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A roadmap for the Human Developmental Cell Atlas.
The Human Developmental Cell Atlas (HDCA) initiative, which is part of the Human Cell Atlas, aims to create a comprehensive reference map of cells during development. This will be critical to understanding normal organogenesis, the effect of mutations, environmental factors and infectious agents on human development, congenital and childhood disorders, and the cellular basis of ageing, cancer and regenerative medicine. Here we outline the HDCA initiative and the challenges of mapping and modelling human development using state-of-the-art technologies to create a reference atlas across gestation. Similar to the Human Genome Project, the HDCA will integrate the output from a growing community of scientists who are mapping human development into a unified atlas. We describe the early milestones that have been achieved and the use of human stem-cell-derived cultures, organoids and animal models to inform the HDCA, especially for prenatal tissues that are hard to acquire. Finally, we provide a roadmap towards a complete atlas of human development.
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γδ T cells are effectors of immunotherapy in cancers with HLA class I defects.
DNA mismatch repair-deficient (MMR-d) cancers present an abundance of neoantigens that is thought to explain their exceptional responsiveness to immune checkpoint blockade (ICB)1,2. Here, in contrast to other cancer types3-5, we observed that 20 out of 21 (95%) MMR-d cancers with genomic inactivation of β2-microglobulin (encoded by B2M) retained responsiveness to ICB, suggesting the involvement of immune effector cells other than CD8+ T cells in this context. We next identified a strong association between B2M inactivation and increased infiltration by γδ T cells in MMR-d cancers. These γδ T cells mainly comprised the Vδ1 and Vδ3 subsets, and expressed high levels of PD-1, other activation markers, including cytotoxic molecules, and a broad repertoire of killer-cell immunoglobulin-like receptors. In vitro, PD-1+ γδ T cells that were isolated from MMR-d colon cancers exhibited enhanced reactivity to human leukocyte antigen (HLA)-class-I-negative MMR-d colon cancer cell lines and B2M-knockout patient-derived tumour organoids compared with antigen-presentation-proficient cells. By comparing paired tumour samples from patients with MMR-d colon cancer that were obtained before and after dual PD-1 and CTLA-4 blockade, we found that immune checkpoint blockade substantially increased the frequency of γδ T cells in B2M-deficient cancers. Taken together, these data indicate that γδ T cells contribute to the response to immune checkpoint blockade in patients with HLA-class-I-negative MMR-d colon cancers, and underline the potential of γδ T cells in cancer immunotherapy.
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Rapid Biofabrication of an Advanced Microphysiological System Mimicking Phenotypical Heterogeneity and Drug Resistance in Glioblastoma.
Microphysiological systems (MPSs) reconstitute tissue interfaces and organ functions, presenting a promising alternative to animal models in drug development. However, traditional materials like polydimethylsiloxane (PDMS) often interfere by absorbing hydrophobic molecules, affecting drug testing accuracy. Additive manufacturing, including 3D bioprinting, offers viable solutions. GlioFlow3D, a novel microfluidic platform combining extrusion bioprinting and stereolithography (SLA) is introduced. GlioFlow3D integrates primary human cells and glioblastoma (GBM) lines in hydrogel-based microchannels mimicking vasculature, within an SLA resin framework using cost-effective materials. The study introduces a robust protocol to mitigate SLA resin cytotoxicity. Compared to PDMS, GlioFlow3D demonstrated lower small molecule absorption, which is relevant for accurate testing of small molecules like Temozolomide (TMZ). Computational modeling is used to optimize a pumpless setup simulating interstitial fluid flow dynamics in tissues. Co-culturing GBM with brain endothelial cells in GlioFlow3D showed enhanced CD133 expression and TMZ resistance near vascular interfaces, highlighting spatial drug resistance mechanisms. This PDMS-free platform promises advanced drug testing, improving preclinical research and personalized therapy by elucidating complex GBM drug resistance mechanisms influenced by the tissue microenvironment.
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Modulation of the maladaptive stress response to manage diseases of protein folding.
Diseases of protein folding arise because of the inability of an altered peptide sequence to properly engage protein homeostasis components that direct protein folding and function. To identify global principles of misfolding disease pathology we examined the impact of the local folding environment in alpha-1-antitrypsin deficiency (AATD), Niemann-Pick type C1 disease (NPC1), Alzheimer's disease (AD), and cystic fibrosis (CF). Using distinct models, including patient-derived cell lines and primary epithelium, mouse brain tissue, and Caenorhabditis elegans, we found that chronic expression of misfolded proteins not only triggers the sustained activation of the heat shock response (HSR) pathway, but that this sustained activation is maladaptive. In diseased cells, maladaptation alters protein structure-function relationships, impacts protein folding in the cytosol, and further exacerbates the disease state. We show that down-regulation of this maladaptive stress response (MSR), through silencing of HSF1, the master regulator of the HSR, restores cellular protein folding and improves the disease phenotype. We propose that restoration of a more physiological proteostatic environment will strongly impact the management and progression of loss-of-function and gain-of-toxic-function phenotypes common in human disease.
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A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS).
Cell state-specific promoters constitute essential tools for basic research and biotechnology because they activate gene expression only under certain biological conditions. Synthetic Promoters with Enhanced Cell-State Specificity (SPECS) can be superior to native ones, but the design of such promoters is challenging and frequently requires gene regulation or transcriptome knowledge that is not readily available. Here, to overcome this challenge, we use a next-generation sequencing approach combined with machine learning to screen a synthetic promoter library with 6107 designs for high-performance SPECS for potentially any cell state. We demonstrate the identification of multiple SPECS that exhibit distinct spatiotemporal activity during the programmed differentiation of induced pluripotent stem cells (iPSCs), as well as SPECS for breast cancer and glioblastoma stem-like cells. We anticipate that this approach could be used to create SPECS for gene therapies that are activated in specific cell states, as well as to study natural transcriptional regulatory networks.
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Targeting TBK1 to overcome resistance to cancer immunotherapy.
Despite the success of PD-1 blockade in melanoma and other cancers, effective treatment strategies to overcome resistance to cancer immunotherapy are lacking1,2. Here we identify the innate immune kinase TANK-binding kinase 1 (TBK1)3 as a candidate immune-evasion gene in a pooled genetic screen4. Using a suite of genetic and pharmacological tools across multiple experimental model systems, we confirm a role for TBK1 as an immune-evasion gene. Targeting TBK1 enhances responses to PD-1 blockade by decreasing the cytotoxicity threshold to effector cytokines (TNF and IFNγ). TBK1 inhibition in combination with PD-1 blockade also demonstrated efficacy using patient-derived tumour models, with concordant findings in matched patient-derived organotypic tumour spheroids and matched patient-derived organoids. Tumour cells lacking TBK1 are primed to undergo RIPK- and caspase-dependent cell death in response to TNF and IFNγ in a JAK-STAT-dependent manner. Taken together, our results demonstrate that targeting TBK1 is an effective strategy to overcome resistance to cancer immunotherapy.
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Electrophysiological Monitoring of Neurochemical-Based Neural Signal Transmission in a Human Brain-Spinal Cord Assembloid.
Combining human brain organoids holds great potential in recapitulating the human brain's histological features and modeling neural disorders. However, current combined-brain organoid models focus on the internal interactions between different brain regions. In this study, we develop an engineered brain-spinal cord assembloid (eBSA) by coculturing cerebral organoids (COs) and motor neuron spheroids (MNSs). By connecting COs and MNSs, we generate a terminal for signal transfer from the brain to the whole body by mimicking the brain-spinal cord connection. After the formation of COs from human induced pluripotent stem cells and MNSs from human neural stem cells, MNSs are prepatterned into specific CO regions and assembled to form an eBSA. Caffeine serves as a neurochemical model to demonstrate neural signal transmission. When the MNSs in the eBSA contact the multielectrode array, the eBSA successfully shows an increased neural spiking speed on the motor neuron region by caffeine treatment, which means that neural stimulation signals transfer from the COs to MNSs. The neural stimulation effects of caffeine are tested on the MNSs only to prove the eBSA system's neural signal transmission, and there were no stimulus effects. Our results demonstrate that the eBSA system can monitor a caffeine-mediated excitatory signal as an output signal from the brain to the spinal cord. We believe that the eBSA system can be utilized as a screening platform to validate the stimulus signal transfer by neurochemicals. In addition, the accumulation of understanding of the neural signal transfer from CNS to PNS will provide better knowledge for controlling muscle actuators with the nervous system.
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Human iPSC-derived microglia: A growing toolset to study the brain's innate immune cells.
Recent advances in the generation of microglia from human induced pluripotent stem cells (iPSCs) have provided exciting new approaches to examine and decipher the biology of microglia. As these techniques continue to evolve to encompass more complex in situ and in vivo paradigms, so too have they begun to yield novel scientific insight into the genetics and function of human microglia. As such, researchers now have access to a toolset comprised of three unique "flavors" of iPSC-derived microglia: in vitro microglia (iMGs), organoid microglia (oMGs), and xenotransplanted microglia (xMGs). The goal of this review is to discuss the variety of research applications that each of these techniques enables and to highlight recent discoveries that these methods have begun to uncover. By presenting the research paradigms in which each model has been successful, as well as the key benefits and limitations of each approach, it is our hope that this review will help interested researchers to incorporate these techniques into their studies, collectively advancing our understanding of human microglia biology.
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Butyrate triggers neuronal signaling via release of colonic serotonin in a microfluidic model of gut-brain axis.
Host-microbiota interactions play a central role in regulating gastrointestinal and cardiometabolic physiology, yet the mechanistic pathways linking microbial metabolites to sensory neuronal activation remain poorly defined. In particular, the rapid signaling events through which short-chain fatty acids such as butyrate influence epithelial and neuronal function in the colon have not been fully resolved due to limitations of existing models. Here, we developed and validated a compartmentalized microfluidic trichannel model that spatially organizes primary colonic epithelial cells, sensory neurons, and microbial inputs to enable real-time, directional analysis of microbial-epithelial-neuronal communication to mimic the in vivo environment of the gastrointestinal tract. Using computational modeling and real-time imaging, we demonstrate a timeline in which butyrate elicits dose-dependent calcium (Ca2+) influx in the sensory neurons, mediated through a multistep signaling cascade: butyrate stimulation of colonic epithelial cells, via epithelial G-protein-coupled receptor 41 (GPR41) and GPR43 receptors, triggering a rapid serotonin (5-hydroxytryptamine, 5-HT) release that subsequently engages 5-HT3a receptors on sensory neurons to induce Ca2+ influx, indicative of neuronal activation. Pharmacological inhibition of epithelial GPR41 and GPR43 receptors or neuronal 5-HT3a receptors abolished these responses, demonstrating the requirement for both (epithelial and neuronal) components in the signaling pathway. Epithelial cells were essential intermediaries, as neurons cultured without them failed to respond to butyrate. Moreover, we establish the feasibility of a live microbiota-epithelial-neuronal triculture model that can be used for future mechanistic dissection of microbiota-gut-brain signaling.NEW & NOTEWORTHY We present a compartmentalized microfluidic trichannel model of the gut-brain axis that reveals how microbial metabolites communicate with neurons. Using this model, we show that butyrate triggers colonic serotonin release, which activates neuronal signaling through calcium influx. This work highlights the power of microfluidic models to uncover mechanisms of gut-brain communication in a controlled, in vitro setting.
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Lecanemab blocks the effects of the Aβ/fibrinogen complex on blood clots and synapse toxicity in organotypic culture.
Proteinaceous brain inclusions, neuroinflammation, and vascular dysfunction are common pathologies in Alzheimer's disease (AD). Vascular deficits include a compromised blood-brain barrier, which can lead to extravasation of blood proteins like fibrinogen into the brain. Fibrinogen's interaction with the amyloid-beta (Aβ) peptide is known to worsen thrombotic and cerebrovascular pathways in AD. Lecanemab, an FDA-approved antibody therapy for AD, clears Aβ plaque from the brain and slows cognitive decline. Here, we show that lecanemab blocks fibrinogen's binding to Aβ protofibrils, preventing Aβ/fibrinogen-mediated delayed fibrinolysis and clot abnormalities in vitro and in human plasma. Additionally, we show that lecanemab dissociates the Aβ/fibrinogen complex and prevents fibrinogen from exacerbating Aβ-induced synaptotoxicity in mouse organotypic hippocampal cultures. These findings reveal a possible protective mechanism by which lecanemab may slow disease progression in AD.