Biology subjects

Fasolino, M.

Publications and source records attributed to Fasolino, M..

8 recordsLinked to original sources

bioRxiv2024

Impact of intragenic NRXN1 deletions on early cortical development

BackgroundDeletions in NRXN1 are strongly associated with neurodevelopmental and psychiatric conditions. While exonic deletions are well-studied, intragenic deletions, particularly in intron 5, are less understood and generally consider benign. Recent studies show exonic deletions impact isoform diversity during neurodevelopment, affecting neurogenesis and neuronal function. However, whether intragenic deletions impact isoform expression and neurodevelopment remains underexplored. MethodsWe used hiPSCs from typically developing individuals (control) and those with NRXN1 intron 5 deletions to study neurodevelopment. HiPSCs were differentiated towards a cortical fate, with NRXN1 isoform expression, molecular differences, and neuronal morphology examined. ResultsWe observed distinct NRXN1 isoform expression dynamics during early neurodevelopment, with two expression peaks post-neuronal induction and NRXN1{beta} being most highly expressed. Both NRXN1 deletion and control lines showed similar acquisition of regional and cell fate identity, but significant differences in NRXN1 isoform expression were observed between deletion and control lines, and between deletion lines. RNA sequencing revealed genotype-dependent alterations, particularly in pathways related to synaptic function and neuronal morphology. Consistent with these findings, NRXN1 deletion lines exhibited altered dendrite outgrowth, with variations between deletion lines. ConclusionsOur results indicate a potential role for intron 5 in controlling NRXN1 isoform expression during neurodevelopment. Alterations in gene expression profiles, correlated with morphological changes, suggest a role for NRXN1 isoforms in shaping dendritic morphology. Molecular and cellular differences observed between lines with identical intronic deletions suggest that additional factors, such as genetic background or biological sex, may also play an important role in these phenotypes. Collectively, these findings indicate that NRXN1 intronic deletions are not benign, influencing isoform expression, cellular phenotypes, and neurodevelopment.

neuroscience↗

bioRxiv2024

Aberrant TNF signaling in pancreatic lymph nodes of patients with Type 1 Diabetes

The therapeutic landscape for Type 1 Diabetes (T1D) is rapidly changing as ongoing clinical trials aim to delay beta-cell loss by inhibiting proinflammatory cytokines. However, the precise timing and cellular contexts of cytokine dysregulation remains unknown. We generated the largest existing measurement of gene expression and chromatin accessibility in [~]1 million immune cells from the pancreatic lymph nodes and spleens of 34 T1D and non-diabetic organ donors. Our study revealed heightened gene activity of the tumor necrosis factor (TNF) pathway and subsequent chromatin remodeling in central memory CD4+ T cells residing in the pancreatic lymph nodes of T1D and non-diabetic islet-autoantibody positive donors. These findings, validated in mice, offer a mechanism underlying the efficacy of TNF inhibitors, currently undergoing clinical trials to delay T1D onset.

immunology↗

bioRxiv2024

Sleep and Activity Patterns in Autism Spectrum Disorder

BackgroundAutism spectrum disorder (ASD) is a highly heritable and heterogeneous neurodevelopmental disorder characterized by impaired social interactions, repetitive behaviors, and a wide range of comorbidities. Between 44-83% of autistic individuals report sleep disturbances, which may share an underlying neurodevelopmental basis with ASD. MethodsWe recruited 382 ASD individuals and 223 of their family members to obtain quantitative ASD-related traits and wearable device-based accelerometer data spanning three consecutive weeks. An unbiased approach identifying traits associated with ASD was achieved by applying the elastic net machine learning algorithm with five-fold cross-validation on 6,878 days of data. The relationship between sleep and physical activity traits was examined through linear mixed-effects regressions using each night of data. ResultsThis analysis yielded 59 out of 242 actimetry measures associated with ASD status in the training set, which were validated in a test set (AUC: 0.777). For several of these traits (e.g. total light physical activity), the day-to-day variability, in addition to the mean, was associated with ASD. Individuals with ASD were found to have a stronger correlation between physical activity and sleep, where less physical activity decreased their sleep more significantly than that of their non-ASD relatives. ConclusionsThe average duration of sleep/physical activity and the variation in the average duration of sleep/physical activity strongly predict ASD status. Physical activity measures were correlated with sleep quality, traits, and regularity, with ASD individuals having stronger correlations. Interventional studies are warranted to investigate whether improvements in both sleep and increased physical activity may improve the core symptoms of ASD.

neuroscience↗

bioRxiv2022

A multi-enhancer hub at the Ets1 locus controls T cell differentiation and allergic inflammation through 3D genome topology

Multi-enhancer hubs are spatial clusters of enhancers which have been recently characterized across numerous developmental programs. Yet, the functional relevance of these three-dimensional (3D) structures is poorly understood. Here we show that the multiplicity of enhancers interacting with the transcription factor Ets1 is essential to control the precise expression level of this gene in response to cellular cues, and the failure to do so can lead to allergic diseases. Focusing on T cells as a model, we identified a highly connected multi-enhancer hub at the Ets1 locus, comprising a noncoding regulatory element that is a hotspot for sequence variation associated with allergic diseases. We deleted this hotspot and found that the multi-enhancer connectivity is dispensable for T cell development but required for CD4+ T helper (Th1) differentiation in response to changes in the cytokine milieu. Mice lacking this hotspot are thus protected from Th1-mediated colitis but demonstrate an overt allergic response to house dust mites, a T cell-mediated response which is dampened by Th1 cells. Mechanistically, the multi-enhancer hub controls the expression level of Ets1 that is dispensable for the active enhancer landscape but required for the Th1-specific genome topology through recruitment of CTCF. Together, we establish a paradigm for the functional and mechanistic relevance of multi-enhancer hubs controlling cellular competence to respond specifically to an inductive cue.

genomics↗

bioRxiv2021

Multiomics single-cell analysis of human pancreatic islets reveals novel cellular states in health and type 1 diabetes

Type 1 diabetes (T1D) is an autoimmune disease of only partially defined etiology in which immune cells destroy insulin-producing beta cells. Using single-cell transcriptomics and an advanced analytical strategy to assess pancreatic islets of T1D, autoantibody-positive, and non-diabetic organ donors, we identified both canonical cell types and rare insulin-expressing cells with a hybrid mixture of endocrine and exocrine gene signatures within all donors. We further found elevated expression of MHC Class II pathway genes in exocrine ductal cells of T1D donors, which we confirmed through CyTOF, in situ imaging mass cytometry, and immunofluorescence analysis. Taken together, our multimodal analyses identify novel cell types and processes that may contribute to T1D immunopathogenesis and provide new cellular and molecular insights into human pancreas function.

genomics↗

bioRxiv2020

SARS-CoV-2 Cell Entry Factors ACE2 and TMPRSS2 are Expressed in the Pancreas but Not in Islet Endocrine Cells

Summary/AbstractReports of new-onset diabetes and diabetic ketoacidosis in individuals with COVID-19 have led to the hypothesis that SARS-CoV-2, the virus that causes COVID-19, is directly cytotoxic to pancreatic islet {beta} cells. This would require binding and entry of SARS-CoV-2 into host {beta} cells via cell surface co-expression of ACE2 and TMPRSS2, the putative receptor and effector protease, respectively. To define ACE2 and TMPRSS2 expression in the human pancreas, we examined six transcriptional datasets from primary human islet cells and assessed protein expression by immunofluorescence in pancreata from donors with and without diabetes. ACE2 and TMPRSS2 transcripts were low or undetectable in pancreatic islet endocrine cells as determined by bulk or single cell RNA sequencing, and neither protein was detected in or {beta} cells from these donors. Instead, ACE2 protein was expressed in the islet and exocrine tissue microvasculature and also found in a subset of pancreatic ducts, whereas TMPRSS2 protein was restricted to ductal cells. The absence of significant ACE2 and TMPRSS2 co-expression in islet endocrine cells reduces the likelihood that SARS-CoV-2 directly infects pancreatic islet {beta} cells through these cell entry proteins.

cell biology↗

bioRxiv2019

Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques

Chromatin loops enable transcription factor-bound distal enhancers to interact with their target promoters to regulate transcriptional programs. Although developmental transcription factors, such as active forms of Notch, can directly stimulate transcription by activating enhancers, the effect of their oncogenic subversion on the 3-dimensional (3D) organization of the cancer genome is largely undetermined. By mapping chromatin looping genome-wide in Notch-dependent triple-negative breast cancer and B-cell lymphoma, we show that far beyond the well-characterized role of Notch as an activator of distal enhancers, Notch regulates its direct target genes through establishing new long-range regulatory interactions. Moreover, a large fraction of Notch-promoted regulatory loops forms highly interacting enhancer and promoter spatial clusters, termed "3D cliques". Loss-and gain-of-function experiments show that Notch preferentially targets hyperconnected 3D cliques that regulate the expression of crucial proto-oncogenes. Our observations suggest that oncogenic hijacking of developmental transcription factors can dysregulate transcription through widespread effects on the spatial organization of cancer genomes.

cancer biology↗

bioRxiv2019

TooManyCells identifies and visualizes relationships of single-cell clades

Transcriptional programs contribute to phenotypic and functional cell states. While elucidation of cell state heterogeneity and its role in biology and pathobiology has been advanced by studying single cell level measurements, the underlying assumptions of current analytical methods limit the identification and exploration of cell clades. Unlike other methods, which produce a single uni-layer partition of cells ignoring echelons of cell states, we present TooManyCells, a software consisting of a suite of graph-based tools for efficient, global, and unbiased identification and visualization of cell clades while maintaining and presenting the relationship between cell states. TooManyCells provides a set of tools based on a matrix-free efficient divisive hierarchical spectral clustering algorithm wholly different from the prevalent Louvain-based methods. BirchBeer, the visualization component of TooManyCells, introduces a new approach for single cell analysis that is built on a concept intentionally orthogonal to the widely used dimensionality reduction methods. Together, this suite of tools provide a paradigm shift in the analysis and interpretation of single cell data by enabling simultaneous comparisons of cell states at context-and application-dependent scales. A byproduct of this shift is the immediate detection and visualization of rare populations that outperforms previous algorithms as demonstrated by applying these tools to existing single cell RNA-seq data sets from various mouse organs.

bioinformatics↗