Polygenic score × intervention moderation: an application of discrete-time survival analysis to modeling the timing of first tobacco use among urban youth

Parenting in the Context of the Child: Genetic and Social Processes

The focus on the role of parenting in child development has a long-standing history. When measures of parenting precede changes in child development, researchers typically infer a causal role of parenting practices and attitudes on child development. However, this research is usually conducted with parents raising their own biological offspring. Such research designs cannot account for the effects of genes that are common to parents and children, nor for genetically influenced traits in children that influence how they are parented and how parenting affects them. The aim of this monograph is to provide a clearer view of parenting by synthesizing findings from the Early Growth and Development Study (EGDS). EGDS is a longitudinal study of adopted children, their birth parents, and their rearing parents studied across infancy and childhood. Families (N = 561) were recruited in the United States through adoption agencies between 2000 and 2010. Data collection began when adoptees were 9 months old (males = 57.2%; White 54.5%, Black 13.2%, Hispanic/Latinx 13.4%, Multiracial 17.8%, other 1.1%). The median child age at adoption placement was 2 days (M = 5.58, SD = 11.32). Adoptive parents were predominantly in their 30s, White, and coming from upper-middle- or upper-class backgrounds with high educational attainment (a mode at 4-year college or graduate degree). Most adoptive parents were heterosexual couples, and were married at the beginning of the project. The birth parent sample was more racially and ethnically diverse, but the majority (70%) were White. At the beginning of the study, most birth mothers and fathers were in their 20s, with a mode of educational attainment at high school degree, and few of them were married. We have been following these family members over time, assessing their genetic influences, prenatal environment, rearing environment, and child development. Controlling for effects of genes common to parents and children, we confirmed some previously reported associations between parenting, parent psychopathology, and marital adjustment in relation to child problematic and prosocial behavior. We also observed effects of children's heritable characteristics, characteristics thought to be transmitted from parent to child by genetic means, on their parents and how those effects contributed to subsequent child development. For example, we found that genetically influenced child impulsivity and social withdrawal both elicited harsh parenting, whereas a genetically influenced sunny disposition elicited parental warmth. We found numerous instances of children's genetically influenced characteristics that enhanced positive parental influences on child development or that protected them from harsh parenting. Integrating our findings, we propose a new, genetically informed process model of parenting. We posit that parents implicitly or explicitly detect genetically influenced liabilities and assets in their children. We also suggest future research into factors such as marital adjustment, that favor parents responding with appropriate protection or enhancement. Our findings illustrate a productive use of genetic information in prevention research: helping parents respond effectively to a profile of child strengths and challenges rather than using genetic information simply to identify some children unresponsive to current preventive interventions.

A systematic review of gene-by-intervention studies of alcohol and other substance use

Alcohol and other substance use problems are common, and the efficacy of current prevention and intervention programs is limited. Genetics may contribute to differential effectiveness of psychosocial prevention and intervention programs. This paper reviews gene-by-intervention (G×I) studies of alcohol and other substance use, and implications for integrating genetics into prevention science. Systematic review yielded 17 studies for inclusion. Most studies focused on youth substance prevention, alcohol was the most common outcome, and measures of genotype were heterogeneous. All studies reported at least one significant G×I interaction. We discuss these findings in the context of the history and current state of genetics, and provide recommendations for future G×I research. These include the integration of genome-wide polygenic scores into prevention studies, broad outcome measurement, recruitment of underrepresented populations, testing mediators of G×I effects, and addressing ethical implications. Integrating genetic research into prevention science, and training researchers to work fluidly across these fields, will enhance our ability to determine the best intervention for each individual across development. With growing public interest in obtaining personalized genetic information, we anticipate that the integration of genetics and prevention science will become increasingly important as we move into the era of precision medicine.

Adolescent cannabis and tobacco use are associated with opioid use in young adulthood-12-year longitudinal study in an urban cohort

BACKGROUND AND AIMS

Cannabis, tobacco and alcohol use are prevalent among youth in the United States and may be risk factors for opioid use. The current study aimed at investigating associations between developmental trajectories of cannabis, tobacco and alcohol use in adolescence and opioid use in young adulthood in an urban cohort over the span of 12 years.

DESIGN

Cohort study of adolescents originally recruited for a randomized prevention trial with yearly assessments into young adulthood.

SETTING

Nine urban elementary schools in Baltimore, MD in the United States.

PARTICIPANTS

Participants (n = 583, 86.8% African American, 54.7% male) were originally recruited as first grade students.

MEASUREMENTS

Cannabis, tobacco and alcohol use were assessed annually from ages 14-18 years and opioid use from ages 19-26. Socio-demographics were assessed at age 6. Intervention status was also randomly assigned at age 6. Gender, race, free/reduced-priced lunch and intervention status were included as covariates in individual and sequential growth models.

FINDINGS

There were significant positive associations between the cannabis use intercept at age 14 and the opioid use intercept at age 19 (beta = 1.43; P = 0.028), the tobacco use intercept at age 14 and the opioid use intercept at age 19 (beta = 0.82; P = 0.042). Specifically, more frequent use of cannabis or tobacco at age 14 was associated with more frequent use of opioids at age 19.

CONCLUSIONS

Cannabis and tobacco use in early adolescence may be risk factors for opioid use in young adulthood among African Americans living in urban areas.

Stability in effects of different smoking-related polygenic risk scores over age and smoking phenotypes

PURPOSE

Polygenic risk scores (PRSs) for smoking behavior largely fail to consider the demonstrated developmental change in genetic influence over age and stage of smoking behaviors. Additionally, few studies have examined how stage-specific smoking PRSs (e.g. for initiation vs. smoking heaviness) generalize to other stages of risk. The current study examines the stability of PRS effects over age, and how specifically calibrated PRSs associate with other smoking phenotypes.

METHODS

7228 participants were from the National Longitudinal Study of Adolescent to Adult Health, who had calculated PRSs for two smoking phenotypes, Centers for Disease Control and Prevention (CDC) smoking initiation status, and cigarettes per day (CPD). Four time-varying effects models estimated associations between both PRSs and four smoking phenotypes (CDC status, cigarettes/day on smoking days, any past-30 day smoking, and past-30 day daily smoking) over adolescence and young adulthood.

FINDINGS

The time-varying effects models demonstrated that both PRSs significantly associated with all four phenotypes age. PRS effects were similar, in both odds ratios and the overlap of 95 % confidence intervals. There were increases in PRS associations with quantity of smoking over age, and a decrease in PRS effects over age for the CDC smoking status phenotype over early to late adolescence.

CONCLUSIONS

Smoking PRSs can be robust predictors of smoking behavior over age. However, the lack of differentiation between specific PRSs and multiple smoking phenotypes, as well as the added contribution of both PRSs to explaining genetic variance, indicates a need to reconceptualize phenotypic measurement used to calibrate smoking PRSs.

Identification of transforming growth factor beta induced (TGFBI) as an immune-related prognostic factor in clear cell renal cell carcinoma (ccRCC)

Clear cell renal cell carcinoma (ccRCC) is the most common subtype among kidney cancer, which has poor prognosis. The aim of this study was to screen out novel prognostic biomarkers and therapeutic targets for immunotherapy, and some novel molecule drugs for ccRCC treatment. Immune scores ranged from -1109.36 to 2920.81 and stromal scores ranged from -1530.11 to 1955.39 were firstly calculated by applying ESTIMATE algorithm. Then 17 DEGs associated with immune score and stromal score were further identified. 6 candidate hub genes were screened out by performing overall survival (OS) and disease-free survival analyses based on TCGA-KIRC data, one of which including TGFBI was further regarded as hub gene associated with prognosis by calculating the R2 (R2 = 0.011, P = 0.018) and AUC (AUC = 0.874). The prognostic value of TGFBI was validated by performing OS, CSS, and PFS analyses based on GSE29609 and E-MTAB-3267. CMap analysis suggested that 3 molecule drugs might be novel choice for ccRCC treatment. Further analysis demonstrated that CNVs of TGFBI was associated with OS of patients with ccRCC. TGFBI expression was also correlated with histologic grade, pathologic stage, and immune infiltration level, significantly. TGFBI was the most relevant gene with OS among the candidate hub genes, which might be novel DNA methylation biomarkers for ccRCC. In conclusion, our findings indicated that TGFBI was correlated with prognosis of patients with ccRCC, which might be novel prognostic biomarkers, and targets for immunotherapy in ccRCC. Three small molecule drugs were also identified, which showed strong potential for ccRCC treatment.

Trajectories and Predictors of Children's Early-Starting Conduct Problems: Child, Family, Genetic, and Intervention Effects

Several research teams have previously traced patterns of emerging conduct problems (CP) from early or middle childhood. The current study expands on this previous literature by using a genetically-informed, experimental, and long-term longitudinal design to examine trajectories of early-emerging conduct problems and early childhood discriminators of such patterns from the toddler period to adolescence. The sample represents a cohort of 731 toddlers and diverse families recruited based on socioeconomic, child, and family risk, varying in urbanicity and assessed on nine occasions between ages 2 and 14. In addition to examining child, family, and community level discriminators of patterns of emerging conduct problems, we were able to account for genetic susceptibility using polygenic scores and the study's experimental design to determine whether random assignment to the Family Check-Up (FCU) discriminated trajectory groups. In addition, in accord with differential susceptibility theory, we tested whether the effects of the FCU were stronger for those children with higher genetic susceptibility. Results augmented previous findings documenting the influence of child (inhibitory control [IC], gender) and family (harsh parenting, parental depression, and educational attainment) risk. In addition, children in the FCU were overrepresented in the persistent low versus persistent high CP group, but such direct effects were qualified by an interaction between the intervention and genetic susceptibility that was consistent with differential susceptibility. Implications are discussed for early identification and specifically, prevention efforts addressing early child and family risk.

The Impact of Genes on Adolescent Substance Use: A Developmental Perspective

Purpose

This review discusses the importance of understanding the impact of genetic factors on adolescent substance use within a developmental framework. Methods for identifying genetic factors, relevant endophenotypes and intermediate phenotypes, and gene-environment interplay effects will be reviewed.

Findings

Prior work supports the role of polygenic variation on adolescent substance use. Mechanisms through which genes impact adolescent phenotypes consist of differences in neural structure and function, early temperamental differences, and problem behavior. Gene-environment interactions are characterized by increased vulnerability to both maladaptive and adaptive contexts.

Summary

Developmental considerations in genetic investigations highlight the critical role that polygenic variation has on adolescent substance use. Yet, determining what to do with this information, especially in terms of personalized medicine, poses ethical and logistic challenges.

Systematic Review of Polygenic Gene-Environment Interaction in Tobacco, Alcohol, and Cannabis Use

Studies testing the effect of single genetic variants on substance use have had modest success. This paper reviewed 39 studies using polygenic measures to test interaction with any type of environmental exposure (G×E) in alcohol, tobacco, and cannabis use. Studies using haplotype combinations, sum scores of candidate-gene risk alleles, and polygenic scores (PS) were included. Overall study quality was moderate, with lower ratings for the polygenic methods in the haplotype and candidate-gene score studies. Heterogeneity in investigated environmental exposures, genetic factors, and outcomes was substantial. Most studies (N = 30) reported at least one significant G×E interaction, but overall evidence was weak. The majority (N = 26) found results in line with differential susceptibility and diathesis-stress frameworks. Future studies should pay more attention to methodological and statistical rigor, and focus on replication efforts. Additional work is needed before firm conclusions can be drawn about the importance of G×E in the etiology of substance use.

Polygenic Score × Intervention Moderation: an Application of Discrete-Time Survival Analysis to Model the Timing of First Marijuana Use Among Urban Youth

The present study examines the interaction between a polygenic score and an elementary school-based universal preventive intervention trial and its effects on a discrete-time survival analysis of time to first smoking marijuana. Research has suggested that initiation of substances is both genetically and environmentally driven (Rhee et al., Archives of general psychiatry 60:1256-1264, 2003; Verweij et al., Addiction 105:417-430, 2010). A previous work has found a significant interaction between the polygenic score and the same elementary school-based intervention with tobacco smoking (Musci et al., in press). The polygenic score reflects the contribution of multiple genes and has been shown in prior research to be predictive of smoking cessation, tobacco use, and marijuana use (Uhl et al., Molecular Psychiatry 19:50-54, 2014). Using data from a longitudinal preventive intervention study (N = 678), we examined age of first marijuana use from sixth grade to age 18. Genetic data were collected during emerging adulthood and were genotyped using the Affymetrix 6.0 microarray (N = 545). The polygenic score was computed using these data. Discrete-time survival analysis was employed to test for intervention main and interaction effects with the polygenic score. We found main effect of the polygenic score approaching significance, with the participants with higher polygenic scores reporting their first smoking marijuana at an age significantly later than controls (p = .050). We also found a significant intervention × polygenic score interaction effect at p = .003, with participants at the higher end of the polygenic score benefiting the most from the intervention in terms of delayed age of first use. These results suggest that genetics may play an important role in the age of first use of marijuana and that differences in genetics may account for the differential effectiveness of classroom-based interventions in delaying substance use experimentation.

Genetic moderation of the effects of the Family Check-Up intervention on children's internalizing symptoms: A longitudinal study with a racially/ethnically diverse sample

Development involves synergistic interplay among genotypes and the physical and cultural environments, and integrating genetics into experimental designs that manipulate the environment can improve understanding of developmental psychopathology and intervention efficacy. Consistent with differential susceptibility theory, individuals can vary in their sensitivity to environmental conditions including intervention for reasons including their genotype. As a consequence, understanding genetic influences on intervention response is critical. Empirically, we tested an interaction between a genetic index representing sensitivity to the environment and the Family Check-Up intervention. Participants were drawn from the Early Steps Multisite randomized prevention trial that included a low-income and racially/ethnically diverse sample of children and their families followed longitudinally (n = 515). As hypothesized, polygenic sensitivity to the environment moderated the effects of the intervention on 10-year-old children's symptoms of internalizing psychopathology, such that children who were genetically sensitive and were randomly assigned to the intervention had fewer symptoms of child psychopathology than genetically sensitive children assigned to the control condition. A significant difference in internalizing symptoms assessed with a clinical interview emerged between the intervention and control groups for those 0.493 SD above the mean on polygenic sensitivity, or 25% of the sample. Similar to personalized medicine, it is time to understand individual and sociocultural differences in treatment response and individualize psychosocial interventions to reduce the burden of child psychopathology and maximize well-being for children growing up in a wide range of physical environments and cultures.

A novel scoring system for gastric cancer risk assessment based on the expression of three CLIP4 DNA methylation-associated genes

Gastric cancer (GC) is the fifth most common cancer and the third leading cause of cancer-associated mortality worldwide. In the current study, comprehensive bioinformatic analyses were performed to develop a novel scoring system for GC risk assessment based on CAP-Gly domain containing linker protein family member 4 (CLIP4) DNA methylation status. Two GC datasets with methylation sequencing information and mRNA expression profiling were downloaded from the The Cancer Genome Atlas and Gene Expression Omnibus databases. Differentially expressed genes (DEGs) between the CLIP4 hypermethylation and CLIP4 hypomethylation groups were screened using the limma package in R 3.3.1, and survival analysis of these DEGs was performed using the survival package. A risk scoring system was established via regression factor-weighted gene expression based on linear combination to screen the most important genes associated with CLIP4 methylation and prognosis. Genes associated with high/low-risk value were selected using the limma package. Functional enrichment analysis of the top 500 DEGs that positively and negatively associated with risk values was performed using DAVID 6.8 online and the gene set enrichment analysis (GSEA) software. In total, 35 genes were identified to be that significantly associated with prognosis and CLIP4 DNA methylation, and three prognostic signature genes, claudin-11 (CLDN11), apolipoprotein D (APOD), and chordin like 1 (CHRDL1), were used to establish a risk assessment system. The prognostic scoring system exhibited efficiency in classifying patients with different prognoses, where the low-risk groups had significantly longer overall survival times than those in the high-risk groups. CLDN11, APOD and CHRDL1 exhibited reduced expression in the hypermethylation and low-risk groups compare with the hypomethylation and high-risk groups, respectively. Multivariate Cox analysis indicated that risk value could be used as an independent prognostic factor. In functional analysis, six functional gene ontology terms and five GSEA pathways were associated with CLDN11, APOD and CHRDL1. The results established the credibility of the scoring system in this study. Additionally, these three genes, which were significantly associated with CLIP4 DNA methylation and GC risk assessment, were identified as potential prognostic biomarkers.

Critical Issues in the Inclusion of Genetic and Epigenetic Information in Prevention and Intervention Trials

Human genetic research in the past decade has generated a wealth of data from the genome-wide association scan era, much of which is catalogued and freely available. These data will typically test the relationship between a single nucleotide variant or polymorphism (SNP) and some outcome, disease, or trait. Ongoing investigations will yield a similar wealth of data regarding epigenetic phenomena. These data will typically test the relationship between DNA methylation at a single genomic location/region and some outcome. Most of these findings will be the result of cross-sectional investigations typically using ascertained cases and controls. Consequently, most methodological consideration focuses on methods appropriate for simple case-control comparisons. It is expected that a growing number of investigators with longitudinal experimental prevention or intervention cohorts will also measure genetic and epigenetic indicators as part of their investigations, harvesting the wealth of information generated by the genome-wide association study (GWAS) era to allow for targeted hypothesis testing in the next generation of prevention and intervention trials. Herein, we discuss appropriate quality control and statistical modelling of genetic, polygenic, and epigenetic measures in longitudinal models. We specifically discuss quality control, population stratification, genotype imputation, pathway approaches, and proper modelling of an interaction between a specific genetic variant and an environment variable (GxE interaction).

Neuroplasticity of selective attention: Research foundations and preliminary evidence for a gene by intervention interaction

This article reviews the trajectory of our research program on selective attention, which has moved from basic research on the neural processes underlying selective attention to translational studies using selective attention as a neurobiological target for evidence-based interventions. We use this background to present a promising preliminary investigation of how genetic and experiential factors interact during development (i.e., gene × intervention interactions). Our findings provide evidence on how exposure to a family-based training can modify the associations between genotype (5-HTTLPR) and the neural mechanisms of selective attention in preschool children from lower socioeconomic status backgrounds.

Genes, Environments, and Sex Differences in Alcohol Research

OBJECTIVE

The study of sex differences has been identified as one way to enhance scientific reproducibility, and the National Institutes of Health (NIH) have implemented a new policy to encourage the explicit examination of sex differences. Our goal here is to address sex differences in behavioral genetic research on alcohol outcomes.

METHOD

We review sex differences for alcohol outcomes and whether the source and magnitude of genetic influences on alcohol consumption and alcohol use disorder (AUD) are the same across sexes; describe common research designs for studying sex-specific gene-by-environment interaction (G × E) effects; and discuss the role of statistical power and theory when testing sex-specific genetic effects.

RESULTS

There are robust sex differences for many alcohol outcomes. The weight of evidence suggests that the source and magnitude of genetic influences on alcohol consumption and AUD are the same across sexes. Whether there are sex-specific G × E effects has received less attention to date.

CONCLUSIONS

The new NIH policy necessitates a systematic approach for studying sex-specific genetic effects in alcohol research. Researchers are encouraged to report power for tests of these effects and to use theory to develop testable hypotheses, especially for studies of G × E.

Polygenic Scores in Epidemiology: Risk Prediction, Etiology, and Clinical Utility

Genes account for a significant proportion of the risk for most common diseases. The genome-wide association scan (GWAS) era of genetic epidemiology has generated a massive amount of data, revolutionized our thinking on the genetic architecture of common diseases and positioned the field to realistically consider risk prediction for common polygenic diseases, such as non-familial cancers, and autoimmune, cardiovascular and psychiatric diseases. Polygenic scoring is an approach that shows promise for understanding the polygenic contribution to common human diseases. This is an approach typically relying on genome-wide SNP data, where a set of SNPs identified in a discovery GWAS are used to construct composite polygenic scores. These scores are then used in additional samples for association testing or risk prediction. This review summarizes the extant literature on the use, power, and accuracy of polygenic scores in studies of the etiology of disease and the promise for disease risk prediction.