Biology subjects

Mei, H.

Publications and source records attributed to Mei, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Spatial transcriptomics defines the mechanisms of hiPSC derived stem cell mediated repair in human articular cartilage

We here determined therapeutic efficacy and mode-of-action of human induced pluripotent-derived therapeutic stem cells (hiMSCs) across in vivo mouse and ex vivo human osteoarthritis models. hiMSC treatment in DMM-mice significantly reduced OARSI damage scores, which was affirmed by a decrease in the catabolic marker Mmp13 and an increase in the anabolic marker Col2. These treatment effects appeared, irrespective of modifying factors such as xeno-free media or thermosensitive hydrogel carrier. Subsequently treatment of hiMSC+gel in human osteoarthritic cartilage explants showed a transcriptome-wide significant activation of the cholesterol and sterol synthesis pathways marked by genes such as MVD, DHCR7, MSMO1, FABP3. Additionally, we showed that these changes alleviated OA-associated imbalances of the cellular Zinc-ion homeostasis pathways, represented by genes such as MT1F, MT1G, MT1H and SLC30A1. Spatial transcriptomics then sensitively captured that hiMSC+gel treatment evoked, specifically at the superficial cartilage layer, a consistent upregulation of healthy chondrocyte markers such as CHAD, ACAN, FRZB, and SOX9, alongside a suppression of catabolic and inflammatory mediators such as SERPINE1, SPP1, MMP13, ADAMTS5. Our findings link therapeutic outcomes of hiMSC treatment to precise spatially resolved molecular changes in human tissue, that would otherwise be obscured by heterogeneous cell populations. Collectively our study highlighted that hiPSC-derived stem cell therapy (hiMSCs) could provide a scalable off-the-shelf solution to treat osteoarthritis, with strong prospects for clinical applications in the near future.

developmental biology↗

bioRxiv2026

Hippocampus-reuniens beta coupling supports goal-directed spatial navigation

Prefrontal-hippocampal communication, supported by both direct and indirect anatomical pathways, is essential for a range of cognitive functions, including spatial navigation. The midline thalamic nucleus reuniens (RE) has been proposed as a key hub along this indirect pathway, coordinating bidirectional interactions between the hippocampus (HC) and prefrontal cortex (PFC). Here, we investigated functional dynamics within the HC-RE-PFC network as adult male rats learned to navigate a complex maze. Initial behavioral analyses revealed three distinct learning phases: exploration, goal-oriented learning, and efficient navigation. Aligning neural data with subject-specific transitions between these phases uncovered distinct neural signatures associated with each learning phase. Notably, the transition from exploratory to goal-directed behavior was accompanied by the emergence of persistent HC-RE beta-band (15-25Hz) interactions, including elevated beta coherence, theta-beta phase-amplitude coupling, and HC-to-RE Granger causality. The interactions further scaled with navigational efficiency, showing increased HC-RE beta coherence in trials without errors. Together, these findings provide new evidence for dynamic HC-RE interactions during goal-directed navigation and support an emerging view that RE functions as a working memory buffer for route-related information, revealing a potential network mechanism underlying flexible spatial behavior. HighlightsO_LIBeta-band hippocampus-reuniens coupling emerges during goal-directed navigation. C_LIO_LIPAC between HC theta and RE beta increased during goal learning. C_LIO_LIHC-RE coupling strength increases with navigational efficiency. C_LIO_LIDirectional hippocampus-to-reuniens communication emerges during learning C_LIO_LIReuniens supports hippocampal-prefrontal integration for flexible behavior C_LI Significance StatementFlexible spatial navigation requires coordinated communication between the hippocampus (HC) and the prefrontal cortex (PFC), yet the thalamic mechanisms coordinating HC-PFC interaction remain poorly understood. This study reveals that the nucleus reuniens (RE) of the midline thalamus plays a critical role in mediating HC-PFC communication during spatial learning. By combining detailed behavioral analysis with simultaneous multi-site electrophysiological recording, we identify beta-band HC-RE coupling as a neural signature of the transition from exploration to goal-directed navigation. The strength and directionality of this interaction tracked improvements in navigational efficiency, revealing a thalamic mechanism for integrating hippocampal output into prefrontal circuits. These findings highlight the RE as a working memory buffer for route-related information and advance our understanding of how thalamic hubs contribute to the circuit-level dynamics underlying flexible behavior.

neuroscience↗

bioRxiv2026

Loss of ABCA4 from photoreceptor discs triggers changes in glial cell homeostasis

Loss-of-function mutations in the ABCA4 gene cause Stargardt disease (STGD1), the most common inherited macular dystrophy leading to progressive central vision loss. Here, we generated hiPSC-derived retinal organoids harboring a premature stop codon in exon-24 of ABCA4 to evaluate the impact of this mutation on mRNA and protein levels in a human model. Immunofluorescence analysis revealed the absence of ABCA4 protein in the mutant photoreceptor outer segment discs, while single-cell RNA sequencing detected no major transcriptional alterations in rods and cones. Unexpectedly, differential gene expression and pathway enrichment analyses of Muller glial cells (MGCs) and astrocytes highlighted disruption of neuronal development, microenvironment of glial cells, intercellular communication, and programmed cell death pathways. These findings suggest that ABCA4 might play a role in maintaining the retinal microenvironment homeostasis, and that the early transcriptomic response of MGCs and astrocytes preceding photoreceptor degeneration could contribute to Stargardt disease development. Significance StatementHuman induced pluripotent stem cell (hiPSC)-derived retinal organoids provide a powerful platform to investigate inherited retinal diseases. In this study, we generated ABCA4-mutant hiPSC lines and differentiated them into retinal organoids to model Stargardt disease. Despite complete loss of ABCA4 protein from the photoreceptor outer segment discs, rods and cones exhibited minimal transcriptional alterations. In contrast, the ABCA4 variant triggered changes in the glial cell homeostasis, suggesting that Muller glial cells and astrocytes might exhibit an early response to photoreceptor dysfunction in the absence of ABCA4. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/718110v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@1d8dbf6org.highwire.dtl.DTLVardef@51239corg.highwire.dtl.DTLVardef@f8fbdborg.highwire.dtl.DTLVardef@5f0b44_HPS_FORMAT_FIGEXP M_FIG Human induced pluripotent stem cells (hiPSCs) were engineered to generate ABCA4-mutant cell lines, later differentiated into retinal organoids as a model of Stargardt disease. The organoids showed loss of ABCA4 from the outer segment discs of rod and cone photoreceptors, while the mutant Muller glial cells and astrocytes exhibited transcriptional changes in pathways involved in neuronal development, microenvironment, and programmed cell death. C_FIG

neuroscience↗

bioRxiv2025

LISA: A Comprehensive R Package for Lentiviral Integration Site Analysis in Gene Therapy Safety Assessment

BackgroundGene therapy using integrating viral vectors has shown remarkable clinical success, but the random integration of vectors into the host genome poses potential safety concerns, particularly insertional mutagenesis. Common Integration Sites (CIS) near oncogenes significantly increase the risk of clonal expansion and malignant transformation. Current tools for integration site (IS) analysis lack comprehensive functionality for safety assessment, particularly in identifying risk-associated genomic regions and tracking clonal dynamics over time. ResultsWe developed LISA (Longitudinal Integration Site Analysis), a comprehensive R package specifically designed for gene therapy safety evaluation. LISA incorporates a novel approach that trains integration site profiles using cumulative curves derived from normal cell infusion samples and normal patient samples, with subsequent statistical testing to distinguish these normal samples from those with exceptional clonal expansion, thereby enabling effective identification of dominant clone formation. For longitudinal studies, LISA monitors fluctuations in clonal dynamics via Richness and Evenness metrics, and integrates this cumulative curve-based statistical testing approach into its early warning system to detect potentially dominant clones. Additionally, LISA features an optimized CIS detection algorithm with O (n log n) time complexity, achieved through chromosome-position encoding and a seed-site strategy, which facilitates efficient analysis of large-scale clinical datasets. The package also provides systematic functional annotations, including annotations for Safe Harbor regions, enhancer/promoter elements, and proximity to three curated gene sets: adverse event-associated genes (AE genes, n=36), cancer-related genes (n=980), and immune-related genes (n=2,485). Furthermore, it encompasses six categories of interactive visualizations and has been validated using real clinical data from gene therapy trials.

bioinformatics↗

bioRxiv2025

Developmental Trajectories of Addition and Subtraction in Early School-aged Children

Mastering basic arithmetic lays the foundation for lifelong mathematical achievement, yet how the neural mechanisms underlying addition and subtraction calculations develop during childhood remain unclear. This study investigated the developmental trajectories of addition and subtraction calculations in school-aged children, and explored how arithmetic-specific neural responses in the right parieto-occipital region are related to age-related improvements in behavioral performance. Here, we recorded electroencephalography (EEG) signals from 115 typically developing children divided into three age groups (7-8-, 9-10-, and 11-12-year-olds) during an arithmetic task involving addition and subtraction calculations. We analyzed the P300 component from the original waveforms and the {Delta}P300 component from the difference waveforms, which were generated by subtracting the event-related potentials (ERPs) elicited by the first operand from those elicited by the second operand to isolate arithmetic-specific neural processes. The results revealed that, in both calculations, older children showed better behavioral performance (faster reaction time and larger PI) and greater right parieto-occipital {Delta}P300 amplitudes, with a key developmental stage at 11-12 years. Furthermore, all groups of children exhibited greater right parieto-occipital P300 and {Delta}P300 amplitudes in subtraction, whereas the smaller right parieto-occipital {Delta}P300 amplitudes in addition significantly mediated the relationship between age and PI. These findings reveal distinct patterns for addition and subtraction calculations over development, highlighting the right parieto-occipital {Delta}P300 amplitude as a neural marker of arithmetic performance, particularly for addition calculation.

neuroscience↗

bioRxiv2025

Biological function and mechanism of flpL gene in regulating pathogenicity of Aeromonas hydrophila

Aeromonas hydrophila is human-animal commensal bacterium that seriously threatens the development of aquaculture and human health. Type IV pili (T4P) are essential for bacterial physiological function. The relationship between the molecular mechanism of flpL gene affiliated to T4P and the pathogenicity is still unclear. In the research, A. hydrophila with a genetically stable deletion of flpL gene ({Delta}flpL) was constructed. The median lethal dose of {Delta}flpL for Crucian carp was 4.87 times higher compared to wild-type strain, suggesting that {Delta}flpL significantly reduced pathogenicity. The attenuation may be attributed to a reduced capacity for biofilm formation and downregulation of the expression levels of virulence-related genes in {Delta}flpL. Meanwhile, the significant increase in swimming capacity and adhesion can be related to the upregulation of flpC, tapM, tapB and tapP genes. In conclusion, flpL gene plays essential role in the pathogenicity, adhesion, motility, and capacity for biofilm formation in A. hydrophila. The research aims to clarify the pathogenesis of A. hydrophila, and lay the foundation for developing live attenuated vaccines through the targeted modification flpL gene.

microbiology↗

bioRxiv2025

Determining off-target effects of splice-switching antisense oligonucleotides using short read RNAseq in neuronally differentiated human induced pluripotent stem cells

Antisense oligonucleotides (AONs) are small pieces of chemically modified DNA or RNA that bind to RNA in a sequence-specific manner based on Watson-Crick base-pairing. Splice-switching AONs are designed to modulate pre-mRNA splicing, thereby for instance restoring protein expression or modifying the eventual protein to restore its function or reduce its toxicity. Given the current lack of in silico methods that adequately predict off-target splicing events, assessment of off-target effects of AONs in human cells using RNAseq could be a promising approach. The identification and prioritization of potential off-target effects for validation and further investigation into the biological relevance would contribute to the development of safe and effective AONs. In this study, we used three different splice-switching AONs targeting three different human transcripts to study their transcriptome-wide, hybridization-dependent off-target effects with short read RNAseq. Using the computational tools rMATS and Whippet, we identified differential splicing events of which only a minority could be explained by hybridization, illustrating the difficulty of predicting off-target effects based on sequence homology. The main splicing events could all be validated with RT-PCR. Furthermore, from the three AONs studied, one AON induced considerably more changes in gene expression and splicing compared to the two other AONs assessed, which was confirmed in a validation experiment. Our study demonstrates that the interpretation of short read RNAseq data to determine off-target effects is challenging. Nonetheless, we showed that valuable results can be obtained as it allows the comparison of toxicity between different AONs within an experiment and identification of AON-specific off-target profiles.

genetics↗

bioRxiv2025

LncRNA-BERT: An RNA Language Model for classifying Coding and Long Non-Coding RNA

Understanding (novel) RNA transcripts generated in next generation sequencing experiments requires accurate classification, given the increasing evidence that long non-coding RNAs (lncRNAs) play crucial regulatory roles. Recent developments in Large Language Models present opportunities for classifying RNA coding potential with sequence-based algorithms that can overcome the limitations of classical approaches that assess coding potential based on a set of predefined features. We present lncRNA-BERT, an RNA language model pre-trained and fine-tuned on human RNAs collected from the GENCODE, RefSeq, and NONCODE databases to classify lncRNAs. LncRNA-BERT matches and outperforms state-of-the-art classifiers on three test datasets, including the cross-species RNAChallenge benchmark. The pre-trained lncRNA-BERT model distinguishes coding from long non-coding RNA without supervised learning which confirms that coding potential is a sequenceintrinsic characteristic. LncRNA-BERT has been shown to benefit from pre-training on human data from GENCODE, RefSeq, and NONCODE, improving upon configurations pre-trained on the commonly used RNAcentral dataset. In addition, we propose a novel Convolutional Sequence Encoding method that is shown to be more effective and efficient than K-mer Tokenization and Byte Pair Encoding for training with long RNA sequences that are otherwise above the common context window size. lncRNA-BERT is available at https://github.com/luukromeijn/lncRNA-Py.

bioinformatics↗

bioRxiv2024

Identification of SENP7 and UTF1/VENTX as new loci influencing clusteredprotocadherin methylation across blood and brain using a genome-wide associationstudy

The epigenetic regulation of clustered protocadherin (cPCDH) genes is tightly linked to their function as specific cell surface barcodes for neural self-nonself discrimination. Differential cPCDH DNA methylation in both blood and brain has been implicated in diverse human traits and diseases ranging from BMI, aging, cancer and brain disorders. However, the unique regulation of cPCDH methylation remains poorly understood. Therefore, we performed a genome-wide association study to evaluate the association of >7 million genetic variants with DNA methylation at 607 cPCDH CpGs measured in whole blood of 3777 individuals and validated findings in prefrontal cortex samples obtained from 523 brain donors. We observed concordant cPCDH methylation patterns in blood and prefrontal cortex, which switched between hypo-, intermediate and hypermethylation over short distances with the former overlapping with the promoter regions of each cPCDH member. Through methylation quantitative trait locus (meQTL) analysis in trans, we first confirmed the broad effect of the candidate gene SMCHD1 on cPCDH methylation in blood which validated in prefrontal cortex. Through a genome-wide analysis, we next identified the SENP7 and UTF1/VENTX loci to have widespread, subcluster-specific effects on cPCDH methylation in blood which was validated in prefrontal cortex. While SENP7 can indirectly affect DNA methylation through the deSUMOylation of the chromatin repressor KAP1, UTF1 and VENTX are two genes involved in embryonic development not previously implicated in epigenetic regulation. Our findings shed new light on the processes involved in cPCDH methylation that may underlie associations with disease.

genetics↗

bioRxiv2024

Industrialization of three-dimensional hiPSC-cardiac microtissues for high-throughput cardiac safety and drug discovery screening

Current cardiac cell models for drug screening often face a trade-off between cellular maturity and achieving high throughput. While three-dimensional human induced pluripotent stem cell-based heart models typically exhibit more adult-like features, their application is hindered by the need for large cell numbers or complex equipment. Here, we developed cost-effective methods to scale up production of three-dimensional cardiac microtissues (cMTs) containing three cardiac cell types, and assess calcium transients and action potential metrics for high-throughput screening (HTS). Automating the procedure revealed reproducible drug responsiveness and predictive accuracy in a reference compound screen. Furthermore, an arrhythmic phenotype was reliably triggered in cMTs containing cardiomyocytes with a RYR2 mutation. A screen of FDA-approved drugs identified 17 drugs that rescued the arrhythmic phenotype. Our findings underscore the scalability of cMTs and their utility in disease modelling and HTS. The advanced "technology-readiness-level" of cMTs supports their regulatory uptake and acceptance within the pharmaceutical industry.

cell biology↗

bioRxiv2024

High-throughput DNA engineering by mating bacteria

To reduce the operational friction and scale DNA engineering, we report here an in vivo DNA assembly technology platform called SCRIVENER (Sequential Conjugation and Recombination for In Vivo Elongation of Nucleotides with low ERrors). SCRIVENER combines bacterial conjugation, in vivo DNA cutting, and in vivo homologous recombination to seamlessly stitch blocks of DNA together by mating E. coli in large arrays or pools. This workflow is simpler, cheaper, and higher throughput than current DNA assembly approaches that require DNA to be moved in and out of cells at different procedural steps. We perform over 5,000 assemblies with two to 13 DNA blocks that range from 240 bp to 8 kb and show that SCRIVENER is capable of assembling constructs as long as 23 kb at relatively high throughput and fidelity. Most SCRIVENER errors are deletions between long interspersed repeats. However, SCRIVENER can overcome these errors by enabling assembly and sequence verification at high replication at a nominal additional cost per replicate. We show that SCRIVENER can be used to build combinatorial libraries in arrays or pools, and that DNA blocks onboarded into the platform can be repurposed and reused with any other DNA block in high throughput without a PCR step. Because of these features, DNA engineering with SCRIVENER has the potential to accelerate design-build-test-learn cycles of DNA products.

synthetic biology↗

bioRxiv2024

Oleic acid triggers CD4+ T cells to be metabolically rewired and poised to differentiate into proinflammatory T cell subsets upon activation

T cells are the most common immune cells in atherosclerotic plaques and the function of T cells can be altered by fatty acids. Here, we show that pre-exposure of CD4+ T cells to oleic acid, an abundant fatty acid linked to cardiovascular events, results in a preferential differentiation into pro-inflammatory subsets upon activation by upregulating core metabolic pathways. RNA-sequencing of non-activated CD4+ T cells revealed that oleic acid upregulates genes encoding enzymes responsible for cholesterol and fatty acid biosynthesis. Transcription footprint analysis linked this rewiring to the differentiation of pro-inflammatory subsets. Indeed, spectral flow cytometry showed that pre-exposure to oleic acid results in a skew toward IL-9, IL-17A, IL-5 and IL-13 producing T cells upon activation. Importantly, inhibition of either cholesterol or fatty acid biosynthesis abolishes this effect, suggesting a beneficial role for statins beyond cholesterol lowering. Taken together, fatty acids may affect inflammatory diseases by influencing T cell metabolism.

genomics↗

bioRxiv2023

Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries

Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput and adding cost. Here, we develop an arrayed in vivo plasmid barcoding platform that enables pooled plasmid extraction and library preparation for Oxford Nanopore sequencing. This method has a high accuracy and recovery rate, and greatly increases throughput and reduces cost relative to other plasmid barcoding methods or Sanger sequencing. We use in vivo barcoding to sequence verify >45,000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel.

synthetic biology↗

bioRxiv2023

Multimodal profiling of peripheral blood identifies proliferating circulating effector CD4+ T cells as predictors for response to integrin α4β7-blocking therapy in patients with inflammatory bowel disease

Despite the success of biological therapies in inflammatory bowel disease (IBD), patient management remains challenging due to a lack of therapy response predictors. Here we prospectively sampled two cohorts of IBD patient cohorts receiving the anti-integrin 4{beta}7 antibody vedolizumab. Samples were subjected to mass cytometry, single-cell RNA sequencing, single-cell V(D)J sequencing, serum proteomics, and multidimensional flow cytometry to comprehensively assess vedolizumab-induced immunological changes in the peripheral blood and their potential associations with treatment response. Vedolizumab induced changes in the abundance of both circulating innate and adaptive immune cell compartments and modified the T cell receptor diversity of circulating gut-homing CD4+ memory T cells. Through integration of multimodal parameters and machine learning, we identify that pretreatment activated proliferating CD4+ memory T cell abundance is associated with treatment failure, independent of clinical variables, thereby providing a reliable predictive classifier with significant implications for the personalized management of IBD patients.

immunology↗

bioRxiv2023

Integration of eQTL and Machine Learning Methods to Dissect Causal Genes with Pleiotropic effects in Genetic Regulation Networks of Seed Cotton Yield

Expression quantitative trait loci (eQTL) provide a powerful means of investigating the biological basis of genome-wide association study (GWAS) results and exploring complex traits or phenotypes. In addition to identifying the causal gene in cis, eQTL analysis also reveals a large number of trans-regulated genes located on different chromosomes, which form a gene regulatory network (GRN) that complements the GWAS locus. However, the dissection of a GRN and the crosstalk underlying multiple agronomical traits, along with prioritizing important genes in eQTL-derived GRNs, remains a major challenge. In this study, we generated 558 transcriptional profiles of lint-bearing ovules at one day post-anthesis (DPA) from a selective core cotton germplasm, from which we identified 12,207 eQTLs. By integrating with a GWAS catalog, we found that 66 out of 187 (35.29%) known phenotypic GWAS loci are colocalized with 1,090 eQTLs, forming 38 major functional GRNs predominantly (30 out of 38) associated with seed size-related phenotypes. Of the eGenes, 34 were shared between at least two functional GRNs, exhibiting pleiotropic effects, such as NF-YB3, GRDP1, and IDD7. Narrow-sense heritability analysis showed that the heritability increased with combining the eQTLs with GRNs compared to those with previous yield trait GWAS loci. The extreme gradient boosting (XGBoost) machine learning approach was then applied to predict seed cotton yield phenotypes based on gene expression. Top-ranking eGenes (NF-YB3, FLA2, and GRDP1) derived by XGBoost with pleiotropic effects on yield traits were validated, along with their potential roles by correlation analysis, domestication selection analysis, and transgenic plants. This study provides insights into the mining of GRNs in relation to the pleiotropy of phenotype. The combination of eQTL and machine learning approaches is efficient in improving the genetic dissection of agricultural traits.

genetics↗

bioRxiv2023

Defective Schwann cell lipid metabolism alters plasma membrane dynamics in Charcot-Marie-Tooth disease 1A

Duplication of PMP22 causes Charcot-Marie-Tooth disease type 1A (CMT1A) and is known to disrupt the lipid metabolism in myelinating Schwann cells by unknown mechanisms. By using two CMT1A mouse models overexpressing human PMP22, we discovered that PMP22 dose-dependently downregulates genes that are involved in lipid and cholesterol metabolism. Lipidomic analysis on CMT1A mouse sciatic nerves confirmed lipid metabolic abnormalities primarily associated with cholesterol and sphingolipids. We observed similar lipidomic profiles and downregulation of genes associated with lipid metabolism in human CMT1A patient induced pluripotent stem cell-derived Schwann cell precursors (iPSC-SCPs). We confirmed these findings by demonstrating altered lipid raft dynamics and plasma membrane fluidity in CMT1A iPSC-SCPs. Additionally, we identified impaired cholesterol incorporation in the plasma membrane due to altered lipid storage homeostasis in CMT1A iPSC-SCPs, which could be modulated by changing the lipid composition of the cell culture medium. These findings suggest that PMP22 plays a role in regulating the lipid composition of the plasma membrane and lipid storage homeostasis. Targeting lipid metabolism may hold promise as a potential treatment for CMT1A patients. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC="FIGDIR/small/535224v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@17d4e84org.highwire.dtl.DTLVardef@1adce4forg.highwire.dtl.DTLVardef@1c3e1eborg.highwire.dtl.DTLVardef@12525da_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPMP22 copy number causes a dose-dependent suppression of cholesterol and lipid biosynthesis in peripheral nerves of CMT1A mice C_LIO_LILipid composition is altered in the sciatic nerves of CMT1A mice and in the membranes of patient derived iPSC-SCPs, with a significant reduction in sphingolipids C_LIO_LICMT1A iPSC-SCPs show decreased plasma membrane lipids required for regulating lipid raft dynamics, membrane fluidity, and membrane order C_LIO_LILipid storage misregulation is key in the pathogenesis of CMT1A C_LI

neuroscience↗

bioRxiv2023

EXO1-mediated DNA repair by single-strand annealing is essential for BRCA1-deficient cells

Deficiency for the repair of DNA double-strand breaks (DSBs) via homologous recombination (HR) leads to chromosomal instability and diseases such as cancer. Yet, defective HR also results in vulnerabilities that can be exploited for targeted therapy. Here, we identify such a vulnerability and show that BRCA1-deficient cells are dependent on the long-range end-resection factor EXO1 for survival. EXO1 loss results in DNA replication-induced lesions decorated by poly(ADP-ribose)-chains. In cells that lack both BRCA1 and EXO1, this is accompanied by unresolved DSBs due to impaired single-strand annealing (SSA), a DSB repair process that requires the activity of both proteins. In contrast, BRCA2-deficient cells have increased SSA, also in the absence of EXO1, and hence are not dependent on EXO1 for survival. In agreement with our mechanistic data, BRCA1-mutated tumours have elevated EXO1 expression and contain more genomic signatures of SSA compared to BRCA1-proficient tumours. Collectively, our data indicate that EXO1 is a promising novel target for treatment of BRCA1-deficient tumours.

molecular biology↗

bioRxiv2022

Tissue microenvironment dictates the state of human induced pluripotent stem cell-derived endothelial cells of distinct developmental origin in 3D cardiac microtissues

Each tissue and organ in the body has its own type of vasculature. Here we demonstrate that organotypic vasculature for the heart can be recreated in a three-dimensional cardiac microtissue (MT) model composed of human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes (CMs), cardiac fibroblasts (CFs) and endothelial cells (ECs). ECs in cardiac MTs upregulated expression of markers enriched in human intramyocardial ECs (iECs), such as CD36, CLDN5, APLNR, NOTCH4, IGFBP3, ARHGAP18, which were previously identified in the single-cell RNA-seq dataset from the human fetal heart (6.5-7 weeks post coitum). We further show that the local microenvironment largely dictates the organ-specific identity of hiPSC-derived ECs: we compared ECs of different developmental origins derived from two distinct mesoderm subtypes (cardiac and paraxial mesoderm) and found that independent of whether the ECs were cardiac or paraxial mesoderm derived, they acquired similar identities upon integration into cardiac microtissues. This was confirmed by single-cell RNA-seq. Overall, the results indicated that whilst the initial gene profile of ECs was dictated by developmental origin, this could be modified by the local tissue environment such that the original identity was lost and the organotypic identity acquired through local environmental signals. This developmental "plasticity" in ECs has implications for multiple pathological and disease states.

developmental biology↗