Transcriptome profiling of human dermal MDPL fibroblasts reveals a characteristic molecular signature providing insights into pathogenic mechanisms

Michela Murdocca; Gerardo Pepe; Serena Maccaroni; Paola Spitalieri; Manuela Helmer-Citterich; Giuseppe Novelli; Federica Sangiuolo

doi:10.1007/s00109-025-02597-y

Transcriptome profiling of human dermal MDPL fibroblasts reveals a characteristic molecular signature providing insights into pathogenic mechanisms

J Mol Med (Berl). 2025 Oct 13. doi: 10.1007/s00109-025-02597-y. Online ahead of print.

Authors

Michela Murdocca¹, Gerardo Pepe², Serena Maccaroni¹, Paola Spitalieri¹, Manuela Helmer-Citterich², Giuseppe Novelli¹, Federica Sangiuolo³

Affiliations

¹ Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.
² Department of Biology, University of Rome "Tor Vergata", Via Della Ricerca Scientifica 1, 00133, Rome, Italy.
³ Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy. sangiuolo@med.uniroma2.it.

PMID: 41083899
DOI: 10.1007/s00109-025-02597-y

Abstract

The emerging perception that the mammalian dermis encloses fibroblasts with differing functional identities has profound implications for understanding a wide range of genetic pathological states, including aging. MDPL syndrome (mandibular hypoplasia, deafness, progeroid characteristics, and lipodystrophy; MIM #615381) is an extremely rare, genetic progeroid disorder. Patients reported variants in the POLD1 gene (NM_002691.3), encoding for the evolutionarily conserved catalytic subunit of DNA polymerase delta (Polδ). The protein is a critical enzyme reliable for synthesizing nascent DNA strands in the eukaryotic genome. Importantly, Polδ also serves to repair DNA lesions due to mutagen exposure. As the natural history of MDPL still remains poorly known, we have performed RNA sequencing analyses on human dermal fibroblasts (HDFs) of two MDPL patients, heterozygotes for p.Ser605del, compared to WT HDFs. The bioinformatic analyses identify differentially expressed transcripts related to the extracellular matrix of connective tissue and transduction signal markers. Successively, we shed light on the capacity of MDPL cells to respond to and repair DNA damage by comparing transcript levels between X-irradiated MDPL HDFs and non-irradiated ones. Importantly, the results allowed us to identify specific downregulated molecular traits in irradiated MDPL HDFs, including those genes closely involved in the mechanisms of DNA replication and repair. These data were further validated at the functional level, choosing four pivotal proteins (CDC6 (Cell Division Cycle 6), CLSPN (Claspin), XRCC3 (X-Ray Repair Cross Complementing 3), RAD51 (DNA repair protein RAD51 homolog 1)) involved in interconnected pathways ensuring genomic stability. This work provides critical insights into the pathogenesis and the regulatory mechanisms of MDPL syndrome and related diseases, paving the way for future therapeutic interventions. KEY MESSAGES: We identified a molecular signature in MDPL human dermal fibroblasts by transcriptomic profiling. We identified specific markers linked to the extracellular matrix of connective tissue and transduction signal markers. We ascertained in irradiated MDPL human dermal fibroblasts specific downregulated molecular traits, involved in the mechanisms of DNA replication and repair. We validated at functional and biochemical level specific those proteins involved in pathways ensuring genomic stability. The markers identified could be targeted for therapeutic intervention in MDPL syndrome and aging-related diseases.

Keywords: Aging; DNA repair; MDPL syndrome; POLD1; RNA sequencing.

Abstract

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