Small nucleic acids and the path to the clinic for anti-CRISPR

CRISPR-based therapeutics have entered clinical trials but no methods to inhibit Cas enzymes have been demonstrated in a clinical setting. The ability to inhibit CRISPR-based gene editing or gene targeting drugs should be considered a critical step in establishing safety standards for many CRISPR-Cas therapeutics. Inhibitors can act as a failsafe or as an adjuvant to reduce off-target effects in patients. In this review we discuss the need for clinical inhibition of CRISPR-Cas systems and three existing inhibitor technologies: anti-CRISPR (Acr) proteins, small molecule Cas inhibitors, and small nucleic acid-based CRISPR inhibitors, CRISPR SNuBs. Due to their unique properties and the recent successes of other nucleic acid-based therapeutics, CRISPR SNuBs appear poised for clinical application in the near-term.

Maple syrup urine disease: Clinical outcomes, metabolic control, and genotypes in a screened population after four decades of newborn bloodspot screening in the Republic of Ireland

Since 1972, 18 patients (10 females/8 males) have been detected by newborn bloodspot screening (NBS) with neonatal-onset maple syrup urine disease (MSUD) in Ireland. Patients were stratified into three clusters according to clinical outcome at the time of data collection, including developmental, clinical, and IQ data. A fourth cluster comprised of two early childhood deaths; a third patient died as an adult. We present neuroimaging and electroencephalography together with clinical and biochemical data. Incidence of MSUD (1972-2018) was 1 in 147 975. Overall good clinical outcomes were achieved with 15/18 patients alive and with essentially normal functioning (with only the lowest performing cluster lying beyond a single SD on their full scale intelligence quotient). Molecular genetic analysis revealed genotypes hitherto not reported, including a possible digenic inheritance state for the BCKDHA and DBT genes in one family. Treatment has been based on early implementation of emergency treatment, diet, close monitoring, and even dialysis in the setting of acute metabolic decompensation. A plasma leucine ≥400 μmol/L (outside therapeutic range) was more frequently observed in infancy or during adolescence, possibly due to infections, hormonal changes, or noncompliance. Children require careful management during metabolic decompensations in early childhood, and this represented a key risk period in our cohort. A high level of metabolic control can be achieved through diet with early implementation of a "sick day" regime and, in some cases, dialysis as a rescue therapy. The Irish cohort, despite largely classical phenotypes, achieved good outcomes in the NBS era, underlining the importance of early diagnosis and skilled multidisciplinary team management.

Multimorbidity among persons aged 25-64 years: a population-based study of social determinants and all-cause mortality

BACKGROUND

Despite increasing multimorbidity across the lifespan, little is known about the co-occurrence of conditions and risk factors among younger adults. This population-based study examines multimorbidity, social determinants and associated mortality among younger and middle-age adults.

METHOD

Analysis was based on the Northern Ireland population aged 25-64 years enumerated in the 2011 Census (n = 878 345), with all-cause mortality follow-up to 2014 (8659 deaths). Logistic regression was used to examine social determinants and Cox proportional hazards models in the analysis of associated mortality.

RESULTS

Prevalence of multimorbidity was 13.7% in females and 12.7% in males. There was a strong association between multimorbidity that included mental/cognitive illness and deprivation. Among those never married, multimorbid physical conditions were less likely [relative risk ratios (RRR) = 0.92: 95% confidence interval (CI) = 0.88, 0.95 for males; and RRR = 0.90: 0.87, 0.94 for females]. Rurality was associated with lower physical multimorbidity (RRR = 0.92: 0.89, 0.95) but higher mental/cognitive multimorbidity (RRR = 1.35: 1.12, 1.64) among females. All multimorbid categories were associated with elevated risk of mortality.

CONCLUSION

The health and economic challenges created by multimorbidity should be addressed further 'upstream'. Future multimorbidity research should include younger adults to inform the development of preventative interventions and align health and social care services more closely with patients' needs.

Current opinion and emerging trends on the treatment, diagnosis, and prevention of pregnancy-associated venous thromboembolic disease: a review

Pregnancy associated venous thromboembolism (PA-VTE) is a leading cause of maternal morbidity and mortality worldwide. Despite the availability of international guidance on the prevention, diagnosis and treatment, practice differs between countries and clinical institutions. The evidence base in this area is limited due to the vulnerable population who are affected, with the majority of guidelines deriving their recommendations from experience in surgical and medical venous thromboembolic disease. This review includes best evidence in PA-VTE management, highlighting specific literature which supports current diagnosis, prevention, and treatment strategies. Additionally, we hope to demonstrate emerging trends in the field through discussion of ongoing trials designed to progress towards evidence-based practice in the context of PA-VTE.

Perspective: The Role of Human Breast-Milk Extracellular Vesicles in Child Health and Disease

Human breast milk (HM) contains multiple bioactive substances determining its impact on children's health. Extracellular vesicles (EVs) are a heterogeneous group of secreted nanoparticles that are present in HM and may be partially responsible for its beneficial effects. The precise roles and content of EVs in HM remain largely unknown. To examine this, we performed a short narrative review on the literature focusing on HM EVs to contextualize the available data, followed by a scoping review of MEDLINE and Embase databases. We identified 424 nonduplicate citations with 19 original studies included. In this perspective, we summarize the evidence around HM EVs, highlight some theoretical considerations based on existing evidence, and provide an overview of some challenges associated with the complexity and heterogeneity of EV research. We consider how the existing data from HM studies conform to the minimal information for studies of EVs (MISEV) guidelines. Across the studies a variety of research methods were utilized involving both bench-based and translational methods, and a range of different EV contents were examined including RNA, proteins, and glycopeptides. We observed a variety of health outcomes in these studies, including allergy and atopy, necrotizing enterocolitis, and HIV. While some promising results have been demonstrated, the heterogeneity in outcomes of interest, methodological limitations, and relatively small number of studies in the field make comparison between studies or further translational work problematic. To date, no studies have examined normative values of HM EVs in a large, diverse population or with respect to potentially important influencing factors such as timing (hind- vs. foremilk), stage (colostrum vs. mature milk), and infant age (preterm vs. term), which makes extrapolation from bench or "basic" research impossible. Future research should focus on addressing the current inadequacies in the literature and utilize MISEV guidelines to inform study design.

Mechanochemical Synthesis of Short DNA Fragments

We demonstrate the first mechanochemical synthesis of DNA fragments by ball milling, enabling the synthesis of oligomers of controllable sequence and length using multi-step, one-pot reactions, without bulk solvent or the need to isolate intermediates. Mechanochemistry allowed for coupling of phosphoramidite monomers to the 5'-hydroxyl group of nucleosides, iodine/water oxidation of the resulting phosphite triester linkage, and removal of the 5'-dimethoxytrityl (DMTr) protecting group in situ in good yields (up to 60 % over three steps) to produce DNA dimers in a one-pot manner. H-Phosphonate chemistry under milling conditions enabled coupling and protection of the H-phosphonate linkage, as well as removal of the 5'-DMTr protecting group in situ, enabling a one-pot process with good yields (up to 65 % over three steps, or ca. 87 % per step). Sulfurization of the internucleotide linkage was possible using elemental sulfur (S8) or sulfur transfer reagents, yielding the target DNA phosphorothioate dimers in good yield (up to 80 % over two steps). This work opens the door to creation of solvent-free synthesis methodologies for DNA and RNA therapeutics.

Unmet need for chronic mental ill health: A population-based record linkage study

Introduction

Many people with chronic mental ill health do not receive the treatment they require, though the true extent of the associated socio-demographic and socio-economic factors is unknown.

Objectives

This unique record linkage study quantifies the characteristics of those reporting chronic poor mental health and the likelihood of being in receipt of pharmacological treatment for those who report chronic mental ill health.

Methods

The Northern Ireland Longitudinal Study (NILS), a random 28% of the 2011 Census returns (aged 25-74), was linked to a population-wide electronic database of prescribed medications. All cohort attributes, including presence of chronic poor mental health were derived from the Census. Logistic regression was used to test the likelihood of people with poor mental health being prescribed psychotropic medication. These findings were compared against similarly derived characteristics of those with respiratory illness on treatment.

Results

Overall, 23,803 (8.3%) of the enumerated 286,717 reported poor mental health and, while 81.5% received pharmacological treatment, those of non-white background (OR=0.38: 95%CI=0.26-0.54), never married (OR=0.67: 95%CI=061-0.73), unemployed (OR=0.65: 95%CI=0.53-0.81) or living in a rural area (OR=0.88: 95%CI=0.79-0.98) were less likely than their respective peers to receive medication for poor mental health. Non-treatment of respiratory illness was less socially patterned.

Conclusions

Some but not all of the observed variation in receipt of psychotropic medicines may represent unmet need. Further studies are required to clarify the patterning of and possible reasons for underuse, including understanding of and attitudes towards healthcare services of groups who are identified as being less likely to receive treatment (for example ethnic minorities and unemployed).

Highlights

Extensive CRISPR RNA modification reveals chemical compatibility and structure-activity relationships for Cas9 biochemical activity

CRISPR (clustered regularly interspaced short palindromic repeat) endonucleases are at the forefront of biotechnology, synthetic biology and gene editing. Methods for controlling enzyme properties promise to improve existing applications and enable new technologies. CRISPR enzymes rely on RNA cofactors to guide catalysis. Therefore, chemical modification of the guide RNA can be used to characterize structure-activity relationships within CRISPR ribonucleoprotein (RNP) enzymes and identify compatible chemistries for controlling activity. Here, we introduce chemical modifications to the sugar–phosphate backbone of Streptococcus pyogenes Cas9 CRISPR RNA (crRNA) to probe chemical and structural requirements. Ribose sugars that promoted or accommodated A-form helical architecture in and around the crRNA ‘seed’ region were tolerated best. A wider range of modifications were acceptable outside of the seed, especially D-2′-deoxyribose, and we exploited this property to facilitate exploration of greater chemical diversity within the seed. 2′-fluoro was the most compatible modification whereas bulkier O-methyl sugar modifications were less tolerated. Activity trends could be rationalized for selected crRNAs using RNP stability and DNA target binding experiments. Cas9 activity in vitro tolerated most chemical modifications at predicted 2′-hydroxyl contact positions, whereas editing activity in cells was much less tolerant. The biochemical principles of chemical modification identified here will guide CRISPR-Cas9 engineering and enable new or improved applications.

Rationally Designed Anti-CRISPR Nucleic Acid Inhibitors of CRISPR-Cas9

Clustered regularly interspaced short palindromic repeat (CRISPR) RNAs and their associated effector (Cas) enzymes are being developed into promising therapeutics to treat disease. However, CRISPR-Cas enzymes might produce unwanted gene editing or dangerous side effects. Drug-like molecules that can inactivate CRISPR-Cas enzymes could help facilitate safer therapeutic development. Based on the requirement of guide RNA and target DNA interaction by Cas enzymes, we rationally designed small nucleic acid-based inhibitors (SNuBs) of Streptococcus pyogenes (Sp) Cas9. Inhibitors were initially designed as 2'-O-methyl-modified oligonucleotides that bound the CRISPR RNA guide sequence (anti-guide) or repeat sequence (anti-tracr), or DNA oligonucleotides that bound the protospacer adjacent motif (PAM)-interaction domain (anti-PAM) of SpCas9. Coupling anti-PAM and anti-tracr modules together was synergistic and resulted in high binding affinity and efficient inhibition of Cas9 DNA cleavage activity. Incorporating 2'F-RNA and locked nucleic acid nucleotides into the anti-tracr module resulted in greater inhibition as well as dose-dependent suppression of gene editing in human cells. CRISPR SNuBs provide a platform for rational design of CRISPR-Cas enzyme inhibitors that should translate to other CRISPR effector enzymes and enable better control over CRISPR-based applications.

A retrospective study (2001-2017) of acute and chronic morbidity and mortality associated with Staphylococcus aureus bacteraemia in a tertiary neonatal intensive care unit

BACKGROUND

Staphylococcus aureus bacteraemia (SAB) in NICU patients can cause significant morbidity and mortality.

AIMS

To review early and late neonatal SAB with regard to risk factors, treatment, acute complications and long-term outcomes.

METHODS

A retrospective study of laboratory confirmed SAB over a 16-year period (November 2001-January 2017) in a tertiary neonatal unit in Ireland.

FINDINGS

A total of 74 neonates (MSSA n = 72, MRSA n = 2) were identified; 8.1% (n = 6) early sepsis, 91.8% (n = 68) late sepsis. Low birth weight neonates (born weighing less than 2500 g) 80% (n = 59). Median age to bacteraemia 11 days post-delivery (range = 0-100 days); median onset early sepsis 1.5 days versus late sepsis 12 days. Complications of SAB; cellulitis n = 17, pneumonia n = 12, necrotising enterocolitis n = 7, thromobophlebitis n = 5, skin abscess formation n = 4, osteomyelitis n = 3, endocarditis n = 1. Late SAB mortality 6.4% (n = 3).

CONCLUSIONS

Preterm and low birth weight infants were at highest risk of SAB. Only a small proportion of affected children had long-term clinical sequelae on follow-up. The high rate of recurrence and breakthrough bacteraemia suggests that early implementation of a targeted anti-staphylococcal antimicrobial regimen may be of particular benefit.

Critical care usage after major gastrointestinal and liver surgery: a prospective, multicentre observational study

BACKGROUND

Patient selection for critical care admission must balance patient safety with optimal resource allocation. This study aimed to determine the relationship between critical care admission, and postoperative mortality after abdominal surgery.

METHODS

This prespecified secondary analysis of a multicentre, prospective, observational study included consecutive patients enrolled in the DISCOVER study from UK and Republic of Ireland undergoing major gastrointestinal and liver surgery between October and December 2014. The primary outcome was 30-day mortality. Multivariate logistic regression was used to explore associations between critical care admission (planned and unplanned) and mortality, and inter-centre variation in critical care admission after emergency laparotomy.

RESULTS

Of 4529 patients included, 37.8% (n=1713) underwent planned critical care admissions from theatre. Some 3.1% (n=86/2816) admitted to ward-level care subsequently underwent unplanned critical care admission. Overall 30-day mortality was 2.9% (n=133/4519), and the risk-adjusted association between 30-day mortality and critical care admission was higher in unplanned [odds ratio (OR): 8.65, 95% confidence interval (CI): 3.51-19.97) than planned admissions (OR: 2.32, 95% CI: 1.43-3.85). Some 26.7% of patients (n=1210/4529) underwent emergency laparotomies. After adjustment, 49.3% (95% CI: 46.8-51.9%, P<0.001) were predicted to have planned critical care admissions, with 7% (n=10/145) of centres outside the 95% CI.

CONCLUSIONS

After risk adjustment, no 30-day survival benefit was identified for either planned or unplanned postoperative admissions to critical care within this cohort. This likely represents appropriate admission of the highest-risk patients. Planned admissions in selected, intermediate-risk patients may present a strategy to mitigate the risk of unplanned admission. Substantial inter-centre variation exists in planned critical care admissions after emergency laparotomies.

Next-Generation Peptide Nucleic Acid Chimeras Exhibit High Affinity and Potent Gene Silencing

We present a new design of mixed-backbone antisense oligonucleotides (ASOs) containing both DNA and peptide nucleic acid (PNA). Previous generations of PNA-DNA chimeras showed low binding affinity, reducing their potential as therapeutics. The addition of a 5'-wing of locked nucleic acid as well as the combination of a modified nucleotide and a PNA monomer at the junction between PNA and DNA yielded high-affinity chimeras. The resulting ASOs demonstrated high serum stability and elicited robust RNase H-mediated cleavage of complementary RNA. These properties allowed the chimeric ASOs to demonstrate high gene silencing efficacy and potency in cells, comparable with those of LNA gapmer ASOs, via both lipid transfection and gymnosis.

Activating frataxin expression by single-stranded siRNAs targeting the GAA repeat expansion

Friedreich's ataxia (FRDA) is an incurable neurodegenerative disorder caused by reduced expression of the mitochondrial protein frataxin (FXN). The genetic cause of the disease is an expanded GAA repeat within the FXN gene. Agents that increase expression of FXN protein are a potential approach to therapy. We previously described anti-trinucleotide GAA duplex RNAs (dsRNAs) and antisense oligonucleotides (ASOs) that activate FXN protein expression in multiple patient derived cell lines. Here we test two distinct series of compounds for their ability to increase FXN expression. ASOs with butane linkers showed low potency, which is consistent with the low Tm values and suggesting that flexible conformation impairs activity. By contrast, single-stranded siRNAs (ss-siRNAs) that combine the strengths of dsRNA and ASO approaches had nanomolar potencies. ss-siRNAs provide an additional option for developing nucleic acid therapeutics to treat FRDA.

Evidence-based dentistry can effectively be taught to dental care professional students - A mixed methods study

BACKGROUND

Little research exists in the teaching of evidence-based dentistry (EBD) to students in the fields of dental hygiene, dental nursing and orthodontic therapy. This study aims to analyse the effect of a 1-day EBD programme on knowledge and confidence whilst also gaining insight into students' experience of the intervention.

METHOD

A mixed methods study was utilised with explanatory sequential design. The population consisted of dental hygiene (DH), dental nursing (DN) and orthodontic therapy (OT) students (N = 44). The intervention consisted of a 1-day active learning EBD programme, delivered via group projects and lectures. In the initial quantitative phase, a standardised questionnaire pre- and post -intervention measured changes in confidence for all participants, whilst change in knowledge was measured for DH and OT students only. Following this, focus groups were scheduled for all members of each discipline 3 months post-intervention for DN and 2 months post-intervention for DH and OT students. Semi-structured focus group schedules were drawn up, and groups organised according to the outcomes of quantitative data analysis. Qualitative results were analysed using a deductive adaptation of Burnard's thematic content analysis.

RESULTS

Forty-two students took part (94.45%) in this study. Median knowledge scores increased from zero to two of five (P < .001), whilst median confidence score doubled from four to eight of eight (P < .001). Results of thematic content analysis were coincident with quantitative results; however, it also provided constructive feedback regarding design and content of the course.

CONCLUSIONS

A 1-day bespoke programme in EBD increased students' confidence and knowledge in EBD skills. However, the findings further suggest that two successive half-day training sessions instead of one full-day training, tied in with coursework that requires the application of the acquired skills, may increase the learning experience further.

Activation of Frataxin Protein Expression by Antisense Oligonucleotides Targeting the Mutant Expanded Repeat

Friedreich's Ataxia (FA) is an inherited neurologic disorder caused by an expanded GAA repeat within intron 1 of the frataxin (FXN) gene that reduces expression of FXN protein. Agents that increase expression of FXN have the potential to alleviate the disease. We previously reported that duplex RNAs (dsRNAs) and antisense oligonucleotides (ASOs) complementary to the GAA repeat could enhance expression of FXN protein. We now explore the potential of a diverse group of chemically modified dsRNAs and ASOs to define the breadth of repeat-targeted synthetic nucleic acids as a platform for therapeutic development for FA. ASOs and dsRNAs can activate FXN protein expression in FA patient-derived cell lines that possess varied numbers of GAA repeats. Increased FXN protein expression was achieved by ASOs incorporating diverse chemical modifications with low nanomolar potencies, suggesting substantial flexibility in choosing compounds for further chemical optimization and animal studies. Our data encourage further development of ASOs as agents to treat FA.