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Ciciani, M.

Publications and source records attributed to Ciciani, M..

6 recordsLinked to original sources
bioRxiv2026

Single-vector AAV delivery of En-ISPmu1 and donor DNA for in vivo targeted genome integration

TnpBs are compact RNA-guided nucleases ideally suited for in vivo delivery. By screening novel TnpBs identified from large metagenomic datasets, ISPmu1 was discovered and its protein and {omega}RNA were engineered to generate En-ISPmu1, which achieved editing efficiencies exceeding 65% across 12 human loci. Owing to its compact size, En-ISPmu1 was delivered together with a donor DNA in a single AAV vector, yielding up to 12.7% targeted integration in mouse liver. These findings establish En-ISPmu1 as a promising versatile platform for in vivo therapeutic genome editing applications.

bioengineering↗
bioRxiv2026

Enhancing hypercompact Cas{Phi}2 activity through EPICA.2, an optimized eukaryotic directed evolution platform

Compact Cas nucleases offer advantages over the widely used SpCas9 due to their smaller size, which enables more efficient delivery for in vivo applications. Among these, the phage-encoded Cas{Phi}2 (Cas12j2) is highly promising due to its relaxed PAM requirement (5-TTN-3) and compact size (757 aa); however, its translational potential is limited by low editing activity. To enhance the efficacy of Cas{Phi}2, we optimized the previously reported EPICA system, developing EPICA.2, a eukaryotic directed evolution platform to improve nucleases with nearly undetectable activity. EPICA.2 integrates additional yeast evolution rounds to enrich for active variants along with a low background mammalian reporter system that improves detection and selection of enhanced variants. Finally, we set up a long-read sequencing protocol which uses unique molecular identifiers (UMIs) to reduce sequencing errors, enabling accurate identification of the mutation combinations in each evolved variant. Among the most frequent variants, we obtained evoCas{Phi}2, which contains six activity-boosting mutations with a synergistic effect not predictable by rational engineering. Overall, evoCas{Phi}2 showed up to 70-fold increased activity in human cells compared to wild-type and outperformed variants generated through rational approaches, highlighting the potential of EPICA.2 as a powerful strategy to evolve genome editing tools with low native activity.

bioengineering↗
bioRxiv2024

Functional rescue of F508del-CFTR through revertant mutations introduced by CRISPR base editing

Cystic Fibrosis (CF) is a life-shortening autosomal recessive disease caused by mutations in the CFTR gene, resulting in functional impairment of the encoded ion channel. F508del mutation, a trinucleotide deletion, is the most frequent cause of CF affecting approximately 80% of patients. Even though current pharmacological treatments alleviate the F508del-CF disease symptoms there is no definitive cure. Here we leveraged revertant mutations (RMs) in cis with F508del to rescue CFTR protein folding and restore its function. We developed CRISPR base editing strategies to efficiently and precisely introduce the desired mutations in the F508del locus. Both editing and CFTR function recovery were verified in CF cellular models including primary epithelial cells derived from CF patients. The efficacy of the CFTR recovery strategy was validated in cultures of pseudostratified epithelia from patients cells showing full recovery of ion transport. Additionally, we observed an additive effect by combining our strategy with small molecules that enhance F508del activity, thus paving the way to combinatorial therapies.

bioengineering↗
bioRxiv2024

Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples

Viruses are an abundant and crucial component of the human microbiome, but accurately discovering them via metagenomics is still challenging. Currently, the available viral reference genomes poorly represent the diversity in microbiome samples, and expanding such a set of viral references is difficult. As a result, many viruses are still undetectable through metagenomics even when considering the power of de novo metagenomic assembly and binning, as viruses lack universal markers. Here, we describe a novel approach to catalog new viral members of the human gut microbiome and show how the resulting resource improves metagenomic analyses. We retrieved >3,000 viral-like particles (VLP) enriched metagenomic samples (viromes), evaluated the efficiency of the enrichment in each sample to leverage the viromes of highest purity, and applied multiple analysis steps involving assembly and comparison with hundreds of thousands of metagenome-assembled genomes to discover new viral genomes. We reported over 162,000 viral sequences passing quality control from thousands of gut metagenomes and viromes. The great majority of the retrieved viral sequences ([~]94.4%) were of unknown origin, most had a CRISPR spacer matching host bacteria, and four of them could be detected in >50% of a set of 18,756 gut metagenomes we surveyed. We included the obtained collection of sequences in a new MetaPhlAn 4.1 release, which can quantify reads within a metagenome matching the known and newly uncovered viral diversity. Additionally, we released the viral database for further virome and metagenomic studies of the human microbiome.

microbiology↗
bioRxiv2023

Eukaryotic-driven directed evolution of Cas9 nucleases

Full exploitation of the natural reservoir of CRISPR-Cas nucleases from prokaryotes for genome editing is limited by the suboptimal activity of these enzymes in mammalian cells. Here we developed a Eukaryotic Platform to Improve Cas Activity (EPICA) to steer weakly active Cas9 nucleases into highly active enzymes by directed evolution. The EPICA platform is obtained by coupling Cas nuclease activity with yeast auxotrophic selection followed by mammalian cell selection through a sensitive reporter system. EPICA was validated with a poorly efficient Cas9 nuclease from Campylobacter jejuni, CjCas9, generating an enhanced variant, UltraCjCas9, following directed evolution rounds. UltraCjCas9 was up to 12-fold more active in mammalian endogenous genomic loci, while preserving high genome-wide specificity. Here we report a eukaryotic pipeline allowing enhancement of Cas9 systems, setting the ground to unlock the multitude of RNA-guided nucleases existing in nature.

bioengineering↗