Biology subjects

Christensen, E.

Publications and source records attributed to Christensen, E..

12 recordsLinked to original sources

bioRxiv2026

Investigating the impact of stressful life events on neuroanatomy across adolescence

Early-life stress elevates the risk of developing neuropsychiatric disorders. However, the mechanism underlying this vulnerability, and how they contribute to sex differences in these disorders, remain to be understood. Here, we use multivariate brain-based predictive models to examine how the number, positive or negative appraisal, and impact of adolescent stressful life events reported either by the youth or their caregivers are reflected in neuroanatomy (cortical thickness, surface area, cortical and subcortical gray matter volume, and T1 intensity measures). We used data from the Adolescent Brain Cognitive Development (ABCD) study at 2-year (N = 6,301, age 11-12), 4-year (N = 5,000, age 13-14) and 6-year (N = 3,226, age 15-16) follow-up time points to examine the sex-independent and sex-specific neural correlates of stressful life events. Our analyses showed mostly non-significant associations between stressful life events and neuroanatomy. However, we did find that the number of positively appraised stressful life events reported by the caregivers at the 4-year follow-up was significantly associated with cortical thickness, independent of sex, and with surface area in females only. Across three developmental timepoints, seven neuroanatomical measures, two reporting perspectives, and both sex-independent and sex-specific analyses, we show that the number, appraisal, and impact of stressful life events are largely not reflected in adolescent neuroanatomy.

neuroscience↗

bioRxiv2025

Shared Neural Signatures of Socioeconomic Status, Scarcity, and Neighborhood Threat in Youth

Early life adversity is a known risk factor for psychopathology, yet the neurodevelopmental impacts of distinct types of adversity remain unclear. Using machine learning, we examined how adversity (physical and sexual abuse, neighborhood threat, scarcity, household dysfunction, prenatal substance exposure, parental psychopathology) and socioeconomic status are associated with cortical thickness in youth. We used data from the Adolescent Brain Cognitive Development Study at three time points: baseline (N=6,908, ages 9-10), two-year follow-up (N=5,808), and four-year follow-up (N=2,245). Cortical thickness was linked to socioeconomic status and neighborhood threat at all time points, and scarcity at baseline. The strongest negative associations were in medial temporal and occipital regions. Our analyses revealed neural effects of socioeconomic status, neighborhood threat, and scarcity, converging on regions involved in memory, visual processing, and higher-order cognition. These findings suggest consistent neural signatures linked to socioeconomic disadvantage, highlighting the importance of addressing inequality to promote neurodevelopmental health.

neuroscience↗

bioRxiv2025

Neuroanatomy Reflects Individual Variability In Impulsivity in Youth

Individual differences in neural circuits underlying emotional regulation, motivation, and decision-making are implicated in many psychiatric illnesses. Interindividual variability in these circuits may manifest, at least in part, as individual differences in impulsivity at both normative and clinically significant levels. Impulsivity reflects a tendency towards rapid, unplanned reactions to internal or external stimuli without considering potential negative consequences coupled with difficulty inhibiting responses. Here, we use multivariate brain-based predictive models to explore the neural bases of impulsivity across multiple behavioral scales, neuroanatomical features (cortical thickness, surface area, and gray matter volume), and sexes (females and males) in a large sample of youth from the Adolescent Brain Cognitive Development (ABCD) Study at baseline (n=9,099) and two-year follow-up (n=6,432). Impulsivity is significantly associated with neuroanatomical variability, and these associations vary across behavioral scales and neuroanatomical features. Impulsivity broadly maps onto cortical thickness in dispersed regions (e.g., inferior frontal, lateral occipital, superior frontal, entorhinal), as well as surface area and gray matter volume in specific medial (e.g., parahippocampal, cingulate) and polar (e.g., frontal and temporal) territories. Importantly, while many relationships are stable across sexes and time points, others are sex-specific and dynamic. These results highlight the complexity of the relationships between neuroanatomy and impulsivity across scales, features, sexes, and time points in youth. These findings suggest that neuroanatomy, in combination with other biological and environmental factors, reflects a key driver of individual differences in impulsivity in youth. As such, neuroanatomical markers may help identify youth at increased risk for developing impulsivity-related illnesses. Furthermore, this work emphasizes the importance of adopting a multidimensional and sex-specific approach in neuroimaging and behavioral research.

neuroscience↗

bioRxiv2023

Field cancerization impacts tumor development, T-cell exhaustion and clinical outcomes in bladder cancer

Bladder field cancerization may be associated with disease outcome in patients with bladder cancer. To investigate this, we analyzed biopsies from bladder urothelium and urine samples by genomics and proteomics analyses. Samples were procured from multiple timepoints from 134 patients with early stage bladder cancer and detailed long term follow-up. We measured the field cancerization in normal-appearing bladder biopsies and found that high levels were associated with high tumor mutational burden, high neoantigen load, and high tumor-associated CD8 T-cell exhaustion. Non-synonymous mutations in known bladder cancer driver genes such as KDM6A and TP53 were identified as early disease drivers in normal urothelium. High field cancerization was associated with worse outcome but not with response to BCG. The level of urinary tumor DNA (utDNA) reflected the bladder tumor burden and originated from both tumors and field cancerization. High utDNA levels after BCG were associated with worse clinical outcomes for the patients. Our results indicate that the level of field cancerization may affect clinical outcome, tumor development and immune responses. utDNA measurements have significant prognostic value and reflect the disease status of the bladder.

cancer biology↗

bioRxiv2020

CReSCENT: CanceR Single Cell ExpressioN Toolkit

CReSCENTCanceR Single Cell ExpressioN Toolkit (https://crescent.cloud), is an intuitive and scalable web portal incorporating a containerized pipeline execution engine for standardized analysis of single-cell RNA sequencing (scRNA-seq) data. While scRNA-seq data for tumour specimens are readily generated, subsequent analysis requires high-performance computing infrastructure and user expertise to build analysis pipelines and tailor interpretation for cancer biology. CReSCENT uses public data sets and preconfigured pipelines that are accessible to computational biology non-experts and are user-editable to allow optimization, comparison, and reanalysis for specific experiments. Users can also upload their own scRNA-seq data for analysis and results can be kept private or shared with other users.

bioinformatics↗

bioRxiv2020

Models of the ventral stream that categorize and visualize images

An open question in systems neuroscience is which objective function (or computational "goal") best describes the computations performed by the ventral stream (VS) of primate visual cortex. Substantial past research has suggested that object categorization could be such a goal. Recent experiments, however, showed that information about object positions, sizes, etc. is encoded with increasing explicitness along this pathway. Because that information is not necessarily needed for object categorization, this motivated us to ask whether primate VS may do more than "just" object recognition. To address that question, we trained deep neural networks, all with the same architecture, with three different objectives: a supervised object categorization objective; an unsupervised autoencoder objective; and a semi-supervised objective that combined autoencoding with categorization. We then compared the image representations learned by these models to those observed in areas V4 and IT of macaque monkeys using canonical correlation analysis (CCA). We found that the semi-supervised model provided the best match the monkey data, followed closely by the unsupervised model, and more distantly by the supervised one. These results suggest that multiple objectives - including, critically, unsupervised ones - might be essential for explaining the computations performed by primate VS.

neuroscience↗

bioRxiv2020

Rare protein coding variants implicate genes involved in risk of suicide death

Suicide death is a worldwide health crisis, claiming close to 800,000 lives per year. Recent evidence suggests that prediction and prevention challenges may be aided by discoveries of genetic risk factors. Here we focus on the role of rare (MAF <1%), putatively functional single nucleotide polymorphisms (SNPs) in suicide death using the large genetic resources available in the Utah Suicide Genetic Risk Study (USGRS). We conducted a single-variant association analysis of 30,377 rare putatively functional SNPs present on the PsychArray genotyping array in 2,672 USGRS suicides of non-Finnish European (NFE) ancestry and 51,583 publicly available NFE controls from gnomAD, with additional follow-up analyses using an independent control sample of 21,324 NFE controls from the Psychiatric Genomics Consortium. SNPs underwent rigorous quality control, and among SNPs meeting significance thresholds, we considered only those that were validated in sequence data. We identified five novel, high-impact, rare SNPs with significant associations with suicide death (SNAPC1, rs75418419; TNKS1BP1, rs143883793; ADGRF5, rs149197213; PER1, rs145053802; and ESS2, rs62223875). Both PER1 and SNAPC1 have other supporting gene-level evidence of suicide risk, and an association with bipolar disorder has been reported for PER1 and with schizophrenia for PER1, TNKS1BP1, and ESS2. Three genes (PER1, TNKS1BP1, and ADGRF5), with additional genes implicated by GWAS studies on suicidal behavior, showed significant enrichment in immune system, homeostatic and signal transduction processes. Pain, depression, and accidental trauma were the most prevalent phenotypes in electronic medical record data for the categories assessed. These findings suggest an important role for rare variants in suicide risk and provide new insights into the genetic architecture of suicide death. Furthermore, we demonstrate the added utility of careful assessment of genotyping arrays in rare variant discovery.

genetics↗

bioRxiv2019

Analysis of synapse-level neuronal morphology in human post-mortem brain tissue

Many cognitive and psychiatric disorders are thought to be disorders of the synapse, yet the precise synapse defects underlying these disorders remain unknown. Because synapses are highly specialized anatomical structures, defects in synapse formation and function can often be observed as changes in micro-scale neuroanatomy. Unfortunately, few methods are available for accurate analysis of synapses in human post-mortem tissues. Here, we present a new methodological pipeline for assessing synapse-level neuron morphology in human post-mortem tissue that is accurate, rapid, and relatively inexpensive. Our method uses small tissue blocks from postmortem human brains, immersion fixation, single cell resolution by dye labeling, and confocal microscopy. As proof of principle, we analyzed pre-and postsynaptic structures from hippocampi of 13 individuals aged 4 months to 71 years. Our results suggest that postsynaptic CA1 dendritic spine shape and density are stable across ages, while presynaptic DG mossy fiber boutons undergo significant structural rearrangements with normal aging. This suggests that mossy fiber synapses, which play a major role in learning and memory, remain dynamic throughout life. Importantly, we find no effect of postmortem intervals up to 28 hours on neuron morphology. Thus, the ease of our new protocol should facilitate higher powered studies of human synapse structure in healthy and diseased states.

neuroscience↗

bioRxiv2019

Mutational analysis of field cancerization in bladder cancer

The multifocal and recurrent nature of bladder cancer has been explained by field cancerization of the bladder urothelium. To shed light on field cancerization in the bladder, we investigated the mutational landscape of normal appearing urothelium and paired bladder tumors from four patients. Sequencing of 509 cancer driver genes revealed the presence of 2-16 mutations exclusively localized in normal tissue (average target read depth 634x). Furthermore, 6-13 mutations were shared between tumor and normal samples and 8-75 mutations were exclusively detected in tumor samples. More mutations were observed in normal samples from patients with multifocal disease compared to patients with unifocal disease. Mutations in normal samples had low allele frequencies compared to tumor mutations (p<2.2*10-16). Furthermore, significant differences in the type of nucleotide changes between tumor, normal and shared mutations (p=2.7*10-8) were observed, and mutations in APOBEC context were observed primarily among tumor mutations (p=0.026). No differences in functional impact between normal, shared and tumor mutations were observed (p=0.23). Overall, these findings support the theory of multiple fields in the bladder, and document non-tumor specific driver mutations to be present in normal appearing bladder tissue.

cancer biology↗

bioRxiv2018

The Portal Project: a long-term study of a Chihuahuan desert ecosystem

This is a data paper for the Portal Project, a long-term ecological study of rodents, plants, and ants located in southeastern Arizona, U.S.A. This paper contains an overview of methods and information about the structure of the data files and the relational structure among the files. This is a living data paper and will be updated with new information as major changes or additions are made to the data. All data - along with more detailed data collection protocols and site information - is archived at: https://doi.org/10.5281/zenodo.1215988.

ecology↗

bioRxiv2017

Identification of genome-wide significant shared genomic segments in large extended Utah families at high risk for completed suicide

Suicide is the 10th leading cause of death in the US. While environment has undeniable impact, evidence suggests genetic factors play a significant role in completed suicide. We linked a resource of >4,500 DNA samples from completed suicides obtained from the Utah Medical Examiner to genealogical records and medical records data available on over 8 million individuals. This linking has resulted in the identification of high-risk extended families (7-9 generations) with significant familial risk of completed suicide. Familial aggregation across distant relatives minimizes effects of shared environment, provides more genetically homogeneous risk groups, and magnifies genetic risks through familial repetition. We analyzed Illumina PsychArray genotypes from suicide cases in 43 high-risk families, identifying 30 distinct shared genomic segments with genome-wide evidence (p=2.02E-07 to 1.30E-18) of segregation with completed suicide. The 207 genes implicated by the shared regions provide a focused set of genes for further study; 18 have been previously associated with suicide risk. While PsychArray variants do not represent exhaustive variation within the 207 genes, we investigated these for specific segregation within the high-risk families, and for association of variants with predicted functional impact in ~1300 additional Utah suicides unrelated to the discovery families. None of the limited PsychArray variants explained the high-risk family segregation; sequencing of these regions will be needed to discover segregating risk variants, which may be rarer or regulatory. However, additional association tests yielded four significant PsychArray variants (SP110, rs181058279; AGBL2, rs76215382; SUCLA2, rs121908538; APH1B, rs745918508), raising the likelihood that these genes confer risk of completed suicide.

genetics↗

bioRxiv2017

Repeated regime shifts in a desert rodent community

While studies increasingly document long-term change in community composition, whether long-term change occurs gradually or via rapid reorganization events remains unclear. We used Latent Dirichlet Allocation (LDA) and a change-point model to examine the long-term dynamics of a desert rodent community undergoing compositional change over a 38-year span. Our approach detected three rapid reorganization events, where changes in the relative abundances of dominant and rare species occurred, and a separate period of increased variance in the structure of the community. These events coincided with time periods--possibly related to climate events--where the total abundance of rodents was extremely low. There are a variety of processes that could link low abundance events with a higher probability of rapid ecological transitions, including higher importance of stochastic processes (i.e., competitive interactions or priority effects) and the removal of structuring effects of competitive dominants or incumbent species. Continued study of the dynamics of community change will provide important information not only on the processes structuring communities, but will also provide guidance for forecasting how communities will undergo change in the future.

ecology↗