[Theoretical models for influenza vaccination behavior at the individual level]

Influenza imposes a significant disease burden on society and individuals annually, and influenza vaccination is considered a significant public health measure to prevent influenza and reduce influenza-related severe disease and death. The low influenza vaccination rate in China is partly due to certain factors affecting the willingness and behavior of individuals to receive them. Scientific research and targeted interventions on these factors can effectively improve the vaccination situation. Commonly used individual-level theoretical models for influenza vaccination behavior include the health belief model, protection motivation theory, and theory of planned behavior. This study reviews theoretical models commonly employed in researching influenza vaccination willingness and behavior. An overview of these practical applications and challenges models is presented to provide references for relevant research and intervention programs in China.

Discovery of deaminase functions by structure-based protein clustering

The elucidation of protein function and its exploitation in bioengineering have greatly advanced the life sciences. Protein mining efforts generally rely on amino acid sequences rather than protein structures. We describe here the use of AlphaFold2 to predict and subsequently cluster an entire protein family based on predicted structure similarities. We selected deaminase proteins to analyze and identified many previously unknown properties. We were surprised to find that most proteins in the DddA-like clade were not double-stranded DNA deaminases. We engineered the smallest single-strand-specific cytidine deaminase, enabling efficient cytosine base editor (CBE) to be packaged into a single adeno-associated virus (AAV). Importantly, we profiled a deaminase from this clade that edits robustly in soybean plants, which previously was inaccessible to CBEs. These discovered deaminases, based on AI-assisted structural predictions, greatly expand the utility of base editors for therapeutic and agricultural applications.

Comparison of In-Frame Deletion, Homology-Directed Repair, and Prime Editing-Based Correction of Duchenne Muscular Dystrophy Mutations

Recent progress in CRISPR gene editing tools has substantially increased the opportunities for curing devastating genetic diseases. Here we compare in-frame deletion by CRISPR-based non-homologous blunt end joining (NHBEJ), homology-directed repair (HDR), and prime editing (PE, PE2, and PE3)-based correction of two Duchenne Muscular Dystrophy (DMD) loss-of-function mutations (c.5533G>T and c.7893delC). To enable accurate and rapid evaluation of editing efficiency, we generated a genomically integrated synthetic reporter system (VENUS) carrying the DMD mutations. The VENUS contains a modified enhanced green fluorescence protein (EGFP) gene, in which expression was restored upon the CRISPR-mediated correction of DMD loss-of-function mutations. We observed that the highest editing efficiency was achieved by NHBEJ (74-77%), followed by HDR (21-24%) and PE2 (1.5%) in HEK293T VENUS reporter cells. A similar HDR (23%) and PE2 (1.1%) correction efficiency is achieved in fibroblast VENUS cells. With PE3 (PE2 plus nicking gRNA), the c.7893delC correction efficiency was increased 3-fold. Furthermore, an approximately 31% correction efficiency of the endogenous DMD: c.7893delC is achieved in the FACS-enriched HDR-edited VENUS EGFP+ patient fibroblasts. We demonstrated that a highly efficient correction of DMD loss-of-function mutations in patient cells can be achieved by several means of CRISPR gene editing.

Massively targeted evaluation of therapeutic CRISPR off-targets in cells

Methods for sensitive and high-throughput evaluation of CRISPR RNA-guided nucleases (RGNs) off-targets (OTs) are essential for advancing RGN-based gene therapies. Here we report SURRO-seq for simultaneously evaluating thousands of therapeutic RGN OTs in cells. SURRO-seq captures RGN-induced indels in cells by pooled lentiviral OTs libraries and deep sequencing, an approach comparable and complementary to OTs detection by T7 endonuclease 1, GUIDE-seq, and CIRCLE-seq. Application of SURRO-seq to 8150 OTs from 110 therapeutic RGNs identifies significantly detectable indels in 783 OTs, of which 37 OTs are found in cancer genes and 23 OTs are further validated in five human cell lines by targeted amplicon sequencing. Finally, SURRO-seq reveals that thermodynamically stable wobble base pair (rG•dT) and free binding energy strongly affect RGN specificity. Our study emphasizes the necessity of thoroughly evaluating therapeutic RGN OTs to minimize inevitable off-target effects.

CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context

A major challenge of CRISPR/Cas9-mediated genome engineering is that not all guide RNAs (gRNAs) cleave the DNA efficiently. Although the heterogeneity of gRNA activity is well recognized, the current understanding of how CRISPR/Cas9 activity is regulated remains incomplete. Here, we identify a sweet spot range of binding free energy change for optimal efficiency which largely explains why gRNAs display changes in efficiency at on- and off-target sites, including why gRNAs can cleave an off-target with higher efficiency than the on-target. Using an energy-based model, we show that local gRNA-DNA interactions resulting from Cas9 "sliding" on overlapping protospacer adjacent motifs (PAMs) profoundly impact gRNA activities. Combining the effects of local sliding for a given PAM context with global off-targets allows us to better identify highly specific, and thus efficient, gRNAs. We validate the effects of local sliding on gRNA efficiency using both public data and in-house data generated by measuring SpCas9 cleavage efficiency at 1024 sites designed to cover all possible combinations of 4-nt PAM and context sequences of 4 gRNAs. Our results provide insights into the mechanisms of Cas9-PAM compatibility and cleavage activation, underlining the importance of accounting for local sliding in gRNA design.

Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs

BACKGROUND

Extrachromosomal circular deoxyribonucleic acid (eccDNA) is evolving as a valuable biomarker, while little is known about its presence in urine.

METHODS

Here, we report the discovery and analysis of urinary cell-free eccDNAs (ucf-eccDNAs) in healthy controls and patients with advanced chronic kidney disease (CKD) by Circle-Seq.

RESULTS

Millions of unique ucf-eccDNAs were identified and comprehensively characterised. The ucf-eccDNAs are GC-rich. Most ucf-eccDNAs are less than 1000 bp and are enriched in four pronounced peaks at 207, 358, 553 and 732 bp. Analysis of the genomic distribution of ucf-eccDNAs shows that eccDNAs are found on all chromosomes but enriched on chromosomes 17, 19 and 20 with a high density of protein-coding genes, CpG islands, short interspersed transposable elements (SINEs) and simple repeat elements. Analysis of eccDNA junction sequences further suggests that microhomology and palindromic repeats might be involved in eccDNA formation. The ucf-eccDNAs in CKD patients are significantly higher than those in healthy controls. Moreover, eccDNA with miRNA genes is highly enriched in CKD ucf-eccDNA.

CONCLUSIONS

This work discovers and provides the first deep characterisation of ucf-eccDNAs and suggests ucf-eccDNA as a valuable noninnvasive biomarker for urogenital disorder diagnosis and monitoring.

Systematical analysis reveals a strong cancer relevance of CREB1-regulated genes

The transcription factor cyclic-AMP response element-binding protein 1 (CREB1) responds to cAMP level and controls the expression of target genes, which regulates nutrition partitioning. The promoters of CREB1-targeted genes responsive to cAMP have been extensively investigated and characterized with the presence of both cAMP response element and TATA box. Compelling evidence demonstrates that CREB1 also plays an essential role in promoting tumor development. However, only very few genes required for cell survival, proliferation and migration are known to be constitutively regulated by CREB1 in tumors. Their promoters mostly do not harbor any cAMP response element. Thus, it is very likely that CREB1 regulates the expressions of distinct sets of target genes in normal tissues and tumors. The whole gene network constitutively regulated by CREB1 in tumors has remained unrevealed. Here, we employ a systematical and integrative approach to decipher this gene network in the context of both tissue cultured cancer cells and patient samples. We combine transcriptomic, Rank-Rank Hypergeometric Overlap, and Chipseq analysis, to define and characterize CREB1-regulated genes in a multidimensional fashion. A strong cancer relevance of those top-ranked targets, which meet the most stringent criteria, is eventually verified by overall survival analysis of cancer patients. These findings strongly suggest the importance of genes constitutively regulated by CREB1 for their implicative involvement in promoting tumorigenesis.

Efficient correction of Duchenne muscular dystrophy mutations by SpCas9 and dual gRNAs

CRISPR gene therapy is one promising approach for treatment of Duchenne muscular dystrophy (DMD), which is caused by a large spectrum of mutations in the dystrophin gene. To broaden CRISPR gene editing strategies for DMD treatment, we report the efficient restoration of dystrophin expression in induced myotubes by SpCas9 and dual guide RNAs (gRNAs). We first sequenced 32 deletion junctions generated by this editing method and revealed that non-homologous blunt-end joining represents the major indel type. Based on this predictive repair outcome, efficient in-frame deletion of a part of DMD exon 51 was achieved in HEK293T cells with plasmids expressing SpCas9 and dual gRNAs. More importantly, we further corrected a frameshift mutation in human DMD (exon45del) fibroblasts with SpCas9-dual gRNA ribonucleoproteins. The edited DMD fibroblasts were transdifferentiated into myotubes by lentiviral-mediated overexpression of a human MYOD transcription factor. Restoration of DMD expression at both the mRNA and protein levels was confirmed in the induced myotubes. With further development, the combination of SpCas9-dual gRNA-corrected DMD patient fibroblasts and transdifferentiation may provide a valuable therapeutic strategy for DMD.

Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning

The design of CRISPR gRNAs requires accurate on-target efficiency predictions, which demand high-quality gRNA activity data and efficient modeling. To advance, we here report on the generation of on-target gRNA activity data for 10,592 SpCas9 gRNAs. Integrating these with complementary published data, we train a deep learning model, CRISPRon, on 23,902 gRNAs. Compared to existing tools, CRISPRon exhibits significantly higher prediction performances on four test datasets not overlapping with training data used for the development of these tools. Furthermore, we present an interactive gRNA design webserver based on the CRISPRon standalone software, both available via https://rth.dk/resources/crispr/ . CRISPRon advances CRISPR applications by providing more accurate gRNA efficiency predictions than the existing tools.

Haplotyping by CRISPR-mediated DNA circularization (CRISPR-hapC) broadens allele-specific gene editing

Allele-specific protospacer adjacent motif (asPAM)-positioning SNPs and CRISPRs are valuable resources for gene therapy of dominant disorders. However, one technical hurdle is to identify the haplotype comprising the disease-causing allele and the distal asPAM SNPs. Here, we describe a novel CRISPR-based method (CRISPR-hapC) for haplotyping. Based on the generation (with a pair of CRISPRs) of extrachromosomal circular DNA in cells, the CRISPR-hapC can map haplotypes from a few hundred bases to over 200 Mb. To streamline and demonstrate the applicability of the CRISPR-hapC and asPAM CRISPR for allele-specific gene editing, we reanalyzed the 1000 human pan-genome and generated a high frequency asPAM SNP and CRISPR database (www.crispratlas.com/knockout) for four CRISPR systems (SaCas9, SpCas9, xCas9 and Cas12a). Using the huntingtin (HTT) CAG expansion and transthyretin (TTR) exon 2 mutation as examples, we showed that the asPAM CRISPRs can specifically discriminate active and dead PAMs for all 23 loci tested. Combination of the CRISPR-hapC and asPAM CRISPRs further demonstrated the capability for achieving highly accurate and haplotype-specific deletion of the HTT CAG expansion allele and TTR exon 2 mutation in human cells. Taken together, our study provides a new approach and an important resource for genome research and allele-specific (haplotype-specific) gene therapy.

A SNP in PLAG1 is associated with body height trait in Chinese cattle

Stature is an important quantitative trait for cattle performance, which influences herd productivity. Previous studies have reported that an SNP (AC_000171.1:g.25015640G>T, rs109815800) in Pleomorphic adenoma gene 1 (PLAG1) on chromosome 14 (CHR14) is associated with bovine stature. To validate whether rs109815800 is associated with the body height of Chinese cattle, we carried out an association analysis using 558 adult cattle samples from seven populations. Then, 1038 samples from 38 Chinese cattle breeds were used to show the geographical distribution of this variant in China. The results showed that the Q allele (G allele) increased the height of cattle. Furthermore, the frequencies of Q allele in Chinese native breeds tend to decrease from northern China to southern China, and the frequency of Q allele in two Chinese beef cattle breeds is much higher than that in another 36 Chinese local cattle breeds. Our data suggest that the prevalence of the Q allele is correlated with latitude in China.

LION: a simple and rapid method to achieve CRISPR gene editing

The RNA-guided CRISPR-Cas9 technology has paved the way for rapid and cost-effective gene editing. However, there is still a great need for effective methods for rapid generation and validation of CRISPR/Cas9 gRNAs. Previously, we have demonstrated that highly efficient generation of multiplexed CRISPR guide RNA (gRNA) expression array can be achieved with Golden Gate Assembly (GGA). Here, we present an optimized and rapid method for generation and validation in less than 1 day of CRISPR gene targeting vectors. The method (LION) is based on ligation of double-stranded gRNA oligos into CRISPR vectors with GGA followed by nucleic acid purification. Using a dual-fluorescent reporter vector (C-Check), T7E1 assay, TIDE assay and a traffic light reporter assay, we proved that the LION-based generation of CRISPR vectors are functionally active, and equivalent to CRISPR plasmids generated by traditional methods. We also tested the activity of LION CRISPR vectors in different human cell types. The LION method presented here advances the rapid functional validation and application of CRISPR system for gene editing and simplified the CRISPR gene-editing procedures.

Comprehensive analysis of the mitochondrial DNA diversity in Chinese cattle

Complete mitochondrial DNA D-loop sequences of 1105 individuals were used to assess the diversity of maternal lineages of cattle populations in China. In total, 250 taurine and 88 zebu haplotypes were identified. Five main haplogroups-T1a, T2, T3, T4 and T5-were identified in Bos taurus, whereas Bos indicus harbored two haplogroups-I1 and I2. Our results suggest that the distribution of T1a in Asia was concentrated mainly in the northeast region (northeast China, Korea and Japan); haplogroups T2, T3 and T4 were predominant in Chinese cattle; and T5 was sporadically detected in Mongolian and Pingwu cattle. In contrast to the widespread presence of I1, I2 was distributed only in southwestern China (Yunnan-Guizhou Plateau and the Tibet Autonomous Region) and Xinjiang Uygur Autonomous Region. This is the first time that all five taurine haplogroups and two zebu haplogroups have been found in Mongolian cattle. In addition, eight individuals in Tibetan cattle carried the Bos grunniens mtDNA type. The high mtDNA diversity (H = 0.904 ± 0.008) and the weak genetic structure among the 57 Chinese cattle breeds/populations are consistent with their complex historical background, migration route and ecological environment.

Genetic diversity of Chinese cattle revealed by Y-SNP and Y-STR markers

With its vast territory and complex natural environment, China boasts rich cattle genetic resources. To gain the further insight into the genetic diversity and paternal origins of Chinese cattle, we analyzed the polymorphism of Y-SNPs (UTY19 and ZFY10) and Y-STRs (INRA189 and BM861) in 34 Chinese cattle breeds/populations, including 606 males representative of 24 cattle breeds/populations collected in this study as well as previously published data for 302 bulls. Combined genotypic data identified 14 Y-chromosome haplotypes that represented three haplogroups. Y2-104-158 and Y2-102-158 were the most common taurine haplotypes detected mainly in northern and central China, whereas the indicine haplotype Y3-88-156 predominates in southern China. Haplotypes Y2-108-158, Y2-110-158, Y2-112-158 and Y3-92-156 were private to Chinese cattle. The population structure revealed by multidimensional scaling analysis differentiated Tibetan cattle from the other three groups of cattle. Analysis of molecular variance showed that the majority of the genetic variation was explained by the genetic differences among groups. Overall, our study indicates that Chinese cattle retain high paternal diversity (H = 0.607 ± 0.016) and probably much of the original lineages that derived from the domestication center in the Near East without strong admixture from commercial cattle carrying Y1 haplotypes.

Traditional Herbal Medicine-Derived Sulforaphene LFS-01 Reverses Colitis in Mice by Selectively Altering the Gut Microbiota and Promoting Intestinal Gamma-Delta T Cells

Sulforaphene (LFS-01) is a natural compound derived from traditional herbal medicine. Here, we show that oral administration of LFS-01 is able to dramatically alter the skewed gut microbiota and reverse colitis in model mice associated with an increase of intestinal γδT cells. Through 16S rDNA sequencing, we showed that LFS-01 can selectively suppress enteric pathogens such as Escherichia–Shigella and Helicobacter whereas the protective strains including Lactobacillus and Lachnospiraceae were significantly expanded after LFS-01 treatment. Interestingly, we demonstrated that LFS-01 administration can significantly promote the IL-17+γδT cells in model mice in response to the expanded Lactobacillus. We verified that the intracellular components of Lactobacillus can stimulate the growth of IL-17+γδT cells upon preincubation. The increased IL-17A after LFS-01 treatment in turn recovers the disrupted occludin subcellular location and protects the epithelial barrier in the colon of model mice. Remarkably, LFS-01 does not show apparent toxicity to animals and we demonstrated that LFS-01 also exerts strong protective effects in TNBS-induced colitis rats. Therefore, LFS-01 holds great promise for the treatment of inflammatory bowel disease (IBD) and warrants translation for use in clinical trials. Our work provided a new avenue for the treatment of IBD based on the strategy of harnessing intestinal symbiosis.

Synbiotic dietary supplement affects growth, immune responses and intestinal microbiota of Apostichopus japonicus

A feeding experiment was conducted to investigate the effects of dietary administration of synbiotic with Bacillus lincheniformis WS-2 (CGMCC No. 12813) and alginate oligosaccharides (AOS) on the growth, innate immune response, and intestinal microbiota of the sea cucumber Apostichopus japonicus and its resistance to Vibrio infection. Sea cucumbers were given a control diet (non-supplemented), pro diet (basal diet plus 1 × 10⁹ cfu (g diet)^-1B. lincheniformis WS-2), syn diet (basal diet plus 1 × 10⁹ cfu (g diet)^-1B. lincheniformis WS-2 and 10 g (kg diet) ^-1 AOS) or pre diet (basal diet plus 10 g (kg diet) ^-1 AOS) over a period of 60 days, and the growth performance and various innate immune parameters of the animals were evaluated after 30 and 60 days of feeding. No significant difference in growth performance was observed between the group fed with the syn and the group fed with the pro diet, but both these groups exhibited significant (P < 0.05) enhancement in growth performance compared to the control group. At the same time, both syn and pro diets also resulted in the animals having significantly higher levels of amylase, protease and alginate lyase activities compared to the con diet. Individuals fed with the syn or pro diet showed enhanced levels of various immune enzyme activities, compared to those fed with the con diet. At the end of the growth period, the sea cucumbers were challenged with Vibrio splendidus via intraperitoneal injection. The survival rates of sea cucumbers fed with the syn, pro or pre diet were significantly improved compared to that of sea cucumbers fed with the con diet, with sea cucumbers fed with synbiotic having the highest survival. In addition, increased proportions of Bacillus and Lactococcus were found in the intestinal tract of sea cucumbers fed with the syn diet (9.5% and 7.3%) compared to those of sea cucumbers fed with the pro diet (6.1% and 4.6%), con diet (4.0% and 3.4%), or pre diet (5.2% and 6.8%) after 60 days of feeding. Furthermore, the proportion of Vibrio in the intestinal tracts of sea cucumbers fed with the pro diet (2%) or syn diet (3.1%) was lower than that of sea cucumbers fed with the con diet (5.5%) or pre diet (3.8%), although no significant difference was detected between the pro diet and syn diet groups (P > 0.05). Overall, the results suggested that dietary synbiotic consisting of Bacillus lincheniformis and alginate oligosaccharides (AOS) could have positive benefit for sea cucumber aquaculture.

Use of Bacteriophages to Control Escherichia coli O157:H7 in Domestic Ruminants, Meat Products, and Fruits and Vegetables

Escherichia coli O157:H7 is an important foodborne pathogen that causes severe bloody diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome. Ruminant manure is a primary source of E. coli O157:H7 contaminating the environment and food sources. Therefore, effective interventions targeted at reducing the prevalence of fecal excretion of E. coli O157:H7 by cattle and sheep and the elimination of E. coli O157:H7 contamination of meat products as well as fruits and vegetables are required. Bacteriophages offer the prospect of sustainable alternative approaches against bacterial pathogens with the flexibility of being applied therapeutically or for biological control purposes. This article reviews the use of phages administered orally or rectally to ruminants and by spraying or immersion of fruits and vegetables as an antimicrobial strategy for controlling E. coli O157:H7. The few reports available demonstrate the potential of phage therapy to reduce E. coli O157:H7 carriage in cattle and sheep, and preparation of commercial phage products was recently launched into commercial markets. However, a better ecological understanding of the phage E. coli O157:H7 will improve antimicrobial effectiveness of phages for elimination of E. coli O157:H7 in vivo.

Liver Transplantation Using Donation After Brain and Cardiac Death: A Single-Center Experience in China

BACKGROUND

Liver transplantation (LTx) using donation after brain and cardiac death (DBCD) has increased steadily in China. The aims of this study were to evaluate the outcomes of DBCD LTx and to assess its feasibility to expand the donor pool.

METHODS

We retrospectively analyzed the clinical characteristics of DBCD donors and recipients, survival of allografts and recipients, and prognostic factors in DBCD LTx recipients from March 2010 to December 2014 in our institution.

RESULTS

DBCD LTx (n = 102) were performed in our institution during the research period, and the successful donation rate was 26.0%. Mean warm ischemia time and cold ischemia time were 14.39 minutes and 5.29 hours, respectively. The overall and biliary complication rates were 45.1% and 16.7%, respectively. Donor age (P = .043), intra-operative blood loss (P = .048), and operation time (P = .045) were significantly different between the complication and non-complication groups. The 1-, 2-, and 3-year survival rates of patients and grafts were 88.0%, 84.6%, 84.6%, and 85.7%, 78.6%, and 78.6%, respectively. The 1- and 2-year overall survival rates of hepatocellular carcinoma patients were 91.9% and 80.5%, respectively whereas the recurrence-free survival rates were 84.9% and 77.2%, respectively. The patient and graft survival rates were not statistically different between the <55-year and ≥55 year groups, but complication rate was higher in the older group than in the younger group (P = .003).

CONCLUSIONS

The outcome of DBCD LTx is favorable in our institution, with careful donor and recipient selection and careful peri-operative management. DBCD is an optimized solution for organ shortage in today's China.

PD03-09: Breast Cancer Recurrence Risk Probed by Whole Transcriptome Next Generation Sequencing in 136 Patients

Background: RNA biomarkers discovered by RT-PCR-based gene expression profiling of archival formalin-fixed paraffin-embedded (FFPE) tissue are the basis for very precise and sensitive clinical diagnostic tests, such as the 21 gene Oncotype DX® breast cancer assay. Both inherent limits of technical scalability and the small amounts of patient FFPE RNA available place practical constraints on the number of transcripts that can be interrogated by RT-PCR. We developed new methods for RNA profiling through massively parallel “next generation” sequencing (RNA-Seq) of archival FFPE specimens. We report here the technical performance of this methodology and compare the results to RT-PCR results obtained in one of the studies that were carried out to develop the 21 gene assay.

Methods: RNA was extracted in 2002 from 136 invasive breast tumors that were formalin-fixed and paraffin-embedded between 1990 and 1997. RNA-Seq was carried out using minor modifications to methods we have reported previously (Sinicropi et al., Advances in Genome Biology and Technology Conference, p. 170, 2010 and p. 198, 2011). Briefly, 0.1 mg of total RNA was selectively depleted of ribosomal RNA and sequencing libraries were prepared using a modification of the ScriptSeq™ kit from Epicentre. The libraries were sequenced on an Illumina HiSeq 2000 instrument with multiplexing of two libraries per lane for 50 cycles in one direction. The resulting FASTQ sequences were mapped to version hg19 of the human genome using the Illumina CASAVA pipeline. The total number of sequences (reads) that uniquely mapped to all exons of each RefSeq entry was used for quantification of expression levels.

Results: On average, there were 43 million reads per sample (range 31 - 58 million; SD=4.6 million) of which 69% uniquely mapped to the human genome. Ribosomal RNA was effectively removed and accounted for &lt;0.3% of total counts. Significant coverage of a high proportion of the human genome was obtained, with 40% of RefSeq transcripts represented by a median of more than 100 reads. Using Cox proportional hazards analysis to evaluate the association of quantitative gene expression with breast cancer recurrence, the standardized hazard ratios and p-values for the 21 Oncotype DX genes determined by RNA-Seq were comparable to those originally obtained using RT-PCR. Moreover, whole transcriptome RNA-Seq identified more than 1800 new coding, intronic, and intergenic transcripts that strongly associated with breast cancer recurrence risk (at a false discovery rate &lt;10%) and revealed heretofore unappreciated co-expressed gene networks. Summary: New methodology has been developed for application of next generation sequencing-based whole transcriptome profiling to small amounts of archival FFPE tissue. This technology has sensitivity and selectivity comparable to RT-PCR, can provide a vast increase in the number of interrogated transcripts, can reveal new biological relationships, and has excellent performance suitable for the discovery of RNA biomarkers.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr PD03-09.

Understanding stem cell differentiation through self-organization theory

The mechanism underling stem cells' key property, the ability to either divide into two replicate cells or a replicate and a differentiated daughter, still is not understood. We tested a hypothesis that stem cell asymmetric division/differentiation is spontaneously created by the coupling of processes within each daughter and the resulting biochemical feedbacks via the exchange of molecules between them during mitotic division. We developed a mathematical/biochemical model that accounts for dynamic processes accompanying division, including signaling initiation and transcriptional, translational and post-translational (TTP) reactions. Analysis of this model shows that it could explain how stem cells make the decision to divide symmetrically or asymmetrically under different microenvironmental conditions. The analysis also reveals that a stem cell can be induced externally to transition to an alternative state that does not have the potentiality to have the option to divide symmetrically or asymmetrically. With this model, we initiated a search of large databases of transcriptional regulatory network (TRN), protein-protein interaction, and cell signaling pathways. We found 12 subnetworks (motifs) that could support human stem cell asymmetric division. A prime example of the discoveries made possible by this tool, two groups of the genes in the genetic model are revealed to be strongly over-represented in a database of cancer-related genes.

Hydrogen sulfide: neurochemistry and neurobiology

Current evidence suggests that hydrogen sulfide (H2S) plays an important role in brain functions, probably acting as a neuromodulator as well as an intracellular messenger. In the mammalian CNS, H2S is formed from the amino acid cysteine by the action of cystathionine beta-synthase (CBS) with serine (Ser) as the by-product. As CBS is a calcium and calmodulin dependent enzyme, the biosynthesis of H2S should be acutely controlled by the intracellular concentration of calcium. In addition, it is also regulated by S-adenosylmethionine which acts as an allosteric activator of CBS. H2S, as a sulfhydryl compound, has similar reducing properties as glutathione. In neurons, H2S stimulates the production of cAMP probably by direct activation of adenylyl cyclase and thus activate cAMP-dependent processes. In astrocytes, H2S increases intracellular calcium to an extent capable of inducing and propagating a "calcium wave", which is a form of calcium signaling among these cells. Possible physiological functions of H2S include potentiating long-term potentials through activation of the NMDA receptors, regulating the redox status, maintaining the excitatory/inhibitory balance in neurotransmission, and inhibiting oxidative damage through scavenging free radicals and reactive species. H2S is also involved in CNS pathologies such as stroke and Alzheimer's disease. In stroke, H2S appears to act as a mediator of ischemic injuries and thus inhibition of its production has been suggested to be a potential treatment approach in stroke therapy.

ELISA system for detection of immune responses to FVIII: a study of 246 samples and correlation with the Bethesda assay

Inhibitors of FVIII are usually IgG polyclonal antibodies that develop as alloimmune responses in patients with congenital haemophilia A or as autoimmune responses resulting in acquired haemophilia. Their recognition can be difficult, especially when the titre is low. Furthermore, results from a Bethesda assay often require several days as samples are referred to a specialty laboratory. The aim of this study is to assess the utility of an ELISA system for detecting immune responses to FVIII. A total of 246 plasma samples submitted from 176 individuals with immune responses to FVIII, as verified with the Bethesda assay, and samples from 50 control subjects were tested for the presence of FVIII-specific IgG using an ELISA-based assay. Paired sera from 18 of the patients were also tested by the ELISA. Of the 246 samples that were positive for a FVIII inhibitor by the Bethesda assay, 235 (95.5%) were also positive by ELISA. The regression coefficient, using Log BU was r = 0.82. The correlation data were strengthened when 27 inhibitor samples were diluted further. There was a strong correlation between ELISA results for the 18-paired serum and plasma samples (r = 0.99). There is a strong correlation between the ELISA and Bethesda methods in detecting immune responses to FVIII. The ELISA provides rapid screening that could be available well in advance of confirmation by the Bethesda assay.

Cancer onset and progression: A genome-wide, nonlinear dynamical systems perspective on onconetworks

It is hypothesized that the many human cell types corresponding to multiple states is supported by an underlying nonlinear dynamical system (NDS) of transcriptional regulatory network (TRN) processes. This hypothesis is validated for epithelial cells whose TRN is found to support an extremely complex array of states that we term a "bifurcation nexus", for which we introduce a quantitative measure of complexity. The TRN used is constructed and analyzed by integrating a database of TRN information, cDNA microarray data analyzers, bioinformatics modules, a transcription/translation/post-translation kinetic model, and NDS analysis software. Results of this genome-wide approach suggest that a cell can be induced to persist in one state or to transition between distinct states; apparently irreversible transitions can be reversed when the high dimensional space of extracellular and intracellular parameters is understood. As conditions change, certain cellular states (cell lines) are no longer supported, new ones emerge, and transitions (cell differentiation or death) occur. The accumulation of simulated point mutations (minor changes which individually are insignificant) lead to occasional dramatic transitions. The genome-wide scope of many of these transitions is shown to arise from the cross-linked TRN structure. These notions imply that studying individual oncogenes may not be sufficient to understand cancer; rather, "onconetworks" (subsets of strongly coupled genes supporting multiple cell states) should be considered. Our approach reveals several epithelial onconetworks, each involving oncogenes and anti-tumor and supporting genes.

Alternative method to construct equilibrium distribution functions in lattice-Boltzmann method simulation of inviscid compressible flows at high Mach number

A method is proposed to construct an equilibrium density distribution function in the simulation of compressible flows at high Mach number by the lattice-Boltzmann method. In this method, the conventional Maxwellian distribution function is replaced by a circular function which is very simple and satisfies all needed statistical relations to recover the compressible Navier-Stokes equations. The circular function is then distributed to the lattice velocity directions by Lagrangian interpolation in such a way that all the needed statistical relations are exactly satisfied when the integral in the phase space is replaced by the summation in the context of the lattice-Boltzmann (LB) method. In this framework, the equilibrium distribution functions and the associated lattice velocity model can be derived naturally without assuming specific forms. Two LB models with adjustable specific heat ratio, respectively, for one-dimensional (1D) and two-dimensional (2D) compressible flows are shown in the paper. Some test cases of compressible flows with strong shock waves are simulated to validate the present approach. Excellent results are obtained. Note that in the simulation, the total variation diminishing (TVD) scheme was used to capture the discontinuity with coarse mesh.

Real-time reverse transcription-polymerase chain reaction for detection of SYT-SSX translocation in synovial sarcoma

9553

Background: Synovial sarcoma is the most common non-rhabdomyosarcomatous soft tissue sarcoma in children and adolescents. A specific translocation, t(X;18), induces fusion of the SYT gene on chromosome 18 to an SSX gene on chromosome X. The resulting fusion gene consists of at least 2 subtypes with different breakpoints: SYT-SSX1(X;18)(p11.23;q11.2) and SYT-SSX2 (X;18)(p11.21;q11.2). Because t(X;18) transcripts occur in >90% of synovial sarcoma subtypes, this marker may be useful for diagnosis. We evaluated the accuracy of a multiplex real-time reverse transcription-polymerase chain reaction (RT-PCR) assay for detection of the primary SYT-SSX fusion transcript types in formalin-fixed, paraffin-embedded (FFPE) tissues and frozen tissues. Methods: 17 tumors (7 synovial sarcomas, 4 Ewing’s sarcomas, 5 rhabdomyosarcomas, 1 small round blue-cell tumor), 4 normal tissues, and 4 control samples were tested for SYT-SSX translocations using real-time RT-PCR. Results were compared to those obtained with gel electrophoresis detection of amplified transcripts; discrepant results were confirmed by sequencing. Results: Concordance between real time RT-PCR and gel electrophoresis was 100% (25/25) for internal control genes and SYT-SSX1, and 92% (23/25) for SYT-SSX2. Of the 2 samples with discordant SYT-SSX2 results, 1 was positive by real-time RT-PCR but not gel electrophoresis and 1 was positive by electrophoresis but not real-time RT-PCR; in both cases, DNA sequencing confirmed the real-time RT-PCR results. The minimum percentage of tumor to normal cells required for detection of SYT-SSX fusion transcripts by real-time RT-PCR was 6.25%. Conclusions: This real-time RT-PCR assay appears to provide greater accuracy than gel electrophoresis for identification of SYT-SSX translocation and fusion types.

No significant financial relationships to disclose.

Distribution of UGT1A1 (TA) polymorphisms in Caucasian and Asian subjects

2063

Background: The hepatic isoform 1A1 of uridine diphosphate glucuronosyltransferase (UGT) is responsible for glucuronidation and detoxification of SN-38, the active metabolite of irinotecan. The presence of an additional TA repeat in the TATA sequence of the UGT1A1 gene is a common polymorphism, leading to a significant decrease in SN-38 glucuronidation. Patients with the UGT1A1 (TA)7 allele (either [TA]6/7 or [TA]7/7 ) are more likely to experience severe neutropenia and diarrhea following irinotecan chemotherapy. We assessed the distribution of the UGT1A1 (TA) polymorphism in Caucasian and Asian subjects. Methods: We used a fluorescent PCR-based assay to detect UGT1A1 (TA) polymorphisms in 129 healthy subjects (52 Caucasian, 34 Chinese, 36 Filipino, and 7 Japanese). The chi-square test was used to assess between-group differences in the distribution of UGT1A1 (TA) genotypes. Results: UGT1A1 (TA) genotype distribution differed significantly between Caucasian and Asian subjects (P = 0.003). The UGT1A1 (TA)6/7 and (TA)7/7 genotypes were more common in Caucasians than Asians. Genotype distributions did not differ significantly between men and women in either group ( Table ). Conclusions: The frequency of the deleterious UGT1A1 (TA)7 polymorphism was greater in Caucasians than in Asians; genotype frequencies were consistent with previous reports. In both groups, UGT1A1 (TA) genotype distributions were similar in men and women.

[Table: see text]

No significant financial relationships to disclose.

Identification of cancer of unknown primary with gene expression profiling

10052

Background: Patients with metastatic cancer of unknown primary (CUP) generally have a poor prognosis, with a median survival of 2–10 months. Conventional diagnostic approaches for identifying the primary tumor site are successful in only 20%-30% of cases; however, such identification provides prognostic information and helps with selection of tumor-specific therapy, leading to improved survival. Recent studies indicate that gene expression-based classification of CUP is highly successful in predicting the site of origin. We report herein development and validation of a method that determines the site of tumor origin by comparing the gene expression profiles of CUP cases to those in a database created from known tumor types. Methods: RNA extracted from frozen and formalin-fixed, paraffin-embedded (FFPE) tissue wasis purified and amplified using the Paradise Reagent System System (Arcturus, Mountain View, CA). Following reverse-transcription, cDNA products wereare used in a semi-quantitative real-time PCR to detect 87 tumor-associated genes and 5 reference genes in an ABI PRISM 7900HT Detection System (Applied Biosystems, Foster City, CA). Gene expression data wereare then compared to those in a database, composed of gene expression profiles of 571 samples from 39 different tumor types, using k-nearest neighbor analysis to predict the most likely site of tumor origin. Intra- and interassay reproducibility was determined. Frozen and FFPE tissues (n=57) from a well-characterized, independent sample set were also tested in a blinded manner to further validate the method. Results: Based on the real-time PCR cycle threshold, the intra- and interassay reproducibility ranged from 0.1%-4.3% and 0.5%-8.2%, respectively. The primary tumor type was identified in 77% of cases. The assay determined the correct tumor type in 88% (44/50) of the samples. Seven samples were not reported: 3 failed to amplify adequately and 4 had an unacceptably low confidence level. Conclusions: We have shown that gene expression profiling can determine the most likely site of tumor origin. Our data suggest that this new method is able tomay identify the primary site of tumor origin in 77% of CUP cases.

No significant financial relationships to disclose.

Treatment of factor XI inhibitor using recombinant activated factor VIIa

A 30-year-old female with severe factor XI deficiency of 0-2% acquired factor XI inhibitor following many infusions for fresh frozen plasma (FFP) for surgical procedures starting at 4 years of age. Seven months before this inhibitor was diagnosed, surgery was complicated by prolonged bleeding resistant to FFP, requiring epsilon aminocaproic acid (EACA) and surgical packing. The inhibitor was measured at 2.2 Bethesda units, 7 months since the last FFP. The inhibitor was confirmed as specific anti-XI and anti-XIa binding by patient's IgG to immobilized factor XI and factor XIa from whole plasma and purified IgG. For repair of a painful anterior cruciate ligament (ACL) defect she was given recombinant factor VIIa (rVIIa) at 90 mug kg(-1), starting one-half hour preoperatively and continued every 2 h for 8 h when haemostasis was complete. Thereafter the rVIIa was given every 3 h for two doses, and then every 4 h for four doses at which time she was discharged on EACA which was continued for 6 days. There was excellent haemostasis during and following the surgery. There was no evidence of consumptive coagulopathy, with no change in the fibrinogen, platelet count, or D-D dimer; and no increase of platelet factor 4, beta-thromboglobulin, or prothrombin fragment F 1.2. The thrombin-antithrombin complex increased over baseline after 24 h. There was no postoperative deep vein thrombosis or pulmonary embolus. In this patient with a factor XI inhibitor, the recombinant factor VIIa was effective and safe, ensuring adequate haemostasis with no thrombotic complications. This product which was designed for patients with inhibitors to factor VIII or factor IX, and factor VII deficiency, has now been given successfully to four patients with factor XI inhibitors.

[A preliminary study on influence of N and P on population constituent of planktonic diatoms in seawater]

Experiment was conducted to study the influence of N and P on population constiuent of planktonic diatoms in seawater. The concentrations of N and P and their ratios might significantly affect the population constituent of planktonic diatoms in seawater, the more the concentrations of N and P and the bigger the N/P ratio to Redfield ratio, the less the species of planktonic diatoms and Shannon's index. The experimental result was verified in the investigation from shrimp culturing ponds.

Bayesian protein family classifier

A Bayesian procedure for the simultaneous alignment and classification of sequences into subclasses is described. This Gibbs sampling algorithm iterates between an alignment step and a classification step. It employs Bayesian inference for the identification of the number of conserved columns, the number of motifs in each class, their size, and the size of the classes. Using Bayesian prediction, inter-class differences in all these variables are brought to bare on the classification. Application to a superfamily of cyclic nucleotide-binding proteins identifies both similarities and differences in the sequence characteristics of the five subclasses identified by the procedure: 1) cNMP-dependent kinases, 2) prokaryotic cAMP-dependent regulatory proteins, CRP-type, 3) prokaryotic regulatory proteins, FNR-type, 4) cAMP gated ion channel proteins of animals, and 5) cAMP gated ion channels of plants.

Motifs and structural fold of the cofactor binding site of human glutamate decarboxylase

The pyridoxal-P binding sites of the two isoforms of human glutamate decarboxylase (GAD65 and GAD67) were modeled by using PROBE (a recently developed algorithm for multiple sequence alignment and database searching) to align the primary sequence of GAD with pyridoxal-P binding proteins of known structure. GAD's cofactor binding site is particularly interesting because GAD activity in the brain is controlled in part by a regulated interconversion of the apo- and holoenzymes. PROBE identified six motifs shared by the two GADs and four proteins of known structure: bacterial ornithine decarboxylase, dialkylglycine decarboxylase, aspartate aminotransferase, and tyrosine phenol-lyase. Five of the motifs corresponded to the alpha/beta elements and loops that form most of the conserved fold of the pyridoxal-P binding cleft of the four enzymes of known structure; the sixth motif corresponded to a helical element of the small domain that closes when the substrate binds. Eight residues that interact with pyridoxal-P and a ninth residue that lies at the interface of the large and small domains were also identified. Eleven additional conserved residues were identified and their functions were evaluated by examining the proteins of known structure. The key residues that interact directly with pyridoxal-P were identical in ornithine decarboxylase and the two GADs, thus allowing us to make a specific structural prediction of the cofactor binding site of GAD. The strong conservation of the cofactor binding site in GAD indicates that the highly regulated transition between apo- and holoGAD is accomplished by modifications in this basic fold rather than through a novel folding pattern.

Kinetics and motional dynamics of spin-labeled yeast iso-1-cytochrome c: 1. Stopped-flow electron paramagnetic resonance as a probe for protein folding/unfolding of the C-terminal helix spin-labeled at cysteine 102

The kinetics of chemically induced folding and unfolding processes in spin-labeled yeast iso-1-cytochrome c were measured by stopped-flow electron paramagnetic resonance (EPR). Stopped-flow EPR, based on a new dielectric resonator structure [Sienkiewicz, A., Qu, K., & Scholes, C. P. (1994) Rev. Sci. Instrum. 65, 68-74], gives a new temporal component to probing nanosecond molecular tumbling motions that are modulated by macromolecular processes requiring time resolution of milliseconds to seconds. The stopped-flow EPR technique presented in this work is a kinetic technique that has not been previously used with such a time resolution on spin-labeled systems, and it has the potential for application to numerous spin-labeled sites in this and other proteins. The cysteine-specific spin-label, methanethiosulfonate spin-label (MTSSL), was attached to yeast iso-1-cytochrome c at the single naturally occurring cysteine102, and the emphasis for this work was on this disulfide-attached spin-labeled prototype. This probe has the advantage of reflecting the protein tertiary fold, as shown by recent, systematic site-directed spin labeling of T4 lysozyme [Mchaourab, H. S. Lietzow, M. A., Hideg, K., & Hubbell, W. L. (1996) Biochemistry 35, 7692-7704], and protein backbone dynamics, as also shown by model peptide studies [Todd, A. P., & Millhauser, G. L. (1991) Biochemistry 30, 5515-5523]. The C-terminal cytochrome c helix where the label is attached is thought to be critical in the initial steps of protein folding and unfolding. Stopped-flow EPR resolved the monoexponential, guanidinium-induced unfolding process at pH 6.5 with an approximately 20 ms time constant; this experiment required less than 150 microL of 80 microM spin-labeled protein. We observed an approximately 50-fold decrease of this unfolding time from the 1 s range to the 20 ms time range as the guanidinium denaturant concentration was increased from 0.6 to 2.0 M. The more complex refolding kinetics of our labeled cytochrome were studied by stopped-flow EPR at pH 5.0 and 6.5. The spin probe showed a fast kinetic process compatible with the time range over which hydrogen/deuterium amide protection indicates helix formation; this process was monoexponential at pH 5.0. At pH 6.5, there was evidence of an additional slower kinetic phase resolved by stopped-flow EPR and by heme-ligation-sensitive UV-Vis that indicated a slower folding where heme misligation may be involved. Since the disulfide-attached probe has reported folding and backbone dynamics in other systems, the implication is that our kinetic experiments were directly sensing events of the C-terminal helix formation and possibly the N- and C-terminal helical interaction. The cysteine-labeled protein was also studied under equilibrium conditions to characterize probe mobility and the effect of the probe on protein thermodynamics. The difference in spin probe mobility between folded and denatured protein was marked, and in the folded protein, the motion of the probe was anisotropically restricted. The motion of the attached nitroxide in the folded protein appears to be restricted about the carbon and sulfur bonds which tether it to the cysteine. The original point of cysteine sulfur attachment is approximately 11 A from the heme iron within the C-terminal helix near its interface with the N-terminal helix, but the low-temperature EPR spin probe line width showed that the probe lies more distant (> 15 A) from the heme iron. By all physical evidence, the protein labeled at cysteine102 folded, but the spin probe in this prototype system perturbed packing which lowered the thermal melting temperature, the free energy of folding, the guanidinium concentration at the midpoint of the unfolding transition, the m parameter of the denaturant, and the helical CD signature. This study prepares the way for study of protein folding/unfolding kinetics using EPR spectroscopy of spin-labels placed at specific cysteine-mutated sites within

Evaluation of Bacillus thuringiensis and Bacillus sphaericus Strains from Chinese Soils Toxic to Mosquito Larvae

During our research to isolate and screen microbial agents, eight Bacillus thuringiensis isolates and five Bacillus sphaericus isolates were shown to have high toxicity to mosquito larvae. Comparing the LC50 values, four B. sphaericus isolates with LC50 values ranging from 0.50 to 1.47 ng/ml were about two to six times more toxic than strain 1593 (LC50 3.00 ng/ml) against larvae of Culex quinquefasciatus. Four B. thuringiensis isolates (LC50 values ranging from 3.80 to 7.54 ng/ml) and four B. sphaericus isolates with LC50 of 17.0 to 43.7 ng/ml were more toxic to Aedes aegypti than strain 1897 (LC50 8.46 ng/ml) and strain 1593 (LC50 67.3 ng/ml). As to Anopheles hyrcanus, the LC50 values of three B. sphaericus isolates ranging from 3.63 to 5.73 ng/ml were three to five times smaller than that of strain 1593 (LC50 16.1 ng/ml). Two B. sphaericus isolates showed high toxicity against mosquito larvae in the three genera Culex, Aedes, and Anopheles.