Biology subjects

Duan, J.

Publications and source records attributed to Duan, J..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Nuclear effects play an important role in determining codon usage-dependent human gene expression

Codon usage biases play a significant role in determining gene expression levels. Codon usage was thought to primarily influence translation-dependent processes. Here we show that codon usage optimality correlates genome-wide with nuclear mRNA and transcription levels in human cells, suggesting a nuclear role for codon usage. A genome-wide non-biased CRISPR-Cas9 screen was performed to identify factors involved in codon usage effects on gene expression. The identified factors include the CCR4-NOT complex subunit CNOT4 and many nuclear factors, including nuclear RNA exosome, PAXT complex components, and transcription factors. The CCR4-NOT complex has been shown to affect codon usage-dependent co-translational mRNA decay in yeast. Surprisingly, human CNOT4 was found to be highly enriched in nucleus and its influence on codon usage-dependent gene expression is largely caused by its impact on nuclear RNA levels due to transcriptional effect. On the other hand, nuclear exosome and PAXT complex, regulates nuclear mRNA stability through the RNA quality control pathway, leading to preferential cytoplasmic accumulation of mRNAs with optimal codon usage. Overall, our findings suggest that codon usage biases are due to selection on both translation-dependent and independent processes; different nuclear mechanisms play a key role in determining nucleotide composition-dependent gene expression levels in human cells.

genomics↗

bioRxiv2024

Mutations of schizophrenia risk gene SETD1A dysregulate synaptic function in human neurons

Schizophrenia (SCZ) is a complex neuropsychiatric disorder associated with both common risk variants of small effect sizes and rare risk variants of high penetrance. Rare protein truncating variants (PTVs) in SETD1A (SET Domain Containing 1A) show a strong association with SCZ; however, it remains largely unclear how rare PTVs in SETD1A contribute to the pathophysiology of SCZ. To understand the impact of SETD1A rare PTVs in human neurons, we CRISPR/Cas9-engineered five isogenic pairs of human induced pluripotent stem cells (iPSCs), with a recurrent heterozygous patient-specific PTV mutation c.4582-2delAG in two donor lines and a heterozygous frameshift mutation c.4596_4597insG (p. Leu1533fs) in three donor lines. These two mutations are predicted to cause a premature stop codon in exon 16 of SETD1A, leading to the loss of the conserved SET domain that is critical for its histone methyltransferase activity. We found that these presumably loss-of-function (LoF) mutations caused the SETD1A mRNAs to be degraded by nonsense-mediated decay (NMD), accompanied by a reduction of full-length SETD1A protein level in iPSCs. We then characterized the morphological, electrophysiological, and transcriptomic impacts of the SETD1A+/- LoF mutations in iPSC-derived human excitatory neurons induced by NGN2. We found that the SETD1A+/- exon-16 LoF mutations altered dendrite complexity, dysregulated synaptic transmission, and synaptic plasticity, likely by dysregulating genes involved in synaptic function. These results provide mechanistic insights into how SETD1A+/-exon-16 patient-specific LoF mutations affect neuron phenotypes that may be relevant to the pathophysiology of SCZ.

neuroscience↗

bioRxiv2024

TOMM40-APOE chimera linking Alzheimer's highest risk genes: a new pathway for mitochondria regulation and APOE4 pathogenesis

The patho-mechanism of apolipoprotein variant, APOE4, the strongest genetic risk for late-onset Alzheimers disease (AD) and longevity, remains unclear. APOEs neighboring gene, TOMM40 (mitochondria protein transport channel), is associated with brain trauma outcome and aging-related cognitive decline, however its role in AD APOE4-independently is controversial. We report that TOMM40 is prone to transcription readthrough into APOE that can generate spliced TOMM40-APOE mRNA chimera (termed T9A2) detected in human neurons and other cells and tissues. T9A2 translation tethers APOE (normal APOE3 or APOE4) to near-full-length TOM40 that is targeted to mitochondria. Importantly, T9A2-APOE3 boosts mitochondrial bioenergetic capacity and decreases oxidative stress significantly more than T9A2-APOE4 and APOE3, and lacking in APOE4. We describe detailed interactomes of these actors that may inform about the activities and roles in pathogenesis. T9A2 uncovers a new candidate pathway for mitochondria regulation and oxidative stress-protection that are impaired in APOE4 genotypes and could initiate neurodegeneration.

cell biology↗

bioRxiv2024

Twist is the key to the gating of mechanosensitive ion channel NOMPC

NOMPC, a tethered mechanosensitive ion channel belonging to the transient receptor potential (TRP) family, converts mechanical stimuli into ionic electric signals that excite neuronal cells. Previous investigations have demonstrated that a pushing force applied to the linker helix domain or the compression of NOMPCs ankyrin repeat (AR) domain can trigger channel opening. In this study, we explored the direct mechanical causes of NOMPC channel opening as well as the torsional properties of the AR domain, using all-atom molecular dynamics simulations. Our results indicate that a torque directed toward the extracellular side, exerted on the amphipathic TRP domain, is the primary factor driving channel opening. The coupling between compression and twisting of the AR domain ensures that both types of deformation can induce channel opening. Therefore, we propose a twist-to-open model, facilitated by the compression-twist coupling property of the AR domain, to provide further insight into the gating mechanism of the NOMPC channel.

biophysics↗

bioRxiv2024

Long-Range Enhancer Networks Gradually Emerge as Key Regulators During Human Cortical Neurogenesis

The chromatin in the human brain cortex shows more enhancer-enhancer contacts than in macaques and mice, yet the organization of these contacts across cellular states and their mechanisms remain unclear. Here, we developed SCOPE-C, a cost-effective technique designed for mapping DNase I Hypersensitive Sites and their spatial interactions, with the potential for scalability to single-cell resolution. Employing SCOPE-C, we generated a comprehensive chromatin map detailing cis-regulatory elements in four cell types during neurogenesis in human, macaque, and mouse fetal cortex. This map introduces a model of long-range enhancer networks that regulate gene transcription during human cortical neurogenesis. In this model, CTCF-mediated loop extrusion forms stripes of enhancer interaction hubs extending up to 10 Mb in human Excitatory Neurons. Enriched with human-specific enhancers and neuropsychiatric disorder-linked SNPs, these remarkably long-range networks predominantly control EN marker genes, suggesting their critical role in robust gene expression during human cortical neurogenesis.

genomics↗

bioRxiv2024

Robust prediction of relative binding energies for protein-protein complex mutations using free energy perturbation calculations

Computational free energy-based methods have the potential to significantly improve throughput and decrease costs of protein design efforts. Such methods must reach a high level of reliability, accuracy, and automation to be effectively deployed in practical industrial settings in a way that impacts protein design projects. Here, we present a benchmark study for the calculation of relative changes in protein-protein binding affinity for single point mutations across a variety of systems from the literature, using free energy perturbation (FEP+) calculations. We describe a method for robust treatment of alternate protonation states for titratable amino acids, which yields improved correlation with and reduced error compared to experimental binding free energies. Following careful analysis of the largest outlier cases in our dataset, we assess limitations of the default FEP+ protocols and introduce an automated script which identifies probable outlier cases that may require additional scrutiny and calculates an empirical correction for a subset of charge-related outliers. Through a series of three additional case study systems, we discuss how protein FEP+ can be applied to real-world protein design projects, and suggest areas of further study. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/590325v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1c5e607org.highwire.dtl.DTLVardef@1810ee5org.highwire.dtl.DTLVardef@1f8f1acorg.highwire.dtl.DTLVardef@c28053_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIReliable calculation of relative binding free energy changes for most protein mutations to within [~]1 kcal/mol. C_LIO_LIAutomated Protein FEP+ Groups treatment of alternate protonation states for titratable residues. C_LIO_LIApplication of FEP+ methodology to "real-world" protein design projects. C_LI

biophysics↗

bioRxiv2024

Widespread transcription initiation within coding sequences marks tissue identity and accessible chromatin

Alternative transcription initiation (ATI) appears to be a ubiquitous regulatory mechanism of gene expression in eukaryotes, but the extent to which it affects the products of gene expression, and how it evolves and is regulated remain unknown. We first identified transcription start sites (TSSs) in eight soybean tissues using recently developed STRIPE-seq and then analyzed ATI in the context of tissue identity and chromatin architecture. We defined 193,579 TSS clusters/regions (TSRs) in 37,911 annotated genes, with 56.5% located in putative regulatory regions upstream of start codons and 43.5% from start codons to 3 untranslated regions, which, together, are responsible for changes in open reading frames of 24,131 genes. Overall, duplicated genes possess more TSRs, exhibited lower degrees of tissue-specificity, and have undergone stronger purifying selection than singletons. Strikingly, 6,845 genes possess ATI within coding sequences (CDSs). These CDS-TSRs are highly tissue-specific, shorter than those located in canonical regulatory regions, and do not have TATA-boxes typical for the core promoters. Furthermore, the CDS-TSRs are embedded in nucleosome-free regions and flanked by nucleosomes with enhanced levels of active histone marks associated with transcriptionally active chromatin, suggesting that non-canonical ATI is epigenetically regulated and largely responsible for tissue-specific functions and tissue identity. Our study highlights the genomic and epigenomic factors shaping the distribution patterns and tissue-specificity of ATI in regulatory and coding sequences, as well as the significance of ATI in the alternation of proteins encoded by tissue-specifically expressed genes in the context of genome duplication and fractionation.

genomics↗

bioRxiv2024

Scaled and Efficient Derivation of Loss of Function Alleles in Risk Genes for Neurodevelopmental and Psychiatric Disorders in Human iPSC

Translating genetic findings for neurodevelopmental and psychiatric disorders (NPD) into actionable disease biology would benefit from large-scale and unbiased functional studies of NPD genes. Leveraging the cytosine base editing (CBE) system, here we developed a pipeline for clonal loss-of-function (LoF) allele mutagenesis in human induced pluripotent stem cells (hiPSCs) by introducing premature stop-codons (iSTOP) that lead to mRNA nonsense-mediated-decay (NMD) or protein truncation. We tested the pipeline for 23 NPD genes on 3 hiPSC lines and achieved highly reproducible, efficient iSTOP editing in 22 NPD genes. Using RNAseq, we confirmed their pluripotency, absence of chromosomal abnormalities, and NMD. Interestingly, for three schizophrenia risk genes (SETD1A, TRIO, CUL1), despite the high efficiency of base editing, we only obtained heterozygous LoF alleles, suggesting their essential roles for cell growth. We replicated the reported neural phenotypes of SHANK3-haploinsufficiency and found CUL1-LoF reduced neurite branches and synaptic puncta density. This iSTOP pipeline enables a scaled and efficient LoF mutagenesis of NPD genes, yielding an invaluable shareable resource.

genetics↗

bioRxiv2024

de Novo Sequencing of Antibodies for Identification of Neutralizing Antibodies in Human Plasma Post SARS-CoV-2 Vaccination

We present a method for sequencing polyclonal IgG enriched from human plasma, employing a combination of de novo sequencing, proteomics, bioinformatics, protein separation, sequencing, and peptide separations. Our study analyzes a single patients IgG antibody response triggered by the Moderna Spikevax mRNA COVID-19 vaccine. From the sequencing data of the natural polyclonal response to vaccination, we generated 12 recombinant antibodies. Six derived recombinant antibodies, including four generated with de novo sequencing, exhibited similar or higher binding affinities than the original natural polyclonal antibody. Our neutralization tests revealed that the six antibodies possess neutralizing capabilities against the target antigen. This research provides insights into sequencing polyclonal IgG antibodies while highlighting the effectiveness and potential of our approach in generating recombinant antibodies with robust binding affinity and neutralization capabilities. Our proposed approach is an advancement in characterizing the IgG response by directly investigating the circulating pool of IgG without relying exclusively on the B-cell repertoire or population. This is crucial as the B-cell analysis may not accurately represent the circulating antibodies. Interestingly, a large proportion (80 to 90%) of the human antibody sequences generated against SARS-CoV-2 in the literature have been derived solely from B-cell analysis. Therefore, the ability to offer a different perspective is crucial in gaining a comprehensive understanding of the IgG response. Significance StatementWe investigate human IgG targeting the receptor binding domain using de novo proteomics. The peripheral B-cell repertoire may not adequately cover all the circulating IgG for human IgG sequencing. Our approach overcomes this limitation by using a de novo protein sequencing on top of standard proteomics. We obtained distinct de novo sequences, showcasing our methods potential. The recombinant proteins we generate possess traits comparable to or surpassing the naturally occurring polyclonal antibodies (pAbs). This study highlights similarities and differences between IgG populations in blood and circulating B-cells, which is crucial for future biologics development.

immunology↗

bioRxiv2024

A Drosophila model to screen Alport syndrome COL4A5 variants for their functional pathogenicity

Alport syndrome is a hereditary chronic kidney disease, attributed to rare pathogenic variants in either of three collagen genes (COL4A3/4/5) with most localized in COL4A5. Trimeric type IV Collagen 345 is essential for the glomerular basement membrane that forms the kidney filtration barrier. A means to functionally assess the many candidate variants and determine pathogenicity is urgently needed. We used Drosophila, an established model for kidney disease, and identify Col4a1 as the functional homolog of human COL4A5 in the fly nephrocyte (equivalent of human podocyte). Fly nephrocytes deficient for Col4a1 showed an irregular and thickened basement membrane and significantly reduced nephrocyte filtration function. This phenotype was restored by expressing human reference (wildtype) COL4A5, but not by COL4A5 carrying any of three established pathogenic patient-derived variants. We then screened seven additional patient COL4A5 variants; their ClinVar classification was either likely pathogenic or of uncertain significance. The findings support pathogenicity for four of these variants; the three others were found benign. Thus, demonstrating the effectiveness of this Drosophila in vivo kidney platform in providing the urgently needed variant-level functional validation. SUMMARY STATEMENTDrosophila, an established model of kidney disease, was used to develop an in vivo functional screen to determine causation for COL4A5 genetic variants linked to Alport syndrome, a progressive nephropathy.

genetics↗

bioRxiv2024

JAK-STAT pathway activation compromises nephrocyte function in a Drosophila high-fat diet model of chronic kidney disease

Chronic kidney disease is a major health issue and is gaining prevalence. Using a Drosophila model for chronic kidney disease, we show that a high-fat diet (HFD) disrupts the slit diaphragm filtration structure in nephrocytes, the fly functional equivalent of mammalian podocytes. The structural disruption resulted in reduced filtration function in the affected nephrocytes. We demonstrate that HFD activates the JAK-STAT pathway in nephrocytes, which has previously been linked to diabetic kidney disease. JAK-STAT activation was initiated by increased expression and release of the adipokine, Upd2, from the fat body. This leptin-like hormone is a known ligand of JAK-STAT. Both genetic and pharmacological inhibition of JAK-STAT restored nephrocyte HFD-associated dysfunction. Altogether, our study reveals the importance of the JAK-STAT signaling pathway in the adipose tissue-nephrocyte axis and its contribution to HFD-associated nephropathy. These findings open new avenues for intervention in treating diabetic nephropathy and chronic kidney disease. HIGHLIGHTSO_LIHigh-fat diet (HFD) disrupt nephrocyte slit diaphragm structure and filtration C_LIO_LIHFD releases fat body adipokine, Upd2, which activates JAK-STAT in nephrocytes C_LIO_LIGenetic/pharmacological inhibition of JAK-STAT reverses HFD nephrocyte dysfunction C_LIO_LIJAK-STAT signaling mediates adipose-nephrocyte axis in HFD-associated nephropathy C_LI IMPACT STATEMENTUsing a Drosophila model for chronic kidney disease, Zhao et al. show that a high-fat diet induces excretion of a leptin-like JAK-STAT ligand from the fat body. Thus, driving the adipose-nephrocyte (podocyte equivalent) axis through activated JAK-STAT signaling. These findings link obesity to kidney disease, implicating new avenues for therapeutics.

molecular biology↗

bioRxiv2024

Polygenic Risk for Alcohol Use Disorder Affects Cellular Responses to Ethanol Exposure in a Human Microglial Cell Model

Polygenic risk scores (PRS) assess genetic susceptibility to Alcohol Use Disorder (AUD), yet their molecular implications remain underexplored. Neuroimmune interactions, particularly in microglia, are recognized as significant contributors to AUD pathophysiology. We investigated the interplay between AUD PRS and ethanol in human microglia derived from iPSCs from individuals with high- or low-PRS (HPRS or LPRS) of AUD. Ethanol exposure induced elevated CD68 expression and morphological changes in microglia, with differential responses between HPRS and LPRS microglial cells. Transcriptomic analysis revealed expression differences in MHCII complex and phagocytosis-related genes following ethanol exposure; HPRS microglial cells displayed enhanced phagocytosis and increased CLEC7A expression, unlike LPRS microglial cells. Synapse numbers in co-cultures of induced neurons with microglia after alcohol exposure were lower in HRPS co-cultures, suggesting possible excess synapse pruning. This study provides insights into the intricate relationship between AUD PRS, ethanol, and microglial function, potentially influencing neuronal functions in developing AUD.

neuroscience↗

bioRxiv2023

A direct estrogenic involvement in the expression of human hypocretin

BackgroundHypocretin-1 may play an important role in depression, which was increased in female depression in LHA in our previous study. Estrogen acts through its nuclear transcriptional receptors. MethodsWe studied the possibility of a direct action of estrogen receptors on the expression of human hypocretin. To explore the activation of ERs by hypocretin, we first investigated the potential presence of co-localization of the estrogen receptors (ERs) in hypocretin-immunoreactive neurons in the lateral hypothalamic area (LHA) in human and nuclear ERs in hypocretin immunoreactive neuroblastoma SK-N-SH cells. We investigated the relationship between E2 and hypocretin in female rats. After we explored the regulating role of exogenous estrogen on hypocretin gene expression via ERs through Chromatin immunoprecipitation, Electrophoretic mobility shift assay and Luciferase assay. ResultsWe found that hypocretin-1 plasma level was significantly higher in female depression. Estrogen receptors (ER and ER{beta}) and hypocretin are co-localized in female depression LHA, PC12 and SK-N-SH cell lines. The estrogen receptor response elements (EREs) existing in the hypocretin promoter region may directly regulate the expression of hypocretin, the synchronicity of change of hypocretin and estradiol both in hypothalamus and plasma was verified in female rats. With the presence of estradiol, there is specific binding between human ER and the Hypocretin-ERE. Expression of ER combined with estradiol repressed hypocretin promoter activity through the ERE. Conclusionswe defined that estradiol may affect hypocretin neurons in the human hypothalamus via ER binding to the Hypocretin-ERE directly, which may thus lead to the sex-specific pathogenesis of depression.

neuroscience↗

bioRxiv2023

Cardiac neurons expressing a glucagon-like receptor mediate cardiac arrhythmia induced by high-fat diet in Drosophila

Cardiac arrhythmia leads to increased risks for stroke, heart failure, and cardiac arrest. Arrhythmic pathology is often rooted in the cardiac conduction system, but the mechanism is complex and not fully understood. For example, how metabolic diseases, like obesity and diabetes, increase the risk for cardiac arrhythmia. Glucagon regulates glucose production, mobilizes lipids from the fat body, and affects cardiac rate and rhythm, attributes of a likely key player. Drosophila is an established model to study metabolic diseases and cardiac arrhythmias. Since glucagon signaling is highly conserved, we used high-fat diet (HFD)-fed flies to study its effect on heart function. HFD led to increased heartbeat and an irregular rhythm. The HFD-fed flies showed increased levels of adipokinetic hormone (Akh), the functional equivalent to human glucagon. Both genetic reduction of Akh and eliminating the Akh producing cells (APC) rescued HFD-induced arrhythmia, whereas heart rhythm was normal in Akh receptor mutants (AkhRnull). Furthermore, we discovered a pair of cardiac neurons that express high levels of Akh receptor. These are located near the posterior heart, make synaptic connections at the heart muscle, and regulate heart rhythm. Altogether, this Akh signaling pathway provides new understanding of the regulatory mechanisms between metabolic disease and cardiac arrhythmia. HIGHLIGHTSO_LIHigh-fat diet activates Akh (glucagon-like)-producing neurons near the esophagus in Drosophila C_LIO_LIReducing Akh prevents high-fat diet-induced cardiac arrhythmia in flies C_LIO_LIDiscovery of two neurons located at the posterior end of the heart that express the Akh receptor (AkhR) and innervate the heart C_LIO_LIEliminating one of the two AkhR-expressing cardiac neurons (ACN) results in cardiac arrhythmia, whereas the absence of functional AkhR prevents high-fat diet-induced cardiac arrhythmia in flies C_LI

molecular biology↗

bioRxiv2023

The microbial community of rust layer biofilm was driven by seawater microbial community

Microbiologically influenced corrosion (MIC) accounts for approximately 20% of the total corrosion-related losses worldwide, causing significant economic damage each year, particularly in Marine environments. However, there are still no truly effective and eco-friendly protection solutions against MIC, among which the incomplete understanding of the microbial biofilm development on metallic surface is a key limitation. Using 16S rRNA and ITS sequencing, we studied bacterial and fungal communities in rust layer biofilm and seawater. The results showed that Proteobacteria, Cyanobacteria and Bacteroidota were the dominant bacterial phyla, and Ascomycota and Basidiomycota were the dominant fungal phyla both in the rust layer biofilm and seawater. Bacteria like Erythrobacter and Aquimarina, as well as fungi like Aspergillus and Acremonium were were notable microorganisms in the rust layer biofilm. Source analysis revealed differences between biofilm and seawater communities, with 23.08% bacterial and 21.48% fungal communities originating from seawater. Stochastic processes governed biofilm and seawater microbial communities, and network analysis showed coexistence and interaction among bacteria and fungi. IMPORTANCEThe composition and source analysis of bacterial and fungal communities in the rust layer and seawater were studied, and the interaction of bacteria and fungi in the rust layer was discussed for the first time. Based on these findings, we provided a framework to explain the observed characteristics of microbial communities in rust layer biofilm and presented key evidence supporting the relationship between different microbial structures and interactions with metal corrosion. These findings, from the perspective of microbial ecology, provide a theoretical foundation for studying microbial corrosion in marine environments.

microbiology↗

bioRxiv2023

The CLAMP GA-binding transcription factor regulates heat stress-induced transcriptional repression by associating with 3D loop anchors.

To survive exposure to heat stress (HS), organisms activate stress response genes and repress constitutive gene expression, thereby preventing the accumulation of potentially toxic RNA and protein products. Although many studies have elucidated the mechanisms that drive HS-induced activation of stress response genes across species, little is known about the mechanisms that repress constitutively expressed genes. Using nascent RNA-sequencing, we identify the first reported transcription factor (TF) that regulates repression of constitutive genes upon heat stress across species and define direct and indirect mechanisms of action by integrating 3D genomic approaches. We demonstrate that the CLAMP (Chromatin-linked adaptor for MSL complex proteins) GA-binding transcription factor (TF) regulates [~]75% of the HS-induced repression in Drosophila, a well-established model for understanding the mechanisms of HS-induced gene regulation. Using Micro-C, we demonstrate that heat stress induces widespread changes in local 3D chromatin looping, which are significantly associated with HS-induced transcriptional changes. Overall, we identify CLAMP as the first reported TF that induces HS repression, which modulates 3D chromatin looping through both direct mechanisms and indirect mechanisms. Moreover, we present the highest-resolution heat stress 3D genomic dataset available in Drosophila, providing a key resource for generating mechanistic insights into how temperature regulates 3D genomic contacts.

genomics↗

bioRxiv2023

Prominent contributions of selective neuronal subtypes to pediatric drug-resistant focal dysplasia

About 75% cases of epilepsy begin during childhood, and 10 - 30% of pediatric epilepsy patients are resistant to drug treatment. The predominant seizure type in children is focal cortical dysplasia (FCD) which is highly associated with drug-resistant epilepsy, but its underlying cause is poorly understood. We performed single-cell RNA sequencing and patch-clamp recording on fresh brain tissues obtained from pediatric FCD patients shortly after surgery to reveal critical factors contributing to FCD. We report that known epilepsy genes or significant transcriptomic alterations occur in only a few neuronal subgroups, suggesting that epilepsy-associated neurons cluster into only a few neuronal subtypes. These epilepsy-subtypes displayed significant epilepsy-related transcriptomic alterations, especially in the genes associated with excitation/inhibition balance and neuron functional signal pathways. Among eight epilepsy-subtypes, L2_4_CUX2_YWHAH and PVALB_RGS5 subtypes showed the most prominent alterations in FCD patient tissues. Supporting PV-neurons being important, recording from fast-spiking/parvalbumin-containing neurons in acute FCD patient brain slices revealed reduced excitatory synaptic inputs, implicating lower activity in these neurons and fewer synaptic inputs onto them. A higher percentage of mitochondria genes, and likely higher activity in the pathways associated with oxidative phosphorylation and ATP biosynthetic process, was observed in the epilepsy-subtypes, suggesting a high energy expenditure in them. Interestingly, the activity of the above two pathways in most epilepsy-subtypes was lower in the FCD patients, suggesting these subtypes may be more vulnerable to energy deficit in epilepsy. Altogether, transcriptomics is significantly altered in only a few neuronal subtypes in pediatric FCD patient brains. These selective epilepsy-subtypes may play prominent roles in the genesis of pediatric drug-resistant seizure and targeting them may provide new treatment options.

bioinformatics↗

bioRxiv2023

tauFisher accurately predicts circadian time from a single sample of bulk and single-cell transcriptomic data

As the circadian clock regulates fundamental biological processes, disrupted clocks are often observed in patients and diseased tissues. Determining the circadian time of the patient or the tissue of focus is essential in circadian medicine and research. Here we present tau-Fisher, a computational pipeline that accurately predicts circadian time from a single transcriptomic sample by finding correlations between rhythmic genes within the sample. We demonstrate tauFishers out-standing performance in both bulk and single-cell transcriptomic data collected from multiple tissue types and experimental settings. Application of tauFisher at a cell-type level in a single-cell RNA-seq dataset collected from mouse dermal skin implies that greater circadian phase heterogeneity may explain the dampened rhythm of collective core clock gene expression in dermal immune cells compared to dermal fibroblasts. Given its robustness and generalizability across assay platforms, experimental setups, and tissue types, as well as its potential application in single-cell RNA-seq data analysis, tauFisher is a promising tool that facilitates circadian medicine and research.

bioinformatics↗