Gene network analysis shows immune-signaling and ERK1/2 as novel genetic markers for multiple addiction phenotypes: alcohol, smoking and opioid addiction

A review on the reciprocal interactions between neuroinflammatory processes and substance use and misuse, with a focus on alcohol misuse

Background: The last decade has witnessed a surge of findings implicating neuroinflammatory processes as pivotal players in substance use disorders. The directionality of effects began with the expectation that the neuroinflammation associated with prolonged substance misuse contributes to long-term neuropathological consequences. As the literature grew, however, it became evident that the interactions between neuroinflammatory processes and alcohol and drug intake were reciprocal and part of a pernicious cycle in which disease-relevant signaling pathways contributed to an escalation of drug intake, provoking further inflammation-signaling and thereby exacerbating the neuropathological effects of drug misuse.Objectives: The goal of this review and its associated special issue is to provide an overview of the emergent findings relevant to understanding these reciprocal interactions. The review highlights the importance of preclinical and clinical studies in testing and validation of immunotherapeutics as viable targets for curtailing substance use and misuse, with a focus on alcohol misuse.Methods: A narrative review of the literature on drug and neuroinflammation was conducted, as well as articles published in this Special Issue on Alcohol- and Drug-induced Neuroinflammation: Insights from Pre-clinical Models and Clinical Research.Results: We argue that (a) demographic variables and genetic background contribute unique sensitivity to drug-related neuroinflammation; (b) co-morbidities between substance use disorders and affect dysfunction may share common inflammation-related signatures that predict the efficacy of immunotherapeutic drugs; and (c) examination of polydrug interactions with neuroinflammation is a critical area where greater research emphasis is needed.Conclusions: This review provides an accessible and example-driven review of the relationship between drug misuse, neuroinflammatory processes, and their resultant neuropathological outcomes.

Stress- and drug-induced neuroimmune signaling as a therapeutic target for comorbid anxiety and substance use disorders

Stress and substance use disorders remain two of the most highly prevalent psychiatric conditions and are often comorbid. While individually these conditions have a debilitating impact on the patient and a high cost to society, the symptomology and treatment outcomes are further exacerbated when they occur together. As such, there are few effective treatment options for these patients, and recent investigation has sought to determine the neural processes underlying the co-occurrence of these disorders to identify novel treatment targets. One such mechanism that has been linked to stress- and addiction-related conditions is neuroimmune signaling. Increases in inflammatory factors across the brain have been heavily implicated in the etiology of these disorders, and this review seeks to determine the nature of this relationship. According to the "dual-hit" hypothesis, also referred to as neuroimmune priming, prior exposure to either stress or drugs of abuse can sensitize the neuroimmune system to be hyperresponsive when exposed to these insults in the future. This review completes an examination of the literature surrounding stress-induced increases in inflammation across clinical and preclinical studies along with a summarization of the evidence regarding drug-induced alterations in inflammatory factors. These changes in neuroimmune profiles are also discussed within the context of their impact on the neural circuitry responsible for stress responsiveness and addictive behaviors. Further, this review explores the connection between neuroimmune signaling and susceptibility to these conditions and highlights the anti-inflammatory pharmacotherapies that may be used for the treatment of stress and substance use disorders.

Genetic Addiction Risk and Psychological Profiling Analyses for "Preaddiction" Severity Index

Since 1990, when our laboratory published the association of the DRD2 Taq A1 allele and severe alcoholism in JAMA, there has been an explosion of genetic candidate association studies, including genome-wide association studies (GWAS). To develop an accurate test to help identify those at risk for at least alcohol use disorder (AUD), a subset of reward deficiency syndrome (RDS), Blum's group developed the genetic addiction risk severity (GARS) test, consisting of ten genes and eleven associated risk alleles. In order to statistically validate the selection of these risk alleles measured by GARS, we applied strict analysis to studies that investigated the association of each polymorphism with AUD or AUD-related conditions, including pain and even bariatric surgery, as a predictor of severe vulnerability to unwanted addictive behaviors, published since 1990 until now. This analysis calculated the Hardy-Weinberg Equilibrium of each polymorphism in cases and controls. Pearson's χ2 test or Fisher's exact test was applied to compare the gender, genotype, and allele distribution if available. The statistical analyses found the OR, 95% CI for OR, and the post risk for 8% estimation of the population's alcoholism prevalence revealed a significant detection. Prior to these results, the United States and European patents on a ten gene panel and eleven risk alleles have been issued. In the face of the new construct of the "preaddiction" model, similar to "prediabetes", the genetic addiction risk analysis might provide one solution missing in the treatment and prevention of the neurological disorder known as RDS.

FOXN3 and GDNF Polymorphisms as Common Genetic Factors of Substance Use and Addictive Behaviors

Epidemiological and phenomenological studies suggest shared underpinnings between multiple addictive behaviors. The present genetic association study was conducted as part of the Psychological and Genetic Factors of Addictions study (n = 3003) and aimed to investigate genetic overlaps between different substance use, addictive, and other compulsive behaviors. Association analyses targeted 32 single-nucleotide polymorphisms, potentially addictive substances (alcohol, tobacco, cannabis, and other drugs), and potentially addictive or compulsive behaviors (internet use, gaming, social networking site use, gambling, exercise, hair-pulling, and eating). Analyses revealed 29 nominally significant associations, from which, nine survived an FDRbl correction. Four associations were observed between FOXN3 rs759364 and potentially addictive behaviors: rs759364 showed an association with the frequency of alcohol consumption and mean scores of scales assessing internet addiction, gaming disorder, and exercise addiction. Significant associations were found between GDNF rs1549250, rs2973033, CNR1 rs806380, DRD2/ANKK1 rs1800497 variants, and the “lifetime other drugs” variable. These suggested that genetic factors may contribute similarly to specific substance use and addictive behaviors. Specifically, FOXN3 rs759364 and GDNF rs1549250 and rs2973033 may constitute genetic risk factors for multiple addictive behaviors. Due to limitations (e.g., convenience sampling, lack of structured scales for substance use), further studies are needed. Functional correlates and mechanisms underlying these relationships should also be investigated.

FcER1: A Novel Molecule Implicated in the Progression of Human Diabetic Kidney Disease

Diabetic kidney disease (DKD) is a key microvascular complication of diabetes, with few therapies for targeting renal disease pathogenesis and progression. We performed transcriptional and protein studies on 103 unique blood and kidney tissue samples from patients with and without diabetes to understand the pathophysiology of DKD injury and its progression. The study was based on the use of 3 unique patient cohorts: peripheral blood mononuclear cell (PBMC) transcriptional studies were conducted on 30 patients with DKD with advancing kidney injury; Gene Expression Omnibus (GEO) data was downloaded, containing transcriptional measures from 51 microdissected glomerulous from patients with DKD. Additionally, 12 independent kidney tissue sections from patients with or without DKD were used for validation of target genes in diabetic kidney injury by kidney tissue immunohistochemistry and immunofluorescence. PBMC DKD transcriptional analysis, identified 853 genes (p < 0.05) with increasing expression with progression of albuminuria and kidney injury in patients with diabetes. GEO data was downloaded, normalized, and analyzed for significantly changed genes. Of the 325 significantly up regulated genes in DKD glomerulous (p < 0.05), 28 overlapped in PBMC and diabetic kidney, with perturbed FcER1 signaling as a significantly enriched canonical pathway. FcER1 was validated to be significantly increased in advanced DKD, where it was also seen to be specifically co-expressed in the kidney biopsy with tissue mast cells. In conclusion, we demonstrate how leveraging public and private human transcriptional datasets can discover and validate innate immunity and inflammation as key mechanistic pathways in DKD progression, and uncover FcER1 as a putative new DKD target for rational drug design.

Reductions in tobacco use in naltrexone, relative to buprenorphine-maintained individuals with opioid use disorder: Secondary analysis from the National Drug Abuse Treatment Clinical Trials Network

BACKGROUND

Smoking prevalence in individuals with opioid use disorder (OUD) is over 80%. Research suggests that opioid use significantly increases smoking, which could account for the strikingly low smoking-cessation rates observed in both methadone- and buprenorphine-maintained patients, even with the use of first-line smoking-cessation interventions. If opioids present a barrier to smoking-cessation, then better smoking outcomes should be observed in OUD patients treated with extended-release naltrexone (XR-NTX, an opioid antagonist) compared to those receiving buprenorphine (BUP-NX, a partial opioid agonist).

METHODS

The current study is a secondary analysis of a 24-week, multi-site, open-label, randomized clinical trial conducted within the National Drug Abuse Treatment Clinical Trials Network comparing the effectiveness of XR-NTX vs. BUP-NX for adults with OUD. Longitudinal mixed effects models were used to determine if there was a significant reduction in cigarette use among daily smokers successfully inducted to treatment (n = 373) and a subset of those who completed treatment (n = 169).

RESULTS

Among daily smokers inducted onto OUD medication, those in the XR-NTX group smoked fewer cigarettes per day (M = 11.36, SE = 0.62) relative to smokers in the BUP-NX group (M = 13.33, SE = 0.58) across all study visits, (b (SE) = -1.97 (0.55), p < .01). Results were similar for the treatment completers.

CONCLUSIONS

OUD patients treated with XR-NTX reduced cigarette use more than those treated with BUP-NX, suggesting that XR-NTX in combination with other smoking cessation interventions might be a better choice for OUD smokers interested in reducing their tobacco use.

Identification of novel risk loci with shared effects on alcoholism, heroin, and methamphetamine dependence

Different substance dependences have common effects on reward pathway and molecular adaptations, however little is known regarding their shared genetic factors. We aimed to identify the risk genetic variants that are shared for substance dependence (SD). First, promising genome-wide significant loci were identified from 3296 patients (521 alcoholic/1026 heroin/1749 methamphetamine) vs 2859 healthy controls and independently replicated using 1954 patients vs 1904 controls. Second, the functional effects of promising variants on gene expression, addiction characteristics, brain structure (gray and white matter), and addiction behaviors in addiction animal models (chronic administration and self-administration) were assessed. In addition, we assessed the genetic correlation among the three SDs using LD score regression. We identified and replicated three novel loci that were associated with the common risk of heroin, methamphetamine addiction, and alcoholism: ANKS1B rs2133896 (P_meta = 3.60 × 10^-9), AGBL4 rs147247472 (P_meta = 3.40 × 10^-12), and CTNNA2 rs10196867 (P_meta = 4.73 × 10^-9). Rs2133896 in ANKS1B was associated with ANKS1B gene expression and had effects on gray matter of the left calcarine and white matter of the right superior longitudinal fasciculus in heroin dependence. Overexpression of anks1b gene in the ventral tegmental area decreased addiction vulnerability for heroin and methamphetamine in self-administration rat models. Our findings could shed light on the root cause for substance dependence and will be helpful for the development of cost-effective prevention strategies for general addiction disorders.

Opioid use disorder research and the Council for the Advancement of Nursing Science priority areas

BACKGROUND

Chronic diseases, such as opioid use disorder (OUD) require a multifaceted scientific approach to address their evolving complexity. The Council for the Advancement of Nursing Science's (Council) four nursing science priority areas (precision health; global health, determinants of health, and big data/data analytics) were established to provide a framework to address current complex health problems.

PURPOSE

To examine OUD research through the nursing science priority areas and evaluate the appropriateness of the priority areas as a framework for research on complex health conditions.

METHOD

OUD was used as an exemplar to explore the relevance of the nursing science priorities for future research.

FINDINGS

Research in the four priority areas is advancing knowledge in OUD identification, prevention, and treatment. Intersection of OUD research population focus and methodological approach was identified among the priority areas.

DISCUSSION

The Council priorities provide a relevant framework for nurse scientists to address complex health problems like OUD.

Bi-directional Acceleration of Alcohol Use and Opioid Use Disorder

Alcohol is the most widely used addictive substance. Severe alcohol abuse is diagnosed as "alcohol use disorder" (AUD). A common and harmful drinking pattern is binge drinking that elevates a person's blood alcohol concentration to ≥ 0.08%. Such drinking may be an early indicator of AUD. Opioid misuse and dependence have become worldwide crises. Patterned consumption of various opioids can develop into opioid use disorder (OUD). An intertwined epidemic exists between opioid abuse, alcohol addiction, and binge drinking. Currently, studies on the interaction of AUD and OUD are limited and the underlying mechanisms linking these disorders remains unclear. We reviewed studies on AUD and OUD and utilized Ingenuity Pathway Analysis (IPA) to identify mechanisms of AUD and OUD interaction and potential gene targets for therapeutic agents. According to IPA Canonical Pathways Analysis, Gamma-aminobutyric Acid (GABA) Receptor Signaling, Neuroinflammation Signaling Pathway, Opioid Signaling Pathway and Dopamine-DARPP32 Feedback in cAMP Signaling are potential contributors to the interaction of AUD and OUD.

Persistence of extra-medical prescription pain reliever use and alcohol involvement among United States 12-20 year olds

The peak risk of first extramedical use of prescription pain relievers (PPRs) is in mid-adolescence, often after underage drinking has begun. This research aims to investigate discrete classes of similar young people based on their newly incident extramedical use of PPR and alcohol involvement, with empirical evaluation of the underlying structure of identified subgroups and their epidemiological distributions in the United States. The U.S. National Surveys on Drug Use and Health, 2002-2013, sampled, recruited, and assessed 24,789 newly incident extramedical PPR users ages 12-20 years, with self-interviews on PPR, alcohol, and covariates. Latent classes of persistence were formed using PPR and alcohol status variables. Then, age and sex were studied as potentially important predictors of class membership. Analysis-weighted estimates and delta method variances were derived. Three classes were distinguished by extramedical PPR and alcohol use patterns: (a) nonpersistent (79%), (b) intermittent (15%), and (c) persistent (6%). There were no differences across classes by age, but being female was associated with greater odds of being in the intermittent class or persistent class compared to the nonpersistent class. Presenting clinical features of alcohol and/or opioid dependence that have become manifest at or near time of first PPR use can be indicators of persisting in extramedical use of PPR, particularly for young people who have recently started extramedical PPR use. Persistent adolescent and young adult extramedical PPR users require tailored public health prevention and intervention strategies based on their vulnerability to continue use over time. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Translational genomic research: the role of genetic polymorphisms in MBSR program among breast cancer survivors (MBSR[BC])

Genetic variations of breast cancer survivors (BCS) may contribute to level of residual symptoms, such as depression, stress, fatigue, and cognitive impairment. The objective of this study was to investigate whether particular single-nucleotide polymorphisms (SNPs) moderated symptom improvement resulting from the Mindfulness-Based Stress Reduction for Breast Cancer (MBSR[BC]) program. An overarching goal of personalized medicine is to identify individuals as risk for disease and tailor interventions based on genetic profiles of patients with diseases including cancer. BCS were recruited from Moffitt Cancer Center and University of South Florida's Breast Health Program and were randomized to either the 6-week MBSR(BC) program (n = 92) or Usual Care (n = 93). Measures of symptoms, demographic, and clinical history data were attained at baseline, 6 weeks, and 12 weeks. A total of 10 SNPs from eight genes known to be related to these symptoms were studied using genomic DNA extracted from blood. Our results were examined for effect sizes, consistency, and statistical significance (p < .05). Three SNPs (rs4680 in COMT, rs6314 in HTR2A, and rs429358 in APOE) emerged as having the strongest (though relatively weak) and most consistent effects in moderating the impact of the MBSR program on symptom outcomes. Although effects were generally weak, with only one effect withstanding multiple comparisons correction for statistical significance, this translational behavioral research may help start the identification of genetic profiles that moderate the impact of MBSR(BC). The ultimate goal of this study is the development of personalized treatment programs tailored to the genetic profile of each patient.

Lactate: A Novel Signaling Molecule in Synaptic Plasticity and Drug Addiction

l-Lactate is emerging as a crucial regulatory nexus for energy metabolism in the brain and signaling transduction in synaptic plasticity, memory processes, and drug addiction instead of being merely a waste by-product of anaerobic glycolysis. In this review, the role of lactate in various memory processes, synapse plasticity and drug addiction on the basis of recent studies is summarized and discussed. To this end, three main parts are presented: first, lactate as an energy substrate in energy metabolism of the brain is described; second, lactate as a novel signaling molecule in synaptic plasticity, neural circuits, memory, and drug addiction is described; and third, in light of the above descriptions, it is plausible to speculate that lactate is predominantly a signaling molecule in specific memory processes and partly acts as an energy substrate. The future perspective in lactate signaling involving microglia and associated precise signaling pathways in the brain is highlighted.

Single-Cell Glia and Neuron Gene Expression in the Central Amygdala in Opioid Withdrawal Suggests Inflammation With Correlated Gut Dysbiosis

Drug-seeking in opioid dependence is due in part to the severe negative emotion associated with the withdrawal syndrome. It is well-established that negative emotional states emerge from activity in the amygdala. More recently, gut microflora have been shown to contribute substantially to such emotions. We measured gene expression in single glia and neurons gathered from the amygdala using laser capture microdissection and simultaneously measured gut microflora in morphine-dependent and withdrawn rats to investigate drivers of negative emotion in opioid withdrawal. We found that neuroinflammatory genes, notably Tnf, were upregulated in the withdrawal condition and that astrocytes, in particular, were highly active. We also observe a decreased Firmicutes to Bacteroides ratio in opioid withdrawal indicating gut dysbiosis. We speculate that these inflammatory and gut microflora changes contribute to the negative emotion experienced in opioid withdrawal that motivates dependence.

Underage drinking, alcohol dependence, and young people starting to use prescription pain relievers extra-medically: A zero-inflated Poisson regression model

Among young people who start using prescription pain relievers (PPRs) for feeling-states such as "to get high" or otherwise beyond boundaries intended by prescribers, the most recent epidemiological incidence estimates show 2%-9% with rapid-onset opioid dependence. In this work, we study recently active underage alcohol dependence as a susceptibility marker and estimate alcohol dependence-associated PPR rates of use, once use starts. In recent U.S. epidemiological samples, we identified 16,125 community-dwelling 12-to-20-year-olds with standardized assessments of both problem drinking and newly incident extra-medical PPR use. We applied zero-inflated Poisson (ZIP) regressions to estimate (a) alcohol dependence associations with susceptibility-to-persist after the very first occasion of extra-medical PPR use, and (b) the rate of PPR use, conditional on persistence. Underage drinkers with alcohol dependence were more susceptible to persistence in their extra-medical PPR use (p < .001). In addition, given susceptibility-to-persistence, there was an alcohol dependence-associated excess rate of extra-medical PPR use (risk ratio = 1.3; 95% confidence interval = 1.1, 1.6). Using ZIP regressions, we can see that underage alcohol dependence signals membership in a susceptible-to-persistence class of extra-medical PPR users and excess rates of extra-medical use. Underage drinking can be an indicator of greater vulnerability to start and persist in extra-medical use of PPR, particularly if presenting clinical features of alcohol dependence already are seen at or near time of first onset of such PPR use. For alcohol dependence-affected adolescent patients, nondrug pain management plans deserve consideration, with special surveillance if analgesic drugs are prescribed. Implications for genetic susceptibility research are discussed. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

A prospective, longitudinal study to evaluate the clinical utility of a predictive algorithm that detects risk of opioid use disorder

Purpose

The purpose of this study was to determine the clinical utility of an algorithm-based decision tool designed to assess risk associated with opioid use. Specifically, we sought to assess how physicians were using the profile in patient care and how its use affected patient outcomes.

Patients and methods

A prospective, longitudinal study was conducted to assess the utility of precision medicine testing in 5,397 patients across 100 clinics in the USA. Using a patent-protected, validated algorithm combining specific genetic risk factors with phenotypic traits, patients were categorized into low-, moderate-, and high-risk patients for opioid abuse. Physicians who ordered precision medicine testing were asked to complete patient evaluations and document their actions, decisions, and perceptions regarding the utility of the precision medicine tests. The patient outcomes associated with each treatment action were carefully documented.

Results

Physicians used the profile to guide treatment decisions for over half of the patients. Of those, guided treatment decisions for 24.5% of the patients were opioid related, including changing the opioid prescribed, starting an opioid, or titrating a patient off the opioid. Treatment guidance was strongly influenced by profile-predicted opioid use disorder (OUD) risk. Most importantly, patients whose physicians used the profile to guide opioid-related treatment decisions had improved clinical outcomes, including better pain management by medication adjustments, with an average pain decrease of 3.4 points on a scale of 1–10.

Conclusion

Patients whose physicians used the profile to guide opioid-related treatment decisions had improved clinical outcomes, as measured by decreased pain levels resulting from better pain management with prescribed medications. The clinical utility of the profile is twofold. It provides clinically actionable recommendations that can be used to 1) prevent OUD through limiting initial opioid prescriptions and 2) reduce pain in patients at low risk of developing OUD.

Infrequently expressed miRNAs influence survival after diagnosis with colorectal cancer

Half of miRNAs expressed in colorectal tissue are expressed < 50% of the population. Many infrequently expressed miRNAs have low levels of expression. We hypothesize that less frequently expressed miRNAs, when expressed at higher levels, influence both disease stage and survival after diagnosis with colorectal cancer (CRC); low levels of expression may be background noise.

We examine 304 infrequently expressed miRNAs in 1893 population-based cases of CRC with paired carcinoma and normal mucosa miRNA profiles. We evaluate miRNAs with disease stage and survival after adjusting for age, study center, sex, MSI status, and AJCC stage. These miRNAs were further evaluated with RNA-Seq data to identify miRNA::mRNA associations that may provide insight into the functionality of miRNAs.

Eleven miRNAs were associated with advanced disease stage among colon cancer patients (Q value = 0.10). Eight infrequently expressed miRNAs influenced survival if highly expressed in overall CRC. Of these, five increased likelihood of dying if they were highly expressed, i.e. miR-124-3p, miR-143-5p, miR-145-3p, miR31-5p, and miR-99b-5p, while three were associated with better survival if highly expressed, i.e. miR-362-5p, miR-374a-5p, and miR-590-5p. Thirteen miRNAs infrequently expressed in colon-specific carcinoma tissue were associated with CRC survival if highly expressed. Evaluation of miRNAs::mRNA associations showed that mRNA expression influenced by infrequently expressed miRNA contributed to networks and pathways shown to influence disease progression and prognosis.

Our large study enabled us to examine the implications of infrequently expressed miRNAs after removal of background noise. These results require replication in other studies. Confirmation of our findings in other studies could lead to important markers for prognosis.

Infrequently expressed miRNAs in colorectal cancer tissue and tumor molecular phenotype

We have previously shown that commonly expressed miRNAs influenced tumor molecular phenotype in colorectal cancer. We hypothesize that infrequently expressed miRNAs, when showing higher levels of expression, help to define tumor molecular phenotype. In this study, we examine 304 miRNAs expressed in at least 30 individuals, but in <50% of the population and with a mean level of expression above 1.0 relative florescent unit. We examine associations in 1893 individuals who have the tumor molecular phenotype data as well as miRNA expression levels for both carcinoma and normal colorectal tissue. We compare miRNAs uniquely associated with tumor molecular phenotype to the RNAseq data to identify genes associated with these miRNAs. This information is used to further identify unique pathways associated with tumor molecular phenotypes of TP53-mutated, KRAS-mutated, CpG island methylator phenotype and microsatellite instability tumors. Thirty-seven miRNAs were uniquely associated with TP53-mutated tumors; 30 of these miRNAs had higher level of expression in TP53-mutated tumors, while seven had lower levels of expression. Of the 34 miRNAs associated with CpG island methylator phenotype-high tumors, 16 were more likely to have a CpG island methylator phenotype-high tumor and 19 were less likely to be CpG island methylator phenotype-high. For microsatellite instability, 13 of the 22 infrequently expressed miRNAs were significantly less likely to be expressed in microsatellite unstable tumors. KRAS-mutated tumors were not associated with any miRNAs after adjustment for multiple comparisons. Of the dysregulated miRNAs, 17 were more likely to be TP53-mutated tumors while simultaneously being less likely to be CpG island methylator phenotype-high and/or microsatellite instability tumors. Genes regulated by these miRNAs were involved in numerous functions and pathways that influence cancer risk and progression. In summary, some infrequently expressed miRNAs, when expressed at higher levels, appear to have significant biological meaning in terms of tumor molecular phenotype and gene expression profiles.

Identifying novel genes and biological processes relevant to the development of cancer therapy-induced mucositis: An informative gene network analysis

Mucositis is a complex, dose-limiting toxicity of chemotherapy or radiotherapy that leads to painful mouth ulcers, difficulty eating or swallowing, gastrointestinal distress, and reduced quality of life for patients with cancer. Mucositis is most common for those undergoing high-dose chemotherapy and hematopoietic stem cell transplantation and for those being treated for malignancies of the head and neck. Treatment and management of mucositis remain challenging. It is expected that multiple genes are involved in the formation, severity, and persistence of mucositis. We used Ingenuity Pathway Analysis (IPA), a novel network-based approach that integrates complex intracellular and intercellular interactions involved in diseases, to systematically explore the molecular complexity of mucositis. As a first step, we searched the literature to identify genes that harbor or are close to the genetic variants significantly associated with mucositis. Our literature review identified 27 candidate genes, of which ERCC1, XRCC1, and MTHFR were the most frequently studied for mucositis. On the basis of this 27-gene list, we used IPA to generate gene networks for mucositis. The most biologically significant novel molecules identified through IPA analyses included TP53, CTNNB1, MYC, RB1, P38 MAPK, and EP300. Additionally, uracil degradation II (reductive) and thymine degradation pathways (p = 1.06-08) were most significant. Finally, utilizing 66 SNPs within the 8 most connected IPA-derived candidate molecules, we conducted a genetic association study for oral mucositis in the head and neck cancer patients who were treated using chemotherapy and/or radiation therapy (186 head and neck cancer patients with oral mucositis vs. 699 head and neck cancer patients without oral mucositis). The top ranked gene identified through this association analysis was RB1 (rs2227311, p-value = 0.034, odds ratio = 0.67). In conclusion, gene network analysis identified novel molecules and biological processes, including pathways related to inflammation and oxidative stress, that are relevant to mucositis development, thus providing the basis for future studies to improve the management and treatment of mucositis in patients with cancer.

Dietary intake alters gene expression in colon tissue: possible underlying mechanism for the influence of diet on disease

Supplemental Digital Content is available in the text.

Background

Although the association between diet and disease is well documented, the biologic mechanisms involved have not been entirely elucidated. In this study, we evaluate how dietary intake influences gene expression to better understand the underlying mechanisms through which diet operates.

Methods

We used data from 144 individuals who had comprehensive dietary intake and gene expression data from RNAseq using normal colonic mucosa. Using the DESeq2 statistical package, we identified genes that showed statistically significant differences in expression between individuals in high-intake and low-intake categories for several dietary variables of interest adjusting for age and sex. We examined total calories, total fats, vegetable protein, animal protein, carbohydrates, trans-fatty acids, mutagen index, red meat, processed meat, whole grains, vegetables, fruits, fiber, folate, dairy products, calcium, and prudent and western dietary patterns.

Results

Using a false discovery rate of less than 0.1, meat-related foods were statistically associated with 68 dysregulated genes, calcium with three dysregulated genes, folate with four dysregulated genes, and nonmeat-related foods with 65 dysregulated genes. With a more stringent false discovery rate of less than 0.05, there were nine meat-related dysregulated genes and 23 nonmeat-related genes. Ingenuity pathway analysis identified three major networks among genes identified as dysregulated with respect to meat-related dietary variables and three networks among genes identified as dysregulated with respect to nonmeat-related variables. The top networks (Ingenuity Pathway Analysis network score >30) associated with meat-related genes were (i) cancer, organismal injury, and abnormalities, tumor morphology, and (ii) cellular function and maintenance, cellular movement, cell death, and survival. Among genes related to nonmeat consumption variables, the top networks were (i) hematological system development and function, nervous system development and function, tissue morphology and (ii) connective tissue disorders, organismal injury, and abnormalities.

Conclusion

Several dietary factors were associated with gene expression in our data. These findings provide insight into the possible mechanisms by which diet may influence disease processes.

Validation Study of a Predictive Algorithm to Evaluate Opioid Use Disorder in a Primary Care Setting

BACKGROUND

Opioid abuse in chronic pain patients is a major public health issue. Primary care providers are frequently the first to prescribe opioids to patients suffering from pain, yet do not always have the time or resources to adequately evaluate the risk of opioid use disorder (OUD).

PURPOSE

This study seeks to determine the predictability of aberrant behavior to opioids using a comprehensive scoring algorithm ("profile") incorporating phenotypic and, more uniquely, genotypic risk factors.

METHODS AND RESULTS

In a validation study with 452 participants diagnosed with OUD and 1237 controls, the algorithm successfully categorized patients at high and moderate risk of OUD with 91.8% sensitivity. Regardless of changes in the prevalence of OUD, sensitivity of the algorithm remained >90%.

CONCLUSION

The algorithm correctly stratifies primary care patients into low-, moderate-, and high-risk categories to appropriately identify patients in need for additional guidance, monitoring, or treatment changes.

From genetic studies to precision medicine in alcohol dependence

Genetic factors contribute to more than 50% of the variation in the vulnerability to alcohol dependence (AD). Although significant advances have been made in medications for AD, these medications do not work for all people. Precise tailoring of medicinal strategies for individual alcoholic patients is needed to achieve optimal outcomes. This review updates the most promising information on genetic variants in AD, which may be useful for improving diagnostic, therapeutic, and monitoring strategies. We describe genetic candidates of various neurotransmitter and enzyme systems. In addition to biological and allelic associations with AD, genetic effects on AD-related phenotypes and treatment responses have also been described. Gene-gene and gene-environment interactions have been considered. Potential applications of genomewide and epigenetic approaches for identifying genetic biomarkers of AD have been discussed. Overall, the application of genetic findings in precision medicine for AD will likely involve an integrated approach that distinguishes effect sizes of specific genetic predictors with regard to sex, pharmacotherapy, ethnicity, and AD-related aspects and considers gene-gene and gene-environment interactions. Our work may pave the way toward more precise treatment for AD that could ultimately improve clinical management and interventions.

Exploring experimental cerebral malaria pathogenesis through the characterisation of host-derived plasma microparticle protein content

Cerebral malaria (CM) is a severe complication of Plasmodium falciparum infection responsible for thousands of deaths in children in sub-Saharan Africa. CM pathogenesis remains incompletely understood but a number of effectors have been proposed, including plasma microparticles (MP). MP numbers are increased in CM patients’ circulation and, in the mouse model, they can be localised within inflamed vessels, suggesting their involvement in vascular damage. In the present work we define, for the first time, the protein cargo of MP during experimental cerebral malaria (ECM) with the overarching hypothesis that this characterisation could help understand CM pathogenesis. Using qualitative and quantitative high-throughput proteomics we compared MP proteins from non-infected and P. berghei ANKA-infected mice. More than 360 proteins were identified, 60 of which were differentially abundant, as determined by quantitative comparison using TMT^TM isobaric labelling. Network analyses showed that ECM MP carry proteins implicated in molecular mechanisms relevant to CM pathogenesis, including endothelial activation. Among these proteins, the strict association of carbonic anhydrase I and S100A8 with ECM was verified by western blot on MP from DBA/1 and C57BL/6 mice. These results demonstrate that MP protein cargo represents a novel ECM pathogenic trait to consider in the understanding of CM pathogenesis.

MAPK1/ERK2 as novel target genes for pain in head and neck cancer patients

Background

Genetic susceptibility plays an important role in the risk of developing pain in individuals with cancer. As a complex trait, multiple genes underlie this susceptibility. We used gene network analyses to identify novel target genes associated with pain in patients newly diagnosed with squamous cell carcinoma of the head and neck (HNSCC).

Results

We first identified 36 cancer pain-related genes (i.e., focus genes) from 36 publications based on a literature search. The Ingenuity Pathway Analysis (IPA) analysis identified additional genes that are functionally related to the 36 focus genes through pathway relationships yielding a total of 82 genes. Subsequently, 800 SNPs within the 82 IPA-selected genes on the Illumina HumanOmniExpress-12v1 platform were selected from a large-scale genotyping effort. Association analyses between the 800 candidate SNPs (covering 82 genes) and pain in a patient cohort of 1368 patients with HNSCC (206 patients with severe pain vs. 1162 with non-severe pain) showed the highest significance for MAPK1/ERK2, a gene belonging to the MAP kinase family (rs8136867, p value = 8.92 × 10⁻⁴; odds ratio [OR] = 1.33, 95 % confidence interval [CI]: 1.13–1.58). Other top genes were PIK3C2G (a member of PI3K [complex], rs10770367, p value = 1.10 × 10⁻³; OR = 1.46, 95 % CI: 1.16–1.82), TCRA (the alpha chain of T-cell receptor, rs6572493, p value = 2.84 × 10⁻³; OR = 0.70, 95 % CI: 0.55–0.88), PDGFC (platelet-derived growth factor C, rs6845322, p value = 4.88 × 10⁻³; OR = 1.32, 95 % CI: 1.09–1.60), and CD247 (a member of CD3, rs2995082, p value = 7.79 × 10⁻³; OR = 0.76, 95 % CI: 0.62–0.93).

Conclusions

Our findings provide novel candidate genes and biological pathways underlying pain in cancer patients. Further study of the variations of these candidate genes could inform clinical decision making when treating cancer pain.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0348-7) contains supplementary material, which is available to authorized users.