Targeted resequencing of the microRNAome and 3'UTRome reveals functional germline DNA variants with altered prevalence in epithelial ovarian cancer

Ovarian cancer is a major cause of cancer deaths, yet there have been few known genetic risk factors identified, the best known of which are disruptions in protein coding sequences (BRCA1 and 2). Recent findings indicate that there are powerful genetic markers of cancer risk outside of these regions, in the noncoding mRNA control regions. To identify additional cancer-associated, functional non-protein-coding sequence germline variants associated with ovarian cancer risk, we captured DNA regions corresponding to all validated human microRNAs and the 3' untranslated regions (UTRs) of ~6000 cancer-associated genes from 31 ovarian cancer patients. Multiple single-nucleotide polymorphisms in the 3'UTR of the vascular endothelial growth factor receptor/FLT1, E2F2 and PCM1 oncogenes were highly enriched in ovarian cancer patients compared with the 1000 Genome Project. Sequenom validation in a case-control study (267 cases and 89 controls) confirmed a novel variant in the PCM1 3'UTR is significantly associated with ovarian cancer (P=0.0086). This work identifies a potential new ovarian cancer locus and further confirms that cancer resequencing efforts should not ignore the study of noncoding regions of cancer patients.

Relative importance of seed drying rate, desiccation tolerance, and cryotolerance for the conservation of Ardisia elliptica, A. brunnescens and A. virens

BACKGROUND

The pan-tropical genus Ardisia has more than 400 species and is of high horticultural and medicinal value. Due to overexploitation it is important to conserve the germplasm of this genus.

OBJECTIVE

To investigate the feasibility and methods of cryopreservation for long-term seed storage of three Ardisia species: A. elliptica Thunb., A. brunnescens Walker, and A. virens Kurz.

METHODS

We tested whether rapid desiccation can increase desiccation tolerance and cryotolerance, and whether the thawing rate can affect cryopreservation success. Seeds were subjected to three desiccation treatments: 1) activated silica gel at 25 +/- 2 degree C, and 4% relative humidity (RH); 2) saturated NaCl solution in closed jars in 25 +/- 2 degree C and 75% RH; and 3) air-drying at room conditions at 27 +/- 2 degree C and RH 60% for different desiccation durations (12h, 24h, 48h, 96h, and 196h). Seeds were then assessed for desiccation tolerance and cryotolerance after rapid thawing (direct immersion in 36 degree C water bath for 2 min) or slow thawing (at 27°C for 1 h).

RESULTS

For all three species, desiccation method and duration significantly affected cryotolerance (P < 0.0001). Fast desiccation did not improve germination compared to slower desiccation (P < 0.01). Whereas A. elliptica germination was unaffected by desiccation duration, drying time significantly (P < 0.0001) affected germination percentage in the other two species especially after 48h. Although slow thawing improved cryotolerance of A. brunnescens seeds (P < 0.05), there was no significant effect of thawing rate on A. elliptica. A. virens seed did not survive cryopreservation.

CONCLUSIONS

Cryopreservation protocols of Ardisia species may be species-specific and should be established for each species in the genus so that cryopreservation can be used as a successful conservation strategy.

Promyelocytic leukaemia zinc finger maintains self-renewal of male germline stem cells (mGSCs) and its expression pattern in dairy goat testis

OBJECTIVES

Previous studies have shown that promyelocytic leukaemia zinc finger (PLZF) is a spermatogonia-specific transcription factor in the testis, required to regulate self-renewal and maintenance of the spermatogonia stem cell. Up to now, expression and function of PLZF in the goat testis has not been known. The objectives of this study were to investigate PLZF expression pattern in the dairy goat and its effect on male goat germline stem cell (mGSC) self-renewal and differentiation.

MATERIALS AND METHODS

Testis development and expression patterns of PLZF in the dairy goat were analysed by haematoxylin and eosin staining, immunohistochemistry and reverse transcription-polymerase chain reaction (RT-PCR). Furthermore, effects of PLZF overexpression on mGSC self-renewal and differentiation were evaluated by quantitative RT-PCR (QRT-PCR), immunofluorescence and BrdU incorporation assay.

RESULTS

Promyelocytic leukaemia zinc finger was essential for dairy goat testis development and expression of several proliferation and pluripotency-associated proteins including OCT4, C-MYC were upregulated by PLZF overexpression. The study demonstrated that PLZF played a key role in maintaining self-renewal of mGSCs and its overexpression enhanced expression of proliferation-associated genes.

CONCLUSIONS

Promyelocytic leukaemia zinc finger could function in the dairy goat as well as in other species in maintaining self-renewal of germline stem cells and this study provides a model to study the mechanism on self-renewal and differentiation of mGSCs in livestock.

RNA-Seq profiling reveals aberrant RNA splicing in patient with adult acute myeloid leukemia during treatment

BACKGROUND

Multiple genetic alterations that affect the process of acute myeloid leukemia (AML) have been discovered, and more evidence also indicates that aberrant splicing plays an important role in cancer.

MATERIALS AND METHODS

We present a RNA-Seq profiling of an AML patient with complete remission after treatment, to analyze the aberrant splicing of genes during treatment. We sequenced 3.97 and 3.32 Gbp clean data of the AML and remission sample, respectively. Firstly, by analyzing biomarkers associated with AML, to assist normal clinical tests, we confirmed that the patient was anormal karyo type, with NPM1 and IDH2 mutations and deregulation patterns of related genes, such as BAALC, ERG, MN1 and HOX family. Then, we performed alternative splicing detection of the AML and remission sample.

RESULTS

We detected 91 differentially splicing events in 68 differentially splicing genes (DSGs) by mixture of isoforms (MISO). Considering Psi values (Ψ) and confidence intervals, 25 differentially expressed isoforms were identified as more confident isoforms, which were associated with RNA processing, cellular macromolecule catabolic process and DNA binding according to GO enrichment analysis. An exon2-skipping event in oncogene FOS (FBJ murine osteosarcoma viral oncogene homolog) were detected and validated in this study. FOS has a critical function in regulating cell proliferation, differentiation and transformation. The exon2-skipping isoform of FOS was increased significantly after treatment.

CONCLUSIONS

All the data and information of RNA-Seq provides highly accurate and comprehensive supplements to conventional clinical tests of AML. Moreover, the splicing aberrations would be another source for biomarker and even therapeutic target discovery. More information of splicing may also assist the better understanding of leukemogenesis.

Acceptability and psychometric properties of Brøset Violence Checklist in psychiatric care settings in China

Short-term risk assessment instrument owns great importance for psychiatric nurses in China; however, the lack of a standardized violence risk assessment instrument has disadvantaged them in clinical practice. The Brøset Violence Checklist (BVC), a behavioural observation tool, is the most frequently cited instrument available for evaluating violence risk in psychiatric inpatients, then worth to be tested in Chinese culture. This study, conducted in two closed wards in a psychiatric hospital in Beijing, revealed that the instrument has favourable reliability, validity and predictive accuracy in Chinese population. BVC provides nurses with a quick and easily administered method to screening out patients with violence potential, thus allowing for early intervention. Feedback from the nurses was quite encouraging and the further use of BVC seems promising. The lack of standardized violence risk assessment instrument has disadvantaged nurses in clinical practice in China, where violent behaviour is an increasing problem. This study conducted a validation of the Brøset Violence Checklist that has proven effective in violence risk prediction in other countries. A sample of 296 patients consecutively admitted to two wards of a psychiatric hospital in Beijing was recruited. These patients were assessed on day shift and evening shift for the first seven days of hospitalization. Violence data and preventive measures were concurrently collected from nursing records and case reports. A total of 3707 assessments for 281 patients were collected revealing 93 episodes of violence among 55 patients. Receiver operating characteristics yielded an area under the curve of 0.85. At the cut-off point of one, its sensitivity/specificity was 78.5%/88.2% and the corresponding positive/negative predictive value was 14.6%/99.4%. In some false positive cases, intense preventive measures had been implemented. Positive feedback from the nurses was gained. The Brøset Violence Checklist was proved as an easy-to-use and time-saving instrument, therefore, regarded as a promising tool to determine if the psychiatric users are potentially violent in the short term.

A Fourier transform infrared spectroscopy analysis of carious dentin from transparent zone to normal zone

It is well known that caries invasion leads to the differentiation of dentin into zones with altered composition, collagen integrity and mineral identity. However, understanding of these changes from the fundamental perspective of molecular structure has been lacking so far. In light of this, the present work aims to utilize Fourier transform infrared spectroscopy (FTIR) to directly extract molecular information regarding collagen's and hydroxyapatite's structural changes as dentin transitions from the transparent zone (TZ) into the normal zone (NZ). Unembedded ultrathin dentin films were sectioned from carious teeth, and an FTIR imaging system was used to obtain spatially resolved FTIR spectra. According to the mineral-to-matrix ratio image generated from large-area low-spectral-resolution scan, the TZ, the NZ and the intermediate subtransparent zone (STZ) were identified. High-spectral-resolution spectra were taken from each zone and subsequently examined with regard to mineral content, carbonate distribution, collagen denaturation and carbonate substitution patterns. The integrity of collagen's triple helical structure was also evaluated based on spectra collected from demineralized dentin films of selected teeth. The results support the argument that STZ is the real sclerotic layer, and they corroborate the established knowledge that collagen in TZ is hardly altered and therefore should be reserved for reparative purposes. Moreover, the close resemblance between the STZ and the NZ in terms of carbonate content, and that between the STZ and the TZ in terms of being A-type carbonate-rich, suggest that the mineral that initially occludes dentin tubules is hydroxyapatite newly generated from odontoblastic activities, which is then transformed into whitlockite in the demineralization/remineralization process as caries progresses.

Expression pattern of Ngn3 in dairy goat testis and its function in promoting meiosis by upregulating Stra8

OBJECTIVES

Ngn3 is a typical transcription factor and marker of differentiating spermatogonial stem cells (SSCs) in mouse, belonging to the basic helix-loop-helix (bHLH) family. Its gene is specifically expressed in A type spermatogonia in mouse testis, thus plays a critical role in controlling differentiation of SSCs. However, roles of Ngn3 and its protein in dairy goat testis remain unknown.

MATERIALS AND METHODS

Testis development and expression patterns of Ngn3 were analysed by immunofluorescence and quantitative reverse transcription-polymerase chain reaction (QRT-PCR) in the dairy goat. Furthermore, effects of its overexpression on male germline stem cells (mGSCs) were evaluated by QRT-PCR, immunofluorescence, luciferase reporter assay and western blotting.

RESULTS

Revealed that Ngn3 was expressed more highly during puberty and in the adult than in testis of other ages. Overexpression of Ngn3 promoted expression of meiosis-related gene Stra8 and stem-cell differentiation marker CD117, but suppressed expression of Plzf, a classical marker of SSCs. Furthermore, Ngn3 did not promote expression of Stra8 directly as shown in transcription and translation levels detected by luciferase reporter assay and western blotting.

CONCLUSIONS

Taken together, these results suggest that Ngn3 plays an important role in spermatogenesis and that overexpression of Ngn3 can promote meiosis in testis of the dairy goat.

Protection against hepatitis E virus infection by naturally acquired and vaccine-induced immunity

Immunity acquired from infection or vaccination protects humans from symptomatic hepatitis E. However, whether the risk of hepatitis E virus (HEV) infection is reduced by the immunity remains unknown. To understand this issue, a cohort with 12 409 participants randomized to receive the hepatitis E vaccine Hecolin(®) or placebo were serologically followed up for 2 years after vaccination. About half (47%) of participants were initially seropositive. A total of 139 infection episodes, evidenced by four-fold or greater rise of anti-HEV level or positive seroconversion, occurred in participants who received three doses of treatment. Risk of infection was highest among the baseline seronegative placebo group participants (2.04%). Pre-existing immunity and vaccine-induced immunity lower the risk significantly, to 0.52% and 0.30%, respectively. In conclusion, both vaccine-induced and naturally acquired immunity can effectively protect against HEV infection.

Detection of prostate cancer related copy number variations with SNP genotyping array

AIM

Prostate cancer is characterized by the accumulation of multiple copy number variants (CNVs) across the genome. We aim to identify potential prostate cancer related CNVs.

MATERIALS AND METHODS

Whole-genome SNP genotyping data of 18 prostate cancer patients was downloaded from the GEO (Gene Expression Omnibus) database. PennCNV was used to detect CNVs. All genes and miRNAs affected by CNVs were annotated. We also identified biological processes where these genes over-represented to capture the characteristics of prostate cancer.

RESULTS

Dominance of deletions was identified in all subjects. A total of 131 genes and 2 miRNAs which were affected by CNVs supported by at least two samples were detected. Over-representations of biological processes related with immune or inflammation response and cell cycle were identified. Two miRNAs, hsa-miR-1302 and hsa-miR-548j, were affected by CNVs and their target genes were reported to be related with prostate cancer according to the Mendelian Inheritance in Man database.

CONCLUSIONS

We identified genes known to be affected by prostate cancer associated CNVs in previous studies; we also identified new genes and miRNAs not reported as interesting. The discoveries in this study may advance the knowledge of the prostate cancer pathogenesis.

Identifying magnetic anisotropy of the topological surface state of Cr(0.05)Sb(1.95)Te(3) with spin-polarized STM

The surface magnetic property plays a key role in determining magnetic related quantum phenomena of magnetic topological insulators. Using spin-polarized scanning tunneling microscopy, we investigate the surface magnetism and anisotropy of a Cr doped topological insulator: Cr(0.05)Sb(1.95)Te(3). It is found that the topological surface state of Cr(0.05)Sb(1.95)Te(3) is spin polarized in the surface plane while the bulk shows a ferromagnetism with an out-of-plane easy axis. The upper and lower branch of the helical Dirac cone harbors the opposite spin polarization and the polarization at the Dirac point is zero. Our results show the complexity of surface magnetism of magnetic doped topological insulators.

Chemotherapy (gemcitabine, docetaxel plus gemcitabine, doxorubicin, or trabectedin) in inoperable, locally advanced, recurrent, or metastatic uterine leiomyosarcoma: a clinical practice guideline

QUESTIONS

Does chemotherapy-that is, gemcitabine, gemcitabine plus docetaxel, doxorubicin, or trabectedin-improve clinical outcomes in women with inoperable, locally advanced, recurrent, or metastatic uterine leiomyosarcoma (lms)? Is there a difference in the tumour response rate to chemotherapy between recurrent pelvic disease and extrapelvic metastases in the target patients?

METHODS

This guideline was developed by Cancer Care Ontario's Program in Evidence-Based Care, the Sarcoma Disease Site Group (dsg), and the Gynecologic Cancer dsg. The core methodology was the systematic review. The medline and embase databases (2004 to June 2011), the Cochrane Library, main guideline Web sites, and relevant annual meeting abstracts (2005-2010) were searched. Internal and external reviews were conducted, with final approval by the dsgs and the Program in Evidence-Based Care.

CLINICAL PRACTICE GUIDELINE

Based on currently available evidence from the medical literature (four single-arm phase ii studies, one arm of a randomized controlled trial, and one abstract), doxorubicin alone, gemcitabine alone, or gemcitabine plus docetaxel may be treatment options in first- or second-line therapy (or both) for women with inoperable, locally advanced, recurrent, or metastatic uterine lms. Hematologic toxicity is common and should be monitored, and granulocyte colony-stimulating factor should be considered when gemcitabine plus docetaxel is used. Other toxicities, such as neurotoxicity, pulmonary toxicity, and cardiovascular toxicity should be monitored. No recommendation is made for or against the use of trabectedin in the targeted patients. No data were available concerning differences in response in recurrent pelvic disease or extrapelvic metastases, or concerning quality of life.

Fine-needle aspiration biopsy versus core-needle biopsy in diagnosing lung cancer: a systematic review

BACKGROUND

Lung cancer leads cancer-related mortality in the world. The objective of the present systematic review was to compare fine-needle aspiration biopsy (fnab) with core-needle biopsy (cnb) for diagnostic characteristics and yields for diagnosing lung cancer in patients with lung lesions.

METHODS

The medline and embase databases (from January 1, 1990, to September 14, 2009), the Cochrane Library (to Issue 4, 2009), and selected guideline Web sites were searched for relevant articles.

RESULTS

For overall diagnostic characteristics (benign vs. malignant) of fnab and cnb, the ranges of sensitivity were 81.3%-90.8% and 85.7-97.4% respectively; of specificity, 75.4%-100.0% and 88.6%-100.0%; and of accuracy, 79.7%-91.8% and 89.0%-96.9%. For specific diagnostic characteristics of fnab and cnb (identifying the histologic subtype of malignancies or the specific benign diagnoses), the ranges of sensitivity were 56.3%-86.5% and 56.5-88.7% respectively; of specificity, 6.7%-57.1% and 52.4%-100.0%; and of accuracy, 40.4%-81.2% and 66.7%-93.2%. Compared with fnab, cnb did not result in a higher complication rate (pneumothorax or hemoptysis). No study has yet compared the diagnostic yields of fnab and of cnb for molecular predictive-marker studies in patients with lung lesions.

DISCUSSION AND CONCLUSIONS

The evidence is currently insufficient to support a difference between fnab and cnb in identifying lung malignancies in patients with lung lesions. Compared with fnab, cnb might have a higher specificity to diagnose specific benign lesions. Well-designed, good-quality studies comparing fnab with cnb for diagnostic characteristics and yields in diagnosing lung cancer should be encouraged.

Variations in circulating sex steroid levels in metastatic prostate cancer patients with combined androgen blockade: observation and implication

Testosterone is the major precursor of estradiol (E2) in men. We hypothesized that, in metastatic prostate cancer, androgen deprivation therapy suppression of serum androgen to the castration level may also disrupt serum E2 level, and variation in serum E2 level might play a role in the development of castration-resistant prostate cancer. Our investigation was designed to observe the variation in circulating oestrogen and androgen levels in metastatic prostate cancer patients after combined androgen blockade, and to explore the possible clinical significance. We recruited 105 consecutive metastatic prostate cancer patients who were treated with combined androgen blockade from June to August 2011, and divided them into three groups according to different hormone-sensitivity status, including 58 hormone-sensitive prostate cancers, 27 after failure of first-line hormone therapy (androgen-independent prostate cancer) and 20 castration-resistant prostate cancers. Another 36 consecutive patients with treatment-naive metastatic prostate cancer during the same period were used as controls. Serum testosterone, E2 and E2/testosterone (E2/T) ratio were analysed and compared between the groups. After combined androgen blockade, testosterone was suppressed to a low level, regardless of different hormone sensitivity (p > 0.05). Mean serum testosterone was 4.07, 0.15, 0.11 and 0.09 ng/mL in treatment-naive, hormone-sensitive, androgen-independent and castration-resistant prostate cancer respectively. For each group, mean E2 was 33.06, 9.23, 9.13 and 15.05 pg/mL respectively. Mean E2/T was 9.58, 269.29, 292.06 and 996.67 respectively. Recovery of E2 and increased E2/T ratio were more significantly associated with combined androgen blockade failure, especially in castration-resistant prostate cancer (p < 0.001). This study indicated that metabolism of oestrogen might change during combined androgen blockade in metastatic prostate cancer patients, and oestrogen-related pathways might play a role in the development of castration-resistant prostate cancer.

Systematic chemotherapy for inoperable, locally advanced, recurrent, or metastatic uterine leiomyosarcoma: a systematic review

The goal of this systematic review was to investigate and compare the treatment effects of systemic chemotherapy (i.e. doxorubicin, gemcitabine, gemcitabine plus docetaxel, or trabectedin) in women with inoperable, locally advanced, recurrent, or metastatic uterine leiomyosarcoma. A 2005 systematic review (searching the literature from 1980 to June 2004) on systemic therapy in advanced uterine sarcoma was used as the basis for this updated review. MEDLINE and EMBASE (from January 2004 to June 2011), the Cochrane Library, some main guideline websites and the American Society of Clinical Oncology and the Connective Tissue Oncology Society annual meeting abstracts were searched. One arm from a randomised controlled trial (RCT), four single-arm phase II trials and one abstract were included in this systematic review. The studies of gemcitabine plus docetaxel have reported numerically longer median overall survival (14.7-17.9 months versus 12.1 months) and numerically higher objective response rates (27-53% versus 25%) than those reported in the study of doxorubicin alone. The combination of gemcitabine plus docetaxel resulted in more toxicity than doxorubicin alone. The available study for single-agent gemcitabine reported a tumour response rate of 21%, which is not superior to the 25% response rate with doxorubicin alone. One abstract (pooling data from two RCTs) failed to show the superiority of gemcitabine plus docetaxel over gemcitabine alone for tumour response rate (23% versus 18%) and progression-free survival (6 versus 4.9 months). To date, there is insufficient evidence to support or refute the use of trabectedin in the target patients. Doxorubicin, gemcitabine, and gemcitabine plus docetaxel are treatment options in women with inoperable, locally advanced, recurrent, or metastatic uterine leiomyosarcoma as first- or second-line therapy. Well-designed and good-quality RCTs are required to investigate the efficacy of chemotherapy and quality of life in target patients with uterine leiomyosarcoma.