Cell Types Research Articles

Origin and cell type specificity of mitochondrial DNA mutations in C9ORF72 ALS-FTLD human brain organoids.

Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are primarily genetic in ~20% of patients. Mutations in C9ORF72 are the most frequent cause, but it is not understood why there is notable regional pathology. An increased burden of mitochondrial DNA (mtDNA) mutations in ALS-FTLD brains implicates mitochondrial mechanisms; however, it remains unclear how and when these mutations arise. To address this, we generated cerebral organoids derived from human-induced pluripotent stem cells (hiPSCs) of patients with ALS-FTLD harboring the C9ORF72 hexanucleotide repeat expansion alongside CRISPR-corrected isogenic and healthy controls. Here, we show a higher mtDNA single-nucleotide variant (mtSNV) burden in astroglia derived from C9ORF72-mutant organoids, with some de novo mtSNVs likely due to the C9ORF72 repeat and others evading selection to reach higher heteroplasmy levels. Thus, the functional consequences of the regional accumulation of mtSNVs in C9ORF72 ALS-FTLD brains are likely to manifest through astroglial mitochondrial dysfunction.

Methods for the Generation of Single-Payload Antibody-Drug Conjugates.

Antibody-drug conjugates (ADCs) have emerged as a powerful form of targeted therapy that can deliver drugs with a high level of selectivity towards a specific cell type, reducing off-target effects and increasing the therapeutic window compared to small molecule therapeutics. However, creating ADCs that are stable, homogeneous, and with controlled drug-to-antibody ratio (DAR) remains a significant challenge. Whilst a myriad of methods have been reported to generate ADCs with a DAR of 2, 4, and 8, strategies to generate DAR 1 constructs are seldom reported despite the advantages of low drug loading to tune ADC properties or to allow access to antibody-antibody and antibody-protein constructs. This concept article highlights the diversity of methods that have been employed to access single-payload ADCs and explores the outlook for the field.

Dynamics of Cell Fate Decisions during Chemically Induced Multi-Lineage Trans-Differentiation at Single-Cell Level.

Cell trans-differentiation offers a powerful means to manipulate cell identities. By exposing cells to a combination of small molecules (SMs), cell trans-differentiation can be induced in a simple and cost-effective manner. However, a comprehensive atlas detailing chemical-induced cell trans-differentiation across multiple cell fates has yet to be established. In this study, the underlying mechanisms of trans-differentiation is investigated and constructed an in-depth single-cell atlas of this process. The time-course trajectory is demonstrated for trans-differentiation of mouse embryonic fibroblasts (MEFs) into multiple cell lineages including epithelial, neural, extraembryonic endoderm like (XEN-like) cells, and endothelial cells, when induced by SMs cocktail 6TCF (E616452, tranylcypromine, CHIR99021, and forskolin). These trans-differentiated cells closely resemble various somatic cell types in the fetus. It is found that trans-differentiation is marked by dynamic shifts in entropy and the cell cycle during cell fate transitions. A common intermediate feature is revealed characterized by high ribosomal gene expression. This study combines high-resolution landscape with comparative analyses of trans-differentiation dynamics, providing new insights into the complex mechanisms driving cell fate determination in vitro. Future study shall explore the applicability of the model in human cell trans-differentiation.

Glycosylation Regulation by TMEM230 in Aging and Autoimmunity

Aging is often a choice between developing cancer or autoimmune disorders, often due in part to loss of self-tolerance or loss of immunological recognition of rogue-acting tumor cells. Self-tolerance and cell recognition by the immune system are processes very much dependent on the specific signatures of glycans and glycosylated factors present on the cell plasma membrane or in the stromal components of tissue. Glycosylated factors are generated in nearly innumerable variations in nature, allowing for the immensely diverse role of these factors in aging and flexibility necessary for cellular interactions in tissue functionality. In previous studies, we showed that differential expression of TMEM230, an endoplasmic reticulum (ER) protein was associated with specific signatures of enzymes regulating glycan synthesis and processing and glycosylation in rheumatoid arthritis synovial tissue using single-cell transcript sequencing. In this current study, we characterize the genes and pathways co-modulated in all cell types of the synovial tissue with the enzymes regulating glycan synthesis and processing, as well as glycosylation. Genes and biological and molecular pathways associated with hallmarks of aging were in mitochondria-dependent oxidative phosphorylation and reactive oxygen species synthesis, ER-dependent stress and unfolded protein response, DNA repair (UV response and P53 signaling pathways), and senescence, glycolysis and apoptosis regulation through PI3K-AKT-mTOR signaling have been shown to play important roles in aging or neurodegeneration (such as Parkinson’s and Alzheimer’s disease). We propose that the downregulation of TMEM230 and RNASET2 may represent a paradigm for the study of age-dependent autoimmune disorders due to their role in regulating glycosylation, unfolded protein response, and PI3K-AKT-mTOR signaling.

Aging activates escape of the silent X chromosome in the female mouse hippocampus.

Women live longer than men and exhibit less cognitive aging. The X chromosome contributes to sex differences, as females harbor an inactive X (Xi) and active X (Xa), in contrast to males with only an Xa. Thus, reactivation of silent Xi genes may contribute to sex differences. We use allele-specific, single-nucleus RNA sequencing to show that aging remodels transcription of the Xi and Xa across hippocampal cell types. Aging preferentially changed gene expression on the X's relative to autosomes. Select genes on the Xi underwent activation, with new escape across cells including in the dentate gyrus, critical to learning and memory. Expression of the Xi escapee Plp1, a myelin component, was increased in the aging hippocampus of female mice and parahippocampus of women. AAV-mediated Plp1 elevation in the dentate gyrus of aging male and female mice improved cognition. Understanding how the Xi may confer female advantage could lead to novel targets that counter brain aging and disease in both sexes.

Mucociliary cell type compositions - bridging the gap between genes and emergent tissue functions.

Mucociliary cell type compositions - bridging the gap between genes and emergent tissue functions.

Alginate-Dialdehyde-Based Reporter Ink Enabling Online Detection of Matrix Metalloproteinase Activity of Encapsulated Cells.

Biofabrication and three-dimensional (3D) bioprinting enable precise spatial arrangement of cells within biomaterial scaffolds. We developed an alginate-based and Förster resonance energy transfer (FRET)-responsive "turn-on" reporter ink platform to enable real-time monitoring of matrix metalloproteinase (MMP) activity. Three distinct MMP-cleavable turn-on peptide reporters were synthesized and characterized for their cell-specific cleavage profiles using recombinant MMPs, cell-derived media, and different cell cultures (NIH3T3, HEK293, and MelHo). All turn-on reporters were covalently and site-specifically incorporated into alginate dialdehyde (ADA) to yield an MMP reporter ink. The ADA reporter ink with an MMP 13 turn-on reporter was responsive to all tested cell types over time within the cast bulk constructs. The ADA reporter ink material blended with gelatin had comparable print resolution and structural fidelity as observed for ADA. The extrusion-based bioprinted MelHo cell grids, measuring 2 × 2 cm2 and containing 1 × 106 cells/mL, exhibited MMP activity responses comparable to those of the casted reporter ink system, with a 3-fold increase observed at 24 h. This study introduces a versatile, FRET-based alginate bioink platform for the real-time monitoring of MMP activities, expanding the toolkit to understand cellular performance in bioprinted 3D constructs.

Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina.

The vast majority of protein-coding genes in the human genome produce multiple mRNA isoforms through alternative splicing, significantly enhancing the complexity of the transcriptome and proteome. To establish an efficient method for characterizing transcript isoforms within tissue samples, we conducted a systematic comparison between single-cell long-read and conventional short-read RNA sequencing techniques. The transcriptome of approximately 30,000 mouse retina cells was profiled using 1.54 billion Illumina short reads and 1.40 billion Oxford Nanopore Technologies long reads. Consequently, we identify 44,325 transcript isoforms, with a notable 38% previously uncharacterized and 17% expressed exclusively in distinct cellular subclasses. We observe that long-read sequencing not only matches the gene expression and cell-type annotation performance of short-read sequencing but also excel in the precise identification of transcript isoforms. While transcript isoforms are often shared across various cell types, their relative abundance shows considerable cell type-specific variation. The data generated from our study significantly enhance the existing repertoire of transcript isoforms, thereby establishing a resource for future research into the mechanisms and implications of alternative splicing within retinal biology and its links to related diseases.

Inhibition of TGF-β signaling enhances osteogenic potential of iPSC-derived MSCs.

Mesenchymal stem cells (MSCs) represent the most commonly utilized type of stem cell in clinical applications. However, variability in quality and quantity between different tissue sources and donors presents a significant challenge to their use. Induced pluripotent stem cells (iPSCs) are a promising and abundant alternative source of MSCs, offering a potential solution to the limitations of adult MSCs. Nevertheless, a standardized protocol for the differentiation of iPSCs into iPSC-derived mesenchymal stem cells (iMSCs) has yet to be established, as the existing methods vary significantly in terms of complexity, duration, and outcome. Many straightforward methods induce differentiation by culturing iPSCs in MSC media which are supplemented with fetal bovine serum (FBS) or human platelet lysate (hPL), followed by selection of MSC-like cells by passaging. However, in our hands, this approach yielded inconsistent quality of iMSCs, particularly in terms of osteogenic potential and premature senescence. This study examines the impact of the selective TGF-β inhibitor SB431542 on iMSC differentiation, demonstrating that TGF-β inhibition enhances osteogenic potential and reduces premature senescence. Additionally, we present a reliable, xeno-free method for producing high-quality iMSCs that can be adapted for Good Manufacturing Practice (GMP) compliance, thus enhancing the potential for clinical applications.

Ribosome-associated proteins: unwRAPping ribosome heterogeneity in the twenty-first century.

The definition of the ribosome as the monolithic machinery in cells that synthesizes all proteins in the cell has persisted for the better part of a century. Yet, research has increasingly revealed that ribosomes are dynamic, multimodal complexes capable of fine-tuning gene expression. This translation regulation may be achieved by ribosome-associated proteins (RAPs), which play key roles as modular trans-acting factors that are dynamic across different cellular contexts and can mediate the recruitment of specific transcripts or the modification of RNA or ribosomal proteins. As a result, RAPs have the potential to rapidly regulate translation within specific subcellular regions, across different cell or tissue types, in response to signalling, or in disease states. In this article, we probe the definition of the eukaryotic ribosome and review the major layers of additional proteins that expand the definition of ribosomes in the twenty-first century. We pose RAPs as key modulators that impart ribosome function in cellular processes, development and disease.This article is part of the discussion meeting issue 'Ribosome diversity and its impact on protein synthesis, development and disease'.

A Single-Cell Transcriptome Atlas Characterizes the Immune Landscape of Human Testes During Aging.

Aging disrupts immune regulation, affecting tissue function and increasing vulnerability to various diseases. However, the effects of aging on immune cells within human testes are not well understood. In this study, we utilized single-cell RNA sequencing to profile immune cells from 33 human testis samples from individuals aged 21 to 69. Our analysis revealed key immune cell types, including CD8+ T cells, monocytes, cDC2 cells, and various macrophage subtypes within the testes. We observed an age-related change in monocytes and MRC1hi tissue-resident macrophage (TRM), a pattern consistent in both human and mouse testes. Individuals aged 40 and older showed notable shifts in pathways related to phagocytosis, cytokine signaling, and antigen presentation. Monocytes also exhibited pro-inflammatory characteristics, potentially contributing to the low-grade inflammation commonly associated with aging. Together, these findings provide insights into age-related immune cell alterations in human testes and uncover molecular mechanisms underlying these shifts, offering a valuable resource for understanding immune aging in the reproductive system.

Single-cell transcriptomics of melanoma sentinel lymph nodes identifies unique immune cell signatures associated with metastasis.

The sentinel lymph node (SLN) is the first lymph node encountered by a metastatic cancer cell and serves as a predictor of poor prognosis, as patients with clinically occult SLN metastases are classified as stage III with elevated rates of recurrence and diminished overall survival. However, the dynamics of immune infiltrates in SLNs remain poorly characterized. Here, using an unbiased Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) technique, we profiled 97,777 cells from SLN tissues obtained from patients with stages I/II and III cutaneous melanoma. We describe the transcriptional programs of a multitude of T, B, and myeloid cell subtypes in SLNs. Based on the proportions of cell types, we determined that SLN subtypes are stratified along a naive → activated axis; patients with a 'high activated' signature score appear to be undergoing a robust melanoma antigen-driven adaptive immune response and thus, could be responsive to immunotherapy. Additionally, we identified transcriptomic signatures of SLN-infiltrating dendritic cell subsets that compromise anti-tumor immune responses. Our analyses provide valuable insights into tumor-driven immune changes in the SLN tissue, offering a powerful tool for the informed design of immune therapies for high-risk melanoma patients.

Macrophage-mediated interleukin-6 signaling drives ryanodine receptor-2 calcium leak in postoperative atrial fibrillation.

Postoperative atrial fibrillation (poAF) is AF occurring days after surgery with a prevalence of 33% among patients undergoing open-heart surgery. The degree of postoperative inflammation correlates with poAF risk, but less is known about the cellular and molecular mechanisms driving postoperative atrial arrhythmogenesis. We performed single-cell RNA sequencing comparing atrial non-myocytes from mice with versus without poAF, which revealed infiltrating CCR2+ macrophages to be the most altered cell type. Pseudotime trajectory analyses identified Il-6 as a top gene in macrophages, which we confirmed in pericardial fluid collected from human patients after cardiac surgery. Indeed, macrophage depletion and macrophage-specific Il6ra conditional knockout (cKO) prevented poAF in mice. Downstream STAT3 inhibition with TTI-101 and cardiomyocyte-specific Stat3 cKO rescued poAF, indicating a pro-arrhythmogenic role of STAT3 in poAF development. Confocal imaging in isolated atrial cardiomyocytes (ACMs) uncovered a novel link between STAT3 and CaMKII-mediated ryanodine receptor-2 (RyR2)-Ser(S)2814 phosphorylation. Indeed, non-phosphorylatable RyR2S2814A mice were protected from poAF, and CaMKII inhibition prevented arrhythmogenic Ca2+ mishandling in ACMs from mice with poAF. Altogether, we provide multiomic, biochemical, and functional evidence from mice and humans that IL-6-STAT3-CaMKII signaling driven by infiltrating atrial macrophages is a pivotal driver of poAF that portends therapeutic utility for poAF prevention.

DNMT3A regulates murine megakaryocyte-biased hematopoietic stem cell fate decisions.

Hematopoietic stem cells (HSCs) are defined by their capacity to regenerate all main components of the peripheral blood, but individual HSCs exhibit a range of preferences for generating downstream cell types. Their propensities are thought to be epigenetically encoded, but few differential regulatory mechanisms have been identified. In this work, we explored the role of the DNA methyltransferase 3A (DNMT3A) in the megakaryocyte-biased HSC population, which is thought to reside at the top of the hematopoietic hierarchy. We demonstrate that heterozygous loss of DNMT3A (Dnmt3a+/-) in these megakaryocyte-biased HSCs has consequences distinct from the rest of the HSC pool. These megakaryocyte-biased HSCs become delayed in their lymphoid-repopulating ability but can ultimately regenerate all lineages. We further demonstrate that Dnmt3a+/- mice have increased numbers of megakaryocytes in the bone marrow. Analysis of DNA methylation differences between WT and Dnmt3a+/- HSC subsets, megakaryocyte-erythroid progenitors (MEP), and megakaryocytes revealed that DNA methylation is eroded in the mutants in a cell type-specific fashion. While transcriptional differences between the WT and Dnmt3a+/- megakaryocyte-biased HSCs are subtle, the pattern of DNA methylation loss in this HSC subset is almost completely different from that in non-megakaryocyte-biased HSCs. Together, our findings establish the role of epigenetic regulation in the fate of megakaryocyte-biased HSCs and their downstream progeny and suggest that the outcomes of DNMT3A loss might vary depending on the identity of the HSC that acquires the mutation.

Impaired yolk sac NAD metabolism disrupts murine embryogenesis with relevance to human birth defects.

Congenital malformations can originate from numerous genetic or non-genetic factors but in most cases the causes are unknown. Genetic disruption of nicotinamide adenine dinucleotide (NAD) de novo synthesis causes multiple malformations, collectively termed Congenital NAD Deficiency Disorder (CNDD), highlighting the necessity of this pathway during embryogenesis. Previous work in mice shows that NAD deficiency perturbs embryonic development specifically when organs are forming. While the pathway is predominantly active in the liver postnatally, the site of activity prior to and during organogenesis is unknown. Here, we used a mouse model of human CNDD and assessed pathway functionality in embryonic livers and extraembryonic tissues via gene expression, enzyme activity and metabolic analyses. We found that the extra-embryonic visceral yolk sac endoderm exclusively synthesises NAD de novo during early organogenesis before the embryonic liver takes over this function. Under CNDD-inducing conditions, visceral yolk sacs had reduced NAD levels and altered NAD-related metabolic profiles, affecting embryo metabolism. Expression of requisite pathway genes is conserved in the equivalent yolk sac cell type in humans. Our findings show that visceral yolk sac-mediated NAD de novo synthesis activity is essential for mouse embryogenesis and its perturbation causes CNDD. As mouse and human yolk sacs are functionally homologous, our data improve the understanding of human congenital malformation causation.

T cell-derived adenosine regulates fibroblast IL-6 formation via A2B receptors in the infarcted heart.

Elevated interleukin-6 (IL-6) levels are linked to an increased risk of cardiovascular mortality in myocardial infarction (MI). Targeting IL-6 and its downstream signalling pathways represents a therapeutic strategy; however, its cellular sources and regulatory mechanisms of IL-6 remain incompletely understood. In this study, Alter and colleagues investigated the primary cell type that produces IL-6 in post-MI murine heart and the role of purinergic signalling in regulating IL-6 formation. Using cellular and mouse models, the authors identified cardiac fibroblasts as the predominant source of IL-6. Further analysis revealed that the IL-6 formation in cardiac fibroblasts is regulated by adenosine A2B receptors. Of further importance, they elucidated that T cells highly express CD73, leading to significant adenosine formation, which in turn enhances IL-6 production via Gq activation in cardiac fibroblasts following MI. These findings reveal a dynamic interplay between immune cells and fibroblasts in shaping the post-MI inflammatory response. This study suggests the adenosine-A2B receptor-IL6 axis as a potential therapeutic target to mitigate inflammation and improve cardiomyocytes salvage in MI.

ScHeteroNet: A Heterophily-Aware Graph Neural Network for Accurate Cell Type Annotation and Novel Cell Detection.

Single-cell RNA sequencing (scRNA-seq) has unveiled extensive cellular heterogeneity, yet precise cell type annotation and the identification of novel cell populations remain significant challenges. scHeteroNet, a novel graph neural network framework specifically designed to leverage heterophily in scRNA-seq data, is presented. Unlike traditional methods that assume homophily, scHeteroNet captures complex cell-cell interactions by integrating information from both immediate and extended cellular neighborhoods, resulting in highly accurate cell representations. Additionally, scHeteroNet incorporates an innovative novelty propagation mechanism that robustly detects previously uncharacterized cell types. Comprehensive evaluations across diverse scRNA-seq datasets demonstrate that scHeteroNet consistently outperforms state-of-the-art approaches in both cell type classification and novel cell detection. This heterophily-aware approach enhances the ability to uncover cellular diversity, providing deeper insights into complex biological systems and advancing the field of single-cellanalysis.

Sensory input, sex and function shape hypothalamiccelltype development.

Mammalian behaviour and physiology undergo major changes in early life. Young animals rely on conspecifics to meet their needs and start showing nutritional independence and sex-specific social interactions at weaning and puberty, respectively. How neuronal populations regulating homeostatic functions and social behaviours develop during these transitions remains unclear. We used paired transcriptomic and chromatin accessibility profiling to examine the developmental trajectories of neuronal populations in the hypothalamic preoptic region, where cell types with key roles in physiological and behavioural control have been identified1-6. These data show a markeddiversity of developmental trajectories shaped by the sex of the animal, and the location and behavioural or physiological function of the corresponding cell types. We identify key stages of preoptic development, including early diversification, perinatal emergence of sex differences, postnatal maturation and refinement of signalling networks, and nonlinear transcriptional changes accelerating at the time of weaning and puberty. We assessed preoptic development in various sensory mutants and find a major role for vomeronasal sensing in the timing of preoptic cell type maturation. These results provide new insights into the development of neurons controlling homeostatic functions and social behaviours and lay ground for examining the dynamics of these functions in early life.

Evolution of irreversible differentiation under stage-dependent cell differentiation

The specialization of cells is a hallmark of complex multicellularity. Cell differentiation enables the emergence of specialized cell types that carry out separate functions previously executed by a multifunctional ancestor cell. One view about the origin of cell differentiation is that it first occurred randomly in genetically identical cells exposed to the same life history environment. Under these conditions, differentiation trajectories producing more offspring could be favored by natural selection; yet, how dynamic variation in differentiation probabilities can affect the evolution of differentiation patterns is unclear. We develop a theoretical model to investigate the effect of dynamic—stage-dependent—cell differentiation on the evolution of optimal differentiation patterns. Concretely, we model trajectories in which cells can randomly differentiate into germ or soma cell types at each cell division. After comparing many of these trajectories, we found that irreversible differentiation, where cells gradually lose their ability to produce the other cell type, is more favored in small organisms under dynamic than under constant (stage-independent) cell differentiation. Furthermore, we found that the irreversible differentiation of germ cells, where germ cells gradually lose their ability to produce soma cells, is prominent among irreversible patterns. Only large variations in the differentiation probabilities prohibit irreversible trajectories from being the optimal pattern.

Single-Cell RNA Sequencing Reveals an Atlas of Meihua Pig Testis Cells

Mammalian spermatogenesis is a complex biological process that is regulated by multiple types of cells. The heterogeneity of these cells poses a challenge for analyzing different cell types at different developmental stages. To characterize the transcriptomic landscape of porcine spermatogenesis and identify potential marker genes for spermatogonia, an unbiased transcriptomic study of spermatogenesis in neonatal and sexually mature six-month-old Meihua pigs was performed using 10× Genomics single-cell RNA sequencing (scRNA-seq). Through the collection of scRNA-seq data from 13,839 cells from Meihua pig testes, three germ cells (spermatogonia, spermatocytes and spermatids) and eight somatic cells (Sertoli cells, Leydig cells, myoid/stromal cells, endothelial cells, T cells/macrophages and erythroblasts) were identified. Pseudo-timing analysis showed that myoid cells and stromal cells originated from common progenitors in Meihua pigs. Functional enrichment analysis revealed that the differentially expressed genes (DEGs) in testicular somatic cells were enriched in the pathways of Ribosome, Oxidative phosphorylation, Protein processing in endoplasmic reticulum, Retrograde endocannabinoid signaling, Cellular senescence and Insulin signaling. Meanwhile, in the three different germ cells, except for pathways which were the same as the first three pathways for somatic cells, DEGs were also enriched in the Spliceosome, Cell cycle, Autophagy and Mitophagy pathways. Furthermore, the candidate marker gene TKTL1 in spermatogonia was identified using immunohistochemistry and immunofluorescence. In conclusion, we collected transcription datasets and constructed single-cell developmental maps of germ cells and somatic cells during the testicular development of Meihua pigs, which provided new insights into the spermatogenesis of Meihua pigs and the development of various types of cells in their testes.