Biology subjects

Riccardi, A.

Publications and source records attributed to Riccardi, A..

4 recordsLinked to original sources

bioRxiv2025

Mapping the Transcriptional Landscape of Drug Responses in Primary Human Cells Using High-Throughput DRUG-seq

To advance our understanding of drug action in physiologically-relevant systems, we developed a high-throughput transcriptomic atlas of compound responses in primary human cell types. Leveraging the scalable and cost-effective Digital RNA with the pertUrbation of Genes (DRUG-seq) assay, we profiled gene expression responses to 89 pharmacologically-active compounds across six concentrations in four distinct primary cell types: aortic smooth muscle cells (AoSMCs), skeletal muscle myoblasts (SkMMs), dermal fibroblasts, and melanocytes. Through rigorous quality control and normalization, we generated reproducible and cell type-resolved transcriptomic signatures, enabling the discovery of both shared and divergent regulatory programs. This dataset revealed core cellular responses, such as brefeldin A-mediated ER stress across all cell types, as well as lineage-specific effects, including dexamethasone-induced hypoxia signaling in AoSMCs, complex inflammatory responses linked to epithelial-to-mesenchymal transition pathways in SkMMs, TGF-{beta}-modulated states in fibroblasts, and dabrafenib-driven transcriptional shifts towards quiescence in melanocytes. By integrating systematic perturbations with primary models, this dataset serves as a resource for building systems-level models of drug response and mechanism. Ultimately, we aim to accelerate predictive pharmacology by enabling high-throughput data generation grounded in human biology and readily usable by artificial intelligence models.

systems biology↗

bioRxiv2024

Impacts of urbanization on the health of American Robins (Turdus migratorus) in Chicagoland

Wild animals in urbanized environments face several unique challenges, including increased anthropogenic stressors, decreased natural food availability and quality, and increased pollutant exposure. While some work has shown that individual urbanization stressors can have negative impacts on aspects of wild bird physiology, other studies have demonstrated ambiguous or sometimes positive interactions. As such, the impact of multiple, coincident urban stressors on avian health still needs to be fully understood. Here, we addressed this knowledge gap by holistically measuring multiple physiological markers of American robin (Turdus migratorius) health across a gradient of urbanization throughout Chicagoland. We predicted that birds using highly urbanized habitats would experience higher heavy metal contamination, higher oxidative stress, lower body condition, higher avian malaria burden, and decreased measures of immune response compared to exurban birds in the Chicagoland area. Multiple linear models revealed that robins in more urbanized areas exhibited higher levels of heavy metal contamination and slightly elevated levels of associated physiological impairments compared to their counterparts in exurban sites. Additionally, noise and light pollution were significantly associated with oxidative stress and infection status, respectively, albeit in different directions. Overall, our findings underscore how the complex environmental changes that accompany urbanization can impact the health of urban bird populations.

ecology↗

bioRxiv2024

DNA damage response defects induced by the formation of TDP-43 and mutant FUS cytoplasmic inclusions and their pharmacological rescue.

Formation of cytoplasmic inclusions (CIs) of TDP-43 and FUS, along with DNA damage accumulation, is a hallmark of affected motor neurons in Amyotrophic Lateral Sclerosis (ALS). However, the impact of CIs on DNA damage response (DDR) and repair in this pathology remains unprobed. Here, we show that CIs of TDP-43 and FUSP525L, co-localizing with stress granules, lead to a dysfunctional DDR activation associated with physical DNA breakage. Inhibition of the activity of the DDR kinase ATM, but not of ATR, abolishes DDR signaling, indicating that DNA double-strand breaks (DSBs) are the primary source of DDR activation. In addition, cells with TDP-43 and FUSP525L CIs exhibit reduced DNA damage-induced RNA synthesis at DSBs. We previously showed that the two endoribonucleases DROSHA and DICER, also known to interact with TDP-43 and FUS during small RNA processing, contribute to DDR signaling at DSBs. Treatment with enoxacin, which stimulates DDR and repair by boosting the enzymatic activity of DICER, restores a proficient DDR and reduces DNA damage accumulation in cultured cells with CIs and in vivo in a murine model of ALS. In Drosophila melanogaster, Dicer-2 overexpression rescues TDP-43-mediated retinal degeneration. In summary, our results indicate that the harmful effects caused by TDP-43 and FUS proteinopathies include genotoxic stress and that the pharmacological stimulation of the DNA damage signaling and repair counteracts it.

molecular biology↗

bioRxiv2024

DROSHA, DICER and Damage-Induced long ncRNA control BMI1-dependent transcriptional repression at DNA double-strand break

Genome integrity is safeguarded by the DNA damage response (DDR). Controlled transcriptional dampening of genes surrounding DNA double-strand breaks (DSBs) has been shown to facilitate DNA repair. This phenomenon, defined as DSB-induced silencing in cis (DISC), involves the DDR apical kinase ATM and the Polycomb Repressive Complex 1 (PRC1). Conversely, DSBs have also been reported to induce de novo transcription of damaged-induced long non-coding RNAs (dilncRNAs) in a MRE11-RAD50-NBS1 (MNR) complex-dependent manner. MRN also controls the recruitment to DSB of the ribonuclease DROSHA, which together with DICER, stimulates DDR signaling and DNA repair. Here, we reconcile these apparently contrasting observations by showing that dilncRNA, together with DROSHA and DICER, but not GW182-like proteins required for miRNA-mediated gene silencing, controls DISC. Indeed, similarly to ATM, MRN inhibition abolishes DISC while pharmacological enhancement of DICER ribonuclease activity by Enoxacin improves DISC. Importantly, Enoxacin administration restores DISC upon ATM inhibition, demonstrating that DICER promotes DISC independently from ATM. Differently, Enoxacin does not restore DISC upon MRN inhibition, suggesting that DICER acts downstream to dilncRNA biogenesis and DROSHA recruitment. Mechanistically, we show that DROSHA and DICER control the recruitment of the PRC1 component BMI1 at DSBs and the consequent H2A-K119 ubiquitination. Upon DSBs formation, BMI1 and DROSHA interact in an RNA-dependent manner. Indeed, BMI1 associates to dilncRNA and do so in a DROSHA- and DICER-dependent manner. Importantly, inhibition of dilncRNA function by antisense oligonucleotides or Cas13-mediated targeting is sufficient to reduce BMI1 recruitment and DISC at individual loci. We propose that dilncRNAs together with DROSHA and DICER control DISC at genomic DSB by supporting PRC1 recruitment and chromatin ubiquitination.

molecular biology↗