Biology subjects

Berk, M.

Publications and source records attributed to Berk, M..

11 recordsLinked to original sources

bioRxiv2026

iPSC-Derived Myotubes from ME/CFS Patients Reveal Signature Genes, Isoforms and Pathways with Drug Repurposing Potential

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a complex multisystem disorder. Its hallmark feature, post-exertional malaise (PEM), is a delayed and prolonged worsening of symptoms following even minor exertion. As PEM commonly includes muscle pain, weakness, exercise intolerance and impaired recovery, skeletal muscle dysfunction may contribute to its pathophysiology, but the underlying molecular processes remain poorly understood. We generated induced pluripotent stem cell-derived skeletal muscle myotubes from individuals with ME/CFS (n = 6) and healthy controls (n = 7) to investigate disease-associated transcriptomic alterations and identify potential therapeutic candidates. Myogenic progenitor cells from both groups differentiated into elongated, multinucleated myotubes expressing titin and myosin heavy chain, while qPCR profiling of myogenic differentiation markers further supported successful differentiation. Gene-level analysis identified three differentially expressed genes at an FDR-adjusted p < 0.05: ERVH48-1, CDX4 and SLC2A14. Isoform-switching analysis identified 16 genes with significant differential isoform usage, including CACNA1H, MIEF2, SMAD2 and CHD4. Gene set enrichment analysis identified broader pathway-level alterations involving RNA processing, protein synthesis, proteostasis, mitochondrial quality control, metabolism and muscle-related processes. Library of Integrated Network-based Cellular Signatures Phase 2 (LINCS2) analysis further prioritised 14 compounds associated with mitochondrial metabolism, glucose and lipid regulation, PPAR signalling, calcium and excitatory signalling, neuroimmune activity and cellular stress responses. Overall, ME/CFS iPSC-derived myotubes showed modest gene-level differences alongside broader isoform- and pathway-level alterations, supporting their use for investigating skeletal muscle biology and prioritising candidates for functional validation.

cell biology↗

bioRxiv2026

The toll-like receptor signalling pathway is altered in iPSC-derived cortical networks from people with bipolar disorder.

BackgroundInduced pluripotent stem cell (iPSC)-derived brain cells are widely utilized as in vitro models for several neuropsychiatric disorders, as they retain the donors genetic profile, offering a unique opportunity to study living human brain cells and perform controlled experimental manipulations. In this study, we conducted whole transcriptome sequencing of cortical networks (co-cultures of neurons and astrocytes) derived from 12 participants with bipolar disorder (BD) and 12 participants without a history of mental health disorders. We aimed to identify new molecular mechanisms underlying the pathophysiology of bipolar disorder. MethodsiPSCs were generated by reprogramming peripheral blood mononuclear cells using episomal vectors. They were then differentiated into neural progenitor cells and matured into cortical networks that express markers of neurons and astrocytes. Whole transcriptome data were obtained using the Illumina NovaSeq X sequencing platform. ResultsDifferential expression analysis was performed using DESeq2 in R, and the identified genes were used for gene set enrichment analysis, which identified 191 enriched pathways in BD. Of these, the toll-like signalling pathway, which is downregulated in BD, was further investigated. ConclusionOur results suggest a profound immune dysregulation in BD, particularly highlighting the immune systems role as a complex signalling network.

neuroscience↗

bioRxiv2025

From iPSCs to NPCs to cortical neurons: bioenergetic, neuronal, and calcium signaling phenotypes in bipolar disorder with and without familial mitochondrial disease

BackgroundPsychiatric disorders frequently accompany primary mitochondrial diseases (PMDs), implicating mitochondrial dysfunction as a shared biological substrate for psychiatric vulnerability. To determine how familial mitochondrial risk influences neuronal development in bipolar disorder (BD), we generated induced pluripotent stem cells (iPSCs), neural progenitor cells (NPCs), and cortical neurons (CNs) from three healthy controls (CT), three patients with BD, and three patients with BD and a family history of mitochondrial disease (BD-FMD). MethodsAcross differentiation, we assessed mitochondrial function (ATP production, mitochondrial membrane potential, ROS generation, cytosolic cell-free mtDNA), metabolomic signatures, calcium imaging, and neuronal electrophysiological activity through multi-electrode arrays (MEA). ResultsBD neurons uniquely exhibited pronounced hyperexcitability in comparison to CT and BD-FMD groups. The BD-FMD group displayed prolonged mitochondrial calcium transients, altered membrane potential, and aberrant ROS, in comparison to CT and BD, consistent with a sustained energetic deficit. Metabolomic profiling revealed distinct pathway enrichments in BD and BD-FMD, indicating divergent bioenergetic adaptations to mitochondrial burden. ConclusionsOur findings reveal that familial mitochondrial liability actively reshapes neuronal differentiation and function, producing distinct trajectories of mitochondrial performance, calcium signaling, and network excitability. These results suggest that mitochondrial dysfunction in BD is not a secondary byproduct of illness, but a mechanistic contributor to altered neuronal energetics and communication. Together, these findings delineate how inherited mitochondrial vulnerability reshapes neuronal excitability and metabolism, revealing bioenergetic phenotypes that may inform precision stratification and therapeutic targeting in BD.

neuroscience↗

bioRxiv2025

Investigating the role of melatonin in bipolar disorder using transcriptomics

Melatonin may be a potential therapeutic target for bipolar disorder (BD) treatment; however, its role in BD pathophysiology remains poorly understood. This study aimed to investigate the therapeutic and mechanistic role of melatonin in BD using transcriptomics. RNA sequencing (RNAseq) data from 216 post-mortem dorsolateral prefrontal cortex samples (156 controls, 60 BD) were used to generate gene regulatory networks (GRNs). These were compared to lists of melatonin-related genes using gene set enrichment analysis (GSEA) to assess differential expression between people with BD and controls. Furthermore, RNAseq data from NT2-N cells treated with lithium, lamotrigine, valproate, or quetiapine were compared to lists of melatonin-related genes using GSEA. Finally, BD-associated gene regulatory patterns were compared to GRNs induced by melatoninergic agents to evaluate the repurposing potential of these pharmacotherapies for BD. Genes involved in inhibiting melatonin signalling were nominally upregulated in the BD post-mortem gene expression dataset. Transcription factors (TFs) activating melatonin signalling tended to be downregulated in BD females, while TFs inhibiting melatonin signalling were significantly downregulated in BD males. Regarding current treatments, quetiapine caused the greatest number of significant alterations in melatonin-related gene expression, followed by valproate, lithium, and then lamotrigine. Valproate was found to significantly upregulate genes involved in melatonin degradation. Finally, the melatonin receptor agonist GR-135531 was identified as a possible repurposing candidate for BD. Overall, this study provides new evidence that dysregulation of melatonin-related genes may play a role in the pathophysiology of BD, and suggests a number of melatoninergic agents as potential therapeutic candidates for BD.

molecular biology↗

bioRxiv2025

iPSC-Derived Cerebral Organoids Reveal Mitochondrial, Inflammatory and Neuronal Vulnerabilities in Bipolar Disorder

Bipolar disorder (BD) is increasingly recognized as a disorder with both mitochondrial dysfunction and heightened inflammatory reactivity, yet their contribution to neuronal activity remains unclear. To address these gaps, this study utilizes iPSC-derived cerebral organoids (COs) from BD patients and healthy controls to model disease-specific metabolic and inflammatory dysfunction in a physiologically relevant system. BD COs exhibited mitochondrial impairment, dysregulated metabolic function, and increased nod-leucine rich repeat and pyrin domain containing protein 3 (NLRP3) inflammasome activation sensitivity. Treatment with MCC950, a selective NLRP3 inhibitor, effectively rescued mitochondrial function and reduced inflammatory activation in both BD and control COs. Additionally, a Bioactive Flavonoid Extract (BFE) was explored as a potential therapeutic, demonstrating partial rescue of inflammasome activation. These findings highlight a mitochondria-inflammasome axis in BD pathophysiology and establish a novel platform for studying BD-associated cellular mechanisms, ultimately bridging the gap between molecular dysfunction and therapeutic development.

neuroscience↗

bioRxiv2024

Multiscale heterogeneity of white matter morphometry in psychiatric disorders

BackgroundInter-individual variability in neurobiological and clinical characteristics in mental illness is often overlooked by classical group-mean case-control studies. Studies using normative modelling to infer person-specific deviations of grey matter volume have indicated that group means are not representative of most individuals. The extent to which this variability is present in white matter morphometry, which is integral to brain function, remains unclear. MethodsWe applied Warped Bayesian Linear Regression normative models to T1- weighted magnetic resonance imaging data and mapped inter-individual variability in person-specific white matter volume deviations in 1,294 cases (58% male) diagnosed with one of six disorders (attention-deficit/hyperactivity, autism, bipolar, major depressive, obsessive-compulsive and schizophrenia) and 1,465 matched controls (54% male) recruited across 25 scan sites. We developed a framework to characterize deviation heterogeneity at multiple spatial scales, from individual voxels, through inter- regional connections, specific brain regions, and spatially extended brain networks. ResultsThe specific locations of white matter volume deviations were highly heterogeneous across participants, affecting the same voxel in fewer than 8% of individuals with the same diagnosis. For autism and schizophrenia, negative deviations (i.e., areas where volume is lower than normative expectations) aggregated into common tracts, regions and large-scale networks in up to 35% of individuals. ConclusionsThe prevalence of white matter volume deviations was lower than previously observed in grey matter, and the specific location of these deviations was highly heterogeneous when considering voxel-wise spatial resolution. Evidence of aggregation within common pathways and networks was apparent in schizophrenia and autism but not other disorders.

neuroscience↗

bioRxiv2023

Plasma neurofilament light protein provides evidence of accelerated brain ageing in treatment-resistant schizophrenia

BackgroundAccelerated brain aging has been observed across multiple psychiatric disorders. Blood markers of neuronal injury such as Neurofilament Light (NfL) protein may therefore represent biomarkers of accelerated brain aging in these disorders. The current study aimed to examine whether relationships between age and plasma NfL were increased in individuals with primary psychiatric disorders compared to healthy individuals. MethodsPlasma NfL was analysed in major depressive disorder (MDD, n = 42), bipolar affective disorder (BPAD, n = 121), treatment-resistant schizophrenia (TRS, n = 82), a large reference normative healthy control (HC) group (n= 1,926) and a locally-acquired HC sample (n = 59). A general linear model (GLM) was used to examine diagnosis by age interactions on NfL z-scores using the large normative HC sample as a reference group. Significant results were then validated using the locally-acquired HC sample. Resultsa GLM identified a significant age by diagnosis interaction for TRS vs HCs and BPAD vs HCs. Post hoc analyses revealed a positive correlation between NfL levels and age among individuals with TRS, whereas a negative correlation was found among individuals with BPAD. However, only the TRS findings were replicated using the locally-acquired HC sample. Post hoc analyses revealed that individuals with TRS aged <40 had lower NfL levels compared to same-age HCs, whereas individuals with TRS aged >40 had higher NfL levels compared to same-age HCs. ConclusionsThese findings add to the growing literature supporting the notion of accelerated brain ageing in schizophrenia-spectrum disorders.

neuroscience↗

bioRxiv2023

Anti-manic effect of deep brain stimulation of the ventral tegmental area in an animal model of mania induced by methamphetamine

BackgroundTreatment of refractory bipolar disorder (BD) is extremely challenging. Deep brain stimulation (DBS) holds promise as an effective treatment intervention. However, we still understand very little about the mechanisms of DBS and its application on BD. AimThe present study aimed to investigate the behavioural and neurochemical effects of ventral tegmental area (VTA) DBS in an animal model of mania induced by methamphetamine (m-amph). MethodsWistar rats were given 14 days of mamph injections, in the last day animals were submitted to 20 minutes of VTA DBS in two different patterns: intermittent low frequency stimulation (LFS) or continuous high frequency stimulation (HFS). Immediately after DBS, manic-like behaviour and nucleus accumbens (NAc) phasic dopamine (DA) release were evaluated in different groups of animals through open-field test and fast-scan cyclic voltammetry. Levels of NAc dopaminergic markers were evaluated by immunohistochemistry. ResultsM-amph induced hyperlocomotion in the animals and both DBS parameters reversed this alteration. Mamph increased DA reuptake time post-sham compared to baseline levels, and both LFS and HFS were able to block this alteration. LFS was also able to reduce phasic DA release when compared to baseline. LFS was able to increase dopamine transporter (DAT) expression in the NAc. ConclusionThese results demonstrate that both VTA LFS and HFS DBS exert anti-manic effects and modulation of DA dynamics in the NAc. More specifically the increase in DA reuptake driven by increased DAT expression may serve as a potential mechanism by which VTA DBS exerts its anti-manic effects.

neuroscience↗

bioRxiv2023

The landscape of tolerated genetic variation in humans and primates

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases. One Sentence SummaryDeep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.

genomics↗

bioRxiv2020

No evidence that androgen regulation of pulmonary TMPRSS2 explains sex-discordant COVID-19 outcomes

The sex discordance in COVID-19 outcomes has been widely recognized, with males generally faring worse than females and a potential link to sex steroids. A plausible mechanism is androgen-induced expression of TMPRSS2 and/or ACE2 in pulmonary tissues that may increase susceptibility or severity in males. This hypothesis is the subject of several clinical trials of anti-androgen therapies around the world. Here, we investigated the sex-associated TMPRSS2 and ACE2 expression in human and mouse lungs and interrogated the possibility of pharmacologic modification of their expression with anti-androgens. We found no evidence for increased TMPRSS2 expression in the lungs of males compared to females in humans or mice. Furthermore, in male mice, treatment with the androgen receptor antagonist enzalutamide did not decrease pulmonary TMPRSS2. On the other hand, ACE2 and AR expression was sexually dimorphic and higher in males than females. ACE2 was moderately suppressible with enzalutamide therapy. Our work suggests that sex differences in COVID-19 outcomes attributable to viral entry are independent of TMPRSS2. Modest changes in ACE2 could account for some of the sex discordance.

physiology↗

bioRxiv2019

Neurovegetative symptom subtypes in young people with major depressive disorder and their structural brain correlates

BackgroundDepression is a leading cause of burden of disease among young people. Current treatments are not uniformly effective, in part due to the heterogeneous nature of major depressive disorder (MDD). Refining MDD into more homogeneous subtypes is an important step towards identifying underlying pathophysiological mechanisms and improving treatment of young people. In adults, symptom-based subtypes of depression identified using data-driven methods mainly differed in patterns of neurovegetative symptoms (sleep and appetite/weight). These subtypes have been associated with differential biological mechanisms, including immuno-metabolic markers, genetics and brain alterations (mainly in the ventral striatum and insular cortex).\n\nMethodsK-means clustering was applied to individual depressive symptoms from the Quick Inventory of Depressive Symptoms (QIDS) in 275 young people (15-25 years old) with MDD to identify symptom-based subtypes, and in 244 young people from an independent dataset (a subsample of the STAR*D dataset). Insula surface area and thickness and ventral striatum volume were compared between the subtypes using structural MRI.\n\nResultsThree subtypes were identified in the discovery dataset and replicated in the independent dataset; severe depression with increased appetite, severe depression with decreased appetite and severe insomnia, and moderate depression. The severe increased appetite subtype showed lower surface area in the anterior insula compared to both healthy controls and the moderate subtype.\n\nConclusionsOur findings in young people replicate the previously identified symptom-based depression subtypes in adults. The structural alterations of the anterior insular cortex add to the existing evidence of different pathophysiological mechanisms involved in this subtype.

neuroscience↗