Cascio, A. | Search bioRxiv

bioRxiv2026

An improved CRISPR-LICHT screen of 120 Tdark genes illuminates new biologically relevant SOX2 targets in human brain organoids

SOX2 is a transcription factor and central regulator of neural progenitor identity, yet the downstream molecular networks through which it supports human brain development remain incompletely characterized. Here, we applied CRISPR-lineage tracing at cellular resolution in heterogeneous tissue (CRISPR-LICHT) to human cerebral organoids to functionally interrogate SOX2-dependent regulatory networks. Using a SOX2-focused library targeting SOX2 together with conserved neurodevelopmental regulators expressed in neural progenitor cells, we showed that CRISPR-LICHT detects reproducible lineage- depletion phenotypes across genes already known to be involved in progenitor maintenance, fate specification, glial differentiation and neuronal maturation. This extends the application of CRISPR-LICHT beyond the severe neural progenitor phenotypes previously characterized for microcephaly-associated genes and demonstrates its ability to detect perturbation effects across a broader set of neurodevelopmental regulators, involving SOX2 targets previously defined in mouse and now open to further understanding in a human model setting. We further screened 120 evolutionarily conserved, poorly characterized SOX2-dependent genes classified as Tdark within the Illuminating the Druggable Genome framework and identified 28 candidate hits whose disruption impaired neural progenitor lineage expansion and/or survival. These candidates included proteins associated with cytoskeletal organization, membrane dynamics and intracellular architecture, suggesting that SOX2-dependent developmental programmes may engage cellular processes beyond transcriptional regulation. Individual downregulation of CDC42EP4, a poorly characterized CDC42 effector linked to cytoskeletal organization, revealed altered distribution of targeted progenitors between ventricular- and subventricular- like compartments, with changes consistent with altered progenitor-state progression. Together, these findings expand the functional landscape of SOX2-dependent regulation in human neural progenitors and identify cellular architecture as a potential component of SOX2-associated developmental programs.

developmental biology↗

bioRxiv2021

Antiparasitic effect of stilbene and terphenyl compounds against Trypanosoma cruzi parasites

BackgroundChagas disease, also known as American trypanosomiasis, is a potentially life-threatening illness caused by the protozoan parasite Trypanosoma cruzi. No progress in the treatment of this pathology has been made since Nifurtimox was introduced more than fifty years ago and is considered very aggressive and may cause several adverse effects. Currently, this drug has severe limitations, including high frequency of undesirable side effects and limited efficacy and availability and the research to discover new drugs for the treatment of Chagas disease is imperative. Many drugs available in the market are natural products as found in nature or compounds designed based on the structure and activity of these natural products. Methodology/Principal FindingsThis study evaluated the in vitro antiparasitic activity in T. cruzi epimastigotes and intracellular amastigotes of a series of stilbene and terphenyl compounds previously synthesized. The action of the most selective compounds has been investigated by flow cytometry analysis to evaluate the mechanism of cell death. The ability to induce apoptosis or caspase-1 inflammasome were assayed in macrophages infected with T. cruzi after treatment comparing with Nifurtimox. Conclusions/SignificanceThe stilbene ST18 was the most potent compound of the series. It was slightly less active than Nifurtimox in epimastigotes but most active in intracellular amastigotes. Compared to Nifurtimox, it was markedly less cytotoxic when tested in vitro on normal cells. ST18 was able to induce a marked increase of parasites positive to Annexin V and monodansylcadaverine. Moreover, ST18 induced the activation in infected macrophages of caspase-1, a conserved enzyme which plays a main role in controlling parasitemia, host survival, and the onset of adaptive immune response in Trypanosoma infection. The antiparasitic activity of ST18 together to its ability to activate caspase-1 in infected macrophages and its low toxicity on normal cells makes this compound interesting for further clinical investigations. Author SummaryChagas disease is a pathology caused by the protozoan parasite Trypanosoma cruzi. No progress in the treatment of this pathology has been made since benznidazole and Nifurtimox were introduced more than fifty years ago. However, these drugs have severe limitations and the research to discover new drugs for the treatment of Chagas disease is imperative. We evaluated the in vitro antiparasitic activity in T. cruzi epimastigotes of a series of stilbene and terphenyl compounds previously synthesized. The stilbene ST18 was the most potent compound of the series. It was slightly less active than nifurtimox in epimastigotes but most active in intracellular amastigotes. Compared to Nifurtimox, it was markedly less cytotoxic when tested in vitro on normal cells. ST18 was able to induce a marked increase of parasites positive to Annexin V and monodansylcadaverine. Moreover, this compound induced the activation in infected macrophages of caspase-1, an evolutionarily conserved enzyme which plays a main role in controlling parasitemia, host survival, and the onset of adaptive immune response in T. cruzi infection. The antiparasitic activity of ST18 together to its ability to activate caspase-1 in infected macrophages and its low toxicity on normal cells makes this compound interesting for further clinical investigations.

microbiology↗