Commentary on the Special Issue on Posttraumatic Stress and Suicide: Recognizing that simple things save lives.

This article offers commentary on the special issue of the Journal of Traumatic Stress dedicated to posttraumatic stress and suicide, with a specific focus on practical recommendations that can be integrated into day-to-day clinical practice. Given the complexity of the myriad associations among posttraumatic stress symptoms, the nature of trauma, and suicidality demonstrated in the articles in this issue, it is important for practitioners to utilize evidence-based approaches to clinical practice in order to be effective. The articles in this special issue offer findings that do just that, providing a foundation rich in practical applications to clinical work, including an understanding of potential mechanisms of action and related targeted interventions.

A study on the use of thermal imaging as a diagnostic tool for the detection of digital dermatitis in dairy cattle.

Our aims were to (1) determine how interdigital skin temperature (IST), measured using infrared thermography, was associated with different stages of digital dermatitis (DD) lesions and (2) develop and validate models that can use IST measurements to identify cows with an active DD lesion. Between March 2019 and March 2020, infrared thermographic images of hind feet were taken from 2,334 Holstein cows across 4 farms. We recorded the maximum temperature reading from infrared thermographic images of the interdigital skin between the heel bulbs on the hind feet. Pregnant animals were enrolled approximately 1 to 2 mo precalving, reassessed 1 wk after calving, and again at approximately 50 to 100 d postpartum. At these time points, IST and the clinical stage of DD (M-stage scoring system: M1-M4.1) were recorded in addition to other data such as the ambient environmental temperature, height, body condition score, parity, and the presence of other foot lesions. A mixed effect linear regression model with IST as the dependent variable was fitted. Interdigital skin temperature was associated with DD lesions; compared to healthy feet, IST was highest in feet with M2 lesions, followed by M1 and M4.1 lesions. Subsequently, the capacity of IST measurements to detect the presence or absence of an active DD lesion (M1, M2, or M4.1) was explored by fitting logistic regression models, which were tested using 10-fold validation. A mixed effect logistic regression model with the presence of active DD as the dependent variable was fitted first. The average area under the curve for this model was 0.80 when its ability to detect presence of active DD was tested on 10% of the data that were not used for the model's training; an average sensitivity of 0.77 and an average specificity of 0.67 was achieved. This model was then restricted so that only explanatory variables that could be practically recorded in a nonresearch, external setting were included. Validation of this model demonstrated an average area under the curve of 0.78, a sensitivity of 0.88, and a specificity of 0.66 for 1 of the time points (precalving). Lower sensitivity and specificity were achieved for the other 2 time points. Our study adds further evidence to the relationship between DD and foot skin temperature using a large data set with multiple measurements per animal. Additionally, we highlight the potential for infrared thermography to be used for routine on-farm diagnosis of active DD lesions.

Human Structural Variation: Mechanisms of Chromosome Rearrangements.

Chromosome structural variation (SV) is a normal part of variation in the human genome, but some classes of SV can cause neurodevelopmental disorders. Analysis of the DNA sequence at SV breakpoints can reveal mutational mechanisms and risk factors for chromosome rearrangement. Large-scale SV breakpoint studies have become possible recently owing to advances in next-generation sequencing (NGS) including whole-genome sequencing (WGS). These findings have shed light on complex forms of SV such as triplications, inverted duplications, insertional translocations, and chromothripsis. Sequence-level breakpoint data resolve SV structure and determine how genes are disrupted, fused, and/or misregulated by breakpoints. Recent improvements in breakpoint sequencing have also revealed non-allelic homologous recombination (NAHR) between paralogous long interspersed nuclear element (LINE) or human endogenous retrovirus (HERV) repeats as a cause of deletions, duplications, and translocations. This review covers the genomic organization of simple and complex constitutional SVs, as well as the molecular mechanisms of their formation.

Next-generation sequencing of duplication CNVs reveals that most are tandem and some create fusion genes at breakpoints.

Interpreting the genomic and phenotypic consequences of copy-number variation (CNV) is essential to understanding the etiology of genetic disorders. Whereas deletion CNVs lead obviously to haploinsufficiency, duplications might cause disease through triplosensitivity, gene disruption, or gene fusion at breakpoints. The mutational spectrum of duplications has been studied at certain loci, and in some cases these copy-number gains are complex chromosome rearrangements involving triplications and/or inversions. However, the organization of clinically relevant duplications throughout the genome has yet to be investigated on a large scale. Here we fine-mapped 184 germline duplications (14.7 kb-25.3 Mb; median 532 kb) ascertained from individuals referred for diagnostic cytogenetics testing. We performed next-generation sequencing (NGS) and whole-genome sequencing (WGS) to sequence 130 breakpoints from 112 subjects with 119 CNVs and found that most (83%) were tandem duplications in direct orientation. The remainder were triplications embedded within duplications (8.4%), adjacent duplications (4.2%), insertional translocations (2.5%), or other complex rearrangements (1.7%). Moreover, we predicted six in-frame fusion genes at sequenced duplication breakpoints; four gene fusions were formed by tandem duplications, one by two interconnected duplications, and one by duplication inserted at another locus. These unique fusion genes could be related to clinical phenotypes and warrant further study. Although most duplications are positioned head-to-tail adjacent to the original locus, those that are inverted, triplicated, or inserted can disrupt or fuse genes in a manner that might not be predicted by conventional copy-number assays. Therefore, interpreting the genetic consequences of duplication CNVs requires breakpoint-level analysis.

Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis.

Unbalanced translocations are a relatively common type of copy number variation and a major contributor to neurodevelopmental disorders. We analyzed the breakpoints of 57 unique unbalanced translocations to investigate the mechanisms of how they form. Fifty-one are simple unbalanced translocations between two different chromosome ends, and six rearrangements have more than three breakpoints involving two to five chromosomes. Sequencing 37 breakpoint junctions revealed that simple translocations have between 0 and 4 base pairs (bp) of microhomology (n = 26), short inserted sequences (n = 8), or paralogous repeats (n = 3) at the junctions, indicating that translocations do not arise primarily from nonallelic homologous recombination but instead form most often via nonhomologous end joining or microhomology-mediated break-induced replication. Three simple translocations fuse genes that are predicted to produce in-frame transcripts of SIRPG-WWOX, SMOC2-PROX1, and PIEZO2-MTA1, which may lead to gain of function. Three complex translocations have inversions, insertions, and multiple breakpoint junctions between only two chromosomes. Whole-genome sequencing and fluorescence in situ hybridization analysis of two de novo translocations revealed at least 18 and 33 breakpoints involving five different chromosomes. Breakpoint sequencing of one maternally inherited translocation involving four chromosomes uncovered multiple breakpoints with inversions and insertions. All of these breakpoint junctions had 0-4 bp of microhomology consistent with chromothripsis, and both de novo events occurred on paternal alleles. Together with other studies, these data suggest that germline chromothripsis arises in the paternal genome and may be transmitted maternally. Breakpoint sequencing of our large collection of chromosome rearrangements provides a comprehensive analysis of the molecular mechanisms behind translocation formation.

Monosomy X rescue explains discordant NIPT results and leads to uniparental isodisomy.

Noninvasive prenatal testing accurately detects trisomy for chromosomes 13, 21, and 18, but has a significantly lower positive predictive value for monosomy X. Discordant monosomy X results are often assumed to be due to maternal mosaicism, usually without maternal follow-up. We describe a case of monosomy X-positive noninvasive prenatal testing that was discordant with the 46,XX results from amniocentesis and postnatal testing. This monosomy X pregnancy doubled the single X chromosome, leading to 45,X/46,XX mosaicism in the placenta and uniparental isodisomy X in the amniotic fluid. Thus, at least some discordant monosomy X results are due to true mosaicism in the pregnancy, which has important implications for clinical outcome and patient counseling.

Large inverted duplications in the human genome form via a fold-back mechanism.

Inverted duplications are a common type of copy number variation (CNV) in germline and somatic genomes. Large duplications that include many genes can lead to both neurodevelopmental phenotypes in children and gene amplifications in tumors. There are several models for inverted duplication formation, most of which include a dicentric chromosome intermediate followed by breakage-fusion-bridge (BFB) cycles, but the mechanisms that give rise to the inverted dicentric chromosome in most inverted duplications remain unknown. Here we have combined high-resolution array CGH, custom sequence capture, next-generation sequencing, and long-range PCR to analyze the breakpoints of 50 nonrecurrent inverted duplications in patients with intellectual disability, autism, and congenital anomalies. For half of the rearrangements in our study, we sequenced at least one breakpoint junction. Sequence analysis of breakpoint junctions reveals a normal-copy disomic spacer between inverted and non-inverted copies of the duplication. Further, short inverted sequences are present at the boundary of the disomic spacer and the inverted duplication. These data support a mechanism of inverted duplication formation whereby a chromosome with a double-strand break intrastrand pairs with itself to form a "fold-back" intermediate that, after DNA replication, produces a dicentric inverted chromosome with a disomic spacer corresponding to the site of the fold-back loop. This process can lead to inverted duplications adjacent to terminal deletions, inverted duplications juxtaposed to translocations, and inverted duplication ring chromosomes.

Mouse model implicates GNB3 duplication in a childhood obesity syndrome.

Obesity is a highly heritable condition and a risk factor for other diseases, including type 2 diabetes, cardiovascular disease, hypertension, and cancer. Recently, genomic copy number variation (CNV) has been implicated in cases of early onset obesity that may be comorbid with intellectual disability. Here, we describe a recurrent CNV that causes a syndrome associated with intellectual disability, seizures, macrocephaly, and obesity. This unbalanced chromosome translocation leads to duplication of over 100 genes on chromosome 12, including the obesity candidate gene G protein ß3 (GNB3). We generated a transgenic mouse model that carries an extra copy of GNB3, weighs significantly more than its wild-type littermates, and has excess intraabdominal fat accumulation. GNB3 is highly expressed in the brain, consistent with G-protein signaling involved in satiety and/or metabolism. These functional data connect GNB3 duplication and overexpression to elevated body mass index and provide evidence for a genetic syndrome caused by a recurrent CNV.

Recurrent deletions and duplications of chromosome 2q11.2 and 2q13 are associated with variable outcomes.

Copy number variation (CNV) in the long arm of chromosome 2 has been implicated in developmental delay (DD), intellectual disability (ID), autism spectrum disorder (ASD), congenital anomalies, and psychiatric disorders. Here we describe 14 new subjects with recurrent deletions and duplications of chromosome 2q11.2, 2q13, and 2q11.2-2q13. Though diverse phenotypes are associated with these CNVs, some common features have emerged. Subjects with 2q11.2 deletions often exhibit DD, speech delay, and attention deficit hyperactivity disorder (ADHD), whereas those with 2q11.2 duplications have DD, gastroesophageal reflux, and short stature. Congenital heart defects (CHDs), hypotonia, dysmorphic features, and abnormal head size are common in those with 2q13 deletions. In the 2q13 duplication cohort, we report dysmorphic features, DD, and abnormal head size. Two individuals with large duplications spanning 2q11.2-2q13 have dysmorphic features, hypotonia, and DD. This compilation of clinical features associated with 2q CNVs provides information that will be useful for healthcare providers and for families of affected children. However, the reduced penetrance and variable expressivity associated with these recurrent CNVs makes genetic counseling and prediction of outcomes challenging. © 2015 Wiley Periodicals, Inc.

DEPRESSION MEDIATES THE RELATION OF INSOMNIA SEVERITY WITH SUICIDE RISK IN THREE CLINICAL SAMPLES OF U.S. MILITARY PERSONNEL.

BACKGROUND: A growing body of empirical research suggests insomnia severity is directly related to suicide ideation, attempts, and death in nonmilitary samples, even when controlling for depression and other suicide risk factors. Few studies have explored this relationship in U.S. military personnel. METHODS: The present study entailed secondary data analyses examining the associations of insomnia severity with suicide ideation and attempts in three clinical samples: Air Force psychiatric outpatients (n = 158), recently discharged Army psychiatric inpatients (n = 168), and Army psychiatric outpatients (n = 54). Participants completed the Beck Scale for Suicide Ideation, the Beck Depression Inventory-II or Patient Health Questionnaire-9, the Insomnia Severity Index, and the Posttraumatic Stress Disorder Checklist at baseline; two samples also completed these measures during follow-up. RESULTS: Sleep disturbance was associated with concurrent (ß's > 0.21; P's < 0.059) and prospective (ß's > 0.39; P's < 0.001) suicide ideation in all three samples. When adjusting for age, gender, depression, and posttraumatic stress, insomnia severity was no longer directly associated with suicide ideation either concurrently (ß's < 0.19; P's > 0.200) or prospectively (ß's < 0.26; P's > 0.063), but depression was (ß's > 0.22; P's < 0.012). Results of a latent difference score mediation model indicated that depression mediated the relation of insomnia severity with suicide ideation. CONCLUSIONS: Across three clinical samples of military personnel, depression explained the relationship between insomnia severity and suicide risk.

An investigation of the interactive effects of the capability for suicide and acute agitation on suicidality in a military sample.

BACKGROUND: According to the interpersonal theory of suicide (1, 2), the difficulties inherently associated with death by suicide deter many individuals from engaging in suicidal behavior. Consistent with the notion that suicide is fearsome, acute states of heightened arousal are commonly observed in individuals immediately prior to lethal and near-lethal suicidal behavior. We suggest that among individuals who possess elevated levels of the capability for suicide, the heightened state of arousal experienced during periods of acute agitation may facilitate suicidal behavior in part because it would provide the necessary energy to approach a potentially lethal stimulus. Among individuals who are low on capability, the arousal experienced during agitation may result in further avoidance. METHODS: In the present project we examine how acute agitation may interact with the capability for suicide to predict suicidality in a large military sample (n = 1,208) using hierarchical multiple regression. RESULTS: Results were in line with a priori hypotheses: among individuals high on capability, as agitation increases, suicidality increases whereas as agitation increases among individuals low on capability, suicidality decreases. Results held beyond the effects of thwarted belongingness, perceived burdensomeness, and suicidal cognitions. CONCLUSIONS: Beyond further substantiating the link between agitation and suicide, findings of the present study provide evidence for the construct validity of the acquired capability as well as offer initial evidence for moderating role of capability on the effect of agitation on suicide. Limitations of the current study highlight a need for future research that improves upon the techniques used in the present study. Implications for science and practice are discussed.

Nonsuicidal self-injury as a prospective predictor of suicide attempts in a clinical sample of military personnel.

BACKGROUND: Nonsuicidal self-injury (NSSI) is a risk factor for suicide attempts, but it has received little attention in military populations, for whom suicide rates have doubled over the past decade. In the current study, the relationship of NSSI with future suicide attempts was prospectively examined in a sample of active duty Soldiers receiving outpatient psychiatric treatment for suicide ideation and/or a recent suicide attempt. METHODS: Data were collected as part of a two-year prospective study of 152 active duty Soldiers (87% male, 71% Caucasian, mean age=27.53) in outpatient mental health care who reported current suicide ideation and/or a suicide attempt during the month preceding intake. Suicide attempts and NSSI were assessed using the Suicide Attempt Self Injury Interview. RESULTS: Forty percent of Soldiers with a history of nonsuicidal self-injury and 25% of Soldiers with a history of suicide attempt made a suicide attempt during the 2-year follow-up. Soldiers with a history of nonsuicidal self-injury were more than twice as likely to make a subsequent suicide attempt (hazard ratio [HR]=2.25, P=.045). Soldiers with a history of suicide attempt were no more likely to make a subsequent suicide attempt than Soldiers without a previous suicide attempt (HR=.88, P=.787). Thirty percent of Soldiers with a history of suicide attempt had also engaged in nonsuicidal self-injury. Forty-two percent of Soldiers with histories of both nonsuicidal self-injury and suicide attempt made a subsequent suicide attempt and were more likely to make a suicide attempt during follow-up than Soldiers with a history of suicide attempt only. Number of NSSI episodes, but not number of suicide attempts, was significantly associated with increased risk for future suicide attempt. Results were unchanged when adjusting for baseline symptom severity. LIMITATIONS: Predominantly male, active duty Army sample. CONCLUSIONS: Among Soldiers in outpatient mental health care, a history of NSSI is a stronger predictor of future suicide attempts than a history of suicide attempts. Soldiers with a history of both NSSI and suicide attempt are at especially increased risk.

Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells.

Covalent modification of DNA distinguishes cellular identities and is crucial for regulating the pluripotency and differentiation of embryonic stem (ES) cells. The recent demonstration that 5-methylcytosine (5-mC) may be further modified to 5-hydroxymethylcytosine (5-hmC) in ES cells has revealed a novel regulatory paradigm to modulate the epigenetic landscape of pluripotency. To understand the role of 5-hmC in the epigenomic landscape of pluripotent cells, here we profile the genome-wide 5-hmC distribution and correlate it with the genomic profiles of 11 diverse histone modifications and six transcription factors in human ES cells. By integrating genomic 5-hmC signals with maps of histone enrichment, we link particular pluripotency-associated chromatin contexts with 5-hmC. Intriguingly, through additional correlations with defined chromatin signatures at promoter and enhancer subtypes, we show distinct enrichment of 5-hmC at enhancers marked with H3K4me1 and H3K27ac. These results suggest potential role(s) for 5-hmC in the regulation of specific promoters and enhancers. In addition, our results provide a detailed epigenomic map of 5-hmC from which to pursue future functional studies on the diverse regulatory roles associated with 5-hmC.

Uncovering the role of substance use in suicide attempts using a mixed-methods approach.

INTRODUCTION: Substance use is an established risk factor for suicide attempt. Clarifying the role of substance use in suicide attempts may identify modifiable treatment targets. This study used mixed methods to associate substance use with suicide attempt history and identify pathways through which substance use contributes to attempts. METHODS: Study 1 included 213 adult inpatients (n = 127 with substance use disorder [SUD]), who completed assessments of suicide attempt history as well as demographic and clinical suicide risk factors. Study 2 was a narrative analysis of suicide attempt stories described by 20 inpatients diagnosed with SUD. RESULTS: In Study 1, patients with co-occurring alcohol and drug use disorders reported more actual lifetime suicide attempts than did those without SUD. In addition, alcohol and drug use disorders were independently associated with lifetime suicide attempts after controlling for demographic and clinical confounders. In Study 2, substance use played a role in all suicide attempts through at least one pathway before, during, or after a triggering stressor, or as suicide attempt method. CONCLUSIONS: Substances play a role in suicide attempt baseline risk, acute risk and as means. It is important to target chronic and acute substance use in suicide prevention treatment plans.

Borderline Personality Traits Do Not Moderate the Relationship Between Depression, Beliefs, and Suicidal Thoughts and Behaviors.

Adults with clinically significant borderline personality disorder traits (BPTs) are at high risk of experiencing suicidal thoughts and behaviors (STBs). STBs among those with BPTs have been associated with suicidal beliefs (e.g., that one is unlovable or that distress is intolerable). However, the extent to which suicidal beliefs uniquely mediate the relationship between emotional distress and STBs among individuals with BPTs is not known. Individuals admitted to an inpatient unit (N = 198) with recent STBs completed assessments of BPTs, depression, suicidal beliefs, suicidal ideation, and suicide attempt history. Moderated mediation models were used to explore whether suicidal beliefs mediated the relationship between depression and STBs conditional on BPTs. Suicidal patients with versus without BPTs reported stronger suicidal beliefs and more severe STBs (i.e., suicidal ideation, lifetime attempts). Exploratory moderated mediation analysis demonstrated that suicidal beliefs mediated the relationship between depression and suicidal ideation as well as suicide attempts. The mediation effect of suicidal beliefs on the depression-ideation and depression-attempt relationship was not significantly moderated by BPTs. This study was cross-sectional and therefore the estimated mediation models must be considered exploratory. Longitudinal research will be needed to assess the potential causal mediation of suicidal beliefs on the relationship between depression and STBs. The results of this study suggest that suicidal beliefs may play a significant role in the relationship between depression and STBs for inpatients with a history of suicidality regardless of BPTs. This suggests suicidal beliefs may be an important treatment target for adults with a history of STBs.

Diverse mutational mechanisms cause pathogenic subtelomeric rearrangements.

Chromosome rearrangements are a significant cause of intellectual disability and birth defects. Subtelomeric rearrangements, including deletions, duplications and translocations of chromosome ends, were first discovered over 40 years ago and are now recognized as being responsible for several genetic syndromes. Unlike the deletions and duplications that cause some genomic disorders, subtelomeric rearrangements do not typically have recurrent breakpoints and involve many different chromosome ends. To capture the molecular mechanisms responsible for this heterogeneous class of chromosome abnormality, we coupled high-resolution array CGH with breakpoint junction sequencing of a diverse collection of subtelomeric rearrangements. We analyzed 102 breakpoints corresponding to 78 rearrangements involving 28 chromosome ends. Sequencing 21 breakpoint junctions revealed signatures of non-homologous end-joining, non-allelic homologous recombination between interspersed repeats and DNA replication processes. Thus, subtelomeric rearrangements arise from diverse mutational mechanisms. In addition, we find hotspots of subtelomeric breakage at the end of chromosomes 9q and 22q; these sites may correspond to genomic regions that are particularly susceptible to double-strand breaks. Finally, fine-mapping the smallest subtelomeric rearrangements has narrowed the critical regions for some chromosomal disorders.

Microdeletions of 3q29 confer high risk for schizophrenia.

Schizophrenia (SZ) is a severe psychiatric illness that affects approximately 1% of the population and has a strong genetic underpinning. Recently, genome-wide analysis of copy-number variation (CNV) has implicated rare and de novo events as important in SZ. Here, we report a genome-wide analysis of 245 SZ cases and 490 controls, all of Ashkenazi Jewish descent. Because many studies have found an excess burden of large, rare deletions in cases, we limited our analysis to deletions over 500 kb in size. We observed seven large, rare deletions in cases, with 57% of these being de novo. We focused on one 836 kb de novo deletion at chromosome 3q29 that falls within a 1.3-1.6 Mb deletion previously identified in children with intellectual disability (ID) and autism, because increasing evidence suggests an overlap of specific rare copy-number variants (CNVs) between autism and SZ. By combining our data with prior CNV studies of SZ and analysis of the data of the Genetic Association Information Network (GAIN), we identified six 3q29 deletions among 7545 schizophrenic subjects and one among 39,748 controls, resulting in a statistically significant association with SZ (p = 0.02) and an odds ratio estimate of 17 (95% confidence interval: 1.36-1198.4). Moreover, this 3q29 deletion region contains two linkage peaks from prior SZ family studies, and the minimal deletion interval implicates 20 annotated genes, including PAK2 and DLG1, both paralogous to X-linked ID genes and now strong candidates for SZ susceptibility.

Identification of a recurrent microdeletion at 17q23.1q23.2 flanked by segmental duplications associated with heart defects and limb abnormalities.

Segmental duplications, which comprise approximately 5%-10% of the human genome, are known to mediate medically relevant deletions, duplications, and inversions through nonallelic homologous recombination (NAHR) and have been suggested to be hot spots in chromosome evolution and human genomic instability. We report seven individuals with microdeletions at 17q23.1q23.2, identified by microarray-based comparative genomic hybridization (aCGH). Six of the seven deletions are approximately 2.2 Mb in size and flanked by large segmental duplications of >98% sequence identity and in the same orientation. One of the deletions is approximately 2.8 Mb in size and is flanked on the distal side by a segmental duplication, whereas the proximal breakpoint falls between segmental duplications. These characteristics suggest that NAHR mediated six out of seven of these rearrangements. These individuals have common features, including mild to moderate developmental delay (particularly speech delay), microcephaly, postnatal growth retardation, heart defects, and hand, foot, and limb abnormalities. Although all individuals had at least mild dysmorphic facial features, there was no characteristic constellation of features that would elicit clinical suspicion of a specific disorder. The identification of common clinical features suggests that microdeletions at 17q23.1q23.2 constitute a novel syndrome. Furthermore, the inclusion in the minimal deletion region of TBX2 and TBX4, transcription factors belonging to a family of genes implicated in a variety of developmental pathways including those of heart and limb, suggests that these genes may play an important role in the phenotype of this emerging syndrome.