Identification of putative miRNAs from the deep-branching unicellular flagellates

MicroRNAs (miRNAs) are a class of extensively studied RNAi-associated small RNAs that play a critical role in eukaryotic gene regulation. However, knowledge on the miRNA and its regulation in unicellular eukaryotes is very limited. In order to obtain a better understanding on the origin of miRNA regulation system, we used deep-sequencing technology to investigate the miRNA expression pattern in four deep-branching unicellular flagellates: Giardia lamblia, Trichomonas vaginalis, Tritrichomonas foetus, and Pentatrichomonas hominis. In addition to the known miRNAs that have been described in G. lamblia and T. vaginalis, we identified 14 ancient animal miRNA families and 13 plant-specific families. Bioinformatics analysis also identified four novel miRNA candidates with reliable precursor structures derived from mature tRNAs. Our results indicated that miRNAs are likely to be a general feature for gene regulation throughout unicellular and multicellular eukaryotes and some of them may derive from unconventional ncRNAs such as snoRNA and tRNA.

Increasing liver transplantation waiting list mortality: a report from the Australian National Liver Transplantation Unit, Sydney

BACKGROUND

We aimed to describe the demand for liver transplantation (LTx) and patient outcomes on the waiting list at the Australian National Liver Transplantation Unit, Sydney over the last 20 years.

METHODS

We performed a retrospective analysis with the data divided into three eras: 1985-1993, 1994-2000 and 2001-2008.

RESULTS

The number of patients accepted for LTx increased from 320 to 372 and 548 (P < 0.001) with the number of LTx being performed increasing from 262 to 312 and 452 respectively (P < 0.001). The median adult recipient age increased from 45 to 48 and 52 years (P < 0.001) while it decreased in children from 4 to 2 and 1 years respectively (P = 0.001). In parallel, the deceased donor offers decreased from 1003 to 720 and 717 (P < 0.001). Methods to improve access to donor livers have been used with the use of split livers, extended criteria and non-heart beating donors, resulting in increased acceptance of deceased donor offers by 65% and 115% in the second and third eras when compared with the first era (P < 0.001). However, the adult median waiting time has increased from 23 to 41 and 120 days respectively (P < 0.001). This was associated with increased adult mortality on the waiting list from 23 to 40 and 122 respectively (P < 0.001).

CONCLUSIONS

Despite the increasing proportion of donor offers being used, the waiting list mortality is increasing. A solution to this problem is an increase in organ donation to keep pace with the escalating demand for LTx.

A transcriptomic study on the pepsin-activated infective larvae of Angiostrongylus cantonensis

To investigate the pepsin-activated infective (third-stage) larvae of Angiostrongylus cantonensis at the transcriptomic level, 1496 ESTs were generated from a cDNA library and clustered into 161 contigs and 757 singletons. Among these unigenes, 54.5% had significant sequence homology with known proteins. The most abundantly expressed transcripts were cathepsin B-like cysteine protease 1 and 2, metalloprotease I, metalloprotease 1 precursor, and extracellular superoxide dismutase. Protein complex was the most common Gene Ontology classification within the 'cellular component' category, embryonic development ending in birth or egg hatching within 'biological process', and protein binding within 'molecular function'. Moreover, 280 clusters were mapped to 158 KEGG pathways and 134 had unique EC numbers. These findings suggest that treatment with pepsin-HCl not only digests the tissues of the snail host but also activates the infective larvae.

Mycobacterium heckeshornense peritonitis in a peritoneal dialysis patient: a case report and review of the literature

We report the first case of peritonitis attributed to Mycobacterium heckeshornense. This is a rare, non-tuberculous mycobacterium that has been reported as an aetiological agent in a growing number and widening spectrum of infections.

DSAP: deep-sequencing small RNA analysis pipeline

DSAP is an automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology. DSAP uses a tab-delimited file as an input format, which holds the unique sequence reads (tags) and their corresponding number of copies generated by the Solexa sequencing platform. The input data will go through four analysis steps in DSAP: (i) cleanup: removal of adaptors and poly-A/T/C/G/N nucleotides; (ii) clustering: grouping of cleaned sequence tags into unique sequence clusters; (iii) non-coding RNA (ncRNA) matching: sequence homology mapping against a transcribed sequence library from the ncRNA database Rfam (http://rfam.sanger.ac.uk/); and (iv) known miRNA matching: detection of known miRNAs in miRBase (http://www.mirbase.org/) based on sequence homology. The expression levels corresponding to matched ncRNAs and miRNAs are summarized in multi-color clickable bar charts linked to external databases. DSAP is also capable of displaying miRNA expression levels from different jobs using a log₂-scaled color matrix. Furthermore, a cross-species comparative function is also provided to show the distribution of identified miRNAs in different species as deposited in miRBase. DSAP is available at http://dsap.cgu.edu.tw.

Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics

Background

Trichomonas vaginalis is the most common non-viral human sexually transmitted pathogen and importantly, contributes to facilitating the spread of HIV. Yet very little is known about its surface and secreted proteins mediating interactions with, and permitting the invasion and colonisation of, the host mucosa. Initial annotations of T. vaginalis genome identified a plethora of candidate extracellular proteins.

Results

Data mining of the T. vaginalis genome identified 911 BspA-like entries (TvBspA) sharing TpLRR-like leucine-rich repeats, which represent the largest gene family encoding potential extracellular proteins for the pathogen. A broad range of microorganisms encoding BspA-like proteins was identified and these are mainly known to live on mucosal surfaces, among these T. vaginalis is endowed with the largest gene family. Over 190 TvBspA proteins with inferred transmembrane domains were characterised by a considerable structural diversity between their TpLRR and other types of repetitive sequences and two subfamilies possessed distinct classic sorting signal motifs for endocytosis. One TvBspA subfamily also shared a glycine-rich protein domain with proteins from Clostridium difficile pathogenic strains and C. difficile phages. Consistent with the hypothesis that TvBspA protein structural diversity implies diverse roles, we demonstrated for several TvBspA genes differential expression at the transcript level in different growth conditions. Identified variants of repetitive segments between several TvBspA paralogues and orthologues from two clinical isolates were also consistent with TpLRR and other repetitive sequences to be functionally important. For one TvBspA protein cell surface expression and antibody responses by both female and male T. vaginalis infected patients were also demonstrated.

Conclusions

The biased mucosal habitat for microbial species encoding BspA-like proteins, the characterisation of a vast structural diversity for the TvBspA proteins, differential expression of a subset of TvBspA genes and the cellular localisation and immunological data for one TvBspA; all point to the importance of the TvBspA proteins to various aspects of T. vaginalis pathobiology at the host-pathogen interface.

Bikunin loss in urine as useful marker for bladder carcinoma

PURPOSE

We searched for bladder tumor markers by analyzing urine samples from patients with bladder cancer and normal individuals.

MATERIALS AND METHODS

Proteins in urine samples of patients with cancer and normal subjects were systematically examined by 2-dimensional electrophoresis combined with matrix assisted laser desorption ionization time-of-flight mass spectrometry. Of the proteins bikunin expression was confirmed by Western blot analysis and further evaluated. To correlate urinary bikunin levels with clinical significance we examined urine samples from patients with bladder cancer and normal controls for bikunin expression in parallel with pro-urolinase-plasminogen activator, which was previously shown to be associated with advanced bladder carcinoma.

RESULTS

A significant relationship was established between the low level and absence of bikunin, and pro-urolinase-plasminogen activator in urine samples from patients with bladder tumors.

CONCLUSIONS

Analysis of urinary proteomes may be a feasible, noninvasive and efficient strategy for searching for potential bladder tumor biomarkers. We identified bikunin loss in urine as a potential bladder carcinoma marker.

Malate dehydrogenase is negatively regulated by miR-1 in Trichomonas vaginalis

MicroRNAs are highly conserved small noncoding RNAs that can suppress protein translation through complementary binding to target mRNAs. We used a novel approach to identify miRNA targets in the protist Trichomonas vaginalis by comparing the levels of differentially expressed proteins and genes in the trophozoite and amoeboid stages. We observed that the T. vaginalis malate dehydrogenase (Tv_MDH) gene was upregulated 20-fold in the amoeboid stage, but the protein level was reduced by 4.5-fold. Bioinformatics analysis revealed that the Tv_MDH mRNA contains putative target sites of the miR-1 family. The expression level of endogenous tva-miR-1 in the amoeboid stage was 50-fold higher than in the trophozoite stage. Transfection of trophozoites with tva-miR-1 mimics reduced Tv_MDH protein expression by 60%. Based on these experimental data, we conclude that Tv_MDH is negatively regulated by tva-miR-1. The results of this study demonstrate that a combination of proteomic and transcriptomic approaches is a powerful tool for identifying miRNA targets.

Effect of siRNA targeting HIF-1alpha combined L-ascorbate on biological behavior of hypoxic MiaPaCa2 cells

The aim of the study was to observe the effect of small interference RNA (siRNA) targeting hypoxia-inducible factor 1alpha (HIF-1alpha) combined L-ascorbate on proliferation, migration, and apoptosis of hypoxic MiaPaCa2 human pancreatic cancer cells. A cassette encoding siRNA targeting HIF-1alpha mediated by recombinant adeno-associated virus (rAAV) was constructed, giving rAAV-siHIF. rAAV-siHIF and L-ascorbate, which were used alone or in combination, were delivered to exponentially growing MiaPaCa2 cells under hypoxic conditions. Then, we observed the expression of HIF-1alpha mRNA and protein, the proliferation, apoptosis, and migration of MiaPaCa2 cells by real-time PCR, Western blot, MTT, TUNEL, and Transwell assay, respectively. Under hypoxic conditions, rAAV-siHIF inhibited the expression of HIF-1alpha mRNA in MiaPaCa2 cells but L-ascorbate did not. However, rAAV-siHIF and L-ascorbate both inhibited the expression of HIF-1alpha protein and the proliferation and migration of MiaPaCa2 cells and induced MiaPaCa2 cell apoptosis. The effect in the combined group was more efficient than that seen when rAAV-siHIF or L-ascorbate was used separately. rAAV-siHIF and L-ascorbate both affect biological behavior of hypoxic MiaPaCa2 cells through modulating HIF-1alpha protein expression and rAAV-siHIF and L-ascorbate have synergy under hypoxic conditions.

Genome-wide association study reveals multiple nasopharyngeal carcinoma-associated loci within the HLA region at chromosome 6p21.3

Nasopharyngeal carcinoma (NPC) is a multifactorial malignancy closely associated with genetic factors and Epstein-Barr virus infection. To identify the common genetic variants linked to NPC susceptibility, we conducted a genome-wide association study (GWAS) in 277 NPC patients and 285 healthy controls within the Taiwanese population, analyzing 480,365 single-nucleotide polymorphisms (SNPs). Twelve statistically significant SNPs were identified and mapped to chromosome 6p21.3. Associations were replicated in two independent sets of case-control samples. Two of the most significant SNPs (rs2517713 and rs2975042; p(combined) = 3.9 x 10(-20) and 1.6 x 10(-19), respectively) were located in the HLA-A gene. Moreover, we detected significant associations between NPC and two genes: specifically, gamma aminobutyric acid b receptor 1 (GABBR1) (rs29232; p(combined) = 8.97 x 10(-17)) and HLA-F (rs3129055 and rs9258122; p(combined) = 7.36 x 10(-11) and 3.33 x 10(-10), respectively). Notably, the association of rs29232 remained significant (residual p < 5 x 10(-4)) after adjustment for age, gender, and HLA-related SNPs. Furthermore, higher GABA(B) receptor 1 expression levels can be found in the tumor cells in comparison to the adjacent epithelial cells (p < 0.001) in NPC biopsies, implying a biological role of GABBR1 in NPC carcinogenesis. To our knowledge, it is the first GWAS report of NPC showing that multiple loci (HLA-A, HLA-F, and GABBR1) within chromosome 6p21.3 are associated with NPC. Although some of these relationships may be attributed to linkage disequilibrium between the loci, the findings clearly provide a fresh direction for the study of NPC development.

A phase II study of Halichondrin B analog eribulin mesylate (E7389) as second-line therapy for patients with advanced pancreatic cancer

e15634

Background: Eribulin mesylate is a halichondrin B analog that inhibits microtubule dynamics by a mechanism that is distinct from other tubulin-targeted agents. Preclinical studies suggest that Eribulin may be effective in pancreatic cancer. The primary objective of this study was to determine the objective response rate (complete and partial) to Eribulin in patients with advanced, pancreatic adenocarcinoma that had progressed after gemcitabine based therapy. Methods: Eligibility criteria included histologically confirmed pancreatic adenocarcinoma; measurable locally advanced, or metastatic disease; disease progression after gemcitabine; and ECOG performance status 0–2. Patients (pts) received Eribulin mesylate 1.4 mg/m2 IV on days 1 and 8. Treatment was repeated every 3 weeks in the absence of disease progression or unacceptable toxicity. Response was assessed by CT scans every 6 weeks while on treatment. Initially 12 pts were to be accrued, if 1 or more pt(s) had an objective response the accrual would increase to a total of 37. Results: 15 pts were accrued,14 received treatment and 12 were evaluable for response. Median age 61; M:F = 8:7; ECOG 1:2 = 11:4; Median number of cycles 2 (1–15). Grade 3+ adverse events included neutropenia (29%), fatigue (14%), peripheral neuropathy (7%) and thrombosis (7%). There were no complete or partial responses, and therefore the study was closed at the first accrual cut off. The best response was stable disease (SD) in 5/12 (42%) pts. Of these 5 pts, 3 (42%) had SD for 12 cycles or greater. Survival data is pending. Conclusions: Eribulin was well tolerated and did not result in any objective responses in refractory pancreatic cancer. However, 42% of pts had stable disease and for 3 pts this was maintained for more than 9 months. Further studies of eribulin in pancreatic cancer may be warranted.

No significant financial relationships to disclose.