Detecting significant genotype-phenotype association rules in bipolar disorder: market research meets complex genetics

First-in-human, double-blind, randomized phase 1b study of peptide immunotherapy IMCY-0098 in new-onset type 1 diabetes: an exploratory analysis of immune biomarkers

BACKGROUND

IMCY-0098, a synthetic peptide developed to halt disease progression via elimination of key immune cells in the autoimmune cascade, has shown a promising safety profile for the treatment of type 1 diabetes (T1D) in a recent phase 1b trial. This exploratory analysis of data from that trial aimed to identify the patient biomarkers at baseline associated with a positive response to treatment and examined the associations between immune response parameters and clinical efficacy endpoints (as surrogates for mechanism of action endpoints) using an artificial intelligence-based approach of unsupervised explainable machine learning.

METHODS

We conducted an exploratory analysis of data from a phase 1b, dose-escalation, randomized, placebo-controlled study of IMCY-0098 in patients with recent-onset T1D. Here, a panel of markers of T cell activation, memory T cells, and effector T cell response were analyzed via descriptive statistics. Artificial intelligence-based analyses of associations between all variables, including immune responses and clinical responses, were performed using the Knowledge Extraction and Management (KEM®) v 3.6.2 analytical platform.

RESULTS

The relationship between all available patient data was investigated using unsupervised machine learning implemented in the KEM® environment. Of 15 associations found for the dose C group (450 μg subcutaneously followed by 3 × 225 μg subcutaneously), seven involved human leukocyte antigen (HLA) type, all of which identified improvement/absence of worsening of disease parameters in DR4+ patients and worsening/absence of improvement in DR4- patients. This association with DR4+ and non-DR3 was confirmed using the endpoints normalized area under the curve C-peptide from mixed meal tolerance tests where presence of DR4 HLA haplotype was associated with an improvement in both endpoints. Exploratory immune analysis showed that IMCY-0098 dose B (150 μg subcutaneously followed by 3 × 75 μg subcutaneously) and dose C led to an increase in presumed/potentially protective antigen-specific cytolytic CD4+ T cells and a decrease in pathogenic CD8+ T cells, consistent with the expected mechanism of action of IMCY-0098. The analysis identified significant associations between immune and clinical responses to IMCY-0098.

CONCLUSIONS

Promising preliminary efficacy results support the design of a phase 2 study of IMCY-0098 in patients with recent-onset T1D.

TRIAL REGISTRATION

ClinicalTrials.gov NCT03272269; EudraCT: 2016-003514-27.

The diabetes mellitus multimorbidity network in hospitalized patients over 50 years of age in China: data mining of medical records

OBJECTIVE

Many diabetes mellitus (DM) patients suffer from multimorbidity. Understanding the DM multimorbidity network should be given priority. The purpose of this study is characterize the DM multimorbidity network in people over 50 years.

METHODS

Data on 75 non-communicable diseases (NCDs) were extracted from electronic medical records of 309,843 hospitalized patients older than 50 years who had at least one NCD. The association rules analysis was used as a novel classification method and combined with the Chi-square tests to identify associations between NCDs and DM.

RESULT

A total of 12 NCDs were closely related to DM, {cholelithiasis, DM} was an unexpected combination. {dyslipidemia, DM} and {gout, DM} had the largest lift in the male and female groups, respectively. The negative related group included 7 NCDs. There were 9 NCDs included in the strong association rules. Most combinations were different by age and sex. In males, the strongest rule was {peripheral vascular disease (PVD), dyslipidemia, DM}, while {hypertension, dyslipidemia, chronic liver disease (CLD), DM} was the strongest in females. In patients younger than 70 years, hypertension, CLD, and dyslipidemia were the most dominant NCDs in the DM multimorbidity network. In patients 70 years or older, chronic kidney disease (CKD), CVD, CHD, and heart disease (HD) frequently co-occurred with DM.

CONCLUSION

Future primary healthcare policies for DM should be formulated based on age and sex. In patients younger than 70 years, more attention to hypertension, CLD, and dyslipidemia is required, while attention to CKD, CVD, CHD and HD is needed in patients older than 70 years.

Characteristics of insulin resistance in Korean adults from the perspective of circadian and metabolic sensing genes

BACKGROUND

The biological clock allows an organism to anticipate periodic environmental changes and adjust its physiology and behavior accordingly.

OBJECTIVE

This retrospective cross-sectional study examined circadian gene polymorphisms and clinical characteristics associated with insulin resistance (IR).

METHODS

We analyzed data from 1,404 Korean adults aged 30 to 55 with no history of cancer and cardio-cerebrovascular disease. The population was classified according to sex and homeostasis model assessment of insulin resistance (HOMA-IR) values. Demographics, anthropometric and clinical characteristics, and single nucleotide polymorphisms (SNPs) were analyzed with respect to sex, age, and HOMA-IR values. We used association rule mining to identify sets of SNPs from circadian and metabolic sensing genes that may be associated with IR.

RESULTS

Among the subjects, 15.0% of 960 women and 24.3% of 444 men had HOMA-IR values above 2. Most of the parameters differed significantly between men and women, as well as between the groups with high and low insulin sensitivity. Body fat mass of the trunk, which was significantly higher in insulin-resistant groups, had a higher correlation with high sensitivity C-reactive protein and hemoglobin levels in women, and alanine aminotransferase and aspartate aminotransferase levels in men. Homozygous minor allele genotype sets of SNPs rs17031578 and rs228669 in the PER3 gene could be more frequently found among women with HOMA-IR values above 2 (p = .014).

CONCLUSION

Oxidative stress enhanced by adiposity and iron overload, which may also be linked to NRF2 and PER3-related pathways, is related to IR in adulthood. However, due to the small population size in this study, more research is needed.

Prevalence of eating disorders in patients with bipolar disorder: a scoping review of the literature

BACKGROUND

Eating disorder (ED) and bipolar disorder (BD) exhibit certain phenomenological similarities rooted in eating behavior and emotional regulation. However, despite the growing body of research on the comorbidity of ED and BD, scientific data on the concurrent course of these disorders has remained poorly systematized.

AIM

To conduct a scoping review of published data on the prevalence of various types of ED among patients with BD types I and II in the context of the sex and clinical features of the concurrent course of these disorders.

METHODS

The analysis was reported following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for scoping reviews. The search was conducted in the MEDLINE electronic database. Studies were included if they were focused samples of patients diagnosed with BD and ED, and the Diagnostic and Statistical Manual of Mental Disorders, fourth and fifth editions (DSM-IV, DSM-5), or International Statistical Classification of Diseases and Related Health Problems, tenth Revision (ICD-10), were used for the verification of the ED and BD diagnoses. The descriptive analysis method was used to summarize the review findings.

RESULTS

A total of 41 studies were selected for the review. Lifetime ED in patients with BD ranged from 2.2% to 31.1%, and the prevalence rates of BD among patients with ED varied from 11.3% to 68.1%. ED nominally had a higher prevalence among individuals with BD type II and females. Additionally, the presence of ED in patients with BD was associated with earlier onset of mood disorder, a higher number of depressive episodes, higher levels of atypical depressive symptoms, suicide attempts, as well as a higher frequency of comorbid obsessive-compulsive and anxiety disorders, addictions, and various metabolic disorders.

CONCLUSION

Despite the high degree of volatility in the results, the prevalence rates of a concurrent course of ED and BD are rather high. For this reason, screening for ED in patients with BD and vice versa holds significant value in the accurate diagnosis and selection of the most effective therapy. The patterns of comorbidity among different types of ED and BD, depending on gender, need further exploration in future research.

Overview of frequent pattern mining

Various methods of frequent pattern mining have been applied to genetic problems, specifically, to the combined association of two genotypes (a genotype pattern, or diplotype) at different DNA variants with disease. These methods have the ability to come up with a selection of genotype patterns that are more common in affected than unaffected individuals, and the assessment of statistical significance for these selected patterns poses some unique problems, which are briefly outlined here.

A precision medicine framework using artificial intelligence for the identification and confirmation of genomic biomarkers of response to an Alzheimer's disease therapy: Analysis of the blarcamesine (ANAVEX2-73) Phase 2a clinical study

INTRODUCTION

The search for drugs to treat Alzheimer's disease (AD) has failed to yield effective therapies. Here we report the first genome-wide search for biomarkers associated with therapeutic response in AD. Blarcamesine (ANAVEX2-73), a selective sigma-1 receptor (SIGMAR1) agonist, was studied in a 57-week Phase 2a trial (NCT02244541). The study was extended for a further 208 weeks (NCT02756858) after meeting its primary safety endpoint.

METHODS

Safety, clinical features, pharmacokinetic, and efficacy, measured by changes in the Mini-Mental State Examination (MMSE) and the Alzheimer's Disease Cooperative Study-Activities of Daily Living scale (ADCS-ADL), were recorded. Whole exome and transcriptome sequences were obtained for 21 patients. The relationship between all available patient data and efficacy outcome measures was analyzed with unsupervised formal concept analysis (FCA), integrated in the Knowledge Extraction and Management (KEM) environment.

RESULTS

Biomarkers with a significant impact on clinical outcomes were identified at week 57: mean plasma concentration of blarcamesine (slope MMSE:P < .041), genomic variants SIGMAR1 p.Gln2Pro (ΔMMSE:P < .039; ΔADCS-ADL:P < .063) and COMT p.Leu146fs (ΔMMSE:P < .039; ΔADCS-ADL:P < .063), and baseline MMSE score (slope MMSE:P < .015). Their combined impact on drug response was confirmed at week 148 with linear mixed effect models.

DISCUSSION

Confirmatory Phase 2b/3 clinical studies of these patient selection markers are ongoing. This FCA/KEM analysis is a template for the identification of patient selection markers in early therapeutic development for neurologic disorders.

Patterns of Multimorbidity in Adults: An Association Rules Analysis Using the Korea Health Panel

This study aimed to identify the prevalence and patterns of multimorbidity among Korean adults. A descriptive study design was used. Of 11,232 adults aged 18 and older extracted from the 2014 Korean Health Panel Survey, 7118 had one or more chronic conditions. The chronic conditions code uses the Korean Standard Classification of Diseases. Association rule analysis and network analysis were conducted to identify patterns of multimorbidity among 4922 participants with multimorbidity. The prevalence of multimorbidity in the overall population was 34.8%, with a higher prevalence among women (40.8%) than men (28.6%). Hypertension had the highest prevalence in both men and women. In men, diabetes mellitus and hypertension yielded the highest probability of comorbidity (10.04%). In women, polyarthrosis and hypertension yielded the highest probability of comorbidity (12.51%). The results of the network analysis in four groups divided according to gender and age showed different characteristics for each group. Public health practitioners should adopt an integrated approach to manage multimorbidity rather than an individual disease-specific approach, along with different strategies according to age and gender groups.

Investigating the relationship between melatonin levels, melatonin system, microbiota composition and bipolar disorder psychopathology across the different phases of the disease

Background

Bipolar disorder (BD) is characterized by recurrent episodes of depression and mania/hypomania alternating with intervals of well-being. The neurobiological underpinnings of BD are still veiled although there is evidence pointing to a malfunction of the circadian clock system that is regulated by the neuromodulator melatonin (MLT). Small sample size studies in BD patients have shown that changes in the levels of MLT are associated with shifts in illness status. Moreover, mood stabilizers (including lithium and valproic acid) influence the MLT system. Of interest, MLT also modulates intestinal microbiota, and recent work suggests an important role of microbiota alterations in neuropsychiatric disorders, including BD. This study is designed to explore whether the possible patterns of associations between changes in the levels of MLT and its precursors and BD mood phases are modulated by variants within the genes encoding for the elements of the MLT system and/or by the microbiota composition.

Methods

We will conduct a 2-year follow-up study in 50 BD patients during the three different mood phases of the disease. For each phase, we will perform a blood withdrawal for the analysis of MLT levels and of variants of the genes related to the MLT pathway between 8 and 10 a.m. after an overnight fasting, a stool specimen collection for the analysis of microbiota composition, and a detailed psychometric assessment for depression, mania, impulsivity and cognitive abilities. We will also recruit 50 healthy age-matched controls in whom we will perform a blood withdrawal between 8 and 10 a.m. after an overnight fasting, a stool specimen collection, and a psychometric assessment to exclude the presence of psychiatric disorders.

Discussion

In this cross sectional (case–control vs. BD comparisons) and longitudinal (24 months) study, we expect to clarify the link between the MLT system, microbiota and BD psychopathology. We expect to identify some typical BD symptomatic clusters that will be more strictly associated with variations in the MLT system. In a personalized medicine perspective, this subgroup of BD patients may benefit from a pharmacological therapy targeting the MLT system.

Trial registration This study protocol was approved by the Ethics Committee of the University Hospital Agency of Cagliari (PG/2019/6277)