IMPARTER, Phase 1 of an intervention to improve patients’ understanding of gene expression profiling tests in breast cancer

Purpose To compare participants’ knowledge about gene expression profiling (GEP) tests and recurrence risks after reading an information leaflet with that following viewing of an information film. Methods Using a randomised cross-over design, at time-point one (T1), women aged 45–75 years without breast cancer either read leaflets or watched information films about Oncotype DX or Prosigna tests. Participants answered nine questions assessing knowledge (maximum score 18). Next-day information in the opposite modality was provided and knowledge re-assessed. Additional questions probed which format was easiest to understand, participants’ preferences for film or leaflet and their reasons for these. Results 120 women participated (60 received OncotypeDX films and leaflets; 60 received the Prosigna versions). T1 mean knowledge scores were higher following film viewing (13.37) compared with that after reading leaflets (9.25) (mean difference 4.1; p < 0.0001; 95% CI 3.2, 5.0). When participants read leaflets first and subsequently viewed films, all increased their scores (mean + 6.08, from T1 of 9.25, p < 0.0001; 95% CI 5.44, 6.72). When films were viewed first, followed by leaflets, (36/60, 60%), participants’ scores declined (mean-1.55 from T1 of 13.37, p < 0.001; 95% CI -2.32, -0.78). A majority of participants expressed preferences for the films (88/120, 73.3%) irrespective as to whether they described OncotypeDX or Prosigna. Reasons included the clarity, ease of understanding, visual material and reassuring voice-over. Conclusion Discussions between oncologists and patients about recurrence risk results can be challenging. Information leaflets may aid understanding but often employ complex language. Information films significantly improved knowledge and were preferred by participants.

Gingival Epithelial Cell-Derived Microvesicles Activate Mineralization in Gingival Fibroblasts

Soft tissue calcification occurs in many parts of the body, including the gingival tissue. Epithelial cell-derived MVs can control many functions in fibroblasts but their role in regulating mineralization has not been explored. We hypothesized that microvesicles (MVs) derived from gingival epithelial cells could regulate calcification of gingival fibroblast cultures in osteogenic environment. Human gingival fibroblasts (HGFs) were cultured in osteogenic differentiation medium with or without human gingival epithelial cell-derived MV stimulation. Mineralization of the cultures, localization of the MVs and mineral deposits in the HGF cultures were assessed. Gene expression changes associated with MV exposure were analyzed using gene expression profiling and real-time qPCR. Within a week of exposure, epithelial MVs stimulated robust mineralization of HGF cultures that was further enhanced by four weeks. The MVs taken up by the HGF's did not calcify themselves but induced intracellular accumulation of minerals. HGF gene expression profiling after short exposure to MVs demonstrated relative dominance of inflammation-related genes that showed increases in gene expression. In later cultures, OSX, BSP and MMPs were significantly upregulated by the MVs. These results suggest for the first time that epithelial cells maybe associated with the ectopic mineralization process often observed in the soft tissues.

Comprehensive Analysis of Myoferlin in Human Pancreatic Cancer via Bioinformatics

Pancreatic cancer is the fourth leading cause of cancer-related death and urgently needs biomarkers for clinical diagnosis and prognosis. It has been reported that myoferlin (MYOF) is implicated in the regulation of proliferation, invasion, and migration of tumor cells in many cancers including pancreatic cancer. To confirm the prognostic value of MYOF in pancreatic cancer, a comprehensive cancer versus healthy people analysis was conducted using public data. MYOF mRNA expression levels were compared in many kinds of cancers including pancreatic cancer via the Oncomine and Gene Expression Profiling Interactive Analysis (GEPIA) databases. The results have shown that MYOF mRNA expression levels were upregulated in most types of cancers, especially in pancreatic cancer, compared with healthy people’s tissues. Data from the Cancer Cell Line Encyclopedia (CCLE) and European Bioinformatics Institute (EMBL-EML) database also revealed that MYOF mRNA is highly expressed in most cancer cells, particularly in pancreatic cancer cell lines. Furthermore, the prognostic value of MYOF was evaluated using GEPIA and Long-term Outcome and Gene Expression Profiling Database of pan-cancers (LOGpc) database. Higher expression of MYOF was associated with poorer overall survival, especially in the lower stage and lower grade. Coexpressed genes, possible regulators, and the correlation between MYOF expressions were analyzed via the GEPIA and LinkedOmics database. Nineteen coexpressed genes were identified, and most of these genes were related to cancer. The Tumor Immune Estimation Resource (TIMER) database was used to analyze the correlation between MYOF and immune response. Notably, we found that MYOF might have a potential novel immune regulatory role in tumor immunity. These results support that MYOF is a candidate prognostic biomarker for pancreatic cancer, which calls for further genomics research of pancreatic cancer and deeply functional studies on MYOF.

Single cell gene expression profiling of nasal ciliated cells reveals distinctive biological processes related to epigenetic mechanisms in patients with severe COVID-19

Objective: To explore the molecular processes associated with cellular regulatory programs in patients with COVID-19, including gene activation or repression mediated by epigenetic mechanisms. We hypothesized that a comprehensive gene expression profiling of nasopharyngeal epithelial cells might expand understanding of the pathogenic mechanisms of severe COVID-19. Methods: We used single-cell RNA sequencing (scRNAseq) profiling of ciliated cells (n = 12725) from healthy controls (SARS-CoV-2 negative n =13) and patients with mild/moderate (n =13) and severe (n =14) COVID-19. ScRNAseq data at the patient level were used to perform gene set and pathway enrichment analyses. We prioritized candidate miRNA-target interactions and epigenetic mechanisms. Results: Pathways linked to mitochondrial function, misfolded proteins, and membrane permeability were upregulated in patients with mild/moderate disease compared to healthy controls. Besides, we noted that compared to mild/moderate disease, cells derived from severe COVID-19 patients had downregulation of sub-networks associated with epigenetic mechanisms, including DNA and histone H3K4 methylation and chromatin remodeling regulation. We found 11-ranked miRNAs that may explain miRNA-dependent regulation of histone methylation, some of which share seed sequences with SARS-CoV-2 miRNAs. Conclusion: Our results may provide novel insights into the epigenetic mechanisms mediating the clinical course of SARS-CoV-2 infection.

Evidence in support of gene regulatory hypothesis: Gene expression profiling manifests homeopathy effect as more than placebo

Background: Use of ultra-high diluted remedies in homeopathy and their claimed efficacy in curing diseases has been challenged time and again by non-believers despite many evidence-based positive results published in favor of their efficacy in curing/ameliorating disease symptoms. Aims: To test the ability of ultra-high diluted homeopathic remedies beyond Avogadro’s limit, if any, in manifesting gene modulating effects in controlled in vitro experimental model. Methods: Since cancer cells manifest aberrant epigenetic gene expressions, we conducted global microarray gene expression profiling of HeLa cells (an established epigenetic model of HPV18 positive cell line) treated with two different potentized homeopathic remedies, namely, Condurango 30c and Hydrastis canadensis 30C (used in the treatment of cancer), as compared to that of placebo (succussed alcohol 30c). Results: Data revealed distinctly different expression patterns of over 100 genes as a consequence of treatment with both homeopathc remedies compared to placebo. Conclusion: Results indicate that action of the potentized drugs was “more than placebo” and these ultra-highly diluted drugs acted primarily through modulation of gene expression.