Ranking Research Methodology by Risk - a cross-sectional study to determine the opinion of research ethics committee members

BACKGROUND

When reviewing a protocol, research ethics committees (RECs, equivalent to institutional review boards - IRBs) have the responsibility to consider whether the proposed research is justified. If research is not justified, it can waste participants' time, researchers' time and resources. As RECs are not constituted to cover all areas of scientific or academic expertise, it can be difficult for RECs to decide whether research is scientifically or methodologically justified especially in the absence of authoritative (often in the form of systematic) reviews. Where such reviews are absent, some have argued that RECs should insist on a new review of existing evidence as a condition of the REC favourable opinion. However, as RECs review a wide range of research, such requests must be proportionate to the type, and extent, of proposed projects. Risk is one factor that may influence the extent of evidence need for a REC to determine that the new project is justified, but not the only factor. The aim of the work described here was to determine whether REC members and researchers specifically link risk to the type of research methodology, and if so, whether this link could be used to help guide the need for systematic, or other, types of reviews.

METHOD

We conducted a cross-sectional study, gathering data between November 2020 and January 2021, to examine whether proposed research methodologies impact how RECs perceive risk to participants. We presented 31 research methodologies to REC members and researchers in the form of an international survey.

RESULTS

We collected 283 responses that included both qualitative and quantitative data as to how research methodology impacts perceptions of risk to participants. We used the data to conclude that RECs did see a link between risk and type of research. We therefore constructed a hierarchy of risk with Phase 1 and 2 clinical trials, and clinical psychology/psychiatry intervention studies, at the top (i.e. viewed as most risky).

CONCLUSIONS

We discuss whether this hierarchy is useful for guiding RECs as to the level of scientific justification that they should seek when reviewing proposed research protocols, and present a one-page guidance sheet to help RECs during their reviews.

Benefits of using exchangeable copper and the ratio of exchangeable copper in a real-world cohort of patients with Wilson disease

Wilson disease (WD) is a complex disease in which diagnosis and long-term metabolic copper control remains challenging. The absence of accurate biomarkers requires the combination of different parameters to ensure copper homeostasis. Exchangeable copper and its ratio (REC) have been suggested to be useful biomarkers in this setting. We aimed at introducing these measurements and evaluate their performance and accuracy in our real-world cohort of WD patients. Exchangeable copper and REC were measured in 48 WD patients and 56 control individuals by inductively coupled plasma-mass-spectrometry. Demographic and clinical characteristics were collected. REC was shown to be significantly higher among WD patients compared to controls and useful for WD identification by using the previously established cutoffs: 71.4% of WD patients with a recent diagnosis had REC ≥18.5% and 95.1% of long-term treated WD had REC ≥14%; only four patients of the cohort presented discordant levels. Moreover, REC values were below 15% in all the control individuals. Exchangeable copper was significantly higher in WD patients compared to controls and tended to be reduced among WD patients who were compliant to medication. This real-life study confirmed that exchangeable copper and REC are useful serum biomarkers that can be used as complementary tests to ensure WD diagnosis (REC) and copper homeostasis whithin time (exchangeable copper). The desirable target levels for this last objective still needs to be validated in prospective cohorts.

Regulating the disenfranchised: Reciprocity & resistance under the Mental Capacity Act

This paper interrogates the legitimacy of formal ethical regulation regarding people with dementia under the Mental Capacity Act, 2005 in England and Wales. Under the Act, research among people diagnosed with dementia must be approved by Health Research Authority committees, irrespective of whether that research engages with health organisations or service users. As examples, I discuss two ethnographic dementia studies that do not engage with healthcare services, but which nonetheless require HRA approval. These instances raise questions regarding legitimacy and reciprocity in the governance of dementia. Through capacity legislation, the state exerts control over people with dementia, automatically delineating them as healthcare subjects because of their diagnoses. This diagnosis functions as a form of administrative medicalisation, rendering dementia a medical entity and those diagnosed with it the property of formal healthcare. However, many people with dementia in England and Wales do not receive related health or care services beyond diagnosis. This institutional imbalance of high governance and low support undermines the contractual citizenship of people with dementia, wherein state-citizen rights and responsibilities should be reciprocal. In response, I consider resistance to this system in ethnographic research. "Resistance" here is not necessarily deliberate, hostile, difficult or perceived, but rather encompasses micropolitical effects that are contrary to power or control, sometimes emerging from systems themselves rather than individual resistive actors. Resistance can be unintentional, through mundane failures to satisfy specific aspects of governance bureaucracies. It can also be deliberate, through refusals to comply with restrictions that seem cumbersome, inapplicable or unethical, potentially raising questions of malpractice and misconduct. I suggest that resistance is made more probable due to the expansion of governance bureaucracies. On the one hand, the potential for both unintentional and intentional transgression increases, while on the other hand, the capacity for those transgressions to be discovered and rectified decreases, because the maintenance of control over such a system requires vast resources. Behind this ethico-bureaucratic tumult, people with dementia themselves are largely invisible. People with dementia often have no interaction with committees that determine their research participation. This further renders ethical governance a particularly disenfranchising facet of the dementia research economy. The state stipulates that people with dementia must be treated differently because of their diagnoses, without consulting those people. In response, resistance to unethical governance could be intuitively deemed ethical per se, but I suggest that such a simplistic binary is somewhat misleading.

Shifts in UNAIDS ethics guidance and implications for ethics review of preventive HIV vaccine trials

INTRODUCTION

A major change in the ethics framework for preventive HIV vaccine trials worldwide is the release of the UNAIDS 2021 ethical considerations in HIV prevention trials. This new guidance comes at an exciting time when there are multiple HIV vaccine efficacy trials in the field. Research Ethics Committees (RECs) or Institutional Review Boards are a most likely audience for these guidelines. Our objective is to highlight shifts in ethics recommendations from the earlier 2012 UNAIDS guidance.

DISCUSSION

We review recommendations related to four key issues, namely standard of prevention, post-trial access to safe and effective vaccines, enrolment of adolescents and enrolment of pregnant women. We outline implications and make recommendations for the ethics review process, including suggested lines of inquiry by RECs and responses by applicants.

CONCLUSIONS

There have been several shifts in the UNAIDS ethics guidance with implications for HIV vaccine researchers submitting applications for initial ethics review or re-certification, and for RECs conducting such reviews. This review may assist RECs in a more efficient and consistent application of ethics recommendations. However, additional tools and training may further help stakeholders comply with new UNAIDS ethics recommendations during protocol development and ethics review.

Research approvals iceberg: helping it melt away

BACKGROUND

In their paper "Research approvals iceberg: how a 'low-key' study in England needed 89 professionals to approve it and how we can do better" Petrova and Barclay highlight concerns with the health research regulatory environment in the UK.

DISCUSSION

As long-standing chairs of NHS research ethics committees, researchers, and also academics in research ethics, we are also often frustrated with the regulatory process in the UK. However, we think that Petrova and Barclay's analysis is misleading because it conflates research ethics with governance and funding processes, thus failing to adequately distinguish between the national coordinating function of the Health Research Authority, local research governance processes, and interactions with research sponsors and/or the Clinical Research Network.

Evaluation of the accuracy of exchangeable copper and relative exchangeable copper (REC) in a mouse model of Wilson's disease

Wilson's disease (WD) is caused by mutations in the ATP7B gene responsible for a toxic copper overload mainly in the liver and the central nervous system. Phenotypic heterogeneity may challenge the diagnostic confirmation. Exchangeable copper (CuEXC) has recently been proposed as a new marker of WD, and its ratio to the total serum copper (Cus), Relative Exchangeable Copper (REC = CuEXC/Cus), as a diagnostic marker. This study aimed to investigate whether this could be confirmed in Atp7b^-/- mice, an engineered WD animal model. Atp7b^-/- (n = 137) and wild type (WT; n = 101) mice were investigated under the same conditions at 6-8, 20, 39, or 50 weeks of age. Twenty-four Atp7b^-/- mice received D-penicillamine treatment from 39 to 50 weeks of age. Serum and liver [histology and intrahepatic copper (IHCu)] data were evaluated. In the WT group, all serum and liver data were normal. Atp7b^-/- livers developed a chronic injury from isolated moderate inflammation (6-8 weeks: 16/33 = 48%) to inflammatory fibrosis with cirrhosis (50 weeks: 25/25 = 100% and 16/25 = 64% respectively). Cus and CuEXC increased until week 39, whereas IHCu and REC were stable with increasing age and much higher than in WT mice (mean ± SD: 669 ± 269 vs. 13 ± 3 μg/g dry liver and 39 ± 12 vs. 11 ± 3%, respectively). A threshold value of 20% for REC provided a diagnostic sensitivity and specificity of 100%, regardless of sex, age, or the use of D-penicillamine. Eleven weeks of 100 mg/kg D-penicillamine reduced liver fibrosis (p = 0.001), IHCu (p = 0.026) and CuEXC (p = 0.175). In conclusion, this study confirms REC as a WD diagnostic marker in a mouse model of chronic liver disease caused by copper overload. Further studies are needed to assess the usefulness of CuEXC to monitor the evolution of WD, particularly during treatment.

miR-146a suppresses STAT3/VEGF pathways and reduces apoptosis through IL-6 signaling in primary human retinal microvascular endothelial cells in high glucose conditions

microRNA (miRNA) play critical roles in the pathological processes of diabetic retinopathy, including inflammatory responses, insulin signaling, and angiogenesis. In addition to their regulatory functions on gene expression, miRNA is considered as a potential therapeutic target, as well as a diagnostic marker for many diseases. Our understanding on the pathological mechanisms underlying diabetic retinopathy is still incomplete and additional investigations are required to develop novel therapeutic strategies. The aim of this study was to investigate our hypothesis that miR-146a plays a role in suppressing pro-inflammatory pathways, involving STAT3 and VEGF, through regulating IL-6 signaling to reduce apoptosis of human retinal endothelial cells (REC) in high glucose conditions. Human REC were cultured in normal (5mM) glucose or high glucose medium (25mM) for 3days. We performed transfections on REC with miRNA mimics (hsa-miR-146a-5p). Overexpression of miR-146a reduced IL-6 levels, STAT3 phosphorylation, and VEGF levels in REC cultured in high glucose. Cellular apoptosis was decreased in REC overexpressing miR-146a, as demonstrated by the inhibition of DNA fragmentation. More importantly, we demonstrated that the regulatory role of miR-146a on STAT3/VEGF and apoptosis was mediated by IL-6 receptor signaling in REC. Overall, we report that miR-146a suppressed IL-6 signaling, leading to reduced levels of STAT3 and VEGF in REC in high glucose conditions, leading to decreased apoptosis. The outcome suggests that miR-146a is a potential molecular target for inhibiting inflammation and apoptosis in the diabetic retina through the suppression of the IL-6-mediated STAT3/VEGF pathway.

Protein engineering of Cas9 for enhanced function

CRISPR/Cas systems act to protect the cell from invading nucleic acids in many bacteria and archaea. The bacterial immune protein Cas9 is a component of one of these CRISPR/Cas systems and has recently been adapted as a tool for genome editing. Cas9 is easily targeted to bind and cleave a DNA sequence via a complementary RNA; this straightforward programmability has gained Cas9 rapid acceptance in the field of genetic engineering. While this technology has developed quickly, a number of challenges regarding Cas9 specificity, efficiency, fusion protein function, and spatiotemporal control within the cell remain. In this work, we develop a platform for constructing novel proteins to address these open questions. We demonstrate methods to either screen or select active Cas9 mutants and use the screening technique to isolate functional Cas9 variants with a heterologous PDZ domain inserted within the protein. As a proof of concept, these methods lay the groundwork for the future construction of diverse Cas9 proteins. Straightforward and accessible techniques for genetic editing are helping to elucidate biology in new and exciting ways; a platform to engineer new functionalities into Cas9 will help forge the next generation of genome-modifying tools.

Cloning of TPS gene from eelgrass species Zostera marina and its functional identification by genetic transformation in rice

The full-length cDNA sequence (2613 bp) of the trehalose-6-phosphate synthase (TPS) gene of eelgrass Zostera marina (ZmTPS) was identified and cloned. Z. marina is a kind of seed-plant growing in sea water during its whole life history. The open reading frame (ORF) region of ZmTPS gene encodes a protein of 870 amino acid residues and a stop codon. The corresponding genomic DNA sequence is 3770 bp in length, which contains 3 exons and 2 introns. The ZmTPS gene was transformed into rice variety ZH11 via Agrobacterium-mediated transformation method. After antibiotic screening, molecular characterization, salt-tolerance and trehalose content determinations, two transgenic lines resistant to 150 mM NaCL solutions were screened. Our study results indicated that the ZmTPS gene was integrated into the genomic DNA of the two transgenic rice lines and could be expressed well. Moreover, the detection of the transformed ZmTPS gene in the progenies of the two transgenic lines was performed from T1 to T4 generations; and results suggested that the transformed ZmTPS gene can be transmitted from parent to the progeny in transgenic rice.

Metabolomics and transcriptomics demonstrate severe oxidative stress in both localized chemotherapy-treated and bystander tumors

BACKGROUND

Localized radiotherapy is long known to cause damages to not only targeted but also non-targeted cells, the so-called bystander (BS) effect. Recently, BS effect was demonstrated in response to chemotherapy. To get further insight into the mechanism of chemotherapy-induced BS effect in vivo, we investigated the response of normal tissues and untreated BS melanomas, at distance from localized chemotherapy-treated melanomas.

METHODS

B16 melanoma cells were inoculated sc in one flank, in mice. Chemotherapy was administered intratumorally. After 3 weeks, untreated melanomas were implanted into the other flank. Tumors were analyzed morphologically, and using metabolomics and transcriptomics.

RESULTS

Locally-treated melanomas showed growth inhibition and pleiotropic metabolic and transcriptional alterations. Tumors recovered slow proliferation while exhibiting prominent oxidative stress response (decreased glutathione level, and increased expression of genes including Mt1, Gpx3, Sod3, and Hmox1). Plasma contained increased levels of oxidative stress products. However, liver and soleus muscle displayed unaltered morphological characteristics. In contrast, untreated BS melanomas induced from naive B16 cells showed reduced growth, marked oxidative stress response (decreased glutathione level, and increased expression of genes including Sod2, Gpx1 and Gsr), and ras oncogene expression alterations. Furthermore, metabolomics and transcriptomics enabled to estimate the proportion of cells undergoing the BS effect within treated tumors.

CONCLUSION

Treatment of tumors with chemotherapy induces BS effects, underpinned by oxidative stress, in abnormal proliferating tissues in vivo, not in normal tissue, that significantly contribute to overall tumor response. General significance BS effect significantly contributes to response to chemotherapy, and may be exploited to improve overall response to cancer treatment.

Reduction in HPV 16/18 prevalence in sexually active young women following the introduction of HPV immunisation in England

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We monitor HPV infection in sexually active young women in England.

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The prevalence of HPV 16/18 has reduced within 3 years of HPV immunisation.

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Reductions in HPV 16/18 were greatest at ages with highest immunisation coverage.

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The data suggest reductions in HPV 16/18 amongst unvaccinated young women and men.

Background

Reduction in the prevalence of vaccine type HPV infection in young women is an early indication of the impact of the HPV immunisation programme and a necessary outcome if the subsequent impact on cervical cancer is to be realised.

Methods

Residual vulva-vaginal swab (VVS) specimens from young women aged 16–24 years undergoing chlamydia screening in community sexual health services (formerly known as family planning clinics), general practice (GP), and youth clinics in 2010–2012 were submitted from 10 laboratories in seven regions around England. These specimens were linked to demographic and sexual behaviour data reported with the chlamydia test, anonymised, and tested for type-specific HPV DNA using a multiplex PCR and Luminex-based genotyping test. Estimated immunisation coverage was calculated and findings were compared to a baseline survey conducted prior to the introduction of HPV immunisation in 2008.

Results

A total of 4664 eligible specimens were collected and 4178 had a valid test result. The post-immunisation prevalence of HPV 16/18 infection was lowest in this youngest age group (16–18 years) and increased with age. This increase with age was a reversal of the pattern seen prior to immunisation and was inversely associated with estimates of age-specific immunisation coverage (65% for 16–18 year olds). The prevalence of HPV 16/18 infection in the post-immunisation survey was 6.5% amongst 16–18 year olds, compared to 19.1% in the similar survey conducted prior to the introduction of HPV immunisation.

Conclusions

These findings are the first indication that the national HPV immunisation programme is successfully preventing HPV 16/18 infection in sexually active young women in England. The reductions seen suggest, for the estimated coverage, high vaccine effectiveness and some herd-protection benefits. Continued surveillance is needed to determine the effects of immunisation on non-vaccine HPV types.

Association between JY-1 gene polymorphisms and reproductive traits in beef cattle

Reproductive traits have a high economic value and it is interesting to include them in the selection objectives of an animal breeding program. These traits generally show low heritability and molecular markers may therefore be used in genetic evaluations to improve the accuracy of predictions. The JY-1 gene is expressed in the oocyte and it is associated with folliculogenesis and early embryo development. It has been suggested to affect reproductive traits. In this study, exons 1 and 2 of the JY-1 gene were studied in 385 Nellore females by PCR-sequencing. Seventeen polymorphisms were identified. After analysis of linkage disequilibrium, association tests were performed between eight SNPs and the occurrence of early pregnancy, age at first calving, days to calving, and reconception of primiparous heifers. Seven SNPs were significant for three traits. The most significant was chr29:12,999 T/A (p=0.003) which was associated with the occurrence of early pregnancy. This SNP might be involved in protein translation inhibition since it affects the initial methionine codon. The JY-1, an oocyte specific gene, influences reproductive traits; further studies investigating other regions of the gene or other genes expressed in tissues of the female reproductive system would be interesting to be performed.

Metabolic impact assessment for heterologous protein production in Streptomyces lividans based on genome-scale metabolic network modeling

The metabolic impact exerted on a microorganism due to heterologous protein production is still poorly understood in Streptomyces lividans. In this present paper, based on exometabolomic data, a proposed genome-scale metabolic network model is used to assess this metabolic impact in S. lividans. Constraint-based modeling results obtained in this work revealed that the metabolic impact due to heterologous protein production is widely distributed in the genome of S. lividans, causing both slow substrate assimilation and a shift in active pathways. Exchange fluxes that are critical for model performance have been identified for metabolites of mouse tumor necrosis factor, histidine, valine and lysine, as well as biomass. Our results unravel the interaction of heterologous protein production with intracellular metabolism of S. lividans, thus, a possible basis for further studies in relieving the metabolic burden via metabolic or bioprocess engineering.

Overexpression of tomato enhancer of SOS3-1 (LeENH1) in tobacco enhanced salinity tolerance by excluding Na+ from the cytosol

The salt overly sensitive pathway has an important function in plant salinity tolerance. The enhancer of SOS3-1 (ENH1) participates in a new salinity stress pathway with SOS2 but without SOS3. To investigate the physiological effects and functional mechanism of ENH1 under salt stress, ENH1 was isolated from tomato and overexpressed in tobacco. Under salt stress, the sprouting percentage, fresh weight, and dry weight of transgenic plants were higher than those of wild-type (WT) plants. Under salt stress, the chlorophyll content, net photosynthetic rate, and maximal photochemical efficiency of PSII in transgenic plants decreased more slowly than those in WT plants. The overexpression of LeENH1 in tobacco excluded Na(+) from the cytosol and retained high K(+) levels in the cytosol to reestablish ion homeostasis. Higher thylakoid-bound ascorbate peroxidase activity and lower reactive oxygen species levels were found in transgenic plants under salt stress.

VEGF but not PlGF disturbs the barrier of retinal endothelial cells

Elevated permeability of retinal endothelial cells (REC), as observed in diabetic retinopathy (DR), is induced by extended exposure to ≥25 ng/ml vascular endothelial growth factor A165 (VEGF165) for up to 3 d and this effect is more pronounced when equimolar amounts of basic fibroblast growth factor (bFGF) and insulin-like growth factor (IGF-1) are present. Down-regulation of the tight-junction protein claudin-1 and its loss from the plasma membrane is associated with induced higher permeability, whereas other tight-junction proteins (e.g. claudin-3, claudin-5, ZO-1) show only subtle changes in our experimental setting. Using immortalized bovine REC (iBREC) as a well-established model, we investigated effects of other members of the VEGF family, i.e. VEGF121, placental growth factor (PlGF-1 and PlGF-2) and viral VEGF-E which activate different sets of VEGF receptors, on barrier function after extended treatment: iBREC were incubated with 1-100 ng/ml of the growth factors for up to 2 days before barrier function was assessed by measuring transendothelial resistance (TER). Presence of TJ-proteins was determined by western blot analyses and immunofluorescence staining. Similar experiments were performed to evaluate whether the primary actions of PlGF-1, PlGF-2 or VEGF121 are modulated by bFGF or IGF-1 when all growth factors (each at 25 ng/ml, but 10 ng/ml IGF-1) act simultaneously at equimolar concentrations. We also studied the potential normalization of the barrier disturbed with combinations of growth factors by addition of the VEGF-specific Fab fragment ranibizumab or the recombinant protein aflibercept which binds VEGF and PlGF. Whereas 1 ng/ml VEGF-E were sufficient to impair the iBREC barrier, a higher concentration of 100 ng/ml VEGF121 was needed to reduce TER and expression of claudin-1 over 2 days. By PlGF-1 or PlGF-2, the barrier was not affected even at the highest concentration tested (100 ng/ml) and these factors also did not modulate the effect of VEGF165. The weak barrier derangement caused by VEGF121 was slightly enhanced by bFGF and IGF-1. After induction of the barrier breakdown with various combinations of all growth factors included in the study, normal TER and claudin-1 expression was re-established by ranibizumab. Both VEGF inhibitors ranibizumab and aflibercept similarly reinstated lost claudin-1, even when applied at a small fraction of the clinically relevant concentrations. These results show that VEGF-A, but not PlGF impairs the barrier function of iBREC and that the longer isoform VEGF165 is more potent than VEGF121. To induce barrier dysfunction in iBREC, activation of VEGF receptor 2 - probably in concert with neuropilin-1 - seems to be sufficient because VEGF-E and VEGF165, but not PlGF-1/-2 reduced TER or claudin-1 expression.

GSTM1 copy number and promoter haplotype as predictors for risk of recurrence and/or second primary tumor in patients with head and neck cancer

The objective of this study was to determine copy number variant (CNV) and promoter genetic variants in glutathione S-transferase Mu class 1 (GSTM1) and the risk of recurrence (REC)/second primary tumor (SPT) in patients with previously diagnosed early stage head and neck cancer. Among 441 subjects, 133 experienced REC and/or an SPT, while 308 had single primary disease. TaqMan real-time polymerase chain reaction was used to measure the exact copy number of GSTM1 and direct sequencing was used to determine genetic variants in the GSTM1 promoter region. Multivariate Cox regression analysis was performed to estimate hazard ratios (HRs) and 95% confidence intervals (95% CIs) associated with copy number and genetic variants. REC/SPT-free survival times were compared by constructing Kaplan–Meier curves and differences between curves were tested by logrank test. Results showed a significantly decreased REC/SPT (HR = 0.57; 95% CI = 0.35–0.95) and longer REC/SPT-free survival in subjects with at least two copies of GSTM1 compared with the GSTM1 homozygous deletion, but not in those with one copy of GSTM1. The −498G, −426G, and −339T alleles were significantly associated with REC/SPT, with HRs of 0.11 (0.02–0.85), 0.28 (0.11–0.74) and 2.02 (1.07–3.82), respectively. Kaplan–Meier survival analysis showed that the −498G, −426G, and −339C alleles were also significantly associated with increased REC/SPT-free survival. Further haplotype analysis showed the haplotype P^{−498G-−426G-−339C} carriers had decreased REC/SPT with a HR of 0.09 (95% CI 0.01–0.71) and increased REC/SPT-free survival compared with those with haplotype P^{−498C-−426A-−339T}. The P^{−498C-−426A-−339T}-containing reporter construct had significantly increased luciferase expression. These results suggest that the GSTM1 CNV and promoter haplotype are better predictors of REC/SPTs of head and neck cancer than just measuring the presence/absence of GSTM1.