Dysregulation Of Networks Research Articles

Association between altered white matter networks and post operative ventricle volume in shunt-treated pediatric hydrocephalus

ObjectiveThe objective of this study was to use probabilistic tractography in combination with white matter microstructure metrics to characterize differences in white matter networks between shunt-treated pediatric hydrocephalus patients relative to healthy controls. We were also able to explore the relationship between these white matter networks and postoperative ventricle volume. MethodsNetwork-based statistics was used in combination with whole-brain probabilistic tractography to determine dysregulated white matter networks in a sample of patients with pediatric hydrocephalus (n = 8), relative to controls (n = 36). Metrics such as streamline count (SC), as well as the mean of the fractional anisotropy along a tract, axial diffusivity (AD), mean diffusivity (MD), and radial diffusivity (RD) were assessed. In networks that were found to be significantly different for patients with hydrocephalus, tracts were evaluated to assess their relationship with postoperative lateral ventricle volume. ResultsPatients with pediatric hydrocephalus had various networks that were either upregulated or downregulated relative to controls across all white matter measures. Predominately, network dysregulation occurred in tracts involving structures located outside of the frontal lobe. Furthermore tracts with values suggesting decreased white matter integrity were not only found between subcortical structures, but also cortical structures. While there were various tracts with white matter metrics that were initially predicted by lateral ventricle volume, only two tracts remained significant following multiple comparisons. ConclusionsThis cross-sectional study in pediatric patients with hydrocephalus and healthy controls demonstrated using whole-brain probabilistic tractography that there are various networks with dysregulated white matter integrity in hydrocephalus patients relative to controls. These dysregulated networks have tracts connecting structures throughout the brain, and the regions were predominately located centrally and posteriorly. Postoperative ventricle volume did not predict the white matter integrity of many tracts. Future studies with larger sample sizes are needed to further understand these results.

Understanding the Impact of HIV-Associated Bone Marrow Alterations on Erythropoiesis

Human Immunodeficiency Virus (HIV) infection presents a multifaceted challenge, extending beyond its primary impact on the immune system to affect various organ systems. Among these, the bone marrow, the primary site for hematopoiesis, undergoes substantial alterations during HIV infection, profoundly influencing erythropoiesis—the process of red blood cell production. Anemia, a prevalent hematologic complication in HIV-infected individuals, often serves as a marker of disease progression and impacts overall health outcomes. This paper aims to delve into the intricate relationship between HIV-associated bone marrow alterations and their consequential effects on erythropoiesis. The mechanisms underlying bone marrow changes in HIV infection, including direct viral effects, dysregulation of cytokine networks, and inflammatory processes, significantly disrupt the delicate balance necessary for efficient erythropoiesis. The impact of these alterations on erythropoiesis manifests through ineffective red blood cell production, decreased erythropoietin responsiveness, and shortened red blood cell lifespan. Chronic inflammation further complicates erythropoietic processes, contributing to the development and perpetuation of anemia in HIV-infected individuals. Therapeutic interventions encompass a multifaceted approach, including antiretroviral therapy (ART) to control viral replication, erythropoiesis-stimulating agents, and adjunctive nutritional support to manage anemia. However, emerging research targeting bone marrow microenvironmental factors and novel agents stimulating erythropoiesis offer promising avenues for future therapeutic development. Keywords: HIV, bone marrow, erythropoiesis, erythropoietin, antiretroviral therapy

Modern trial outcome measures increase trial participation and recruitment of representative peoples

AbstractBackgroundClinical trials have been one size fits all, despite evidence that dementia ensues from a combination of pathologies with effects from environment, sex/gender, race/ethnicity and other factors influencing disease course. Cardiovascular diseases and cancer have measures (imaging and molecular biomarkers) that aid in capturing targetable biology. These biomarkers are used for risk stratification, precise diagnostic classification, in addition to inclusion as outcomes in trials. Clinical trials for brain degenerative disorders would benefit from a similar precision approaches.MethodWe performed proteomics analyses on banked plasma samples from longitudinal observational studies of vascular cognitive impairment and dementia (VCID) and a clinical trial (SPRINT‐MIND) targeting hypertension, a major VCID risk factor. Using multi‐modal analytical approaches we combined molecular measures with imaging and clinical outcomes to identify promising molecular markers for risk stratification for VCID clinical trials and maximizing benefit of interventions for VCID.ResultProteins related to angiogenesis as well as innate immune activation were found to be dysregulated in cases versus controls. With multivariate analyses, components with high loading from proteins involved in these multi‐cellular phenotypes were associated with cognitive outcomes. Using network analyses, key molecular nodes were validated via orthogonal methods.ConclusionA simple molecular panel with key proteins involved in dysregulated molecular networks mediating the effect of vascular disease on cognition could be developed and used for risk stratification in clinical trials of VCID. Greater precision in clinical trials would ensure higher benefit at lower cost, at all levels.

Deciphering the components of Amyloid‐beta (Aβ)‐driven dementia using a novel peptide‐focused global proteomics platform

AbstractBackgroundThe overlap of Alzheimer’s disease (AD) symptomology and pathology with other dementia types is a significant challenge to treatment, patient care, and new drug development. Amyloid‐beta (Aβ) peptides begin to accumulate in AD subjects over a decade prior to clinical symptoms and impair multiple cellular pathways during disease continuum. However, how the brain proteome is remodeled by Aβ burden remains an enigma. Here we compared the cerebrospinal fluid (CSF) proteomes of demented subjects with or without Aβ pathology to unveil alterations specific to Aβ‐driven dementia.MethodMass spectrometry data (PRIDE archive PXD016278) from CSF of cognitively impaired Sweden cohort subjects was reanalyzed using our de novo‐assisted workflow. Peptide raw peak area intensities were quantile normalized and log2 transformed to reduce technical variation and ensure distribution symmetry. Differentially expressed peptides were identified via analysis of covariance after adjusting for age and gender. Multiscale Embedded Gene Co‐expression Network Analysis (MEGENA) was used to explore the dysregulated network from Aβ‐driven brain proteome remodeling.ResultThe de novo‐assisted workflow significantly increased the CSF proteome depth ‐ 4,572 CSF protein groups vs 1542 protein groups reported in PXD016278 analysis. Comparison of peptide‐level CSF proteomes of demented subjects with or without Aβ pathology identified 2,014 differentially regulated peptides (q<0.2). These alterations may reflect the Aβ‐driven brain proteome remodeling in CSF. MEGENA network analysis identified several hubs and network modules. The most significantly altered ALDO‐A peptide represented a hub, a highly connected node within a network module, and exhibited high correlation with AD‐linked neurosecretory protein VGF and MAPT. The top pathways enriched in MEGENA network modules, e.g. extracellular matrix organization, cell adhesion, and neurogenesis, are consistent with other pathway enrichment analyses across other cross‐sectional studies in AD and non‐AD dementias.ConclusionThis is the first study capturing the peptide‐level alterations in CSF to reflect brain proteome remodeling by Aβ burden. This data will serve as an important resource for biomarkers demarcating AD from non‐AD.

Development of MDS in Pediatric Patients with GATA2 Deficiency: Increased Histone Trimethylation and Deregulated Apoptosis as Potential Drivers of Transformation

GATA2 deficiency is a heterogeneous, multisystem disorder associated with a high risk of developing myelodysplastic syndrome (MDS) and the progression to acute myeloid leukemia. The mechanisms underlying malignant transformation in GATA2 deficiency remain poorly understood, necessitating predictive markers to assess an individual’s risk of progression and guide therapeutic decisions. In this study, we performed a systematic analysis of bone marrow biopsies from 57 pediatric MDS patients. Focusing on hematopoiesis and the hematopoietic niche, including its microenvironment, we used multiplex immunofluorescence combined with multispectral imaging, gene expression profiling, and multiplex RNA in situ hybridization. Patients with a GATA2 deficiency exhibited a dysregulated GATA2 transcriptional network. Disease progression (GATA2-EB, n = 6) was associated with increased GATA2 mRNA levels, restored expression of the GATA2 target EZH2, and increased H3K27me3. GATA2-EB was further characterized by the high expression of the anti-apoptotic protein BCL2, a feature absent in children with a GATA2 deficiency and refractory cytopenia of childhood (GATA2-RCC, n = 24) or other pediatric MDS subgroups (RCC, n = 17; MDS-EB, n = 10). The multispectral imaging analysis of additional BCL2 family members revealed significantly elevated Mediators of Apoptosis Combinatorial (MAC) scores in GATA2-EB patients. Taken together, our findings highlight the potential drivers of disease progression in GATA2 deficiency, particularly increased histone trimethylation and dysregulated apoptosis. Furthermore, upregulated BCL2 and EZH2 and increased MAC scores provide a strong rationale for the use of venetoclax and azacitidine in therapeutic regimens for GATA2-EB.

Identifying the driver miRNAs with somatic copy number alterations driving dysregulated ceRNA networks in cancers

BackgroundMicroRNAs (miRNAs) play critical roles in cancer initiation and progression, which were critical components to maintain the dynamic balance of competing endogenous RNA (ceRNA) networks. Somatic copy number alterations (SCNAs) in the cancer genome could disturb the transcriptome level of miRNA to deregulate this balance. However, the driving effects of SCNAs of miRNAs were insufficiently understood.MethodsIn this study, we proposed a method to dissect the functional roles of miRNAs under different copy number states and identify driver miRNAs by integrating miRNA SCNAs profile, miRNA-target relationships and expression profiles of miRNA, mRNA and lncRNA.ResultsApplying our method to 813 TCGA breast cancer (BRCA) samples, we identified 29 driver miRNAs whose SCNAs significantly and concordantly regulated their own expression levels and further inversely dysregulated expression levels of their targets or disturbed the miRNA-target networks they directly involved. Based on miRNA-target networks, we further constructed dynamic ceRNA networks driven by driver SCNAs of miRNAs and identified three different patterns of SCNA interference in the miRNA-mediated dynamic ceRNA networks. Survival analysis of driver miRNAs showed that high-level amplifications of four driver miRNAs (including has-miR-30d-3p, has-mir-30b-5p, has-miR-30d-5p and has-miR-151a-3p) in 8q24 characterized a new BRCA subtype with poor prognosis and contributed to the dysfunction of cancer-associated hallmarks in a complementary way. The SCNAs of driver miRNAs across different cancer types contributed to the cancer development by dysregulating different components of the same cancer hallmarks, suggesting the cancer specificity of driver miRNA.ConclusionsThese results demonstrate the efficacy of our method in identifying driver miRNAs and elucidating their functional roles driven by endogenous SCNAs, which is useful for interpreting cancer genomes and pathogenic mechanisms.

Cell-type brain-region specific changes in prefrontal cortex of a mouse model of alcohol dependence

The prefrontal cortex is a crucial regulator of alcohol drinking, and dependence, and other behavioral phenotypes associated with AUD. Comprehensive identification of cell-type specific transcriptomic changes in alcohol dependence will improve our understanding of mechanisms underlying the excessive alcohol use associated with alcohol dependence and will refine targets for therapeutic development. We performed single nucleus RNA sequencing (snRNA-seq) and Visium spatial gene expression profiling on the medial prefrontal cortex (mPFC) obtained from C57BL/6 J mice exposed to the two-bottle choice-chronic intermittent ethanol (CIE) vapor exposure (2BC-CIE, defined as dependent group) paradigm which models phenotypes of alcohol dependence including escalation of alcohol drinking. Gene co-expression network analysis and differential expression analysis identified highly dysregulated co-expression networks in multiple cell types. Dysregulated modules and their hub genes suggest novel understudied targets for studying molecular mechanisms contributing to the alcohol dependence state. A subtype of inhibitory neurons was the most alcohol-sensitive cell type and contained a downregulated gene co-expression module; the hub gene for this module is Cpa6, a gene previously identified by GWAS to be associated with excessive alcohol consumption. We identified an astrocytic Gpc5 module significantly upregulated in the alcohol-dependent group. To our knowledge, there are no studies linking Cpa6 and Gpc5 to the alcohol-dependent phenotype. We also identified neuroinflammation related gene expression changes in multiple cell types, specifically enriched in microglia, further implicating neuroinflammation in the escalation of alcohol drinking. Here, we present a comprehensive atlas of cell-type specific alcohol dependence mediated gene expression changes in the mPFC and identify novel cell type-specific targets implicated in alcohol dependence.

EPCO-41. MICRORNA-MEDIATED DIRECT NEURONAL REPROGRAMMING OF GLIOBLASTOMAS

Abstract Neuron-specific microRNAs miR-9/9* and miR-124 (miR-9/9*-124) are potent neurogenic molecules whose ectopic expression in non-neuronal somatic cells effectively induces direct cell fate conversion into a neuronal fate. Our recent work indicates that the fate transition occurs in distinct steps where miR-9/9*-124 first represses core gene regulatory networks to erase the original non-neuronal cell identity and subsequently activates the neuronal program to confer neuronal fate. Extending these findings, we reason that repression of similar gene regulatory networks by miR-9/9*-124 can also induce fate erasure in cancerous cells using glioblastoma as a paradigm. Glioblastoma multiforme (GBM) is a type of aggressive brain tumor with poor prognosis. Instead of having specific mutation profiles, GBMs present a global genetic network dysregulation which gives rise to a neural stem cell or progenitor cell-like state resembling embryonic neural development. Whereas miR-9/9*-124 plays a key role in inducing mitotic exit and orchestrating neurogenesis during development and neuronal reprogramming, we hypothesize that miR-9/9*-124 will instruct neuronal reprogramming of GBMs. Our results so far demonstrate that miR-9/9*-124 indeed exerts reprogramming activities in patient-derived GBM cell lines. Ectopic expression of miR-9/9*-124 in vitro readily induces GBM cells to exit cell cycle and promotes neuronal identity over time. In GBM intracerebral xenograft mouse model, mice receiving GBM cells overexpressing miR-9/9*-124 were able to survive longer than those with GBMs overexpressing non-specific microRNAs. We are currently carrying out transcriptomic and chromatin accessibility analyses to infer the epigenetic switch as GBM cells are reprogrammed to neurons. Based on these studies, we will further examine whether the GBM cells undergo irreversible fate erasure and are reprogrammed into a stable post-mitotic neuronal state. Our studies will provide insights into the plasticity of GBM fate that can be controlled by microRNAs and the key downstream regulatory nodes underlying fate transition of GBM to permanent post-mitotic state.

Abstract 17103: The Proteomic Fingerprint in Patients With Single Ventricle Disease in the Interstage Period: Evidence of Chronic Inflammation and Widespread Activation of Biological Networks

Introduction: Children with single ventricle heart disease (SVHD) experience significant morbidity across systems and time: (AKI 70%, neurodevelopmental impairment 33%, growth failure 14%, NEC 5.5%). Proteomics is a novel method to identify new biomarkers and mechanisms of injury in complex physiologic states. Hypothesis: Does the proteome of patients with SVHD differ from healthy children, and which biological systems are activated or repressed? Methods: Infants with SVHD in the interstage period were compared to similar-age healthy controls. Serum samples were collected, stored at -80C, and run on a panel of 1500 proteins in single batch analysis (Somalogic Inc., CO). Partial Least Squares-Discriminant Analysis (PLS-DA) was used to compare the proteomic profile of cases and controls and t-tests to detect differences in individual proteins (FDR < 0.05). Protein network analysis with functional enrichment was performed in STRING and Cytoscape. Results: PLS-DA readily discriminated between cases (n=33) and controls (n=24) based on their proteomic pattern alone (Accuracy=0.96, R2=0.97, Q2=0.80) (Fig 1a). 568 proteins differed between groups (FDR < 0.05). The 15 proteins with the greatest effect on the proteomic phenotype between the groups are shown (Fig 1b). We identified 25 up-regulated functional clusters and 13 down-regulated (5 clusters highlighted in Fig 1c). Active biological systems fell into six key groups: angiogenesis and cell proliferation/turnover, immune system activation and inflammation, altered metabolism, neuronal development, gastrointestinal system, and cardiac development. Conclusions: We report a clear differentiation in the circulating proteome of patients with SVHD and healthy controls with >500 circulating proteins distinguishing the groups. This proteomic data identifies various dysregulated protein networks across multiple organ systems with promising biological plausibility as drivers of SVHD morbidity.

Inhibition of ATR opposes glioblastoma invasion through disruption of cytoskeletal networks and integrin internalization via macropinocytosis.

Glioblastomas have highly infiltrative growth patterns that contribute to recurrence and poor survival. Despite infiltration being a critical therapeutic target, no clinically useful therapies exist that counter glioblastoma invasion. Here, we report that inhibition of ataxia telangiectasia and Rad 3 related kinase (ATR) reduces invasion of glioblastoma cells through dysregulation of cytoskeletal networks and subsequent integrin trafficking. Glioblastoma motility and invasion were assessed in vitro and in vivo in response to ATR inhibition (ATRi) and ATR overexpression using time-lapse microscopy, two orthotopic glioblastoma models, and intravital imaging. Disruption to cytoskeleton networks and endocytic processing were investigated via high-throughput, super-resolution and intravital imaging. High ATR expression was associated with significantly poorer survival in clinical datasets while histological, protein expression, and spatial transcriptomics using glioblastoma tumor specimens revealed higher ATR expression at infiltrative margins. Pharmacological inhibition with two different compounds and RNAi targeting of ATR opposed the invasion of glioblastoma, whereas overexpression of ATR drove migration. Subsequent investigation revealed that cytoskeletal dysregulation reduced macropinocytotic internalization of integrins at growth-cone-like structures, resulting in a tumor microtube retraction defect. The biological relevance and translational potential of these findings were confirmed using two orthotopic in vivo models of glioblastoma and intravital imaging. We demonstrate a novel role for ATR in determining invasion in glioblastoma cells and propose that pharmacological targeting of ATR could have far-reaching clinical benefits beyond radiosensitization.

4 Resting State Functional Connectivity Impairments Implicate CNS Mechanisms Underlying Chronic Pain and Depression in Gulf War Veterans’ Illness

Objective:Around 200,000 veterans (up to 32% of those deployed) of the 1991 Gulf War (GW) suffer from GW veterans’ illness (GWVI). GWVI is a poorly understood chronic medical condition, characterized by symptoms indicative of brain function deficits in multiple domains. Among the symptoms of brain impairment GWVI-related chronic headaches and body muscle and joint pain conditions (GWVI-HAP) are the most debilitating, affecting around 64% of the GWVI veterans. Further, depression carries a very high co-morbid rate (>50%) in patients with chronic pain, including GWVI-HAP. In this preliminary study, we examined the integrity of brain function networks in a group of GWI-HAP veterans, with resting state fMRI (rsfMRI).Participants and Methods:Data from the first twenty-two GWVI-HAP veterans from two ongoing parallel clinical trials was examined. Of these 14 subjects (GWVI-HAP-DM) had mild depression (Hamilton Rating Scale for Depression (HSRD < 13); and 8 subjects (GWVI-HAP-DS) had moderate to severe depression (HSRD > 14). Written informed consent was obtained from all participants in the protocol approved by the local Institutional Review Board. RsfMRI data was acquired on a Siemens 3T Prisma-Fit MRI scanner using a 10-minute whole-brain high resolution simultaneous multi-slice (SMS) gradient echo echo-planar imaging (EPI) sequence: TR/TE/FA = 2.2 sec/ 27 msec/80°, and analyzed with well-established image processing pipelines. Functional connectivity (FC) to different regions implicated in depression and chronic pain was assessed with seed-based correlation analysis. Between group differences in FC were obtained with 2-sample t-tests.Results:GWVI-HAP-DS group exhibited significantly (p < 0.05) reduced FC compared to GWVI-HAP-DM between frontal lobe (medial (mPFC), and dorsolateral (dlPFC) prefrontal cortex) and the striatum. This indicates that malfunction of fronto-striatal circuits could be a source of the increased chronic pain and depression seen in veterans with GWVI- HAP-DS. Dysregulation of fronto-striatal networks has been implicated in major depressive disorder as well as many chronic pain conditions. In addition, FC between mPFC, and salience network (SN; anterior insula and dorsal anterior cingulate) and limbic (subgenual and ventral anterior cingulate) regions were also reduced in GWVI-HAP-DS. Similarly, mPFC and SN also exhibited reduced FC to pain processing regions (posterior insula, centromedian thalamus and cerebellum). These FC impairments could reflect greater deficits in regulation of and salience attribution to emotions and nociception in the GWVI-HAP-DS group. Finally, GWVI-HAP-DS also exhibited reduced FC between nodes of the default mode network. DMN impairments also have been observed in many depressive and chronic pain conditions.Conclusions:The results of this preliminary analysis implicate impairments in cognitive control of emotion and nociception as a mechanism underlying the enhanced chronic pain and depression observed in GWVI-HAP veterans, especially those with moderate to severe depression. A fuller picture of deficits in FC in brain function networks is expected to emerge as more GWI-HAP subjects of both groups along with age matched healthy controls are examined in this ongoing project. Better understanding of impairments in these networks in GWI-HAP will benefit the rehabilitation of veterans with GWI-HAP.

From aging to long COVID: exploring the convergence of immunosenescence, inflammaging, and autoimmunity.

The process of aging is accompanied by a dynamic restructuring of the immune response, a phenomenon known as immunosenescence. This mini-review navigates through the complex landscape of age-associated immune changes, chronic inflammation, age-related autoimmune tendencies, and their potential links with immunopathology of Long COVID. Immunosenescence serves as an introductory departure point, elucidating alterations in immune cell profiles and their functional dynamics, changes in T-cell receptor signaling, cytokine network dysregulation, and compromised regulatory T-cell function. Subsequent scrutiny of chronic inflammation, or "inflammaging," highlights its roles in age-related autoimmune susceptibilities and its potential as a mediator of the immune perturbations observed in Long COVID patients. The introduction of epigenetic facets further amplifies the potential interconnections. In this compact review, we consider the dynamic interactions between immunosenescence, inflammation, and autoimmunity. We aim to explore the multifaceted relationships that link these processes and shed light on the underlying mechanisms that drive their interconnectedness. With a focus on understanding the immunological changes in the context of aging, we seek to provide insights into how immunosenescence and inflammation contribute to the emergence and progression of autoimmune disorders in the elderly and may serve as potential mediator for Long COVID disturbances.

Single-cell RNA sequencing reveals a distinct profile of bone immune microenvironment and decreased osteoclast differentiation in type 2 diabetic mice

The pathogenic effects of type 2 diabetes on bone tissue are gaining attention, but the cellular and molecular mechanisms underlying osteoimmunology are still unclear in diabetes-related bone diseases. We delineated the single-cell transcriptome of bone marrow cells from both wide type and type 2 diabetes mice, which provided the first detailed global profile of bone marrow cells and revealed a distinct bone immune microenvironment at the genetic level under type 2 diabetic condition. It was observed that osteoclast activity was inhibited due to a dysregulated cytokine network, which ultimately led to decreased osteoclast formation and differentiation. In type 2 diabetes mice, a specific Cd36+ cluster (cluster 18, monocytes/macrophages 2) was identified as the precursor of osteoclasts with diminished differentiation potential. AP-1 was demonstrated to be the key transcription factor in the underlying mechanism.

Single-cell RNA sequencing of a new transgenic t(8;21) preleukemia mouse model reveals regulatory networks promoting leukemic transformation.

T(8;21)(q22;q22), which generates the AML1-ETO fusion oncoprotein, is a common chromosomal abnormality in acute myeloid leukemia (AML) patients. Despite having favorable prognosis, 40% of patients will relapse, highlighting the need for innovative models and application of the newest technologies to study t(8;21) leukemogenesis. Currently, available AML1-ETO mouse models have limited utility for studying the pre-leukemic stage because AML1-ETO produces mild hematopoietic phenotypes and no leukemic transformation. Conversely, overexpression of a truncated variant, AML1-ETO9a (AE9a), promotes fully penetrant leukemia and is too potent for studying pre-leukemic changes. To overcome these limitations, we devised a germline-transmitted Rosa26 locus AE9a knock-in mouse model that moderately overexpressed AE9a and developed leukemia with long latency and low penetrance. We observed pre-leukemic alterations in AE9a mice, including skewing of progenitors towards granulocyte/monocyte lineages and replating of stem and progenitor cells. Next, we performed single-cell RNA sequencing to identify specific cell populations that contribute to these pre-leukemic phenotypes. We discovered a subset of common myeloid progenitors that have heightened granulocyte/monocyte bias in AE9a mice. We also observed dysregulation of key hematopoietic transcription factor target gene networks, blocking cellular differentiation. Finally, we identified Sox4 activation as a potential contributor to stem cell self-renewal during the pre-leukemic stage.

Joint analysis of the metabolomics and transcriptomics uncovers the dysregulated network and develops the diagnostic model of high-risk neuroblastoma

High-risk neuroblastoma (HR-NB) has a significantly lower survival rate compared to low- and intermediate-risk NB (LIR-NB) due to the lack of risk classification diagnostic models and effective therapeutic targets. The present study aims to characterize the differences between neuroblastomas with different risks through transcriptomic and metabolomic, and establish an early diagnostic model for risk classification of neuroblastoma.Plasma samples from 58 HR-NB and 38 LIR-NB patients were used for metabolomics analysis. Meanwhile, NB tissue samples from 32 HR-NB and 23 LIR-NB patients were used for transcriptomics analysis. In particular, integrative metabolomics and transcriptomic analysis was performed between HR-NB and LIR-NB. A total of 44 metabolites (P < 0.05 and fold change > 1.5) were altered, including 12 that increased and 32 that decreased in HR-NB. A total of 1,408 mRNAs (P < 0.05 and |log2(fold change)|> 1) showed significantly altered in HR-NB, of which 1,116 were upregulated and 292 were downregulated. Joint analysis of both omic data identified 4 aberrant pathways (P < 0.05 and impact ≥ 0.5) consisting of glycerolipid metabolism, retinol metabolism, arginine biosynthesis and linoleic acid metabolism. Importantly, a HR-NB risk classification diagnostic model was developed using plasma circulating-free S100A9, CDK2, and UNC5D, with an area under receiver operating characteristic curve of 0.837 where the sensitivity and specificity in the validation set were both 80.0%. This study presents a novel pioneering study demonstrating the metabolomics and transcriptomics profiles of HR-NB. The glycerolipid metabolism, retinol metabolism, arginine biosynthesis and linoleic acid metabolism were altered in HR-NB. The risk classification diagnostic model based on S100A9, CDK2, and UNC5D can be clinically used for HR-NB risk classification.

Resting-state EEG dynamics help explain differences in response control in ADHD: Insight into electrophysiological mechanisms and sex differences.

Reductions in response control (greater reaction time variability and commission error rate) are consistently observed in those diagnosed with attention-deficit/hyperactivity disorder (ADHD). Previous research suggests these reductions arise from a dysregulation of large-scale cortical networks. Here, we extended our understanding of this cortical-network/response-control pathway important to the neurobiology of ADHD. First, we assessed how dynamic changes in three resting-state EEG network properties thought to be relevant to ADHD (phase-synchronization, modularity, oscillatory power) related with response control during a simple perceptual decision-making task in 112 children/adolescents (aged 8-16) with and without ADHD. Second, we tested whether these associations differed in males and females who were matched in age, ADHD-status and ADHD- subtype. We found that changes in oscillatory power (as opposed to phase-synchrony and modularity) are most related with response control, and that this relationship is stronger in ADHD compared to controls. Specifically, a tendency to dwell in an electrophysiological state characterized by high alpha/beta power (8-12/13-30Hz) and low delta/theta power (1-3/4-7Hz) supported response control, particularly in those with ADHD. Time in this state might reflect an increased initiation of alpha-suppression mechanisms, recruited by those with ADHD to suppress processing unfavourable to response control. We also found marginally significant evidence that this relationship is stronger in males compared to females, suggesting a distinct etiology for response control in the female presentation of ADHD.

Association of Inflammatory Cytokine Levels with Extra Glandular Manifestations, Fatigue, and Disease Activity in Primary Sjögren's Syndrome in Saudi Patients: A Cross-Sectional Study.

Primary Sjögren's syndrome (pSS) is an autoimmune disease that can cause fatigue and extraglandular manifestations (EGMs). pSS is associated with cytokine network dysregulation, which may be related to the immune-mediated destruction of exocrine glands. We determined cytokine levels and their relationship to EGMs, the European League Against Rheumatism (EULAR) Sjögren's syndrome disease activity index (ESSDAI), and fatigue in Saudi patients with pSS. This study was a cross-sectional, single-center study. We included forty-one patients and 71 controls. Serum samples were collected from random healthy people and pSS patients who were followed in the rheumatology and pulmonary clinics of King Saud University Medical City in Riyadh, Saudi Arabia. Levels of the frequently studied cytokines were measured using Luminex xMAP technology. Each ESSDAI score and EGM were recorded, and the Arabic version of the fatigue severity scale (FSS) was applied to assess fatigue. The main outcome measures were cytokine levels in pSS Saudi patients using/not using immune-suppressive medications (ISMs). Thirty-six (87.8%) patients had one or more EGMs, and the mean ESSDAI score was 9.95 ± 7.73. There was a significant decrease in TNFα and IL-21 levels in the pSS group compared to those in the control group (p = 0.034 and p < 0.001, respectively), whereas IL-12 levels were significantly elevated in the pSS group (p = 0.002). Cytokine levels in patients who used ISMs were the same as those in patients who did not use medications. Decreased IL-1β (p = 0.014), IL-2 (p = 0.035), IL-6 (p = 0.014), and IL-35 (p = 0.010) levels were observed in patients who had EGMs. Patients who had low disease activity exhibited low IL-10 (p = 0.018) and high IFN-α (p = 0.049), IFN-β (p = 0.049), IL-1β (p = 0.006), and IL-35 (p = 0.032) levels compared to patients with high disease activity. A negative association between a positive fatigue score and IL-1β (p = 0.010), IL-2 (p = 0.037), IFN-α (p = 0.025), TNFα (p = 0.030), IL-17 (p = 0.029), IL-12 (p = 0.046), and IL-21 (p = 0.005) levels was found. Cytokine profiles correlate with EGMs, ESSDAI, and fatigue. Patients with controlled disease activity have a normal cytokine profile that is similar to that of controls.

Unraveling the Molecular Puzzle: Exploring Gene Networks across Diverse EMT Status of Cell Lines.

Understanding complex disease mechanisms requires a comprehensive understanding of the gene regulatory networks, as complex diseases are often characterized by the dysregulation and dysfunction of molecular networks, rather than abnormalities in single genes. Specifically, the exploration of cell line-specific gene networks can provide essential clues for precision medicine, as this methodology can uncover molecular interplays specific to particular cell line statuses, such as drug sensitivity, cancer progression, etc. In this article, we provide a comprehensive review of computational strategies for cell line-specific gene network analysis: (1) cell line-specific gene regulatory network estimation and analysis of gene networks under varying epithelial-mesenchymal transition (EMT) statuses of cell lines; and (2) an explainable artificial intelligence approach for interpreting the estimated massive multiple EMT-status-specific gene networks. The objective of this review is to help readers grasp the concept of computational network biology, which holds significant implications for precision medicine by offering crucial clues.

Whole transcriptome analysis reveals dysregulation of molecular networks in schizophrenia.

To characterize the regulatory relationships between different types of transcripts and the altered molecular networks in schizophrenia (SCZ), we performed a whole transcriptome study by quantifying mRNAs, long noncoding RNAs (lncRNAs), miRNAs, and circular RNAs (circRNAs) in the same individuals simultaneously. A total of 807 dysregulated genes showed differential expression in SCZ cases compared with controls. Network-based analysis revealed dysregulation of molecular networks in SCZ. Finally, integration of the transcriptome data with published data identified promising SCZ candidate genes. Our study reveals that dysregulated molecular networks and regulatory relationships between different types of transcript may have a role in SCZ.

289-OR: Defining Pathway-Selective Insulin Resistance in Type 2 Diabetes Using iPS Cell-Derived Hepatocytes

Hepatic insulin resistance is central to type 2 diabetes (T2D), fatty liver disease, and metabolic syndrome. To identify the fundamental, cell-autonomous defects underlying hepatic insulin resistance in T2D, we have used inducible human pluripotent stem (iPS) cells derived from 16 individuals with and without T2D differentiated to hepatocytes (iHeps) and studied in vitro. Consistent with pathway selective insulin resistance, we find that insulin failed to suppress gene expression of critical gluconeogenic enzymes (PCK1, G6PC) but continued to stimulate increased expression of the lipogenic enzymes, fatty acid synthase and acetyl Co-A carboxylase 1 in T2D iHeps. iHeps from T2D also displayed reduced insulin receptor tyrosine phosphorylation and reduced phosphorylation through the IRS/Akt pathway. Global phosphoproteomics in control and T2D iHeps identified 378 unique phosphosites regulated by insulin, and many dysregulated phosphosites within the classical insulin signaling pathway (IRS, AKT1/2, GSK3, FOXO1, RPS6KB1, TSC2) and components of gene transcription regulation, membrane trafficking, Rho-GTPases, vesicle transport. Using a kinome-wide data set created with synthetic peptide libraries to profile almost all functional known human serine/threonine kinases, we found the alterations in insulin signaling mapped to AKT, P70S6K, P90S6K, RSK, PKCτ, and SGK kinases. Thus, iHeps from T2D patients show pathway-selective insulin resistance with a loss of suppression of gluconeogenesis by insulin yet persistent activation of lipogenesis, even in vitro, in the absence of any circulating factor exposure. T2D iHeps also show a dysregulated phosphorylation network that provides new clues to the kinases whose action is altered in T2D and hepatic insulin resistance. Disclosure A.Gattu: None. A.Krook: None. J.R.Zierath: None. M.Mann: None. C.Kahn: None. Funding National Institutes of Health (T32DK007260-46)