From genes to behavior: placing cognitive models in the context of biological pathways

DRDs and Brain-Derived Neurotrophic Factor Share a Common Therapeutic Ground: A Novel Bioinformatic Approach Sheds New Light Toward Pharmacological Treatment of Cognitive and Behavioral Disorders

Cognitive and behavioral disorders are subgroups of mental health disorders. Both cognitive and behavioral disorders can occur in people of different ages, genders, and social backgrounds, and they can cause serious physical, mental, or social problems. The risk factors for these diseases are numerous, with a range from genetic and epigenetic factors to physical factors. In most cases, the appearance of such a disorder in an individual is a combination of his genetic profile and environmental stimuli. To date, researchers have not been able to identify the specific causes of these disorders, and as such, there is urgent need for innovative study approaches. The aim of the present study was to identify the genetic factors which seem to be more directly responsible for the occurrence of a cognitive and/or behavioral disorder. More specifically, through bioinformatics tools and software as well as analytical methods such as systemic data and text mining, semantic analysis, and scoring functions, we extracted the most relevant single nucleotide polymorphisms (SNPs) and genes connected to these disorders. All the extracted SNPs were filtered, annotated, classified, and evaluated in order to create the "genomic grammar" of these diseases. The identified SNPs guided the search for top suspected genetic factors, dopamine receptors D and neurotrophic factor BDNF, for which regulatory networks were built. The identification of the "genomic grammar" and underlying factors connected to cognitive and behavioral disorders can aid in the successful disease profiling and the establishment of novel pharmacological targets and provide the basis for personalized medicine, which takes into account the patient's genetic background as well as epigenetic factors.

Selection of Mice for Object Permanence Cognitive Task Solution

The selection of mice for high (“plus”) and low (“minus”) scores in the puzzle-box test was performed over five generations. This test evaluates the success (or failure) in finding the underpass, leading to the dark part of the box, when it is blocked. This means that the mouse is either able or unable to operate the “object permanence rule” (one of the index’s cognitive abilities). For the “+” strain, animals were bred who solved the test when the underpass test blocked with a plug; the “−” strain comprised those who were unable to solve this task. In mice of the “+” strain, the proportion of animals that was able to solve “plug” stages of the test was higher than in the “−” strain and in the non-selected genetically heterogeneous population. The “+” mice ate significantly more new food in the hyponeophagia test. Animals of both strains demonstrated the ability to “manipulate” the plug blocking the underpass, touching the plug with their paws and muzzle, although the majority of “−” mice were unable to open the underpass effectively. Thus, mice of both selected strains demonstrated that they were able to understand that the underpass does exist, but only “+”-strain animals (at least the majority of them) were able to realize the solution. The selection for plug-stage solution success affected the mouse’s ability to open the hidden underpass.

Selection of Laboratory Mice for the Cognitive Task Successful Solution and for the Inability to Solve It

Using the selected mouse strain EX as the founding population (selection for extrapolation ability) three selection generations of mice were obtained, which were selected for successful solution of object permanence test (plus-sub-strain) and for lack of such solution (minus-sub-strain). The successful solution required not only the ability to operate the object permanence rule (by J. Piajet), but the performance of complicated action (executive function) which was significantly higher in plus-substrain, and this is the unique example of successful selection for cognitive trait.

BLASSO: integration of biological knowledge into a regularized linear model

Background

In RNA-Seq gene expression analysis, a genetic signature or biomarker is defined as a subset of genes that is probably involved in a given complex human trait and usually provide predictive capabilities for that trait. The discovery of new genetic signatures is challenging, as it entails the analysis of complex-nature information encoded at gene level. Moreover, biomarkers selection becomes unstable, since high correlation among the thousands of genes included in each sample usually exists, thus obtaining very low overlapping rates between the genetic signatures proposed by different authors. In this sense, this paper proposes BLASSO, a simple and highly interpretable linear model with l₁-regularization that incorporates prior biological knowledge to the prediction of breast cancer outcomes. Two different approaches to integrate biological knowledge in BLASSO, Gene-specific and Gene-disease, are proposed to test their predictive performance and biomarker stability on a public RNA-Seq gene expression dataset for breast cancer. The relevance of the genetic signature for the model is inspected by a functional analysis.

Results

BLASSO has been compared with a baseline LASSO model. Using 10-fold cross-validation with 100 repetitions for models’ assessment, average AUC values of 0.7 and 0.69 were obtained for the Gene-specific and the Gene-disease approaches, respectively. These efficacy rates outperform the average AUC of 0.65 obtained with the LASSO. With respect to the stability of the genetic signatures found, BLASSO outperformed the baseline model in terms of the robustness index (RI). The Gene-specific approach gave RI of 0.15±0.03, compared to RI of 0.09±0.03 given by LASSO, thus being 66% times more robust. The functional analysis performed to the genetic signature obtained with the Gene-disease approach showed a significant presence of genes related with cancer, as well as one gene (IFNK) and one pseudogene (PCNAP1) which a priori had not been described to be related with cancer.

Conclusions

BLASSO has been shown as a good choice both in terms of predictive efficacy and biomarker stability, when compared to other similar approaches. Further functional analyses of the genetic signatures obtained with BLASSO has not only revealed genes with important roles in cancer, but also genes that should play an unknown or collateral role in the studied disease.

Genetically-Driven Enhancement of Dopaminergic Transmission Affects Moral Acceptability in Females but Not in Males: A Pilot Study

Moral behavior has been a key topic of debate for philosophy and psychology for a long time. In recent years, thanks to the development of novel methodologies in cognitive sciences, the question of how we make moral choices has expanded to the study of neurobiological correlates that subtend the mental processes involved in moral behavior. For instance, in vivo brain imaging studies have shown that distinct patterns of brain neural activity, associated with emotional response and cognitive processes, are involved in moral judgment. Moreover, while it is well-known that responses to the same moral dilemmas differ across individuals, to what extent this variability may be rooted in genetics still remains to be understood. As dopamine is a key modulator of neural processes underlying executive functions, we questioned whether genetic polymorphisms associated with decision-making and dopaminergic neurotransmission modulation would contribute to the observed variability in moral judgment. To this aim, we genotyped five genetic variants of the dopaminergic pathway [rs1800955 in the dopamine receptor D4 (DRD4) gene, DRD4 48 bp variable number of tandem repeat (VNTR), solute carrier family 6 member 3 (SLC6A3) 40 bp VNTR, rs4680 in the catechol-O-methyl transferase (COMT) gene, and rs1800497 in the ankyrin repeat and kinase domain containing 1 (ANKK1) gene] in 200 subjects, who were requested to answer 56 moral dilemmas. As these variants are all located in genes belonging to the dopaminergic pathway, they were combined in multilocus genetic profiles for the association analysis. While no individual variant showed any significant effects on moral dilemma responses, the multilocus genetic profile analysis revealed a significant gender-specific influence on human moral acceptability. Specifically, those genotype combinations that improve dopaminergic signaling selectively increased moral acceptability in females, by making their responses to moral dilemmas more similar to those provided by males. As females usually give more emotionally-based answers and engage the "emotional brain" more than males, our results, though preliminary and therefore in need of replication in independent samples, suggest that this increase in dopamine availability enhances the cognitive and reduces the emotional components of moral decision-making in females, thus favoring a more rationally-driven decision process.

Dopamine-System Genes and Cultural Acquisition: The Norm Sensitivity Hypothesis

Previous research in cultural psychology shows that cultures vary in the social orientation of independence and interdependence. To date, however, little is known about how people may acquire such global patterns of cultural behavior or cultural norms. Nor is it clear what genetic mechanisms may underlie the acquisition of cultural norms. Here, we draw on recent evidence for certain genetic variability in the susceptibility to environmental influences and propose a norm sensitivity hypothesis, which holds that people acquire culture, and rules of cultural behaviors, through reinforcement-mediated social learning processes. One corollary of the hypothesis is that the degree of cultural acquisition should be influenced by polymorphic variants of genes involved in dopaminergic neural pathways, which have been widely implicated in reinforcement learning. We reviewed initial evidence for this prediction and discussed challenges and directions for future research.