Matteo Ciciani

Systematic investigation of prokaryotic mobile genetic elements and programmable nucleases using large metagenomic data

Matteo Ciciani

In Bacteria and Archaea, mobile genetic elements (MGEs) are extremely diverse in terms of size, structure and mobilization mechanism, ranging from minimal non-autonomous sequences (<100 bp) to complex elements (>100,000 bp) capable of mobilizing many passenger genes. MGEs drive genome evolution and …

Enhancing hypercompact CasΦ2 activity through EPICA.2, an optimized eukaryotic directed evolution platform

Giulia Vittoria Ruta, Matteo Ciciani, Veronica De Sanctis, Roberto Bertorelli et autres

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 CasΦ2 (Cas12j2) is highly promising due to its relaxed PAM requirement (5′-TTN-3′) and compact …

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Functional correction of the untreatable CFTR 1717-1G>A mutation through mRNA- and sgRNA-optimized base editing

Alessandro Umbach, Annalisa Santini, Mattijs Bulcaen, Daniela Guidone et autres

The 1717-1G>A is a prevalent splicing mutation causing cystic fibrosis (CF) for which no pharmacological treatments have been approved. This mutation disrupts a canonical 3′ AG splice acceptor site in the cystic fibrosis transmembrane conductance regulator ( CFTR ) gene, leading to …

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Baby-to-baby strain transmission shapes the developing gut microbiome

Liviana Ricci, Vitor Heidrich, Michal Punčochář, Federica Armanini et autres

The early infant microbiome is largely primed by microbial transmission from the mother between birth and the first few weeks of life1–3, but how interpersonal transmission further shapes the developing microbiome in the first year remains unexplored. Here we report a metagenomic …

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

Irene Carrozzo, Giulia Maule, Carmelo Gentile, Alessandro Umbach et autres

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 persons …

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Characterization of a novel thermostable NAD+-dependent formate dehydrogenase from Methylacidiphilum kamchatkense Kam1 (MkaFDH)

Matteo Ciciani, Ágata Sofia Assunção Carreira, Martina Paganin, Sara Pozzo et autres

Metal-independent NAD + -dependent formate dehydrogenases (FDHs) are enzymes responsible for catalyzing the conversion of formate (HCOO – ) to carbon dioxide (CO 2 ), a biological reaction involved in microbial carbon processing and cofactor regeneration. These enzymes show large potential for …

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271 Prime editing functionally corrects rare and common cystic fibrosis–causing mutations in patient-derived organoids and airway epithelia

M. Bulcaen, Phéline Kortleven, R. Liu, G. Maule et autres

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

Irene Carrozzo, Giulia Maule, Carmelo Gentile, Alessandro Umbach et autres

Summary 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 …

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WITHDRAWN: DNA polymerase λ-driven targeted mutagenesis for directed evolution in human cells

Davide Aiello, Matteo Ciciani, Federica Marelli, Marta Stancampiano et autres

Withdrawal Statement The authors have withdrawn this manuscript due to the need for further modifications in the experimental setup. Therefore, the authors do not wish this work to be cited as reference for this project. If you have any questions, please contact …

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Prime editing functionally corrects cystic fibrosis-causing CFTR mutations in human organoids and airway epithelial cells

Mattijs Bulcaen, Phéline Kortleven, Ronald B. Liu, Giulia Maule et autres

Prime editing is a recent, CRISPR-derived genome editing technology capable of introducing precise nucleotide substitutions, insertions, and deletions. Here, we present prime editing approaches to correct L227R- and N1303K-CFTR, two mutations that cause cystic fibrosis and are not eligible for current market-approved …

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CoCas9 is a compact nuclease from the human microbiome for efficient and precise genome editing

Eleonora Pedrazzoli, Michele Demozzi, Elisabetta Visentin, Matteo Ciciani et autres

The expansion of the CRISPR-Cas toolbox is highly needed to accelerate the development of therapies for genetic diseases. Here, through the interrogation of a massively expanded repository of metagenome-assembled genomes, mostly from human microbiomes, we uncover a large variety (n = 17,173) …

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Eukaryotic-driven directed evolution of Cas9 nucleases

Giulia Vittoria Ruta, Matteo Ciciani, Eyemen Kheir, Michele Domenico Gentile et autres

BACKGROUND: Further advancement of genome editing highly depends on the development of tools with higher compatibility with eukaryotes. A multitude of described Cas9s have great potential but require optimization for genome editing purposes. Among these, the Cas9 from Campylobacter jejuni, CjCas9, has …

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