Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria

Accumulating evidence suggests that cardiovascular disease (CVD) is associated with an altered gut microbiome. Our understanding of the underlying mechanisms has been hindered by lack of matched multi-omic data with diagnostic biomarkers. To comprehensively profile gut microbiome contributions to CVD, we generated stool metagenomics and metabolomics from 1,429 Framingham Heart Study participants. We identified blood lipids and cardiovascular health measurements associated with microbiome and metabolome composition. Integrated analysis revealed microbial pathways implicated in CVD, including flavonoid, γ-butyrobetaine, and cholesterol metabolism. Species from the Oscillibacter genus were associated with decreased fecal and plasma cholesterol levels. Using functional prediction and in vitro characterization of multiple representative human gut Oscillibacter isolates, we uncovered conserved cholesterol-metabolizing capabilities, including glycosylation and dehydrogenation. These findings suggest that cholesterol metabolism is a broad property of phylogenetically diverse Oscillibacter spp., with potential benefits for lipid homeostasis and cardiovascular health.

Care or Complicity? Medical Personnel in Prisons

Imprisonment may sometimes be a justified form of punishment. Yet the U.S. carceral system suffers from appalling problems of justice-in who is put into prisons, in how imprisoned people are treated, and in downstream personal and community health impacts. Medical personnel working in prisons and jails take on risky work for highly vulnerable and underserved patients. They are to be lauded for their professional commitments. Yet at the same time, prison care undercuts the ability of medical personnel to uphold their own professional standards and sometimes fails in even basic health protection. Doctors in prisons are stuck between their commitment to vulnerable patients and complicity in a system that requires their participation to uphold its constitutionality. Medical ethics is frayed in prisons, and the problem deserves our attention.

Lectin-Seq: A method to profile lectin-microbe interactions in native communities

Soluble human lectins are critical components of innate immunity. Genetic models suggest that lectins influence host-resident microbiota, but their specificity for commensal and mutualist species is understudied. Elucidating lectins' roles in regulating microbiota requires an understanding of which microbial species they bind within native communities. To profile human lectin recognition, we developed Lectin-Seq. We apply Lectin-Seq to human fecal microbiota using the soluble mannose-binding lectin (MBL) and intelectin-1 (hItln1). Although each lectin binds a substantial percentage of the samples (10 to 20%), the microbial interactomes of MBL and hItln1 differ markedly in composition and diversity. MBL binding is highly selective for a small subset of species commonly associated with humans. In contrast, hItln1's interaction profile encompasses a broad range of lower-abundance species. Our data uncover stark differences in the commensal recognition properties of human lectins.

Cross-ancestry, cell-type-informed atlas of gene, isoform, and splicing regulation in the developing human brain

Genomic regulatory elements active in the developing human brain are notably enriched in genetic risk for neuropsychiatric disorders, including autism spectrum disorder (ASD), schizophrenia, and bipolar disorder. However, prioritizing the specific risk genes and candidate molecular mechanisms underlying these genetic enrichments has been hindered by the lack of a single unified large-scale gene regulatory atlas of human brain development. Here, we uniformly process and systematically characterize gene, isoform, and splicing quantitative trait loci (xQTLs) in 672 fetal brain samples from unique subjects across multiple ancestral populations. We identify 15,752 genes harboring a significant xQTL and map 3,739 eQTLs to a specific cellular context. We observe a striking drop in gene expression and splicing heritability as the human brain develops. Isoform-level regulation, particularly in the second trimester, mediates the greatest proportion of heritability across multiple psychiatric GWAS, compared with eQTLs. Via colocalization and TWAS, we prioritize biological mechanisms for ~60% of GWAS loci across five neuropsychiatric disorders, nearly two-fold that observed in the adult brain. Finally, we build a comprehensive set of developmentally regulated gene and isoform co-expression networks capturing unique genetic enrichments across disorders. Together, this work provides a comprehensive view of genetic regulation across human brain development as well as the stage-and cell type-informed mechanistic underpinnings of neuropsychiatric disorders.

Mission Creep or Mission Lapse? Scientific Review in Research Oversight

BACKGROUND

The ethical use both of human and non-human animals in research is predicated on the assumption that it is of a high quality and its projected benefits are more significant than the risks and harms imposed on subjects. Yet questions remain about whether and how IRBs and IACUCs should consider the scientific value of proposed research studies.

METHODS

We draw upon 45 interviews with IRB and IACUC members and researchers with oversight experience about their perceptions of their own roles in reviewing the quality and value of scientific protocols. Interview transcripts were memoed to highlight specific findings, which were then used to identify key themes through an iterative process.

RESULTS

IRB and IACUC members expressed broad trust in the need for and value of research, and they often assumed that protocols had social value or that prior review, especially when associated with funding, affirmed both the rigor and merit of those protocols. Some oversight members also took an explicit stance against scientific review by stating that such review is not within the regulatory mandates governing their parts in the oversight system. Yet other interviewees expressed uneasiness about the current paradigm for evaluating the quality and overall value of science, suggesting that IRB and IACUC members perceive gaps in the oversight systems.

CONCLUSIONS

These findings reveal many similarities in how IRB and IACUC members understand the roles and limitations of their respective oversight committees. We conclude with a discussion of how the lack of a clear mandate regarding scientific review within US federal regulations may undermine ethical engagement of whether human and animal research is scientifically justified, resulting in a "mission lapse" wherein no organizational body is clearly responsible for ensuring that the research being conducted has the potential to advance science and benefit society.

Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine

Colonization of the intestine by oral microbes has been linked to multiple diseases such as inflammatory bowel disease and colon cancer, yet mechanisms allowing expansion in this niche remain largely unknown. Veillonella parvula, an asaccharolytic, anaerobic, oral microbe that derives energy from organic acids, increases in abundance in the intestine of patients with inflammatory bowel disease. Here we show that nitrate, a signature metabolite of inflammation, allows V. parvula to transition from fermentation to anaerobic respiration. Nitrate respiration, through the narGHJI operon, boosted Veillonella growth on organic acids and also modulated its metabolic repertoire, allowing it to use amino acids and peptides as carbon sources. This metabolic shift was accompanied by changes in carbon metabolism and ATP production pathways. Nitrate respiration was fundamental for ectopic colonization in a mouse model of colitis, because a V. parvula narG deletion mutant colonized significantly less than a wild-type strain during inflammation. These results suggest that V. parvula harness conditions present during inflammation to colonize in the intestine.

Ethical Criteria for Improved Human Subject Protections in Phase I Healthy Volunteer Trials

Phase I healthy volunteer trials test the safety and tolerability of investigational pharmaceuticals. In them, participants are exposed to study-drug risks without the possibility of direct medical benefit and typically must spend days or weeks in a residential research facility. Monetary payments are used to incentivize enrollment and compensate participants for their time. Together, these features of phase I healthy volunteer trials create a research context that differs markedly from most other clinical research, including by enrolling disproportionate numbers of economically disadvantaged people of color as participants. Due to these unique trial features and participation patterns, traditional biomedical research oversight offers inadequate ethical and policy guidance for phase I healthy volunteer research. This article details five ethical criteria crafted to be responsive to the particularities of this type of research: translational science value, fair opportunity and burden sharing, fair compensation for service, experiential welfare, and enhanced voice and recourse.

Translational science: a survey of US biomedical researchers' perspectives and practices

This national survey aimed to identify how biomedical researchers using vertebrate animals viewed issues of significance for translational science, including oversight and public engagement, and to analyze how researcher characteristics and animal model choice correlate with those views. Responses from 1,187 researchers showed awareness of, and concerns about, problems of translation, reproducibility and rigor. Surveyed scientists were nevertheless optimistic about the value of animal studies, were favorable about research oversight and reported openness with non-scientists in discussing their animal work. Differences in survey responses among researchers also point to diverse perspectives within the animal research community on these matters. Most significant was variability associated with the primary type of animal that surveyed scientists used in their work. Other significant divergence in opinion appeared on the basis of professional role factors, including the type of degree held, workplace setting, type of funding, experience on an institutional animal care and use committee and personal demographic characteristics of age and gender.

Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease

BACKGROUND

The human gut harbors trillions of microbes that play dynamic roles in health. While the microbiome contributes to many cardiometabolic traits by modulating host inflammation and metabolism, there is an incomplete understanding regarding the extent that and mechanisms by which individual microbes impact risk and development of cardiovascular disease (CVD). The Framingham Heart Study (FHS) is a multi-generational observational study following participants over decades to identify risk factors for CVD by correlating genetic and phenotypic factors with clinical outcomes. As a large-scale population-based cohort with extensive clinical phenotyping, FHS provides a rich landscape to explore the relationships between the gut microbiome and cardiometabolic traits.

METHODS

We performed 16S rRNA gene sequencing on stool from 1423 participants of the FHS Generation 3, OMNI2, and New Offspring Spouse cohorts. Data processing and taxonomic assignment were performed with the 16S bioBakery workflow using the UPARSE pipeline. We conducted statistical analyses to investigate trends in overall microbiome composition and diversity in relation to disease states and systematically examined taxonomic associations with a variety of clinical traits, disease phenotypes, clinical blood markers, and medications.

RESULTS

We demonstrate that overall microbial diversity decreases with increasing 10-year CVD risk and body mass index measures. We link lifestyle factors, especially diet and exercise, to microbial diversity. Our association analyses reveal both known and unreported microbial associations with CVD and diabetes, related prescription medications, as well as many anthropometric and blood test measurements. In particular, we observe a set of microbial species that demonstrate significant associations with CVD risk, metabolic syndrome, and type 2 diabetes as well as a number of shared associations between microbial species and cardiometabolic subphenotypes.

CONCLUSIONS

The identification of significant microbial taxa associated with prevalent CVD and diabetes, as well as risk for developing CVD, adds to increasing evidence that the microbiome may contribute to CVD pathogenesis. Our findings support new hypothesis generation around shared microbe-mediated mechanisms that influence metabolic syndrome, diabetes, and CVD risk. Further investigation of the gut microbiomes of CVD patients in a targeted manner may elucidate microbial mechanisms with diagnostic and therapeutic implications.

DIAPH1 Variants in Non-East Asian Patients With Sporadic Moyamoya Disease

Importance

Moyamoya disease (MMD), a progressive vasculopathy leading to narrowing and ultimate occlusion of the intracranial internal carotid arteries, is a cause of childhood stroke. The cause of MMD is poorly understood, but genetic factors play a role. Several familial forms of MMD have been identified, but the cause of most cases remains elusive, especially among non-East Asian individuals.

Objective

To assess whether ultrarare de novo and rare, damaging transmitted variants with large effect sizes are associated with MMD risk.

Design, Setting, and Participants

A genetic association study was conducted using whole-exome sequencing case-parent MMD trios in a small discovery cohort collected over 3.5 years (2016-2019); data were analyzed in 2020. Medical records from US hospitals spanning a range of 1 month to 1.5 years were reviewed for phenotyping. Exomes from a larger validation cohort were analyzed to identify additional rare, large-effect variants in the top candidate gene. Participants included patients with MMD and, when available, their parents. All participants who met criteria and were presented with the option to join the study agreed to do so; none were excluded. Twenty-four probands (22 trios and 2 singletons) composed the discovery cohort, and 84 probands (29 trios and 55 singletons) composed the validation cohort.

Main Outcomes and Measures

Gene variants were identified and filtered using stringent criteria. Enrichment and case-control tests assessed gene-level variant burden. In silico modeling estimated the probability of variant association with protein structure. Integrative genomics assessed expression patterns of MMD risk genes derived from single-cell RNA sequencing data of human and mouse brain tissue.

Results

Of the 24 patients in the discovery cohort, 14 (58.3%) were men and 18 (75.0%) were of European ancestry. Three of 24 discovery cohort probands contained 2 do novo (1-tailed Poisson P = 1.1 × 10-6) and 1 rare, transmitted damaging variant (12.5% of cases) in DIAPH1 (mammalian diaphanous-1), a key regulator of actin remodeling in vascular cells and platelets. Four additional ultrarare damaging heterozygous DIAPH1 variants (3 unphased) were identified in 3 other patients in an 84-proband validation cohort (73.8% female, 77.4% European). All 6 patients were non-East Asian. Compound heterozygous variants were identified in ena/vasodilator-stimulated phosphoproteinlike protein EVL, a mammalian diaphanous-1 interactor that regulates actin polymerization. DIAPH1 and EVL mutant probands had severe, bilateral MMD associated with transfusion-dependent thrombocytopenia. DIAPH1 and other MMD risk genes are enriched in mural cells of midgestational human brain. The DIAPH1 coexpression network converges in vascular cell actin cytoskeleton regulatory pathways.

Conclusions and Relevance

These findings provide the largest collection to date of non-East Asian individuals with sporadic MMD harboring pathogenic variants in the same gene. The results suggest that DIAPH1 is a novel MMD risk gene and impaired vascular cell actin remodeling in MMD pathogenesis, with diagnostic and therapeutic ramifications.

Phase I trial compensation: How much do healthy volunteers actually earn from clinical trial enrollment?

Background/aims

Financial compensation for research participation is a major focus of ethical concern regarding human subject recruitment. Phase I trials are sometimes considered to be a lucrative source of income for healthy volunteers, encouraging some people to become “professional guinea pigs.” Yet, little is known about how much these clinical trials actually pay and how much healthy volunteers earn from them.

Methods

As part of a mixed-methods, longitudinal study of healthy volunteers, we required participants to complete clinical trial diaries, or surveys that captured detailed information about screening and enrollment in Phase I trials. Over a 3-year period, participants provided information online or via telephone about each clinical trial for which they screened (e.g. the clinic name, the study’s therapeutic area, the length of the trial, the number of nights spent in the clinic, and the study compensation), and whether they qualified for trial inclusion. Clinical trial diaries generated data about whether participants continued to screen for and enroll in clinical trials and how much money they earned from their participation.

Results

131 participants routinely completed clinical trial diaries or confirmed that they had not screened for any new clinical trials. Together, these participants screened for 1001 clinical trials at 73 research facilities during a 3-year period. Overall, the median clinical trial compensation was US$3070 (range = US$150–US$13,000). Participants seeking new healthy volunteer trials tended to screen for three studies per year, participate in one or two studies, and earn roughly US$4000 annually. Participants who were unemployed earned the most income from clinical trials compared to those with full-time or part-time jobs, and those individuals whom we label “occupational” participants because of their persistent pursuit of clinical trials earned more than people who screened occasionally. Notably, the median annual trial compensation was well below US$10,000 for all employment groups, and most occupational healthy volunteers also earned less than US$10,000 each year. The 10% of participants who earned the most had a median annual income of US$18,885 from clinical trials, and there was significant volatility in these individuals’ earnings from year to year.

Conclusion

Despite the perception that Phase I enrollment can generate significant earnings, it was exceedingly rare for anyone in this study to make more than US$20,000 in a single year, and unusual to earn even between US$10,000 and US$20,000. From an ethics perspective, individual trials might appear to unduly induce enrollment by offering significant sums of money, but given our findings, the larger problem for low-income participants may be the unrealistic perception that clinical trials alone could be a way of earning a living.

Biomedical Researchers' Perceptions of the NIH's Sex as a Biological Variable Policy for Animal Research: Results from a U.S. National Survey

Background: In 2015, the National Institutes of Health (NIH) established a policy on sex as a biological variable (SABV) in an effort to address the overrepresentation of men and male animals in biomedical research and the lack of attention to sex-based responses to medical treatments. However, questions remain regarding how U.S. biomedical researchers perceive the impact of the SABV policy on their own research and on translational science more broadly. Materials and Methods: A national survey of U.S. scientists who use vertebrate animals in their research was conducted. Respondents were asked how they select and use animal species as model organisms as well as how they perceive the impact of the SABV policy on their research practices. Results: Almost all respondents reported that they had previously heard of the NIH SABV policy, and over one-third had altered their study designs to comply with the policy. There were robust differences in perceptions of the SABV policy based on researchers' primary species of model organism. However, there was no significant difference in the likelihood of researchers analyzing their results by sex based on whether they had received recent NIH funding. Conclusions: While many researchers report adhering to the SABV policy requirements, more work needs to be done to ensure that the policy is being evenly applied to researchers using all types of animal models and that researchers adhere to the policy after receiving NIH funding, particularly in terms of reporting on and analyzing SABV in their study findings for publication.

Correction to: Picking and Choosing Among Phase I Trials

The article "Picking and Choosing Among Phase I Trials", written by Jill A. Fisher, Torin Monahan and Rebecca L. Walker, was originally published Online First without Open Access. After publication in volume 16, issue 4, page 535-549 the author decided to opt for Open Choice and to make the article an Open Access publication.

A New Governance Approach to Regulating Human Genome Editing

For years, genomic medicine-medicine based on the growing understanding of the genetic contribution to many diseases and conditions-has been hailed as the future of medical treatment, but it has thus far had limited effect on day-to-day medical practice. The ultimate goal of genomic medicine has always been the ability not just to identify dangerous gene mutations, but to fix them. Now CRISPR and related genome-editing technologies may have the potential to provide a safe and effective way to repair dangerous mutations. In the wake of ethically dubious experiments with human embryos in China, the international governance of human genome editing is emerging as an urgent topic for scientists, regulators, and the public. Efforts to develop a governance model are underway at national and international levels. These efforts are the subject of multiple initiatives by national and international health and science organizations and are topics of discussion at scientific conferences, summits, and meetings. This Article reports on the Authors' multi-year, interdisciplinary project to identify and investigate the practical, ethical, and policy considerations that are emerging as the greatest concerns about human genome editing, and ultimately to develop policy options. The project involves monitoring the discussions of groups, both government-sponsored and private, that are considering how genome editing should be governed; observing conferences where the topic is discussed; analyzing emerging policy reports by national and international bodies; and interviewing a wide range of stakeholders, including scientists, ethicists, and those who make and comment on public policy. The Article identifies several stakeholder concerns that are especially prominent in the research to date and begins to explore the implications of these concerns for alternative models of governance. There are current indications that, for practical purposes, a focus on "soft," hybrid forms of governance based on networks of multiple public and private stakeholders may turn out to be the most promising course to pursue. The "new governance" paradigm developed in the corporate and financial sectors offers a useful model for understanding the dynamics of this approach.

Evaluating the National Institutes of Health's Sex as a Biological Variable Policy: Conflicting Accounts from the Front Lines of Animal Research

Background: Since the National Institutes of Health (NIH) Revitalization Act of 1993, focus on the equitable inclusion of women in clinical research has been ongoing. NIH's 2015 sex as a biological variable (SABV) policy aims to transform research design, analysis, and reporting in the preclinical sphere by including male and female organisms in vertebrate animal research as well as human studies. However, questions remain regarding how researchers and members of research oversight committees perceive the value and need of the SABV policy. Materials and Methods: Based on 62 interviews with animal researchers and oversight personnel, we analyze what the animal research community knows about the policy and sees as the benefits and challenges of implementation. Results: We found that the 62 interviewees disagreed about the need for the policy, with some being supportive and others questioning whether the policy is based on science or is politically motivated. There were also tensions in how interviewees conceptualized the challenges to and resources needed for implementing the SABV policy. For instance, while some thought implementation would require a significant increase in numbers of animals used for each study, others explicitly rejected this claim. Conclusions: We conclude by discussing the practical and social implications of our findings about the views of members of the animal research community regarding the SABV policy.

Exome sequencing implicates genetic disruption of prenatal neuro-gliogenesis in sporadic congenital hydrocephalus

Congenital hydrocephalus (CH), characterized by enlarged brain ventricles, is considered a disease of excessive cerebrospinal fluid (CSF) accumulation and thereby treated with neurosurgical CSF diversion with high morbidity and failure rates. The poor neurodevelopmental outcomes and persistence of ventriculomegaly in some post-surgical patients highlight our limited knowledge of disease mechanisms. Through whole-exome sequencing of 381 patients (232 trios) with sporadic, neurosurgically treated CH, we found that damaging de novo mutations account for >17% of cases, with five different genes exhibiting a significant de novo mutation burden. In all, rare, damaging mutations with large effect contributed to ~22% of sporadic CH cases. Multiple CH genes are key regulators of neural stem cell biology and converge in human transcriptional networks and cell types pertinent for fetal neuro-gliogenesis. These data implicate genetic disruption of early brain development, not impaired CSF dynamics, as the primary pathomechanism of a significant number of patients with sporadic CH.

Can We Do without Respect and Justice in Animal Research Ethics?

This book review essay discusses Principles of Animal Research Ethics (2020), by Tom L. Beauchamp and David DeGrazia.

The Unfinished Business of Respect for Autonomy: Persons, Relationships, and Nonhuman Animals

This essay explores three issues in respect for autonomy that pose unfinished business for the concept. By this, I mean that the dialogue over them is ongoing and essentially unresolved. These are: (1) whether we ought to respect persons or their autonomous choices; (2) the role of relational autonomy; and (3) whether nonhuman animals can be autonomous. In attending to this particular set of unfinished business, I highlight some critical moral work left aside by the concept of respect for autonomy as understood in Beauchamp and Childress’ Principles of Biomedical Ethics. Specifically, while significant pragmatic traction is gained by the authors’ focus on autonomous choice, carving such a focus out from the broader questions of moral respect and the autonomy of the person leaves aside a number of questions that we might have thought a view about respect for autonomy in biomedicine ought to answer. These include: How should physicians respond when autonomous patients make decisions that appear nonautonomous? What is the impact of the view that autonomy is “relational” for cross-cultural differences in how autonomy is respected? If chimpanzees (and by extension young children) can be autonomous, what does that mean for how they should be treated?

Picking and Choosing Among Phase I Trials : A Qualitative Examination of How Healthy Volunteers Understand Study Risks

This article empirically examines how healthy volunteers evaluate and make sense of the risks of phase I clinical drug trials. This is an ethically important topic because healthy volunteers are exposed to risk but can gain no medical benefit from their trial participation. Based on in-depth qualitative interviews with 178 healthy volunteers enrolled in various clinical trials, we found that participants focus on myriad characteristics of clinical trials when assessing risk and making enrolment decisions. These factors include the short-term and long-term effects; required medical procedures; the type of trial, including its design, therapeutic area of investigation, and dosage of the drug; the amount of compensation; and trust in the research clinic. In making determinations about the study risks, participants rely on information provided during the consent process, their own and others' experiences in clinical trials, and comparisons among studies. Our findings indicate that the informed consent process succeeds in communicating well about certain types of risk information while simultaneously creating lacunae that are problematically filled by participants through their collective experiences and assumptions about risk. We discuss the ethical implications of these findings and make recommendations for improving the consent process in healthy volunteer trials.

Serial Participation and the Ethics of Phase 1 Healthy Volunteer Research

Phase 1 healthy volunteer clinical trials-which financially compensate subjects in tests of drug toxicity levels and side effects-appear to place pressure on each joint of the moral framework justifying research. In this article, we review concerns about phase 1 trials as they have been framed in the bioethics literature, including undue inducement and coercion, unjust exploitation, and worries about compromised data validity. We then revisit these concerns in light of the lived experiences of serial participants who are income-dependent on phase 1 trials. We show how participant experiences shift attention from discrete exchanges, behaviors, and events in the research enterprise to the ongoing and dynamic patterns of serial participation in which individual decision-making is embedded in collective social and economic conditions and shaped by institutional policies. We argue in particular for the ethical significance of structurally diminished voluntariness, routine powerlessness in setting the terms of exchange, and incentive structures that may promote pharmaceutical interests but encourage phase 1 healthy volunteers to skirt important rules.

Genetic Control of Expression and Splicing in Developing Human Brain Informs Disease Mechanisms

Tissue-specific regulatory regions harbor substantial genetic risk for disease. Because brain development is a critical epoch for neuropsychiatric disease susceptibility, we characterized the genetic control of the transcriptome in 201 mid-gestational human brains, identifying 7,962 expression quantitative trait loci (eQTL) and 4,635 spliceQTL (sQTL), including several thousand prenatal-specific regulatory regions. We show that significant genetic liability for neuropsychiatric disease lies within prenatal eQTL and sQTL. Integration of eQTL and sQTL with genome-wide association studies (GWAS) via transcriptome-wide association identified dozens of novel candidate risk genes, highlighting shared and stage-specific mechanisms in schizophrenia (SCZ). Gene network analysis revealed that SCZ and autism spectrum disorder (ASD) affect distinct developmental gene co-expression modules. Yet, in each disorder, common and rare genetic variation converges within modules, which in ASD implicates superficial cortical neurons. More broadly, these data, available as a web browser and our analyses, demonstrate the genetic mechanisms by which developmental events have a widespread influence on adult anatomical and behavioral phenotypes.

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder

Most genetic risk for psychiatric disease lies in regulatory regions, implicating pathogenic dysregulation of gene expression and splicing. However, comprehensive assessments of transcriptomic organization in diseased brains are limited. In this work, we integrated genotypes and RNA sequencing in brain samples from 1695 individuals with autism spectrum disorder (ASD), schizophrenia, and bipolar disorder, as well as controls. More than 25% of the transcriptome exhibits differential splicing or expression, with isoform-level changes capturing the largest disease effects and genetic enrichments. Coexpression networks isolate disease-specific neuronal alterations, as well as microglial, astrocyte, and interferon-response modules defining previously unidentified neural-immune mechanisms. We integrated genetic and genomic data to perform a transcriptome-wide association study, prioritizing disease loci likely mediated by cis effects on brain expression. This transcriptome-wide characterization of the molecular pathology across three major psychiatric disorders provides a comprehensive resource for mechanistic insight and therapeutic development.

Advancing Ethics and Policy for Healthy-Volunteer Research through a Model-Organism Framework

Nonhuman animal research and phase I healthy-volunteer clinical trials are both critical components of testing the safety of investigational drugs as part of the development of new pharmaceuticals. In addition, these types of research share important structural features, as both take place in confinement and both use subjects that are dissimilar to the target population. By mobilizing a model-organism framework for phase I trials, we employ concepts and mechanisms typical to animal research to query gaps in the human subjects ethics and policy framework. By bringing these two research worlds together, we aim to illustrate how the model-organism framework can enhance healthy volunteers' welfare during trials, improve research oversight, and more critically assess the science value of current phase I trials.

"My Body is One of the Best Commodities": Exploring the Ethics of Commodification in Phase I Healthy Volunteer Clinical Trials

In phase I clinical trials, healthy volunteers are dosed with investigational drugs and subjected to blood draws and other bodily monitoring procedures while they are confined to clinic spaces. In exchange, they are paid. These participants are, in a direct sense, selling access to their bodies for pharmaceutical companies and their associates to run drugs through. However, commodification is rarely investigated as an ethical dimension of phase I trial participation. We address this gap in the literature by bringing the voices of phase I healthy volunteers into conversation with philosophical perspectives on body commodification. Querying the intersection of commodification and phase I clinical trials illuminates important features of healthy volunteers' experiences, disentangles commodification from a dominant narrative about exploitation, and brings focus to the question of what, if any, market norms will best protect the multiple ways in which healthy volunteers' welfare is impacted by clinical trial participation.

Healthy Volunteers' Perceptions of the Benefits of Their Participation in Phase I Clinical Trials

Other than the financial motivations for enrolling in Phase I trials, research on how healthy volunteers perceive the benefits of their trial participation is scant. Using qualitative interviews conducted with 178 U.S. healthy volunteers enrolled in Phase I trials, we investigated how participants described the benefits of their study involvement, including, but not limited to, the financial compensation, and we analyzed how these perceptions varied based on participants' sociodemographic characteristics and clinical trial history. We found that participants detailed economic, societal, and noneconomic personal benefits. We also found differences in participants' perceived benefits based on gender, age, ethnicity, educational attainment, employment status, and number of clinical trials completed. Our study indicates that many healthy volunteers believe they gain more than just the financial compensation when they accept the risks of Phase I participation.

Is Enhancement the Price of Prevention in Human Gene Editing?

New gene-editing tools challenge conventional policy proscriptions of research aimed at either human germline gene editing or human enhancement by potentially lowering technical barriers to both kinds of intervention. Some recent gene-editing reports have begun to take up the prospect of germline editing, but most experts are in broad agreement that research should prioritize medical applications over attempts to enhance human traits. However, there is little consensus about what counts as human enhancement in this context, or how to deal with the issues it flags. Moreover, several influential reports interpret medical applications to include disease prevention as well as treatment as a goal for gene-editing research. This challenges the current policy consensus because using gene editing to prevent disease would incidentally facilitate human enhancement applications in a variety of ways. If such research efforts are penalized by policy concerns about enhancement, then their preventive health benefits could be lost. To avoid being caught off guard by such challenges, science policy makers will need to think more carefully about what "prevention" might mean in the gene-editing context, and develop research governance that can anticipate and address the human enhancement concerns it will raise. To accomplish the latter, the scope of policy making will need to expand from its narrow focus on human clinical trials to engage with basic researchers driving the translational pipeline toward preventive gene editing and the science policy makers who have to address its "off-label" uses.

Healthy volunteers' perceptions of risk in US Phase I clinical trials: A mixed-methods study

BACKGROUND

There is limited research on healthy volunteers' perceptions of the risks of Phase I clinical trials. In order to contribute empirically to long-standing ethical concerns about healthy volunteers' involvement in drug development, it is crucial to assess how these participants understand trial risks. The objectives of this study were to investigate (1) participants' views of the overall risks of Phase I trials, (2) their views of the risk of personally being harmed in a trial, and (3) how risk perceptions vary across participants' clinical trial history and sociodemographic characteristics.

METHODS AND FINDINGS

We qualitatively and quantitatively analyzed semi-structured interviews conducted with 178 healthy volunteers who had participated in a diverse range of Phase I trials in the United States. Participants had collective experience in a reported 1,948 Phase I trials (mean = 10.9; median = 5), and they were interviewed as part of a longitudinal study of healthy volunteers' risk perceptions, their trial enrollment decisions, and their routine health behaviors. Participants' qualitative responses were coded, analyzed, and subsequently quantified in order to assess correlations between their risk perceptions and demographics, such as their race/ethnicity, gender, age, educational attainment, employment status, and household income. We found that healthy volunteers often viewed the overall risks of Phase I trials differently than their own personal risk of harm. The majority of our participants thought that Phase I trials were medium, high, or extremely high risk (118 of 178), but most nonetheless felt that they were personally safe from harm (97 of 178). We also found that healthy volunteers in their first year of clinical trial participation, racial and ethnic minority participants, and Hispanic participants tended to view the overall trial risks as high (respectively, Jonckheere-Terpstra, -2.433, p = 0.015; Fisher exact test, p = 0.016; Fisher exact test, p = 0.008), but these groups did not differ in regard to their perceptions of personal risk of harm (respectively, chi-squared, 3.578, p = 0.059; chi-squared, 0.845, p = 0.358; chi-squared, 1.667, p = 0.197). The main limitation of our study comes from quantitatively aggregating data from in-depth interviews, which required the research team to interpret participants' nonstandardized risk narratives.

CONCLUSIONS

Our study demonstrates that healthy volunteers are generally aware of and reflective about Phase I trial risks. The discrepancy in healthy volunteers' views of overall and personal risk sheds light on why healthy volunteers might continue to enroll in clinical trials, even when they view trials on the whole as risky.

Beyond Primates: Research Protections and Animal Moral Value

Should monkeys be used in painful and often deadly infectious disease research that may save many human lives? This is the challenging question that Anne Barnhill, Steven Joffe, and Franklin G. Miller take on in their carefully argued and compelling article "The Ethics of Infection Challenges in Primates." The authors offer a nuanced and even-handed position that takes philosophical worries about nonhuman primate moral status seriously and still appreciates the very real value of such research for human welfare. Overall, they argue for an extension and revision of the recommendations regarding chimpanzee research offered by the Institute of Medicine in 2011; the practical upshot of their argument would allow for infection challenge research for promising interventions for Ebola and Marburg virus diseases but not for smallpox or the common cold. The IOM recommendations regarding chimpanzee research put in motion an exceptionalist policy for this great ape population. Barnhill and colleagues' proposal would enlarge the scope of that exceptionalism to embrace NHPs other than great apes. But is such exceptionalism warranted? It is not obvious to me either that the more sophisticated capacities of a species as a whole give it greater ethical protections or that less intellectually or socially sophisticated animals ought to therefore receive less protection when it comes to painful experimental interventions.

ASD restricted and repetitive behaviors associated at 17q21.33: genes prioritized by expression in fetal brains

Autism spectrum disorder (ASD) is a behaviorally defined condition that manifests in infancy or early childhood as deficits in communication skills and social interactions. Often, restricted and repetitive behaviors (RRBs) accompany this disorder. ASD is polygenic and genetically complex, so we hypothesized that focusing analyses on intermediate core component phenotypes, such as RRBs, can reduce genetic heterogeneity and improve statistical power. Applying this approach, we mined Caucasian genome-wide association studies (GWAS) data from two of the largest ASD family cohorts, the Autism Genetics Resource Exchange and Autism Genome Project (AGP). Of the 12 RRBs measured by the Autism Diagnostic Interview-Revised, seven were found to be significantly familial and substantially variable, and hence, were tested for genome-wide association in 3104 ASD-affected children from 2045 families. Using a stringent significance threshold (P<7.1 × 10-9), GWAS in the AGP revealed an association between 'the degree of the repetitive use of objects or interest in parts of objects' and rs2898883 (P<6.8 × 10-9), which resides within the sixth intron of PHB. To identify the candidate target genes of the associated single-nucleotide polymorphisms at that locus, we applied chromosome conformation studies in developing human brains and implicated three additional genes: SLC35B1, CALCOCO2 and DLX3. Gene expression, brain imaging and fetal brain expression quantitative trait locus studies prioritize SLC35B1 and PHB. These analyses indicate that GWAS of single heritable features of genetically complex disorders followed by chromosome conformation studies in relevant tissues can be successful in revealing novel risk genes for single core features of ASD.

The Ethics of General Population Preventive Genomic Sequencing: Rights and Social Justice

Advances in DNA sequencing technology open new possibilities for public health genomics, especially in the form of general population preventive genomic sequencing (PGS). Such screening programs would sit at the intersection of public health and preventive health care, and thereby at once invite and resist the use of clinical ethics and public health ethics frameworks. Despite their differences, these ethics frameworks traditionally share a central concern for individual rights. We examine two putative individual rights-the right not to know, and the child's right to an open future-frequently invoked in discussions of predictive genetic testing, in order to explore their potential contribution to evaluating this new practice. Ultimately, we conclude that traditional clinical and public health ethics frameworks, and these two rights in particular, should be complemented by a social justice perspective in order adequately to characterize the ethical dimensions of general population PGS programs.

Virtue, Vice, and "Voracious" Science: How should we approach the ethics of primate research?

Philosophical approaches to animal research have typically asked whether nonhuman animals have rights that would prohibit such research or whether the benefit of such research on the whole balances out the harms to animals. The professional ethics approach instead promotes compliance with regulatory norms that aim to support science progress. In Voracious Science and Vulnerable Animals: A Primate Scientist's Ethical Journey (2016), John Gluck struggles with issues that relate to each of these ethical frameworks, but the notion of an ethical "journey" also raises questions of character that are underdeveloped in animal research ethics. This essay considers how virtue ethics may allow us to revisit the ethical significance of the research of one of Gluck's mentors, Harry F. Harlow. Harlow's torturous, but highly influential, experiments with infant macaques made him one of the most controversial figures in animal research in the second half of the 20th century. A virtue ethical approach to his case poses a unique set of questions, including: Was Harlow compassionate or cruel? Why are human-animal bonds important in ethical primate research? And what is a good life for a research monkey?

Histochemical and Immunohistochemical Evidence of a Bacterium Associated with Lesions of Epizootic Bovine Abortion

Epizootic bovine abortion (EBA), a tick-transmitted disease of pregnant cattle grazing foothill pastures, is a major cause of reproductive failure in California and adjacent states. Affected fetuses develop a chronic disease, resulting in late-term abortion or premature calving. Despite investigations spanning 50 years, to the authors' knowledge, the etiologic agent of EBA has not yet been isolated from affected fetuses or the tick vector. The diagnosis of EBA is based on gross and microscopic lesions. Recently, documentation that the etiologic agent is susceptible to antibiotics and identification of a unique 16S deltaproteobacterial rDNA gene sequence in 90% of thymus tissues from aborted fetuses have supported the role of a bacterial infection as the cause of EBA. To determine whether bacteria could be detected in the tissues, histochemical staining and immunohistochemical procedures were used on formalin-fixed, paraffin-embedded tissues. Use of a modified Steiner silver stain revealed small numbers of intracytoplasmic bacterial rods in 37 of 42 thymic samples from EBA-affected fetuses. Improved detection was achieved by use of immunohistochemical staining with serum from EBA-affected fetuses that resulted in detection of numerous bacterial rods in the cytoplasm of histiocytic cells in the thymus from all 42 EBA-affected fetuses. Immunohistochemical examination of additional tissues from 21 field and experimental EBA cases revealed positively stained intracytoplasmic bacterial rods in many organs with inflammatory lesions. Use of the modified Steiner stain and immunohistochemical staining of tissues from negative-control fetuses failed to reveal organisms. To the authors' knowledge, this is the first report to document morphologic evidence of a bacterium associated with the lesions of EBA.

Looking for Trouble: Preventive Genomic Sequencing in the General Population and the Role of Patient Choice

Advances in genomics have led to calls for developing population-based preventive genomic sequencing (PGS) programs with the goal of identifying genetic health risks in adults without known risk factors. One critical issue for minimizing the harms and maximizing the benefits of PGS is determining the kind and degree of control individuals should have over the generation, use, and handling of their genomic information. In this article we examine whether PGS programs should offer individuals the opportunity to selectively opt out of the sequencing or analysis of specific genomic conditions (the menu approach) or whether PGS should be implemented using an all-or-nothing panel approach. We conclude that any responsible scale-up of PGS will require a menu approach that may seem impractical to some, but that draws its justification from a rich mix of normative, legal, and practical considerations.

Bioethics methods in the ethical, legal, and social implications of the human genome project literature

While bioethics as a field has concerned itself with methodological issues since the early years, there has been no systematic examination of how ethics is incorporated into research on the Ethical, Legal and Social Implications (ELSI) of the Human Genome Project. Yet ELSI research may bear a particular burden of investigating and substantiating its methods given public funding, an explicitly cross-disciplinary approach, and the perceived significance of adequate responsiveness to advances in genomics. We undertook a qualitative content analysis of a sample of ELSI publications appearing between 2003 and 2008 with the aim of better understanding the methods, aims, and approaches to ethics that ELSI researchers employ. We found that the aims of ethics within ELSI are largely prescriptive and address multiple groups. We also found that the bioethics methods used in the ELSI literature are both diverse between publications and multiple within publications, but are usually not themselves discussed or employed as suggested by bioethics method proponents. Ethics in ELSI is also sometimes undistinguished from related inquiries (such as social, legal, or political investigations).

A mutant p53/let-7i-axis-regulated gene network drives cell migration, invasion and metastasis

Most p53 mutations in human cancers are missense mutations resulting in a full-length mutant p53 protein. Besides losing tumor suppressor activity, some hotspot p53 mutants gain oncogenic functions. This effect is mediated in part, through gene expression changes due to inhibition of p63 and p73 by mutant p53 at their target gene promoters. Here, we report that the tumor suppressor microRNA let-7i is downregulated by mutant p53 in multiple cell lines expressing endogenous mutant p53. In breast cancer patients, significantly decreased let-7i levels were associated with missense mutations in p53. Chromatin immunoprecipitation and promoter luciferase assays established let-7i as a transcriptional target of mutant p53 through p63. Introduction of let-7i to mutant p53 cells significantly inhibited migration, invasion and metastasis by repressing a network of oncogenes including E2F5, LIN28B, MYC and NRAS. Our findings demonstrate that repression of let-7i expression by mutant p53 has a key role in enhancing migration, invasion and metastasis.

Genomic research with the newly dead: a crossroads for ethics and policy

Recent advances in next generation sequencing along with high hopes for genomic medicine have inspired interest in genomic research with the newly dead. However, applicable law does not adequately determine ethical or policy responses to such research. In this paper we propose that such research stands at a crossroads between other more established biomedical clinical and research practices. In addressing the ethical and policy issues raised by a particular research project within our institution comparatively with these other practices, we illustrate the moral significance of paying careful heed to where one looks for guidance in responding to ethical questions raised by a novel endeavor.

Methodology of the 2009 Survey on Living with Chronic Diseases in Canada--hypertension component

INTRODUCTION

The Survey on Living with Chronic Diseases in Canada--hypertension component (SLCDC-H) is a 20-minute cross-sectional telephone survey on hypertension diagnosis and management. Sampled from the 2008 Canadian Community Health Survey (CCHS), the SLCDC-H includes Canadians (aged ≥ 20 years) with self-reported hypertension from the ten provinces.

METHODS

The questionnaire was developed by Delphi technique, externally reviewed and qualitatively tested. Statistics Canada performed sampling strategies, recruitment, data collection and processing. Proportions were weighted to represent the Canadian population, and 95% confidence intervals (CIs) were derived by bootstrap method.

RESULTS

Compared with the CCHS population reporting hypertension, the SLCDC-H sample (n = 6142) is slightly younger (SLCDC-H mean age: 61.2 years, 95% CI: 60.8-61.6; CCHS mean age: 62.2 years, 95% CI: 61.8-62.5), has more post-secondary school graduates (SLCDC-H: 52.0%, 95% CI: 49.7%-54.2%; CCHS: 47.5%, 95% CI: 46.1%-48.9%) and has fewer respondents on hypertension medication (SLCDC-H: 82.5%, 95% CI: 80.9%-84.1%; CCHS: 88.6%, 95% CI: 87.7%-89.6%).

CONCLUSION

Overall, the 2009 SLCDC-H represents its source population and provides novel, comprehensive data on the diagnosis and management of hypertension. The survey has been adapted to other chronic conditions--diabetes, asthma/chronic obstructive pulmonary disease and neurological conditions. The questionnaire is available on the Statistics Canada website; descriptive results have been disseminated by the Public Health Agency of Canada.

Funding and Forums for ELSI Research: Who (or What) is Setting the Agenda?

BACKGROUND: Discussion of the influence of money on bioethics research seems particularly salient in the context of research on the ethical, legal and social implications (ELSI) of human genomics, as this research may be financially supported by the ELSI Research Program. Empirical evidence regarding the funding of ELSI research and where such research is disseminated, in relation to the specific topics of the research and methods used, can help to further discussions regarding the appropriate influence of specific institutions and institutional contexts on ELSI and other bioethics research agendas. METHODS: We reviewed 642 ELSI publications (appearing between 2003-2008) for reported sources of funding, forum for dissemination, empirical and non-empirical methods, and topic of investigation. RESULTS: Most ELSI research is independent of direct grant-based funding sources; 66% reported no such sources of funding. The National Human Genome Research Institute (NHGRI) is the most dominant source of funding; 16% of publications acknowledged at least one source of NHGRI grant funding. Funding is acknowledged more frequently in empirical than non-empirical publications, and more frequently in publications in public health journals than in any other ELSI research dissemination forums. Dominant research topics vary by publication forum and by reported funding. CONCLUSIONS: ELSI research is surprisingly independent of direct grant-based funding, yet correlations are apparent between this type of funding and publication placement, topics addressed, and methods used, implying a not insignificant influence on ELSI research agenda-setting. However, given the relatively low percentage of publications acknowledging external grant-based funding, as well as other significant correlations between publication placement and topics addressed, additional institutional contexts, perhaps related to professional advancement or valuation, may shape research agendas in ways that potentially exceed the direct influences of grant-based funding in this area. In some cases, grant-based funding may actually counter other potentially problematic institutional influences.

Biodefense research and the U.S. regulatory structure whither nonhuman primate moral standing?

Biodefense and emerging infectious disease animal research aims to avoid or ameliorate human disease and suffering arising from the natural outbreak or intentional deployment of some of the world's most dreaded pathogens. Research to develop medical countermeasures to these diseases faces a difficult challenge since the products usually cannot be tested for efficacy in human beings. The U.S. Food and Drug Administration's Animal Rule may be increasingly used to overcome this challenge by allowing researchers to translate animal data into medical countermeasures without human subject efficacy testing. Yet the Animal Rule also has significant implications for increased intensive nonhuman primate research. We argue that despite the common belief that nonhuman primates have a fairly high level of moral standing and the protections for animals that are crucial to the U.S. regulations guiding animal research, the Animal Rule specifically and the regulations generally raise serious problems for the attribution of moral standing to nonhuman primates. We argue, however, that the burden of proof is on a position denying all moral standing to nonhuman primates and compare the implications of the U.S. regulatory structure in this regard with some recent developments in the European Union.

Perception of uncontrolled blood pressure and behaviours to improve blood pressure: findings from the 2009 Survey on Living with Chronic Diseases in Canada

Individuals with hypertension should lower and maintain their blood pressure levels through lifestyle modification and/or pharmacotherapy. To determine whether perception of blood pressure control is related to behaviours and intentions for improving blood pressure, data from 6142 Canadians age 20+ years with self-reported hypertension were analysed. Relationships between perception of control, current behaviours for blood pressure control and intentions to improve these behaviours were examined. Although individuals who reported uncontrolled blood pressure were equally likely to report engaging in lifestyle behaviours for blood pressure control, they were more likely to indicate an intention to improve their health, compared with those who reported well-controlled/low blood pressure. These individuals were also less likely to report having enough information to control their blood pressure. In addition, they were less likely to report having been advised to take antihypertensive medication, and to be taking and adhering to medications. Individuals who perceive their blood pressure as uncontrolled have intentions to make health-enhancing changes but may lack the information to do so. The study highlights the potential need for programmes/services to help those with uncontrolled blood pressure make lifestyle changes and/or take appropriate medication.

Enhanced nutrient removal MBR system with chemical addition for low effluent TP

A pilot study was conducted to test an membrane bioreactor (MBR) process for combined biological and chemical P removal to achieve a very low effluent total phosphorus (TP) concentration of 0.025 mg P/L. With the data from the pilot test, a simulation study was performed to demonstrate that: (1) the pilot system behaviour (effluent quality, MLSS, etc.) can be modelled accurately with an activated sludge model combined with a chemical precipitation model; and (2) with the calibrated model, simulation scenarios can be performed to further understand the pilot MBR process, and provide information for optimizing design and operation when applied at full-scale. Results from the pilot test indicated that the system could achieve very low effluent TP concentration through biological P removal with a limited chemical addition, and chemical addition to remove P to very low level did not affect other biological processes, i.e., organic and nitrogen removal. Simulation studies indicate that the process behaviour can be modelled accurately with an activated sludge model combined with a chemical precipitation model, and the calibrated model can be used to provide information to optimize system design and operation, e.g., chemical addition control under dynamic loading conditions is important for maintaining biological P removal.