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Supplementary Tables A-F from Rapid Identification of UCA1 as a Very Sensitive and Specific Unique Marker for Human Bladder Carcinoma

Purpose: The most common genitourinary malignancy in China is bladder transitional cell carcinoma (TCC). Early diagnosis of new and recurrent bladder cancers, followed by timely treatment, will help decrease mortality. There are currently no satisfactory markers for bladder cancer available in clinics. Better diagnostic methods are highly demanded.Experimental Design: In this research, we have used comprehensive expressed sequence tag analysis, serial analysis of gene expression, and microarray analysis and quickly discovered a candidate marker, urothelial carcinoma associated 1 (UCA1). The UCA1 gene was characterized and its performance as a urine marker was analyzed by reverse transcription-PCR with urine sediments. A total of 212 individuals were included in this study, 94 having bladder cancers, 33 ureter/pelvic cancers, and 85 normal and other urinary tract disease controls.Results:UCA1 was identified as a novel noncoding RNA gene dramatically up-regulated in TCC and it is the most TCC-specific gene yet identified. The full-length cDNA was 1,439 bp, and sequence analysis showed that it belonged to the human endogenous retrovirus H family. Clinical tests showed that UCA1 assay was highly specific (91.8%, 78 of 85) and very sensitive (80.9%, 76 of 94) in the diagnosis of bladder cancer and was especially valuable for superficial G2-G3 patients (sensitivity 91.1%, 41 of 45). It showed excellent differential diagnostic performance in various urinary tract diseases without TCC.Conclusions: UCA1 is a very sensitive and specific unique marker for bladder cancer. It could have important implications in postoperative noninvasive follow-up. This research also highlights a shortcut to new cancer diagnostic assays through integration of in silico isolation methods with translational clinical tests based on RNA detection protocols.

PDF file - 179K, Includes HEPA analysis data, Calculation of DP score, and supplementary references

PDF file - 104K, Literature references reporting the clinical applications of known TSAs and the top 100 genes nominated by HEPA analysis

PDF file - 66K, Detailed information for the adult somatic tissues and cancer tissues from the five Affymetrix U133 plus2 gene expression datasets compiled for HEPA analysis

PDF file - 504K, 1) The principle and algorithm of HEPA analysis; 2) The parameters of HEPA analysis; 3) The HEPA score and expression profile of the TSA genes identified in this study; 4) Comparing PARSE and ELISA assay using IGF2BP3 antigen, and detecting autoantibody responses in an independent cohort of 149 lung cancer patients and 123 healthy individuals with PARSE assay; 5) The application of HEPA analysis in discovering therapeutically relevant overexpressed antigens

PDF file - 56K, Age and sex distribution of the lung patient and healthy cohorts, and the autoantibody responses in lung cancer patients at different clinical stages

PDF file - 98K, The detailed information and RT-PCR validation results for the TSA candidates nominated by HEPA analysis

PDF file - 41K, The weights for normal adult somatic tissues for the calculation of Depreciatory Penalty score

Intestinal ischemia/reperfusion (I/R) injury (IIRI) is associated with high prevalence and mortality rate. Recently, mesenchymal stem cell (MSC) therapy attracted more attentions. However, the function and regulatory mechanism of MSC-derived exosomal miRNAs during IIRI remain largely uninvestigated. The in vitro and in vivo IIRI models were established. MSC were characterized by immunofluorescent staining and flow cytometry. Purified exosomes were characterized by transmission electron microscopy (TEM), flow cytometry, and western blot. The expression of key molecules was detected by western blot and qRT-PCR. CCK-8, TUNEL, and transepithelial electrical resistance (TER) assays were employed to assess cell viability, apoptosis, and intestinal integrity, respectively. Pre-miR-34A m

It is a challenging issue to achieve propeller chirality for triarylboranes owing to the low transition barrier between the P and M forms of the boron center. Herein, we report a new strategy to achieve propeller chirality of triarylboranes. It was found that the chirality relay from axially chiral 1,1'-binaphthyl to propeller chirality of the trivalent boron center can be realized when a Me2 N and a Mes2 B group (Mes=mesityl) are introduced at the 2,2'-positions of the 1,1'-binaphthyl skeleton (BN-BNaph) owing to the strong π-π interaction between the Me2 N-bonded naphthyl ring and the phenyl ring of one adjacent Mes group, which not only exerts great steric hindrance on the rotation of the two Mes groups but also gives unequal stability to the two configurations of the boron center for a given configuration of the binaphthyl moiety. The stereostructures of the boron center were fully characterized through 1 H NMR spectroscopy, X-ray crystal analyses, and theoretical calculations. Detailed comparisons with the analog BN-Ph-BNaph, in which the Mes2 B group is separated from 1,1'-binaphthyl by a para-phenylene spacer, confirmed the essential role of π-π interaction for the successful chirality relay in BN-BNaph.

No effective method has been developed to distinguish sperm cells originating from different men in multi-suspect sexual assault cases. Here we combined MACS and FACS to isolate single donor sperm cells from forensic mixture samples including female vaginal epithelial cells and sperm cells from multiple contributors. Sperms from vaginal swab were isolated by MACS using FITC-conjugated A kinase anchor protein 3 (AKAP3) antibody; target individual sperm cells involving two or three donors were separated by FACS using FITC-labeled blood group A/B antigen antibody. This procedure was further tested in two mock multi-suspect sexual assault samples and one practical casework sample. Our results showed that complete single donor STR profiles could be successfully obtained from sperm/epithelial cell and sperm mixtures from two contributors. For unbalanced sperm/epithelial cells and sperm cells mixtures, sensitivity results revealed that target cells could be detected at as low as 1:32 and 1:8 mixed ratios, respectively. Although highly relies on cell number and blood types or secretor status of the individuals, this procedure would still be useful tools for forensic DNA analysis of multi-suspect sexual assault cases by the combined use of FACS and MACS based on sperm-specific AKAP3 antigen and human blood type antigen.

To explore the feasibility of detecting of Y-STR of fetal DNA in maternal plasma using Ion Torrent PGM™ System.A total of 16 fetal DNA samples from maternal plasmas (8 cases from 38 weeks gestational age and 8 ones from 12 weeks) were prepared and a multiplex assay with 7 STR loci (DYS390, DYS391, DYS393, DYS438, DYS437, DYS456, DYS635) was designed for multiplex-PCR amplification. Using Ion Torrent PGM™ System, the results of Y-STR sequences and capillary electrophoresis were obtained and compared.Y-STR specific alleles were detected in the maternal plasma of all the pregnant women having male babies of second and third trimester, which were higher than that detected by capillary electrophoresis. Consistent Y-STR genotypes were observed between fetal DNA from maternal plasma and genomic DNA from the newborn babies.Based on Ion Torrent PGM™ System, the prenatal Y-STR detection method may provide a high-sensitive and high-throughput choice for prenatal STR detection in forensic testing.

A series of organoboron-based biphenyls o,o'-NMe2, o,p'-NMe2, p,p'-NMe2, which contain an electron-donating NMe2 and an electron-accepting BMes2 groups at o,o'-, o,p'-, p,p'-positions of biphenyl skeleton, respectively, as well as o,o'-NBn2, which contains more bulky NBn2 rather than NMe2, were fully characterized to explore the effect of structural modification on the intramolecular charge-transfer emissions. In addition to significant effect of substitution position on photophysical properties, remarkable influence of conformation was also observed for o,o'-substituted compounds. The emission is substantially blue-shifted as conformation changes from the location of NMe2 and BMes2 at same side of biphenyl axis with a close B···N distance, and thus direct B···N electronic interaction in o,o'-NMe2, to the location of NBn2 and BMes2 on two opposite sides in o,o'-NBn2. And o,o'-NMe2 exhibits the longest emission wavelength, but the shortest absorption wavelength, and thus largest Stokes shift among these four organoboron-based biphenyls in both solution and solid state. The theoretical calculations demonstrated that the unique structure of o,o'-NMe2, in which boryl and amino located at the same side of biphenyl axis with close B···N distance and direct B···N electronic interaction, is helpful to stabilize the lowest singly occupied orbital in the exited state.

A triarylborane derivative BN-S, which contains a Hg(2+)-responsive dithioacetal group and a F(-)-responsive boryl group, has been designed and synthesized via the functionalization of 2-dimesitylboryl-2'-(N,N-dimethylamino)biphenyl core skeleton with a dithioacetal substituent. This compound displays intense intramolecular charge transfer fluorescence, even for its nano-aggregates in water. The Hg(2+)-promoted deprotection of the dithioacetal group and complexation of F(-) with the tri-coordinate boron center cause hypochromism of fluorescence to different extents. And thus BN-S behaves as a promising ratiometric bifunctional fluorescence probe to detect Hg(2+) and F(-) simultaneously. In addition, the detection of Hg(2+) is performable in aqueous medium using its nano-aggregates.

Previous studies have suggested anti-tumor effects of asiatic acid in some human cancer cell lines. This agent is reported to increase the levels of p21 WAF1/CIP1 in human breast cancer cell lines. However, the molecular mechanisms have not been established. Here we report that asiatic acid up-regulates p21 WAF1/CIP1 protein expression but not the level of p21 WAF1/CIP1 mRNA in HepG2 human hepatoma cells. Furthermore, we found that the asiatic acid induced increase of p21 WAF1/CIP1 protein was associated with decreased phosphorylation (ser-146) of p21 WAF1/CIP1 . Knockdown of NDR1/2 kinase, which directly phosphorylates p21 WAF1/CIP1 protein at ser-146 and enhances its proteasomal degradation, increased the levels of p21 WAF1/CIP1 protein and eliminated the regulation of p21 WAF1/ CIP1 stability by asiatic acid. At the same time, the expression of NDR1/2 kinase decreased during treatment with asiatic acid in HepG2 cells. Moreover, asiatic acid inhibited the proliferation of HepG2 cells, this being attenuated by knockdown of p21 WAF1/CIP1 . In conclusion, we propose that asiatic acid inhibits the expression NDR1/2 kinase and promotes the stability of p21 WAF1/CIP1 protein through attenuating NDR1/2 dependent phosphorylation of p21 WAF1/CIP1 in HepG2 cells.

To explore the feasibility of biological method to identify the biological attribute of samples at crime scene.Thirty samples of ten blood stains, ten saliva stains and ten semen stains were selected, and all the samples were processed by the routine method and biomolecular method, respectively. Both RNA and DNA were isolated using DNA-RNA co-extraction technology and the mRNA was converted into cDNA using reverse transcription PCR (RT-PCR). Three pairs of specific primers were designed for blood stain, saliva stain and semen stain based on the different target genes in three specific tissues and the primers were amplified using real-time fluorescent quantitative PCR. The differences in these biological samples were evaluated by melting temperature (Tm) values and the size of the amplification fragment.The Tm values of blood stain, saliva stain and semen stain were (84.5 +/- 0.2) degrees C, (76.9 +/- 0.3) degrees C and (88.5 +/- 0.2) degrees C, respectively. The length of PCR fragments of them was 177bp, 134bp and 294bp, respectively.Compared with the routine method, RT-PCR with real-time fluorescent quantitative PCR is highly specific, sensitive and reliable to identify the biological attribute of evidence, and can be potentially applied to determine evidence attribute in forensic practice.

Previous studies have indicated that borneol has double side effects on the central nervous system (CNS), but the mechanism is unknown. The aim of this study was to clarify the relationship between excitation ratio [contents of excitatory amino acids (AAs) versus that of inhibitory] and the content of natural borneol after a single oral dose. Mice were administered a 1.2 g/kg dose of natural borneol (containing 98% D: -borneol) by oral ingestion. Brain samples were collected before administration and at 0.083, 0.167, 0.25, 0.333, 0.5, 0.75, 1, 1.5, 2, 2.5, 3, 4 and 5 h after administration. The brain concentration of natural borneol and contents of AA neurotransmitters in mice brain were determined by GC-MS and HPLC-FLU, respectively. After per oral application, natural borneol was absorbed rapidly into the brain and could be determined 5 min after dosing. The maximal brain concentration (86.52 μg/g) was reached after 1 h post-dosing. Natural borneol could affect the contents of AA neurotransmitters in mice brain: L: -aspartic acid increased significantly from 0.083 to 1 h after administration, L: -glutamic acid increased significantly at 0.333 h and decreased from 1.5 to 5 h, gamma-amino-N-butyric acid increased significantly from 0.167 to 5 h, whereas glycine was not affected. The excitation ratio is the contents of excitatory AAs versus that of inhibitory AAs, which reflects the excitatory or inhibitory state of the body. The excitation ratio elevated transitorily and then declined 0.5 h post-dosing; there were significant differences between 1.5-5 h post-dose compared with pre-dose. The present study indicated that natural borneol could affect the contents of AA neurotransmitters, and the change in excitatory ratio led to borneol's double side effects on the CNS.

To compare the effectiveness of two methods of DNA extraction from different colour costal cartilages in STR genotyping.DNA fragments were extracted from costal cartilages of different colour of 30 corrupt corpses using Chelex-100 and Phenol-Chloroform methods. STR loci were analyzed by ABI 3100 genetic analyzer after PCR amplification by using Profiler Plus kit.STR loci were completely detected in all 30 samlpes of costal cartilages when using Phenol-Chloroform DNA extraction methods. While using Chelex-100 methods, all STR loci were identified in 22 cases (11 white, 8 light-yellow and 3 yellow cases). Partial STR loci were detected in 7 cases (3 yellow and 4 yellow-brown cases) and none in 1 brown-black cases.Suitable DNA extracion methods will be chosen depends on the colour of costal cartilage. Phenol-Chloroform methods is more effective in STR genotyping especially in dark colour costal cartilage cases.

To investigate the effect of different PCR amplification volume on the accuracy of human identification test.Human genome DNA samples were amplified using ABI PRISM Profiler Plus kits in 50 microliters, 25 microliters, 12.5 microliters, and 6.25 microliters reaction volume, respectively. The thermocycle parameters were the same. All PCR products were then electrophoresized on ABI PRISM 310 Genetic Analyzer, 377 DNA Sequencer, and 3100 Genetic Analyzer. Data were processed by ABI PRISM GeneScan and Genotyper software.The less reaction volume, the more alleles losing or alleles adding observed.Non-standard volume of PCR amplification reaction should be used carefully in human identification test, especially when the sample DNA quality is not so satisfied.