Biology subjects

Cohen, L.

Publications and source records attributed to Cohen, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Multiplexed optical barcoding and sequencing for spatial omics

Spatial omics has brought a fundamental change in the way that we study cell and tissue biology in health and disease. Among various spatial omics methods, genome-scale imaging allows transcriptomic, 3D-genomic, and epigenomic profiling of individual cells with high spatial (subcellular) resolution but often requires a preselection of targeted genes or genomic loci. On the other hand, spatially dependent barcoding of molecules followed by sequencing provides untargeted, genome-wide profiling but typically lacks single-cell resolution. Here, we report a spatial omics method that could potentially combine the power of the two approaches by optically controlled spatial barcoding followed by sequencing. Specifically, we utilize patterned light to encode the locations of cells in tissues using oligonucleotide-based barcodes and then identify the barcoded molecular content, such as mRNAs, by sequencing. This optical barcoding method is designed with multiplexing and error-correction capacity and achieved by a light-directed ligation chemistry that attaches distinct nucleic-acid sequences to the reverse transcribed cDNA products at different locations. As a proof of principle for this method, we demonstrated high-efficiency in situ light-directed ligation, spatially dependent barcoding with multiplexed light-controlled ligations, and high-accuracy detection of spatially barcoded mRNAs in cells.

genomics↗

bioRxiv2024

The reparative immunologic consequences of stem cell transplantation as a cellular therapy for refractory Crohn's disease

BackgroundTreatment strategies for Crohns disease (CD) suppress diverse inflammatory pathways but many patients remain refractory to treatment. Autologous hematopoietic stem cell transplantation (SCT) has emerged as a therapy for medically refractory CD. SCT was developed to rescue cancer patients from myelosuppressive chemotherapy but its use for CD and other immune diseases necessitates reimagining SCT as a cellular therapy that restores appropriately responsive immune cell populations from hematopoietic progenitors in the stem cell autograft (i.e. immune "reset"). Here we present a paradigm to understand SCT as a cellular therapy for immune diseases and reveal how SCT re-establishes cellular immunity utilizing high-dimensional cellular phenotyping and functional studies of the stem cell grafts. MethodsImmunophenotyping using CyTOF, single cell RNA sequencing (scRNA-seq) and T cell receptor (TCR) sequencing was performed on peripheral blood and intestinal tissue samples from refractory CD patients who underwent SCT. The stem cell graft from these patients was analyzed using flow cytometry and functionally interrogated using a murine model for engraftment. ResultsOur study revealed a remodeling of intestinal macrophages capable of supporting mucosal healing that was independently validated using multimodal studies of immune reconstitution events including CyTOF and scRNA-seq. Functional interrogation of hematopoietic stem cells (HSCs) using a xenograft model demonstrated that HSCs shape the timing of immune reconstitution, the selected reconstitution of specific cell lineages and potentially the clinical efficacy of SCT. ConclusionsThese studies indicate that SCT serves as a myeloid-directed cellular therapy re-establishing homeostatic intestinal macrophages that support intestinal healing and suggest refractory CD evolves from impairment of restorative functions in myeloid cells. Furthermore, we report heterogeneity among HSCs from CD patients which may drive SCT outcomes and suggests an unrecognized impact of CD pathophysiology on HSC in the marrow niche.

immunology↗

bioRxiv2024

Multiparametric quantitative MRI uncovers putamen microstructural changes in Parkinson's Disease

Parkinsons disease (PD) is a progressive neurodegenerative disorder dominated by motor and non-motor dysfunction. Despite extensive research, the in vivo characterization of PD-related microstructural brain changes remains an ongoing challenge, limiting advancements in diagnostic and therapeutic strategies. The putamen, a critical structure within the basal ganglia, plays a key role in regulating movement and is profoundly affected in early PD-related neurodegeneration. In this study, we collected multiparametric quantitative MRI (qMRI) brain data of PD patients and healthy controls, to investigate microstructural alterations in the putamen in PD. We utilized a gradient analysis technique to analyze the spatial variations of various qMRI parameters, including relaxation rates (R1, R2, R2*), water fraction (WF), susceptibility, magnetization transfer saturation (MTsat), and diffusion metrics (MD, FA). Our findings reveal significant spatial gradients and interhemispheric asymmetries in these biophysical properties along the anterior-posterior axis of the putamen. Notably, PD patients exhibited increased water fraction and altered transverse relaxation rate R2*, particularly in the posterior putamen, correlated with motor symptom laterality. These microstructural changes suggest underlying tissue atrophy or neuroinflammatory processes associated with PD. The study underscores the importance of the posterior putamen as a focal point for PD pathology and highlights the potential of localized gradient analysis in detecting subtle yet clinically significant brain changes. The new qMRI dataset provides valuable insights into PD pathology, potentially aiding in the development of more precise diagnostic tools and targeted therapies.

neuroscience↗

bioRxiv2023

Specification and survival of post-metamorphic branchiomeric neurons in the hindbrain of a non-vertebrate chordate.

Tunicates are the sister group to the vertebrates, yet most species have a life cycle split between swimming larva and sedentary adult phases. During metamorphosis, larval neurons are largely replaced by adult-specific ones. Yet the regulatory mechanisms underlying this neural replacement remain largely unknown. Using tissue-specific CRISPR/Cas9-mediated mutagenesis in the tunicate Ciona, we show that orthologs of conserved hindbrain and branchiomeric neuron regulatory factors Pax2/5/8 and Phox2 are required to specify the "Neck", a compartment of cells set aside in the larva to give rise to cranial motor neuron-like neurons in the adult. Using bulk and single-cell RNAseq analyses, we also characterize the transcriptome of the Neck downstream of Pax2/5/8. Surprisingly, we find that Neck-derived adult ciliomotor neurons begin to differentiate in the larva, contrary to the long-held assumption that the adult nervous system is formed only after settlement and the death of larval neurons during metamorphosis. Finally, we show that manipulating FGF signaling during the larval phase alters the patterning of the Neck and its derivatives. Suppression of FGF converts Neck cells into larval neurons that fail to survive metamorphosis, while prolonged FGF signaling promotes an adult neural stem cell-like fate instead.

developmental biology↗

bioRxiv2023

Ultra-high field fMRI of visual mental imagery in typical imagers and aphantasic individuals

Most of us effortlessly describe visual objects, whether seen or remembered. Yet, around 4% of people report congenital aphantasia: they struggle to visualize objects despite being able to describe their visual appearance. What neural mechanisms create this disparity between subjective experience and objective performance? Aphantasia can provide novel insights into conscious processing and awareness. We used ultra-high field 7T fMRI to establish the neural circuits involved in visual mental imagery and perception, and to elucidate the neural mechanisms associated with the processing of internally generated visual information in the absence of imagery experience in congenital aphantasia. Ten typical imagers and 10 aphantasic individuals performed imagery and perceptual tasks in five domains: object shape, object color, written words, faces, and spatial relationships. In typical imagers, imagery tasks activated left-hemisphere frontoparietal areas, the relevant domain-preferring areas in the ventral temporal cortex partly overlapping with the perceptual domain-preferring areas, and a domain-general area in the left fusiform gyrus (the Fusiform Imagery Node). The results were valid for each individual participant. In aphantasic individuals, imagery activated similar visual areas, but there was reduced functional connectivity between the Fusiform Imagery Node and frontoparietal areas. Our results unveil the domain-general and domain-specific circuits of visual mental imagery, their functional disorganization in aphantasia, and support the general hypothesis that conscious visual experience - whether perceived or imagined - depends on the integrated activity of high-level visual cortex and frontoparietal networks.

neuroscience↗

bioRxiv2023

Nf1 Deficiency Increases Mammary Collagen Deposition and Restricts Adipocyte Differentiation Before Tumor Formation

BACKGROUNDNeurofibromin, coded by the NF1 tumor suppressor gene, is the main negative regulator of the RAS pathway and is frequently mutated in various cancers. Women with Neurofibromatosis Type I (NF1) - a tumor predisposition syndrome caused by a germline NF1 mutation - have an increased risk of developing aggressive breast cancer with poorer prognosis. The mechanism by which NF1 mutations lead to breast cancer tumorigenesis is not well understood. Therefore, the objective of this work was to identify stromal alterations before tumor formation that result in the increased risk and poorer outcome seen among NF1 patients with breast cancer. METHODSTo accurately model the germline monoallelic NF1 mutations in NF1 patients, we utilized an Nf1-deficient rat model with accelerated mammary development before presenting with highly penetrant breast cancer. RESULTSWe identified increased collagen content in Nf1-deficient rat mammary glands before tumor formation that correlated with age of tumor onset. Additionally, gene expression analysis revealed that Nf1-deficient mature adipocytes in the rat mammary gland have increased collagen expression and shifted to a fibroblast and preadipocyte expression profile. This alteration in lineage commitment was also observed with in vitro differentiation, however, flow cytometry analysis did not show a change in mammary adipose-derived mesenchymal stem cell abundance. CONCLUSIONCollectively, these studies uncovered the previously undescribed role of Nf1 in mammary collagen deposition and regulating adipocyte differentiation. In addition to unraveling the mechanism of tumor formation, further investigation of adipocytes and collagen modifications in preneoplastic mammary glands will create a foundation for developing early detection strategies of breast cancer among NF1 patients. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/539442v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@d4aeeforg.highwire.dtl.DTLVardef@128d9a5org.highwire.dtl.DTLVardef@e8f9e0org.highwire.dtl.DTLVardef@16d0164_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

A molecularly defined and spatially resolved cell atlas of the whole mouse brain

In mammalian brains, tens of millions to billions of cells form complex interaction networks to enable a wide range of functions. The enormous diversity and intricate organization of cells in the brain have so far hindered our understanding of the molecular and cellular basis of its functions. Recent advances in spatially resolved single-cell transcriptomics have allowed systematic mapping of the spatial organization of molecularly defined cell types in complex tissues1-3. However, these approaches have only been applied to a few brain regions1-11 and a comprehensive cell atlas of the whole brain is still missing. Here, we imaged a panel of >1,100 genes in [~]8 million cells across the entire adult mouse brain using multiplexed error-robust fluorescence in situ hybridization (MERFISH)12 and performed spatially resolved, single-cell expression profiling at the whole-transcriptome scale by integrating MERFISH and single-cell RNA-sequencing (scRNA-seq) data. Using this approach, we generated a comprehensive cell atlas of >5,000 transcriptionally distinct cell clusters, belonging to [~]300 major cell types, in the whole mouse brain with high molecular and spatial resolution. Registration of the MERFISH images to the common coordinate framework (CCF) of the mouse brain further allowed systematic quantifications of the cell composition and organization in individual brain regions defined in the CCF. We further identified spatial modules characterized by distinct cell-type compositions and spatial gradients featuring gradual changes in the gene-expression profiles of cells. Finally, this high-resolution spatial map of cells, with a transcriptome-wide expression profile associated with each cell, allowed us to infer cell-type-specific interactions between several hundred pairs of molecularly defined cell types and predict potential molecular (ligand-receptor) basis and functional implications of these cell-cell interactions. These results provide rich insights into the molecular and cellular architecture of the brain and a valuable resource for future functional investigations of neural circuits and their dysfunction in diseases.

neuroscience↗

bioRxiv2023

Breast adipose tissue-derived extracellular vesicles from women with obesity stimulate mitochondrial-induced dysregulated tumor cell metabolism

Breast adipose tissue is an important contributor to the obesity-breast cancer link. Dysregulated cell metabolism is now an accepted hallmark of cancer. Extracellular vesicles (EVs) are nanosized particles containing selective cargo, such as miRNAs, that act locally or circulate to distant sites to modulate target cell functions. Here, we found that long-term education of breast cancer cells (MCF7, T47D) with EVs from breast adipose tissue of women who are overweight or obese (O-EVs) leads to sustained increased proliferative potential. RNA-Seq of O-EV-educated cells demonstrates increased expression of genes, such as ATP synthase and NADH: ubiquinone oxidoreductase, involved in oxidative phosphorylation. O-EVs increase respiratory complex protein expression, mitochondrial density, and mitochondrial respiration in tumor cells. Mitochondrial complex I inhibitor, metformin, reverses O-EV-induced cell proliferation. Several miRNAs, miR-155-5p, miR-10a-3p, and miR-30a-3p, which promote mitochondrial respiration and proliferation, are enriched in O-EVs relative to EVs from lean women. O-EV-induced proliferation and mitochondrial activity are associated with stimulation of the Akt/mTOR/P70S6K pathway, and are reversed upon silencing of P70S6K. This study reveals a new facet of the obesity-breast cancer link with human breast adipose tissue-derived EVs causing the metabolic reprogramming of ER+ breast cancer cells.

cancer biology↗

bioRxiv2023

Ultrasensitive detection of circulating LINE-1 ORF1p as a specific multi-cancer biomarker

Improved biomarkers are needed for early cancer detection, risk stratification, treatment selection, and monitoring treatment response. While proteins can be useful blood-based biomarkers, many have limited sensitivity or specificity for these applications. Long INterspersed Element-1 (LINE-1, L1) open reading frame 1 protein (ORF1p) is a transposable element protein overexpressed in carcinomas and high-risk precursors during carcinogenesis with negligible detectable expression in corresponding normal tissues, suggesting ORF1p could be a highly specific cancer biomarker. To explore the potential of ORF1p as a blood-based biomarker, we engineered ultrasensitive digital immunoassays that detect mid-attomolar (10-17 M) ORF1p concentrations in patient plasma samples across multiple cancers with high specificity. Plasma ORF1p shows promise for early detection of ovarian cancer, improves diagnostic performance in a multi-analyte panel, and provides early therapeutic response monitoring in gastric and esophageal cancers. Together, these observations nominate ORF1p as a multi-cancer biomarker with potential utility for disease detection and monitoring. Statement of SignificanceLINE-1 ORF1p transposon protein is pervasively expressed in many cancers and a highly specific biomarker of multiple common, lethal carcinomas and their high-risk precursors in tissue and blood. Ultrasensitive ORF1p assays from as little as 25 L plasma are novel, rapid, cost-effective tools in cancer detection and monitoring.

cancer biology↗

bioRxiv2022

Does the visual word form area split in bilingual readers? A millimeter-scale 7T fMRI study

In expert readers, a brain region known as the visual word form area (VWFA) is highly sensitive to written words, exhibiting a posterior-to-anterior gradient of increasing sensitivity to orthographic stimuli whose statistics match those of real words. Using high-resolution 7T fMRI, we ask whether, in bilingual readers, distinct cortical patches specialize for different languages. In 21 English-French bilinguals, unsmoothed 1.2 mm fMRI revealed that the VWFA is actually composed of several small cortical patches highly selective for reading, with a posterior-to-anterior word similarity gradient, but with near-complete overlap between the two languages. In 10 English-Chinese bilinguals, however, while most word-specific patches exhibited similar reading specificity and word-similarity gradients for reading in Chinese and English, additional patches responded specifically to Chinese writing and, surprisingly, to faces. Our results show that the acquisition of multiple writing systems can indeed tune the visual cortex differently in bilinguals, sometimes leading to the emergence of cortical patches specialized for a single language.

neuroscience↗

bioRxiv2022

Seeing speech: The cerebral substrate of tickertape synesthesia.

Reading acquisition is enabled by deep changes in the brains visual system and language areas, and in the links subtending their collaboration. Disruption of those plastic processes commonly results in developmental dyslexia. However, atypical development of reading mechanisms may occasionally result in ticker-tape synesthesia (TTS), a condition described by Francis Galton in 1883 wherein individuals "see mentally in print every word that is uttered (...) as from a long imaginary strip of paper". While reading is the bottom-up translation of letters into speech, TTS may be viewed as its opposite, the top-down translation of speech into internally visualized letters. In a series of functional MRI experiments, we studied MK, a man with TTS. We showed that a set of left-hemispheric areas were more active in MK than in controls during the perception of normal than reversed speech, including frontoparietal areas involved in speech processing, and the Visual Word Form Area, an occipitotemporal region subtending orthography. Those areas were identical to those involved in reading, supporting the construal of TTS as upended reading. Using dynamic causal modeling, we further showed that, parallel to reading, TTS induced by spoken words and pseudowords relied on top-down flow of information along distinct lexical and phonological routes, involving the middle temporal and supramarginal gyri, respectively. Future studies of TTS should shed new light on the neurodevelopmental mechanisms of reading acquisition, their variability and their disorders. Significance statementSome individuals, whenever they are hearing speech, see vividly in their minds eye the corresponding words in written form, as mental subtitles. This unusual condition, termed ticker-tape synesthesia (TTS), far from being purely anecdotal, actually touches on the core of the brain mechanisms of normal and impaired reading acquisition. Through 3 fMRI experiments, plus brain connectivity analyses, we propose an in-depth study of a single individual with such ticker-tape synesthesia. We propose that TTS, a situation in some sense symmetrical to developmental dyslexia, reflects an inverted flow of information through the reading system, such that speech is automatically translated into internally visualized letters. Future studies of TTS should shed new light on the neurodevelopmental mechanisms of reading acquisition.

neuroscience↗

bioRxiv2022

Axial encoding schematics of neural representations of 3D space in freely navigating goldfish

Navigation is one of the most fundamental cognitive skills for the survival of fish, the largest vertebrate class, and almost all other animal classes. A critical component of the neural basis of navigation is the encoding of space in the activity of single neurons. To study this basic cognitive component in fish, we recorded the activity of single neurons in the central area of the goldfish telencephalon while the fish were freely navigating in a 3D water tank. We found neurons with firing patterns that gradually increased or decreased along spatial axes distributed in all directions. Some of these cells exhibited beta rhythm oscillations. This type of axial coding for spatial representation in the brains of fish is unique among space encoding cells in vertebrates and provides insights into spatial cognition in this lineage.

neuroscience↗

bioRxiv2022

Numerical discrimination in Drosophila melanogaster

Sensitivity to numbers is a crucial and evolutionarily conserved cognitive ability. The lack of experimental models amenable to systematic genetic and neural manipulation has precluded discovering circuits required for numerical cognition. Here, we demonstrate that in a two-choice task Drosophila fruit flies spontaneously prefer sets containing more objects. This preference is determined by the ratio between the two numerical quantities tested, a characteristic signature of numerical cognition across species. Individual flies maintained their numerical choice over consecutive days. Using a numerical visual conditioning paradigm, we found that flies are capable of associating sucrose with numerical quantities and can be trained to reverse their spontaneous preference for large quantities. Finally, we show that silencing LC11 neurons reduces the preference for more objects, thus identifying a neuronal substrate for numerical cognition in invertebrates. This discovery paves the way for the systematic analysis of the behavioral and neural mechanisms underlying sensitivity to numerosity.

neuroscience↗

bioRxiv2021

MEK1/2 inhibition transiently alters the tumor immune microenvironment to enhance immunotherapy efficacy against head and neck cancer

Although the mitogen-activated protein kinases (MAPK) pathway is hyperactive in head and neck cancer (HNC), inhibition of MEK1/2 in HNC patients has not shown clinically meaningful activity. Using pre-clinical HNC models, we demonstrated that treatment with the MEK1/2 blocker trametinib delays HNC initiation and progression by reducing tumor cell proliferation and enhancing the anti-tumor immunity of CD8+ T cells. Further activation of CD8+ T cells by supplementation with anti-programmed death-1 (PD-1) antibody eliminated tumors and induced an immune memory in the cured mice. Mechanistically, an early response to trametinib treatment sensitized tumors to PD-1-supplementation by attenuating the expression of tumor-derived colony-stimulating factor-1 (CSF-1), which reduced the abundance of two CSF-1R+CD11c+ myeloid-derived suppressor cell (MDSC) populations in the tumor microenvironment (TME). In contrast, prolonged treatment with trametinib abolished the anti-tumor activity of PD-1, because tumor cells undergoing the epithelial to mesenchymal transition (EMT) in response to trametinib restored CSF-1 expression and re-created an immune-suppressive TME. These findings provide the rationale for testing the trametinib/PD-1 combination in HNC and highlight the importance of sensitizing tumors to immunotherapies by using targeted therapies to interfere with the host-tumor interaction. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/457244v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1c65286org.highwire.dtl.DTLVardef@1541becorg.highwire.dtl.DTLVardef@f557f3org.highwire.dtl.DTLVardef@16134dc_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

cancer biology↗

bioRxiv2021

Simulating the emergence of the Visual Word Form Area: Recycling a convolutional neural network for reading

The visual word form area (VWFA) is a region of human inferotemporal cortex that emerges at a fixed location in occipitotemporal cortex during reading acquisition, and systematically responds to written words in literate individuals. According to the neuronal recycling hypothesis, this region arises through the repurposing, for letter recognition, of a subpart of the ventral visual pathway initially involved in face and object recognition. Furthermore, according to the biased connectivity hypothesis, its universal localization is due to pre-existing connections from this subregion to areas involved in spoken language processing. Here, we evaluate those hypotheses in an explicit computational model. We trained a deep convolutional neural network of the ventral visual pathway, first to categorize pictures, and then to recognize written words invariantly for case, font and size. We show that the model can account for many properties of the VWFA, particularly when a subset of units possesses a biased connectivity to word output units. The network develops a sparse, invariant representation of written words, based on a restricted set of reading-selective units. Their activation mimics several properties of the VWFA, and their lesioning causes a reading-specific deficit. Our simulation fleshes out the neuronal recycling hypothesis, and make several testable predictions concerning the neural code for written words.

neuroscience↗

bioRxiv2020

Statistical learning occurs during practice while high-order rule learning during rest period

Knowing when the brain learns is crucial for both the comprehension of memory formation and consolidation, and for developing new training and neurorehabilitation strategies in healthy and patient populations. Recently, a rapid form of offline learning developing during short rest periods has been shown to account for most of procedural learning, leading to the hypothesis that the brain mainly learns during rest between practice periods. Nonetheless, procedural learning has several subcomponents not disentangled in previous studies investigating learning dynamics, such as acquiring the statistical regularities of the task, or else the high-order rules that regulate its organization. Here, we analyzed 506 behavioral sessions of implicit visuomotor deterministic and probabilistic sequence learning tasks, allowing the distinction between general skill learning, statistical learning and high-order rule learning. Our results show that the temporal dynamics of apparently simultaneous learning processes differ. While general skill and high-order rule learning are acquired offline, statistical learning is evidenced online. These findings open new avenues on the short-scale temporal dynamics of learning and memory consolidation and reveal a fundamental distinction between statistical and high-order rule learning, the former benefiting from online evidence accumulation and the latter requiring short rest periods for rapid consolidation.

neuroscience↗

bioRxiv2020

Color naming and categorization depend on distinct functional brain networks

Naming a color can be understood as an act of categorization, i.e. identifying it as a member of category of colors that are referred to by the same name. But are naming and categorization equivalent cognitive processes, and consequently rely on same neural substrates? Here, we used task and resting-state fMRI, as well as behavioral measures to identify functional brain networks that modulated naming and categorization of colors. Color naming and categorization response times were modulated by different resting state connectivity networks spanning from the color-sensitive regions in the ventro-occipital cortex. Color naming correlated with the connectivity between the left posterior color region, the left medial temporal gyrus, and the left angular gyrus; whereas color categorization involved the connectivity between the bilateral posterior color regions, the left frontal, right temporal and bilateral parietal areas. The networks supporting naming and categorization did not overlap, suggesting that the two processes rely on different neural mechanisms. SignificanceWhen we name a color, we also identify it as a member of a color category, e.g. blue or yellow. Are neural processes underlying color categorization equivalent to those of color naming? Here, we address this question by measuring how individual differences in color categorization and naming response times relate to the strength of functional connections in the brain. Color naming speed correlated with left-hemispheric connectivity between the color-sensitive visual regions and the anterior temporal lobe. Color categorization speed was modulated by a different brain network, encompassing bilateral color-sensitive visual areas, and high-level executive and semantic regions. Thus, color categorization and naming performance involved distinct, non-overlapping brain networks, suggesting that the two processes depend on different neural mechanisms.

neuroscience↗

bioRxiv2019

Lymph node follicle formation and vaccination responses reconstituted in vitro in a human Organ Chip

Lymphoid follicles (LFs) are responsible for generation of adaptive immune responses in secondary lymphoid organs and form ectopically during chronic inflammation. A human model of LF formation would provide a tool to understand LF development and an alternative to non-human primate models for preclinical evaluation of vaccines. Here, we show that primary human blood B- and T-lymphocytes autonomously assemble into ectopic LFs when cultured in a three-dimensional (3D) extracellular matrix gel within an organ-on-a-chip microfluidic device. Dynamic fluid flow is required for LF formation and prevention of lymphocyte autoactivation. These germinal center-like LFs contain B cells expressing Activation-Induced Cytidine Deaminase and exhibit plasma cell (PC) differentiation upon activation. To explore their utility for vaccine testing, autologous monocyte-derived dendritic cells were integrated into LF Chips. The human LF chips demonstrated improved antibody responses to split virion influenza vaccination compared to 2D cultures, which were enhanced by addition of a squalene-in-water emulsion adjuvant, and this was accompanied by increases in LF size and number. When inoculated with commercial influenza vaccine, PC formation and production of anti-hemagglutinin IgG were observed, as well as secretion of cytokines similar to those observed in vaccinated humans over clinically relevant timescales.

immunology↗