histories of multiple mesotheliomas and melanomas and/or multiple cancers. We identified four families that shared an identical BAP1 mutation: they lived across the US and did not appear to be related. By combining family histories, molecular genetics, and genealogical approaches, we uncovered a BAP1 cancer syndrome kindred of ~80,000 descendants with a core of 106 individuals, whose members descend from a couple born in Germany in the early 1700s who immigrated to North America. Their descendants spread throughout the country with mutation carriers affected by multiple malignancies. Our data show that, once a proband is identified, extended analyses of these kindreds, using genomic and genealogical studies to identify the most recent common ancestor, allow investigators to uncover additional branches of the family that may carry BAP1 mutations. Using this knowledge, we have identified new branches of this family carrying BAP1 mutations. We have also implemented early-detection strategies that help identify cancers at early-stage, when they can be cured (melanomas) or are more susceptible to therapy (MM and other malignancies).

Germline BAP1 mutations cause a cancer syndrome characterized by high incidence of mesothelioma (MM), uveal melanoma and other cancers, and by very high penetrance, as all individuals carrying BAP1 mutations developed at least one, and usually several, malignancies throughout their lives. Through screening MM patients with histories of multiple cancers, we found four supposedly unrelated patients that shared an identical germline BAP1 mutation. We investigated whether this BAP1 mutation occurred in a ‘hot-spot’ for “de novo” mutations or whether these four MM patients shared a common ancestor. Using molecular genomics analyses we found that they are related. By genealogic studies we traced their ancestor to a couple that emigrated from Germany to North America in the early 1700’s; we traced the subsequent migration of their descendants, who are now living in at least three different US States. Our findings demonstrate that BAP1 mutations are transmitted among subsequent generations over the course of centuries. This knowledge and methodology is being used to identify additional branches of the family carrying BAP1 mutations. Our study shows that the application of modern genomic analyses, coupled with “classical” family histories collected by the treating physician, and with genealogical searches, offer a powerful strategy to identify high-risk germline BAP1 mutation carriers that will benefit from genetic counseling and early detection cancer screening.

Abstract 3944: High incidence of somatic BAP1 alterations in sporadic malignant mesothelioma

Background: Malignant mesothelioma (MM) is a lethal tumor whose pathogenesis results from complex interactions between host genetics and environmental carcinogens. BAP1 mutations were reported in 22% and 23% of sporadic MM in two US Caucasian studies whereas BAP1 mutations were found in 61% of sporadic MM in a Japanese study. The significant discrepancy in frequency of BAP1 mutations suggested either a possible influence of ethnicity or differences related to the methodological approaches. Methods: To investigate this apparent discrepancy, we carried out comprehensive genomic analyses using multiple techniques in order to detect somatic alterations of the BAP1 gene in tumors of 22 US Caucasian MM patients. Results: Six mutations were detected by Sanger sequencing, gross gene alterations were found in 7 MM specimens by Multiplex Ligation-Dependent Probe Amplification and copy number analysis, and a new splice variant was identified by cDNA sequencing. Changes in methylation were not observed in our study. Immunohistochemistry (IHC) revealed nuclear BAP1 staining in the 8 MM tumors containing wild-type BAP1 while tumor cells in the 14 biopsies with mutated BAP1 did not show any nuclear staining. We extended our BAP1 IHC analysis to an independent cohort of MM samples from the National Virtual Mesothelioma Bank and we found loss of BAP1 nuclear staining in 46 out of 67 biopsies. Moreover we found similar frequency of BAP1 loss across different MM histological subtypes. Conclusions: We identified somatic alterations of the BAP1 gene in 73.7% of Caucasian MM tumors in two independent cohorts of somatic MMs, underscoring the need to apply integrated genomic analyses to scrutinize the BAP1 gene for its alterations. Immunohistochemistry was the most reliable technique to detect BAP1 mutations in MM biopsies. The high incidence of alterations establishes BAP1 as the most commonly mutated gene in MM, regardless of ethnic background or histological subtype.

Citation Format: Masaki Nasu, Sandra Pastorino, Hugh Luk, Erin Flores, Francine Baumann, Amy Powers, Shreya Kanodia, Giovanni Gaudino, Yu-an Zhang, Adi Gazdar, Haining Yang, Harvey I. Pass, Mitsuru Emi, Michele Carbone. High incidence of somatic BAP1 alterations in sporadic malignant mesothelioma. [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 3944. doi:10.1158/1538-7445.AM2015-3944

Abstract 4796: A founder mutation in the BAP1 gene among four caucasian families with high incidences of malignant peritoneal mesothelioma and uveal melanoma: a molecular and genealogical study in a 10-generation BAP1 cancer syndrome kindred

The BAP1 cancer syndrome is characterized by a high incidence of malignant mesothelioma (MM), uveal melanoma (UM), cutaneous melanoma (CM), clear cell renal cell carcinoma (ccRCC), and it is expected that the clinical phenotype will continue to broaden in scope. Molecular screening for BAP1 gene mutations among 29 patients selected for clinically apparent familial MM led to the identification of a heterozygous C base deletion mutation (c.1832delC, p.Leu573fs*3) shared by four of those patients. The frame shift deletion is predicted to truncate the BAP1 protein, and immunohistochemistry analysis of tumor specimens revealed predominant cytoplasmic staining. We genotyped 650K SNPs of the four MM samples and four controls and carried out principal component analysis and whole-genome identity-by-descent analysis using publicly available genotype data from the 1000 Genomes Project, UK10K Project, and NHIBL Exome Sequencing Project. These analyses showed that the four MM patients are of Central Europe ancestry and that some are related by a kinship coefficient of 0.0186. Haplotype analysis showed the presence of significantly shared segments around the BAP1 gene (LOD&gt;37.1). The pairwise extent of shared segments between any of the four MM patients ranged in length from 9.1 to 34.2 Mbp and indicates the c.1832delC variant originated in a recent common ancestor within five to ten generations. Through a combined molecular genomic and genealogical approach, we ascertained, to our knowledge, the largest known genealogically connected BAP1 cancer syndrome kindred (K4), whose members can trace descent from a common ancestor in the 17th century. This pedigree provided a unique opportunity to examine effects of BAP1 alteration on tumor expression on various body sites and would facilitate study of gene-gene and gene-environment interaction involving the BAP1 gene. It also suggests that molecular screening of the BAP1 gene, coupled with genealogical research, would be an effective strategy for the early detection and early intervention for BAP1-associated malignancies.

Citation Format: Erin Flores, Mitsuru Emi, Todd Johnson, Tatsuhiko Tsunoda, Dusty Behner, Harriet Hoffman, Mary Hesdorffer, Masaki Nasu, Andrea Napolitano, Francine Baumann, Haining Yang, Michele Carbone. A founder mutation in the BAP1 gene among four caucasian families with high incidences of malignant peritoneal mesothelioma and uveal melanoma: a molecular and genealogical study in a 10-generation BAP1 cancer syndrome kindred. [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 4796. doi:10.1158/1538-7445.AM2015-4796

BAP1 hereditary cancer predisposition syndrome: a case report and review of literature

A 72-year-old woman was diagnosed with uveal melanoma, peritoneal mesothelioma and a primary biliary tract adenocarcinoma. She had a strong family history of mesothelioma as well as other malignancies including renal cell carcinoma. The recently described BAP1 hereditary cancer predisposition syndrome was suspected, but immunohistochemical labeling was not conclusive. Genetic testing confirmed a novel and unusual germline mutation in the ubiquitin hydrolase domain of the BAP1 gene (p.Tyr173Cys) and the patient was diagnosed with the BAP1 hereditary cancer predisposition syndrome. This case demonstrates the importance of clinically recognizing this rare syndrome and its manifestations, some which are still being characterized. It also highlights the importance of genetic testing in cases where there is a high clinical suspicion, even when screening tests, such as immunohistochemistry, in this case, are inconclusive. The diagnosis of a germline BAP1 mutation may have important implications for both the patient and their families with regards to further genetic testing and active surveillance programs. Further research is needed to fully understand the extent and clinical implications of this rare cancer syndrome.

Abstract 446: BAP1 mutation in mesothelioma and “BAP1 Cancer Syndrome”

Malignant mesothelioma (MM) is a lethal cancer whose pathogenesis results from complex interactions between host genetics and environmental carcinogens, such as asbestos and erionite fibers. Recently, BAP1 (BRCA associated protein 1) has been identified as a novel MM tumor suppressor gene located at 3p21, a region frequently deleted in MM, which encodes for a deubiquitinase enzyme known to target histones and other proteins.

We discovered that germline BAP1 mutations cause a novel cancer syndrome characterized by a significant excess of both pleural and peritoneal MM, uveal and cutaneous melanoma and possibly other tumors. In the same study, we reported that 22% sporadic MM tumors, among the Caucasian population, harbored somatic BAP1 mutations. Several other studies supported a relevant role of BAP1 in MM. However, a significant variation in the frequency of BAP1 mutation was found across different studies and populations. In fact, one research group found BAP1 gene altered in 61% of tumor samples from a Japanese cohort, pointing out to a possible influence of ethnicity on the prevalence of BAP-1 alterations among MM patients. However, the limitations in tumor sample sizes and methodological differences across studies do not allow for conclusive associations. We are now further analyzing BAP1 status and possible clinicopathological associations using different and more sensitive methods, such as MPLA, DNA and RNA sequencing, DNA copy number and methylation. Our preliminary results indicate that, regardless of ethnicity, BAP1 plays a crucial role in MM pathogenesis. More experiments are urgently needed to see whether BAP1 expression could be used in diagnostic, prognostic, or therapeutic settings. The impact of this work will extend to other cancers with BAP1 mutations.

Citation Format: Masaki Nasu, Andrea Napolitano, Sandra Pastorino, Mika Tanji, Erin Flores, Francine Baumann, Amy Powers, Giovanni Gaudino, Harvey I. Pass, Haining Yang, Michele Carbone. BAP1 mutation in mesothelioma and “BAP1 Cancer Syndrome”. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 446. doi:10.1158/1538-7445.AM2014-446

Ranpirnase Interferes with NF-κB Pathway and MMP9 Activity, Inhibiting Malignant Mesothelioma Cell Invasiveness and Xenograft Growth

The ribonuclease ranpirnase (Onconase) has been used empirically to treat malignant mesothelioma (MM) patients, and some of them had prolonged survivals. The aim of this study was to investigate the mechanisms of the therapeutic function of ranpirnase in MM cells. The effects of ranpirnase were studied in vivo and in vitro on 2 MM cell lines (epithelioid REN and sarcomatoid PPM-Mill). We found that ranpirnase was able to inhibit NF-κB nuclear translocation, evaluated by cell fractionation and immunoblotting as well as by immunofluorescence. Also, MMP9 secretion by MM cells was decreased by ranpirnase treatment, as assessed by the reduction of metalloproteinase activity, evaluated by zymography on culture-conditioned media. Ranpirnase induced apoptosis of MM cells in vitro and in vivo, causing a powerful inhibition of MM tumor growth in SCID xenografts, determined by In Vivo Imaging System (IVIS) of tumor cells engineered by lentiviral transduction of the luciferase gene. Finally, mice treated with ranpirnase showed a significantly prolonged survival. Our data provide a mechanistic rationale to explain the beneficial antitumor activity observed in some patients treated with ranpirnase and demonstrate that ranpirnase interferes with the NF-κB pathway, thus influencing MM tumor cell invasiveness and survival. It is hoped that this information will also facilitate the identification of those patients who are more likely to benefit from this drug and will also open a new frontier for the use of this drug in tumor types other than MM.

Maillard reaction, mitochondria and oxidative stress: potential role of antioxidants

Glycation and oxidative stress are two important processes known to play a key role in complications of many disease processes. Oxidative stress, either via increasing reactive oxygen species (ROS), or by depleting the antioxidants may modulate the genesis of early glycated proteins in vivo. Maillard Reactions, occur in vivo as well as in vitro and are associated with the chronic complications of diabetes, aging and age-related diseases. Hyperglycaemia causes the autoxidation of glucose, glycation of proteins, and the activation of polyol metabolism. These changes facilitate the generation of reactive oxygen species and decrease the activity of antioxidant enzymes such as Cu,Zn-superoxide dismutase, resulting in a remarkable increase of oxidative stress. A large body of evidence indicates that mitochondria alteration is involved and plays a central role in various oxidative stress-related diseases. The damaged mitochondria produce more ROS (increase oxidative stress) and less ATP (cellular energy) than normal mitochondria. As they are damaged, they cannot burn or use glucose or lipid and cannot provide cell with ATP. Further, glucose, amino acids and lipid will not be correctly used and will accumulate outside the mitochondria; they will undergo more glycation (as observed in diabetes, obesity, HIV infection and lipodystrophia). The objective of this paper is to discuss how to stop the vicious circle established between oxidative stress, Maillard Reaction and mitochondria. The potential application of some antioxidants to reduce glycation phenomenon and to increase the antioxidant defence system by targeting mitochondria will be discussed. Food and pharmaceutical companies share the same challenge, they must act now, urgently and energetically.

Scanning electron microscope imaging of bacteria based on DNA sequence

AIMS

To develop a scanning electron microscopic approach using in situ hybridization (SEM-ISH) for gaining both genetic and morphological information about target bacteria.

METHODS AND RESULTS

Target cells were hybridized with DNA-targeted polynucleotide probes, and a tyramide signal amplification system was used to increase the sensitivity. The protocol of SEM-ISH enabled to detect low copy number target DNA sequences in individual cells.

CONCLUSIONS

SEM-ISH allowed the in situ detection of bacteria carrying a specific gene.

SIGNIFICANCE AND IMPACT OF THE STUDY

Combining morphological study with SEM and ISH techniques appears to be a valuable tool to understand the spatial distribution of target cells in complex microbial communities on various materials.

Heat island mitigation using water retentive pavement sprinkled with reclaimed wastewater

In Japan, reclaimed wastewater has been recycled widely for non-potable urban applications and it is to be used for sprinkling roads to mitigate heat island in urban areas. To assess the heat island mitigation effects of the sprinkling reclaimed wastewater on water retentive pavement, we carried out a survey at Shiodome-District, Tokyo. The temperatures of air and roads, humidity, and WBGT (Wet-bulb globe temperature) were measured and heat flux was estimated to compare the condition of the areas with/without sprinkling. The following results were obtained. 1) Sprinkling reclaimed wastewater decreased the road surface temperature by 8 degrees during the daytime and by 3 degrees at night: temperatures equal to those on planting zones. Nevertheless sprinkling was done only in the daytime, the temperature decrease effect was not only obtained during the daytime: it continued through the night, due to the water retentive pavement. 2) Sprinkling reclaimed wastewater reduced the amount of sensible heat flux and increased that of latent heat flux. These results suggest that sprinkling reclaimed wastewater on water retentive pavement can effectively mitigate the heat island phenomenon.

Somatostatin inhibits the excitability of rat small-diameter trigeminal ganglion neurons that innervate nasal mucosa and project to the upper cervical dorsal horn via activation of somatostatin 2a receptor

This study investigated whether somatostatin (SST) modulates the excitability of nociceptive trigeminal ganglion (TRG) neurons that innervate the nasal mucosa and project to the upper cervical (C(1)) dorsal horn by using perforated-patch clamping, retrograde-labeling, and immunohistochemistry. Fluorogold (FG) retrograde labeling was used to identify the rat TRG neurons innervating the nasal mucosa, while microbeads (MB) were used to label neurons projected onto the superficial layer of the C(1) dorsal horn. FG-labeled small-diameter TRG neurons exhibited SST(2A) receptor immunoreactivity (19%) and half of these neurons were also labeled with MB. In whole-cell current-clamp mode, most (72%) of the dissociated FG-/MB-labeled TRG neurons were hyperpolarized by application of SST. The hyperpolarization was evoked by SST in a concentration-dependent manner (0.1-10 microM) and the responses were associated with a decrease in the cell input resistance. The minimum concentration to elicit a significant hyperpolarization was 1 microM. The repetitive firings during a depolarizing pulse were significantly reduced by SST (1 microM) application. The hyperpolarization and decreased firing evoked by SST were both blocked by the SST(2) receptor antagonist, CYN154806 (1 microM). Under voltage-clamp conditions, SST (1 microM) significantly increased the voltage-gated K(+) transient (I(A)) and sustained (I(K)) currents and these increases were abolished by coapplication of CYN154806 (1 microM). In the presence of both 4-aminopyridine (6 mM) and tetraethylammonium (10 mM), no significant changes in the membrane potential in response to SST application were found. These results suggest that modulation of trigeminal nociceptive transmission in the C(1) dorsal horn by activation of SST(2A) receptors occurs at the level of small-diameter TRG cell bodies and/or their afferent terminals, and that this may be related to regulation of protective upper-airway reflexes.

Normal esophageal mucosae adjacent to esophageal adenocarcinomas in both Japanese and U.S. patients have a field defect of methylation changes

4636

Background: Esophageal mucosae that reside next to gross cancer are often without histological premalignant changes. We hypothesized that DNA hypermethylation could be detected in “normal” tissues adjacent to esophageal adenocarcinomas (EAC). Methods: A cohort of patients from Japan (J, n=14) and the United States (US, n=41) with locally advanced EAC were evaluated for methylation status. Esophagectomy specimens provided a source of paired normal and tumor tissues. After DNA extraction, methylation specific PCR was used to evaluate the promoters of APC, p16 and MGMT in all samples. Methylation frequency was calculated for each patient and expressed as a percentage of total. Results: Age, gender, pathologic stage and epigenetic analyses of primary tumors were similar in each cohort. Methylation frequency of tumors was: APC (66% US; 70% J). p16 (39% US; 20% J). MGMT (63% US; 75% J). In adjacent histologically “normal” esophageal mucosae, the percentage of patients with methylation at 0, 1, 2 or 3 genes was 79%, 14%, 0%, 7% for the J group and 56%, 44%, 10% and 2% for the U.S. group. In both cohorts, the majority of the normal samples had no methylation changes. In over half of the total cohort, however, there was at least one gene in the adjacent histologically “normal” tissue positive for DNA hypermethylation. Very few samples in either group, however, had more than one gene methylated in histologically “normal” esophageal mucosae. In general, the same methylation pattern present in the “normal” tissue persisted in the primary malignancy. Conclusions: Histologically negative esophageal mucosae adjacent to cancer frequently show at least one hypermethylated gene in a multiple gene panel. These data suggest that for patients with EAC, regardless of nationality, there is a field defect of promoter hypermethylation changes in adjacent esophageal mucosae. These events reflect those of the primary malignancy, and are probably early and cumulative during carcinogenesis.

No significant financial relationships to disclose.

Unavoidable arterioplasty of the pulmonary main trunk for complete resection of mediastinal paraganglima--a case report

Anterior mediastinal paraganglioma is a rare neoplasm and its pathogenesis has not yet been fully understood. The treatment of choice is complete surgical resection, however, its hypervascular nature and proximity to the great vessels makes resection challenging. Operations for paraganglioma have been referred to as a surgical challenge. Moreover, definitive preoperative diagnoses of mediastinal paraganglioma are rarely made, which has made it difficult for thoracic surgeons to prepare for such a challenge preoperatively. We report a case of anterior mediastinal paraganglioma, which was resected successfully under cardiopulmonary bypass, followed by arterioplasty of the pulmonary main trunk.

Simple detection of small amounts of Pseudomonas cells in milk by using a microfluidic device

AIMS

Flow cytometry offers rapid and reliable analyses of bacteria in milk. However, a flow cytometer is relatively expensive and operation is rather complicated for an unskilled operator. We applied flow cytometry using a microfluidic device (on-chip flow cytometry) in detection of small amounts of milk-spoiling bacteria.

METHODS AND RESULTS

Pseudomonas cells in milk were in situ hybridized with Cy5-labelled probe specific for Pseudomonas spp. under optimized condition. Numbers of Pseudomonas cells in the stationary phase and in the starved state determined by on-chip flow cytometry were compared with those determined by conventional plate counting, and on-chip flow cytometry detected targeted cells in milk that were undetectable as colony forming units(CFU) on Standards Methods Agar.

CONCLUSIONS

The contamination in milk with fewer than 10 CFU ml(-1) of targeted cells in starved state was detectable with simple procedure (0.5 h milk-clearing, 1 h fixation, 2 h hybridization and 0.5 h on-chip flow cytometry following 12 h enrichment of cells).

SIGNIFICANCE AND IMPACT OF THE STUDY

On-chip flow cytometry following fluorescence in situ hybridization could be applicable to simple detection of milk-spoiling bacteria.

Activation of α2-adrenoreceptors suppresses the excitability of C1 spinal neurons having convergent inputs from tooth pulp and superior sagittal sinus in rats

The aim of the present study was to test the hypothesis that activation of alpha(2)-adrenoreceptors modulates the excitability of C1 neurons having convergent inputs from both the tooth pulp (TP) and the superior sagittal sinus (SSS), by using the microiontophoretic techniques of drug application and immunohistochemical approaches. Extracellular single-unit recordings were made from 38 C1 neurons responding to electrical stimulation of TP under pentobarbital-anesthetized rats. Seventy-one percent of C1 neurons (27/38) that responded to TP stimulation also responded to electrical stimulation of the SSS. In these neurons, L: -glutamate-evoked C1 neuronal discharge firings were increased in a dose-dependent manner. The mean glutamate-evoked firing rates were dose-dependently inhibited after microiontophoretic application of clonidine (alpha(2)-adrenoreceptor/imidazoline I(1) receptor agonist). The inhibition of glutamate-evoked C1 mean firings by clonidine was antagonized by the co-application of idazoxan (alpha(2)-adrenoreceptor/imidazoline I(2) receptor antagonist), yohimbine (alpha(2)-adrenoreceptor) but not the alpha(1)-adrenoreceptor antagonist, prazosin with affinity for alpha(2B)- and alpha(2C)-adrenoreceptors. The mean spontaneous discharge frequencies were significantly inhibited by the microiontophoretic application of clonidine and this inhibition was reversed by the co-application of idazoxan, yohimbine. Microiontophoresis of clonidine also resulted in a reduction of TP-/SSS-evoked activity and this effect was reversed by the co-application of yohimbine. Immunoreactivity for alpha(2A)-adrenoreceptor was found in the superficial layers of I-III in the C1 region. These results suggest that alpha(2)-adrenoreceptor agonist clonidine inhibits the excitability of C1 neurons having convergent inputs from TP and SSS afferents, and that the activation of alpha(2A)-adrenoreceptors onto C1 dorsal horn neurons may contribute as a useful therapeutic target for the alleviation of trigeminal referred pain associated with migraine and tooth pain.

Enhanced excitability of rat trigeminal root ganglion neurons via decrease in A-type potassium currents following temporomandibular joint inflammation

The aim of the present study was to investigate the effect of temporomandibular joint inflammation on the excitability of trigeminal root ganglion neurons innervating the temporomandibular joint using a perforated patch-clamp technique. Inflammation was induced by injection of complete Freund's adjuvant into the rat temporomandibular joint. The threshold for escape from mechanical stimulation in the temporomandibular joint-inflamed rats was significantly lower than that in control rats. Fluorogold labeling was used to identify the trigeminal root ganglion neurons innervating the site of inflammation. When voltage-clamp (V(h)=-60 mV) conditions were applied to these Fluorogold-labeled small diameter trigeminal root ganglion neurons (<30 mum), voltage-dependent transient K(+) current densities were significantly reduced in the inflamed rats compared with controls. In addition, the voltage-dependence of inactivation of the voltage-dependent transient K(+) current was negatively shifted in the labeled temporomandibular joint-inflamed trigeminal root ganglion neurons. Furthermore, temporomandibular joint inflammation significantly reduced the threshold current and significantly increased action potential firings evoked at two-fold threshold in the Fluorogold-labeled small trigeminal root ganglion neurons. Application of 4-aminopyridine (0.5mM) to control trigeminal root ganglion neurons mimicked the changes in the firing properties observed after complete Freund's adjuvant treatment. Together, these results suggest that temporomandibular joint inflammation increases the excitability of trigeminal root ganglion neurons innervating temporomandibular joint by suppressing voltage-dependent transient K(+) current via a leftward shift in the inactivation curve. These changes may contribute to trigeminal inflammatory allodynia in temporomandibular joint disorder.

Current bioremediation practice and perspective

The use of microbes to clean up polluted environments, bioremediation, is a rapidly changing and expanding area of environmental biotechnology. Although bioremediation is a promising approach to improve environmental conditions, our limited understanding of biological contribution to the effect of bioremediation and its impact on the ecosystem has been an obstacle to make the technology more reliable and safer. Providing fundamental data to resolve these issues, i.e., the behavior of the target bacteria directly related to the degradation of contaminants and the changes in microbial communities during bioremediation, has been a challenge for microbiologists since many environmental bacteria cannot yet be cultivated by conventional laboratory techniques. The application of culture-independent molecular biological techniques offers new opportunities to better understand the dynamics of microbial communities. Fluorescence in situ hybridization (FISH), in situ PCR, and quantitative PCR are expected to be powerful tools for bioremediation to detect and enumerate the target bacteria that are directly related to the degradation of contaminants. Nucleic acid based molecular techniques for fingerprinting the 16S ribosomal DNA (rDNA) of bacterial cells, i.e., denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP), enable us to monitor the changes in bacterial community in detail. Such advanced molecular microbiological techniques will provide new insights into bioremediation in terms of process optimization, validation, and the impact on the ecosystem, which are indispensable data to make the technology reliable and safe.

Multicolour digital image analysis system for identification of bacteria and concurrent assessment of their respiratory activity

AIMS

To develop a rapid and simple multicolour digital image analysis system for simultaneous identification of bacteria and assessment of their metabolic activity.

METHODS AND RESULTS

We developed an image analyser capable of distinguishing triple-stained bacterial cells. Bacteria were stained with a nucleic acid stain, a fluorescent antibody and a fluorescent metabolic indicator for enumeration, species identification and assessment of metabolic activity. This multicolour image analyser was used to simultaneously identify Escherichia coli O157:H7 in milk samples and assess their respiratory activity. The images of the triple-stained bacteria were captured using a combination of blue light and u.v. excitation and an epifluorescence microscope and were processed by our image analyser. We found a good correlation between the counts of actively respiring (r = 0.93) and total (r = 0.94) E. coli O157:H7 measured by digital image analysis and visual observation.

CONCLUSION

The multicolour digital image analysis system described here was able to quantify active pathogenic micro-organisms within 2 h.

SIGNIFICANCE AND IMPACT OF THE STUDY

This multicolour image analysis allows the rapid and simultaneous quantification of bacteria, identification of species and assessment of metabolic activity.

Role of capsaicin-sensitive primary afferent inputs from the masseter muscle in the C1 spinal neurons responding to tooth-pulp stimulation in rats

The aim of the present study was to demonstrate the convergence of inputs from masseter muscle (MM) and tooth pulp (TP) onto C1 spinal neurons and to determine whether the afferent fibers express the functional vanilloid receptor (VR1). Extracellular single-unit recordings were made from 61 C1 units responding to TP electrical stimulation with a constant temporal relationship to a digastric electromyogram signal in pentobarbital anesthetized rats. Eighty-four percent of C1 neurons responding to TP stimulation also responded to the ipsilateral MM stimulation. Of these neurons, 61% were considered to be afferent inputs from Adelta-fibers and the remaining units (39%) were C-fibers, based on calculation of the nerve conduction velocity. Intramuscular injection of capsaicin (0.05 and 0.1%) produced a reduction in a MM-induced C1 neuronal activity in a dose-dependent manner and this effect was antagonized by pretreatment with an antagonist of VR1, capsazepine. Some of these units were also excited by noxious heat stimulation (> 43 degrees C). The trigeminal root ganglion (TRG) neurons that innervated the MM were retrogradely labeled with Fluorogold (FG) and the small-diameter FG-labeled TRG neurons expressed the immunoreactivity for VR1. After intramuscular mustard oil injection (noxious chemical stimulation), the C1 neuronal activity induced by both touch and pinch stimuli was enhanced and their receptive field sizes were significantly expanded. These changes were reversed within 15-20 min. These results suggest that there may be the convergence of noxious afferents inputs from the MM and TP afferents on the same C1 neurons in rats, and that the afferent fibers expressing the functional VR1 may contribute to the hyperalgesia and/or referred pain associated with temporomandibular joint disorder.

High plasma concentrations of osteopontin in patients with interstitial pneumonia

Osteopontin (OPN) produced by alveolar macrophages functions as a fibrogenic cytokine in the development of bleomycin (BLM)-induced murine pulmonary fibrosis, and OPN mRNA is expressed on lung tissues from patients with idiopathic pulmonary fibrosis (IPF). The present study investigates plasma OPN levels in human interstitial pneumonia (IP) and their relationships with disease severity by analyzing the correlation between plasma OPN concentrations and pulmonary functions. The concentrations of OPN in plasma were measured in 17 patients with IP, in 9 with sarcoidosis and in 20 healthy controls using an antigen-capture enzyme-linked immunosorbent assay. The concentrations of OPN in plasma were significantly higher in IP patients than in those with sarcoidosis or in controls. Based on a Receiver Operating Characteristic curve analysis, cut-off points between 300 and 380 ng/ml discriminated between IP and control subjects with 100% sensitivity and 100% specificity. In such case, the sensitivity for sarcoidosis decreased (55.5-33.3%) in cut-offs with 100% specificity. Plasma OPN levels inversely and closely correlated with arterial oxygen tension (PaO2) in patients with IP. Immunohistochemically, OPN was localized predominantly in macrophages and airway epithelium. These findings suggest that plasma OPN levels were found to be associated with the presence of IP, and that OPN play an important role in the development of IP.

Rapid monitoring of microbial contamination on herbal medicines by fluorescent staining method

AIMS

To apply fluorescent staining method for fast assessment of microbial quality of herbal medicines.

METHODS AND RESULTS

The number of total bacteria and esterase-active bacteria on powdered traditional Chinese medicines were enumerated by fluorescent staining method using 6-carboxyfluorescein diacetate (6CFDA) and 4',6-diamidino-2-phenylindole (DAPI), and they were compared with colony-forming units (CFU). The CFU was approximately 10(3) per gram in ginseng radix, and no bacterial colonies were detected from others. However, the total bacterial number (TDC) was more than 10(7) per gram, and number of bacteria possessing esterase activity ranged from 1 to 3% of TDC.

CONCLUSIONS, SIGNIFICANCE AND IMPACT OF THE STUDY

Many bacteria in each Chinese medicine had enzyme activity and most of them could not be detected by conventional plate counting technique. Enumeration of bacterial cells on traditional Chinese medicines by fluorescent staining method requires less than 1 h. The double staining method with 6CFDA and DAPI could be applicable to rapid microbial monitoring of crude drugs.

Real-time PCR assays based on distinct genomic regions for cytomegalovirus reactivation following hematopoietic stem cell transplantation

Real-time PCR has many advantages compared with antigenemia and qualitative PCR assays for detecting cytomegalovirus (CMV) infection in patients following SCT. However, the procedure used in each report was not standardized. This study compares the CMV load detected by real-time PCR assays amplifying distinct genomic regions. Real-time PCR assays based on US17, UL65, immediate early protein (IE) and glycoprotein B(gB) were selected and comparisons were made between each genomic region, and with antigenemia and nested PCR (IE region) in 18 SCT patients. The CMV load detected by real-time PCR using all combinations of primers targeting distinct genomic regions and by antigenemia assays correlated well. However, US17 and UL65-PCR could detect CMV earlier than gB-PCR, antigenemia and nested PCR assays. In longitudinal analysis, gB-PCR demonstrated a trend for showing a lower viral load in some patients than US17-, UL65- and IE-PCR. Moreover, the results suggest that a cutoff level of 500 copies/ml might be used to decide when to initiate treatment. We propose that monitoring should be carried out using real-time PCR assays targeting the US17 region and that a CMV load of 500 copies/ml could be used as a cutoff value for initiating treatment in patients following SCT, receiving immunoglobulin prophylaxis.

Bacterial population dynamics and community structure in a pharmaceutical manufacturing water supply system determined by real-time PCR and PCR-denaturing gradient gel electrophoresis

AIMS

To control bacteria in the pharmaceutical water supply system.

METHODS AND RESULTS

Bacteria were enumerated by conventional culture method and fluorescent vital staining. Activated carbon treatment and storage in a tank provided favourable environments for bacterial growth. The bacterial population of the water in both the post-activated carbon treatment and the tank was analysed by denaturing gradient gel electrophoresis (DGGE) with PCR-amplified 16S rDNA fragments including V6, -7, and -8 regions. The bacterial community structure in activated carbon treated water was stable throughout the year. Several kinds of bacteria such as genus Aquaspirillum and Methylobacterium were found in the water after activated carbon treatment. The bacterial community structure was changed and other bacteria such as mycobacteria were detected after storage. Mycobacteria were quantified in water samples using real-time PCR targeting the 16S rDNA gene. Mycobacteria were also detected in tap water and their number was increased 10(3)-10(4)-fold higher after storage.

CONCLUSION

These data suggest the importance of culture-independent methods for quality control of water used in pharmaceutical manufacturing.

SIGNIFICANCE AND IMPACT OF THE STUDY

Critical steps and specified bacteria that should be controlled in the water supply system were recognized by culture-independent methods. These data will enable effective control of water used in the pharmaceutical industry.

Opioidergic modulation of excitability of rat trigeminal root ganglion neuron projections to the superficial layer of cervical dorsal horn

The aim of the present study was to investigate the effect of a micro-opioid receptor agonist DAMGO (Tyr-d-Ala-Gly-NMe-Phe-Gly-ol) on the excitability of trigeminal root ganglion (TRG) neurons, projecting onto the superficial layer of the cervical dorsal horn, by using the perforated-patch technique and to determine whether TRG neurons show the expression of mRNA or functional protein for micro-opioid receptors by using reverse transcription-polymerase chain reaction (RT-PCR) and immunohistochemistry. TRG neurons projecting onto the superficial layer of the cervical dorsal horn were retrogradely labeled with Fluorogold (FG). The cell diameter of FG-labeled TRG neurons was small (<30 microm). Under voltage-clamp (V(h)=-60 mV), voltage-dependent K(+) currents were recorded in the TRG neurons and isolated by blocking Na(+) and Ca(2+) currents with appropriate ion replacement. Separation of the K(+) current components was achieved by the response to variation in the conditioning voltage. Two distinct K(+) current components, a transient (I(A)) and sustained (I(K)), were identified. DAMGO significantly increased I(A) by 57% (20 microM) and in a dose-dependent manner (1-50 microM). Similarly, I(K) was also enhanced by DAMGO administration (42%, 20 microM). The augmentation of both I(A) and I(K) was antagonized by a micro-opioid receptor antagonist, CTOP (d-Phe-Cys-Thr-d-Trp-Orn-Thr-Pen-Thr-NH(2)). Hyperpolarization of the membrane potential was elicited by DAMGO (20 microM) and the response was associated with a decrease in the input resistance. DAMGO induced hyperpolarization was blocked by CTOP. DAMGO-sensitive I(A) and I(K) currents were antagonized by K(+) channel blockers, 4-aminopyridine (4-AP) and tetraethylammonium (TEA). In the presence of both 4-AP and TEA, no significant changes in membrane potential induced by DAMGO application were observed. In the presence of BaCl(2), DAMGO evoked hyperpolarization with decreased resistance was observed. The firing rate of action potentials and the first spike duration induced by depolarizing step pulses were decreased in the presence of DAMGO. RT-PCR analysis demonstrated the expression of mRNA for micro-opioid receptors in the trigeminal ganglia. The micro-opioid receptor immunoreactivity was expressed in the small diameter FG-labeled TRG neurons. These results suggest that the activation of micro-opioid receptors inhibits the excitability of rat small diameter TRG neurons projecting on the superficial layer of the cervical dorsal horn and this inhibition is mediated by potentiation of voltage-dependent K(+) currents. We therefore concluded that modulation of nociceptive transmission in the trigeminal system, resulting in the functional activation of micro-opioid receptors, occurs at the level of small TRG cell bodies and/or their primary afferent terminals, which contribute to opioid analgesia in the trigeminal pain.