Biology subjects

Crisci, E.

Publications and source records attributed to Crisci, E..

6 recordsLinked to original sources

bioRxiv2026

Route of Adenovirus Type 5-Vectored Influenza Vaccination Shapes Systemic and Mucosal Immunity in a Maternal-Neonatal Pig Model

Influenza A virus can cause severe complications in pregnant women and infants, yet no influenza vaccines are approved for infants younger than six months. To address this, novel maternal vaccination strategies are needed to increase global access and coverage in these vulnerable populations. This study evaluated a hemagglutinin (HA) A/California/2009 (H1N1)-based human adenovirus 5 (huAd5) vector vaccine, adjuvanted with a TLR3 agonist, for its ability to induce influenza-specific passive immunity from pregnant and lactating pigs to their piglets following different immunization routes. Influenza naive pregnant dams were vaccinated via oral, intranasal (IN), or intramuscular (IM) routes three weeks prepartum and boosted four weeks later. Serum, colostrum and milk samples were collected longitudinally to assess HA-specific antibody induced by vaccination. H1N1-Ca/09 neutralizing antibodies were evaluated in serum and IFN{gamma} producing cells were assessed in blood, spleen and lymph node cells. IN and IM routes elicited robust serum HA-specific antibody responses when compared to control animals at one- and four-weeks post-boost, whereas the oral route resulted in poor antibody induction across all samples tested. Piglets nursing from IN and IM vaccinated dams showed a significantly higher level of HA-specific antibodies in serum at 2-3 weeks post-partum compared to control piglets. Notably, IN immunized dams and their piglets showed significantly elevated influenza neutralizing antibodies compared to controls. This work demonstrated that both IN and IM immunization with a huAd5-vectored vaccine robustly induced maternal influenza-specific immunity that supported passive transfer to nursing piglets, with IN immunization resulting in superior transfer of neutralizing antibodies.

immunology↗

bioRxiv2024

Defining Cellular Diversity at the Swine Maternal-Fetal Interface Using Spatial Transcriptomics and Organoids

The placenta is a dynamic, embryo-derived organ essential for fetal growth and development. While all eutherian mammals have placentas composed of fetal-derived trophoblasts that mediate maternal-fetal exchange, their anatomical and histological structures vary across species due to evolutionary divergence. Despite the cellular heterogeneity of porcine trophoblasts in vivo, understanding the mechanisms driving porcine placental development has been limited by the lack of in vitro models replicating this heterogeneity. In this study, we derived swine trophoblast organoids (sTOs) from full-term porcine placentas, retaining key transcriptional signatures of in vivo trophoblasts. To identify conserved cell populations, we integrated Visium spatial transcriptomics from mid-gestation porcine placentas with single-cell transcriptomics from sTOs. Spatial transcriptomics revealed novel markers of the porcine uterus and placenta, enabling precise separation of histological structures at the maternal-fetal interface. The integration of tissue and sTO transcriptomics showed that sTOs spontaneously differentiate into distinct trophoblast populations, with conserved gene expression and cell communication programs. These findings demonstrate that sTOs recapitulate porcine placental trophoblast populations, offering a powerful model for advancing placentation research. Our work also provides a spatially resolved whole-transcriptome dataset of the porcine maternal-fetal interface, opening new avenues for discoveries in placental development, evolution, and health across mammals.

developmental biology↗

bioRxiv2024

Human long noncoding RNA, VILMIR, is induced by major respiratory viral infections and modulates the host interferon response

Long noncoding RNAs (lncRNAs) are a newer class of noncoding transcripts identified as key regulators of biological processes. Here we aimed to identify novel lncRNA targets that play critical roles in major human respiratory viral infections by systematically mining large-scale transcriptomic datasets. Using bulk RNA-sequencing (RNA-seq) analysis, we identified a previously uncharacterized lncRNA, named virus inducible lncRNA modulator of interferon response (VILMIR), that was consistently upregulated after in vitro influenza infection across multiple human epithelial cell lines and influenza A virus subtypes. VILMIR was also upregulated after SARS-CoV-2 and RSV infections in vitro. We experimentally confirmed the response of VILMIR to influenza infection and interferon-beta (IFN-{beta}) treatment in the A549 human epithelial cell line and found the expression of VILMIR was robustly induced by IFN-{beta} treatment in a dose and time-specific manner. Single cell RNA-seq analysis of bronchoalveolar lavage fluid (BALF) samples from COVID-19 patients uncovered that VILMIR was upregulated across various cell types including at least five immune cells. The upregulation of VILMIR in immune cells was further confirmed in the human T cell and monocyte cell lines, SUP-T1 and THP-1, after IFN-{beta} treatment. Finally, we found that knockdown of VILMIR expression reduced the magnitude of host transcriptional responses to IFN-{beta} treatment in A549 cells. Together, our results show that VILMIR is a novel interferon-stimulated gene (ISG) that regulates the host interferon response and may be a potential therapeutic target for human respiratory viral infections upon further mechanistic investigation. IMPORTANCEIdentifying host factors that regulate the immune response to human respiratory viral infection is critical to developing new therapeutics. Human long noncoding RNAs (lncRNAs) have been found to play key regulatory roles during biological processes, however the majority of lncRNA functions within the host antiviral response remain unknown. In this study, we identified that a previously uncharacterized lncRNA, VILMIR, is upregulated after major respiratory viral infections including influenza, SARS-CoV-2, and RSV. We demonstrated that VILMIR is an interferon-stimulated gene that is upregulated after interferon-beta (IFN-{beta}) in several human cell types. We also found that knockdown of VILMIR reduced the magnitude of host transcriptional responses to IFN-{beta} treatment in human epithelial cells. Our results reveal that VILMIR regulates the host interferon response and may present a new therapeutic target during human respiratory viral infections.

immunology↗

bioRxiv2024

Prolonged airway explant culture enables study of health, disease, and viral pathogenesis

In vitro models play a major role in studying airway physiology and disease. However, the native lungs complex tissue architecture and non-epithelial cell lineages are not preserved in these models. Ex vivo tissue models could overcome in vitro limitations, but methods for long-term maintenance of ex vivo tissue has not been established. We describe methods to culture human large airway explants, small airway explants, and precision-cut lung slices for at least 14 days. Human airway explants recapitulate genotype-specific electrophysiology, characteristic epithelial, endothelial, stromal and immune cell populations, and model viral infection after 14 days in culture. These methods also maintain mouse, rabbit, and pig tracheal explants. Notably, intact airway tissue can be cryopreserved, thawed, and used to generate explants with recovery of function 14 days post-thaw. These studies highlight the broad applications of airway tissue explants and their use as translational intermediates between in vitro and in vivo studies.

bioengineering↗

bioRxiv2022

A Rapid, High Throughput, Viral Infectivity Assay using Automated Brightfield Microscopy with Machine Learning

Infectivity assays are essential for the development of viral vaccines, antiviral therapies and the manufacture of biologicals. Traditionally, these assays take 2-7 days and require several manual processing steps after infection. We describe an automated assay (AVIA), using machine learning (ML) and high-throughput brightfield microscopy on 96 well plates that can quantify infection phenotypes within hours, before they are manually visible, and without sample preparation. ML models were trained on HIV, influenza A virus, coronavirus 229E, vaccinia viruses, poliovirus, and adenoviruses, which together span the four major categories of virus (DNA, RNA, enveloped, and non-enveloped). A sigmoidal function, fit to virus dilution curves, yielded an R2 higher than 0.98 and a linear dynamic range comparable to or better than conventional plaque or TCID50 assays. Because this technology is based on sensitizing AIs to specific phenotypes of infection, it may have potential as a rapid, broad-spectrum tool for virus identification.

microbiology↗

bioRxiv2018

Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig.

BackgroundFunctional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project (http://www.fragencode.org) aimed to profile the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in four livestock species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells).\n\nResultsRNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically Associating Domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species.\n\nConclusionsWe report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species.

genomics↗