Omics Approaches to Investigate the Pathogenesis of Suicide.

Suicide is the second leading cause of death in U.S. adolescents and young adults and is generally associated with a psychiatric disorder. Suicidal behavior has a complex etiology and pathogenesis. Moderate heritability suggests genetic causes. Associations between childhood and recent life adversity indicate contributions from epigenetic factors. Genomic contributions to suicide pathogenesis remain largely unknown. This article is based on a workshop held to design strategies to identify molecular drivers of suicide neurobiology that would be putative new treatment targets. The panel determined that while bulk tissue studies provide comprehensive information, single-nucleus approaches that identify cell type-specific changes are needed. While single-nuclei techniques lack information on cytoplasm, processes, spines, and synapses, spatial multiomic technologies on intact tissue detect cell alterations specific to brain tissue layers and subregions. Because suicide has genetic and environmental drivers, multiomic approaches that combine cell type-specific epigenome, transcriptome, and proteome provide a more complete picture of pathogenesis. To determine the direction of effect of suicide risk gene variants on RNA and protein expression and how these interact with epigenetic marks, single-nuclei and spatial multiomics quantitative trait loci maps should be integrated with whole-genome sequencing and genome-wide association databases. The workshop concluded with a recommendation for the formation of an international suicide biology consortium that will bring together brain banks and investigators with expertise in cutting-edge omics technologies to delineate the biology of suicide and identify novel potential treatment targets to be tested in cellular and animal models for drug and biomarker discovery to guide suicide prevention.

Ultra-secure storage and analysis of genetic data for the advancement of precision medicine.

Cloud computing provides the opportunity to store the ever-growing genotype-phenotype data sets needed to achieve the full potential of precision medicine. However, due to the sensitive nature of this data and the patchwork of data privacy laws across states and countries, additional security protections are proving necessary to ensure data privacy and security. Here we present SQUiD, a secure queryable database for storing and analyzing genotype-phenotype data. With SQUiD, genotype-phenotype data can be stored in a low-security, low-cost public cloud in the encrypted form, which researchers can securely query without the public cloud ever being able to decrypt the data. We demonstrate the usability of SQUiD by replicating various commonly used calculations such as polygenic risk scores, cohort creation for GWAS, MAF filtering, and patient similarity analysis both on synthetic and UK Biobank data. Our work represents a new and scalable platform enabling the realization of precision medicine without security and privacy concerns.

Defining the Core Skills and Activities of the Attending Physician in Post-Acute and Long-Term Care.

The American Board of Post-Acute and Long-Term Care Medicine (ABPLM) contracted with a psychometric firm to perform a 3-phase Job Analysis following best practices. Literature was reviewed, a task force of subject matter experts was convened, a survey was developed and sent via Survey Monkey to attending physicians practicing in post-acute and long-term care settings (PALTC). The task force refined a comprehensive list of the tasks, knowledge, and medical knowledge needed in the role of attending physician in PALTC. These items were written as statements and edited until consensus was reached on their accuracy, conciseness, and lack of overlap. Task statements described distinct, identifiable, and specific practice-related activities relevant across multiple care settings. Knowledge statements described previously acquired information considered necessary to effectively perform such tasks. The survey consisted of 260 items, including 21 demographic questions, 115 task statements, 73 knowledge statements, and 72 medical knowledge statements. The survey was disseminated via e-mail invitations to Society for Post-Acute and Long-Term Care (AMDA) members and through an online link available through ABPLM's website. A total of 389 respondents participated. Survey data were analyzed with statistical analysis software SPSS. For each task and knowledge statement, an Overall Task Rating and Knowledge Rating were developed by combining the importance rating weighted at 65% and (for task) the frequency rating or (for knowledge) the cognitive level weighted at 35%. One task statement and 1 medical knowledge statement had a mean importance rating lower than 2.5 and were dropped from further review, resulting in a final count of 114 task, 73 knowledge, and 71 medical knowledge statements (258 total). The results of this Job Analysis highlight the unique and specific nature of medical care provided by attending physicians across a range of PALTC settings. These findings lay a foundation for Focused Practice Designation or Subspecialty in PALTC and changes in practice and policy.

The epidemiology of psychiatric disorders in Africa: a scoping review.

This scoping review of population-based epidemiological studies was done to provide background information on the prevalences and distribution of psychiatric disorders in Africa for calls to broaden diversity in psychiatric genetic studies. We searched PubMed, EMBASE, and Web of Science to retrieve relevant literature in English, French, and Portuguese from Jan 1, 1984, to Aug 18, 2020. In 36 studies from 12 African countries, the lifetime prevalence ranged from 3·3% to 9·8% for mood disorders, from 5·7% to 15·8% for anxiety disorders, from 3·7% to 13·3% for substance use disorders, and from 1·0% to 4·4% for psychotic disorders. Although the prevalence of mood and anxiety disorders appears to be lower than that observed in research outside the continent, we identified similar distributions by gender, although not by age or urbanicity. This review reveals gaps in epidemiological research on psychiatric disorders and opportunities to leverage existing epidemiological and genetic research within Africa to advance our understanding of psychiatric disorders. Studies that are methodologically comparable but diverse in geographical context are needed to advance psychiatric epidemiology and provide a foundation for understanding environmental risk in genetic studies of diverse populations globally.

The impact of ventilation during postharvest ripening on the development of flavour compounds and sensory quality of mangoes (Mangifera indica L.) cv. Kent.

The postharvest ripening behaviour of mangoes (Mangifera indica L.) and particularly the development of colour, volatiles, sensory properties and texture, were investigated. Mangoes cv. Kent from Peru were arranged in a postharvest ripening chamber in two different ways enabling different ventilation of the fruits. Fruit properties were investigated in comparison to reference fruits after postharvest ripening for 78 h. Volatile compounds were analysed by HS-SPME GC-MS; an expert panel performed sensory analysis using descriptive methods. The arrangement of the mangoes significantly impacted the ripening procedures. Dense fruit arrangement induced a degradation of terpenes, a reduced formation of reaction products from the lipoxygenase pathway and less pronounced fruitiness and mango flavour. Principal component analysis based on volatile compounds and sensory properties showed a high correlation with the position in the ripening chamber. These data demonstrate the urgent need for further investigations of the postharvest ripening processes to increase mango quality.

Schizophrenia research in the era of Team Science and big data.

The last decade has provided new insights into the genetic architecture of schizophrenia. For the first time researchers have identified genetic factors conferring risk that can be mapped to tissue and cell specific perturbations of the molecular machinery underlying disease processes. However, it has also become clear that attempts to gain mechanistic insights into disease processes that span multiple levels of biological complexity, from genes to cells to circuits to behaviors, are inherently difficult and will require interdisciplinary efforts. Here we discuss the opportunities and pitfalls of developing causal models of SCZ that will lead to novel treatments and prevention strategies. We make the case that integrated large-scale Team Science efforts will be necessary to achieve this goal and that a systems level approach that includes genetics and integrative modelling is needed.

A framework for the investigation of rare genetic disorders in neuropsychiatry.

De novo and inherited rare genetic disorders (RGDs) are a major cause of human morbidity, frequently involving neuropsychiatric symptoms. Recent advances in genomic technologies and data sharing have revolutionized the identification and diagnosis of RGDs, presenting an opportunity to elucidate the mechanisms underlying neuropsychiatric disorders by investigating the pathophysiology of high-penetrance genetic risk factors. Here we seek out the best path forward for achieving these goals. We think future research will require consistent approaches across multiple RGDs and developmental stages, involving both the characterization of shared neuropsychiatric dimensions in humans and the identification of neurobiological commonalities in model systems. A coordinated and concerted effort across patients, families, researchers, clinicians and institutions, including rapid and broad sharing of data, is now needed to translate these discoveries into urgently needed therapies.

Arsenic Trioxide Impacts Viral Latency and Delays Viral Rebound after Termination of ART in Chronically SIV-Infected Macaques.

The latent viral reservoir is the source of viral rebound after interruption of antiretroviral therapy (ART) and is the major obstacle in eradicating the latent human immunodeficiency virus-1 (HIV-1). In this study, arsenic class of mineral, arsenic trioxide, clinically approved for treating acute promyelocytic leukemia, is demonstrated to reactivate latent provirus in CD4+ T cells from HIV-1 patients and Simian immunodeficiency virus (SIV)-infected macaques, without significant systemic T cell activation and inflammatory responses. In a proof-of-concept study using chronically SIVmac239-infected macaques, arsenic trioxide combined with ART delays viral rebound after ART termination, reduces the integrated SIV DNA copies in CD4+ T cells, and restores CD4+ T cells counts in vivo. Most importantly, half of arsenic trioxide-treated macaques show no detectable viral rebound in the plasma for at least 80 days after ART discontinuation. Mechanistically, the study reveals that CD4 receptors and CCR5 co-receptors of CD4+ T cells are significantly downregulated by arsenic trioxide treatment, which reduces susceptibility to infection after provirus reactivation. Furthermore, an increase in SIV-specific immune responses after arsenic trioxide treatment may contribute to suppression of viral rebound. This work suggests that arsenic trioxide in combination with ART is a novel regimen in down-sizing or even eradicating latent HIV-1 reservoir.

From genetics to biology: advancing mental health research in the Genomics ERA.

The Genomics Workgroup of the National Advisory Mental Health Council (NAMHC) recently issued a set of recommendations for advancing the NIMH psychiatric genetics research program and prioritizing subsequent follow-up studies. The report emphasized the primacy of rigorous statistical support from properly designed, well-powered studies for pursuing genetic variants robustly associated with disease. Here we discuss the major points NIMH program staff consider when assessing research applications based on common and rare variants, as well as genetic syndromes, associated with psychiatric disorders. These are broad guiding principles for investigators to consider prior to submission of their applications. NIMH staff weigh these points in the context of reviewer comments, the existing literature, and current investments in related projects. Following the recommendations of the NAMHC, statistical strength and robustness of the underlying genetic discovery weighs heavily in our funding considerations as does the suitability of the proposed experimental approach. We specifically address our evaluation of applications motivated in whole, or in part, by an association between human DNA sequence variation and a disease or trait relevant to the mission of the NIMH.

The Open Translational Science in Schizophrenia (OPTICS) project: an open-science project bringing together Janssen clinical trial and NIMH data.

Clinical trial data are the gold standard for evaluating pharmaceutical safety and efficacy. There is an ethical and scientific imperative for transparency and data sharing to confirm published results and generate new knowledge. The Open Translational Science in Schizophrenia (OPTICS) Project was an open-science initiative aggregating Janssen clinical trial and NIH/NIMH data from real-world studies and trials in schizophrenia. The project aims were to show the value of using shared data to examine: therapeutic safety and efficacy; disease etiologies and course; and methods development. The success of project investigators was due to collaboration from project applications through analyses, with support from the Harvard Catalyst. Project work was independent of Janssen; all intellectual property was dedicated to the public. Efforts such as this are necessary to gain deeper insights into the biology of disease, foster collaboration, and to achieve the goal of developing better treatments, reducing the overall public health burden of devastating brain diseases.

Publisher Correction: Whole genome sequencing in psychiatric disorders: the WGSPD consortium.

In the version of this article initially published, the consortium authorship and corresponding authors were not presented correctly. In the PDF and print versions, the Whole Genome Sequencing for Psychiatric Disorders (WGSPD) consortium was missing from the author list at the beginning of the paper, where it should have appeared as the seventh author; it was present in the author list at the end of the paper, but the footnote directing readers to the Supplementary Note for a list of members was missing. In the HTML version, the consortium was listed as the last author instead of as the seventh, and the line directing readers to the Supplementary Note for a list of members appeared at the end of the paper under Author Information but not in association with the consortium name itself. Also, this line stated that both member names and affiliations could be found in the Supplementary Note; in fact, only names are given. In all versions of the paper, the corresponding author symbols were attached to A. Jeremy Willsey, Steven E. Hyman, Anjene M. Addington and Thomas Lehner; they should have been attached, respectively, to Steven E. Hyman, Anjene M. Addington, Thomas Lehner and Nelson B. Freimer. As a result of this shift, the respective contact links in the HTML version did not lead to the indicated individuals. The errors have been corrected in the HTML and PDF versions of the article.

Gene Discovery for Complex Traits: Lessons from Africa.

The genetics of African populations reveals an otherwise "missing layer" of human variation that arose between 100,000 and 5 million years ago. Both the vast number of these ancient variants and the selective pressures they survived yield insights into genes responsible for complex traits in all populations.

A novel mechanism linking memory stem cells with innate immunity in protection against HIV-1 infection.

HIV infection affects 37 million people and about 1.7 million are infected annually. Among the phase III clinical trials only the RV144 vaccine trial elicited significant protection against HIV-1 acquisition, but the efficacy and immune memory were inadequate. To boost these vaccine functions we studied T stem cell memory (TSCM) and innate immunity. TSCM cells were identified by phenotypic markers of CD4+ T cells and they were further characterised into 4 subsets. These expressed the common IL-2/IL-15 receptors and another subset of APOBEC3G anti-viral restriction factors, both of which were upregulated. In contrast, CD4+ TSCM cells expressing CCR5 co-receptors and α4ß7 mucosal homing integrins were decreased. A parallel increase in CD4+ T cells was recorded with IL-15 receptors, APOBEC3G and CC chemokines, the latter downmodulating CCR5 molecules. We suggest a novel mechanism of dual memory stem cells; the established sequential memory pathway, TSCM →Central →Effector memory CD4+ T cells and the innate pathway consisting of the 4 subsets of TSCM. Both pathways are likely to be activated by endogenous HSP70. The TSCM memory stem cell and innate immunity pathways have to be optimised to boost the efficacy and immune memory of protection against HIV-1 in the clinical trial.

Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network.

Neuropsychiatric disorders have a complex genetic architecture. Human genetic population-based studies have identified numerous heritable sequence and structural genomic variants associated with susceptibility to neuropsychiatric disease. However, these germline variants do not fully account for disease risk. During brain development, progenitor cells undergo billions of cell divisions to generate the ~80 billion neurons in the brain. The failure to accurately repair DNA damage arising during replication, transcription, and cellular metabolism amid this dramatic cellular expansion can lead to somatic mutations. Somatic mutations that alter subsets of neuronal transcriptomes and proteomes can, in turn, affect cell proliferation and survival and lead to neurodevelopmental disorders. The long life span of individual neurons and the direct relationship between neural circuits and behavior suggest that somatic mutations in small populations of neurons can significantly affect individual neurodevelopment. The Brain Somatic Mosaicism Network has been founded to study somatic mosaicism both in neurotypical human brains and in the context of complex neuropsychiatric disorders.

The Effect of Cellular Stress on T and B Cell Memory Pathways in Immunized and Unimmunized BALB/c Mice.

Immunological memory is a fundamental function of vaccination. The antigenic breakdown products of the vaccine may not persist, and undefined tonic stimulation has been proposed to maintain the specific memory. We have suggested that cellular stress agents to which the immune cells are constantly exposed may be responsible for tonic stimulation. Here we have studied four stress agents: sodium arsenite, an oxidative agent; Gramicidin, eliciting K(+) efflux and calcium influx; dithiocarbamate, a metal ionophore; and aluminum hydroxide (alum), an immunological adjuvant. The aims of this study are to extend these investigations to T and B cell responses of unimmunized and ovalbumin (OVA)-immunized BALB/c mice, and furthermore, to ascertain whether stress is involved in optimal expression of memory B cells, as demonstrated in CD4(+) T cells. Examination of the homeostatic pathway defined by IL-15/IL-15R (IL-15 receptor) interaction and the inflammasome pathway defined by the IL-1-IL-1R interaction between dendritic cells (DC) and CD4(+) T cells suggests that both pathways are involved in the development of optimal expression of CD4(+)CD45RO(+) memory T cells in unimmunized and OVA-immunized BALB/c mice. Furthermore, significant direct correlation was found between CD4(+)CD44(+) memory T cells and both IL-15 of the homeostatic and IL-1ß of the inflammasome pathways. However, CD19(+)CD27(+) memory B cells in vivo seem to utilize only the IL-15/IL-15R homeostatic pathway, although the proliferative responses are enhanced by the stress agents. Altogether, stress agents may up-regulate unimmunized and OVA-immunized CD4(+)CD44(+) memory T cells by the homeostatic and inflammasome pathways. However, the CD19(+)CD27(+) memory B cells utilize only the homeostatic pathway.

Stress-activated Dendritic Cells (DC) Induce Dual Interleukin (IL)-15- and IL1ß-mediated Pathways, Which May Elicit CD4+ Memory T Cells and Interferon (IFN)-stimulated Genes.

The prevailing evidence suggests that immunological memory does not require antigenic re-stimulation but is maintained by low level tonic stimulation. We examined the hypothesis that stress agents contribute to tonic cellular activation and maintain immunological memory. Stimulation of monocyte-derived dendritic cells (DC) with stress agents elicits reactive oxygen species and HSP70. NFκB is activated, which up-regulates membrane-associated (ma) IL-15, caspase-1 and IL-1ß. Co-culture of stress-treated DC with mononuclear cells activates IL-15 and IL-1ß receptors on CD4(+) T cells, eliciting CD40L, proliferation, and up-regulation of CD45RO(+) memory T cells. The transcription factors Tbet(high) and RORγt are up-regulated, whereas FoxP3 is down-regulated, resulting in enhanced Th1 and Th17 expression and the corresponding cytokines. The interaction between maIL-15 expressed by DC and IL-15R on CD4(+) T cells results in one pathway and the corresponding cells expressing IL-1ß and IL1ßR as a second pathway. Importantly, inhibition studies with IL-15 antibodies and IL-1ßR inhibitor suggest that both pathways may be required for optimum CD4(+) CD45RO(+) memory T cell expression. Type 1 IFN expression in splenic CD11c DC of stress-treated mice demonstrated a significant increase of IFN-α in CD11c CD317(+) and CD8α(+) DC. Analysis of RNA in human CD4(+) memory T cells showed up-regulation of type 1 IFN-stimulated genes and inhibition with histone methyltransferase inhibitor. We suggest the paradigm that stress-induced tonic stimulation might be responsible for the robust persistence of the immune response in vaccination and that epigenetic changes are involved in maintaining CD4(+) T cell memory.

Comorbidity of physical and mental disorders in the neurodevelopmental genomics cohort study.

OBJECTIVES: To examine patterns of associations between a broad range of mental and physical conditions by using a large, systematically obtained pediatric registry. METHODS: The sample included 9014 youth ages 8 to 21 years (4349 males and 4665 females; 3585 aged <13 years, 3678 aged 13 to 18 years, and 1751 aged 19 to 21 years) from the Philadelphia Neurodevelopmental Cohort identified through pediatric clinics at the Children's Hospital of Philadelphia health care network by the Center for Applied Genomics. Measures were as follows: physical condition based on electronic medical records and interview data on 42 physical conditions of 14 organ systems/specialties and mental disorders based on an abbreviated version of the structured Kiddie-Schedule for Affective Disorders and Schizophrenia psychiatric diagnostic interview. RESULTS: There was a direct association between the severity of the physical condition and most classes of mental disorders, as well as with functional impairment. Models adjusted for sociodemographic correlates, other physical and mental disorders, and false discovery and revealed broad patterns of associations between neurodevelopmental disorders with behavior disorders (odds ratio [OR]: 1.5; 95% confidence interval [CI]: 1.3-1.8; P < .004) and attention-deficit/hyperactivity disorder (OR: 3.1; 95% CI: 2.7-3.6; P < .0001), and neurologic/central nervous system conditions (OR: 1.3; 95% CI: 1.1-1.9; P < .05) with mood disorders and attention-deficit/hyperactivity disorder (OR: 1.3; 95% CI: 1.1-1.5; P < .001), and autoimmune/inflammatory conditions with mood disorders (OR: 1.4; 95% CI: 1.1-1.8, P < .05). CONCLUSIONS: Findings show the strong overlap between physical and mental conditions and their impact on severity and functional impairment in youth. Specific patterns of comorbidity have important implications for etiology. Prospective tracking of cross-disorder morbidity will be important to establish more effective mechanisms for prevention and intervention.