The Middle East respiratory syndrome coronavirus (MERS-CoV), an emerging human coronavirus, causes severe acute respiratory illness with a 35% mortality rate. In light of the recent surge in reported ...infections we have developed asymmetric five-primer reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for detection of MERS-CoV. Isothermal amplification assays will facilitate the development of portable point-of-care diagnostics that are crucial for management of emerging infections. The RT-LAMP assays are designed to amplify MERS-CoV genomic loci located within the open reading frame (ORF)1a and ORF1b genes and upstream of the E gene. Additionally we applied one-step strand displacement probes (OSD) for real-time sequence-specific verification of LAMP amplicons. Asymmetric amplification effected by incorporating a single loop primer in each assay accelerated the time-to-result of the OSD-RT-LAMP assays. The resulting assays could detect 0.02 to 0.2 plaque forming units (PFU) (5 to 50 PFU/ml) of MERS-CoV in infected cell culture supernatants within 30 to 50 min and did not cross-react with common human respiratory pathogens.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Intrahepatic cholangiocellular carcinoma (ICC) is the second most common type of primary liver cancer. However, its tumor heterogeneity and molecular characteristics are largely unknown. In this ...study, we conducted transcriptomic profiling of 23 ICC and combined hepatocellular cholangiocarcinoma tumor specimens from Asian patients using Affymetrix messenger RNA (mRNA) and NanoString microRNA microarrays to search for unique gene signatures linked to tumor subtypes and patient prognosis. We validated the signatures in an additional 68 ICC cases derived from Caucasian patients. We found that both mRNA and microRNA expression profiles could independently classify Asian ICC cases into two main subgroups, one of which shared gene expression signatures with previously identified hepatocellular carcinoma (HCC) with stem cell gene expression traits. ICC‐specific gene signatures could predict survival in Asian HCC cases and independently in Caucasian ICC cases. Integrative analyses of the ICC‐specific mRNA and microRNA expression profiles revealed that a common signaling pathway linking miR‐200c signaling to epithelial‐mesenchymal transition (EMT) was preferentially activated in ICC with stem cell gene expression traits. Inactivation of miR‐200c resulted in an induction of EMT, whereas activation of miR‐200c led to a reduction of EMT including a reduced cell migration and invasion in ICC cells. We also found that miR‐200c and neural cell adhesion molecule 1 (NCAM1) expression were negatively correlated and their expression levels were predictive of survival in ICC samples. NCAM1, a known hepatic stem/progenitor cell marker, was experimentally demonstrated to be a direct target of miR‐200c. Conclusion: Our results indicate that ICC and HCC share common stem‐like molecular characteristics and poor prognosis. We suggest that the specific components of EMT may be exploited as critical biomarkers and clinically relevant therapeutic targets for an aggressive form of stem cell‐like ICC. (HEPATOLOGY 2012;56:1792–1803)
Abstract Middle East Respiratory Syndrome Coronavirus (MERS-CoV) continues to be a threat to human health in the Middle East. Development of countermeasures is ongoing; however, an animal model that ...faithfully recapitulates human disease has yet to be defined. A recent study indicated that inoculation of common marmosets resulted in inconsistent lethality. Based on these data we sought to compare two isolates of MERS-CoV. We followed disease progression in common marmosets after intratracheal exposure with: MERS-CoV-EMC/2012, MERS-CoV-Jordan-n3/2012, media, or inactivated virus. Our data suggest that common marmosets developed a mild to moderate non-lethal respiratory disease, which was quantifiable by computed tomography (CT), with limited other clinical signs. Based on CT data, clinical data, and virological data, MERS-CoV inoculation of common marmosets results in mild to moderate clinical signs of disease that are likely due to manipulations of the marmoset rather than as a result of robust viral replication.
Ebola virus (EBOV) is a single-stranded negative-sense RNA virus belonging to the Filoviridae family. The leader and trailer non-coding regions of the EBOV genome likely regulate its transcription, ...replication, and progeny genome packaging. We investigated the cis-acting RNA signals involved in RNA-RNA and RNA-protein interactions that regulate replication of eGFP-encoding EBOV minigenomic RNA and identified heat shock cognate protein family A (HSC70) member 8 (HSPA8) as an EBOV trailer-interacting host protein. Mutational analysis of the trailer HSPA8 binding motif revealed that this interaction is essential for EBOV minigenome replication. Selective 2'-hydroxyl acylation analyzed by primer extension analysis of the secondary structure of the EBOV minigenomic RNA indicates formation of a small stem-loop composed of the HSPA8 motif, a 3' stem-loop (nucleotides 1868-1890) that is similar to a previously identified structure in the replicative intermediate (RI) RNA and a panhandle domain involving a trailer-to-leader interaction. Results of minigenome assays and an EBOV reverse genetic system rescue support a role for both the panhandle domain and HSPA8 motif 1 in virus replication.
Intronic miRNAs, residing in intronic regions of host genes, are thought to be co-transcribed from their host genes and present consistent expression patterns with host genes. Recent studies reported ...a few intronic miRNAs with discordant expression with their host genes. We therefore aimed to understand the expression pattern of intronic miRNAs and their host genes in hepatocellular carcinoma (HCC) and reveal possible associated molecular mechanisms. Our genome wide integration analysis of miRNA and mRNA transcriptomes, in three dataset from 550 patients with HCC, found that a large amount of miRNA-host gene pairs were discordantly expressed. Consistent results were also revealed in 775 breast cancer patients. Further, most of HCC-related intronic miRNAs were predicted to have distinct upstream regulators and independent proximal promoter signals from host genes. The discordant expression of representative pairs, miR-26s/CTDSPs, was validated experimentally. We have also identified the independent transcriptional start site, promoter signal, and transcriptional factor of miR-26b from its host gene. Collectively, discordant expression of intronic miRNAs and their host genes was relatively ubiquitous and the intronic miRNA "independent transcription" may partially contribute to such a phenotype.
Single photon emission computed tomography (SPECT) is frequently used in oncology and cardiology to evaluate disease progression and/or treatment efficacy. Such technology allows for real-time ...evaluation of disease progression and when applied to studying infectious diseases may provide insight into pathogenesis. Insertion of a SPECT-compatible reporter gene into a virus may provide insight into mechanisms of pathogenesis and viral tropism. The human sodium iodide symporter (hNIS), a SPECT and positron emission tomography reporter gene, was inserted into Middle East respiratory syndrome coronavirus (MERS-CoV), a recently emerged virus that can cause severe respiratory disease and death in afflicted humans to obtain a quantifiable and sensitive marker for viral replication to further MERS-CoV animal model development. The recombinant virus was evaluated for fitness, stability, and reporter gene functionality. The recombinant and parental viruses demonstrated equal fitness in terms of peak titer and replication kinetics, were stable for up to six
passages, and were functional. Further
evaluation indicated variable stability, but resolution limits hampered
functional evaluation. These data support the further development of hNIS for monitoring infection in animal models of viral disease.
Advanced medical imaging such as single photon emission computed tomography with computed tomography (SPECT/CT) enhances fields such as oncology and cardiology. Application of SPECT/CT, magnetic resonance imaging, and positron emission tomography to infectious disease may enhance pathogenesis studies and provide alternate biomarkers of disease progression. The experiments described in this article focus on insertion of a SPECT/CT-compatible reporter gene into MERS-CoV to demonstrate that a functional SPECT/CT reporter gene can be inserted into a virus.
Kidney fibrosis constitutes the shared final pathway of nearly all chronic nephropathies, but biomarkers for the non-invasive assessment of kidney fibrosis are currently not available. To address ...this, we characterize five candidate biomarkers of kidney fibrosis: Cadherin-11 (CDH11), Sparc-related modular calcium binding protein-2 (SMOC2), Pigment epithelium-derived factor (PEDF), Matrix-Gla protein, and Thrombospondin-2. Gene expression profiles in single-cell and single-nucleus RNA-sequencing (sc/snRNA-seq) datasets from rodent models of fibrosis and human chronic kidney disease (CKD) were explored, and Luminex-based assays for each biomarker were developed. Plasma and urine biomarker levels were measured using independent prospective cohorts of CKD: the Boston Kidney Biopsy Cohort, a cohort of individuals with biopsy-confirmed semiquantitative assessment of kidney fibrosis, and the Seattle Kidney Study, a cohort of patients with common forms of CKD. Ordinal logistic regression and Cox proportional hazards regression models were used to test associations of biomarkers with interstitial fibrosis and tubular atrophy and progression to end-stage kidney disease and death, respectively. Sc/snRNA-seq data confirmed cell-specific expression of biomarker genes in fibroblasts. After multivariable adjustment, higher levels of plasma CDH11, SMOC2, and PEDF and urinary CDH11 and PEDF were significantly associated with increasing severity of interstitial fibrosis and tubular atrophy in the Boston Kidney Biopsy Cohort. In both cohorts, higher levels of plasma and urinary SMOC2 and urinary CDH11 were independently associated with progression to end-stage kidney disease. Higher levels of urinary PEDF associated with end-stage kidney disease in the Seattle Kidney Study, with a similar signal in the Boston Kidney Biopsy Cohort, although the latter narrowly missed statistical significance. Thus, we identified CDH11, SMOC2, and PEDF as promising non-invasive biomarkers of kidney fibrosis.
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Background: Small bowel neuroendocrine tumors (SB-NET) are rare, and often small and multifocal. They are difficult to localize preoperatively and can be overlooked during operative ...exploration. The optimal work-up and operative approach is not known. Methods: Patients who underwent resection of SB-NET at a single institution from 2000-2014 were included. Primary aim was to describe the diagnostic work-up, pathologic characteristics, and compare minimally-invasive (MIS) to open resection. Results: 93pts underwent resection for SB-NET. Median age was 61yrs; 52% were male. On presentation, 71% of pts were symptomatic and underwent an average of 3 diagnostic tests prior to resection: 45% had octreoscans, which identified the region of primary disease in 85%; 11% had small bowel enteroscopy, with a 10% diagnostic yield; 19% had capsule endoscopy, which saw a lesion in 83%, but in only 21% was the correct number of tumors seen. The diagnostic yield of capsule was 28% overall, but 82% in pts presenting with GI bleeding. 79pts (85%) underwent curative-intent resections. Median tumor size was 1.8cm and multiple primary tumors were seen in 34pts(42%), of whom 50% had > 3 tumors. 37% had metastatic and 70% had LN positive disease. 27pts underwent MIS resections vs 66 open. MIS pts were younger (56vs61yrs;p0.035) and less likely to have obstructive symptoms (4vs24%;p = 0.19) and metastatic disease at resection (19vs44%;p = 0.038). Compared to open, the MIS group had smaller (1.7vs2.4cm;p = 0.03) and fewer tumors resected (2vs5;p = 0.049), but similar LN yield (13vs12;p = 0.7). In pts without metastases undergoing curative-intent resection, MIS approach was still associated with fewer tumors removed compared to open (1.5vs4;p = 0.034). Conclusions: Capsule endoscopy appears to be better than small bowel enteroscopy at identifying occult small bowel neuroendocrine tumors, particularly when pts present with bleeding, but still may underestimate tumor burden. While MIS may be appropriate in select patients, recognizing the limitations of preoperative evaluation is critical when selecting the operative approach for these tumors, as heightened operative vigilance is often required.
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Background: The prognostic implications on outcomes of symptomatic presentation of gastroenteropancreatic (GEP) neuroendocrine tumors (NETs) remains unclear. Methods: Patients who ...underwent curative-intent resection of nonfunctional, well-differentiated GEP NETs from 2000-2014 at a single institution were analyzed. Patients were classified as symptomatic if clinical symptoms were present at diagnosis. Primary end points were distant recurrence-free survival (DRFS) and overall survival (OS). Results: A total of 339pts were identified, of which 208pts (61%) were symptomatic at presentation. Symptomatic presentation was associated with younger age at presentation (55vs59yrs, p = 0.001), higher tumor grade (38vs21%, p = 0.027), LVI (58vs33%, p < 0.001), PNI (53vs30%, p = 0.002), and advanced disease (T3/T4/N1/M1 63vs44%, p = 0.002), but not tumor size (2.6vs2.5cm, p = 0.74). Symptomatic presentation was associated with decreased DRFS but not OS. When accounting for race, tumor size, positive resection margins, presence of metastatic disease, and positive lymph nodes on multivariate analysis (MVA), symptomatic presentation remained independently associated with reduced DRFS (HR 3.51, p = 0.007). On subgroup analysis of patients only with advanced disease (T3/T4/N1/M1), symptomatic presentation was still associated with decreased 3-yr DRFS (67vs79%, p = 0.012), but not OS. On MVA, symptomatic presentation persisted as an independent factor associated with decreased DRFS in patients with advanced disease (HR 2.89, p = 0.014). Conclusions: Symptomatic presentation of GEP NETs is associated with more aggressive pathologic features and worse DRFS than incidentally diagnosed NETs irrespective of tumor size. As our armamentarium of therapeutic agents for NETs expands and improves, trials assessing the value of adjuvant therapy for advanced GEP NETs are needed, and symptomatic presentation may be considered as one inclusion criterion. Following resection, symptomatic presentation should be taken into account when planning follow-up strategies, as these patients may require closer surveillance than their incidentally diagnosed counterparts.
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