@article{%a1.%Y_160,

title = {Blocking lipid synthesis induces DNA damage in prostate cancer and increases cell death caused by PARP inhibition},

author = {Ribeiro CF and Rodrigues S and Bastos DC and Fanelli GN and Pakula H and Foiani M and Zadra G and Loda M},

url = {https://www.science.org/doi/10.1126/scisignal.adh1922?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed},

doi = {10.1126/scisignal.adh1922},

year  = {2024},

date = {2024-05-28},

journal = {Science signaling},

volume = {17},

issue = {831},

abstract = {Androgen deprivation therapy (ADT) is the primary treatment for prostate cancer; however, resistance to ADT invariably develops, leading to castration-resistant prostate cancer (CRPC). Prostate cancer progression is marked by increased de novo synthesis of fatty acids due to overexpression of fatty acid synthase (FASN), making this enzyme a therapeutic target for prostate cancer. Inhibition of FASN results in increased intracellular amounts of ceramides and sphingomyelin, leading to DNA damage through the formation of DNA double-strand breaks and cell death. We found that combining a FASNi with the poly-ADP ribose polymerase (PARP) inhibitor olaparib, which induces cell death by blocking DNA damage repair, resulted in a more pronounced reduction in cell growth than that caused by either drug alone. Human CRPC organoids treated with a combination of PARP and FASNi were smaller, had decreased cell proliferation, and showed increased apoptosis and necrosis. Together, these data indicate that targeting FASN increases the therapeutic efficacy of PARP inhibitors by impairing DNA damage repair, suggesting that combination therapies should be explored for CRPC.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_159,

title = {4-Trifluoromethyl bithiazoles as broad-spectrum antimicrobial agents for virus-related bacterial infections or co-infections},

author = {Barbieri F and Carlen V and Martina MG and Sannio F and Cancade S and Perini C and Restori M and Crespan E and Maga G and Docquier JD and Cagno V and Radi M.},

url = {https://pubs.rsc.org/en/content/articlelanding/2024/md/d3md00686g},

doi = {10.1039/d3md00686g},

year  = {2024},

date = {2024-05-28},

journal = {RSC medicinal chemistry},

volume = {15},

issue = {5},

pages = {1589-1600},

abstract = {Respiratory tract infections involving a variety of microorganisms such as viruses, bacteria, and fungi are a prominent cause of morbidity and mortality globally, exacerbating various pre-existing respiratory and non-respiratory conditions. Moreover, the ability of bacteria and viruses to coexist might impact the development and severity of lung infections, promoting bacterial colonization and subsequent disease exacerbation. Secondary bacterial infections following viral infections represent a complex challenge to be overcome from a therapeutic point of view. We report herein our efforts in the development of new bithiazole derivatives showing broad-spectrum antimicrobial activity against both viruses and bacteria. A series of 4-trifluoromethyl bithiazole analogues was synthesized and screened against selected viruses (hRVA16, EVD68, and ZIKV) and a panel of Gram-positive and Gram-negative bacteria. Among them, two promising broad-spectrum antimicrobial compounds (8a and 8j) have been identified: both compounds showed low micromolar activity against all tested viruses, 8a showed synergistic activity against E. coli and A. baumannii in the presence of a subinhibitory concentration of colistin, while 8j showed a broader spectrum of activity against Gram-positive and Gram-negative bacteria. Activity against antibiotic-resistant clinical isolates is also reported. Given the ever-increasing need to adequately address viral and bacterial infections or co-infections, this study paves the way for the development of new agents with broad antimicrobial properties and synergistic activity with common antivirals and antibacterials.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_158,

title = {TERRA ONTseq: a long read-based sequencing pipeline to study the human telomeric transcriptome},

author = {Rodrigues J and Alfieri R and Bione S and Azzalin C.},

url = {https://rnajournal.cshlp.org/content/early/2024/05/22/rna.079906.123.long},

doi = {10.1261/rna.079906.123},

year  = {2024},

date = {2024-05-28},

journal = {RNA},

abstract = {The long noncoding RNA TERRA is transcribed from telomeres in virtually all eukaryotes with linear chromosomes. In humans, TERRA transcription is driven in part by promoters comprising CpG dinucleotide-rich repeats of 29 base pairs (29 bp repeats), believed to be present in half of the subtelomeres. Thus far, TERRA expression has been analyzed mainly using molecular biology-based approaches that only generate partial and somehow biased results. Here, we present a novel experimental pipeline to study human TERRA based on long read sequencing (TERRA ONTseq). By applying TERRA ONTseq to different cell lines, we show that the vast majority of human telomeres produce TERRA and that the cellular levels of TERRA transcripts varies according to their chromosomes of origin. Using TERRA ONTseq, we also identified regions containing TERRA transcription start sites (TSSs) in more than half of human subtelomeres. TERRA TSS regions are generally found immediately downstream of 29 bp repeat-related sequences, which appear to be more widespread than previously estimated. Finally, we isolated a novel TERRA promoter from the highly expressed subtelomere of the long arm of chromosome 7. With the development of TERRA ONTseq, we provide a refined picture of human TERRA biogenesis and expression and we equip the scientific community with an invaluable tool for future studies.},

keywords = {},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{%a1.%Y,

title = {An Adapted Questionnaire Tailored for Assessing the Risk of Vitamin D Deficiency in Children That Is Proving Useful in Guiding Clinical Interventions},

author = {Calcaterra V and Cena H and De Giuseppe R and Biino G and Grazi R and Manuelli M and Zanelli S and Tagi V and Vincenti A and Zuccotti G and Fabiano V.},

url = {https://www.mdpi.com/2072-6643/16/7/971},

doi = {10.3390/nu16070971},

year  = {2024},

date = {2024-05-28},

urldate = {2024-05-28},

journal = {Nutrients},

volume = {16},

issue = {7},

pages = {971},

abstract = {Background: The identification of vitamin D (VitD) deficiency in pediatric populations is essential for preventive healthcare. We refined and tested the Evaluation of Deficiency Questionnaire (EVIDENCe-Q) for its utility in detecting VitD insufficiency among children. Patients and methods: We enrolled 201 pediatric patients (aged between 3 and 18 years). Clinical evaluation and serum vitamin D levels were assessed in all subjects. The EVIDENCe-Q was updated to incorporate factors influencing VitD biosynthesis, intake, assimilation, and metabolism, with scores spanning from 0 (optimal) to 36 (poor). Results: We established scores for severe deficiency (<10 mg/dL) at 20, deficiency (<20 mg/dL) at 22, and insufficiency (<30 mg/dL) at 28. A score of 20 or greater was determined as the optimal cut-off for distinguishing VitD deficient from sufficient statuses, as evidenced by ROC curve analysis AUC = 0.7066; SE = 0.0841; sensitivity 100%, 95% CI 0.561-1. The most accurate alignment was seen with VitD insufficiency, defined as 25-OH-D3 < 20 ng/mL. Conclusions: This study confirms that the EVIDENCe-Q is a valid instrument for assessing the risk of vitamin D deficiency and insufficiency in children. It offers a practical approach for determining the need for clinical intervention and dietary supplementation of VitD in the pediatric population.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_156,

title = {Histochemical and ultrastructural localization of triterpene saponins in Medicago truncatula},

author = {Zannino L and Carelli M and Milanesi G and Croce AC and Biggiogera M and Confalonieri M},

url = {https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/jemt.24591},

doi = {10.1002/jemt.24591},

year  = {2024},

date = {2024-05-28},

journal = {Microscopy research and technique},

abstract = {"In the Medicago genus, saponins are complex mixtures of triterpene pentacyclic glycosides extensively studied for their different and economically relevant biological and pharmaceutical properties. This research is aimed at determining for the first time the tissue and cellular localization of triterpene saponins in vegetative organs of Medicago truncatula, a model plant species for legumes, by histochemistry and transmission electron microscopy. The results showed that saponins are present mainly in the palisade mesophyll layer of leaves, whereas in stems they are mostly located in the primary phloem and the subepidermal cells of cortical parenchyma. In root tissue, saponins occur in the secondary phloem region. Transmission electron microscopy revealed prominent saponin accumulation within the leaf and stem chloroplasts, while in the roots the saponins are found in the vesicular structures. Our results demonstrate the feasibility of using histochemistry and transmission electron microscopy to localize M. truncatula saponins at tissue and cellular levels and provide important information for further studies on biosynthesis and regulation of valuable bioactive saponins on agronomic relevant Medicago spp., such as alfalfa (Medicago sativa L.). RESEARCH HIGHLIGHTS: The Medicago genus represents a valuable rich source of saponins, one of the most interesting groups of secondary plant metabolites, which possess relevant biological and pharmacological properties. Plant tissue and cellular localization of saponins is of great importance to better understand their biological functions, biosynthetic pathway, and regulatory mechanisms. We elucidate the localization of saponins in Medicago truncatula with histochemical and transmission electron microscopy studies.

"},

keywords = {},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{%a1.%Y,

title = {The NFATc1/P2X7 receptor relationship in human intervertebral disc cells},

author = {Notarangelo MP and Penolazzi L and Lambertini E and Falzoni S and De Bonis P and Capanni C and Di Virgilio F and Piva R.},

url = {https://www.frontiersin.org/articles/10.3389/fcell.2024.1368318/full},

doi = {10.3389/fcell.2024.1368318},

year  = {2024},

date = {2024-05-28},

urldate = {2024-05-28},

journal = {Frontiers in cell and developmental biology},

volume = {12},

pages = {1368318},

abstract = {A comprehensive understanding of the molecules that play key roles in the physiological and pathological homeostasis of the human intervertebral disc (IVD) remains challenging, as does the development of new therapeutic treatments. We recently found a positive correlation between IVD degeneration (IDD) and P2X7 receptor (P2X7R) expression increases both in the cytoplasm and in the nucleus. Using immunocytochemistry, reverse transcription PCR (RT-PCR), overexpression, and chromatin immunoprecipitation, we found that NFATc1 and hypoxia-inducible factor-1α (HIF-1α) are critical regulators of P2X7R. Both transcription factors are recruited at the promoter of the P2RX7 gene and involved in its positive and negative regulation, respectively. Furthermore, using the proximity ligation assay, we revealed that P2X7R and NFATc1 form a molecular complex and that P2X7R is closely associated with lamin A/C, a major component of the nuclear lamina. Collectively, our study identifies, for the first time, P2X7R and NFATc1 as markers of IVD degeneration and demonstrates that both NFATc1 and lamin A/C are interaction partners of P2X7R.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_153,

title = {Replicative senescence and high glucose induce the accrual of self-derived cytosolic nucleic acids in human endothelial cells},

author = {Ramini D and Giuliani A and Kwiatkowska KM and Guescini M and Storci G and Mensa' E and Recchioni R and Xumerle L and Zago E and Sabbatinelli J and Santi S and Garagnani P and Bonafe' M and Olivieri F.},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11032409/},

doi = {10.1038/s41420-024-01954-z},

year  = {2024},

date = {2024-05-28},

urldate = {2024-05-28},

journal = {Cell death discovery},

volume = {10},

number = {184},

issue = {1},

abstract = {Recent literature shows that loss of replicative ability and acquisition of a proinflammatory secretory phenotype in senescent cells is coupled with the build-in of nucleic acids in the cytoplasm. Its implication in human age-related diseases is under scrutiny. In human endothelial cells (ECs), we assessed the accumulation of intracellular nucleic acids during in vitro replicative senescence and after exposure to high glucose concentrations, which mimic an in vivo condition of hyperglycemia. We showed that exposure to high glucose induces senescent-like features in ECs, including telomere shortening and proinflammatory cytokine release, coupled with the accrual in the cytoplasm of telomeres, double-stranded DNA and RNA (dsDNA, dsRNA), as well as RNA:DNA hybrid molecules. Senescent ECs showed an activation of the dsRNA sensors RIG-I and MDA5 and of the DNA sensor TLR9, which was not paralleled by the involvement of the canonical (cGAS) and non-canonical (IFI16) activation of the STING pathway. Under high glucose conditions, only a sustained activation of TLR9 was observed. Notably, senescent cells exhibit increased proinflammatory cytokine (IL-1β, IL-6, IL-8) production without a detectable secretion of type I interferon (IFN), a phenomenon that can be explained, at least in part, by the accumulation of methyl-adenosine containing RNAs. At variance, exposure to exogenous nucleic acids enhances both IL-6 and IFN-β1 expression in senescent cells. This study highlights the accrual of cytoplasmic nucleic acids as a marker of senescence-related endothelial dysfunction, that may play a role in dysmetabolic age-related diseases.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_152,

title = {Epithelial-to-mesenchymal transition and NF-kB pathways are promoted by a mutant form of DDB2, unable to bind PCNA, in UV-damaged human cells},

author = {Perucca P and Bassi E and Vetro M and Tricarico A and Prosperi E and Stivala LA and Cazzalini O},

url = {https://bmccancer.biomedcentral.com/articles/10.1186/s12885-024-12368-6},

doi = {10.1186/s12885-024-12368-6},

year  = {2024},

date = {2024-05-28},

journal = {BMC CANCER},

volume = {24},

issue = {1},

pages = {616},

abstract = {Background: DNA-Damaged Binding protein 2 (DDB2) is a protein involved in the early step of Nucleotide Excision Repair. Recently, it has been reported that DDB2 is involved in epithelial-to-mesenchymal transition (EMT), key process in tumour invasiveness and metastasis formation. However, its role is not completely known. Methods: Boyden chamber and cell adhesion assays, and ICELLigence analysis were performed to detect HEK293 adhesion and invasion. Western blotting and gelatine zymography techniques were employed to assess the EMT protein levels and MMP enzymatic activity. Immunofluorescence analysis and pull-down assays facilitated the detection of NF-kB sub-cellular localization and interaction. Results: We have previously demonstrated that the loss of DDB2-PCNA binding favours genome instability, and increases cell proliferation and motility. Here, we have investigated the phenotypic and molecular EMT-like changes after UV DNA damage, in HEK293 clones stably expressing DDB2Wt protein or a mutant form unable to interact with PCNA (DDB2PCNA-), as well as in HeLa cells transiently expressing the same DDB2 constructs. Cells expressing DDB2PCNA- showed morphological modifications along with a reduced expression of E-cadherin, an increased activity of MMP-9 and an improved ability to migrate, in concomitance with a significant upregulation of EMT-associated Transcription Factors (TFs), whose expression has been reported to favour tumour invasion. We observed a higher expression of c-Myc oncogene, NF-kB, both regulating cell proliferation and metastatic process, as well as ZEB1, a TF significantly associated with tumorigenic potential and cell migratory ability. Interestingly, a novel interaction of DDB2 with NF-kB was detected and found to be increased in cells expressing the DDB2PCNA-, suggesting a direct modulation of NF-kB by DDB2. Conclusion: These results highlight the role of DDB2-PCNA interaction in counteracting EMT since DDB2PCNA- protein induces in HEK293 transformed cells a gain of function contributing to the acquisition of a more aggressive phenotype.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_154,

title = {Molecular engineering of a spheroid-penetrating phage nanovector for photodynamic treatment of colon cancer cells},

author = {Turrini E and Ulfo L and Costantini PE and Saporetti R and Di Giosia M and Nigro M and Petrosino A and Pappagallo L and Kaltenbrunner A and Cantelli A and Pellicioni V and Catanzaro E and Fimognari C and Calvaresi M and Danielli A.},

url = {https://link.springer.com/article/10.1007/s00018-024-05174-7},

doi = {10.1007/s00018-024-05174-7},

year  = {2024},

date = {2024-05-14},

journal = {Cellular and molecular life sciences},

volume = {81},

issue = {1},

pages = {144},

abstract = {Photodynamic therapy (PDT) represents an emerging strategy to treat various malignancies, including colorectal cancer (CC), the third most common cancer type. This work presents an engineered M13 phage retargeted towards CC cells through pentavalent display of a disulfide-constrained peptide nonamer. The M13CC nanovector was conjugated with the photosensitizer Rose Bengal (RB), and the photodynamic anticancer effects of the resulting M13CC-RB bioconjugate were investigated on CC cells. We show that upon irradiation M13CC-RB is able to impair CC cell viability, and that this effect depends on i) photosensitizer concentration and ii) targeting efficiency towards CC cell lines, proving the specificity of the vector compared to unmodified M13 phage. We also demonstrate that M13CC-RB enhances generation and intracellular accumulation of reactive oxygen species (ROS) triggering CC cell death. To further investigate the anticancer potential of M13CC-RB, we performed PDT experiments on 3D CC spheroids, proving, for the first time, the ability of engineered M13 phage conjugates to deeply penetrate multicellular spheroids. Moreover, significant photodynamic effects, including spheroid disruption and cytotoxicity, were readily triggered at picomolar concentrations of the phage vector. Taken together, our results promote engineered M13 phages as promising nanovector platform for targeted photosensitization, paving the way to novel adjuvant approaches to fight CC malignancies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_150,

title = {Judith Campisi (1948-2024)},

author = {Wiley CD and Hara E and {d'Adda di Fagagna F}},

url = {https://www.nature.com/articles/s43587-024-00603-5},

doi = {10.1038/s43587-024-00603-5},

year  = {2024},

date = {2024-03-18},

urldate = {2024-03-18},

journal = {Nature Aging},

volume = {4},

number = {435-436},

issue = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_149,

title = {Molecular characterization of ANKRD1 in rhabdomyosarcoma cell lines: expression, localization, and proteasomal degradation.},

author = {Milosevic E and Novkovic M and Cenni V and Bavelloni A and Kojic S and Jasnic J},

url = {https://link.springer.com/article/10.1007/s00418-024-02272-2},

doi = {10.1007/s00418-024-02272-2},

year  = {2024},

date = {2024-03-18},

urldate = {2024-03-18},

journal = {Histochemistry and cell biology},

volume = {161},

issue = {5},

pages = {435},

abstract = {Rhabdomyosarcoma (RMS) is the most common soft tissue malignancy in children and adolescents. Respecting the age of the patients and the tumor aggressiveness, investigation of the molecular mechanisms of RMS tumorigenesis is directed toward the identification of novel therapeutic targets. To contribute to a better understanding of the molecular pathology of RMS, we investigated ankyrin repeat domain 1 (ANKRD1), designated as a potential marker for differential diagnostics. In this study, we used three RMS cell lines (SJRH30, RD, and HS-729) to assess its expression profile, intracellular localization, and turnover. They express wild-type ANKRD1, as judged by the sequencing of the open reading frame. Each cell line expressed a different amount of ANKRD1 protein, although the transcript level was similar. According to western blot analysis, ANKRD1 protein was expressed at detectable levels in the SJRH30 and RD cells (SJRH30 > RD), but not in the HS-729, even after immunoprecipitation. Immunocytochemistry revealed nuclear and cytoplasmic localization of ANKRD1 in all examined cell lines. Moreover, the punctate pattern of ANKRD1 staining in the nuclei of RD and HS-729 cells overlapped with coilin, indicating its association with Cajal bodies. We have shown that RMS cells are not able to overexpress ANKRD1 protein, which can be attributed to its proteasomal degradation. The unsuccessful attempt to overexpress ANKRD1 in RMS cells indicates the possibility that its overexpression may have detrimental effects for RMS cells and opens a window for further research into its role in RMS pathogenesis and for potential therapeutic targeting.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_148,

title = {Proceedings of the annual meeting of the European Consortium of Lipodystrophies (ECLip), Pisa, Italy, 28-29 September 2023.},

author = {Ceccarini G and Akinci B and Araujo-Vilar D and Beghini M and Brown RJ and Tudela JC and Corradin V and Donadille B and Ruiz JJ and Jeru I and Lattanzi G and Maffei M and McIlroy GD and Nobécourt E and Perez de Tudela N and Rochford J and Sanders R and Schnurbein JV and Tews D and Vantyghem MC and Vatier C and Vigouroux C and Santini F.},

url = {https://www.sciencedirect.com/science/article/pii/S0003426624000362?via%3Dihub},

doi = {10.1016/j.ando.2024.03.002},

year  = {2024},

date = {2024-03-18},

urldate = {2024-03-18},

journal = {Annales d'endocrinologie},

volume = {S0003-4266},

issue = {24},

abstract = {Lipodystrophic syndromes are rare diseases affecting primarily the development or maintenance of the adipose tissue but are also distressing indirectly multiple organs and tissues, causing in most of the cases reduced life expectancy and quality of life. Lipodystrophy syndromes are multifaceted disorders caused by genetic mutations or autoimmune and iatrogenic mechanisms, many subtypes are now recognized and classified but the disease remains remarkably underdiagnosed. The European Consortium of Lipodystrophies (ECLip) was founded in 2014 as a non-profit network of European centers of excellence working in the field of lipodystrophies aiming at promoting international collaborations to increase basic scientific understanding and clinical management of these syndromes. The network has developed a European Patient Registry as a collaborative research platform for consortium members. ECLip and ECLip registry activities involve patient advocacy groups to increase public awareness and to advice on research activities relevant from the patients perspective. The annual ECLip congress gives an update on the research results of the various network groups members.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_147,

title = {ZEB1 shapes AML immunological niches, suppressing CD8 T cell activity while fostering Th17 cell expansion},

author = {Bassani B and Simonetti G and Cancila V and Fiorino A and Ciciarello M and Piva A and Khorasani AM and Chiodoni C and Lecis D and Gulino A and Fonzi E and Botti L and Portararo P and Costanza M and Brambilla M and Colombo G and Schwaller J and Tzankov A and Ponzoni M and Ciceri F and Bolli N and Curti A and Tripodo C and Colombo MP and Sangaletti S},

url = {https://www.sciencedirect.com/science/article/pii/S2211124724001220?via%3Dihub},

doi = {10.1016/j.celrep.2024.113794},

year  = {2024},

date = {2024-03-11},

journal = {Cell reports},

volume = {43},

issue = {2},

pages = {113794},

abstract = {Acute myeloid leukemia (AML) progression is influenced by immune suppression induced by leukemia cells. ZEB1, a critical transcription factor in epithelial-to-mesenchymal transition, demonstrates immune regulatory functions in AML. Silencing ZEB1 in leukemic cells reduces engraftment and extramedullary disease in immune-competent mice, activating CD8 T lymphocytes and limiting Th17 cell expansion. ZEB1 in AML cells directly promotes Th17 cell development that, in turn, creates a self-sustaining loop and a pro-invasive phenotype, favoring transforming growth factor beta (TGF-beta), interleukin-23 (IL-23), and SOCS2 gene transcription. In bone marrow biopsies from AML patients, immunohistochemistry shows a direct correlation between ZEB1 and Th17. Also, the analysis of ZEB1 expression in larger datasets identifies two distinct AML groups, ZEB1high and ZEB1low, each with specific immunological and molecular traits. ZEB1high patients exhibit increased IL-17, SOCS2, and TGF-beta pathways and a negative association with overall survival. This unveils ZEB1's dual role in AML, entwining pro-tumoral and immune regulatory capacities in AML blasts.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_145,

title = {SnapShot: Tolerating replication stress},

author = {Szakal B and Giannattasio M and Branzei D},

url = {https://www.sciencedirect.com/science/article/abs/pii/S1097276523009760?via%3Dihub},

doi = {10.1016/j.molcel.2023.11.031},

year  = {2024},

date = {2024-02-13},

urldate = {2024-02-13},

journal = {Molecular cell},

volume = {84},

issue = {1},

pages = {182},

abstract = {Completion of DNA replication relies on the ability of replication forks to traverse various types of DNA damage, actively transcribed regions, and structured DNA. The mechanisms enabling these processes are here referred to as DNA damage tolerance pathways. Here, we depict the stalled DNA replication fork structures with main DNA transactions and key factors contributing to the bypass of such blocks, replication restart, and completion. To view this SnapShot, open or download the PDF.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_144,

title = {A bioartificial and vasculomorphic bone matrix-based organoid mimicking microanatomy of flat and short bones},

author = {Toni R and Barbaro F and Di Conza G and Zini N and Remaggi G and Elviri L and Spaletta G and Quarantini E and Quarantini M and Mosca S and Caravelli S and Mosca M and Ravanetti F and Sprio S and Tampieri A},

url = {https://onlinelibrary.wiley.com/doi/10.1002/jbm.b.35329},

doi = {10.1002/jbm.b.35329},

year  = {2024},

date = {2024-02-12},

journal = {Journal of biomedical materials research. Part B, Applied biomaterials},

volume = {112},

issue = {1},

pages = {e35329},

abstract = {We engineered an in vitro model of bioartificial 3D bone organoid consistent with an anatomical and vascular microenvironment common to mammalian flat and short bones. To achieve this, we chose the decellularized-decalcified matrix of the adult male rat scapula, implemented with the reconstruction of its intrinsic vessels, obtained through an original intravascular perfusion with polylevolactic (PLLA), followed by coating of the PLLA-fabricated vascularization with rat tail collagen. As a result, the 3D bone and vascular geometry of the native bone cortical and cancellous compartments was reproduced, and the rat tail collagen-PLLA biomaterial could in vitro act as a surrogate of the perivascular extracellular matrix (ECM) around the wall of the biomaterial-reconstituted cancellous vessels. As a proof-of-concept of cell compatibility and site-dependent osteoinductive properties of this bioartificial 3D construct, we show that it in vitro leads to a time-dependent microtopographic positioning of rat mesenchymal stromal cells (MSCs), initiating an osteogenic fate in relation to the bone compartment. In addition, coating of PLLA-reconstructed vessels with rat tail collagen favored perivascular attachment and survival of MSC-like cells (mouse embryonic fibroblasts), confirming its potentiality as a perivascular stroma for triggering competence of seeded MSCs. Finally, in vivo radiographic topography of bone lesions in the human jaw and foot tarsus of subjects with primary osteoporosis revealed selective bone cortical versus cancellous involvement, suggesting usefulness of a human 3D bone organoid engineered with the same principles of our rat organoid, to in vitro investigate compartment-dependent activities of human MSC in flat and short bones under experimental osteoporotic challenge. We conclude that our 3D bioartificial construct offers a reliable replica of flat and short bones microanatomy, and promises to help in building a compartment-dependent mechanistic perspective of bone remodeling, including the microtopographic dysregulation of osteoporosis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_143,

title = {Ultrasound Stimulation of Piezoelectric Nanocomposite Hydrogels Boosts Chondrogenic Differentiation in Vitro, in Both a Normal and Inflammatory Milieu},

author = {Ricotti L and Cafarelli A and Manferdini C and Trucco D and Vannozzi L and Gabusi E and Fontana F and Dolzani P and Saleh Y and Lenzi E and Columbaro M and Piazzi M and Bertacchini J and Aliperta A and Cain M and Gemmi M and Parlanti P and Jost C and Fedutik Y and Nessim GD and Telkhozhayeva M and Teblum E and Dumont E and Delbaldo C and Codispoti G and Martini L and Tschon M and Fini M and Lisignoli G},

url = {10.1021/acsnano.3c08738},

doi = {10.1021/acsnano.3c08738},

year  = {2024},

date = {2024-02-12},

journal = {ACS nano},

volume = {18},

issue = {3},

pages = {2047},

abstract = {The use of piezoelectric nanomaterials combined with ultrasound stimulation is emerging as a promising approach for wirelessly triggering the regeneration of different tissue types. However, it has never been explored for boosting chondrogenesis. Furthermore, the ultrasound stimulation parameters used are often not adequately controlled. In this study, we show that adipose-tissue-derived mesenchymal stromal cells embedded in a nanocomposite hydrogel containing piezoelectric barium titanate nanoparticles and graphene oxide nanoflakes and stimulated with ultrasound waves with precisely controlled parameters (1 MHz and 250 mW/cm2, for 5 min once every 2 days for 10 days) dramatically boost chondrogenic cell commitment in vitro. Moreover, fibrotic and catabolic factors are strongly down-modulated: proteomic analyses reveal that such stimulation influences biological processes involved in cytoskeleton and extracellular matrix organization, collagen fibril organization, and metabolic processes. The optimal stimulation regimen also has a considerable anti-inflammatory effect and keeps its ability to boost chondrogenesis in vitro, even in an inflammatory milieu. An analytical model to predict the voltage generated by piezoelectric nanoparticles invested by ultrasound waves is proposed, together with a computational tool that takes into consideration nanoparticle clustering within the cell vacuoles and predicts the electric field streamline distribution in the cell cytoplasm. The proposed nanocomposite hydrogel shows good injectability and adhesion to the cartilage tissue ex vivo, as well as excellent biocompatibility in vivo, according to ISO 10993. Future perspectives will involve preclinical testing of this paradigm for cartilage regeneration.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_142,

title = {Homozygous substitution of threonine 191 by proline in polymerase eta causes Xeroderma pigmentosum variant},

author = {Ricciardiello R and Forleo G and Cipolla L and van Winckel G and Marconi C and Nouspikel T and Halazonetis TD and Zgheib O and Sabbioneda S},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10784498/},

doi = {10.1038/s41598-023-51120-1},

year  = {2024},

date = {2024-02-12},

journal = {Scientific reports},

volume = {14},

issue = {1},

pages = {1117},

abstract = {DNA polymerase eta (Pol-eta) is the only translesion synthesis polymerase capable of error-free bypass of UV-induced cyclobutane pyrimidine dimers. A deficiency in Polη function is associated with the human disease Xeroderma pigmentosum variant (XPV). We hereby report the case of a 60-year-old woman known for XPV and carrying a Pol-eta Thr191Pro variant in homozygosity. We further characterize the variant in vitro and in vivo, providing molecular evidence that the substitution abrogates polymerase activity and results in UV sensitivity through deficient damage bypass. This is the first functional molecular characterization of a missense variant of Pol-eta, whose reported pathogenic variants have thus far been loss of function truncation or frameshift mutations. Our work allows the upgrading of Pol-eta Thr191Pro from 'variant of uncertain significance' to 'likely pathogenic mutant', bearing direct impact on molecular diagnosis and genetic counseling. Furthermore, we have established a robust experimental approach that will allow a precise molecular analysis of further missense mutations possibly linked to XPV. Finally, it provides insight into critical Pol-eta residues that may be targeted to develop small molecule inhibitors for cancer therapeutics.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_141,

title = {Recent Updates on the Therapeutic Prospects of Reversion-Inducing Cysteine-Rich Protein with Kazal Motifs (RECK) in Liver Injuries},

author = {Palladini G and Di Pasqua LG and Croce AC and Ferrigno A and Vairetti M},

url = {https://www.mdpi.com/1422-0067/24/24/17407},

doi = {10.3390/ijms242417407},

year  = {2024},

date = {2024-02-12},

journal = {International journal of molecular sciences},

volume = {24},

issue = {24},

pages = {17407},

abstract = {The reversion-inducing cysteine-rich protein with Kazal motifs (RECK), a membrane-anchored glycoprotein, negatively regulates various membrane proteins involved in the tissue governing extracellular matrix (ECM) remodeling such as metalloproteases (MMPs) and the sheddases ADAM10 and ADAM17. The significance of the present review is to summarize the current understanding of the pathophysiological role of RECK, a newly discovered signaling pathway associated with different liver injuries. Specifically, this review analyzes published data on the downregulation of RECK expression in hepatic ischemia/reperfusion (I/R) injury, liver-related cancers, including hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), as well as in the progression of nonalcoholic fatty liver disease (NAFLD) to non-alcoholic steatohepatitis (NASH). In addition, this review discusses the regulation of RECK by inducers, such as FXR agonists. The RECK protein has also been suggested as a potential diagnostic and prognostic marker for liver injury or as a biomarker with predictive value for drug treatment efficacy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_140,

title = {SnapShot: DNA repair pathways},

author = {Nunomiya A and Szakal B and Branzei D},

url = {https://www.sciencedirect.com/science/article/abs/pii/S1097276523009759?via%3Dihub},

doi = {10.1016/j.molcel.2023.11.030},

year  = {2024},

date = {2024-02-12},

journal = {Molecular cell},

volume = {84},

issue = {1},

pages = {180},

abstract = {The genetic information stored in DNA is under continuous threat by endogenous and environmental sources of DNA damage. Cells have evolved multiple DNA repair pathways that function in overlapping manners, with principles shared across species. Here, we depict the main DNA repair pathways cells rely on, with the primary lesions they are tackling, along with key players and main DNA transactions. To view this SnapShot, open or download the PDF.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_139,

title = {Engagement of CD99 activates distinct programs in Ewing sarcoma and macrophages},

author = {Manara MC and Manferdini C and Cristalli C and Carrabotta M and Santi S and De Feo A and Caldoni G and Pasello M and Landuzzi L and Lollini PL and Salamanna F and Dominici S and Fiori V and Magnani M and Lisignoli G and Scotlandi K},

url = {https://aacrjournals.org/cancerimmunolres/article/doi/10.1158/2326-6066.CIR-23-0440/731506/Engagement-of-CD99-activates-distinct-programs-in},

doi = {10.1158/2326-6066.CIR-23-0440},

year  = {2024},

date = {2024-02-12},

journal = {Cancer immunology research},

volume = {12},

issue = {2},

pages = {247-260},

abstract = {Ewing sarcoma (EWS) is the second most common pediatric bone tumor. The EWS tumor microenvironment is largely recognized as immune-cold, with macrophages being the most abundant immune cells and their presence associated with worse patient prognosis. Expression of CD99 is a hallmark of EWS cells, and its targeting induces inhibition of EWS tumor growth through a poorly understood mechanism. In this study, we analyzed CD99 expression and functions on macrophages and investigated whether the concomitant targeting of CD99 on both tumor and macrophages could explain the inhibitory effect of this approach against EWS. Targeting CD99 on EWS cells downregulated expression of the "don't eat-me" CD47 molecule but increased levels of the "eat-me" phosphatidyl serine and calreticulin molecules on the outer leaflet of the tumor cell membrane, triggering phagocytosis and digestion of EWS cells by macrophages. In addition, CD99 ligation induced reprogramming of undifferentiated M0 macrophages and M2-like macrophages toward the inflammatory M1-like phenotype. These events resulted in the inhibition of EWS tumor growth. Thus, this study reveals what we believe to be a previously unrecognized function of CD99, which engenders a virtuous circle that delivers intrinsic cell death signals to EWS cells, favors tumor cell phagocytosis by macrophages, and promotes the expression of various molecules and cytokines, which are pro-inflammatory and usually associated with tumor regression. This raises the possibility that CD99 may be involved in boosting the antitumor activity of macrophages.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_138,

title = {Leveraging Tissue-Specific Enhancer-Target Gene Regulatory Networks Identifies Enhancer Somatic Mutations That Functionally Impact Lung Cancer},

author = {Hariprakash JM and Salviato E and La Mastra F and Sebestyén E and Tagliaferri I and Silva RS and Lucini F and Farina L and Cinquanta M and Rancati I and Riboni M and Minardi SP and Roz L and Gorini F and Lanzuolo C and Casola S and Ferrari F},

url = {https://aacrjournals.org/cancerres/article/84/1/133/731819/Leveraging-Tissue-Specific-Enhancer-Target-Gene},

doi = {10.1158/0008-5472.CAN-23-1129},

year  = {2024},

date = {2024-02-12},

urldate = {2024-02-12},

journal = {Cancer research},

volume = {84},

issue = {1},

pages = {133-153},

abstract = {Enhancers are noncoding regulatory DNA regions that modulate the transcription of target genes, often over large distances along with the genomic sequence. Enhancer alterations have been associated with various pathological conditions, including cancer. However, the identification and characterization of somatic mutations in noncoding regulatory regions with a functional effect on tumorigenesis and prognosis remain a major challenge. Here, we present a strategy for detecting and characterizing enhancer mutations in a genome-wide analysis of patient cohorts, across three lung cancer subtypes. Lung tissue-specific enhancers were defined by integrating experimental data and public epigenomic profiles, and the genome-wide enhancer-target gene regulatory network of lung cells was constructed by integrating chromatin three-dimensional architecture data. Lung cancers possessed a similar mutation burden at tissue-specific enhancers and exons but with differences in their mutation signatures. Functionally relevant alterations were prioritized on the basis of the pathway-level integration of the effect of a mutation and the frequency of mutations on individual enhancers. The genes enriched for mutated enhancers converged on the regulation of key biological processes and pathways relevant to tumor biology. Recurrent mutations in individual enhancers also affected the expression of target genes, with potential relevance for patient prognosis. Together, these findings show that noncoding regulatory mutations have a potential relevance for cancer pathogenesis and can be exploited for patient classification. Significance: Mapping enhancer-target gene regulatory interactions and analyzing enhancer mutations at the level of their target genes and pathways reveal convergence of recurrent enhancer mutations on biological processes involved in tumorigenesis and prognosis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_137,

title = {FXR agonists INT-787 and OCA increase RECK and inhibit liver steatosis and inflammation in diet-induced ob/ob mouse model of NASH},

author = {Di Pasqua LG and Cagna M and Palladini G and Croce AC and Cadamuro M and Fabris L and Perlini S and Adorini L and Ferrigno A and Vairetti M.},

url = {https://www.sciencedirect.com/science/article/pii/S0171933523000882?via%3Dihub},

doi = {10.1111/liv.15767},

year  = {2024},

date = {2024-02-12},

journal = {Liver international},

volume = {44},

number = {214},

issue = {1},

pages = {227},

abstract = {Background and aims: We have previously shown in a model of hepatic ischaemia/reperfusion injury that the farnesoid X receptor (FXR) agonist obeticholic acid (OCA) restores reversion-inducing-cysteine-rich protein with Kazal motifs (RECK), an inverse modulator of metalloproteases (MMPs) and inhibitor of the sheddases ADAM10 and ADAM17 involved in inflammation and fibrogenesis. Here, the effects of FXR agonists OCA and INT-787 on hepatic levels of RECK, MMPs, ADAM10 and ADAM17 were compared in a diet-induced ob/ob mouse model of non-alcoholic steatohepatitis (NASH). Methods: Lep ob/ob NASH mice fed a high-fat diet (HFD) or control diet (CD) for 9 weeks (wks) were treated with OCA or INT-787 0.05% dosed via HFD admixture (30 mg/kg/day) or HFD for further 12 wks. Serum alanine transaminase (ALT) and inflammatory cytokines, liver RECK, MMP-2 and MMP-9 activity as well as ADAM10, ADAM17, collagen deposition (Sirius red), hepatic stellate cell activation (α-SMA) and pCK+ reactive biliary cells were quantified. Results: Only INT-787 significantly reduced serum ALT, IL-1β and TGF-berta. A downregulation of RECK expression and protein levels observed in HFD groups (at 9 and 21 wks) was counteracted by both OCA and INT-787. HFD induced a significant increase in liver MMP-2 and MMP-9; OCA administration reduced both MMP-2 and MMP-9 while INT-787 markedly reduced MMP-2 expression. OCA and INT-787 reduced both ADAM10 and ADAM17 expression and number of pCK+ cells. INT-787 was superior to OCA in decreasing collagen deposition and α-SMA levels. Conclusion: INT-787 is superior to OCA in controlling specific cell types and clinically relevant anti-inflammatory and antifibrotic molecular mechanisms in NASH.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_136,

title = {Developmental and Nutritional Dynamics of Malpighian Tubule Autofluorescence in the Asian Tiger Mosquito Aedes albopictus},

author = {Croce AC and Garbelli A and Moyano A and Soldano S and Tejeda-Guzman C and Missirlis F and Scolari F},

url = {https://www.mdpi.com/1422-0067/25/1/245},

doi = {10.3390/ijms25010245},

year  = {2024},

date = {2024-02-12},

journal = {International journal of molecular sciences},

volume = {25},

issue = {1},

pages = {245},

abstract = {Malpighian tubules (MTs) are arthropod excretory organs crucial for the osmoregulation, detoxification and excretion of xenobiotics and metabolic wastes, which include tryptophan degradation products along the kynurenine (KYN) pathway. Specifically, the toxic intermediate 3-hydroxy kynurenine (3-HK) is metabolized through transamination to xanthurenic acid or in the synthesis of ommochrome pigments. Early investigations in Drosophila larval fat bodies revealed an intracellular autofluorescence (AF) that depended on tryptophan administration. Subsequent observations documented AF changes in the MTs of Drosophila eye-color mutants genetically affecting the conversion of tryptophan to KYN or 3-HK and the intracellular availability of zinc ions. In the present study, the AF properties of the MTs in the Asian tiger mosquito, Aedes albopictus, were characterized in different stages of the insect's life cycle, tryptophan-administered larvae and blood-fed adult females. Confocal imaging and microspectroscopy showed AF changes in the distribution of intracellular, brilliant granules and in the emission spectral shape and amplitude between the proximal and distal segments of MTs across the different samples. The findings suggest AF can serve as a promising marker for investigating the functional status of MTs in response to metabolic alterations, contributing to the use of MTs as a potential research model in biomedicine.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_135,

title = {CRISPR/Cas9 mediated Y-chromosome elimination affects human cells transcriptome},

author = {Celli L and Gasparini P and Biino G and Zannini L and Cardano M},

url = {https://cellandbioscience.biomedcentral.com/articles/10.1186/s13578-024-01198-5},

doi = {10.1186/s13578-024-01198-5},

year  = {2024},

date = {2024-02-12},

journal = {Cell & bioscience},

volume = {14},

issue = {1},

pages = {15},

abstract = {Background: Sexual dimorphism represents a key concept in the comprehension of molecular processes guiding several sex-specific physiological and pathological mechanisms. It has been reported that genes involved in many disorders show a sex-dependent expression pattern. Moreover, the loss of Y chromosome (LOY), found to be a physiological age-driven phenomenon, has been linked to many neurodegenerative and autoimmune disorders, and to an increased cancer risk. These findings drove us towards the consideration that LOY may cause the de-regulation of disease specific networks, involving genes located in both autosomal and sex chromosomes. Results: Exploiting the CRISPR/Cas9 and RNA-sequencing technologies, we generated a Y-deficient human cell line that has been investigated for its gene expression profile. Our results showed that LOY can influence the transcriptome displaying relevant enriched biological processes, such as cell migration regulation, angiogenesis and immune response. Interestingly, the ovarian follicle development pathway was found enriched, supporting the female-mimicking profile of male Y-depleted cells. Conclusion: This study, besides proposing a novel approach to investigate sex-biased physiological and pathological conditions, highlights new roles for the Y chromosome in the sexual dimorphism characterizing human health and diseases. Moreover, this analysis paves the way for the research of new therapeutic approaches for sex dimorphic and LOY-related diseases.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_134,

title = {FANCJ DNA helicase is recruited to the replisome by AND-1 to ensure genome stability},

author = {Boavida A and Napolitano LM and Santos D and Cortone G and Jegadesan NK and Onesti S and Branzei D and Pisani FM.},

url = {https://www.embopress.org/doi/full/10.1038/s44319-023-00044-y},

doi = {10.1038/s44319-023-00044-y},

year  = {2024},

date = {2024-02-07},

urldate = {2024-02-12},

journal = {EMBO reports},

volume = {25},

issue = {2},

pages = {876-901},

abstract = {FANCJ, a DNA helicase linked to Fanconi anemia and frequently mutated in cancers, counteracts replication stress by dismantling unconventional DNA secondary structures (such as G-quadruplexes) that occur at the DNA replication fork in certain sequence contexts. However, how FANCJ is recruited to the replisome is unknown. Here, we report that FANCJ directly binds to AND-1 (the vertebrate ortholog of budding yeast Ctf4), a homo-trimeric protein adaptor that connects the CDC45/MCM2-7/GINS replicative DNA helicase with DNA polymerase α and several other factors at DNA replication forks. The interaction between FANCJ and AND-1 requires the integrity of an evolutionarily conserved Ctf4-interacting protein (CIP) box located between the FANCJ helicase motifs IV and V. Disruption of the CIP box significantly reduces FANCJ association with the replisome, causing enhanced DNA damage, decreased replication fork recovery and fork asymmetry in cells unchallenged or treated with Pyridostatin, a G-quadruplex-binder, or Mitomycin C, a DNA inter-strand cross-linking agent. Cancer-relevant FANCJ CIP box variants display reduced AND-1-binding and enhanced DNA damage, a finding that suggests their potential role in cancer predisposition.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y,

title = {Desmin and Plectin Recruitment to the Nucleus and Nuclei Orientation Are Lost in Emery-Dreifuss Muscular Dystrophy Myoblasts Subjected to Mechanical Stimulation},

author = {Cenni V and Evangelisti C and Santi S and Sabatelli P and Neri S and Cavallo M and Lattanzi G and Mattioli E},

url = {https://www.mdpi.com/2073-4409/13/2/162},

doi = {10.3390/cells13020162},

year  = {2024},

date = {2024-01-31},

journal = {Cells},

volume = {13},

issue = {2},

pages = {162},

abstract = {n muscle cells subjected to mechanical stimulation, LINC complex and cytoskeletal proteins are basic to preserve cellular architecture and maintain nuclei orientation and positioning. In this context, the role of lamin A/C remains mostly elusive. This study demonstrates that in human myoblasts subjected to mechanical stretching, lamin A/C recruits desmin and plectin to the nuclear periphery, allowing a proper spatial orientation of the nuclei. Interestingly, in Emery-Dreifuss Muscular Dystrophy (EDMD2) myoblasts exposed to mechanical stretching, the recruitment of desmin and plectin to the nucleus and nuclear orientation were impaired, suggesting that a functional lamin A/C is crucial for the response to mechanical strain. While describing a new mechanism of action headed by lamin A/C, these findings show a structural alteration that could be involved in the onset of the muscle defects observed in muscular laminopathies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_106,

title = {Normal and pathogenic variation of RFC1 repeat expansions: implications for clinical diagnosis},

author = {Dominik N and Magri S and Currò R and Abati E and Facchini S and Corbetta M and MacPherson H and Di Bella D and Sarto E and Stevanovski I and Chintalaphani SR and Akcimen F and Manini A and Vegezzi E and Quartesan I and Montgomery KA and Pirota V and Crespan E and Perini C and Grupelli GP and Tomaselli PJ and Marques W andGenomics England Research Consortium; Shaw J and Polke J and Salsano E and Fenu S and Pareyson D and Pisciotta C and Tofaris GK and Nemeth AH and Ealing J and Radunovic A and Kearney S and Kumar KR and Vucic S and Kennerson M and Reilly MM and Houlden H and Deveson I and Tucci A and Taroni F and Cortese A},

url = {https://academic.oup.com/brain/advance-article/doi/10.1093/brain/awad240/7224416?login=true},

doi = {10.1093/brain/awad240},

year  = {2023},

date = {2023-12-27},

urldate = {2023-12-27},

journal = {Brain},

volume = {146},

issue = {12},

pages = {5060-5069},

abstract = {Cerebellar Ataxia, Neuropathy and Vestibular Areflexia Syndrome (CANVAS) is an autosomal recessive neurodegenerative disease, usually caused by biallelic AAGGG repeat expansions in RFC1. In this study, we leveraged whole genome sequencing (WGS) data from nearly 10,000 individuals recruited within the Genomics England sequencing project to investigate the normal and pathogenic variation of the RFC1 repeat. We identified three novel repeat motifs, AGGGC (n=6 from 5 families), AAGGC (n=2 from 1 family), AGAGG (n=1), associated with CANVAS in the homozygous or compound heterozygous state with the common pathogenic AAGGG expansion. While AAAAG, AAAGGG and AAGAG expansions appear to be benign, here we show a pathogenic role for large AAAGG repeat configuration expansions (n=5). Long read sequencing was used to fully characterise the entire repeat sequence and revealed a pure AGGGC expansion in six patients, whereas the other patients presented complex motifs with AAGGG or AAAGG interruptions. All pathogenic motifs seem to have arisen from a common haplotype and are predicted to form highly stable G quadruplexes, which have been previously demonstrated to affect gene transcription in other conditions. The assessment of these novel configurations is warranted in CANVAS patients with negative or inconclusive genetic testing. Particular attention should be paid to carriers of compound AAGGG/AAAGG expansions, since the AAAGG motif when very large (>500 repeats) or in the presence of AAGGG interruptions. Accurate sizing and full sequencing of the satellite repeat with long read is recommended in clinically selected cases, in order to achieve an accurate molecular diagnosis and counsel patients and their families.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_130,

title = {High promiscuity among females of the invasive pest species Drosophila suzukii},

author = {Puppato S and Fiorenza G and Carraretto D and Gomulski LM and Gasperi G and Caceres C and Grassi A and Mancini MV and De Cristofaro A and Ioriatti C and Guilhot R and Malacrida AR},

url = {https://onlinelibrary.wiley.com/doi/10.1111/mec.17161},

doi = {10.1111/mec.17161},

year  = {2023},

date = {2023-12-08},

journal = {Molecular ecology},

volume = {32},

issue = {22},

pages = {6018},

abstract = {Drosophila suzukii (Matsumura, 1931), the spotted-wing drosophila, is a highly invasive fruit fly that spread from Southern Asia across most regions of Asia and, in the last 15 years, has invaded Europe and the Americas. It is an economically important pest of small fruits such as berries and stone fruits. Drosophila suzukii speciated by adapting to cooler, mountainous, and forest environments. In temperate regions, it evolved seasonal polyphenism traits which enhanced its survival during stressful winter population bottlenecks. Consequently, in these temperate regions, the populations undergo seasonal reproductive dynamics. Despite its economic importance, no data are available on the behavioural reproductive strategies of this fly. The presence of polyandry, for example, has not been determined despite the important role it might play in the reproductive dynamics of populations. We explored the presence of polyandry in an established population in Trentino, a region in northern Italy. In this area, D. suzukii overcomes the winter bottleneck and undergoes a seasonal reproductive fluctuation. We observed a high remating frequency in females during the late spring demographic explosion that led to the abundant summer population. The presence of a high degree of polyandry and shared paternity associated with the post-winter population increase raises the question of the possible evolutionary adaptive role of this reproductive behaviour in D. suzukii.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_125,

title = {Proteomic Analysis on Sequential Samples of Cystic Fluid Obtained from Human Brain Tumors},

author = {Magrassi L and Brambilla F and Viganò R and Di Silvestre D and Benazzi L and Bellantoni G and Danesino GM and Comincini S and Mauri P},

url = {https://www.mdpi.com/2072-6694/15/16/4070},

doi = {10.3390/cancers15164070},

year  = {2023},

date = {2023-12-07},

journal = {Cancers-Basel},

volume = {15},

issue = {16},

pages = {4070},

abstract = {Cystic formation in human primary brain tumors is a relatively rare event whose incidence varies widely according to the histotype of the tumor. Composition of the cystic fluid has mostly been characterized in samples collected at the time of tumor resection and no indications of the evolution of cystic content are available. We characterized the evolution of the proteome of cystic fluid using a bottom-up proteomic approach on sequential samples obtained from secretory meningioma (SM), cystic schwannoma (CS) and cystic high-grade glioma (CG). We identified 1008 different proteins; 74 of these proteins were found at least once in the cystic fluid of all tumors. The most abundant proteins common to all tumors studied derived from plasma, with the exception of prostaglandin D2 synthase, which is a marker of cerebrospinal fluid origin. Overall, the protein composition of cystic fluid obtained at different times from the same tumor remained stable. After the identification of differentially expressed proteins (DEPs) and the protein-protein interaction network analysis, we identified the presence of tumor-specific pathways that may help to characterize tumor-host interactions. Our results suggest that plasma proteins leaking from local blood-brain barrier disruption are important contributors to cyst fluid formation, but cerebrospinal fluid (CSF) and the tumor itself also contribute to the cystic fluid proteome and, in some cases, as with immunoglobulin G, shows tumor-specific variations that cannot be simply explained by differences in vessel permeability or blood contamination.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_124,

title = {Impact of heat and cold shock on epigenetics and chromatin structure},

author = {Casali C and Galgano L and Zannino L and Siciliani S and Cavallo M and Mazzini G and Biggiogera M},

url = {https://www.sciencedirect.com/science/article/pii/S0171933523000882?via%3Dihub},

doi = {10.1016/j.ejcb.2023.151373},

year  = {2023},

date = {2023-12-02},

urldate = {2024-01-28},

journal = {European journal of cell biology},

volume = {103},

issue = {1},

pages = {151373},

abstract = {Cells are continuously exposed to various sources of insults, among which temperature variations are extremely common. Epigenetic mechanisms, critical players in gene expression regulation, undergo alterations due to these stressors, potentially leading to health issues. Despite the significance of DNA methylation and histone modifications in gene expression regulation, their changes following heat and cold shock in human cells remain poorly understood. In this study, we investigated the epigenetic profiles of human cells subjected to hyperthermia and hypothermia, revealing significant variations. Heat shock primarily led to DNA methylation increments and epigenetic modifications associated with gene expression silencing. In contrast, cold shock presented a complex scenario, with both methylation and demethylation levels increasing, indicating different epigenetic responses to the opposite thermal stresses. These temperature-induced alterations in the epigenome, particularly their impact on chromatin structural organization, represent an understudied area that could offer important insights into genome function and potential prospects for therapeutic targets.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_128,

title = {A modular phage vector platform for targeted photodynamic therapy of Gram-negative bacterial pathogens},

author = {Petrosino A and Saporetti R and Starinieri F and Sarti E and Ulfo L and Boselli L and Cantelli A and Morini A and Zadran SK and Zuccheri G and Pasquini Z and Di Giosia M and Prodi L and Pompa PP and Costantini PE and Calvaresi M and Danielli A},

url = {https://www.sciencedirect.com/science/article/pii/S2589004223021090?via%3Dihub},

doi = {10.1016/j.isci.2023.108032},

year  = {2023},

date = {2023-10-18},

journal = {ISCIENCE},

volume = {26},

issue = {10},

pages = {108032},

abstract = {Growing antibiotic resistance has encouraged the revival of phage-inspired antimicrobial approaches. On the other hand, photodynamic therapy (PDT) is considered a very promising research domain for the protection against infectious diseases. Yet, very few efforts have been made to combine the advantages of both approaches in a modular, retargetable platform. Here, we foster the M13 bacteriophage as a multifunctional scaffold, enabling the selective photodynamic killing of bacteria. We took advantage of the well-defined molecular biology of M13 to functionalize its capsid with hundreds of photo-activable Rose Bengal sensitizers and contemporarily target this light-triggerable nanobot to specific bacterial species by phage display of peptide targeting moieties fused to the minor coat protein pIII of the phage. Upon light irradiation of the specimen, the targeted killing of diverse Gram(-) pathogens occurred at subnanomolar concentrations of the phage vector. Our findings contribute to the development of antimicrobials based on targeted and triggerable phage-based nanobiotherapeutics.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_132,

title = {Mineralocorticoid Receptor Antagonism Prevents Type 2 Familial Partial Lipodystrophy Brown Adipocyte Dysfunction},

author = {Schena E and Mattioli E and Peres C and Zanotti L and Morselli P and Iozzo P and Guzzardi MA and Bernardini C and Forni M and Nesci S and Caprio M and Cecchetti C and Pagotto U and Gabusi E and Cattini L and Lisignoli G and Blalock WL and Gambineri A and Lattanzi G},

url = {https://www.mdpi.com/2073-4409/12/22/2586},

doi = {10.3390/cells12222586},

year  = {2023},

date = {2023-10-10},

urldate = {2023-10-10},

journal = {CELLS},

volume = {12},

issue = {22},

pages = {2586},

abstract = {Type-2 Familial Partial Lipodystrophy (FPLD2), a rare lipodystrophy caused by LMNA mutations, is characterized by a loss of subcutaneous fat from the trunk and limbs and excess accumulation of adipose tissue in the neck and face. Several studies have reported that the mineralocorticoid receptor (MR) plays an essential role in adipose tissue differentiation and functionality. We previously showed that brown preadipocytes isolated from a FPLD2 patient's neck aberrantly differentiate towards the white lineage. As this condition may be related to MR activation, we suspected altered MR dynamics in FPLD2. Despite cytoplasmic MR localization in control brown adipocytes, retention of MR was observed in FPLD2 brown adipocyte nuclei. Moreover, overexpression of wild-type or mutated prelamin A caused GFP-MR recruitment to the nuclear envelope in HEK293 cells, while drug-induced prelamin A co-localized with endogenous MR in human preadipocytes. Based on in silico analysis and in situ protein ligation assays, we could suggest an interaction between prelamin A and MR, which appears to be inhibited by mineralocorticoid receptor antagonism. Importantly, the MR antagonist spironolactone redirected FPLD2 preadipocyte differentiation towards the brown lineage, avoiding the formation of enlarged and dysmorphic lipid droplets. Finally, beneficial effects on brown adipose tissue activity were observed in an FPLD2 patient undergoing spironolactone treatment. These findings identify MR as a new lamin A interactor and a new player in lamin A-linked lipodystrophies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_122,

title = {Hot on RAD51C: structure and functions of RAD51C-XRCC3},

author = {Szakal B and Branzei D},

url = {https://febs.onlinelibrary.wiley.com/doi/10.1002/1878-0261.13518},

doi = {10.1002/1878-0261.13518},

year  = {2023},

date = {2023-10-05},

urldate = {2023-10-05},

journal = {Molecular oncology},

volume = {17},

issue = {10},

pages = {1950-1952},

abstract = {A new study by Longo, Roy et al. has solved the structure of the RAD51C-XRCC3 (CX3) heterodimer with a bound ATP analog, identifying two main structural interfaces and defining separable replication fork stability roles. One function relates to the ability of RAD51C to bind and assemble CX3 on nascent DNA, with an impact on the ability of forks to restart upon replication stress. The other relates to effective CX3 heterodimer formation, required for 5' RAD51 filament capping, with effects on RAD51 filament disassembly, fork protection and influencing the persistence of reversed forks.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_121,

title = {PCNA recruits cohesin loader Scc2 to ensure sister chromatid cohesion},

author = {Psakhye I and Kawasumi R and Abe T and Hirota K and Branzei D},

url = {https://www.nature.com/articles/s41594-023-01064-x},

doi = {10.1038/s41594-023-01064-x.},

year  = {2023},

date = {2023-10-05},

journal = {Nature structural & molecular biology},

volume = {30},

issue = {9},

pages = {1286-1294},

abstract = {Sister chromatid cohesion, established during replication by the ring-shaped multiprotein complex cohesin, is essential for faithful chromosome segregation. Replisome-associated proteins are required to generate cohesion by two independent pathways. One mediates conversion of cohesins bound to unreplicated DNA ahead of replication forks into cohesive entities behind them, while the second promotes cohesin de novo loading onto newly replicated DNA. The latter process depends on the cohesin loader Scc2 (NIPBL in vertebrates) and the alternative PCNA loader CTF18-RFC. However, the mechanism of de novo cohesin loading during replication is unknown. Here we show that PCNA physically recruits the yeast cohesin loader Scc2 via its C-terminal PCNA-interacting protein motif. Binding to PCNA is crucial, as the scc2-pip mutant deficient in Scc2-PCNA interaction is defective in cohesion when combined with replisome mutants of the cohesin conversion pathway. Importantly, the role of NIPBL recruitment to PCNA for cohesion generation is conserved in vertebrate cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_120,

title = {New Clinical and Immunofluoresence Data of Collagen VI-Related Myopathy: A Single Center Cohort of 69 Patients},

author = {Merlini L and Sabatelli P and Gualandi F and Redivo E and Di Martino A and Faldini C},

url = {https://www.mdpi.com/1422-0067/24/15/12474},

doi = {10.3390/ijms241512474},

year  = {2023},

date = {2023-10-05},

journal = {International journal of molecular sciences},

volume = {24},

issue = {15},

pages = {12474},

abstract = {Pathogenetic mechanism recognition and proof-of-concept clinical trials were performed in our patients affected by collagen VI-related myopathies. This study, which included 69 patients, aimed to identify innovative clinical data to better design future trials. Among the patients, 33 had Bethlem myopathy (BM), 24 had Ullrich congenital muscular dystrophy (UCMD), 7 had an intermediate phenotype (INTM), and five had myosclerosis myopathy (MM). We obtained data on muscle strength, the degree of contracture, immunofluorescence, and genetics. In our BM group, only one third had a knee extension strength greater than 50% of the predicted value, while only one in ten showed similar retention of elbow flexion. These findings should be considered when recruiting BM patients for future trials. All the MM patients had axial and limb contractures that limited both the flexion and extension ranges of motion, and a limitation in mouth opening. The immunofluorescence analysis of collagen VI in 55 biopsies from 37 patients confirmed the correlation between collagen VI defects and the severity of the clinical phenotype. However, biopsies from the same patient or from patients with the same mutation taken at different times showed a progressive increase in protein expression with age. The new finding of the time-dependent modulation of collagen VI expression should be considered in genetic correction trials.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_119,

title = {N-Sulfenylation of beta-Lactams: Radical Reaction of N-Bromo-azetidinones by TEMPO Catalysis},

author = {Giraldi V and Giunchino F and Casacchia ME and Cantelli A and Lucarini M and Giacomini D},

url = {https://pubs.acs.org/doi/10.1021/acs.joc.3c01759},

doi = {10.1021/acs.joc.3c01759},

year  = {2023},

date = {2023-10-05},

urldate = {2023-10-05},

journal = {Journal of organic chemistry},

volume = {88},

number = {14728},

issue = {20},

pages = {14735},

abstract = {Azetidinones with a sulfenyl group on the β-lactam nitrogen atom show interesting biological activities as antimicrobial agents and enzyme inhibitors. We report in the present study a versatile synthesis of N-sulfenylated azetidinones starting from the corresponding N-bromo derivatives by means of the (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) radical as the catalyst and disulfides. Preparation of N-halo-azetidinones was studied and optimized. The reactivity of N-bromo-azetidinone 2a as a model compound in the presence of TEMPO radical was investigated by NMR and electron paramagnetic resonance (EPR) spectroscopy studies. Optimization of the reaction conditions allowed the access of N-alkylthio- or N-arylthio-azetidinones from 55 to 92% yields, and the method exhibited a good substrate scope.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_117,

title = {Epigenomic signature of accelerated ageing in progeroid Cockayne syndrome},

author = {Crochemore C and Chica C and Garagnani P and Lattanzi G and Horvath S and Sarasin A and Franceschi C and Bacalini MG and Ricchetti M},

url = {https://onlinelibrary.wiley.com/doi/10.1111/acel.13959},

doi = {10.1111/acel.13959},

year  = {2023},

date = {2023-10-05},

urldate = {2023-10-05},

journal = {Aging Cell},

volume = {22},

issue = {10},

pages = {e13959},

abstract = {Cockayne syndrome (CS) and UV-sensitive syndrome (UVSS) are rare genetic disorders caused by mutation of the DNA repair and multifunctional CSA or CSB protein, but only CS patients display a progeroid and neurodegenerative phenotype, providing a unique conceptual and experimental paradigm. As DNA methylation (DNAm) remodelling is a major ageing marker, we performed genome-wide analysis of DNAm of fibroblasts from healthy, UVSS and CS individuals. Differential analysis highlighted a CS-specific epigenomic signature (progeroid-related; not present in UVSS) enriched in three categories: developmental transcription factors, ion/neurotransmitter membrane transporters and synaptic neuro-developmental genes. A large fraction of CS-specific DNAm changes were associated with expression changes in CS samples, including in previously reported post-mortem cerebella. The progeroid phenotype of CS was further supported by epigenomic hallmarks of ageing: the prediction of DNAm of repetitive elements suggested an hypomethylation of Alu sequences in CS, and the epigenetic clock returned a marked increase in CS biological age respect to healthy and UVSS cells. The epigenomic remodelling of accelerated ageing in CS displayed both commonalities and differences with other progeroid diseases and regular ageing. CS shared DNAm changes with normal ageing more than other progeroid diseases do, and included genes functionally validated for regular ageing. Collectively, our results support the existence of an epigenomic basis of accelerated ageing in CS and unveil new genes and pathways that are potentially associated with the progeroid/degenerative phenotype.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_118,

title = {Woven bone formation and mineralization by rat mesenchymal stromal cells imply increased expression of the intermediate filament desmin},

author = {{Di Conza G} and Barbaro F and Zini N and Spaletta G and Remaggi G and Elviri L and Mosca S and Caravelli S and Mosca M and Toni R.},

url = {https://www.frontiersin.org/articles/10.3389/fendo.2023.1234569/full},

doi = {10.3389/fendo.2023.1234569},

year  = {2023},

date = {2023-10-04},

journal = {Frontiers in endocrinology},

volume = {14},

pages = {1234569},

abstract = {Background: Disordered and hypomineralized woven bone formation by dysfunctional mesenchymal stromal cells (MSCs) characterize delayed fracture healing and endocrine -metabolic bone disorders like fibrous dysplasia and Paget disease of bone. To shed light on molecular players in osteoblast differentiation, woven bone formation, and mineralization by MSCs we looked at the intermediate filament desmin (DES) during the skeletogenic commitment of rat bone marrow MSCs (rBMSCs), where its bone-related action remains elusive. Results: Monolayer cultures of immunophenotypically- and morphologically - characterized, adult male rBMSCs showed co-localization of desmin (DES) with vimentin, F-actin, and runx2 in all cell morphotypes, each contributing to sparse and dense colonies. Proteomic analysis of these cells revealed a topologically-relevant interactome, focused on cytoskeletal and related enzymes//chaperone/signalling molecules linking DES to runx2 and alkaline phosphatase (ALP). Osteogenic differentiation led to mineralized woven bone nodules confined to dense colonies, significantly smaller and more circular with respect to controls. It significantly increased also colony-forming efficiency and the number of DES-immunoreactive dense colonies, and immunostaining of co-localized DES/runx-2 and DES/ALP. These data confirmed pre-osteoblastic and osteoblastic differentiation, woven bone formation, and mineralization, supporting DES as a player in the molecular pathway leading to the osteogenic fate of rBMSCs. Conclusion: Immunocytochemical and morphometric studies coupled with proteomic and bioinformatic analysis support the concept that DES may act as an upstream signal for the skeletogenic commitment of rBMSCs. Thus, we suggest that altered metabolism of osteoblasts, woven bone, and mineralization by dysfunctional BMSCs might early be revealed by changes in DES expression//levels. Non-union fractures and endocrine - metabolic bone disorders like fibrous dysplasia and Paget disease of bone might take advantage of this molecular evidence for their early diagnosis and follow-up.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_116,

title = {Discovery of first novel sigma/HDACi dual-ligands with a potent in vitro antiproliferative activity},

author = {Barbaraci C and di Giacomo V and Maruca A and Patamia V and Rocca R and Dichiara M and {Di Rienzo} A and Cacciatore I and Cataldi A and Balaha M and Rapino M and Zagni C and Zampieri D and Pasquinucci L and Parenti C and Amata E and Rescifina A and Alcaro S and Marrazzo A.},

url = {https://www.sciencedirect.com/science/article/pii/S0045206823004558?via%3Dihub},

doi = {10.1016/j.bioorg.2023.106794},

year  = {2023},

date = {2023-10-02},

journal = {Bioorganic chemistry},

volume = {140},

pages = {106794},

abstract = {Designing and discovering compounds for dual-target inhibitors is challenging to synthesize new, safer, and more efficient drugs than single-target drugs, especially to treat multifactorial diseases such as cancer. The simultaneous regulation of multiple targets might represent an alternative synthetic approach to optimize patient compliance and tolerance, minimizing the risk of target-based drug resistance due to the modulation of a few targets. To this end, we conceived for the first time the design and synthesis of dual-ligands σR/HDACi to evaluate possible employment as innovative candidates to address this complex disease. Among all synthesized compounds screened for several tumoral cell lines, compound 6 (Kiσ1R = 38 ± 3.7; Kiσ2R = 2917 ± 769 and HDACs IC50 = 0.59 µM) is the most promising candidate as an antiproliferative agent with an IC50 of 0.9 µM on the HCT116 cell line and no significant toxicity to normal cells. Studies of molecular docking, which confirmed the affinity over σ1R and a pan-HDACs inhibitory behavior, support a possible balanced affinity and activity between both targets.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_133,

title = {Aberrant MET activation impairs perinuclear actin cap organization with YAP1 cytosolic relocation},

author = {Sgarzi M and Mazzeschi M and Santi S and Montacci E and Panciera T and Ferlizza E and Girone C and Morselli A and Gelfo V and Kuhre RS and Cavallo C and Valente S and Pasquinelli G and Gyorffy B and D'Uva G and Romaniello D and Lauriola M},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10576810/},

doi = {10.1038/s42003-023-05411-y},

year  = {2023},

date = {2023-08-23},

urldate = {2023-08-23},

journal = {Communications biology},

volume = {6},

issue = {1},

pages = {1044},

abstract = {Little is known about the signaling network responsible for the organization of the perinuclear actin cap, a recently identified structure holding unique roles in the regulation of nuclear shape and cell directionality. In cancer cells expressing a constitutively active MET, we show a rearrangement of the actin cap filaments, which crash into perinuclear patches associated with spherical nuclei, meandering cell motility and inactivation of the mechano-transducer YAP1. MET ablation is sufficient to reactivate YAP1 and restore the cap, leading to enhanced directionality and flattened nuclei. Consistently, the introduction of a hyperactive MET in normal epithelial cells, enhances nuclear height and alters the cap organization, as also confirmed by TEM analysis. Finally, the constitutively active YAP1 mutant YAP5SA is able to overcome the effects of oncogenic MET. Overall, our work describes a signaling axis empowering MET-mediated YAP1 dampening and actin cap misalignment, with implications for nuclear shape and cell motility.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}