Exploring the Stability of Genomic Imprinting and X-Chromosome Inactivation in the Aged Brain

Published: July 31, 2024

Changes in the epigenetic landscape are a hallmark of aging that contributes to irreversible decline organismal fitness ultimately leading aging-related diseases.Epigenetic modifications regulate cellular memory processes genomic imprinting and X-chromosome inactivation (XCI) ensure monoallelic expression imprinted X-linked genes.Whether aging-associated changes affect maintenance XCI has not been comprehensively studied.Here, we investigate allele-specific transcriptional signatures brain, by comparing juvenile old hybrid mice obtained from C57BL/6J (BL6) CAST/EiJ (CAST) reciprocal crosses, with an emphasis on hippocampus (HCP).We confirmed aged HCP showed expected increase DNA hydroxymethylation typical signature.Importantly, was largely unaffected, stable parent-of-origin-specific methylation multiple brain regions including HCP, cerebellum, nucleus accumbens, hypothalamus, prefrontal cortex.Consistently, transcriptomic bulk analysis unaltered HCP.An exception four novel non-coding transcripts (B230209E15Rik, Ube2nl, A330076H08Rik, A230057D06Rik) at Prader-Willi syndrome/Angelman syndrome locus, which lost strict during aging.Similar imprinting, remarkably no signs aging-driven skewing or relaxation genes.Our study provides valuable resource for evaluating reveals that, despite known occurring aging, remain predominantly throughout process physiological mouse brain.

Language: Английский

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Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 11, 2024

Spatially mapping the transcriptome and proteome in same tissue section can significantly advance our understanding of heterogeneous cellular processes connect cell type to function. Here, we present Deterministic Barcoding Tissue sequencing plus (DBiTplus), an integrative multi-modality spatial omics approach that combines sequencing-based transcriptomics image-based protein profiling on enable both single-cell resolution typing genome-scale interrogation biological pathways. DBiTplus begins with in situ reverse transcription for cDNA synthesis, microfluidic delivery DNA oligos barcoding, retrieval barcoded using RNaseH, enzyme selectively degrades RNA RNA-DNA hybrid, preserving intact high-plex imaging CODEX. We developed computational pipelines register data from two distinct modalities. Performing DBiT-seq CODEX slide enables accurate each spot subsequently image-guided decomposition generate resolved atlases. was applied mouse embryos limited markers but still demonstrated excellent integration decomposition, normal human lymph nodes yield a map, lymphoma FFPE explore mechanisms lymphomagenesis progression. DBiTplusCODEX is unified workflow including experimental procedure innovation spatially atlasing exploration pathways cell-by-cell at genome-scale.

Language: Английский

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Transcriptomics and proteomics of projection neurons in a circuit linking hippocampus with dorsolateral prefrontal cortex in human brain

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 13, 2024

Abstract RNA-sequencing studies of brain tissue homogenates have shed light on the molecular processes underlying schizophrenia (SCZ) but lack biological granularity at cell type level. Laser capture microdissection (LCM) can isolate selective populations with intact bodies to allow complementary gene expression analyses mRNA and protein. We used LCM collect excitatory neuron-enriched samples from CA1 subiculum (SUB) hippocampus layer III dorsolateral prefrontal cortex (DLPFC), which we generated gene, transcript, peptide level data. In a machine learning framework, LCM-derived achieved superior regional identity predictions as compared bulk tissue, further improvements when using isoform-level transcript protein quantifications. co-expression also had increased strength neuronal sets homogenates. SCZ risk pathways were identified replicated across networks consistently enriched for glutamate receptor complex post-synaptic functions. Finally, through inter-regional analyses, show that SUB transcriptomic connectivity may be altered in SCZ.

Language: Английский

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Novel single-cell preservation and RNA sequencing technology unlocks field studies forPlasmodiumnatural infections

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 7, 2024

Abstract Single-cell RNA sequencing (scRNA-seq) is a powerful technology used to investigate cellular heterogeneity. When applied unicellular eukaryotes such as Plasmodium parasites, scRNA-seq provides single-cell resolution particularly valuable study complex infections which are often comprised of mixed life stages and clones. Until now, the application has been mainly limited in vitro animal malaria models, despite known transcriptional differences compared circulating parasite populations. This primarily due challenges working with natural endemic settings. We validated sample preparation methods novel for first time P. knowlesi parasites can be effectively implemented analyze low-resource recovered 22,345 transcriptomes containing all asexual blood from 6 culture samples, conditions mimicking infections, generated most extensive dataset date. All samples produced reproducible circular UMAP projections consistent cluster localization high gene expression correlation, regardless used. Biomarker stage annotation using Malaria Cell Atlas reference further confirmed these results. In conclusion, combination adaptable preservation potential fundamentally transform infections. approach unlocks use field studies will lead new insights into biology. Importance Sequencing organisms, at level important understand diversity present cell laboratory models. While models key understanding biological processes, there between lab populations human presents that enables collection Using mock infection, we this marker genes patterns Atlas. demonstrate high-quality various methods, thereby unlocking leading additional biology future.

Language: Английский

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High-throughput gene expression analysis with TempO-LINC sensitively resolves complex brain, lung and kidney heterogeneity at single-cell resolution

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 6, 2024

Abstract We report the development and performance of a novel genomics platform, TempO-LINC, for conducting high-throughput transcriptomic analysis on single cells nuclei. TempO-LINC works by adding cell-identifying molecular barcodes onto highly selective high-sensitivity gene expression probes within fixed cells, without having to first generate cDNA. Using an instrument-free combinatorial-indexing approach, all same cell receive identical barcode, enabling reconstruction single-cell profiles across as few several hundred up 100,000+ per run. The approach is easily scalable based number rounds barcoding performed; however, experiments reported in this study, assay utilized over 5.3 million unique barcodes. has robust protocol fixing banking displays detection from multiple diverse sample types. show that observed multiplet rate less than 1.1% capture ∼50%. Although can accurately profile whole transcriptome (19,683 human or 21,400 mouse genes), it be targeted measure only actionable/informative genes pathways interest – thereby reducing sequencing requirements. In we applied transcriptomes 89,722 types, including nuclei lung, kidney brain tissues. data demonstrated ability identify annotate at least 50 populations positively correlate type-specific markers them. new technology ideal large-scale applications/studies thousands samples with high quality.

Language: Английский

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PURE-seq identifies Egr1 as a Potential Master Regulator in Murine Aging by Sequencing Long-Term Hematopoietic Stem Cells

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 13, 2024

Single-cell transcriptomics is valuable for uncovering individual cell properties, particularly in highly heterogeneous systems. However, this technique often results the analysis of many well-characterized cells, increasing costs and diluting rare populations. To address this, we developed PURE-seq (PIP-seq Rare-cell Enrichment Sequencing) scalable sequencing cells. allows direct loading from FACS into PIP-seq reactions, minimizing handling reducing loss. reliably captures with 60 minutes sorting capturing tens cells at a rarity 1 1,000,000. Using PURE-seq, investigated murine long-term hematopoietic stem their transcriptomes context aging, identifying Egr1 as potential master regulator hematopoiesis aging context. offers an accessible reliable method isolating that are currently too to capture successfully existing methods.

Language: Английский

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PURE-seq identifiesEgr1as a Potential Master Regulator in Murine Aging by Sequencing Long-Term Hematopoietic Stem Cells

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 14, 2024

Abstract Single-cell transcriptomics is valuable for uncovering individual cell properties, particularly in highly heterogeneous systems. However, this technique often results the analysis of many well- characterized cells, increasing costs and diluting rare populations. To address this, we developed PURE-seq (PIP-seq Rare-cell Enrichment Sequencing) scalable sequencing cells. allows direct loading from FACS into PIP-seq reactions, minimizing handling reducing loss. reliably captures with 60 minutes sorting capturing tens cells at a rarity 1 1,000,000. Using PURE-seq, investigated murine long- term hematopoietic stem their transcriptomes context aging, identifying Egr1 as potential master regulator hematopoiesis aging context. offers an accessible reliable method isolating that are currently too to capture successfully existing methods.

Language: Английский

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Genome-wide analysis reveals the MORC3-mediated repression of PD-L1 expression in head and neck cancer

Frontiers in Cell and Developmental Biology, Journal Year: 2024, Volume and Issue: 12

Published: Sept. 12, 2024

Programmed death-ligand 1 (PD-L1) plays essential roles in the negative regulation of anti-tumor immunity. However, regulatory mechanisms PD-L1 expression need further exploration. MORC family CW-type zinc finger 3 (MORC3) is a transcriptional factor that regulates innate immune responses, but and MORC3 cancers remain largely unknown. The present study explored at both translational levels.

Language: Английский

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Identifying cell types by lasso-constraint regularized Gaussian graphical model based on weighted distance penalty

Briefings in Bioinformatics, Journal Year: 2024, Volume and Issue: 25(6)

Published: Sept. 23, 2024

Abstract Single-cell RNA sequencing (scRNA-seq) technology is one of the most cost-effective and efficacious methods for revealing cellular heterogeneity diversity. Precise identification cell types essential establishing a robust foundation downstream analyses prerequisite understanding heterogeneous mechanisms. However, accuracy existing warrants improvement, highly accurate often impose stringent equipment requirements. Moreover, unsupervised learning-based approaches are constrained by need to input number prior, which limits their widespread application. In this paper, we propose novel algorithm framework named WLGG. Initially, capture underlying nonlinear information, introduce weighted distance penalty term utilizing Gaussian kernel function, maps data from low-dimensional space high-dimensional linear space. We subsequently Lasso constraint on regularized graphical model enhance its ability characteristics. Additionally, utilize Eigengap strategy predict obtain predicted labels via spectral clustering. The experimental results 14 test datasets demonstrate superior clustering WLGG over 16 alternative methods. Furthermore, analysis, including marker gene identification, pseudotime inference, functional enrichment analysis based similarity matrix algorithm, substantiates reliability offers valuable insights into biological dynamic processes regulatory

Language: Английский

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Detecting gene expression in Caenorhabditis elegans

Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 18, 2024

Abstract Reliable methods for detecting and analyzing gene expression are necessary tools understanding development investigating biological responses to genetic environmental perturbation. With its fully sequenced genome, invariant cell lineage, transparent body, wiring diagram, detailed anatomy, wide array of tools, Caenorhabditis elegans is an exceptionally useful model organism linking cellular phenotypes. The new techniques in recent years has greatly expanded our ability detect at high resolution. Here, we provide overview C. elegans, including transcripts proteins situ, bulk RNA sequencing whole worms specific tissues cells, single-cell sequencing, high-throughput proteomics. We discuss important considerations choosing among these publicly available online resources data.

Language: Английский

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