Biology subjects

Giacomello, S.

Publications and source records attributed to Giacomello, S..

10 recordsLinked to original sources

bioRxiv2025

A molecular atlas of cell-type specific signatures in the parkinsonian striatum.

The progressive degeneration of dopaminergic projections to the striatum is a key disease mechanism in Parkinsons disease (PD). To define the cellular landscape in the parkinsonian striatum, we mapped the cell-type specific transcriptional landscape in early and progressive PD mouse models and in human PD stages. Our analyses revealed substantial transcriptomic changes across both neuronal and glial populations, with astrocytes and oligodendrocytes exhibiting distinct disease-associated gene expression profiles. Notably, progressive dopamine depletion uncovered differential neuronal vulnerability, identifying eccentric striatal projection neurons (SPNs) and Chst9-expressing direct-pathway SPNs as among the most resilient subtypes in both species. This cross-species resource establishes a comprehensive framework for investigating cell-state dynamics in the parkinsonian striatum and uncovers selectively vulnerable and resistant cell types that can inspire new therapeutic strategies.

neuroscience↗

bioRxiv2025

ProbeST: a custom probe design pipeline for Spatial Transcriptomics

Probe-based Spatial Transcriptomics profiles spatially-resolved transcriptomes using gene-specific probe pairs for both Formalin-fixed paraffin-embedded (FFPE) and Fresh Frozen samples. However, its applicability is restricted to human and mouse studies, due to commercial probe set availability. Here, we present ProbeST, an open-source computational pipeline for designing custom probe sets for any organism of interest. We validated ProbeST on FFPE mouse enteroids infected with Salmonella enterica serovar Typhimurium, using custom pathogen probes with the available mouse probe panel. We simultaneously detected host and pathogen transcripts, demonstrating high probe specificity and enabling identification of inflammatory response host genes Mefv, Tnf, and Anxa1 colocalizing to pathogen genes. The reproducible ProbeST workflow expands probe-based Spatial Transcriptomics to studies of non-model organisms and host-pathogen interactions.

bioinformatics↗

bioRxiv2023

Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton

Single-cell transcriptomics has the potential to provide novel insights into poorly studied microbial eukaryotes. Although several such technologies are available and benchmarked on mammalian cells, few have been tested on protists. Here, we optimized a microarray single-cell sequencing (MASC-seq) technology that generates microscope images of cells in parallel with capturing their transcriptomes. We tested the method on three species representing important plankton groups with different cell structures, the ciliate Tetrahymena thermophila, the diatom Phaeodactylum tricornutum and the dinoflagellate Heterocapsa sp.. Both the cell fixation and permeabilization steps were adjusted. For the ciliate and dinoflagellate, the number of transcripts of microarray spots with single cells were significantly higher than for background spots, and the overall expression patterns were correlated with that of bulk RNA, while for the much smaller diatom cells, it was not possible to separate single-cell transcripts from background. The MASC-seq method holds promise for investigating "microbial dark matter", although further optimizations are necessary to increase the signal-to-noise ratio.

genomics↗

bioRxiv2022

Miniature spatial transcriptomics for studying parasite-endosymbiont relationships at the micro scale

Several important human infectious diseases are caused by microscale-sized parasitic nematodes like filarial worms. Filarial worms have their own spatial tissue organization and to uncover this tissue structure, we need methods that can spatially resolve these miniature specimens. Most filarial worms evolved a mutualistic association with endosymbiotic bacteria Wolbachia, however, the mechanisms underlying the dependency of filarial worms on the fitness of these bacteria remain unknown. As Wolbachia is essential for the development, reproduction, and survival of filarial worms, we focused on studying a posterior region containing reproductive tissue and developing embryos of adult female Brugia malayi worms. To spatially explore how Wolbachia interacts with the worms reproductive system, we performed a spatial characterization using Spatial Transcriptomics (ST) across our region of interest. We provide a proof-of-concept for miniature-ST to explore spatial gene expression patterns in small sample types, demonstrating the methods ability to uncover nuanced tissue region expression patterns, observe the spatial localization of key B. malayi - Wolbachia pathway genes, and co-localize the B. malayi spatial transcriptome in Wolbachia tissue regions. We envision our approach to open up new scenarios for the study of infectious diseases caused by micro-scale parasitic worms.

genomics↗

bioRxiv2022

Spatially resolved host-bacteria-fungi interactomes via spatial metatranscriptomics

All multicellular organisms are closely associated with microbes, which have a major impact on the health of their host. The interactions of microbes among themselves and with the host take place at the microscale, forming complex networks and spatial patterns that are rarely well understood due to the lack of suitable analytical methods. The importance of high-resolution spatial molecular information has become widely appreciated with the recent advent of spatially resolved transcriptomics. Here, we present Spatial metaTranscriptomics (SmT), a sequencing-based approach that leverages 16S/18S/ITS/poly-d(T) multimodal arrays for simultaneous host transcriptome- and microbiome-wide characterization of tissues at 55-{micro}m resolution. We showcase SmT in outdoor-grown Arabidopsis thaliana leaves as a model system, and found tissue-scale bacterial and fungal hotspots. By network analysis, we study inter- and intra-kingdom spatial interactions among microbes, as well as the host response to microbial hotspots. SmT is a powerful new strategy that will be pivotal to answering fundamental questions on host-microbiome interplay.

genomics↗

bioRxiv2022

Enabling automated and reproducible spatially resolved transcriptomics at scale

Tissue spatial information is an essential component to reach a holistic overview of gene expression mechanisms. The sequencing-based Spatial transcriptomics approach allows to spatially barcode the whole transcriptome of tissue sections using microarray glass slides. However, manual preparation of high-quality tissue sequencing libraries is time-consuming and subjected to technical variability. Here, we present an automated adaptation of the 10x Genomics Visium library construction on the widely used Agilent Bravo Liquid Handling Platform. Compared to the manual Visium library preparation, our automated approach reduces hands-on time by over 80% and provides higher throughput and robustness. Our automated Visium library preparation protocol provides a new strategy to standardize spatially resolved transcriptomics analysis of tissues at scale.

genetics↗

bioRxiv2022

Dual spatially resolved transcriptomics for SARS-CoV-2 host-pathogen colocalization studies in humans

To advance our understanding of cellular host-pathogen interactions, technologies that facilitate the co-capture of both host and pathogen spatial transcriptome information are needed. Here, we present an approach to simultaneously capture host and pathogen spatial gene expression information from the same formalin-fixed paraffin embedded (FFPE) tissue section using the spatial transcriptomics technology. We applied the method to COVID-19 patient lung samples and enabled the dual detection of human and SARS-CoV-2 transcriptomes at 55 m resolution. We validated our spatial detection of SARS-CoV-2 and identified an average specificity of 94.92% in comparison to RNAScope and 82.20% in comparison to in situ sequencing (ISS). COVID-19 tissues showed an upregulation of host immune response, such as increased expression of inflammatory cytokines, lymphocyte and fibroblast markers. Our colocalization analysis revealed that SARS-CoV-2+ spots presented shifts in host RNA metabolism, autophagy, NF{kappa}B, and interferon response pathways. Future applications of our approach will enable new insights into host response to pathogen infection through the simultaneous, unbiased detection of two transcriptomes.

genomics↗

bioRxiv2022

High cardiomyocyte diversity in human early prenatal heart development

Cardiomyocytes play key roles during cardiogenesis, but have poorly understood features, especially in prenatal stages. Thus, we have characterized human prenatal cardiomyocytes, 6.5- 7 weeks post-conception, in detail by integrating single-cell RNA sequencing, spatial transcriptomics, and ligand-receptor interaction information. Using a computational workflow developed to dissect cell type heterogeneity, localize cell types, and explore their molecular interactions, we identified eight types of developing cardiomyocyte, more than double compared to the ones identified in the Human Developmental Cell Atlas. These have high variability in cell cycle activity, mitochondrial content, and connexin gene expression, and are differentially distributed in the ventricles, including outflow tract, and atria, including sinoatrial node. Moreover, cardiomyocyte ligand-receptor crosstalk is mainly with non-cardiomyocyte cell types, encompassing cardiogenesis-related pathways. Thus, early prenatal human cardiomyocytes are highly heterogeneous and develop unique location-dependent properties, with complex ligand-receptor crosstalk. Further elucidation of their developmental dynamics may give rise to new therapies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/482029v1_ufig1.gif" ALT="Figure 1"> View larger version (76K): org.highwire.dtl.DTLVardef@1385cb8org.highwire.dtl.DTLVardef@14f62d1org.highwire.dtl.DTLVardef@e0b10borg.highwire.dtl.DTLVardef@1876345_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2019

Prototypical pacemaker neurons are immunocompetent cells

Pacemaker neurons exert control over neuronal circuit function by their intrinsic ability to generate rhythmic bursts of action potential. Recent work has identified rhythmic gut contractions in human, mice and hydra to be dependent on both neurons and the resident microbiota. However, little is known about the evolutionary origin of these neurons and their interaction with microbes. In this study, we identified and functionally characterized prototypical ANO/SCN/TRPM ion channel expressing pacemaker cells in the basal metazoan Hydra by using a combination of single-cell transcriptomics, immunochemistry, and functional experiments. Unexpectedly, these prototypical pacemaker neurons express a rich set of immune-related genes mediating their interaction with the microbial environment. Functional experiments validated a model of the evolutionary emergence of pacemaker cells as neurons using components of innate immunity to interact with the microbial environment and ion channels to generate rhythmic contractions.

developmental biology↗

bioRxiv2017

Single-cell transcriptomic profiling of progenitors of the oligodendrocyte lineage reveals transcriptional convergence during development

Pdgfra+ oligodendrocyte precursor cells (OPCs) arise in distinct specification waves during embryogenesis in the central nervous system (CNS). It is unclear whether there is a correlation between these waves and different transcriptional oligodendrocyte (OL) states at adult stages. Here we present a bulk and single-cell transcriptomics resource providing insights on how transitions between these states occur. We show that E13.5 Pdgfra+ populations are not OPCs, exhibiting instead hallmarks of neural progenitors. A subset of these progenitors, which we refer as pre-OPCs, rewires their transcriptional landscape, converging into indistinguishable OPC states at E17.5 and post-natal stages. P7 brain and spinal cord OPCs present similar transcriptional profiles at the single-cell level, indicating that OPC states are not region-specific. Postnatal OPC progeny of E13.5 Pdgfra+ have electrophysiological and transcriptional profiles similar to OPCs derived from subsequent specification waves. In addition, lineage tracing indicates that a subset of E13.5 Pdgfra+ cells also originate cells of the pericyte lineage. In summary, our results indicate that embryonic Pdgfra+ cells are diverse and give rise at post-natal stages to distinct cell lineages, including OPCs with convergent transcriptional profiles in different CNS regions.

neuroscience↗