Biology subjects

Huang, Q.

Publications and source records attributed to Huang, Q..

At least 109 records · Page 6Linked to original sources

bioRxiv2023

Multi-omics analysis reveals novel interplays between intratumoral bacteria and glioma

Emerging evidence highlights the potential impact of intratumoral microbiota on cancer. However, the microbial composition and function in glioma remains elusive. Consequently, our study aimed to investigate the microbial community composition in glioma tissues and elucidate its role in glioma development. We parallelly performed microbial profiling, transcriptome sequencing and metabolomics detection on tumor and adjacent normal brain tissues obtained from 50 glioma patients. We employed immunohistochemistry, multicolor immunofluorescence and FISH staining to observe the presence and location of bacteria. Furthermore, an animal model was employed to validate the impact of key bacteria on glioma development. Six genera were found to be significantly enriched in glioma tissues compared to its adjacent normal brain tissues, including Fusobacterium, Longibaculum, Intestinimonas, Pasteurella, Limosilactobacillus and Arthrobacter. Both bacterial RNA and LPS were observed in glioma tissues. Multicolor immunofluorescence analysis showed higher bacterial LPS levels in tumor cells than in macrophages and in glioma tissue than in adjacent normal brain tissue. Integrated microbiomics, transcriptomics, and metabolomics revealed that genes associated with intratumoral microbes were enriched in multiple synapse-associated pathways and that metabolites associated with intratumoral microbes were (R)-N-methylsalsolinol, N-acetylaspartylglutamic acid, and N-acetyl-L-aspartic acid. Further mediation analysis suggested that intratumoral microbiome may affect the expression of neuron-related genes through bacteria-associated metabolites. In addition, a glioma mouse model suggested that Fusobacterium nucleatum promoted glioma growth by increasing the levels of N-acetylneuraminic acid and the expression levels of CCL2, CXCL1, and CXCL2. In conclusion, our findings shed light on the intricate interplays between intratumoral bacteria and glioma.

neuroscience↗

bioRxiv2023

MFSD7c functions as a transporter of choline at the blood-brain barrier

Mutations of MFSD7c (also known as Flvcr2), which is an orphan transporter, are linked to Fowler syndrome 1, 2. Here, we use Mfsd7c knockout mice and cell-based assays to reveal that MFSD7c is a choline transporter at the blood-brain barrier (BBB). We performed comprehensive metabolomics and detected differential changes of metabolites in the brains and livers of Mfsd7c knockout (Mfsd7c-/-) embryos. Particularly, we found that choline-related metabolites were altered in the brains but not in the livers of Mfsd7c-/- embryos. Thus, we hypothesized that MFSD7c regulates the levels of choline in the brain. Indeed, expression of human MFSD7c in cells significantly increased choline uptake. Interestingly, we showed that choline uptake by MFSD7c is greatly increased by choline-metabolizing enzymes, leading us to demonstrate that MFSD7c is a facilitative transporter of choline. Furthermore, single-cell patch-clamp showed that the import of choline by MFSD7c is electrogenic. Choline transport function of MFSD7c is conserved in vertebrates, but not in yeasts. We show that human MFSD7c is a functional ortholog of HNM1, the yeast choline importer. Employing our transport assays, we showed that several missense mutations of human MFSD7c from Fowler patients had abolished or reduced choline transport activity. Mice lacking Mfsd7c in the CNS endothelial cells suppressed the import of exogenous choline from blood but unexpectedly had increased choline levels in the brain. Stable-isotope tracing study revealed that MFSD7c is required for exporting choline derived from lysophosphatidylcholine (LPC) in the brain. Collectively, our work identifies MFSD7c as a choline transporter at the BBB. This study suggests that defective export of choline in the brain may be a cause of Fowler syndrome.

biochemistry↗

bioRxiv2023

Activation of a cortical neurogenesis transcriptional program during NEUROD1-induced astrocyte-to-neuron conversion

NEUROD1-induced astrocyte-to-neuron (AtN) conversion has garnered significant attention as a potential therapeutic intervention to neurological disorders. To gain insight into the molecular regulations underlying this neuronal reprogramming process, we applied single-cell multiomics analyses on in vitro ND1-induced AtN conversion to systematically investigate how ND1 changed the fate of astrocytes at transcriptomic and epigenetic levels. Our findings reveal that the initial immature astrocytes go through an intermediate state where both astrocytic and neuronal genes are activated at early stage of AtN conversion. ND1 directly reshapes the chromatin accessibility landscape of astrocytes to that of neurons, promoting expression of endogenous Neurod1 and other neurogenic genes such as Hes6, Insm1 etc. Interestingly, cell proliferation status is highly correlated with conversion rate, and inhibition of cell division significantly reduces the conversion ratio. Moreover, in comparison with another AtN reprogramming transcription factor, ASCL1, external ND1 can activate endogenous Neurod1 and directly promote neuronal gene transcription; whereas external ASCL1 hardly activates endogenous Ascl1, leading to slower and inefficient conversion. Together, our studies demonstrate that in vitro AtN conversion mimics neurogenic transcriptional program in embryonic neurogenesis.

neuroscience↗

bioRxiv2023

Commensal microbiome dysbiosis elicits IL-8 signaling to drive fibrotic skin disease

Commensal bacteria are core players in wound healing whose function in the opposite pathophysiological process-scarring is presently unclear. Here, we document the association between bacteria and a specific skin fibrotic disease-keloid, which might offer a promising avenue for translational practice. ABSTRACTWound healing is an intensely studied topic involved in many relevant pathophysiological processes, including fibrosis. Despite the large interest in fibrosis, the network that related to commensal microbiota and skin fibrosis remain mysterious. Here, we pay attention to keloid, a classical yet intractable skin fibrotic disease to establish the association between commensal microbiota to scaring tissue. Our histological data reveal the presence of microbiota in the keloids. 16S rRNA sequencing characterize microbial composition and divergence between the pathological and normal skin tissue. Moreover, the data show elevation of interleukin-8 both in the circulation and keloid tissue, which elicited the collagen accumulation and migratory program of dermal fibroblasts via CXCR1/2 receptor. Our research provides insights into the pathology of human fibrotic diseases, advocating commensal bacteria and IL-8 signaling as useful targets in future interventions of recurrent keloid disease.

microbiology↗

bioRxiv2023

Replay-triggered Brain-wide Activation in Humans

The consolidation of discrete experiences into a coherent narrative shape our cognitive map, providing a structured mental representation of our experiences. Neural replay, by fostering crucial hippocampal-cortical dialogue, is thought to be pivotal in this process. However, the brain-wide engagement coinciding with replay bursts remains largely unexplored. In this study, by employing simultaneous EEG-fMRI, we capture both the spatial and temporal dynamics of replay. We find that during mental simulation, the strength of on-task replay, as detected via EEG, correlates with heightened fMRI activity in the hippocampus and medial prefrontal cortex. Intriguingly, increased replay strength also enhances the functional connectivity between the hippocampus and the default mode network, a set of brain regions key to representing cognitive map. Furthermore, during the post-learning resting state, we observed a positive association between increased task-related reactivation, hippocampal activity, and augmented connectivity to the entorhinal cortex. Our findings elucidate the neural mechanism of human replay in both time and space, providing novel insights into dynamics of replay and associated brain-wide activation.

neuroscience↗

bioRxiv2023

Reduced SV2A and GABAA receptor levels in the brains of type 2 diabetic rats revealed by flumazenil PET

PurposeType 2 diabetes mellitus (T2DM) is associated with a greater risk of Alzheimers disease. Synaptic impairment and protein aggregates have been reported in the brains of T2DM models. Here, we assessed whether neurodegenerative changes in synaptic vesicle 2A (SV2A), {gamma};-aminobutyric acid type A (GABAA) receptor, amyloid-{beta}, tau and receptor for advanced glycosylation end product (RAGE) can be detected in vivo in T2DM rats. MethodsPositron emission tomography (PET) using [18F]SDM-8 (SV2A), [18F]flumazenil (GABAA receptor), [18F]florbetapir (amyloid-{beta}), [18F]PM-PBB3 (tau), and [18F]FPS-ZM1 (RAGE) was carried out in 12-month-old diabetic Zucker diabetic fatty (ZDF) and Sprague{square}Dawley (SD) rats. Proteomic profiling and pathway analysis of the hippocampus of ZDF and SD rats were performed. ResultsReduced cortical [18F]SDM-8 and cortical and hippocampal [18F]flumazenil uptake were observed in 12-month-old ZDF rats compared to SD rats. [18F]florbetapir and [18F]PM-PBB3 uptake were comparable in the brains of 12-month-old ZDF rats and SD rats. ConclusionThe findings provide in vivo evidence for regional reductions in SV2A and GABAA receptor levels in the brains of aged T2DM ZDF rats.

neuroscience↗

bioRxiv2023

Relationship between reactive astrocytes, by SMBT-1 imaging, with amyloid-beta, tau, glucose metabolism, and microgliosis in mouse models of Alzheimer's disease

PurposeReactive astrocytes play an important role in the development of Alzheimers disease (AD). Here, we aim to investigate the temporospatial relationship between reactive astrocytes, tau and amyloid-{beta}, glucose metabolism, and microgliosis by using multitracer imaging in AD transgenic mouse models. MethodsPositron emission tomography (PET) imaging with [18F]SMBT-1 (monoamine oxidase-B), [18F]florbetapir (A{beta}), [18F]PM-PBB3 (tau), [18F]FDG, and [18F]DPA-714 (translocator protein) was carried out in 5- and 10-month-old APP/PS1, 11-month-old 3xTg mice, and aged-matched wild-type mice. The brain regional referenced standard uptake value (SUVR) was computed with the cerebellum as the reference region. Immunofluorescence staining was performed in mouse brain tissue slices. Results[18F]SMBT-1 and [18F]florbetapir SUVRs were higher in the cortex and hippocampus of 10-month-old APP/PS1 mice than in 5-month-old APP/PS1 mice and wild-type mice. Reduced [18F]FDG SUVR was observed in the thalamus and midbrain of 5-month-old APP/PS1 mice compared to wild-type mice. No significant difference in brain regional [18F]DPA-714 SUVR was observed in 5- and 10-month-old APP/PS1 mice compared to wild- type mice. No significant difference in the SUVRs of any tracers was observed in 11-month-old 3xTg mice compared to age-matched wild-type mice. A positive correlation between the SUVRs of [18F]SMBT-1 and [18F]DPA-714 in the cortex was observed. Immunostaining validated the distribution of MAO-B and TSPO, amyloid and tau inclusions in brain tissue from 10-month-old APP/PS1 mice and limited changes in 11-month- old 3xTg mice. ConclusionThe findings provide in vivo evidence for reactive astrocytes along with amyloid plaque and tau deposition preceding microgliosis in animal models of AD pathologies.

neuroscience↗

bioRxiv2023

Shared structure facilitates working memory of multiple sequences via neural replay

Daily experiences often involve the processing of multiple sequences, yet storing them challenges the limited capacity of working memory (WM). To achieve efficient memory storage, relational structures shared by sequences would be leveraged to reorganize and compress information. Here, participants memorized a sequence of items with different colors and spatial locations and later reproduced the full color and location sequences one after another. Crucially, we manipulated the consistency between location and color sequence trajectories. First, sequences with consistent trajectories demonstrate improved memory performance and a trajectory correlation between reproduced color and location sequences. Second, sequences with consistent trajectories show neural reactivation of common trajectories, and display spontaneous replay of color sequences when recalling locations. Finally, neural reactivation correlates with WM behavior. Our findings suggest that shared common structure is leveraged for storage of multiple sequences through compressed encoding and neural replay, together facilitating efficient information organization in WM.

neuroscience↗

bioRxiv2023

The canonical single-stranded DNA binding protein SSB is not an essential replication protein but an RNA chaperon in the hyperthermophilic archaeon Saccharolobus islandicus REY15A

Single-stranded DNA binding proteins (SSBs) have been regarded as indispensable factors in all three domains of life since they play vital roles in DNA replication. Herein, we report that genes coding for the canonical SSB (SisSSB) and the non-canonical SSB (SisDBP) in the hyperthermophilic archaeon Saccharolobus islandicus REY15A can both be deleted. The growth is not affected, and the cell cycle progression and genome stability of the deletion strains is not impaired, suggesting that SisSSB and SisDBP are not essential for cell viability. Interestingly, at a lower temperature (55{degrees}C), the protein level of SisSSB increases [~]1.8 fold in the wild type and the growth of {Delta}Sisssb and {Delta}Sisssb{Delta}Sisdbp is retarded. SisSSB exhibits melting activity on dsRNA and DNA/RNA hybrid in vitro and unwinding RNA hairpin in Escherichia coli. Furthermore, the core SisSSB domain is able to complement the absence of the cold shock proteins CspABGE in E. coli, suggesting that SisSSB functions as RNA chaperon. We show that a two-fold overexpression of SisSSB is beneficial to the cell growth at lower temperature, but it has detrimental effect on the cell growth and cell cycle progression at normal growth temperature, which differs from bacterial Csp proteins. Importantly, these in vitro and in vivo activities are conserved in SSB subtype SSB-1 in Crenarchaeota species that lack bacterial Csp homologs. Overall, we have clarified the function of the archaeal canonical SSB which does not function as a DNA processing factor, but plays a role in processes requiring dsRNA or DNA/RNA hybrid unwinding.

microbiology↗

bioRxiv2023

Transcriptional changes consistent with impaired neuronal differentiation, angiogenesis, and tumor plasticity induced in human subpallial telencephalic organoid-glioblastoma chimeras.

Glioblastoma multiforme (GBM) is one of the most aggressive and therapy-resistant brain tumors prevalent in both adults and children. Despite extensive research to understand GBM pathology, it remains unclear how neural cells in the human brain interact with GBM cells to support their brain propagation and therapy resistance and whether GBM cells exert any influence on the properties of human neural cells. In this study, we co-culture human stem cell-derived subpallial telencephalic organoids with patient-derived proneural or mesenchymal GBM spheroids to investigate their reciprocal interactions. We show that both proneural and mesenchymal GBM spheroids readily fuse and propagate with human organoids, forming organoid-GBM chimeras, without the need for exogenous growth factors. GBM cells within the chimeras adapt by modulating gene expression profiles consistent with diminished proliferation, heightened hypoxia, increased angiogenesis, and proneural-to-mesenchymal transition in proneural GBM. Both proneural or mesenchymal GBMs also exert an impact on the properties of neural cells in the chimeras, leading to the suppression of neuronal genes and an upregulation expression of genes associated with hypoxia and angiogenesis. Collectively, this study identifies specific genes and molecular pathways that can be altered in GBM and neural cells by reciprocal interactions in a human developing brain-like environment for an increased understanding of GBM pathology and future therapy development.

cancer biology↗

bioRxiv2023

Directed-evolution mutations of adenine base editor ABE8e improve its DNA-binding affinity and protein stability

Adenine base editors (ABEs), consisting of CRISPR-associated (Cas) nickase and deaminase, can convert the A:T base pair to G:C. Previous studies have shown that ABE8e, a directed-evolution variant of ABE7.10 with eight amino-acid mutations in its deaminase TadA-8e, has higher base editing activity than ABE7.10. However, it remains unclear how the directed-evolution mutations of ABE8e increase its editing activity. Here, we combined molecular dynamics (MD) simulations and experimental measurements to elucidate the molecular origin of the activity enhancement by these mutations. MD simulations and microscale thermophoresis measurements showed that TadA-8e has a higher DNA-binding affinity than TadA-7.10, and the main driving force is electrostatic interactions. The directed-evolution mutations increase the positive charge density in the DNA-binding region, thereby enhancing the electrostatic attractions with DNA. We showed that R111 is the key mutation for the enhanced binding to DNA, which explains why the ABE-8e activity was dramatically reduced when R111 was mutated back to the original T. Unexpectedly, we also found that these mutations improve the thermal stability of TadA-8e by [~]12{degrees}C (Tm). Our results indicate that the editing activities of ABEs are closely related to their DNA-binding affinity and protein stability, thus providing a rational basis for their optimization. Author SummaryAdenine-to-guanine mutations account for 47% of known disease-causing point mutations in humans. Adenine base editors (ABEs), which can restore the guanine mutation to adenine, are a promising tool for precision gene therapy. ABE8e is the most widely used editor today due to its high editing efficacy and was derived from the first-generation base editor ABE7.10 by directed evolution. Compared to ABE7.10, ABE8e contains 8 directed-evolution amino-acid mutations. Understanding how these mutations affect the efficiency of ABE8e is important for the development of efficient base editors. In this study, we combined computational and experimental approaches to investigate how these mutations affect the editing activity of ABE8e. Our results showed that these directed-evolution mutations improve the DNA binding affinity and the protein stability of ABE8e, by enhancing electrostatic and hydrogen bonding interactions. Therefore, our study provides valuable insights for the design of more efficient base editors.

molecular biology↗

bioRxiv2023

Pushed to extremes: distinct effects of high temperature vs. pressure on the structure of an atypical phosphatase

Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature vs. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes novel interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Together, our work argues that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.

biophysics↗

bioRxiv2023

Dynamics of the epigenetic landscape during development and in response to drought stress in sorghum

Sorghum bicolor is a C4 plant with the characteristics of high stress tolerance, which may be conferred partly by the underlying epigenetic mechanism unique to sorghum. In this study, we revealed some epigenomic features in sorghum that have never been reported before. The long H3K27me3 regions clustered in four areas, which we defined as H3K27me3 islands, were identified in sorghum. H3K36me3 plays some role in inhibiting the deposition of both H3K27me3 and H2A.Z, which may serve as partial motivation for the removal of H3K27me3 and H2A.Z in leaf and root. All the 7 histone marks are involved in the regulation of tissue-specific genes, especially the specific expression of C4 genes in leaf and peroxidase (POD) encoding genes in root, which are involved in the photosynthesis in leaf and lignin synthesis in root, respectively. These marks except H3K36me3 and H3K27me3 also engage in the regulation of stress genes in response to PEG treatment. However, we found that differential enrichment of histone marks on many tissue-specific genes was observed only between leaf and root but hardly in response to PEG treatment, although expression of these genes changed after PEG treatment.

plant biology↗

bioRxiv2023

PaxDB 5.0: curated protein quantification data suggests adaptive proteome changes

The "Protein Abundances Across Organisms" database (PaxDB) is an integrative meta-resource dedicated to protein abundance levels, in tissue-specific or whole-organism proteomes. PaxDB focuses on computing best-estimate abundances for proteins in normal/healthy contexts, and expresses abundance values for each protein in "parts per million" (ppm) in relation to all other protein molecules in the cell. The uniform data re-processing, quality scoring, and integrated orthology relations have made PaxDB one of the preferred tools for comparisons between individual datasets, tissues or organisms. In describing the latest version 5.0 of PaxDB, we particularly emphasise the data integration from various types of raw data, and how we expanded the number of organisms and tissue groups as well as the proteome coverage. The current collection of PaxDB includes 831 original datasets from 170 species, including 22 Archaea, 81 Bacteria and 67 Eukaryota. Apart from detailing the data update, we also show a comparative analysis of the human proteome subset of PaxDB against the two most widely-used human proteome data resources: Human Protein Atlas (HPA) and Genotype-Tissue Expression (GTEx). Lastly, we present a use case of PaxDB, showing how protein abundance data can be used to study the evolution of relative amino acid usage in Fungi.

bioinformatics↗

bioRxiv2023

Estimating receptive fields of simple and complex cells in early visual cortex: A convolutional neural network model with parameterized rectification

Neurons in the primary visual cortex respond selectively to simple features of visual stimuli, such as orientation and spatial frequency. Simple cells, which have phase-sensitive responses, can be modeled by a single receptive field filter in a linear-nonlinear model. However, it is challenging to analyze phase-invariant complex cells, which require more elaborate models having a combination of nonlinear subunits. Estimating parameters of these models is made additionally more difficult by cortical neurons trial-to-trial response variability. We develop a simple convolutional neural network method to estimate receptive field models for both simple and complex visual cortex cells from their responses to natural images. The model consists of a spatiotemporal filter, a parameterized rectifier unit (PReLU), and a two-dimensional Gaussian "map" of the receptive field envelope. A single model parameter determines the simple vs. complex nature of the receptive field, capturing complex cell responses as a summation of homogeneous subunits, and collapsing to a linear-nonlinear model for simple type cells. The convolutional method predicts simple and complex cell responses to natural image stimuli as well as grating tuning curves. The fitted models yield a continuum of values for the PReLU parameter across the sampled neurons, showing that the simple/complex nature of cells can vary in a continuous manner. We demonstrate that complex-like cells respond less reliably than simple-like cells - compensation for this unreliability reveals good predictive performance on novel sets of natural images, with predictive performance for complex cells proportionately closer to that for simple cells. Most spatial receptive field structures are well fit by Gabor functions, whose parameters confirm well-known properties of cat A17/18 receptive fields. Author summaryMethods for recording increasingly many visual cortex neurons are advancing rapidly, demanding new approaches to characterize diverse receptive fields. We present a compact convolutional neural network model of early cortical neurons, which is uniformly applicable to simple and complex cells, and whose parameters are straightforwardly interpretable and readily estimated from responses to natural image stimuli. This novel approach introduces a single estimated model parameter to capture the simple/complex nature of a neurons receptive field, revealing a continuum of simple vs complex-like behaviour. We show that almost all complex-like cells exhibit a lower response reliability to repeated presentations of the same stimuli, compared to more reliable responses from simple-like cells. Accounting for this "noise ceiling" brings predictive performance for complex cells proportionately closer to that for simple cells. Using this model estimation approach with natural images, we evaluate findings from previous approaches that were restricted to simple-type cells and the use of grating or white noise stimuli, revealing a diversity of Gabor-like spatial receptive field shapes, which lie along a continuum of spatial bandwidths.

neuroscience↗

bioRxiv2023

The Complexity of Functional Connectivity Profiles of the Subgenual Anterior Cingulate Cortex and Dorsal Lateral Prefrontal Cortex in Major Depressive Disorder: a DIRECT Consortium Study

BackgroundThe subgenual anterior cingulate cortex (sgACC) plays a central role in the pathophysiology of major depressive disorder (MDD), and its functional interactive profile with the left dorsal lateral prefrontal cortex (DLPFC) is associated with transcranial magnetic stimulation (TMS) treatment outcomes. Nevertheless, previous research on sgACC functional connectivity (FC) in MDD has yielded inconsistent results, partly due to small sample sizes and limited statistical power. Furthermore, calculating sgACC-FC to target TMS individually is challenging. MethodsLeveraging a large multi-site cross-sectional sample (1660 MDD patients vs. 1341 healthy controls) from Phase II of the Depression Imaging REsearch ConsorTium (DIRECT), we systematically delineated case-control difference maps of sgACC-FC. Then, we explored the potential impact of such group-level abnormality profiles on the TMS target localization and clinical efficacy. Next, we developed an MDD big data-guided individualized TMS targeting algorithm to integrate group-level statistical maps with individual-level brain activity to localize TMS targets individually. ResultsWe found an enhanced sgACC-DLPFC FC in MDD patients compared to healthy controls (HC). Such group differences altered the position of the sgACC anti-correlation peak in the left DLPFC. In two independent clinical samples, we showed that the magnitude of TMS targets case-control differences in sgACC FC was related to clinical improvement. The MDD big data-guided individualized TMS targeting algorithm may generate individualized TMS targets that are clinically superior to group-level targets. InterpretationWe reliably delineated MDD-related abnormalities of sgACC-FC profiles in a large, independently ascertained sample and demonstrated the potential impact of such case-control differences on FC-guided localization of TMS targets. FundingMinistry of Science and Technology of the Peoples Republic of China, National Natural Science Foundation of China, and Chinese Academy of Sciences

neuroscience↗

bioRxiv2023

Structure-dependent spontaneous calcium dynamics in cultured neuronal networks on microcontact-printed substrates

Microcontact printing (CP) is widely used in neuroscience research. However, CP yields reduced cell-substrate adhesion compared with directly coating cell adhesion molecules. Here, we demonstrate that the reduced cell-substrate adhesion caused by CP, high seeding density, and the local restriction would separately contribute to more aggregated (neurons closer to each other in separate clusters) neuronal networks. Calcium recordings revealed that more aggregated networks presented fewer spontaneous calcium activity patterns, and were more likely dominated by synchronized network-wide calcium oscillation (network bursts). First, on a uniform microcontact-printed substrate, densely seeded neurons were reaggregated into a Petri dish-wide network consisting of small clusters, of which the calcium dynamics were dominated by network bursts. Next, further analysis revealed this dominance was maintained since its appearance, and the initiation and propagation of bursts in the small-cluster network shared a similar mechanism with that of homogeneous networks. Then, sparsely seeded neurons formed several networks with different aggregation degrees, in which the less clustered ones presented abundant time-varying subnetwork burst patterns. Finally, by printing locally restricted patterns, highly clustered networks formed, where dominant network bursts reappeared. These findings demonstrate the existence of structure-dependent spontaneous calcium dynamics in cultured networks on microcontact-printed substrates, which provide important insights into designing cultured networks by using CP, and into deciphering the onset and evolution of network bursts in developmental nerve systems.

neuroscience↗

bioRxiv2023

MICA: A multi-omics method to predict gene regulatory networks in early human embryos

Recent advances in single-cell-omics have been transformative to characterise cell types in challenging to study biological contexts. It is technically difficult to infer transcription factor-gene regulatory interactions from these datasets, especially in contexts with limited single-cell sample number such as the early human embryo. Here we systematically assessed the application of four different linear or non-linear gene regulatory network (GRN) prediction strategies to single-cell simulated and human embryo transcriptome datasets. We also compared how gene expression normalisation methods impact on regulatory network predictions, finding that TPM (transcripts per million reads) outperformed alternative methods. We identified more reproducible GRN inferences using a non-linear method based on mutual information (MI) applied to single-cell transcriptome datasets refined with chromatin accessibility (CA) (called MICA), compared to alternative network prediction methods tested. MICA captures complex non-monotonic dependencies and feedback loops. Using MICA, we generated the first GRN inferences in early human development. MICA predicted co-localisation of the AP-1 transcription factor subunit proto-oncogene JUND and the TFAP2C transcription factor AP-2{psi} in human preimplantation embryos. These interactions were supported by previous findings in other developmental and stem cell contexts. Overall, our comparative analysis of gene regulatory network prediction methods defines a pipeline that can be applied to single-cell multi-omics datasets in especially challenging contexts to infer interactions between transcription factor expression and target gene regulation.

developmental biology↗