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Biology subjects

Jolly, A.

Publications and source records attributed to Jolly, A..

At least 19 recordsLinked to original sources

Monocytes promote intraepithelial infiltration of effector memory CD8+ T cells in regressing tumors

Despite the clinical success of cancer immunotherapies, the cellular interactions driving tumor regression remain incompletely understood. Here, we investigated the dynamic remodeling of the tumor immune microenvironment during regression of transplanted PyMT mammary tumors following STING agonist treatment. Using scRNA-seq of sorted CD8+ T cells and myeloid cells, combined with imaging approaches, we identified major changes in both lymphoid and myeloid compartments during tumor regression. Regressing tumors showed a transient accumulation of Ly6Chi monocyte populations associated with a decline in macrophage subsets, while effector and memory CD8+ T-cell populations increased at the expense of exhausted T cells. Interaction analyses predicted enhanced chemotactic and adhesion interactions between CXCL9+ Ly6Chi monocytes and effector CD8+ T cells. Consistently, dynamic imaging revealed increased CD8+ T-cell motility and infiltration into tumor cores following treatment. In particular, CXCR6+ effector CD8+ T cells transiently accumulated within tumor islets during regression before relocalizing to stromal regions. Together, these findings reveal a coordinated spatiotemporal remodeling of myeloid and CD8+ T-cell populations during immunotherapy-induced tumor regression and highlight cooperative interactions that may promote durable anti-tumor immunity.

immunology↗

Cortical gray matter density at age five associated with preceding early longitudinal language profiles: A Voxel-based morphometry analysis of the FinnBrain Birth Cohort Study

Previous studies exploring the connection between early language development and brain anatomy have shown that cortical areas relating to individual differences in language skills are diverse and vary depending on the age of child. However, due to lack of large longitudinal samples, current literature is limited in answering the extent to which individual differences in language development prior to school age are reflected in areas of the cortex. To fill this gap, we compared gray matter density between participants that belonged to different longitudinally defined language profiles from 14 months to five years of age in a large population-based sample. Participants were 166 children from the FinnBrain Birth Cohort Study who had longitudinal language data from 14 months to five years of age and magnetic resonance imaging data at five years of age. Three groups of language development were used as per our prior study: persistent low, stable average, and stable high. Voxel-based morphometry metrics were calculated using SPM12 and the three language profile groups were compared to one another. Covariates included sex and age at brain scan. The statistics were thresholded at p < 0.01 and false discovery rate corrected at the cluster level. Of the three longitudinal language profiles, the stable high group had higher gray matter density than the persistent low group in the right superior frontal gyrus. No differences were found between the stable average and stable high groups, nor persistent low and stable average groups. The identified superior frontal cortical area belongs to executive functions neural network. This finding adds to the cumulating evidence that individual differences in language development are reflected in growth of gray matter supporting general processing ability rather than specialized language regions. The results suggest that cognitive development and early language development are linked through shared principles of neural growth, identifiable already at age five. Key pointsO_LIAn association between early language development from 14 months to five years of age and gray matter density differences of the right superior frontal gyrus was found at the age of five years. Children following the strongest language trajectory were more likely to exhibit higher gray matter density of the right superior frontal gyrus than children following the weakest trajectory. C_LIO_LIAs the superior frontal gyrus is part of executive functions network, we propose that individual differences in early language development are more defined by general learning mechanisms supported by those networks, rather than language specific pathways. C_LI

neuroscience↗

Functional connectome harmonics capture early brain organization and maturity in neonates

The functional organization of the human brain is established early, yet the ontogeny of its large-scale functional gradients remains unclear. Using resting-state fMRI data from 714 neonates in the Developing Human Connectome Project, we mapped neonatal brain gradients via functional connectome harmonics (FCH). We identified adult-like sensory-to-multimodal and cognitive gradient patterns present at birth. Applying three FCH-derived metrics--entropy, power, and energy--we found that power and energy were higher in term-born compared to preterm neonates, while entropy was elevated in preterms. These metrics predicted up to ~30% of postmenstrual age, indicating their biological relevance. Our findings reveal that the neonatal brain possesses a robust gradient architecture underpinning early functional organization, offering novel biomarkers for assessing brain maturity and the impact of prematurity on neurodevelopment.

neuroscience↗

Functional connectome harmonics and dynamic connectivity maps of the preadolescent brain

The maturation of large-scale functional brain networks during preadolescence underpins critical cognitive and behavioral development. However, the spatial and temporal organization of these networks in this age group remains incompletely characterized. Here we applied Functional Connectome Harmonics (FCH) and Leading Eigenvector Dynamics Analysis (LEiDA) to resting-state fMRI data from over 11,000 children aged 9-10 years in the ABCD Study. FCH revealed hierarchical spatial gradients spanning cortical and subcortical regions, while LEiDA identified recurrent dynamic brain states aligned with canonical intrinsic connectivity networks. Linking these spatial and temporal components, we established a low-dimensional harmonic scaffold constraining brain dynamics during this developmental window. These findings provide a large-scale spatiotemporal reference framework of preadolescent functional brain organization, offering a foundation for characterizing neurodevelopmental benchmarks and early neural markers relevant to adolescent mental health.

neuroscience↗

skiftiTools: An R package for reading, writing, analysing, and visualising, tract-based spatial statistics (TBSS) derived diffusion MR images

skiftiTools processes three- and four-dimensional neuroimaging data, facilitating advanced statistical modelling with voxelwise data in any software of choice. Tract-Based Spatial Statistics (TBSS) is a conventionally used tool to make statistical calculations in voxel space for brain imaging data. While pre-existing software packages provide support for general linear model based statistics, there is a clear need for more sophisticated modeling. skiftiTools writes subject-per-volume NIfTI files as tab-separated value ASCII files, which are easily readable by most commonly used statistical tools such as R language (RStudio), SPSS, SAS, and GraphPad Prism. This facilitates a wide range of voxel-level statistical analyses from TBSS data, including estimation of standardised effect sizes, clustering, dimensionality reduction, non-linear and machine learning predictive modelling, which we showcase in this article using FinnBrain and developing Human Connectome Project diffusion MRI data. After statistical processing, the resulting ASCII data can then be read again for visualization. The package supports NIfTI image format, tab-separated ASCII format, and its own stand-alone format for efficient disk usage. It is open source (https://github.com/haanme/skiftiTools), built on R-language and has easy installation from Rs CRAN package repository. In addition, we provide basic functions available in Docker containers for further platform independence. HighlightsO_LIThe skiftiTools R package is an open-source, user-friendly interface for analysing voxelwise diffusion tensor imaging (DTI) data following tract-based spatial statistics (TBSS) processing C_LIO_LIIt supports reading, writing, visualization, mathematical operations, and data manipulation and thus allows comprehensive conventional and advanced statistics, including machine learning C_LIO_LIskiftiTools bridges a critical gap between statistical tools in R and voxelwise neuroimaging data - including comparable means to perform multiple comparison corrections and much needed possibility to use non-linear statistics C_LI

neuroscience↗

Differentiation hierarchy in adult B cell acute lymphoblastic leukemia at clonal resolution

While a differentiation hierarchy with leukemia-initiating stem cells (LICs) at the apex is well documented for acute myeloid leukemia, the existence of LICs and their trajectories in B cell acute lymphoblastic leukemia (B-ALL) are debated. B-ALL is a malignant disease displaying considerable phenotypical and functional heterogeneity, yet the underlying cellular organization remains largely elusive. This study aims to investigate the hierarchical landscape of B-ALL by combining barcoding and multiome single cell data to unveil the differentiation architecture and temporal dynamics of leukemic differentiation at clonal and single cell resolution in vivo. Single-cell transcriptome and AbSeq analysis of lentiviral barcoded and transplanted patient-derived B-ALL cells revealed interconnected subpopulations, which could be prospectively isolated via surface markers and exhibited distinct leukemogenicity. Barcode tracking demonstrated the ability of cells to differentiate from a source cluster into differentiated progeny. Using machine learning we identified expression patterns predicting their differentiation potential of each barcoded cell within the immature cell compartment. To determine the dynamical properties of clones, we have designed a mathematical model that simulates the development of these subpopulations from a clonally diverse stem cell compartment. The model confirmed the most likely cluster of origin, supporting our functional data, and revealed the variability in dynamical properties between clones, while largely excluding plasticity. Hence, our work demonstrates a unidirectional differentiation in B-ALL with an immature population exhibiting a high leukemogenic potential. Key pointsO_LIA differentiation hierarchy with distinct leukemogenesis potential in B-ALL is demonstrated via clonal tracing and mathematical modeling. C_LIO_LIClonal differentiation behavior, while heterogeneous, is cell intrinsically controlled and predictable, yet independent from expansion. C_LI

cancer biology↗

Structural Brain Correlates of Speech Disfluency in Early Childhood: A Dimensional Analysis in a Non-Clinical Cohort

Most neuroimaging studies of speech disfluency have compared individuals who stutter with fluent controls. However, treating speech disfluency as a continuous, dimensional trait offers new insights into the neural basis of fluency during early childhood. This study aimed to investigate whether naturally occurring variation in speech disfluency is associated with grey matter structure in a non-clinical, population-based sample of 5-year-old children. The study included 120 participants (65M, 55F) from the FinnBrain Birth Cohort study. Speech disfluency was evaluated as a continuous measure from audiovisual speech samples, with transcription and analysis conducted using the SALT software. Ambrose & Yairi (1999) classification system was used to categorize speech disfluencies into stuttering-like (SLD) and other disfluency types. T1-weighted images obtained through magnetic resonance imaging were analyzed using voxel-based morphometry (VBM) with the CAT12 toolbox and complemented by surface-based morphometry with FreeSurfer. Whole-brain statistical analysis was employed to examine the association between grey matter metrics and speech disfluency. We found that VBM-derived proportional grey matter volume in the left middle frontal gyrus, left posterior cerebellum, and right superior frontal gyrus was positively associated with speech disfluency, specifically SLD, in children (p <.001; p=.002; p <.001, FDR corrected). No significant associations were found for cortical thickness or surface area. Additionally, no notable sex differences were observed. Our findings suggest that speech disfluency in early childhood is linked to localized structural differences in regions supporting motor planning and cognitive control, without broader changes in cortical thickness or surface area. Importantly, similar brain regions have been implicated in studies comparing children who stutter to those who do not, suggesting that normal variation in disfluency captures meaningful neurobiological differences even in non-clinical populations. This supports the value of treating speech disfluency as a spectrum and underscores the importance of longitudinal, multimodal research to clarify how these structural features evolve and influence later fluency outcomes.

neuroscience↗

Neonatal White Matter Microstructure Predicts Infant Attention Disengagement from Fearful Faces

Infants develop an attentional bias towards faces already at birth, with further specification towards fearful faces emerging at 6 months and diminishing around 11 months of age. However, the neurobiological origins of attentional bias to fear are still poorly understood. To understand the neural structures underlying perception of facial expressions, the current study utilized newborn diffusion magnetic resonance images (N = 86; 41 females; = 27.15 days) and eye tracking from the same infants at 8-months ( = 8.75 months) as a behavioural measure. An overlap paradigm was used to measure attention disengagement from fearful, happy, and neutral faces. Tract-based spatial statistics revealed that higher white matter (WM) mean diffusivity in widespread regions across the brain was associated with lower attention disengagement from fearful faces. The same association was found with happy faces but was limited to only the splenium of the corpus callosum and sensorimotor pathways. Variance in neonatal WM microstructure may reflect individual differences in growth that is related to attentional bias development later in infancy.

neuroscience↗

Pre- and postnatal maternal depressive symptoms associate with localconnectivity of the left amygdala in 5-year-olds.

BackgroundMaternal depressive symptoms can influence brain development in offspring, prenatally through intrauterine programming, and postnatally through caregiving related mother-child interaction. MethodsThe participants were 5-year-old mother-child dyads from the FinnBrain Birth Cohort Study (N = 68; 28 boys, 40 girls). Maternal depressive symptoms were assessed with the Edinburgh Postnatal Depression Scale (EPDS) at gestational week 24, 3 months, 6 months, and 12 months postnatal. Childrens brain imaging data were acquired with task-free functional magnetic resonance imaging (fMRI) at the age of 5 years in 7 min scans while watching the Inscapes movie. The derived brain metrics included whole brain regional homogeneity (ReHo) and seed-based connectivity maps of the bilateral amygdalae. ResultsWe found that maternal depressive symptoms were positively associated with ReHo values of the left amygdala. The association was highly localised and strongest with the maternal depressive symptoms at three months postnatal. Seed-based connectivity analysis did not reveal associations between distal connectivity of the left amygdala region and maternal depressive symptoms. ConclusionsThese results suggest that maternal depressive symptoms soon after birth may influence offsprings neurodevelopment in the local functional coherence in the left amygdala. They underline the potential relevance of postnatal maternal distress exposure on neurodevelopment that has received much less attention than prenatal exposures. These results offer a possible thus far understudied pathway of intergenerational effects of perinatal depression that should be further explored in future studies.

neuroscience↗

Studying the cellular basis of small bowel enteropathy using high-parameter flow cytometry in mouse models of primary antibody deficiency

BackgroundPrimary immunodeficiencies are heritable defects in immune system function. Antibody deficiency is the most common form of primary immunodeficiency in humans, can be caused by abnormalities in both the development and activation of B cells, and may result from B-cell-intrinsic defects or defective responses by other cells relevant to humoral immunity. Inflammatory gastrointestinal complications are commonly observed in antibody-deficient patients, but the underlying immune mechanisms driving this are largely undefined. MethodsIn this study, several mouse strains reflecting a spectrum of primary antibody deficiency (IgA-/-, Aicda-/-, CD19-/- and JH-/-) were used to generate a functional small-bowel-specific cellular atlas using a novel high-parameter flow cytometry approach that allows for the enumeration of 59 unique cell subsets. Using this cellular atlas, we generated a direct and quantifiable estimate of immune dysregulation. This estimate was then used to identify specific immune factors most predictive of the severity of inflammatory disease of the small bowel (small bowel enteropathy). ResultsResults from our experiments indicate that the severity of primary antibody deficiency positively correlates with the degree of immune dysregulation that can be expected to develop in an individual. In the SI of mice, immune dysregulation is primarily explained by defective homeostatic responses in T cell and invariant natural killer-like T (iNKT) cell subsets. These defects are strongly correlated with abnormalities in the balance between protein (MHCII-mediated) versus lipid (CD1d-mediated) antigen presentation by intestinal epithelial cells (IECs) and intestinal stem cells (ISCs), respectively. ConclusionsMultivariate statistical approaches can be used to obtain quantifiable estimates of immune dysregulation based on high-parameter flow cytometry readouts of immune function. Using one such estimate, we reveal a previously unrecognized tradeoff between iNKT cell activation and type 1 immunity that underlies disease in the small bowel. The balance between protein/lipid antigen presentation by ISCs may play a crucial role in regulating this balance and thereby suppressing inflammatory disease in the small bowel.

immunology↗

The FinnBrain Multimodal Neonatal Template and Atlas Collection: T1, T2, and DTI brain templates, and accompanying cortical and subcortical atlases

The accurate processing of neonatal and infant brain MRI data is crucially important for developmental neuroscience, but presents challenges that child and adult data do not. Tissue segmentation and image coregistration accuracy can be improved by optimizing template images and / or related segmentation procedures. Here, we describe the construction of the FinnBrain Neonate (FBN-125) template; a multi-contrast template with T1- and T2-weighted as well as diffusion tensor imaging derived fractional anisotropy and mean diffusivity images. The template is symmetric and aligned to the Talairach-like MNI 152 template and has high spatial resolution (0.5 mm3). In addition, we provide atlas labels, constructed from manual segmentations, for cortical grey matter, white matter, cerebrospinal fluid, brainstem, and cerebellum as well as the bilateral hippocampi, amygdalae, caudate nuclei, putamina, globi pallidi, and thalami. We provide this multi-contrast template along with the labelled atlases for the use of the neuroscience community in the hope that it will prove useful in advancing developmental neuroscience, for example, by helping to achieve reliable means for spatial normalization and measures of neonate brain structure via automated computational methods. Additionally, we provide standard co-registration files that will enable investigators to reliably transform their statistical maps to the adult MNI space, which has the potential to improve the consistency and comparability of neonatal studies or the use of adult MNI space atlases in neonatal neuroimaging.

neuroscience↗

Design and validation of a high-throughput in vitro model of the outer Blood-Retinal Barrier (oBRB) using the Curiochips Microphysiological System

Numerous diseases, including AMD (age-related macular degeneration), arise from the blood-retinal barrier and blood vessel abnormalities in the eye; unfortunately, there is a lack of reliable in-vitro models for their systematic study. This study describes a high-throughput microphysiological system (MPS) designed to model the outer Blood-Retinal Barrier (oBRB). The MPS platform is engineered to integrate seamlessly with high-content screening technologies, utilizing a design with a single oBRB model incorporating RPE (retina pigment epithelial cells) and endothelial cell co-culture to fit within a single 96-well. Arranged in the standard 96-well plate format, the platform allows high-throughput assessment of barrier integrity through 3D confocal imaging (ZO-1 staining), Trans Epithelial Electrical Resistance (TEER), and permeability measurements. The oBRB model enables the investigation of crosstalk among different cell types in co-culture. This includes assessing changes in the barrier integrity of the Retinal Pigment Epithelium (RPE) monolayer and investigating neovascularization events resulting from endothelial cell remodeling. The platform is positioned for utility in drug discovery and development efforts targeting diseases involving oBRB damage and choroidal neovascularization, such as age-related macular degeneration (AMD).

bioengineering↗

An outbreak of SARS-CoV-2 in big hairy armadillos (Chaetophractus villosus) associated with Gamma variant in Argentina three months after being undetectable in humans

The present pandemic produced by SARS-CoV-2 and its variants represents an example of the one health concept in which humans and animals are components of the same epidemiologic chain. Animal reservoirs of these viruses are thus the focus of surveillance programs to monitor their circulation and evolution in potentially new hosts and reservoirs. In this work, we report the detection of SARS-CoV-2 Gamma variant infection in four specimens of Chaetophractus villosus (big hairy armadillo/armadillo peludo) in Argentina. In addition to the finding of a new wildlife species susceptible to SARS-CoV-2 infection, the identification of the Gamma variant three months after its last detection in humans is a noteworthy result, raising the question of potential unidentified viral reservoirs.

microbiology↗

Multi-omics comparison of malignant and normal uveal melanocytes reveals novel molecular features of uveal melanoma.

Uveal Melanoma (UM) is a rare cancer resulting from transformation of melanocytes residing in the uveal tract. Integrative analysis has identified four molecular and clinical subsets in UM. To improve our molecular understanding of UM we performed extensive multi-omics characterization comparing two aggressive UM patient-derived xenograft models with normal choroidal melanocytes, including DNA optical mapping, specific histone modifications, and DNA topology analysis by Hi-C. Our gene expression and cytogenetic analyses suggest that genomic instability is a hallmark of UM. We also identified a recurrent deletion in the BAP1 promoter resulting in loss of expression and associated with high risk of metastases in UM patients. Hi-C revealed chromatin topology changes associated with up-regulation of PRAME, an independent prognostic biomarker in UM and potential therapeutic target. Our findings illustrate how multi-omics approaches can improve the understanding of tumorigenesis and reveals two novel mechanisms of gene expression dysregulation in UM.

genomics↗

Interferon regulates stem cell output via post-transcriptional repression of Sox2 independent of its antiviral function in the brain

Stem cells show intrinsic interferon signalling, which protects them from viral infections at all ages. In the ageing brain, interferon signalling in stem cells also reduces their ability to activate. Whether these functions are linked and at what time interferons start taking on a role in stem cell functioning is unknown. Additionally, the molecular link between interferons and activation in neural stem cells and how this relates to productivity is not well understood. Here we combine single-cell transcriptomics, RiboSeq and animal models of interferon to show that this pathway is important for proper stem cell function at all ages. Interferon orchestrates cell cycle and mTOR activity to post-transcriptionally repress Sox2 and drive the exit from stem cell activation. The interferon response then decreases in the subsequent maturation states. Mathematical simulations indicate that this regulation is beneficial for the young and harmful for the old brain. Our study establishes molecular mechanisms of interferon in stem cells and interferons as genuine regulators of stem cell homeostasis and a potential therapeutic target to repair the ageing brain.

neuroscience↗

CycleFlow quantifies cell-cycle heterogeneity in vivo

While the average cell-cycle length in a cell population can be derived from pulse-chase experiments, proliferative heterogeneity has been difficult to quantify. Here we describe CO_SCPLOWYCLEC_SCPLOWFO_SCPLOWLOWC_SCPLOW, a broadly applicable method that applies Bayesian inference to combined measurements of EdU incorporation and DNA content. CO_SCPLOWYCLEC_SCPLOWFO_SCPLOWLOWC_SCPLOW accurately quantifies the fraction of proliferating versus quiescent cells and the durations of cell-cycle phases of the proliferating cells in vitro and in vivo.

cell biology↗

Transcription factors involved in stem cell maintenance are downstream of Slug/Snail2 and repressed by TGF-β in bronchial epithelial progenitors from Chronic Obstructive Pulmonary Disease

Patients with COPD have many anomalies in their airway epithelium, and their basal stem/progenitor cells show a decrease in self-renewal and differentiation potential. The objective of this study was to identify deregulations in the genetic program of COPD bronchial basal stem/progenitor cells that could account for their exhaustion. TGF-{beta} is found at higher levels in the lungs of COPD subjects. It has been shown to play a role in stem/progenitor cell fate and also to regulate the expression of the EMT-inducing transcription factor Slug/Snail2. In contrast to other transcription factors of the Snail family, Slug is highly expressed in basal progenitor cells, the adult stem/progenitors of human airway epithelium. We aimed at identifying genes downstream of Slug that respond to TGF-{beta}, and whose expression is deregulated in COPD airway basal stem/progenitor cells, and could account for the decrease in count and functional ability of these cells observed in COPD. For this, we knocked down Slug in primary bronchial basal progenitor cells from COPD and normal subjects and, among the genes downstream of Slug, we selected those responding to TGF-{beta} and differentiation. We identified 5 genes coding for transcription factors involved in stem cell maintenance that are repressed downstream of Slug and by TGF-{beta} in COPD but not normal basal progenitor cells. Our results bring a molecular perspective to the exhaustion of airway basal stem/progenitor cells observed in COPD by revealing that stem cell maintenance genes are repressed in these cells, with TGF-{beta} and Slug being involved in this deregulation.

genomics↗

Slug/Snail2 is involved in the repression of proliferation genes by TGF-β in bronchial epithelial progenitor cells and is deregulated in abnormal epithelium

Slug/Snail2 belongs to the Epithelial-Mesenchymal Transition (EMT)-inducing transcription factors involved in development and diseases. Slug is expressed in adult stem/progenitor cells of several epithelia, making it unique among these transcription factors. To investigate Slug role in human bronchial epithelium progenitors, we studied primary bronchial basal/progenitor cells in an air-liquid interface culture system that allows regenerating a bronchial epithelium. To identify Slug downstream genes we knocked down Slug in basal/progenitor cells from normal subjects and subjects with COPD, a respiratory disease presenting anomalies in the bronchial epithelium and high levels of TGF-{beta} in the lungs. We show that normal and COPD bronchial basal/progenitors, even when treated with TGF-{beta}, express both epithelial and mesenchymal markers, and that the epithelial marker E-cadherin is not a target of Slug and, moreover, positively correlates with Slug. We reveal that Slug downstream genes responding to both differentiation and TGF-{beta} are different in normal and COPD progenitors, with in particular a set of proliferation-related genes that are among the genes repressed downstream of Slug in normal but not COPD. In COPD progenitors at the onset of differentiation in presence of TGF-{beta}, we show that there is positive correlations between the effect of differentiation and TGF-{beta} on proliferation-related genes and on Slug protein, and that their expression levels are higher than in normal cells. As well, the expression of Smad3 and {beta}-Catenin, two molecules from TGF-{beta} signaling pathways, are higher in COPD progenitors, and our results indicate that proliferation-related genes and Slug protein are increased by different TGF-{beta}-induced mechanisms. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/674127v2_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@524a15org.highwire.dtl.DTLVardef@7dd1e5org.highwire.dtl.DTLVardef@5f3798org.highwire.dtl.DTLVardef@13ae179_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗