Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer.

BACKGROUND: Previous studies identified microRNAs (miRNAs) and messenger RNAs with significantly different expression between normal pancreas and pancreatic cancer (PDAC) tissues. Due to technological limitations of microarrays and real-time PCR systems these studies focused on a fixed set of targets. Expression of other RNA classes such as long intergenic non-coding RNAs or sno-derived RNAs has rarely been examined in pancreatic cancer. Here, we analysed the coding and non-coding transcriptome of six PDAC and five control tissues using next-generation sequencing. RESULTS: Besides the confirmation of several deregulated mRNAs and miRNAs, miRNAs without previous implication in PDAC were detected: miR-802, miR-2114 or miR-561. SnoRNA-derived RNAs (e.g. sno-HBII-296B) and piR-017061, a piwi-interacting RNA, were found to be differentially expressed between PDAC and control tissues. In silico target analysis of miR-802 revealed potential binding sites in the 3' UTR of TCF4, encoding a transcription factor that controls Wnt signalling genes. Overexpression of miR-802 in MiaPaCa pancreatic cancer cells reduced TCF4 protein levels. Using Massive Analysis of cDNA Ends (MACE) we identified differential expression of 43 lincRNAs, long intergenic non-coding RNAs, e.g. LINC00261 and LINC00152 as well as several natural antisense transcripts like HNF1A-AS1 and AFAP1-AS1. Differential expression was confirmed by qPCR on the mRNA/miRNA/lincRNA level and by immunohistochemistry on the protein level. CONCLUSIONS: Here, we report a novel lncRNA, sncRNA and mRNA signature of PDAC. In silico prediction of ncRNA targets allowed for assigning potential functions to differentially regulated RNAs.

How safe is safe: new human immunodeficiency virus Type 1 variants missed by nucleic acid testing.

BACKGROUND: Nucleic acid amplification techniques (NAT) in routine blood donor screening considerably reduce the diagnostic window phase period. Nevertheless, several reports of false-negative NAT results were published. Here, four cases of human immunodeficiency virus Type 1 (HIV-1) RNA-positive blood donations that escaped detection by NAT screening are described. STUDY DESIGN AND METHODS: A total of 2.7 million blood donations were screened for viral infections between January 2010 and October 2012 in our German Red Cross blood donation service. Four plasma specimens with false-negative NAT results were comparatively investigated with 12 CE-marked NAT assays. In two cases of putative HIV-1 variants the target region of the NAT assay was sequenced allowing comparison with the respective primers and probes. RESULTS: Most of the NAT assays used in routine blood donor screening with the 5'-long terminal repeat (LTR) as target region demonstrated deficiencies in detecting the viral variants and the low-viral-carrier donations. Sequence analysis revealed in one case a deletion of 56 nucleotides within the 5'-LTR preventing the binding of the probe accompanied by a neighbored insertion of another 52 nucleotides and several primer mismatches in another case. No false-negative results were obtained for these cases using dual-target assays. The viral load of the remaining two false-negative results was below the NAT's limit of detection. CONCLUSION: HIV-1 is characterized by a high mutation rate and rapid generation of new viral variants. By the use of one target region for HIV-1 NAT assays there is a certain risk of false-negative results. Employing HIV-1 multi- and dual-target assays in routine blood donor screening seems to be a reasonable possibility to minimize this problem.

Experience of German Red Cross blood donor services with nucleic acid testing: results of screening more than 30 million blood donations for human immunodeficiency virus-1, hepatitis C virus, and hepatitis B virus.

BACKGROUND: The risk of transfusion-transmitted human immunodeficiency virus-1 (HIV-1), hepatitis C virus (HCV), and hepatitis B virus (HBV) infections is predominantly attributable to donations given during the early stage of infection when diagnostic tests may fail. In 1997, nucleic acid amplification technique (NAT)-testing was introduced at the German Red Cross (GRC) blood donor services to reduce this diagnostic window period (WP). STUDY DESIGN AND METHODS: A total of 31,524,571 blood donations collected from 1997 through 2005 were screened by minipool NAT, predominantly with pool sizes of 96 donations. These donations cover approximately 80 percent of all the blood collected in Germany during that period. Based on these data, the WP risk in the GRC blood donor population was estimated by using a state-of-the-art mathematic model. RESULTS: During the observation period, 23 HCV, 7 HIV-1, and 43 HBV NAT-only-positive donations were detected. On the basis of these data and estimated pre-NAT infectious WPs, the residual risk per unit transfused was estimated at 1 in 10.88 million for HCV (95% confidence interval [CI], 7.51-19.72 million), 1 in 4.30 million for HIV-1 (95% CI, 2.39-21.37 million), and 1 in 360,000 for HBV (95% CI, 0.19-3.36 million). Based on observed cases of breakthrough infections, the risk of transfusion-related infections may be even lower. CONCLUSION: The risk of a blood recipient becoming infected with HCV, HIV-1, or HBV has reached an extremely low level. Introduction of individual donation testing for HCV and HIV-1 would have a marginal effect on interception of WP donations.

Nucleic acid test screening of blood donors for orthopoxviruses can potentially prevent dispersion of viral agents in case of bioterrorism.

BACKGROUND: Microbiologic agents such as variola virus (VAR) are very attractive for terrorism. As a result of international collaboration under the WHO eradication campaign, smallpox was declared eradicated in 1980. Therefore, the immunization programs were discontinued worldwide. Because most people are now immunologically naive, VAR is considered to be a potential threat agent or bioterrorist weapon. Real-time polymerase chain reaction (PCR) followed by melting analysis was developed for fast and safe analysis and allows differentiation of VAR from other orthopoxviruses (OPVs) like vaccinia or camelpox virus. STUDY DESIGN AND METHODS: A RealArt Orthopox LC PCR kit (Artus GmbH) was used to amplify OPV sequences from blood donor samples. A total of 31,500 blood donor samples were tested in minipools of up to 96 samples. To evaluate the sensitivity of the assay, routine donor minipools (90 +/- 6 samples per pool) were spiked with vaccinia virus used as positive control. RESULTS: Specificity was 100 percent because none of 31,500 blood donors was positive for the presence OPV. The detection limit of the assay was 10.6 copies per PCR procedure. Therefore, a sensitivity of 1590 copies per mL was calculated. Overall, 0.28 percent of test results had to be considered invalid owing to negative internal controls. CONCLUSION: The RealArt Orthopox LC PCR kit enables reliable detection of OPV DNA in viremic blood donor samples, even at the beginning of the disease when patients present minor clinical symptoms, and could be implemented in our routine screening procedure immediately. Thus, the assay could potentially help to prevent dispersion of viral agents by blood transfusion in case of bioterrorism.

NAT screening of blood donors for severe acute respiratory syndrome coronavirus can potentially prevent transfusion associated transmissions.

BACKGROUND: The severe acute respiratory syndrome (SARS) was first described in February 2003. Close contact with symptomatic patients appears to be the main route of transmission, whereas blood transfusion transmission could not be ruled out. STUDY DESIGN AND METHODS: A SARS coronavirus (SARS-CoV) detection kit developed by C. Drosten (Bernhard Nocht Institute, BNI) was used to amplify SARS-CoV sequences from blood donor samples. We tested 31,151 blood donor samples in minipools of up to 96 samples. To validate the sensitivity of the assay, routine donor minipools (88 +/- 8 samples per pool) were spiked with plasma of an imported case of SARS or of a subsequently infected contact person, respectively. Gamma-irradiated cell culture supernatants of Vero E6 cells, infected with SARS-CoV, were used as positive controls. RESULTS: None of 31,151 blood donors were positive for the presence of SARS. Two 96-member plasma pools that were each spiked with 100 microL of plasma of the German index patient or his wife, respectively, were positive. Overall, 0.85 percent of test results had to be considered invalid owing to negative internal controls. CONCLUSION: A real-time CoV PCR test is able to detect SARS-CoV in viremic blood donor samples even in the beginning of the disease when patients present minor clinical symptoms. Thus the assay could potentially help to prevent transfusion-associated SARS-CoV transmissions.

Yield of HCV and HIV-1 NAT after screening of 3.6 million blood donations in central Europe.

BACKGROUND: HCV and HIV-1 NAT of all blood donations was initiated at our institutions in January 1997 to reduce the residual risk of transfusion-transmitted virus infections. The yield of NAT after testing more than 3.6 million donations in central Europe is reported. STUDY DESIGN AND METHODS: Automated pipetting instruments were used to pool up to 96 donor samples including those that were antibody reactive. To compensate for dilution of the individual donor samples by pooling, viruses were enriched from the pools by centrifugation at 48,000 x g. A commercial PCR (Cobas Amplicor, Roche) and an in-house PCR were applied for HCV and HIV-1 amplification, respectively. RESULTS: Six HCV and 2 HIV-1 PCR confirmed-positive, antibody-negative donations (yield, 1 in 600,000 and 1 in 1.8 million, respectively) were identified. Thirty-nine and 11 multiple-time donors seroconverted for HCV and HIV, respectively, and look-back procedures were initiated. Archived samples from preseroconversion donations were thawed and retested by single-sample PCR and remained negative. The recipients of the blood components were traced and tested. All traced recipients were negative for HCV and HIV antibodies. CONCLUSION: The yield of NAT in central European Red Cross blood donors was less than expected from theoretical calculations for American and German multiple-time donors. Look-back procedures for HCV and HIV indicated that no donation given before seroconversion of the donor was missed by minipool PCR. Sensitivity of minipool PCR testing after virus enrichment seems to be sufficiently high to close the diagnostic window almost completely.

NAT for HBV and anti-HBc testing increase blood safety.

BACKGROUND: Routine HBV PCR screening of blood donations to our institutes was introduced in January 1997 to complete the NAT screening program for transfusion-relevant viruses. Testing was successively extended to customer transfusion services with a total of 1,300,000 samples tested per year. STUDY DESIGN AND METHODS: Minipools of 96 blood donation samples were formed by automatic pipettors. HBsAg-reactive samples were included. HBV particles were enriched from the minipools by centrifugation. Conventional and in-house TaqMan PCRs were successively applied for HBV amplification. Sensitivity reached 1000 genome equivalents per mL for each individual donation. Confirmatory single-sample and single-sample enrichment PCRs were established with sensitivities of 300 and 5 to 10 genome equivalents per mL, respectively. RESULTS: After screening of 3.6 million donor samples, 6 HBV PCR-positive, HBsAg-negative donations were identified. Two samples were from infected donors who had not seroconverted and four were from chronic anti-HBc-positive low-level HBV carriers. Retesting by single-sample PCR of 432 samples confirmed positive for HBsAg identified 37 donations that were negative in minipool PCR. Donor-directed look-back procedures indicated that no infected donor who had not yet seroconverted was missed by minipool PCR. However, recipient-directed look-back procedures revealed two anti-HBc-positive recipients of HBsAg-negative minipool PCR-negative, anti-HBc-positive and single-sample PCR-positive blood components. After testing randomly selected 729 HBsAg-negative minipool PCR-negative, anti-HBc-positive donors by single-sample enrichment PCR, 7 were identified with < or = 10 HBV particles per mL of donor plasma. CONCLUSION: Minipool PCR testing after virus enrichment was sensitive enough to identify HBsAg-negative donors who had seroconverterd and HBsAg-negative, anti-HBc-positive chronic HBV carriers. HBV NAT in conjunction with anti-HBc screening would reduce the residual risk of transfusion-transmitted HBV infection.