Recent advances and current challenges of new approach methodologies in developmental and adult neurotoxicity testing DOI Creative Commons
Melania Maria Serafini, Sara Sepehri, Miriam Midali

et al.

Archives of Toxicology, Journal Year: 2024, Volume and Issue: 98(5), P. 1271 - 1295

Published: March 13, 2024

Abstract Adult neurotoxicity (ANT) and developmental (DNT) assessments aim to understand the adverse effects underlying mechanisms of toxicants on human nervous system. In recent years, there has been an increasing focus so-called new approach methodologies (NAMs). The Organization for Economic Co-operation Development (OECD), together with European American regulatory agencies, promote use validated alternative test systems, but date, guidelines DNT ANT assessment rely primarily classical animal testing. Alternative methods include both non-animal approaches systems non-vertebrates (e.g., nematodes) or non-mammals fish). Therefore, this review summarizes advances NAMs focusing highlights potential current critical issues full implementation these in future. status vitro battery (DNT IVB) is also reviewed as a first step context. Critical such (i) need batteries method integration (from silico vivo alternatives, e.g., zebrafish, C. elegans ) requiring interdisciplinarity manage complexity, (ii) interlaboratory transferability, (iii) urgent validation are discussed.

Language: Английский

Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender DOI
Stephen J. Fleming, Mark Chaffin, Alessandro Arduini

et al.

Nature Methods, Journal Year: 2023, Volume and Issue: 20(9), P. 1323 - 1335

Published: Aug. 7, 2023

Language: Английский

Citations

327
Generation of vascularized brain organoids to study neurovascular interactions DOI Creative Commons

Xin-Yao Sun,

Xiang-Chun Ju, Yang Li

et al.

eLife, Journal Year: 2022, Volume and Issue: 11

Published: May 4, 2022

Brain organoids have been used to recapitulate the processes of brain development and related diseases. However, lack vasculatures, which regulate neurogenesis disorders, limits utility organoids. In this study, we induced vessel organoids, respectively, then fused two types together obtain vascularized The were engrafted with robust vascular network-like structures exhibited increased number neural progenitors, in line possibility that vessels development. Fusion also contained functional blood–brain barrier-like structures, as well microglial cells, a specific population immune cells brain. incorporated microglia responded actively stimuli showed ability engulfing synapses. Thus, fusion established study allow modeling interactions between neuronal non-neuronal components vitro, particularly vasculature niche.

Language: Английский

Citations

235
Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender DOI Creative Commons
Stephen J. Fleming, Mark Chaffin, Alessandro Arduini

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2019, Volume and Issue: unknown

Published: Oct. 3, 2019

Abstract Droplet-based single-cell assays, including scRNA-seq, snRNA-seq, and CITE-seq, produce a significant amount of background noise counts, the hallmark which is non-zero counts in cell-free droplets off-target gene expression unexpected cell types. The presence such systematic potential source batch effect spurious differential expression. Here we develop deep generative model for noise-contaminated data that structured to reflect phenomenology generation droplet-based assays. proposed successfully distinguishes cell-containing from without supervision, learns profile noise, retrieves noise-free quantification an end-to-end fashion. We present scalable robust implementation our method as module open-source software package CellBender . show operates close theoretically optimal denoising limit simulated datasets, extensive evaluations using real datasets experimental benchmarks drawn different tissues, protocols, modalities significantly improves agreement with established patterns, learned provides evidence degraded or uncaptured

Language: Английский

Citations

190
Human cerebral organoids — a new tool for clinical neurology research DOI Open Access
Oliver L. Eichmüller, Juergen A. Knoblich

Nature Reviews Neurology, Journal Year: 2022, Volume and Issue: 18(11), P. 661 - 680

Published: Oct. 17, 2022

Language: Английский

Citations

174
An in vivo neuroimmune organoid model to study human microglia phenotypes DOI Open Access
Simon T. Schafer, Abed AlFatah Mansour, Johannes C. M. Schlachetzki

et al.

Cell, Journal Year: 2023, Volume and Issue: 186(10), P. 2111 - 2126.e20

Published: May 1, 2023

Language: Английский

Citations

123
Expression of the transcription factor PU.1 induces the generation of microglia-like cells in human cortical organoids DOI Creative Commons
Bilal Çakir, Yoshiaki Tanaka, Ferdi Rıdvan Kiral

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Jan. 20, 2022

Microglia play a role in the emergence and preservation of healthy brain microenvironment. Dysfunction microglia has been associated with neurodevelopmental neurodegenerative disorders. Investigating function human health disease challenging due to limited models available. Here, we develop method generate functional cortical organoids (hCOs) from embryonic stem cells (hESCs). We apply this system study during inflammation induced by amyloid-β (Aβ). The overexpression myeloid-specific transcription factor PU.1 generates microglia-like hCOs, producing mhCOs (microglia-containing hCOs), that engraft mouse brain. Single-cell transcriptomics reveals acquire cell cluster an intact complement chemokine system. Functionally, protect parenchyma cellular molecular damage caused Aβ. Furthermore, mhCOs, observed reduced expression Aβ-induced genes apoptosis, ferroptosis, Alzheimer's (AD) stage III. Finally, assess AD-associated highly expressed response Aβ using pooled CRISPRi coupled single-cell RNA sequencing mhCOs. In summary, provide protocol can be used fundamental translational studies as model investigate

Language: Английский

Citations

103
iPS-cell-derived microglia promote brain organoid maturation via cholesterol transfer DOI

Dong Shin Park,

Tatsuya Kozaki, Satish Kumar Tiwari

et al.

Nature, Journal Year: 2023, Volume and Issue: 623(7986), P. 397 - 405

Published: Nov. 1, 2023

Language: Английский

Citations

98
Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution DOI Creative Commons
Alex A. Pollen, Umut Kilik, Craig B. Lowe

et al.

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 24(10), P. 687 - 711

Published: Feb. 3, 2023

Our ancestors acquired morphological, cognitive and metabolic modifications that enabled humans to colonize diverse habitats, develop extraordinary technologies reshape the biosphere. Understanding genetic, developmental molecular bases for these changes will provide insights into how we became human. Connecting human-specific genetic species differences has been challenging owing an abundance of low-effect size changes, limited descriptions phenotypic across development at level cell types lack experimental models. Emerging approaches single-cell sequencing, manipulation stem culture now support descriptive functional studies in defined with a human or ape background. In this Review, describe sequencing genomes from modern archaic hominins, great apes other primates is revealing new cellular - including atlases organoids are enabling exploration candidate causal factors underlie traits.

Language: Английский

Citations

97
Microglia-containing human brain organoids for the study of brain development and pathology DOI Creative Commons
Wendiao Zhang,

Jiamei Jiang,

Zhenhong Xu

et al.

Molecular Psychiatry, Journal Year: 2022, Volume and Issue: 28(1), P. 96 - 107

Published: Dec. 6, 2022

Microglia are resident immune cells in the central nervous system, playing critical roles brain development and homeostasis. Increasing evidence has implicated microglia dysfunction pathogenesis of various disorders ranging from psychiatric to neurodegenerative diseases. Using a human cell-based model illuminate functional mechanisms will promote pathological studies drug development. The recently developed microglia-containing organoids (MC-HBOs), in-vitro three-dimensional cell cultures that recapitulate key features brain, have provided new avenue pathology. However, MC-HBOs generated different methods differ origin, proportion, fidelity within organoids, may produced inconsistent results. To help researchers develop robust reproducible recapitulates in-vivo signatures study pathology, this review summarized current used generate opinions on use for disease modeling studies.

Language: Английский

Citations

87
Exposure of iPSC-derived human microglia to brain substrates enables the generation and manipulation of diverse transcriptional states in vitro DOI Creative Commons
Michael-John Dolan, Martine Therrien,

Saša Jereb

et al.

Nature Immunology, Journal Year: 2023, Volume and Issue: 24(8), P. 1382 - 1390

Published: July 27, 2023

Abstract Microglia, the macrophages of brain parenchyma, are key players in neurodegenerative diseases such as Alzheimer’s disease. These cells adopt distinct transcriptional subtypes known states. Understanding state function, especially human microglia, has been elusive owing to a lack tools model and manipulate these cells. Here, we developed platform for modeling microglia states vitro. We found that exposure stem-cell-differentiated synaptosomes, myelin debris, apoptotic neurons or synthetic amyloid-beta fibrils generated diversity mapped gene signatures identified including disease-associated enriched diseases. Using new lentiviral approach, demonstrated transcription factor MITF drives signature highly phagocytic state. Together, enable manipulation functional interrogation microglial both homeostatic disease-relevant contexts.

Language: Английский

Citations

77