Genomics in medicine: A new era in medicine

Boundary-work in genomic medicine: Safeguarding the future of diagnostic next-generation sequencing in the clinic

Next-generation sequencing (NGS) technologies - which allow to look at large parts or even the whole genome at once - are making their way into diagnostic clinical care. With trends towards 'mainstreaming' genetic services into general medicine, significant ethical challenges, and a disputed clinical utility and cost-benefit ratio, genomic medicine's autonomy and dominance in defining and offering NGS care may come under increased pressure from the outside (e.g., regulators, other healthcare providers and facilities, ethicists, and patients). In this paper, we show how the field of genomic medicine engages in substantial boundary-work in reaction to these circumstances. Building on multi-sited fieldwork in two centers for human genetics in Belgium and the Netherlands, we show how acts of demarcation serve to uphold an image of expertise and authority which helps maintain the field's autonomy and dominance. Through examining the delineations put forward in interviews, practice (based on observations in multidisciplinary meetings and consultations), and grey and academic literature, we show the politics involved in moving NGS forward fairly seamlessly in a way that suits the field. First, we show how genetic healthcare professionals have redefined what makes a genetic test 'valuable' so that it underlines its current value. Secondly, we examine how a genetic imaginary is put forward that both emphasizes the extraordinary character of genomic medicine and the normalcy of NGS testing. By underlining the need for their expertise whilst simultaneously normalizing the ethical challenges and positioning themselves as most capable of reflecting on these, the field minimized external regulation and kept a close grip on defining ethical issues and policy. Despite their current dominance in shaping the future of genomic care, we argue that the closedness of the field hinders it from benefiting from external expertise, reflection, and monitoring to ensure enduring and broad support for this future.

Association between osteoprotegerin and RANKL single nucleotide polymorphisms and destructive rhinosinusitis in patients with granulomatosis with polyangiitis

BACKGROUND

Chronic invasive rhinosinusitis with facial bone damage is a common cause of functional and social impairment in granulomatosis with polyangiitis (GPA) patients. To the best of our knowledge, there is no clinical or laboratory biomarker to predict bone damage.

METHODS

This case-control study included 90 patients with GPA and 270 health controls (HCs). Patients were categorized according to the presence of tomographic facial bone erosions. Frequency of RANKL and osteoprotegerin single nucleotide polymorphisms (SNPs), analyzed by real-time polymerase chain reaction, were compared between patients and HCs, and between patients with and without bone damage. Clinical, therapeutic, and laboratory data were analyzed.

RESULTS

Facial bone erosion was observed in 55.5% of patients. No difference was found in the frequency of SNPs between patients with GPA and HCs. GPA patients were compared according to the presence or absence of bone damage, and a difference was found in the frequencies of osteoprotegerin G1181C (rs2073618) and RANKL A290G (rs2277438). A multivariate analysis showed that the CC genotype of osteoprotegerin 1181 was independently associated with bone erosion (OR = 3.95, CI95%=1.20-13.00, P = 0.02), as were the presence of the G allele in RANKL A290G (OR = 6.13, CI95%=1.95-19.26, P = 0.002) and higher disease duration (OR = 1.08, CI95%=1,01-1.15, P = 0.04).

CONCLUSION

SNPs in osteoprotegerin G1181C and RANKL A290G may play a role in the development of destructive rhinosinusitis in patients with GPA. Genetic assessment may be useful for identifying high-risk individuals. This observational study might work as a basis for further research to better understand this association and clinical trials using RANKL/osteoprotegerin as therapeutic targets.

Identifying Network Biomarkers in Early Diagnosis of Hepatocellular Carcinoma via miRNA-Gene Interaction Network Analysis

BACKGROUND

Hepatocellular carcinoma (HCC) is a highly heterogeneous cancer at the histological level. Despite the emergence of new biological technology, advanced-stage HCC remains largely incurable. The prediction of a cancer biomarker is a key problem for targeted therapy in the disease.

METHODS

We performed a miRNA-gene integrated analysis to identify differentially expressed miRNAs (DEMs) and genes (DEGs) of HCC. The DEM-DEG interaction network was constructed and analyzed. Gene ontology enrichment and survival analyses were also performed in this study.

RESULTS

By the analysis of healthy and tumor samples, we found that 94 DEGs and 25 DEMs were significantly differentially expressed in different datasets. Gene ontology enrichment analysis showed that these 94 DEGs were significantly enriched in the term "Liver" with a statistical p-value of 1.71 × 10-26. Function enrichment analysis indicated that these genes were significantly overrepresented in the term "monocarboxylic acid metabolic process" with a p-value = 2.94 × 10-18. Two sets (fourteen genes and five miRNAs) were screened by a miRNA-gene integrated analysis of their interaction network. The statistical analysis of these molecules showed that five genes (CLEC4G, GLS2, H2AFZ, STMN1, TUBA1B) and two miRNAs (hsa-miR-326 and has-miR-331-5p) have significant effects on the survival prognosis of patients.

CONCLUSION

We believe that our study could provide critical clinical biomarkers for the targeted therapy of HCC.

Insights into the Mechanism of CRISPR/Cas9-Based Genome Editing from Molecular Dynamics Simulations

The CRISPR/Cas9 system is a popular genome-editing tool with immense therapeutic potential. It is a simple two-component system (Cas9 protein and RNA) that recognizes the DNA sequence on the basis of RNA:DNA complementarity, and the Cas9 protein catalyzes the double-stranded break in the DNA. In the past decade, near-atomic resolution structures at various stages of the CRISPR/Cas9 DNA editing pathway have been reported along with numerous experimental and computational studies. Such studies have boosted knowledge of the genome-editing mechanism. Despite such advancements, the application of CRISPR/Cas9 in therapeutics is still limited, primarily due to off-target effects. Several studies aim at engineering high-fidelity Cas9 to minimize the off-target effects. Molecular Dynamics (MD) simulations have been an excellent complement to the experimental studies for investigating the mechanism of CRISPR/Cas9 editing in terms of structure, thermodynamics, and kinetics. MD-based studies have uncovered several important molecular aspects of Cas9, such as nucleotide binding, catalytic mechanism, and off-target effects. In this Review, the contribution of MD simulation to understand the CRISPR/Cas9 mechanism has been discussed, preceded by an overview of the history, mechanism, and structural aspects of the CRISPR/Cas9 system. These studies are important for the rational design of highly specific Cas9 and will also be extremely promising for achieving more accurate genome editing in the future.

Biological Clock and Inflammatory Bowel Disease Review: From the Standpoint of the Intestinal Barrier

Inflammatory bowel disease is a group of chronic, recurrent, nonspecific inflammatory diseases of the intestine that severely affect the quality of life of patients. The pathogenesis of this disease is caused by complex and interactive neural networks composed of factors such as genetic susceptibility, external environment, immune disorders, and intestinal barrier dysfunction. It is well known that there is a strong link between environmental stressors (also known as circadian clocks) that can influence circadian changes and inflammatory bowel disease. Among them, the biological clock is involved in the pathogenesis of inflammatory bowel disease by affecting the function of the intestinal barrier. Therefore, this review is aimed at systematically summarizing the latest research progress on the role of the circadian clock in the pathogenesis of inflammatory bowel disease by affecting intestinal barrier functions (intestinal mechanical barrier, intestinal immune barrier, intestinal microecological barrier, and intestinal chemical barrier) and the potential clinical value of clock genes in the management of inflammatory bowel disease, for the application of circadian clock therapy in the management of inflammatory bowel disease and then the benefit to the majority of patients.