Patterns Of Dysregulation Research Articles

The Impact of Neurotransmitters on the Neurobiology of Neurodegenerative Diseases.

Neurodegenerative diseases affect millions of people worldwide. Neurodegenerative diseases result from progressive damage to nerve cells in the brain or peripheral nervous system connections that are essential for cognition, coordination, strength, sensation, and mobility. Dysfunction of these brain and nerve functions is associated with Alzheimer's disease, Parkinson's disease, Huntington's disease, Amyotrophic lateral sclerosis, and motor neuron disease. In addition to these, 50% of people living with HIV develop a spectrum of cognitive, motor, and/or mood problems collectively referred to as HIV-Associated Neurocognitive Disorders (HAND) despite the widespread use of a combination of antiretroviral therapies. Neuroinflammation and neurotransmitter systems have a pathological correlation and play a critical role in developing neurodegenerative diseases. Each of these diseases has a unique pattern of dysregulation of the neurotransmitter system, which has been attributed to different forms of cell-specific neuronal loss. In this review, we will focus on a discussion of the regulation of dopaminergic and cholinergic systems, which are more commonly disturbed in neurodegenerative disorders. Additionally, we will provide evidence for the hypothesis that disturbances in neurotransmission contribute to the neuronal loss observed in neurodegenerative disorders. Further, we will highlight the critical role of dopamine as a mediator of neuronal injury and loss in the context of NeuroHIV. This review will highlight the need to further investigate neurotransmission systems for their role in the etiology of neurodegenerative disorders.

Integrative analysis reveals early epigenetic alterations in high-grade serous ovarian carcinomas.

High-grade serous ovarian carcinoma (HGSOC) is the most lethal gynecological malignancy. To date, the profiles of gene mutations and copy number alterations in HGSOC have been well characterized. However, the patterns of epigenetic alterations and transcription factor dysregulation in HGSOC have not yet been fully elucidated. In this study, we performed integrative omics analyses of a series of stepwise HGSOC model cells originating from human fallopian tube secretory epithelial cells (HFTSECs) to investigate early epigenetic alterations in HGSOC tumorigenesis. Assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation sequencing (ChIP-seq), and RNA sequencing (RNA-seq) methods were used to analyze HGSOC samples. Additionally, protein expression changes in target genes were confirmed using normal HFTSECs, serous tubal intraepithelial carcinomas (STICs), and HGSOC tissues. Transcription factor motif analysis revealed that the DNA-binding activity of the AP-1 complex and GATA family proteins was dysregulated during early tumorigenesis. The protein expression levels of JUN and FOSL2 were increased, and those of GATA6 and DAB2 were decreased in STIC lesions, which were associated with epithelial-mesenchymal transition (EMT) and proteasome downregulation. The genomic region around the FRA16D site, containing a cadherin cluster region, was epigenetically suppressed by oncogenic signaling. Proteasome inhibition caused the upregulation of chemokine genes, which may facilitate immune evasion during HGSOC tumorigenesis. Importantly, MEK inhibitor treatment reversed these oncogenic alterations, indicating its clinical effectiveness in a subgroup of patients with HGSOC. This result suggests that MEK inhibitor therapy may be an effective treatment option for chemotherapy-resistant HGSOC.

Fibroblast-specific adipocyte enhancer binding protein 1 is a potential pathological trigger and prognostic marker for liver fibrosis independent of etiology.

Aortic carboxypeptidase-like protein (ACLP) is an extracellular protein involved in adipogenesis, epithelial-mesenchymal transition, epithelial cell hyperplasia, and collagen fibrogenesis. This study mainly aimed to analyze the potential role of adipocyte enhancer binding protein 1 (AEBP1), the ACLP-encoding gene, as a pathological target or prognostic marker for liver fibrosis regardless of etiology. Dysregulation pattern, clinical relevance, and biological significance of AEBP1 gene in liver fibrosis were analyzed using publicly available transcriptomic profiles, different liver fibrosis mouse models, biological databases, and AEBP1 gene silencing followed by RNA sequencing in human hepatic stellate cells (HSCs). AEBP1 gene expression was upregulated and positively correlated with liver fibrogenesis independent of etiology, the protein of which was further verified in liver fibrosis mouse models induced by different pathogenic factors. A higher expression of liver AEBP1 gene had the potential to predict poor prognosis in liver fibrosis. Systematic bioinformatic analyses revealed that AEBP1 expression was HSCs-specific and associated with extracellular matrix (ECM) remodeling and its downstream mechanical-chemical signaling transition. AEBP1 knockdown by specific small interfering RNAs (siRNAs) in HSCs inhibited ECM-receptor interaction and immune-related pathways as well as HSC proliferation or activation. A high expression of AEBP1 was specifically associated with liver fibrosis and was related to a poor prognosis and predicted the role of AEBP1 in HSCs, providing a new insight for understanding AEBP1 in liver fibrosis.

Identifying different patterns of emotion dysregulation in adult ADHD

BackgroundEmotion dysregulation (ED) is a core intrinsic feature of adult presenting Attention Deficit Hyperactivity Disorder (ADHD). However, the clinical expressions of ED are diverse and several questionnaires have been used to measure ED in adults with ADHD. Thus, to date, the characteristics of ED in adult ADHD remain poorly defined. The objective of this study is to identify the different patterns of ED in adults with ADHD.MethodsA large sample of 460 newly diagnosed adults with ADHD were recruited. Patients completed a total of 20 self-reported questionnaires. Measures consisted in the several facets of ED, but also other clinical features of adult ADHD such as racing thoughts. A factor analysis with the principal component extraction method was performed to define the symptomatic clusters. A mono-dimensional clustering was then conducted to assess whether participants presented or not with each symptomatic cluster.ResultsThe factor analysis yielded a 5 factor-solution, including “emotional instability”, “impulsivity”, “overactivation”, “inattention/disorganization” and “sleep problems”. ED was part of two out of five clusters and concerned 67.52% of our sample. Among those patients, the combined ADHD presentation was the most prevalent. Emotional instability and impulsivity were significantly predicted by childhood maltreatment. The ED and the “sleep problems” factors contributed significantly to the patients’ functional impairment.ConclusionsED in ADHD is characterized along emotional instability and emotional impulsivity, and significantly contributes to functional impairment. However, beyond impairing symptoms, adult ADHD may also be characterized by functional strengths such as creativity.

Addressing Impaired Sleep Among Adults in the Psychiatric Care Setting

Insomnia is highly comorbid with mental disorders and commonly treated by mental health care clinicians. A review of literature provides evidence for shared pathophysiology in systems regulating arousal and sleep–wake cycles in insomnia, anxiety, and mood disorders. Evidence-based pharmacological treatment rationales, based on patterns of dysregulation, are presented. Sleep quality is essential to mental health, and early identification and treatment of insomnia can aid in recovery. [ Journal of Psychosocial Nursing and Mental Health Services, 61 (9), 6–9.]

The yin and yang of self-regulation in developing vertebrates.

All living organisms are thermodynamic open systems constantly exchanging energy with the environment to maintain organization and structure. In a state of non-equilibrium they undergo a back and forth pattern of self-regulation and dysregulation in energy exchange. This state of dynamic non-equilibrium can be observed during vertebrate development in which high phenotypic variation and plasticity exists, especially in the presence of stressors. While investigations of the effects of stressors on mechanisms of self-regulation are usually measured by systemic changes (e.g. metabolic rate) between baseline (control) and stimulus (or stressor), real world stressors do not switch on and off in predictable patterns, rarely occur alone, and can be acute (short-term) or chronic (long-term). In this short review, application of two processes underlying self-regulation and dysregulation are explored, 1) allostasis, stability through change or the processes underlying self-regulation and, 2) metastasis, instability through change or the processes underlying dysregulation, to understand the effects of environmental stressors on the energetics of fish early life history stages (embryos and larvae). In mammalian physiology, allostasis theory was developed to maximize the probability of survival under stress, while reducing or limiting somatic damage. Yet, allostatic responses have energetic costs. Multiple stress responses over time result in systemic somatic damage accompanied by a loss of resilience due to an inability to self-regulate. Allostatic costs and their systemic effects on neuroendocrine, metabolic, cardiovascular and immune systems are cumulative and understood for adults but not yet for earlier stages. Developing stages with greater challenges for allostatic self-regulation than older stages because of limited resources have higher growth rates, smaller aerobic scopes, elevated metabolic costs, tight energy budgets, and employ compensatory versus additive energy budgets. Along with high mortality, early stages are expected to exhibit decreased physiological resilience and increased vulnerability in response to stressors, but little examination of energetic strategies to preserve functional stability in the face of stressors exists. While dysregulation/metastatic processes are more difficult to document in development, they increase our understanding of how organisms exposed to chronic/multiple stressors may reach allostatic overload leading to either, 1) systemic dysfunction and/or death or possibly, 2) novel physiological adaptive states. Evaluation of factors driving the yin and yang of self-regulation and dysregulation will provide knowledge of factors triggering or retarding metastatic processes, thus identifying those that prevent or reduce their affects, important in a world undergoing rapid global change.

Alignment of multiple metabolomics LC-MS datasets from disparate diseases to reveal fever-associated metabolites.

Acute febrile illnesses are still a major cause of mortality and morbidity globally, particularly in low to middle income countries. The aim of this study was to determine any possible metabolic commonalities of patients infected with disparate pathogens that cause fever. Three liquid chromatography-mass spectrometry (LC-MS) datasets investigating the metabolic effects of malaria, leishmaniasis and Zika virus infection were used. The retention time (RT) drift between the datasets was determined using landmarks obtained from the internal standards generally used in the quality control of the LC-MS experiments. Fitted Gaussian Process models (GPs) were used to perform a high level correction of the RT drift between the experiments, which was followed by standard peakset alignment between the samples with corrected RTs of the three LC-MS datasets. Statistical analysis, annotation and pathway analysis of the integrated peaksets were subsequently performed. Metabolic dysregulation patterns common across the datasets were identified, with kynurenine pathway being the most affected pathway between all three fever-associated datasets.

Epigenetics in myeloproliferative neoplasms.

The myeloproliferative neoplasms (MPNs) are a group of acquired clonal disorders where mutations drive proliferative disease resulting in increased blood counts and in some cases end-stage myelofibrosis. Epigenetic changes are the reversible modifications to DNA- and RNA-associated proteins that impact gene activity without changing the DNA sequence. This review summarizes mechanisms of epigenetic changes and the nucleosome. The drivers and epigenetic regulators in MPNs are outlined. In MPNs, distinct patterns of epigenetic dysregulation have been seen in chronic and in advanced phases. Methylation age and histone modification are altered in MPNs and by further treatment. The alterations found in methylation age in MPNs and with treatment are discussed, and the changes in histone modification with Janus kinase (JAK) inhibition are evaluated. Currently available therapeutic areas where the epigenome can be altered are outlined. Thus, we review the current knowledge and understanding of epigenetics in MPN and consider further management options. Understanding the epigenome and its alteration in MPNs and epigenetic changes associated with the progression of disease will lead to advances in therapeutic options.

Immunologic and vascular biomarkers of mortality in critical COVID-19 in a South African cohort.

Biomarkers predicting mortality among critical Coronavirus disease 2019 (COVID-19) patients provide insight into the underlying pathophysiology of fatal disease and assist with triaging of cases in overburdened settings. However, data describing these biomarkers in Sub-Saharan African populations are sparse. We collected serum samples and corresponding clinical data from 87 patients with critical COVID-19 on day 1 of admission to the intensive care unit (ICU) of a tertiary hospital in Cape Town, South Africa, during the second wave of the COVID-19 pandemic. A second sample from the same patients was collected on day 7 of ICU admission. Patients were followed up until in-hospital death or hospital discharge. A custom-designed 52 biomarker panel was performed on the Luminex® platform. Data were analyzed for any association between biomarkers and mortality based on pre-determined functional groups, and individual analytes. Of 87 patients, 55 (63.2%) died and 32 (36.8%) survived. We found a dysregulated cytokine response in patients who died, with elevated levels of type-1 and type-2 cytokines, chemokines, and acute phase reactants, as well as reduced levels of regulatory T cell cytokines. Interleukin (IL)-15 and IL-18 were elevated in those who died, and levels reduced over time in those who survived. Procalcitonin (PCT), C-reactive protein, Endothelin-1 and vascular cell adhesion molecule-1 were elevated in those who died. These results show the pattern of dysregulation in critical COVID-19 in a Sub-Saharan African cohort. They suggest that fatal COVID-19 involved excessive activation of cytotoxic cells and the NLRP3 (nucleotide-binding domain, leucine-rich-containing family, pyrin domain-containing-3) inflammasome. Furthermore, superinfection and endothelial dysfunction with thrombosis might have contributed to mortality. HIV infection did not affect the outcome. A clinically relevant biosignature including PCT, pH and lymphocyte percentage on differential count, had an 84.8% sensitivity for mortality, and outperformed the Luminex-derived biosignature.

Cortisol Dysregulation and Protective Psychological Factors in Older Adulthood

Stressful experiences may elicit hyper- and hypo-secretion of cortisol, which both can compromise quality of life. Psychological factors that are useful for managing stress experiences may ameliorate such patterns of dysregulation and protect quality of life. It is examined how stress experiences and psychological factors can shape cortisol dysregulation during older adulthood. Data from a 12-year longitudinal study of older adults were analyzed (Montreal Aging and Health Study; N = 215). Participants were assessed every 2 years. Measures included stress experiences, cortisol output, psychological factors (e.g., control strategies or self-compassion), and indicators of quality of life (e.g., well-being and health). Analyses were performed using hierarchical regression analyses and multi-level modeling. Higher, as compared to lower, levels of stress perceptions were associated with increased cortisol output (AUC) at the beginning of the study, but predicted relatively reduced cortisol output after 12 years. In addition, high and increasing stress perceptions predicted a flattening of cortisol slopes over 12 years. In terms of psychological factors, the use of control strategies, self-compassion, and self-esteem modulated cortisol output during the study period. Stressful experiences can be associated with a complex pattern of cortisol dysregulation in older adulthood, changing from hyper- to hypo-secretion of cortisol as stress experiences remain high or increase over longer periods of time. Psychological responses to stress may modulate this pattern and could play an important role in maintaining older adults’ quality of life. Implications for studying cortisol regulation and stress management in older adulthood are discussed.

A biopsychosocial perspective of the effects of stress during development and its relationship to one’s vulnerability to psychopathology

Various stress-related psychopathologies, for which the prevalence is known to increase during late childhood and early adolescence, have been associated with dysregulated patterns of cortisol secretion and distinct cognitive profiles. Most studies have been performed in clinical populations and utilize cross-sectional designs. As such, this has prevented researchers from drawing clear conclusions regarding the temporality of the observed effects. Importantly, different individual, familial, and societal factors are known to impact the regulation of the HPA axis activity. Therefore, these factors may moderate one’s risk of developing certain psychopathologies and/or modulating symptom severity or cognitive profiles that characterize various stress-related psychopathologies. This symposium is composed of four young investigators and will focus on the cognitive and clinical correlates of stress exposure in childhood, as well as the various individual, familial, and societal influences that moderate these effects. First, Catherine Raymond (Université du Québec à Montréal) will present data on cortisol reactivity and emotional cognitive processes in healthy children exhibiting high levels of vulnerability to anxiety, as assessed by various personality traits known to be predictive of clinical anxiety. Then, the two following presentations will address COVID-related stress in children. Alexe Bilodeau-Houle (Université du Québec à Montréal) will first discuss how cortisol levels prior to and following the first COVID-19 lockdown are related to psychological distress symptoms in healthy children. Thereafter, Sydney Yi (University of California) will present data related to the pandemic from a family-related perspective. Of note, she will comment on the effect of COVID-19-related parental job loss and financial stress on executive functioning performance and mental health in a parent and their child. Finally, Christina Cantave (University of Montreal) will present data pertaining to socio-economic status mobility during childhood and adolescence and how this relates to HPA axis activity in twin dyads. Altogether, this data will present a biopsychosocial perspective of how stress during childhood modulates one’s vulnerability to develop stress-related psychopathologies.

Systems analysis of Alzheimer’s disease pathway dysregulation in human subjects is recapitulated in 3d cellular models to reveal P38 MAPK as a therapeutic target that mitigates tau pathology

AbstractBackground3D human neural cell culture models of Alzheimer’s disease (AD) are valuable resources for studying AD pathogenesis mechanisms. Although our 3D models capture cellular heterogeneity and key pathogenic cascades in AD, including β‐amyloid (Aβ) accumulation and Aβ‐induced tau pathology, it is not known to what extent 3D models functionally reflect human AD pathogenesis. We address this gap by capturing functionally active AD pathways in human brain through a granular systems approach that accurately recapitulates the activity of disease‐associated pathways from afflicted brain tissues in 3D models.MethodsWe leveraged transcriptomic data to precisely determine the activity dynamics of biological pathways. We assembled transcriptomic data from AD brains and compared them with a battery of 3D models displaying a broad range of disease‐associated characteristics. Our approach discovered pathways showing concordant dysregulation patterns between human brain and disease models. We prioritized the most consistent AD‐pathways for in‐vitro therapeutic screening.ResultsOne of our 3D models has transmembrane domain APP mutations, but not PS1 mutations and exhibits an elevated Aβ42/40 ratio. It best recapitulated dysregulated AD‐pathways found in both human prefrontal and temporal cortices. Multiple pathways indicated activation of p38 MAPK signaling, coupled with broad transcriptional inactivation in AD. Cellular and biochemical validations demonstrated elevated phosphorylated‐p38 (p‐tau)/total‐p38 ratios. Treatment with a p38 MAPK inhibitor resulted in significant reduction in the total amount of tau, significant reduction in the amount of p‐tau, and suggestive reduction in p‐tau/tau ratio. Our results strongly support a critical role for p38 MAPK signaling in mediating Ab‐induced tau pathology.ConclusionsUsing human brain transcriptomes, we have introduced a broadly‐applicable systems biology approach to rapidly discover therapeutic targets in 3D models. The approach provides a granular determination of the degree to which cellular models accurately reflect dysregulated molecular pathways in afflicted brains. We have detected, validated, and targeted the activated p38 MAPK pathway in AD. We have diminished tau pathology by inhibiting p38 MAPK signaling in cellular models, suggesting that the p38 MAPK pathway is a potent human‐derived target to combat tau pathology.PNY and SSK are co‐first‐authors.RT, WH, and DYK jointly supervised this project.

Characterizing Symptoms and Identifying Biomarkers of Long COVID in People with and without HIV: Protocol for a Remotely-Conducted Prospective Observational Cohort Study.

Living with HIV is a risk factor for severe acute COVID-19, but it is unknown whether living with HIV is a risk factor for long COVID. This study aimed to formally and prospectively characterize symptoms, sequelae, and cognition in the 12 months following SARS-CoV-2 infection in people living with HIV (PWH) as compared to HIV-seronegative people. Additionally, PWH and HIV-seronegative people with no history of SARS-CoV-2 infection were enrolled as controls. The study also aimed to identify blood-based biomarkers or patterns of immune dysregulation that associate with long COVID. This prospective observational cohort study enrolled participants into one of four study arms: PWH who had SARS-CoV-2 infection for the first time no more than four weeks prior to enrollment (HIV+COVID+ arm), HIV-seronegative people who had SARS-CoV-2 infection for the first time within 4 weeks of enrollment (HIV-COVID+ arm), PWH who believe they never had SARS-CoV-2 infection (HIV+COVID- arm), and HIV-seronegative people who believe they never had SARS-CoV-2 infection (HIV-COVID- arm). At enrollment, participants in the COVID+ arms recalled their symptoms, mental health status, and quality of life in the month prior to having SARS-CoV-2 infection via comprehensive survey administered by telephone or online. All participants completed the same symptom, mental health, and quality of life surveys at 1, 2, 4, 6, and 12 months post-acute COVID-19 symptom onset or diagnosis, if asymptomatic, (COVID+ arms) or post-enrollment (COVID- arms) online or by telephone. Eleven cognitive assessments were administered by telephone at 1 and 4 months post-symptom onset (COVID+ arms) or post-enrollment (COVID- arms). A mobile phlebotomist met the participant at a location of their choosing for height and weight measurements, orthostatic vital signs, and a blood draw. Participants in the COVID+ arms donated blood 1 and 4 months post-COVID, and participants in the COVID- arms donated blood 0-1 times. Blood was then shipped overnight to the receiving study laboratory. When received, blood was sent to the local Clinical Laboratory Improvement Amendments of 1988 (CLIA)-certified laboratory for real-time testing and processed and stored as frozen plasma, serum, and PBMC for future testing. This project was funded in early 2021, and recruitment began in June 2021. Data analyses will be completed by summer 2023. As of February 2023, 387 participants enrolled in this study with 345 having completed enrollment/baseline surveys together with at least one other completed study event at month 1, 2, 4, 6, or 12. This includes 76 COVID+HIV+, 121 COVID+HIV-, 78 COVID-HIV+ and 70 COVID-HIV- participants. This study will provide longitudinal data to characterize post-COVID recovery over 12 months in PWH and HIV-seronegative people. Additionally, this study will determine whether biomarkers or patterns of immune dsyregulation associate with decreased cognitive function or symptoms of long COVID. ClinicalTrials.gov NCT04958889.

Immunological Pathways in Sarcoidosis and Autoimmune Rheumatic Disorders-Similarities and Differences in an Italian Prospective Real-Life Preliminary Study.

The pathogenesis of sarcoidosis involves T cells and B lymphocytes that produce autoantibodies. We compared the expression of different T and B cell subsets in sarcoidosis and three B-mediated rheumatic diseases that can affect the lungs in an attempt to identify similarities and differences that distinguish these diseases. The study included patients referred to Siena University Hospital's respiratory disease and rheumatology units. Patients were enrolled prospectively and consecutively. Healthy volunteers were also included. Multicolor flow cytometry was performed on phenotype T and B cell subsets. Multivariate analysis was carried out to reduce the dimensionality of the data. Fifteen patients had a diagnosis of sarcoidosis, fourteen idiopathic inflammatory myopathies (IIM), five granulomatosis with polyangiitis (GPA), ten microscopic polyangiitis (MPA), and seven were controls. Thirty-five T and B cell subsets were phenotyped, 15 of which were significantly different in sarcoidosis, B-mediated rheumatic disorders, and controls. Principal components analysis distinguished the four groups of patients with a total explained variance of 54.7%. A decision tree was constructed to determine which clustering variables would be most useful for distinguishing sarcoidosis, IIM, MPA, and GPA. The model showed regulatory T helper cells (Th-reg) > 5.70% in 91% of sarcoidosis patients as well as Th-reg ≤ 5.70 and Th17 > 43.27 in 100% of MPA. It also showed Th-reg ≤ 5.70, Th17 ≤ 43.27 and Tfh-reg ≥ 7.81 in 100% of GPA patients, and Th-reg ≤ 5.70, Th17 ≤ 43.27 and Tfh-reg ≤ 7.81 in 100% of IIM patients. The immune cell profile sheds light on similarities and differences between sarcoidosis and B-mediated rheumatic diseases. Sarcoidosis and autoimmune diseases show similar patterns of cellular immune dysregulation, suggesting a common pathogenic pathway that may provide an opportunity for further understanding autoimmunity and exploring biological therapies to treat sarcoidosis.

Matrisome gene-based subclassification of patients with liver fibrosis identifies clinical and molecular heterogeneities.

Excessive deposition and crosslinking of extracellular matrix increases liver density and stiffness, promotes fibrogenesis, and increases resistance to fibrinolysis. An emerging therapeutic opportunity in liver fibrosis is to target the composition of the extracellular matrix or block pathogenic communication with surrounding cells. However, the type and extent of extracellular changes triggering liver fibrosis depend on the underlying etiology. Our aim was to unveil matrisome genes not dependent on etiology, which are clinically relevant to liver fibrosis. We used transcriptomic profiles from liver fibrosis cases of different etiologies to identify and validate liver fibrosis-specific matrisome genes (LFMGs) and their clinical and biological relevance. Dysregulation patterns and cellular landscapes of LFMGs were further explored in mouse models of liver fibrosis progression and regression by bulk and single-cell RNA sequencing. We identified 35 LFMGs, independent of etiology, representing an LFMG signature defining liver fibrosis. Expression of the LFMG signature depended on histological severity and was reduced in regressive livers. Patients with liver fibrosis, even with identical pathological scores, could be subclassified into LFMG Low and LFMG High , with distinguishable clinical, cellular, and molecular features. Single-cell RNA sequencing revealed that microfibrillar-associated protein 4 + activated HSC increased in LFMG High patients and were primarily responsible for the LFMG signature expression and dysregulation. The microfibrillar-associated protein 4 + -activated HSC-derived LFMG signature classifies patients with liver fibrosis with distinct clinical and biological characteristics. Our findings unveil hidden information from liver biopsies undetectable using traditional histologic assessments.

Analogy or fallacy, unsafe chemical alternatives: Mechanistic insights into energy metabolism dysfunction induced by Bisphenol analogs in HepG2 cells

Bisphenol analogs (BPs) are widely used as industrial alternatives for Bisphenol A (BPA). Their toxicity assessment in humans has mainly focused on estrogenic activity, while other toxicity effects and mechanisms resulting from BPs exposure remain unclear. In this study, we investigated the effects of three BPs (Bisphenol AF (BPAF), Bisphenol G (BPG) and Bisphenol PH (BPPH)) on metabolic pathways of HepG2 cells. Results from comprehensive cellular bioenergetics analysis and nontarget metabolomics indicated that the most important process affected by BPs exposure was energy metabolism, as evidenced by reduced mitochondrial function and enhanced glycolysis. Compared to the control group, BPG and BPPH exhibited a consistent pattern of metabolic dysregulation, while BPAF differed from both, such as an increased ATP: ADP ratio (1.29-fold, p < 0.05) observed in BPAF and significantly decreased ATP: ADP ratio for BPG (0.28-fold, p < 0.001) and BPPH (0.45-fold, p < 0.001). Bioassay endpoint analysis revealed BPG/BPPH induced alterations in mitochondrial membrane potential and overproductions of reactive oxygen species. Taken together these data suggested that BPG/BPPH induced oxidative stress and mitochondrial damage in cells results in energy metabolism dysregulation. By contrast, BPAF had no effect on mitochondrial health, but induced a proliferation promoting effect on cells, which might contribute to the energy metabolism dysfunction. Interestingly, BPPH induced the greatest mitochondrial damage among the three BPs but did not exhibit Estrogen receptor alpha (ERα) activating effects. This study characterized the distinct metabolic mechanisms underlying energy metabolism dysregulation induced by different BPs in target human cells, providing new insight into the evaluation of the emerging BPA substitutes.

Blood transcriptome sequencing identifies biomarkers able to track disease stages in spinocerebellar ataxia type 3.

Transcriptional dysregulation has been described in spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD), an autosomal dominant ataxia caused by a polyglutamine expansion in the ataxin-3 protein. As ataxin-3 is ubiquitously expressed, transcriptional alterations in blood may reflect early changes that start before clinical onset and might serve as peripheral biomarkers in clinical and research settings. Our goal was to describe enriched pathways and report dysregulated genes, which can track disease onset, severity or progression in carriers of the ATXN3 mutation (pre-ataxic subjects and patients). Global dysregulation patterns were identified by RNA sequencing of blood samples from 40 carriers of ATXN3 mutation and 20 controls and further compared with transcriptomic data from post-mortem cerebellum samples of MJD patients and controls. Ten genes-ABCA1, CEP72, PTGDS, SAFB2, SFSWAP, CCDC88C, SH2B1, LTBP4, MEG3 and TSPOAP1-whose expression in blood was altered in the pre-ataxic stage and simultaneously, correlated with ataxia severity in the overt disease stage, were analysed by quantitative real-time PCR in blood samples from an independent set of 170 SCA3/MJD subjects and 57 controls. Pathway enrichment analysis indicated the Gαi signalling and the oestrogen receptor signalling to be similarly affected in blood and cerebellum. SAFB2, SFSWAP and LTBP4 were consistently dysregulated in pre-ataxic subjects compared to controls, displaying a combined discriminatory ability of 79%. In patients, ataxia severity was associated with higher levels of MEG3 and TSPOAP1. We propose expression levels of SAFB2, SFSWAP and LTBP4 as well as MEG3 and TSPOAP1 as stratification markers of SCA3/MJD progression, deserving further validation in longitudinal studies and in independent cohorts.

Abstract 2057: Pan-cancer analysis of ion channel genes reveals patterns of large-scale transcriptional dysregulation and novel oncogenes with functions in cellular connectivity

Abstract Ion channels (IC) are one of the largest families of highly druggable proteins targeted in therapies for many human diseases; however, their role in cancer remains understudied. IC drug repurposing for cancer therapies is an appealing avenue; however, prioritizing ICs for pre-clinical research, mechanistic elucidation, and target development remains a challenge. Here we performed a systematic, pan-cancer analysis to prioritize IC genes as putative targets for therapeutic and biomarker development. Using machine learning, we studied ~10,000 human transcriptomes from 32 cancer types of The Cancer Genome Atlas (TCGA) to identify ICs whose expression significantly associated with patient survival. IC genes showed dysregulation in all cancer types: elevated IC expression was characteristic of a subset of tumors often associated with poor patient prognosis. Excessive IC expression was unexpectedly frequent and high-magnitude compared to control sets of protein-coding genes and genes of major druggable families. We focused on ICs in glioblastoma (GBM), the most prevalent and lethal form of brain cancer in adults, prioritizing GJB2 (gap junction protein beta 2) and SCN9A (sodium voltage-gated channel alpha subunit 9) as potential GBM oncogenes. High expression of these ICs associated with poor GBM prognosis in TCGA and independent transcriptomics datasets. GJB2 and SCN9A expression was higher in GBMs than normal brain tissues and associated with GBM subtypes, histological features, and immune cell infiltration. At the single-cell level, GJB2 and SCN9A were predominantly expressed in malignant cell types in GBMs. We validated GJB2 and SCN9A with shRNA-mediated knockdowns (KDs) in patient-derived GBM cell lines and mouse xenograft models. First, GJB2 and SCN9A KDs significantly impaired cell viability and spheroid formation. We then validated survival associations, showing that GJB2 and SCN9A KDs prolonged survival of mice with GBM xenografts. Finally, we showed GBJ2 KD impaired tunneling nanotube length in GBM cells. Transcriptome-wide profiling of IC KD cells revealed hundreds of differentially expressed genes. Integrative pathway enrichment across IC KDs in GBM cells and IC-stratified TCGA samples identified dysregulated pathways with functional themes of neuronal development, cancer hallmarks, and regulation of glial cells, including tumor cell connectivity pathways in GBM, corroborating the phenotypes observed in our functional validations. Our pan-cancer analysis prioritized ICs for further pre-clinical development and mechanistic study. The functional validation experiments of GJB2 and SCN9A highlight their possible roles in GBM pathology and lends confidence to our analysis. This study demonstrates the utility of investigating ICs as avenues for drug repurposing and the development of novel cancer therapeutics. Citation Format: Alexander Bahcheli, Hyun Min, Xi Huang, Jüri Reimand. Pan-cancer analysis of ion channel genes reveals patterns of large-scale transcriptional dysregulation and novel oncogenes with functions in cellular connectivity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2057.

Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis.

LncRNAs comprise a heterogeneous class of RNA-encoding genes typified by low expression, nuclear enrichment, high tissue-specificity, and functional diversity, but the vast majority remain uncharacterized. Here, we assembled the mouse liver noncoding transcriptome from >2000 bulk RNA-seq samples and discovered 48,261 liver-expressed lncRNAs, a majority novel. Using these lncRNAs as a single-cell transcriptomic reference set, we elucidated lncRNA dysregulation in mouse models of high fat diet-induced nonalcoholic steatohepatitis and carbon tetrachloride-induced liver fibrosis. Trajectory inference analysis revealed lncRNA zonation patterns across the liver lobule in each major liver cell population. Perturbations in lncRNA expression and zonation were common in several disease-associated liver cell types, including nonalcoholic steatohepatitis-associated macrophages, a hallmark of fatty liver disease progression, and collagen-producing myofibroblasts, a central feature of liver fibrosis. Single-cell-based gene regulatory network analysis using bigSCale2 linked individual lncRNAs to specific biological pathways, and network-essential regulatory lncRNAs with disease-associated functions were identified by their high network centrality metrics. For a subset of these lncRNAs, promoter sequences of the network-defined lncRNA target genes were significantly enriched for lncRNA triplex formation, providing independent mechanistic support for the lncRNA-target gene linkages predicted by the gene regulatory networks. These findings elucidate liver lncRNA cell-type specificities, spatial zonation patterns, associated regulatory networks, and temporal patterns of dysregulation during hepatic disease progression. A subset of the liver disease-associated regulatory lncRNAs identified have human orthologs and are promising candidates for biomarkers and therapeutic targets.

Construction and validation of a competing endogenous RNA network in the thymus of miR-147-/- mice.

Prior evidence has demonstrated that miR-147 can regulate cellular proliferation, migration, apoptotic death, inflammatory responses, and the replication of viruses through its interactions with specific mRNA targets. LncRNA-miRNA-mRNA interactions are often found in various biological processes. No studies have documented lncRNA-miRNA-mRNA regulatory interactions in miR-147-/- mice. Thymus tissue samples from miR-147-/- mice were systematically analyzed to detect patterns of lncRNA, miRNA, and mRNA dysregulation in the absence of this biologically important miRNA. Briefly, RNA-sequencing was used to analyze samples of thymus tissue from wild-type (WT) and miR-147-/- mice. Radiation damage models of miR-147-/- mice were prepared and prophylactic intervention with the drug trt was performed. The validation of miR-47, PDPK1,AKT and JNK were carried out by qRT-PCR, western blot and fluorescence in situ hybridization. Apoptosis was detected by Hoechst staining, and histopathological changes were detected by HE staining. We showed the identification of 235 mRNAs, 63 lncRNAs, and 14 miRNAs that were significantly upregulated in miR-147-/- mice as compared to WT controls, as well as 267 mRNAs, 66 lncRNAs and 12 miRNAs exhibiting significant downregulation. Predictive analyses of the miRNAs targeted by dysregulated lncRNAs and their associated mRNAs were further performed, highlighting the dysregulation of pathways including the Wnt signaling pathway, Thyroid cancer, Endometrial cancer (include PI3K/AKT) and Acute myeloid leukemia pathway(include PI3K/AKT) pathways. Troxerutin (TRT) upregulated PDPK1 via targeting miR-147 to promote AKT activation and inhibit JNK activation in the lungs of mice in radioprotection. Together, these results highlight the potentially important role of miR-147 as a key regulator of complex lncRNA-miRNA-mRNA interacting networks. Further research focusing on PI3K/AKT pathways in miR-147-/- mice in radioprotection will thus benefit current knowledge of miR-147 while also informing efforts to improve radioprotection.