EpiVar Browser: advanced exploration of epigenomics data under controlled access.

MOTIVATION: Human epigenomic data has been generated by large consortia for thousands of cell types to be used as a reference map of normal and disease chromatin states. Since epigenetic data contains potentially identifiable information, similarly to genetic data, most raw files generated by these consortia are stored in controlled-access databases. It is important to protect identifiable information, but this should not hinder secure sharing of these valuable datasets. RESULTS: Guided by the Framework for responsible sharing of genomic and health-related data from the Global Alliance for Genomics and Health (GA4GH), we have developed an approach and a tool to facilitate the exploration of epigenomics datasets' aggregate results, while filtering out identifiable information. Specifically, the EpiVar Browser allows a user to navigate an epigenetic dataset from a cohort of individuals and enables direct exploration of genotype-chromatin phenotype relationships. Because individual genotypes and epigenetic signal tracks are not directly accessible, and rather aggregated in the portal output, no identifiable data is released, yet the interface allows for dynamic genotype-epigenome interrogation. This approach has the potential to accelerate analyses that would otherwise require a lengthy multi-step approval process and provides a generalizable strategy to facilitate responsible access to sensitive epigenomics data. AVAILABILITY AND IMPLEMENTATION: Online portal: https://computationalgenomics.ca/tools/epivar; EpiVar Browser source code: https://github.com/c3g/epivar-browser; bw-merge-window tool source code: https://github.com/c3g/bw-merge-window.

EpiVar Browser: advanced exploration of epigenomics data under controlled access.

Motivation: Human epigenomic data has been generated by large consortia for thousands of cell types to be used as a reference map of normal and disease chromatin states. Since epigenetic data contains potentially identifiable information, similarly to genetic data, most raw files generated by these consortia are stored in controlled-access databases. It is important to protect identifiable information, but this should not hinder secure sharing of these valuable datasets. Results: Guided by the Framework for responsible sharing of genomic and health-related data from the Global Alliance for Genomics and Health (GA4GH), we have developed a tool to facilitate the exploration of epigenomics datasets' aggregate results, while filtering out identifiable information. Specifically, the EpiVar Browser allows a user to navigate an epigenetic dataset from a cohort of individuals and enables direct exploration of genotype-chromatin phenotype relationships. Because the information about individual genotypes is not accessible and aggregated in the output that is made available, no identifiable data is released, yet the interface allows for dynamic genotype - epigenome interrogation. This approach has the potential to accelerate analyses that would otherwise require a lengthy multi-step approval process and provides a generalisable strategy to facilitate responsible access to sensitive epigenomics data. Availability and implementation: Online portal instance: https://computationalgenomics.ca/tools/epivarSource code: https://github.com/c3g/epivar-browser.

Canadians' opinions towards COVID-19 data-sharing: a national cross-sectional survey.

OBJECTIVES: COVID-19 research has significantly contributed to pandemic response and the enhancement of public health capacity. COVID-19 data collected by provincial/territorial health authorities in Canada are valuable for research advancement yet not readily available to the public, including researchers. To inform developments in public health data-sharing in Canada, we explored Canadians' opinions of public health authorities sharing deidentified individual-level COVID-19 data publicly. DESIGN/SETTING/INTERVENTIONS/OUTCOMES: A national cross-sectional survey was administered in Canada in March 2022, assessing Canadians' opinions on publicly sharing COVID-19 datatypes. Market research firm Léger was employed for recruitment and data collection. PARTICIPANTS: Anyone greater than or equal to 18 years and currently living in Canada. RESULTS: 4981 participants completed the survey with a 92.3% response rate. 79.7% were supportive of provincial/territorial authorities publicly sharing deidentified COVID-19 data, while 20.3% were hesitant/averse/unsure. Datatypes most supported for being shared publicly were symptoms (83.0% in support), geographical region (82.6%) and COVID-19 vaccination status (81.7%). Datatypes with the most aversion were employment sector (27.4% averse), postal area (26.7%) and international travel history (19.7%). Generally supportive Canadians were characterised as being ≥50 years, with higher education, and being vaccinated against COVID-19 at least once. Vaccination status was the most influential predictor of data-sharing opinion, with respondents who were ever vaccinated being 4.20 times more likely (95% CI 3.21 to 5.48, p=0.000) to be generally supportive of data-sharing than those unvaccinated. CONCLUSIONS: These findings suggest that the Canadian public is generally favourable to deidentified data-sharing. Identifying factors that are likely to improve attitudes towards data-sharing are useful to stakeholders involved in data-sharing initiatives, such as public health agencies, in informing the development of public health communication and data-sharing policies. As Canada progresses through the COVID-19 pandemic, and with limited testing and reporting of COVID-19 data, it is essential to improve deidentified data-sharing given the public's general support for these efforts.

[Research progress on culture technologies,chemical components,and pharmacological activities of Saussurea involucrata cells].

Saussurea involucrata,a traditional Chinese medicinal material,is effective in the treatment of rheumatoid arthritis with cold-dampness blockage syndrome,cold pain in lower abdomen,and menstrual irregularities. However,due to the specific habitat,low natural reproduction rate,slow growth,and overexploitation,it is at the high risk of extinction. S. involucrata cells can be obtained through callus culture,suspension culture,and hairy root culture. This study highlighted the influences of reactor type,culture system,precursor,elicitor type, and light wavelength on the suspension culture of S. involucrate cells. The chemical components of S. involucrata cells mainly include phenylpropanoids,flavonoids,lignans,and steroids,among which phenylpropanoids are the most abundant. S. involucrata cells have multiple pharmacological activities of anti-inflammation,analgesia,activating blood and resolving stasis,immunoregulation,increasing bone density,lowering blood lipids,anti-hypoxia,anti-exercise fatigue,anti-radiation,anti-obesity,and anti-oxidation. Moreover,it has the potential of treating aplastic anemia. This study reviews the cell culture technologies,chemical components,and pharmacological activities of S. involucrata cells,laying a basis for the further research,development,and utilization.

Addressing Privacy Concerns in Sharing Viral Sequences and Minimum Contextual Data in a Public Repository During the COVID-19 Pandemic.

COVID-19 was declared to be a pandemic in March 2020 by the World Health Organization. Timely sharing of viral genomic sequencing data accompanied by a minimal set of contextual data is essential for informing regional, national, and international public health responses. Such contextual data is also necessary for developing, and improving clinical therapies and vaccines, and enhancing the scientific community's understanding of the SARS-CoV-2 virus. The Canadian COVID-19 Genomics Network (CanCOGeN) was launched in April 2020 to coordinate and upscale existing genomics-based COVID-19 research and surveillance efforts. CanCOGeN is performing large-scale sequencing of both the genomes of SARS-CoV-2 virus samples (VirusSeq) and affected Canadians (HostSeq). This paper addresses the privacy concerns associated with sharing the viral sequence data with a pre-defined set of contextual data describing the sample source and case attribute of the sequence data in the Canadian context. Currently, the viral genome sequences are shared by provincial public health laboratories and their healthcare and academic partners, with the Canadian National Microbiology Laboratory and with publicly accessible databases. However, data sharing delays and the provision of incomplete contextual data often occur because publicly releasing such data triggers privacy and data governance concerns. The CanCOGeN Ethics and Governance Expert Working Group thus has investigated several privacy issues cited by CanCOGeN data providers/stewards. This paper addresses these privacy concerns and offers insights primarily in the Canadian context, although similar privacy considerations also exist in other jurisdictions. We maintain that sharing viral sequencing data and its limited associated contextual data in the public domain generally does not pose insurmountable privacy challenges. However, privacy risks associated with reidentification should be actively monitored due to advancements in reidentification methods and the evolving pandemic landscape. We also argue that during a global health emergency such as COVID-19, privacy should not be used as a blanket measure to prevent such genomic data sharing due to the significant benefits it provides towards public health responses and ongoing research activities.

Inhibition of epidermal growth factor receptor signaling by Saussurea involucrata, a rare traditional Chinese medicinal herb, in human hormone-resistant prostate cancer PC-3 cells.

Prostate carcinoma is the most frequently diagnosed malignancy and the second leading cause of death of men in the United States. To date, no effective therapeutic treatment allows abrogation of the progression of prostate cancer to more invasive forms. In this study, we identified Saussurea involucrata Kar. et Kir., a rare traditional Chinese medicinal herb, as a potential agent for androgen-independent prostate cancer patients and investigated its biological mechanism as an antineoplastic agent. S. involucrata caused a concentration- and time-dependent inhibition of cell proliferation in human hormone-resistant prostate cancer PC-3 cells. Moreover, in vitro studies in a panel of several types of human cancer cell lines revealed that S. involucrata inhibited cell proliferation with high potency. To evaluate the bioactive compounds, we successively extracted the S. involucrata with fractions of methanol (SI-1), ethyl acetate (SI-2), n-butanol (SI-3), and water (SI-4). Among these extracts, SI-2 contains the most effective bioactivity. SI-2 treatment resulted in significant time-dependent growth inhibition together with G1 phase cell cycle arrest and apoptosis in PC3 cells. In addition, SI-2 treatment strongly induced p21WAF1/CIP and p27KIP1 expression, independent of the p53 pathway, and downregulated expression of cyclin D1 and cyclin-dependent kinase 4 (CDK4). SI-2 treatment increased levels of Bax, cytochrome c, activated caspase-3, and active caspase-9 and decreased Bcl-2 expression level. One of the major targets for the therapy in prostate cancer can be epidermal growth factor receptor (EGFR). SI-2 markedly reduced phosphorylation of EGFR and inhibited activation of AKT and STAT3. Moreover, p.o. administration of SI-2 induced a dose-dependent inhibition of PC-3 tumor growth in vivo. In summary, our study identifies S. involucrata as an effective inhibitor of EGFR signaling in human hormone-resistant prostate cancer PC-3 cells. We suggest that S. involucrata could be developed as an agent for the management of EGFR-positive human cancers.