The core exosome proteome of Trichomonas vaginalis

BACKGROUND

Trichomonas vaginalis is parasitic protozoan that causes human urogenital infections. Accumulated reports indicated that exosomes released by this parasite play a crucial role in transmitting information and substances between cells during host-parasite interactions. Current knowledge on the protein contents in T. vaginalis exosome is mainly generated from three previous studies that used different T. vaginalis isolates as an experimental model. Whether T. vaginalis exosomes comprise a common set of proteins (core exosome proteome) is still unclear.

METHODS

To explore the core exosome proteome in T. vaginalis, we used liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify the contents of sucrose ultracentrifugation-enriched exosome and supernatant fractions isolated from six isolates.

RESULTS

Transmission electron microscopy (TEM) confirmed the presence of exosomes in the enriched fraction. Proteomic analysis identified a total of 1870 proteins from exosomal extracts. There were 1207 exosomal-specific proteins after excluding 436 'non-core exosomal proteins'. Among these, 72 common exosomal-specific proteins were expressed in all six isolates. Compared with three published T. vaginalis exosome proteome datasets, we identified 16 core exosomal-specific proteins. These core exosomal-specific proteins included tetraspanin (TvTSP1), the classical exosome marker, and proteins mainly involved in catalytic activity and binding such as ribosomal proteins, ras-associated binding (Rab) proteins, and heterotrimeric G proteins.

CONCLUSIONS

Our study highlighted the importance of using supernatant fraction from exosomal extract as a control to eliminate 'non-core exosomal proteins'. We compiled a reference core exosome proteome of T. vaginalis, which is essential for developing a fundamental understanding of exosome-mediated cell communication and host-parasite interaction.

ProFun: A web server for functional enrichment analysis of parasitic protozoan genes

BACKGROUND

The initial step to interpreting putative biological functions from comparative multi-omics studies usually starts from a differential expressed gene list followed by functional enrichment analysis (FEA). However, most FEA packages are designed exclusively for humans and model organisms. Although parasitic protozoan is the most important pathogen in the tropics, no FEA package is available for protozoan functional (ProFun) enrichment analysis. To speed up comparative multi-omics research on parasitic protozoans, we constructed ProFun, a web-based, user-friendly platform for the research community.

METHODS

ProFun utilizes the Docker container, ShinyProxy, and R Shiny to construct a scalable web service with load-balancing infrastructure. We have integrated a series of visual analytic functions, in-house scripts, and custom-made annotation packages to create three analytical modules for 40 protozoan species: (1) Gene Overlaps; (2) Over-representation Analysis (ORA); (3) Gene Set Enrichment Analysis (GSEA).

RESULTS

We have established ProFun, a web server for functional enrichment analysis of differentially expressed genes. FEA becomes as simple as pasting a list of gene IDs into the textbox of our website. Users can customize enrichment parameters and results with just one click. The intuitive web interface and publication-ready charts enable users to reveal meaningful biological events and pinpoint potential targets for further studies.

CONCLUSION

ProFun is the first web application that enables gene functional enrichment analysis of parasitic protozoans. In addition to supporting FEA analysis, ProFun also allows the comparison of FEA results across complicated experimental designs. ProFun is freely available at http://dalek.cgu.edu.tw:8080/app/profun.

HeapMS: An Automatic Peak-Picking Pipeline for Targeted Proteomic Data Powered by 2D Heatmap Transformation and Convolutional Neural Networks

The process of peak picking and quality assessment for multiple reaction monitoring (MRM) data demands significant human effort, especially for signals with low abundance and high interference. Although multiple peak-picking software packages are available, they often fail to detect peaks with low quality and do not report cases with low confidence. Furthermore, visual examination of all chromatograms is still necessary to identify uncertain or erroneous cases. This study introduces HeapMS, a web service that uses artificial intelligence to assist with peak picking and the quality assessment of MRM chromatograms. HeapMS applies a rule-based filter to remove chromatograms with low interference and high-confidence peak boundaries detected by Skyline. Additionally, it transforms two histograms (representing light and heavy peptides) into a single encoded heatmap and performs a two-step evaluation (quality detection and peak picking) using image convolutional neural networks. HeapMS offers three categories of peak picking: uncertain peak picking that requires manual inspection, deletion peak picking that requires removal or manual re-examination, and automatic peak picking. HeapMS acquires the chromatogram and peak-picking boundaries directly from Skyline output. The output results are imported back into Skyline for further manual inspection, facilitating integration with Skyline. HeapMS offers the benefit of detecting chromatograms that should be deleted or require human inspection. Based on defined categories, it can significantly reduce human workload and provide consistent results. Furthermore, by using heatmaps instead of histograms, HeapMS can adapt to future updates in image recognition models. The HeapMS is available at: https://github.com/ccllabe/HeapMS.

Ten-Year Outcomes of Hypofractionated (45 Gy in 9 Fractions) Intensity Modulated Radiotherapy for Localized Prostate Cancer

PURPOSE/OBJECTIVE(S)

We reported 10-year outcomes of localized prostate cancers treated with hypofractionated intensity-modulated radiotherapy of 45 Gy in 9 consecutive fractions.

MATERIALS/METHODS

From October 2011 to April 2017, thirty patients with localized prostate cancer were enrolled in this prospective trial. The median age of the patients was 72.5 years. According to NCCN recurrence risk criteria, eight patients were at low-risk group, 17 at intermediate risk group, 5 at high-risk group. All patients were treated with hypofractionated intensity-modulated radiotherapy (IMRT) of 45 Gy in 9 consecutive fractions to their prostate with or without seminal vesicles. Before radiotherapy, three gold fiducials were implanted into the prostate. In order to reduce the rectal high dose irradiation volume, an inflated rectal balloon was placed in the rectum at simulation and every treatment and patients were treated with comfortable full bladder. Static Intensity-modulated radiotherapy (SIMRT) was applied in 1 patient, Volumetric Modulated Arc Therapy (VMAT) in 27 patients, and tomotherapy in 2 patients. Image guided radiotherapy (IGRT) with gold fiducial registration was adopted. Twenty-six patients also received androgen deprivation therapy (ADT). The median time of ADT was 6 months. Progression⁃free survival (PFS) and overall survival (OS) were analyzed using Kaplan-Meier analysis. All grade ≥1 genitourinary (GU) and gastrointestinal (GI) toxicities were recorded using Common Terminology Criteria for Adverse Event version 5.0 (CTCAE 5.0) and Radiation Therapy Oncology Group (RTOG) late morbidity criteria, and GU and GI toxicities were cumulatively calculated.

RESULTS

After a median follow-up of 102 months (65∼131 months), the 10-year OS was 90.0% (95% confidence interval, 83.3%-96.7%), and the 10-year PFS was 86.5% (95% confidence interval, 79.1%-93.9%). According to CTCAE 5.0, grade 1 acute gastrointestinal (GI) toxicity developed in 12 patients, grade 2 in 2 patients, grade 3 in 2 patients, and grade 1 acute genitourinary (GU) toxicity developed in 12 patients, grade 2 in 2 patients, and no grade 3 or higher toxicity occurred. According to RTOG late morbidity criteria, late (≥3 months after radiotherapy) grade 1 GI toxicity developed in 4 patients (13.3%), grade 2 in 1 (3.3%), grade 3 in 1 (3.3%), and late grade 1 GU toxicity occurred in 1 patient (3.3%), grade 2 in 1 (3.3%), grade 3 in 1 (3.3%). No grade 4 or higher GI and GU toxicities developed. Only one grade 3 GI and one grade 2 GU toxicities were observed for the maximum toxicity at the last follow-up. The potency was not evaluated.

CONCLUSION

The 10-year oncologic outcomes of this shortened hypofractionated IMRT regimen for mainly low/intermediate risk prostate cancer patients is favorable with acceptable acute and late toxicities.

Metabolomics analysis reveals changes related to pseudocyst formation induced by iron depletion in Trichomonas vaginalis

BACKGROUND

Iron is an essential element for cellular functions, such as energy metabolism. Trichomonas vaginalis, a human urogenital tract pathogen, is capable of surviving in the environment without sufficient iron supplementation. Pseudocysts (cyst-like structures) are an environmentally tolerated stage of this parasite while encountering undesired conditions, including iron deficiency. We previously demonstrated that iron deficiency induces more active glycolysis but a drastic downregulation of hydrogenosomal energy metabolic enzymes. Therefore, the metabolic direction of the end product of glycolysis is still controversial.

METHODS

In the present work, we conducted an LC‒MS-based metabolomics analysis to obtain accurate insights into the enzymatic events of T. vaginalis under iron-depleted (ID) conditions.

RESULTS

First, we showed the possible digestion of glycogen, cellulose polymerization, and accumulation of raffinose family oligosaccharides (RFOs). Second, a medium-chain fatty acid (MCFA), capric acid, was elevated, whereas most detected C18 fatty acids were reduced significantly. Third, amino acids were mostly reduced, especially alanine, glutamate, and serine. Thirty-three dipeptides showed significant accumulation in ID cells, which was probably associated with the decrease in amino acids. Our results indicated that glycogen was metabolized as the carbon source, and the structural component cellulose was synthesized at same time. The decrease in C18 fatty acids implied possible incorporation in the membranous compartment for pseudocyst formation. The decrease in amino acids accompanied by an increase in dipeptides implied incomplete proteolysis. These enzymatic reactions (alanine dehydrogenase, glutamate dehydrogenase, and threonine dehydratase) were likely involved in ammonia release.

CONCLUSION

These findings highlighted the possible glycogen utilization, cellulose biosynthesis, and fatty acid incorporation in pseudocyst formation as well as NO precursor ammonia production induced by iron-depleted stress.

[Clinical features of SF3B1 mutation in patients with myelodysplastic syndrome with excess blasts]

Objective: To exploring the clinical features of SF3B1-mutated myelodysplastic syndrome with excess blasts (MDS-EB) and analyzing the association between SF3B1 mutation, and efficacy and prognostic significance for patients with MDS-EB. Methods: This was a retrospective case series study. The clinical data of 266 patients with MDS-EB diagnosed in the First Affiliated Hospital of Zhengzhou University between April 2016 and November 2021 were analyzed. The observed indicators included blood routine counts, mutated genes, overall response rate (ORR), overall survival (OS), progression-free survival (PFS), and leukemia-free survival (LFS). The Kaplan-Meier method was used to depict the survival curves. The Log-rank test method was equally used to compare survival across groups and performed the Cox proportional hazard regression model for prognostic analysis. Results: In 266 patients with MDS-EB, 166 (62.4%) were men, and the median age was 57 (17-81) years. Moreover, there were included 26 and 240 patients in the SF3B1-mutated and SF3B1 wild-type groups. Patients in the SF3B1-mutated group were older [median age 65 (51, 69) years vs. 56 (46, 66) years, P=0.033], had higher white blood cell (WBC) counts [3.08 (2.35, 4.78) × 10⁹/L vs. 2.13 (1.40, 3.77) × 10⁹/L], platelet (PLT) counts [122.5 (50.5, 215.0) ×10⁹/L vs. 49.0 (24.3, 100.8) × 10⁹/L], absolute neutrophil counts (ANC) [1.83 (1.01, 2.88) × 10⁹/L vs. 0.80 (0.41, 1.99) × 10⁹/L]and occurrence of DNMT3A mutation [23.1% (6/26) vs. 6.7% (16/240)] (all P<0.05). The ORR were similar in both groups after 2 and 4 cycles of therapy (P=0.348, P=1.000). Moreover, the LFS (P=0.218), PFS (P=0.179) and OS (P=0.188) were similar across the groups. Univariate Cox analysis revealed that SF3B1 mutation did not affect the prognosis of patients with MDS-EB (OS: P=0.193; PFS: P=0.184). Conclusions: Patients with SF3B1 mutation were older, with greater WBC, PLT, and ANC, and SF3B1 mutation easily co-occurred with DNMT3A mutation. From this model, there were no significant differences in efficacy and survival of MDS-EB with or without SF3B1 mutation.

Long-term Cardiovascular Risks of Gonadotropin-releasing Hormone Agonists and Antagonists: a Population-based Cohort Study

AIMS

Gonadotropin-releasing hormone (GnRH) agonists and antagonists, critical medications for prostate cancer (PCa) treatment, may differ in cardiovascular safety. This prospective cohort study aimed to compare the long-term cardiovascular risks between GnRH agonists and antagonists.

MATERIALS AND METHODS

Patients with PCa receiving GnRH agonists or antagonists during 2013-2021 in Hong Kong were identified. Patients with <6 months' prescriptions, who were switching between drugs, had missing baseline prostate-specific antigen level or had a prior stroke or myocardial infarction were excluded. Patients were followed up until September 2021. The primary outcome was major adverse cardiovascular events (MACE) as in the PRONOUNCE trial (MACE_PRONOUNCE), i.e. a composite of all-cause mortality, stroke and myocardial infarction. The secondary outcome was MACE_CVM, i.e. a composite of cardiovascular mortality, stroke and myocardial infarction. Inverse probability treatment weighting was used to balance covariates between groups. The Log-rank test was used to compare the cumulative freedom from the primary outcome between groups.

RESULTS

In total, 2479 patients were analysed (162 GnRH antagonist users and 2317 agonist users; median age 75.0 years, interquartile range 68.0-81.6 years). Inverse probability treatment weighting achieved good covariate balance between groups. Over a median follow-up duration of 3.0 years (interquartile range 1.7-5.0 years), 1115 patients (45.0%) had MACE_PRONOUNCE and 344 (13.9%) had MACE_CVM. GnRH agonist users had lower risks of MACE_PRONOUNCE (Log-rank P < 0.001) and MACE_CVM (Log-rank P = 0.027). However, no differences were observed within 1 year of follow-up (MACE_PRONOUNCE: Log-rank P = 0.308; MACE_CVM: Log-rank P = 0.357). Among patients without cardiovascular risk factors at baseline, GnRH agonist users had lower risks of MACE_PRONOUNCE (Log-rank P < 0.001) and MACE_CVM (Log-rank P = 0.001), whereas no differences were observed in those with such risk factor(s) (MACE_PRONOUNCE: Log-rank P = 0.569; MACE_CVM: Log-rank P = 0.615).

CONCLUSIONS

GnRH antagonists may be associated with higher long-term, but not short-term, cardiovascular risks than agonists in Asian patients with PCa, particularly in those without known cardiovascular risk factors.

[The efficacy of radiotherapy based combined therapy for unresectable locally invasive bladder cancer and its associated factors analysis]

Objective: Retrospective analysis of the efficacy and influencing factors of bladder preservation integrated therapy for unresectable invasive bladder cancer confined to the pelvis was done, also including the bladder function preservation and adverse effects analysis. Methods: Sixty-nine patients with unresectable locally invasive bladder cancer who received radiotherapy-based combination therapy from March 1999 to December 2021 at our hospital were selected. Among them, 42 patients received concurrent chemoradiotherapy, 32 underwent neoadjuvant chemotherapyand 43 with transurethral resection of bladder tumors (TURBT) prior to radiotherapy. The late adverse effect of radiotherapy, preservation of bladder function, replase and metastasis and survival were followed-up. Cox proportional hazards models were applied for the multifactorial analysis. Results: The median age was 69 years. There were 63 cases (91.3%) of uroepithelial carcinoma, 64 of stage Ⅲ and 4 of stage Ⅳ. The median duration of follow-up was 76 months. There were 7 grade 2 late genito urinary toxicities, 2 grade 2 gastrointestinal toxicities, no grade 3 or higher adverse events occurred. All patients maintained normal bladder function, except for 8 cases who lost bladder function due to uncontrolled tumor in the bladder. Seventeen cases recurred locally. There were 11 cases in the concurrent chemoradiotherapy group with a local recurrence rate of 26.2% (11/42) and 6 cases in the non-concurrent chemoradiotherapy group with a local recurrence rate of 22.2% (6/27), and the difference in local recurrence rate between the two groups was not statistically significant (P=0.709). There were 23 cases of distant metastasis (including 2 cases of local recurrence with distant metastasis), including 10 cases in the concurrent chemoradiotherapy group with a distant metastasis rate of 23.8% (10/42) and 13 cases in the non-concurrent chemoradiotherapy group with a distant metastasis rate of 48.1% (13/27), and the distant metastasis rate in the non-concurrent chemoradiotherapy group was higher than that in the concurrent chemoradiotherapy group (P=0.036). The median 5-year overall survival (OS) time was 59 months and the OS rate was 47.8%. The 5-year progression-free survival (PFS) time was 20 months and the PFS rate was 34.4%. The 5-year OS rates of concurrent and non-concurrent chemoradiotherapy group were 62.9% and 27.6% (P<0.001), and 5-year PFS rates were 45.4% and 20.0%, respectively (P=0.022). The 5-year OS rates of with or without neoadjuvant chemotherapy were 78.4% and 30.1% (P=0.002), and the 5-year PFS rates were 49.1% and 25.1% (P=0.087), respectively. The 5-year OS rates with or without TURBT before radiotherapy were 45.5% and 51.9% (P=0.233) and the 5-year PFS rates were 30.8% and 39.9% (P=0.198), respectively. Multivariate Cox regression analysis results showed that the clinical stage (HR=0.422, 95% CI: 0.205-0.869) was independent prognostic factor for PFS of invasive bladder cancer. The multivariate analysis showed that clinical stages (HR=0.278, 95% CI: 0.114-0.678), concurrent chemoradiotherapy (HR=0.391, 95% CI: 0.165-0.930), neoadjuvant chemotherapy (HR=0.188, 95% CI: 0.058-0.611), and recurrences (HR=10.855, 95% CI: 3.655-32.638) were independent prognostic factors for OS of invasive bladder cancer. Conclusion: Unresectable localized invasive bladder cancer can achieve satisfactory long-term outcomes with bladder-preserving combination therapy based on radiotherapy, most patients can retain normal bladder function with acceptable late adverse effects and improved survival particularly evident in patients with early, concurrent chemoradiotherapy and neoadjuvant chemotherapy.

[Clinical features and survival analysis of microscopic polyangiitis-associated interstitial lung disease:a retrospective study of 28 patients]

Objective: To explore the clinical features, laboratory examination and imaging features of microscopic polyangiitis (MPA)-associated interstitial lung disease (ILD), and to perform survival analysis. Methods: The records of 28 patients with MPA-ILD who were treated at the Affiliated Hospital of Medical School of Ningbo University were reviewed retrospectively from August 2014 to November 2021. The patients' clinical features, laboratory parameters, pulmonary function test, echocardiography, chest CT scan findings and therapeutic regimen were analyzed, and the relevant data were statistically analyzed. Results: There were 18 males and 10 females, with an average age of (70.1±9.3) years. Among them, 13 patients had a history of smoking. The main clinical manifestations were cough (14/28), fever (12/28), chest tightness, shortness of breath (12/28) and hemoptysis (3/28). Sixteen patients had renal involvement, and 78.57% (22/28) and 89.28% (25/28) of the patients had elevated C-reactive protein (CRP) and ESR respectively. Sixteen (16/28) patients had increased rheumatoid factor (RF), and the positive rate of myeloperoxidase antineutrophil cytoplasmic antibodies (MPO-ANCA) was 82.12% (23/28). 96.43% (27/28) of ILDs were diagnosed before or at the same time as MPA. The chest radiological pattern was mainly usual interstitial pneumonia (UIP) or UIP-like (15/28), followed by nonspecific interstitial pneumonia (NSIP) (8/28). Compared with non-UIP-like patients, UIP or UIP-like patients were older (P=0.018), and had higher serum LDH level (P=0.041), but serum creatinine level was significantly lower (P=0.041). Univariate and multivariate survival analysis showed that inappropriate treatment (HR=9.81, 95%CI: 1.68-57.29, P=0.011) and elevated serum LDH (HR=4.11, 95%CI: 0.99-17.00, P=0.051) were independent risk factors for shortened survival of MPA-ILD, while elevated RF (HR=0.22, 95%CI: 0.06-0.91, P=0.037) was a protective factor for prolonged survival. Conclusions: MPA-ILD patients had fewer systemic vasculitis symptoms. Most of the ILD patients were diagnosed before or at the same time as MPA. The chest radiological pattern was mainly UIP or UIP-like, followed by NSIP. Early use of glucocorticoids combined with immunosuppressant or rituximab could improve the survival rate of MPA-ILD. The elevated serum LDH was an independent risk factor for shortened survival of MPA-ILD, while elevated RF was a protective factor for prolonged survival.

Deep learning-based classification of dermatological lesions given a limited amount of labeled data

BACKGROUND

Artificial intelligence (AI) techniques are promising in early diagnosis of skin diseases. However, a precondition for their success is the access to large-scaled annotated data. Until now, obtaining this data has only been feasible with very high personnel and financial resources.

OBJECTIVES

The aim of this study was to overcome the obstacle caused by the scarcity of labeled data.

METHODS

To simulate the scenario of label shortage, we discarded a proportion of labels of the training set. The training set consisted of both labeled and unlabeled images. We then leveraged a self-supervised learning technique to pre-train the AI model on the unlabeled images. Next, we fine-tuned the pre-trained model on the labeled images.

RESULTS

When the images in the training dataset were fully labeled, the self-supervised pre-trained model achieved 95.7% of accuracy, 91.7% of precision and 90.7% of sensitivity. When only 10% of the data was labeled, the model could still yield 87.7% of accuracy, 81.7% of precision and 68.6% of sensitivity. In addition, we also empirically verified that the AI model and dermatologists are consistent in visually inspecting the skin images.

CONCLUSIONS

The experimental results demonstrate the great potential of the self-supervised learning in alleviating the scarcity of annotated data.

Double-Stranded RNA Viruses Are Released From Trichomonas vaginalis Inside Small Extracellular Vesicles and Modulate the Exosomal Cargo

Trichomonas vaginalis is a parasitic protist that infects the human urogenital tract. During the infection, trichomonads adhere to the host mucosa, acquire nutrients from the vaginal/prostate environment, and release small extracellular vesicles (sEVs) that contribute to the trichomonad adherence and modulate the host-parasite communication. Approximately 40–70% of T. vaginalis strains harbor a double-stranded RNA virus called Trichomonasvirus (TVV). Naked TVV particles have the potential to stimulate a proinflammatory response in human cells, however, the mode of TVV release from trichomonads to the environment is not clear. In this report, we showed for the first time that TVV particles are released from T. vaginalis cells within sEVs. The sEVs loaded with TVV stimulated a higher proinflammatory response of human HaCaT cells in comparison to sEVs from TVV negative parasites. Moreover, a comparison of T. vaginalis isogenic TVV plus and TVV minus clones revealed a significant impact of TVV infection on the sEV proteome and RNA cargo. Small EVs from TVV positive trichomonads contained 12 enriched and 8 unique proteins including membrane-associated BspA adhesine, and about a 2.5-fold increase in the content of small regulatory tsRNA. As T. vaginalis isolates are frequently infected with TVV, the release of TVV via sEVs to the environment represents an important factor with the potential to enhance inflammation-related pathogenesis during trichomoniasis.

Identification of Endosymbiotic Virus in Small Extracellular Vesicles Derived from Trichomonas vaginalis

Accumulated evidence suggests that the endosymbiotic Trichomonasvirus (TVV) may play a role in the pathogenesis and drug susceptibility of Trichomonas vaginalis. Several reports have shown that extracellular vesicles (EVs) released from TVV-positive (TVV+) trichomonads can modulate the immune response in human vaginal epithelial cells and animal models. These results prompted us to examine whether EVs released from TVV+ isolates contained TVV. We isolated small extracellular vesicles (sEVs) from six T. vaginalis isolates that were either TVV free (ATCC 50143), harbored a single (ATCC 30236, ATCC 30238, T1), two (ATCC PRA-98), or three TVV subspecies (ATCC 50148). The presence of TVV subspecies in the six isolates was observed using reverse transcription-polymerase chain reaction (RT-PCR). Transmission electron microscopy (TEM) confirmed the presence of cup-shaped sEVs with a size range from 30–150 nm. Trichomonas vaginalis tetraspanin (TvTSP1; TVAG_019180), the classical exosome marker, was identified in all the sEV preparations. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis showed that all the sEVs isolated from TVV+ isolates contain viral capsid proteins derived from the same TVV subspecies in that isolate as demonstrated by RT-PCR. To provide more comprehensive information on the TVV subspecies population in other T. vaginalis isolates, we investigated the distribution of TVV subspecies in twenty-four isolates by mining the New-Generation Sequencing (NGS) RNAseq datasets. Our results should be beneficial for future studies investigating the role of TVV on the pathogenicity of T. vaginalis and the possible transmission of virus subspecies among different isolates via sEVs.

[Correlation between professional quality of life and social support of Chinese nurses: a meta-analysis]

Objective: To systematically evaluate the correlation between professional quality of life and social support of Chinese nurses based on Pearson and Spearman correlation coefficients. Methods: In databases including PubMed, Cochrane Library, CINAHL, Medline, CBM, CNKI、Wanfang, and other databases were searched by computer for the literatures on correlation between Chinese nurses' professional quality of life and social support from January 2005 to July 2020. The Chinese and English search terms are "nurse" "professional quality of life" "empathy satisfaction" "empathy fatigue" "professional quality of life" "ProQOL" "comparison satisfaction" "comparison fatigue" "social support" "competent social support" "SSRS" "PSSS", etc. Literatures were screened according to the inclusion and exclusion criteria. After evaluating quality and extracting data, meta-analysis was conducted using RevMan 5.3 software. Results: A total of 12 studies were included. The meta analysis showed that nurses' compassion satisfaction, burnout, secondary traumatic stress were related to social support, summary r were 0.35, -0.26 and -0.23 respectively. The correlation between compassion satisfaction and social support were increased with sample, the south was higher than the north, and comprehensive departments were higher than other departments (P<0.05) . The correlation between burnout and social support were increased with time and sample, and the south was higher than the north, oncology was higher than others, non-random sampling was higher than random sampling, using ProQOL and Perceived Social Support Scale (PSSS) was higher than Professional Quality of Life Scale (ProQOL) and Social Support Racting Scale (SSRS) (P<0.05) . The correlation coefficient between secondary traumatic stress and social support in oncology was higher than others, random sampling was higher than non-random sampling, using ProQOL and PSSS was higher than ProQOL and SSRS (P<0.05) . Conclusion: There is a positive and weak correlation between compassion satisfaction and social support, and a negative and weak correlation between burnout and secondary traumatic stress and social support. There are differences in different time, research design, region and department.

[The effectiveness of psychological intervention on nursing staff' compassion fatigue: a meta-analysis]

Objective: To systematically evaluate the impact of psychological intervention on nursing staff' compassion fatigue. Methods: From March to May 2020, PubMed, Cochrane Library, EMbase, Web of Science, CNKI, VIP, Wanfang and other databases were electronically searched to collect randomized controlled trials (RCTs) on the influence of psychological intervention on nursing staff' compassion fatigue with the main search terms including compassion fatigue, nurs*, psychological intervention, mental intervention, RCT and so on from inception to March 31, 2020. Screened literature, extracted data and assessed the risk of bias of included studies. The Stata 16.0 software was used to calculate the pooled effectiveness of psychological intervention on nursing staff' compassion fatigue. Results: All 13 RCTs were enrolled, including 940 nursing staff. Meta-analysis results demonstrated that the psychological intervention group was superior to the control group in the improvement of the compassion fatigue score (SMD=-0.96, 95%CI: -1.17-0.74, P=0.001) , compassion satisfaction score (SMD=0.61, 95%CI: 0.45-0.77, P=0.002) , burnout score (SMD=-0.46, 95%CI: -0.62-0.29, P=0.006) , secondary trauma score (SMD=-0.40, 95%CI: -0.68-0.12, P=0.020) , and the difference was statistically significant. Subgroup analysis found that the psychological intervention group was more effective than the control group in improving compassion satisfaction score, reducing burnout score and secondary trauma score, and the differences were statistically significant (P<0.05) in different intervention time (<8 weeks and ≥8 weeks) and intervention methods. Conclusion: The psychological intervention can improve the level of compassion satisfaction, and reduce the compassion fatigue among nursing staff, and have a certain preventive effect on compassion fatigue.

[Familial interstitial lung disease associated with surfactant protein C gene mutation in adults: report of two cases and literature review]

Objective: To improve the understanding of clinical manifestations, imaging findings, diagnosis and treatment of surfactant protein C gene (SFTPC) mutation associated with familial interstitial lung disease in adults. Methods: Two cases of adult SFTPC gene mutation associated with familial interstitial lung disease diagnosed in the Affiliated Hospital of Medical School of Ningbo University were analyzed retrospectively, and the literature was reviewed. The literatures were retrieved with "family interstitial lung disease" "SFTPC gene" "surface protein C gene" "SFTPC gene mutation associated with familial international lung disease" and "surface protein C gene mutation associated with familial international lung disease" in PubMed, Embase, Ovid, Wanfang database and China National Knowledge Infrastructure (CNKI). Results: There were two patients with familial interstitial lung diseases(one male and one female) with an average age of 27.5 years. Ⅱ-2 patient had symptoms of dry cough and shortness of breath, and Ⅱ-1 patient had no symptoms. There were multiple cysts and fine reticular shadows in both cases. Ⅱ-2 patient had multiple ground glass opacities in both lower lungs. TheⅡ-2 patient was diagnosed with usual interstitial pneumonia (UIP) by transbronchial lung cryobiopsy. A total of 35 patients were included in this literature review, including 20 males, with an average age of 33.5 years. Of all the patients, the clinical symptoms were described in 30 patients. The main manifestations were shortness of breath (22/30), dry cough (18/30), clubbing finger (12/30), and 30% (9/30) of them were found by chest computerized tomography (CT) without symptoms. There were 17 cases with detailed description of chest CT imaging. The most common chest CT findings were multiple intralobular reticular opacities (17/17), multiple cysts (12/17) and ground glass opacities (7/17). The main histopathological pattern was UIP (24/26). Conclusions: The main clinical manifestations of SFTPC gene mutation associated with familial interstitial lung disease in adults are shortness of breath, dry cough and clubbing fingers. The main manifestations are multiple cysts and intralobular reticular opacities in combination with multiple ground glass opacities. There is no specific drug in the treatment at present and early treatment with hydroxychloroquine may have better curative effect. When the imaging findings show multiple cysts and intralobular reticular opacities in combination with multiple ground glass opacities, especially the age of onset is less than 50 years old, this disease should be considered.

Dissecting the Transcriptomes of Multiple Metronidazole-Resistant and Sensitive Trichomonas vaginalis Strains Identified Distinct Genes and Pathways Associated with Drug Resistance and Cell Death

Trichomonas vaginalis is the causative agent of trichomoniasis, the most prevalent non-viral sexually transmitted infection worldwide. Metronidazole (MTZ) is the mainstay of anti-trichomonal chemotherapy; however, drug resistance has become an increasingly worrying issue. Additionally, the molecular events of MTZ-induced cell death in T. vaginalis remain elusive. To gain insight into the differential expression of genes related to MTZ resistance and cell death, we conducted RNA-sequencing of three paired MTZ-resistant (MTZ-R) and MTZ-sensitive (MTZ-S) T. vaginalis strains treated with or without MTZ. Comparative transcriptomes analysis identified that several putative drug-resistant genes were exclusively upregulated in different MTZ-R strains, such as ATP-binding cassette (ABC) transporters and multidrug resistance pumps. Additionally, several shared upregulated genes among all the MTZ-R transcriptomes were not previously identified in T. vaginalis, such as 5′-nucleotidase surE and Na⁺-driven multidrug efflux pump, which are a potential stress response protein and a multidrug and toxic compound extrusion (MATE)-like protein, respectively. Functional enrichment analysis revealed that purine and pyrimidine metabolisms were suppressed in MTZ-S parasites upon drug treatment, whereas the endoplasmic reticulum-associated degradation (ERAD) pathway, proteasome, and ubiquitin-mediated proteolysis were strikingly activated, highlighting the novel pathways responsible for drug-induced stress. Our work presents the most detailed analysis of the transcriptional changes and the regulatory networks associated with MTZ resistance and MTZ-induced signaling, providing insights into MTZ resistance and cell death mechanisms in trichomonads.

Helminth egg analysis platform (HEAP): An opened platform for microscopic helminth egg identification and quantification based on the integration of deep learning architectures

BACKGROUND

Millions of people throughout the world suffer from parasite infections. Traditionally, technicians use manual eye inspection of microscopic specimens to perform a parasite examination. However, manual operations have limitations that hinder the ability to obtain precise egg counts and cause inefficient identification of infected parasites on co-infections. The technician requirements for handling a large number of microscopic examinations in countries that have limited medical resources are substantial. We developed the helminth egg analysis platform (HEAP) as a user-friendly microscopic helminth eggs identification and quantification platform to assist medical technicians during parasite infection examination.

METHODS

Multiple deep learning strategies including SSD (Single Shot MultiBox Detector), U-net, and Faster R-CNN (Faster Region-based Convolutional Neural Network) are integrated to identify the same specimen allowing users to choose the best predictions. An image binning and egg-in-edge algorithm based on pixel density detection was developed to increase the performance. Computers with different operation systems can be gathered to lower the computation time using our easy-to-deploy software architecture.

RESULTS

A user-friendly interface is provided to substantially increase the efficiency of manual validation. To adapt to low-cost computers, we architected a distributed computing structure with high flexibilities.

CONCLUSIONS

HEAP serves not only as a prediction service provider but also as a parasitic egg database of microscopic helminth egg image collection, labeling data and pretrained models. All images and labeling resources are free and accessible at http://heap.cgu.edu.tw. HEAP can also be an ideal education and training resource for helminth egg examination.

Accurate diagnosis of colorectal cancer based on histopathology images using artificial intelligence

BACKGROUND

Accurate and robust pathological image analysis for colorectal cancer (CRC) diagnosis is time-consuming and knowledge-intensive, but is essential for CRC patients' treatment. The current heavy workload of pathologists in clinics/hospitals may easily lead to unconscious misdiagnosis of CRC based on daily image analyses.

METHODS

Based on a state-of-the-art transfer-learned deep convolutional neural network in artificial intelligence (AI), we proposed a novel patch aggregation strategy for clinic CRC diagnosis using weakly labeled pathological whole-slide image (WSI) patches. This approach was trained and validated using an unprecedented and enormously large number of 170,099 patches, > 14,680 WSIs, from > 9631 subjects that covered diverse and representative clinical cases from multi-independent-sources across China, the USA, and Germany.

RESULTS

Our innovative AI tool consistently and nearly perfectly agreed with (average Kappa statistic 0.896) and even often better than most of the experienced expert pathologists when tested in diagnosing CRC WSIs from multicenters. The average area under the receiver operating characteristics curve (AUC) of AI was greater than that of the pathologists (0.988 vs 0.970) and achieved the best performance among the application of other AI methods to CRC diagnosis. Our AI-generated heatmap highlights the image regions of cancer tissue/cells.

CONCLUSIONS

This first-ever generalizable AI system can handle large amounts of WSIs consistently and robustly without potential bias due to fatigue commonly experienced by clinical pathologists. It will drastically alleviate the heavy clinical burden of daily pathology diagnosis and improve the treatment for CRC patients. This tool is generalizable to other cancer diagnosis based on image recognition.

DGCR8 promotes the metastasis in triple-negative breast cancer by epigenetically regulating TGF-β

OBJECTIVE

Breast cancer (BC) is one of the most ordinary fatal cancers. Recent studies have identified the vital role of genes in the development and progression of Tri-negative breast cancer (TNBC). In this research, DGCR8 was studied to identify how it functioned in the metastasis of TNBC.

PATIENTS AND METHODS

DGCR8 expression of tissues was detected by quantitative Real Time-Polymerase Chain Reaction (qRT-PCR) in 50 TNBC patients. Wound healing assay and transwell assay were used to observe the changes in the biological behaviors of TNBC cells through knockdown or overexpression of DGCR8. In addition, qRT-PCR and Western blot assay were performed to discover the potential target protein of DGCR8 in TNBC.

RESULTS

DGCR8 expression level in TNBC samples was higher than that of adjacent ones. Besides, the migration ability and invasion ability of TNBC cells were inhibited after DGCR8 was silenced, while they were promoted after DGCR8 was overexpressed. In addition, TGF-β was downregulated after silencing of DGCR8 in TNBC cells, while TGF-β was upregulated after overexpression of DGCR8 in TNBC cells. Furthermore, TGF-β was upregulated in TNBC tissues, which was positively associated with DGCR8.

CONCLUSIONS

Our study uncovers a new oncogene in TNBC and suggests that DGCR8 can enhance TNBC cell migration and invasion via targeting TGF-β, which provides a novel therapeutic target for TNBC patients.

Protein cysteine S-nitrosylation provides reducing power by enhancing lactate dehydrogenase activity in Trichomonas vaginalis under iron deficiency

BACKGROUND

Iron plays essential roles in the pathogenesis and proliferation of Trichomonas vaginalis, the causative agent of the most prevalent non-viral human sexually transmitted infection. We previously demonstrated that under iron deficiency, the endogenous nitric oxide (NO) is accumulated and capable of regulating the survival of T. vaginalis. Herein, we aim to explore the influence of NO on the activity of the pyruvate-reducing enzyme lactate dehydrogenase in T. vaginalis (TvLDH).

METHODS

Levels of lactate and pyruvate were detected for determining glycolysis activity in T. vaginalis under iron deficiency. Quantitative PCR was performed to determine the expression of TvLDH. S-nitrosylated (SNO) proteomics was conducted to identify the NO-modified proteins. The activities of glyceraldehyde-3-phosphate dehydrogenase (TvGAPDH) and TvLDH were measured after sodium nitrate treatment. The effects of protein nitrosylation on the production of cellular reducing power were examined by measuring the amount of nicotinamide adenine dinucleotide (NAD) and the ratio of the NAD redox pair (NAD+/NADH).

RESULTS

We found that although the glycolytic pathway was activated in cells under iron depletion, the level of pyruvate was decreased due to the increased level of TvLDH. By analyzing the SNO proteome of T. vaginalis upon iron deficiency, we found that TvLDH is one of the glycolytic enzymes modified by SNO. The production of pyruvate was significantly reduced after nitrate treatment, indicating that protein nitrosylation accelerated the consumption of pyruvate by increasing TvLDH activity. Nitrate treatment also induced NAD oxidation, suggesting that protein nitrosylation was the key posttranslational modification controlling cellular redox status.

CONCLUSIONS

We demonstrated that NO-mediated protein nitrosylation plays pivotal roles in the regulation of glycolysis, pyruvate metabolism, and the activity of TvLDH. The recycling of oxidized NAD catalyzed by TvLDH provided the reducing power that allowed T. vaginalis to adapt to the iron-deficient environment.

SAT0453 DELAYED DENOSUMAB INJECTIONS AND FRACTURES RISK AMONG SUBJECTS WITH OSTEOPOROSIS: A POPULATION-BASED COHORT STUDY

Background:

Denosumab is effective for osteoporosis, but discontinuation leads to rapid reversal of its therapeutic effect[1].

Objectives:

To estimate the risk for fracture among users of denosumab who delayed subsequent dosages compared with users who received dosages on time.

Methods:

Population-based cohort study. We included patients aged over 45 years who initiated denosumab for osteoporosis from UK THIN database, 2010 to 2019. Observational data were used to “emulate a hypothetical trial”[2, 3] with three dosing intervals: subsequent denosumab injection 24-28 weeks after prior dose (“on time”), delay by 4-16 weeks (“short delay”), and delay by over 16 weeks (“long delay”). The primary outcome was a composite of all fracture types. Secondary outcomes included major osteoporotic fracture, vertebral fracture, and hip fracture.

Results:

The rate of composite fracture per 1000 person-years was 58.9 for on-time, 61.7 for short delay, and 85.4 for long delay of subsequent denosumab injections. Compared to on-time injections, short delay had a hazard ratio (HR) for composite fracture 1.03 (95% CI 0.63-1.69) and long delay HR 1.44 (95% CI 0.96-2.17; p for trend 0.093). For major osteoporotic fractures, short delay had an HR 0.94 (95% CI 0.57-1.55) and long delay an HR of 1.69 (95% CI 1.01-2.83; p for trend 0.056). For vertebral fractures, short delay had an HR 1.48 (95% CI 0.58-3.79) and long delay 3.91 (95% CI 1.62-9.45; p for trend 0.005).

Conclusion:

While delayed subsequent denosumab dosages over 16 weeks was associated with an increased risk of vertebral and major osteoporotic fracture compared to no delay, composite fracture risk was not increased with longer delays.

References:

[1]Cummings SR, Ferrari S, Eastell R, et al. Vertebral Fractures After Discontinuation of Denosumab: A Post Hoc Analysis of the Randomized Placebo-Controlled FREEDOM Trial and Its Extension. J Bone Miner Res, 2017.

[2]Hernán MA. How to estimate the effect of treatment duration on survival outcomes using observational data. BMJ 2018.

[3]Hernán MA, Robins JM. Using Big Data to Emulate a Target Trial When a Randomized Trial Is Not Available. Am J Epidemiol 2016.

Table.

Rates and Adjusted Hazard Ratios of Fracture

On-timeShort delayLong delayP for linear trendComposite FractureRate (per 1000 person-years)5961.785.4-Unadjusted HR (95 %)Ref1.05 (0.62, 1.76)1.45 (0.95, 2.21)0.097Adjusted HR (95% CI)†Ref1.03 (0.63, 1.69)1.44 (0.96, 2.17)0.093Major Osteoporotic FractureRate (per 1000 person-years)34.831.958-Unadjusted HR (95 %)Ref0.92 (0.55, 1.53)1.67 (0.98, 2.84)0.074Adjusted HR (95% CI)†Ref0.94 (0.57, 1.55)1.69 (1.01, 2.83)0.056Vertebral FractureRate (per 1000 person-years)4.97.319.4-Unadjusted HR (95 %)Ref1.47 (0.58, 3.71)3.93 (1.59, 9.72)0.006Adjusted HR (95% CI)†Ref1.48 (0.58, 3.79)3.91 (1.62, 9.45)0.005Hip FractureRate (per 1000 person-years)10.29.618.3-Unadjusted HR (95 %)Ref0.94 (0.43, 2.04)1.78 (0.80, 3.97)0.18Adjusted HR (95% CI)†Ref0.97 (0.44, 2.12)1.75 (0.81, 3.79)0.173

†Adjusted model: adjusted by age, sex, baseline CCI index, major osteoporotic fracture, oral BP duration (years), 10-year risk of major osteoporotic fracture, prior denosumab doses.

Acknowledgments:

We acknowledge Dr. Dani Prieto-Alhambra for kindly providing Read codes.

Disclosure of Interests:

Houchen Lyu: None declared, Kazuki Yoshida: None declared, Sizheng Steven Zhao: None declared, Xabier García-Albéniz: None declared, Jie Wei: None declared, Chao Zeng: None declared, Sara Tedeschi: None declared, Benjamin Leder Grant/research support from: Research funding from Amgen, Guanghua Lei: None declared, Peifu Tang: None declared, Daniel Solomon Grant/research support from: Funding from Abbvie and Amgen unrelated to this work

Proteomic signatures of metronidazole-resistant Trichomonas vaginalis reveal novel proteins associated with drug resistance

BACKGROUND

Trichomoniasis is the most common non-viral sexually transmitted disease caused by the protozoan parasite Trichomonas vaginalis. Metronidazole (MTZ) is a widely used drug for the treatment of trichomoniasis; however, increased resistance of the parasite to MTZ has emerged as a highly problematic public health issue.

METHODS

We conducted iTRAQ-based analysis to profile the proteomes of MTZ-sensitive (MTZ-S) and MTZ-resistant (MTZ-R) parasites. STRING and gene set enrichment analysis (GESA) were utilized to explore the protein-protein interaction networks and enriched pathways of the differentially expressed proteins, respectively. Proteins potentially related to MTZ resistance were selected for functional validation.

RESULTS

A total of 3123 proteins were identified from the MTZ-S and MTZ-R proteomes in response to drug treatment. Among the identified proteins, 304 proteins were differentially expressed in the MTZ-R proteome, including 228 upregulated and 76 downregulated proteins. GSEA showed that the amino acid-related metabolism, including arginine, proline, alanine, aspartate, and glutamate are the most upregulated pathways in the MTZ-R proteome, whereas oxidative phosphorylation is the most downregulated pathway. Ten proteins categorized into the gene set of oxidative phosphorylation were ATP synthase subunit-related proteins. Drug resistance was further examined in MTZ-S parasites pretreated with the ATP synthase inhibitors oligomycin and bafilomycin A1, showing enhanced MTZ resistance and potential roles of ATP synthase in drug susceptibility.

CONCLUSIONS

We provide novel insights into previously unidentified proteins associated with MTZ resistance, paving the way for future development of new drugs against MTZ-refractory trichomoniasis.

Frequency Characteristics of AEPs in Normal Young Adults and Comparison of Their Response Threshold and Pure Tone Audiometry Threshold

Objective The tests of three types of auditory evoked potentials （AEPs） were performed on normal young adults, to understand the frequency characteristics of different testing methods and the relationship between response threshold and pure tone audiometry threshold of different methods, and to discuss the forensic value of 3 types of AEPs to evaluate hearing function. Methods Twenty normal young adults were selected, their standard pure tone audiometry threshold, short-term pure tone audiometry threshold and the response threshold of 3 types of AEPs （tone burst-auditory brainstem response, 40 Hz auditory event-related potential and slow vertex response） at 0.5 kHz, 1.0 kHz, 2.0 kHz and 4.0 kHz were recorded. The relationship between the response threshold and standard pure tone audiometry threshold, short-term pure tone audiometry threshold of 3 types of AEPs at different frequencies as well as the differences between different types of AEPs were analyzed. Results The short-term pure tone audiometry threshold was higher than the standard pure tone audiometry threshold at each frequency. The response threshold and standard pure tone audiometry threshold of the 3 types of AEPs all had a certain correlation, and the response threshold of the 3 types of AEPs was higher than short-term pure tone audiometry threshold and standard pure tone audiometry threshold at each frequency. The differences in the differences between the response threshold and standard pure tone audiometry threshold of the 3 types of AEPs at different frequencies had statistical significance. Linear regression mathematical models were established to infer the standard pure tone audiometry threshold （hearing level） from response threshold （sound pressure level） of 3 types of AEPs of normal young adults. Conclusion When using response threshold of different types of AEPs to estimate pure tone audiometry threshold, conversion and correction are needed. Combined use of different types of AEPs could improve the accuracy of hearing function evaluation.

Porphyromonas gingivalis Sphingolipid Synthesis Limits the Host Inflammatory Response

Porphyromonas gingivalis, like other bacteria belonging to the phylum Bacteroidetes, synthesizes sphingolipids (SLs). However, their exact roles in microbial physiology and their potential role in mediating interactions with their eukaryotic host are unclear. Our working hypothesis for this study was that synthesis of SLs (host-like lipids) affords a mechanism that allows P. gingivalis to persist in homeostasis with its host. In a previous study, we deleted a gene (PG1780 in strain W83) predicted to encode a serine palmitoyl transferase (SPT)-the enzyme that catalyzes the first conserved step in the synthesis of SLs-and we determined that the mutant was unable to synthesize SLs. Here, we characterized the SPT enzyme encoded by PG1780, analyzed the impact of SPT deletion on P. gingivalis gene expression (RNA-Seq analysis), and began to define the impact of SL synthesis on its interactions with host cells. Enzymatic analysis verified that the protein encoded by PG1780 is indeed an SPT. RNA-Seq analysis determined that a lack of SL synthesis results in differential expression of extracytoplasmic function sigma factors, components of the type IX secretion system (T9SS), and CRISPR and cas genes. Our data demonstrate that when human THP1 macrophage-like cells were challenged with the wild type (W83) and the SL-null mutant (W83 ΔSPT), the SL-null strain elicited a robust inflammatory response (elevated IL-1β, IL-6, IL-10, IL-8, RANTES, and TNFα) while the response to the parent strain W83 was negligible. Interestingly, we also discovered that SLs produced by P. gingivalis can be delivered to host cells independent of cell-to-cell contact. Overall, our results support our working hypothesis that synthesis of SLs by P. gingivalis is central to its ability to manipulate the host inflammatory response, and they demonstrate the integral importance of SLs in the physiology of P. gingivalis.

Comparison of routine field epidemiology and whole genome sequencing to identify tuberculosis transmission in a remote setting

Yukon Territory (YT) is a remote region in northern Canada with ongoing spread of tuberculosis (TB). To explore the utility of whole genome sequencing (WGS) for TB surveillance and monitoring in a setting with detailed contact tracing and interview data, we used a mixed-methods approach. Our analysis included all culture-confirmed cases in YT (2005-2014) and incorporated data from 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) genotyping, WGS and contact tracing. We compared field-based (contact investigation (CI) data + MIRU-VNTR) and genomic-based (WGS + MIRU-VNTR + basic case data) investigations to identify the most likely source of each person's TB and assessed the knowledge, attitudes and practices of programme personnel around genotyping and genomics using online, multiple-choice surveys (n = 4) and an in-person group interview (n = 5). Field- and genomics-based approaches agreed for 26 of 32 (81%) cases on likely location of TB acquisition. There was less agreement in the identification of specific source cases (13/22 or 59% of cases). Single-locus MIRU-VNTR variants and limited genetic diversity complicated the analysis. Qualitative data indicated that participants viewed genomic epidemiology as a useful tool to streamline investigations, particularly in differentiating latent TB reactivation from the recent transmission. Based on this, genomic data could be used to enhance CIs, focus resources, target interventions and aid in TB programme evaluation.

Hepatocyte Transplantation to the Liver via the Splenic Artery in a Juvenile Large Animal Model

Hepatocyte transplantation (HcTx) is a promising approach for the treatment of metabolic diseases in newborns and children. The most common application route is the portal vein, which is difficult to access in the newborn. Transfemoral access to the splenic artery for HcTx has been evaluated in adults, with trials suggesting hepatocyte translocation from the spleen to the liver with a reduced risk for thromboembolic complications. Using juvenile Göttingen minipigs, we aimed to evaluate feasibility of hepatocyte transplantation by transfemoral splenic artery catheterization, while providing insight on engraftment, translocation, viability, and thromboembolic complications. Four Göttingen Minipigs weighing 5.6 kg to 12.6 kg were infused with human hepatocytes (two infusions per cycle, 1.00E08 cells per kg body weight). Immunosuppression consisted of tacrolimus and prednisolone. The animals were sacrificed directly after cell infusion (n=2), 2 days (n=1), or 14 days after infusion (n=1). The splenic and portal venous blood flow was controlled via color-coded Doppler sonography. Computed tomography was performed on days 6 and 18 after the first infusion. Tissue samples were stained in search of human hepatocytes. Catheter placement was feasible in all cases without procedure-associated complications. Repetitive cell transplantations were possible without serious adverse effects associated with hepatocyte transplantation. Immunohistochemical staining has proven cell relocation to the portal venous system and liver parenchyma. However, cells were neither present in the liver nor the spleen 18 days after HcTx. Immunological analyses showed a response of the adaptive immune system to the human cells. We show that interventional cell application via the femoral artery is feasible in a juvenile large animal model of HcTx. Moreover, cells are able to pass through the spleen to relocate in the liver after splenic artery infusion. Further studies are necessary to compare this approach with umbilical or transhepatic hepatocyte administration.

mSignatureDB: a database for deciphering mutational signatures in human cancers

Cancer is a genetic disease caused by somatic mutations; however, the understanding of the causative biological processes generating these mutations is limited. A cancer genome bears the cumulative effects of mutational processes during tumor development. Deciphering mutational signatures in cancer is a new topic in cancer research. The Wellcome Trust Sanger Institute (WTSI) has categorized 30 reference signatures in the COSMIC database based on the analyses of ∼10 000 sequencing datasets from TCGA and ICGC. Large cohorts and bioinformatics skills are required to perform the same analysis as WTSI. The quantification of known signatures in custom cohorts is not possible under the current framework of the COSMIC database, which motivates us to construct a database for mutational signatures in cancers and make such analyses more accessible to general researchers. mSignatureDB (http://tardis.cgu.edu.tw/msignaturedb) integrates R packages and in-house scripts to determine the contributions of the published signatures in 15 780 individual tumors from 73 TCGA/ICGC cancer projects, making comparison of signature patterns within and between projects become possible. mSignatureDB also allows users to perform signature analysis on their own datasets, quantifying contributions of signatures at sample resolution, which is a unique feature of mSignatureDB not available in other related databases.

Pathogenic Protist Transmembranome database (PPTdb): a web-based platform for searching and analysis of protist transmembrane proteins

BACKGROUND

Pathogenic protist membrane transporter proteins play important roles not only in exchanging molecules into and out of cells but also in acquiring nutrients and biosynthetic compounds from their hosts. Currently, there is no centralized protist membrane transporter database published, which makes system-wide comparisons and studies of host-pathogen membranomes difficult to achieve.

RESULTS

We analyzed over one million protein sequences from 139 protists with full or partial genome sequences. Putative transmembrane proteins were annotated by primary sequence alignments, conserved secondary structural elements, and functional domains. We have constructed the PPTdb (Pathogenic Protist Transmembranome database), a comprehensive membrane transporter protein portal for pathogenic protists and their human hosts. The PPTdb is a web-based database with a user-friendly searching and data querying interface, including hierarchical transporter classification (TC) numbers, protein sequences, functional annotations, conserved functional domains, batch sequence retrieving and downloads. The PPTdb also serves as an analytical platform to provide useful comparison/mining tools, including transmembrane ability evaluation, annotation of unknown proteins, informative visualization charts, and iterative functional mining of host-pathogen transporter proteins.

CONCLUSIONS

The PPTdb collected putative protist transporter proteins and offers a user-friendly data retrieving interface. Moreover, a pairwise functional comparison ability can provide useful information for identifying functional uniqueness of each protist. Finally, the host and non-host protein similarity search can fulfill the needs of comprehensive studies of protists and their hosts. The PPTdb is freely accessible at http://pptdb.cgu.edu.tw .

CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts

BACKGROUND

CoMut plot is widely used in cancer research publications as a visual summary of mutational landscapes in cancer cohorts. This summary plot can inspect gene mutation rate and sample mutation burden with their relevant clinical details, which is a common first step for analyzing the recurrence and co-occurrence of gene mutations across samples. The cBioPortal and iCoMut are two web-based tools that allow users to create intricate visualizations from pre-loaded TCGA and ICGC data. For custom data analysis, only limited command-line packages are available now, making the production of CoMut plots difficult to achieve, especially for researchers without advanced bioinformatics skills. To address the needs for custom data and TCGA/ICGC data comparison, we have created CoMutPlotter, a web-based tool for the production of publication-quality graphs in an easy-of-use and automatic manner.

RESULTS

We introduce a web-based tool named CoMutPlotter to lower the barriers between complex cancer genomic data and researchers, providing intuitive access to mutational profiles from TCGA/ICGC projects as well as custom cohort studies. A wide variety of file formats are supported by CoMutPlotter to translate cancer mutation profiles into biological insights and clinical applications, which include Mutation Annotation Format (MAF), Tab-separated values (TSV) and Variant Call Format (VCF) files.

CONCLUSIONS

In summary, CoMutPlotter is the first tool of its kind that supports VCF file, the most widely used file format, as its input material. CoMutPlotter also provides the most-wanted function for comparing mutation patterns between custom cohort and TCGA/ICGC project. Contributions of COSMIC mutational signatures in individual samples are also included in the summary plot, which is a unique feature of our tool. CoMutPlotter is freely available at http://tardis.cgu.edu.tw/comutplotter .

Phenotypic analysis of atopic dermatitis in children aged 1-12 months: elaboration of novel diagnostic criteria for infants in China and estimation of prevalence

BACKGROUND

Atopic dermatitis (AD) is the most common skin disorder in infancy. However, the diagnosis and definite significance of infantile AD remains a debated issue.

OBJECTIVE

To analyse the phenotypes of AD in infancy, to establish diagnostic criteria and to estimate the prevalence of this condition in China.

METHODS

This is a multicentric study, in which 12 locations were chosen from different metropolitan areas of China. Following careful and complete history-taking and skin examination, the definite diagnosis of AD was made and the severity based on the SCORAD index was determined by local experienced dermatologists. Based on the detailed phenotyping, the major and representative clinical features of infantile AD were selected to establish the diagnostic criteria and evaluate their diagnostic efficacy.

RESULTS

A total of 5967 infants were included in this study. The overall point prevalence of AD was 30.48%. The infantile AD developed as early as at the second month of life, and its incidence peaked in the third month of life at 40.81%. The proportion of mild, moderate and severe AD was 67.40%, 30.57% and 2.03%, respectively. The most commonly seen manifestations in the infantile AD were facial dermatitis (72.07%), xerosis (42.72%) and scalp dermatitis (27.93%). We established the novel diagnostic criteria of infants, which included: (i) onset after 2 weeks of birth; (ii) pruritus and/or irritability and sleeplessness comparable with lesions; and (iii) all two items above with one of the following items can reach a diagnosis of AD: (i) eczematous lesions distributed on cheeks and/or scalp and/or extensor limbs, and (ii) eczematous lesions on any other parts of body accompanied by xerosis.

CONCLUSIONS

In China, the prevalence of AD in infancy is 30.48% according to clinical diagnosis of dermatologists. The novel Chinese diagnostic criteria for AD in infants show a higher sensitivity and comparable specificity.

Abstract P1-13-02: Real world outcomes of adjuvant FECD, ddACT and ACT for the treatment of early stage breast cancer - A multicenter retrospective analysis

Background: Adjuvant chemotherapy combining anthracyclines and taxanes for early stage breast cancer (ESBC) have demonstrated disease-free survival (DFS) and overall survival (OS) benefits. Among the 3rd generation regimens, 2 options have been favoured: FEC-Docetaxel (FECD) and AC-Paclitaxel (ACT). ACT may be delivered with dose-dense (ddACT) or weekly taxane scheduling (ddACWT), compared to traditional every 3-weekly (q3ACT) scheduling. Despite literature supporting both FECD and (dd)ACT regimens in the management of ESBC, no direct prospective trial has evaluated their comparative effectiveness.

Methods: A retrospective review of the BC Cancer Breast Cancer Outcomes Unit (BCOU) and the Alberta Health Services (AHS) databases was performed to identify patients with HER2 negative, stage 1-3 ESBC, who received adjuvant chemotherapy between 2007-2014. The primary endpoint was OS and the secondary endpoint was RFS, defined as freedom from local (invasive), regional or distant recurrence or breast cancer death. Outcome comparisons were made between FECD, ddACT/ddACWT and q3ACT using the Kaplan Meier method. Treatment arms were compared using a log-rank test for univariate analysis. A multivariate analysis was also conducted for OS comprising age, stage, grade, receptor status and type of chemotherapy received (FECD vs combined ACT group).

Results: A total of 4047 patients met inclusion criteria, including 2685 FECD, 1259 ddACT and 103 ACT. Median age was 53 (24-77) in the FECD group vs 52 (26-68) in the ddACT/ddACWT group and 58 (43-78) in the q3ACT group. The majority had stage 2 disease, 51.3%, 53.5% and 50.5% in the FECD, ddACT/ddACWT and q3ACT groups, respectively. Most were HR+, 84.5% in the FECD group vs 66.9% in both the ddACT/ddACWT and q3ACT groups. In the FECD group, 42.8% had a grade 2 tumour and 48.2% a grade 3 tumour vs 35.4% and 56.4% in the ddACT/ddACWT group and 35.0% and 58.3% in the q3ACT group. Lymphovascular invasion (LVI) was present in 40.7% of patients who received FECD vs 39.7% for ddACT/ddACWT and 26.2% for ACT. 5-year OS, for the FECD group was 90.3% (95%CI 89.1,91.4) vs 87.0% (95%CI 84.3,89.2) for the ddACT/ddACWT and 84.9% (95%CI 75.5,90.8) for the q3ACT groups, p=0.0907. 5-year RFS was 85.5% (95%CI 84.0-86.8) with FECD vs 84.4% (95% 81.9,86.6) for ddACT/ddACWT and 87.7% (95%CI 79.2,92.8) with q3ACT,p=0.4200. In multivariate analysis: age, stage and grade were significantly associated with OS whereas type of chemotherapy received (FECD vs ACT) was not (p=0.165). Finally, OS rates were compared across provinces and no significant differences were identified, 87.0% vs 88.0% (p=0.6294). Subgroup analyses by receptor type, comparing HR+ and TNBC are ongoing.

Conclusions: The use of FECD as compared to ACT based chemotherapy did not reveal significant differences in OS or RFS in this population-based study. Further, chemotherapy regimen was not associated with differences in overall survival, as compared to other well recognized prognostic factors. While the results were obtained from a retrospective analysis, conclusive prospective data is lacking. These results may therefore reassure physicians and patients alike on a comparable efficacy of these regimens in a real-life setting.

Citation Format: LeVasseur N, Veitch Z, Diocee RM, Gondara L, Cheung W, Khan O, Cossetti R, Gelmon KA, King K, Lupichuk S, Chia SK, Tang P, Simmons C. Real world outcomes of adjuvant FECD, ddACT and ACT for the treatment of early stage breast cancer - A multicenter retrospective analysis [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-13-02.

Combination therapy with parathyroid hormone analogs and antiresorptive agents for osteoporosis: a systematic review and meta-analysis of randomized controlled trials

Combination therapy with parathyroid hormone (PTH) analogs and antiresorptive agents may be more effective than monotherapy for the treatment of osteoporosis. This study aimed to estimate the effectiveness and safety of this combination therapy for osteoporosis. MEDLINE, EMBASE, and Cochrane Library were searched from inception to May 1, 2018, including randomized controlled trials (RCTs) with a duration of at least 6 months on adults with osteoporosis treated with combination therapy versus monotherapy. Outcomes included fractures, bone mineral density (BMD) changes, and adverse events. A meta-analysis was performed using a random-effect model, to estimate risk ratios (RRs) for fractures, and mean differences (MDs) for BMD changes. A total of 19 RCTs and 2177 patients were included. Compared with monotherapy, combination therapy had an advantage of 36% (RR, 0.64; 95% confidence interval (CI), 0.42-0.98) regarding fracture risk reduction. It also appears to improve lumbar spine BMD by 4.06% (95%CI = 2.60-5.53) and total hip BMD by 1.89% (95%CI = 1.25-2.53). No RCT reported an increased risk of serious adverse events. Among patients with osteoporosis, combination therapy was superior to monotherapy regarding improvement of the lumbar spine and total hip BMD, without risk of serious adverse events. Combination therapy also had an advantage over monotherapy on fracture risk reduction. However, owing to the limited sample size, additional larger studies are required to confirm this benefit.

Whole genome sequencing for improved understanding of Mycobacterium tuberculosis transmission in a remote circumpolar region

Few studies have used genomic epidemiology to understand tuberculosis (TB) transmission in rural and remote settings - regions often unique in history, geography and demographics. To improve our understanding of TB transmission dynamics in Yukon Territory (YT), a circumpolar Canadian territory, we conducted a retrospective analysis in which we combined epidemiological data collected through routine contact investigations with clinical and laboratory results. Mycobacterium tuberculosis isolates from all culture-confirmed TB cases in YT (2005-2014) were genotyped using 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) and compared to each other and to those from the neighbouring province of British Columbia (BC). Whole genome sequencing (WGS) of genotypically clustered isolates revealed three sustained transmission networks within YT, two of which also involved BC isolates. While each network had distinct characteristics, all had at least one individual acting as the probable source of three or more culture-positive cases. Overall, WGS revealed that TB transmission dynamics in YT are distinct from patterns of spread in other, more remote Northern Canadian regions, and that the combination of WGS and epidemiological data can provide actionable information to local public health teams.

A Transcriptome Study of Progeroid Neurocutaneous Syndrome Reveals POSTN As a New Element in Proline Metabolic Disorder

Aging is a complex biological process. A study of pyrroline-5-carboxylate reductase 1 (PYCR1) deficiency, which causes a progeroid syndrome, may not only shed light on its genetic contribution to autosomal recessive cutis laxa (ARCL) but also help elucidate the functional mechanisms associated with aging. In this study, we used RNA-Seq technology to examine gene expression changes in primary skin fibroblasts from healthy controls and patients with PYCR1 mutations. Approximately 22 and 32 candidate genes were found to be up- and downregulated, respectively, in fibroblasts from patients. Among the downregulated candidates in fibroblasts with PYCR1 mutations, a strong reduction in the expression of 17 genes (53.1%) which protein products are localized in the extracellular space was detected. These proteins included several important ECM components, periostin (POSTN), elastin (ELN), and decorin (DCN); genetic mutations in these proteins are associated with different phenotypes of aging, such as cutis laxa and joint and dermal manifestations. The differential expression of ten selected extracellular space genes was further validated using quantitative RT-PCR. Ingenuity Pathway Analysis revealed that some of the affected genes may be associated with cardiovascular system development and function, dermatological diseases and conditions, and cardiovascular disease. POSTN, one of the most downregulated gene candidates in affected individuals, is a matricellular protein with pivotal functions in heart valvulogenesis, skin wound healing, and brain development. Perturbation of PYCR1 expression revealed that it is positively correlated with the POSTN levels. Taken together, POSTN might be one of the key molecules that deserves further investigation for its role in this progeroid neurocutaneous syndrome.

[Clinical and prognostic significance of ABO promotor methylation level in adult leukemia and myelodydysplastic syndrome]

Objective: To investigate the clinical and prognostic significance of ABO promotor methylation level in adult patients with leukemia and myelodydysplastic syndrome(MDS). Methods: ABO promoter methylation level of 182 malignant hematological disease patients and 68 normal controls were detected by bisulfite sequencing PCR.Then clinical features and outcome were compared between hypermethylation group and hypomethylation group. Results: The median methylation rate of ABO promoter in newly diagnosed acute myeloid leukemia (AML) and acute lymphocytic leukemia (ALL) were 46.98% and 11.01% respectively, which were both higher than that in controls (2.30%, P<0.05). The methylation rates in remission AML and ALL were 1.58% and 2.30% respectively, which were comparable with that in normal group (P>0.05). As to relapse AML and ALL, methylation rates were 41.26% and 17.50% respectively, also significantly higher than that in controls (P<0.05).In patients with chronic myeloid leukemia (CML) chronic phase, the median methylation rate was 1.00%, which was similar to normal group. But a CML patient who transformed to ALL hadextremely high methylation rate 92.56%. The median methylation rate in patients with MDS significantly elevated as 5.81% compared with that in controls (P<0.05). The median overall survival (OS) of ALL and AML (non-M3) patients with hypermethylation were 12.5 months and 15.3 months, which were significantly shorter than those with hypomethylation (24.0 months and 20.0 months)(P<0.05).The median disease-free survival (DFS) of ALL and AML (non-M3) patients with hypermethylation were 9.9 months and 12.0 months, which were significantly shorter than those with hypomethylation (22.3 months and 18.5 months), (P<0.05). Multivariable analysis suggested that ABO promoter methylation level was an independent predictive factor of OS and DFS in ALL and AML (non-M(3)) patients. Conclusion: ABO promoter hypermethylation is closely related to genesis, development and prognosis of leukemia and MDS. Hypermethylationis related to a clinical poor prognosis compare with hypomethylation.

Large-Scale Proteomic Identification of Targets of Cellular miR-197 Downregulated by Enterovirus A71

MicroRNAs are noncoding RNA species comprising 18-23 nucleotides that regulate host-virus interaction networks. Here, we show that enterovirus A71 infection in human rhabdomyosarcoma (RD) is regulated by miR-197 expression. Transfection of miR-197 mimic into RD cells inhibited virus replication by interfering with the viral RNA synthesis. We employed a combination of mass-spectrometry-based quantitative proteomics with the stable isotope labeling with amino acids in cell culture (SILAC) approach for the identification of the miR-197 target genes in RD cells and to investigate the differential expression of the prospective target proteins. A total of 1822 proteins were repeatedly identified in miR-197-transfected RD cells, 106 of which were predicted to have seed sites by TargetScan. Notably, seven of eight selected genes potentially related to viral replication and immune response were validated as direct miR-197 targets, using a luciferase 3'-untranslated region (UTR) reporter assay. The expression levels of three selected endogenous molecules (ITGAV, ETF1, and MAP2K1/MEK1) were significantly reduced when RD cells were transfected with a miR-197 mimic. Our results provide a comprehensive database of miR-197 targets, which might provide better insights into the understanding of host-virus interaction.

Hip fracture patients who experience a greater fluctuation in RDW during hospital course are at heightened risk for all-cause mortality: a prospective study with 2-year follow-up

This study aims to detect whether there remains valuable prognostic information in fluctuation of red cell distribution width (RDW) in hip fracture patients. Results show that this readily available parameter may provide a more effective strategy for assessment of mortality risk, therefore providing a reference for clinical planning and decision-making.

INTRODUCTION

Prognostic values have been found in the fluctuation of some hematologic parameters. The red cell distribution width (RDW) routinely reported with all complete blood cell counts (CBC) has proven to be associated with poor outcomes in various diseases. However, whether the fluctuation in RDW is predictive of long-term mortality in hip fracture patients treated with surgery remains unknown.

METHODS

One thousand three hundred thirty hip fracture patients who underwent surgery from January 1, 2000 to November 18, 2012 were recruited in this prospective cohort study. Fluctuation in the RDW between admission and discharge was measured, and a Kaplan-Meier (KM) analysis and multivariable Cox regression model were applied to evaluate the relationship between this fluctuation and mortality. Risk factors for a larger fluctuation were detected by using Logistic regression analyses.

RESULTS

In addition to the admission RDW, a high RDW level at the time of discharge was also associated with an increased risk of death, while no significant difference was found in the postoperative RDW. Fluctuation in the RDW between admission and discharge was an independent risk predictor for 2-year mortality (HR 1.45 95%CI 1.06-2.00, p = 0.022). Factors affecting the change in the RDW between admission and discharge included both the demographic characteristics of the patients and clinical interventions.

CONCLUSION

Hip fracture patients who experience a greater fluctuation in RDW during the hospital course are at a heightened risk for 2-year all-cause mortality.

Acute Deep Vein Thrombosis Treated with Porcine Plasmin

The thrombolytic effect of pig plasmin was tested in a double blind trial on patients with deep venous thrombosis in the lower limb. Only patients with not more than three days old thrombi were selected for this study. The diagnosis of deep vein thrombosis was made clinically and confirmed by phlebography. Lysofibrin Novo (porcine plasmin) or placebo (porcine plasminogen) was administered intravenously to the patients. The enzyme and the placebo were delivered as lyophilized powder in labelled bottles - the contents of the bottles were unknown to the doctor in charge of the clinical administration of the trial. An initial dose of plasmin/plasminogen of 30 unit per kg body weight given slowly intravenously (1-1% hours infusion) was followed by a maintenance dosis of 15 per cent the initial dose per hour for the following 5-7 hours. In most cases a similar maintenance dosis was given the next day. In all patients heparin was administered after ending the plasmin/plasminogen infusion. The results of the treatment was evaluated clinically as well as by control phlebo- grams the following days.

A statistically significant improvement was found in the plasmin treated group compared with the placebo (plasminogen) treated group. Thrombolysis was obtained clinically and phlebographically in 65 per cent of the plasmin treated group, but only in 15 per cent of the control patients were improvements found.

This study has thus demonstrated that plasmin treatment according to a standard scheme was able to induce thrombolysis. There were only a few and insignificant side effects. Allergic reactions have not been seen and only very simple tests are required.

Inactivation of the tight junction gene CLDN11 by aberrant hypermethylation modulates tubulins polymerization and promotes cell migration in nasopharyngeal carcinoma

BACKGROUND

Aberrant hypermethylation of cellular genes is a common phenomenon to inactivate genes and promote tumorigenesis in nasopharyngeal carcinoma (NPC).

METHODS

Methyl binding domain (MBD)-ChIP sequencing of NPC cells, microarray data of NPC biopsies and gene ontology analysis were conducted to identify a potential tumor suppressor gene CLDN11 that was both hypermethylated and downregulated in NPC. Bisulfite sequencing, qRT-PCR, immunohistochemistry staining of the NPC clinical samples and addition of methylation inhibitor, 5'azacytidine, in NPC cells were performed to verify the correlation between DNA hypermethylation and expression of CLDN11. Promoter reporter and EMSA assays were used to dissect the DNA region responsible for transcription activator binding and to confirm whether DNA methylation could affect activator's binding, respectively. CLDN11 was transiently overexpressed in NPC cells followed by cell proliferation, migration, invasion assays to characterize its biological roles. Co-immunoprecipitation experiments and proteomic approach were carried out to identify novel interacting protein(s) and the binding domain of CLDN11. Anti-tumor activity of the CLDN11 was elucidated by in vitro functional assay.

RESULTS

A tight junction gene, CLDN11, was identified as differentially hypermethylated gene in NPC. High methylation percentage of CLDN11 promoter in paired NPC clinical samples was correlated with low mRNA expression level. Immunohistochemistry staining of NPC paired samples tissue array demonstrated that CLDN11 protein expression was relatively low in NPC tumors. Transcription activator GATA1 bound to CLDN11 promoter region - 62 to - 53 and its DNA binding activity was inhibited by DNA methylation. Re-expression of CLDN11 reduced cell migration and invasion abilities in NPC cells. By co-immunoprecipitation and liquid chromatography-tandem mass spectrometry LC-MS/MS, tubulin alpha-1b (TUBA1B) and beta-3 (TUBB3), were identified as the novel CLDN11-interacting proteins. CLDN11 interacted with these two tubulins through its intracellular loop and C-terminus. Furthermore, these domains were required for CLDN11-mediated cell migration inhibition. Treatment with a tubulin polymerization inhibitor, nocodazole, blocked NPC cell migration.

CONCLUSIONS

CLDN11 is a hypermethylated and downregulated gene in NPC. Through interacting with microtubules TUBA1B and TUBB3, CLDN11 blocks the polymerization of tubulins and cell migration activity. Thus, CLDN11 functions as a potential tumor suppressor gene and silencing of CLDN11 by DNA hypermethylation promotes NPC progression.

VAReporter: variant reporter for cancer research of massive parallel sequencing

Background

High throughput sequencing technologies have been an increasingly critical aspect of precision medicine owing to a better identification of disease targets, which contributes to improved health care cost and clinical outcomes. In particular, disease-oriented targeted enrichment sequencing is becoming a widely-accepted application for diagnostic purposes, which can interrogate known diagnostic variants as well as identify novel biomarkers from panels of entire human coding exome or disease-associated genes.

Results

We introduce a workflow named VAReporter to facilitate the management of variant assessment in disease-targeted sequencing, the identification of pathogenic variants, the interpretation of biological effects and the prioritization of clinically actionable targets. State-of-art algorithms that account for mutation phenotypes are used to rank the importance of mutated genes through visual analytic strategies. We established an extensive annotation source by integrating a wide variety of biomedical databases and followed the American College of Medical Genetics and Genomics (ACMG) guidelines for interpretation and reporting of sequence variations.

Conclusions

In summary, VAReporter is the first web server designed to provide a “one-stop” resource for individual’s diagnosis and large-scale cohort studies, and is freely available at http://rnd.cgu.edu.tw/vareporter.