Biology subjects

Kim, M. J.

Publications and source records attributed to Kim, M. J..

43 records · Page 3Linked to original sources

bioRxiv2019

On the prediction of protein abundance from RNA

BackgroundProfiling of mRNA expression is an important method to identify biomarkers but complicated by limited correlations between mRNA expression and protein abundance. We hypothesised that these correlations could be improved by mathematical models based on measuring splice variants and time delay in protein translation. MethodsWe characterised time-series of primary human naive CD4+ T cells during early T-helper type 1 differentiation with RNA-sequencing and mass-spectrometry proteomics. We then performed computational time-series analysis in this system and in two other key human and murine immune cell types. Linear mathematical mixed time-delayed splice variant models were used to predict protein abundances, and the models were validated using out-of-sample predictions. Lastly, we re-analysed RNA-Seq datasets to evaluate biomarker discovery in five T-cell associated diseases, validating the findings for multiple sclerosis (MS) and asthma. ResultsThe new models demonstrated median correlations of mRNA-to-protein abundance of 0.79-0.94, significantly out-performing models not including the usage of multiple splice variants and time-delays, as shown in cross-validation tests. Our mathematical models provided more differentially expressed proteins between patients and controls in all five diseases. Moreover, analysis of these proteins in asthma and MS supported their relevance. One marker, sCD27, was clinically validated in MS using two independent cohorts, for treatment response and prognosis. ConclusionOur splice variant and time-delay models substantially improved the prediction of protein abundance from mRNA data in three immune cell-types. The models provided valuable biomarker candidates, which were validated in clinical studies of MS and asthma. We propose that our strategy is generally applicable for biomarker discovery.

bioinformatics↗

bioRxiv2019

Corticolimbic circuit structure moderates an association between early life stress and later trait anxiety

Childhood adversity is associated with a wide range of negative behavioral and neurodevelopmental consequences. However, individuals vary substantially in their sensitivity to such adversity. Here, we examined how individual variability in structural features of the corticolimbic circuit, which plays a key role in emotional reactivity, moderates the association between childhood adversity and later trait anxiety in 798 young adult university students. Consistent with prior research, higher self-reported childhood adversity was significantly associated with higher self-reported trait anxiety. However, this association was attenuated in participants with higher microstructural integrity of the uncinate fasciculus and greater thickness of the orbitofrontal cortex. These structural properties of the corticolimbic circuit may capture a neural profile of relative resiliency to early life stress, especially against the negative effects of childhood adversity on later trait anxiety. More generally, our findings highlight the potential utility in the simultaneous consideration of qualitatively different brain structural measures in explaining complex behavioral associations in future research.

neuroscience↗

bioRxiv2019

Maternal Protection in Childhood is Associated with Amygdala Reactivity and Structural Connectivity in Adulthood

Recently, we reported that variability in early-life caregiving experiences maps onto individual differences in threat-related brain function. Specifically, we found that greater familial affective responsiveness is associated with increased amygdala reactivity to interpersonal threat, particularly in adolescents having experienced relatively low recent stress. Here, we conceptually replicate and extend on our previous work to provide further evidence that subtle variability in specific features of early caregiving shapes structural and functional connectivity between the amygdala and medial prefrontal cortex (mPFC) in a cohort of 312 young adult volunteers. Multiple regression analyses revealed that participants who reported higher maternal but not paternal protection exhibited increased amygdala reactivity to explicit signals of interpersonal threat (i.e., angry facial expressions) but not implicit signals of broad environmental threat (i.e., fearful facial expressions). While amygdala functional connectivity with regulatory regions of the mPFC was not significantly associated with maternal protection, participants who reported higher maternal protection exhibited relatively decreased structural integrity of the uncinate fasciculus (UF), a white matter tract connecting these same brain regions. The observed associations were independent of the potential confounding influences of participant sex, socioeconomic status, and self-reported childhood trauma. There were no significant associations between structural or functional brain measures and either maternal or paternal care ratings. These findings suggest that an over controlling parenting style in mothers during childhood is associated with functional and structural alterations of brain regions involved in generating and regulating responses to threat in young adulthood.

neuroscience↗

bioRxiv2018

General Functional Connectivity: shared features of resting-state and task fMRI drive reliable individual differences in functional brain networks

Intrinsic connectivity, measured using resting-state fMRI, has emerged as a fundamental tool in the study of the human brain. However, due to practical limitations, many studies do not collect enough resting-state data to generate reliable measures of intrinsic connectivity necessary for studying individual differences. Here we present general functional connectivity (GFC) as a method for leveraging shared features across resting-state and task fMRI and demonstrate in the Human Connectome Project and the Dunedin Study that GFC offers better test-retest reliability than intrinsic connectivity estimated from the same amount of resting-state data alone. Furthermore, at equivalent scan lengths, GFC displays higher heritability on average than resting-state functional connectivity. We also show that predictions of cognitive ability from GFC generalize across datasets, performing as well or better than resting-state or task data alone. Collectively, our work suggests that GFC can improve the reliability of intrinsic connectivity estimates in existing datasets and, subsequently, the opportunity to identify meaningful correlates of individual differences in behavior. Given that task and resting-state data are often collected together, many researchers can immediately derive more reliable measures of intrinsic connectivity through the adoption of GFC rather than solely using resting-state data. Moreover, by better capturing heritable variation in intrinsic connectivity, GFC represents a novel endophenotype with broad applications in clinical neuroscience and biomarker discovery.

neuroscience↗

bioRxiv2018

Microstructural integrity of white matter moderates an association between childhood adversity and adult trait anger

Amongst a number of negative life sequelae associated with childhood adversity is the later expression of a higher dispositional tendency to experience anger and frustration to a wide range of situations (i.e., trait anger). We recently reported that an association between childhood adversity and trait anger is moderated by individual differences in both threat-related amygdala activity and executive control-related dorsolateral prefrontal cortex (dlPFC) activity, wherein individuals with relatively low amygdala and high dlPFC activity do not express higher trait anger even when having experienced childhood adversity. Here, we examine possible structural correlates of this functional dynamic using diffusion magnetic resonance imaging data from 647 young adult men and women volunteers. Specifically, we tested whether the degree of white matter microstructural integrity as indexed by fractional anisotropy modulated the association between childhood adversity and trait anger. Our analyses revealed that higher microstructural integrity of multiple pathways was associated with an attenuated link between childhood adversity and adult trait anger. Amongst these pathways was the uncinate fasciculus, which not only provides a major anatomical link between the amygdala and prefrontal cortex but also is associated with individual differences in regulating negative emotion through top-down cognitive reappraisal. These findings suggest that higher microstructural integrity of distributed white matter pathways including but not limited to the uncinate fasciculus may represent an anatomical foundation serving to buffer against the expression of childhood adversity as later trait anger, which is itself associated with multiple negative health outcomes.

neuroscience↗

bioRxiv2018

Brain-Specific Deletion of GIT1 Impairs Cognition and Alters Phosphorylation of Synaptic Protein Networks Implicated in Schizophrenia Susceptibility

Despite tremendous effort, the molecular and cellular basis of cognitive deficits in schizophrenia remain poorly understood. Recent progress in elucidating the genetic architecture of schizophrenia has highlighted the association of multiple loci and rare variants that may impact susceptibility. One key example, given their potential etiopathogenic and therapeutic relevance, is a set of genes that encode proteins that regulate excitatory glutamatergic synapses in brain. A critical next step is to delineate specifically how such genetic variation impacts synaptic plasticity and to determine if and how the encoded proteins interact biochemically with one another to control cognitive function in a convergent manner. Towards this goal, here we study the roles of GPCR-kinase interacting protein 1 (GIT1), a synaptic scaffolding and signaling protein with damaging coding variants found in schizophrenia patients, as well as copy number variants found in patients with neurodevelopmental disorders. We generated conditional neural-selective GIT1 knockout mice and find that these mice have deficits in fear conditioning learning and spatial memory. Using global quantitative phospho-proteomics, we revealed that GIT1 deletion in brain perturbs specific networks of GIT1-interacting synaptic proteins. Importantly, several schizophrenia and neurodevelopmental disorder risk genes are present within these networks. We propose that GIT1 regulates the phosphorylation of a network of synaptic proteins and other critical regulators of neuroplasticity, and that perturbation of these networks may contribute to cognitive deficits observed in schizophrenia and neurodevelopmental disorders.

neuroscience↗

bioRxiv2017

Trajectories of Alcohol Use Initiation and Risk to Develop an Alcohol Use Disorder During Adolescence: A Role for Stress and Amygdala Activity

Early alcohol use initiation predicts onset of alcohol use disorders (AUD) in adulthood. However, little is known about developmental trajectories of alcohol use initiation or their putative biological and environmental correlates. Here we report the results of latent class analyses identifying two trajectories of alcohol use initiation in a prospective study of adolescents selected for the presence or absence of familial risk for depression at baseline. The latent class analyses identified two distinct patterns of initiation: early initiators (EI; n=32) who reported greater baseline alcohol use (M = 1.12, SE = .35) and exhibited a more rapid rate of change in use between baseline and each follow up wave (M = 4.43, SE = .94); and in contrast, late initiators (LI; n=298) who reported lower baseline use (M = .23, SE = .03) and exhibited a slower rate of change between baseline and each of the subsequent follow up waves (M = .12, SE = .03). Early initiators had more positive expectancies regarding alcohol (p = .002 - p = .005) and reported higher levels of stressful life events during the year prior to baseline assessment (p = .001). Additionally, fMRI analyses revealed that EI displayed heightened threat-related amygdala activity at baseline compared to LI (p = .001), but no differences in reward-related ventral striatum activity. Lastly survival analyses revealed that EI initiators were 6.7 times more likely to develop an AUD by age 19 when compared to the LI (p = .005). These patterns, which were independent of broad familial risk for depression, suggest that early initiation of alcohol use during adolescence associated with later risk for AUD is reflected in both higher levels of stressful life events and higher neural reactivity to threat, the combination of which may inform ongoing efforts to prevent persistent dysfunction.

neuroscience↗