@article{%a1:%Ybv,

title = {Prostate Cancer Progression: as a Matter of Fats Natalia},

author = {Scaglia N and Frontini-Lopez YR and Zadra G},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8353450/},

doi = {10.3389/fonc.2021.719865},

year  = {2021},

date = {2021-08-30},

journal = {Frontiers in oncology},

volume = {11},

pages = {719865},

abstract = {Advanced prostate cancer (PCa) represents the fifth cause of cancer death worldwide. Although survival has improved with second-generation androgen signaling and Parp inhibitors, the benefits are not long-lasting, and new therapeutic approaches are sorely needed. Lipids and their metabolism have recently reached the spotlight with accumulating evidence for their role as promoters of PCa development, progression, and metastasis. As a result, interest in targeting enzymes/transporters involved in lipid metabolism is rapidly growing. Moreover, the use of lipogenic signatures to predict prognosis and resistance to therapy has been recently explored with promising results. Despite the well-known association between obesity with PCa lethality, the underlying mechanistic role of diet/obesity-derived metabolites has only lately been unveiled. Furthermore, the role of lipids as energy source, building blocks, and signaling molecules in cancer cells has now been revisited and expanded in the context of the tumor microenvironment (TME), which is heavily influenced by the external environment and nutrient availability. Here, we describe how lipids, their enzymes, transporters, and modulators can promote PCa development and progression, and we emphasize the role of lipids in shaping TME. In a therapeutic perspective, we describe the ongoing efforts in targeting lipogenic hubs. Finally, we highlight studies supporting dietary modulation in the adjuvant setting with the purpose of achieving greater efficacy of the standard of care and of synthetic lethality. PCa progression is "a matter of fats", and the more we understand about the role of lipids as key players in this process, the better we can develop approaches to counteract their tumor promoter activity while preserving their beneficial properties},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {Selective Binding and Redox-Activity on Parallel G-Quadruplexes by Pegylated Naphthalene Diimide-Copper Complexes},

author = {Pirota V and Lunghi E and Benassi A and Crespan E and Freccero M and Doria F},

url = {https://www.mdpi.com/1420-3049/26/16/5025},

doi = {10.3390/molecules26165025},

year  = {2021},

date = {2021-08-30},

urldate = {2021-08-30},

journal = {Molecules},

volume = {26},

number = {16},

pages = {5025},

abstract = {G-quadruplexes (G4s) are higher-order supramolecular structures, biologically important in the regulation of many key processes. Among all, the recent discoveries relating to RNA-G4s, including their potential involvement as antiviral targets against COVID-19, have triggered the ever-increasing need to develop selective molecules able to interact with parallel G4s. Naphthalene diimides (NDIs) are widely exploited as G4 ligands, being able to induce and strongly stabilize these structures. Sometimes, a reversible NDI-G4 interaction is also associated with an irreversible one, due to the cleavage and/or modification of G4s by functional-NDIs. This is the case of NDI-Cu-DETA, a copper(II) complex able to cleave G4s in the closest proximity to the target binding site. Herein, we present two original Cu(II)-NDI complexes, inspired by NDI-Cu-DETA, differently functionalized with 2-(2-aminoethoxy)ethanol side-chains, to selectively drive redox-catalyzed activity towards parallel G4s. The selective interaction toward parallel G4 topology, controlled by the presence of 2-(2-aminoethoxy)ethanol side chains, was already firmly demonstrated by us using core-extended NDIs. In the present study, the presence of protonable moieties and the copper(II) cavity, increases the binding affinity and specificity of these two NDIs for a telomeric RNA-G4. Once defined the copper coordination relationship and binding constants by competition titrations, ability in G4 stabilization, and ROS-induced cleavage were analyzed. The propensity in the stabilization of parallel topology was highlighted for both of the new compounds HP2Cu and PE2Cu. The results obtained are particularly promising, paving the way for the development of new selective functional ligands for binding and destructuring parallel G4s.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {A Meta-Analysis of Brain DNA Methylation Across Sex, Age, and Alzheimer's Disease Points for Accelerated Epigenetic Aging in Neurodegeneration},

author = {Pellegrini C and Pirazzini C and Sala C and Sambati L and Yusipov I and Kalyakulina A and Ravaioli F and Kwiatkowska KM and Durso DF and Ivanchenko M and Monti D and Lodi R and Franceschi C and Cortelli P and Garagnani P and Bacalini MG},

url = {https://www.frontiersin.org/articles/10.3389/fnagi.2021.639428/full},

doi = {10.3389/fnagi.2021.639428},

year  = {2021},

date = {2021-08-30},

journal = {Frontiers in aging neuroscience},

volume = {13},

pages = {639428},

abstract = {Alzheimer's disease (AD) is characterized by specific alterations of brain DNA methylation (DNAm) patterns. Age and sex, two major risk factors for AD, are also known to largely affect the epigenetic profiles in brain, but their contribution to AD-associated DNAm changes has been poorly investigated. In this study we considered publicly available DNAm datasets of four brain regions (temporal, frontal, entorhinal cortex, and cerebellum) from healthy adult subjects and AD patients, and performed a meta-analysis to identify sex-, age-, and AD-associated epigenetic profiles. In one of these datasets it was also possible to distinguish 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) profiles. We showed that DNAm differences between males and females tend to be shared between the four brain regions, while aging differently affects cortical regions compared to cerebellum. We found that the proportion of sex-dependent probes whose methylation is modified also during aging is higher than expected, but that differences between males and females tend to be maintained, with only a few probes showing age-by-sex interaction. We did not find significant overlaps between AD- and sex-associated probes, nor disease-by-sex interaction effects. On the contrary, we found that AD-related epigenetic modifications are significantly enriched in probes whose DNAm varies with age and that there is a high concordance between the direction of changes (hyper or hypo-methylation) in aging and AD, supporting accelerated epigenetic aging in the disease. In summary, our results suggest that age-associated DNAm patterns concur to the epigenetic deregulation observed in AD, providing new insights on how advanced age enables neurodegeneration.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {Immune-tolerance to human iPS-derived neural progenitors xenografted into the immature cerebellum is overridden by species-specific differences in differentiation timing},

author = {Nato G and Corti A and Parmigiani E and Jachetti E and Lecis D and Colombo MP and Delia D and Buffo A and Magrassi L},

url = {https://www.nature.com/articles/s41598-020-79502-9},

doi = {10.1038/s41598-020-79502-9},

year  = {2021},

date = {2021-08-30},

journal = {Scientific reports},

volume = {11},

number = {1},

pages = {651},

abstract = {We xeno-transplanted human neural precursor cells derived from induced pluripotent stem cells into the cerebellum and brainstem of mice and rats during prenatal development or the first postnatal week. The transplants survived and started to differentiate up to 1 month after birth when they were rejected by both species. Extended survival and differentiation of the same cells were obtained only when they were transplanted in NOD-SCID mice. Transplants of human neural precursor cells mixed with the same cells after partial in vitro differentiation or with a cellular extract obtained from adult rat cerebellum increased survival of the xeno-graft beyond one month. These findings are consistent with the hypothesis that the slower pace of differentiation of human neural precursors compared to that of rodents restricts induction of immune-tolerance to human antigens expressed before completion of maturation of the immune system. With further maturation the transplanted neural precursors expressed more mature antigens before the graft were rejected. Supplementation of the immature cells suspensions with more mature antigens may help to induce immune-tolerance for those antigens expressed only later by the engrafted cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {Circulating miR-19a-3p and miR-19b-3p characterize the human aging process and their isomiRs associate with healthy status at extreme ages},

author = {Morsiani C and Terlecki-Zaniewicz L and Skalicky S and Bacalini MG and Collura S and Conte M and Sevini F and Garagnani P and Salvioli S and Hackl M and Grillari J and Franceschi C and Capri M},

url = {https://onlinelibrary.wiley.com/doi/10.1111/acel.13409},

doi = {10.1111/acel.13409},

isbn = {10.1111/acel.13409},

year  = {2021},

date = {2021-08-30},

urldate = {2021-08-30},

journal = {Aging Cell},

volume = {20},

number = {7},

pages = {e13409},

abstract = {Blood circulating microRNAs (c-miRs) are potential biomarkers to trace aging and longevity trajectories to identify molecular targets for anti-aging therapies. Based on a cross-sectional study, a discovery phase was performed on 12 donors divided into four groups: young, old, healthy, and unhealthy centenarians. The identification of healthy and unhealthy phenotype was based on cognitive performance and capabilities to perform daily activities. Small RNA sequencing identified 79 differentially expressed c-miRs when comparing young, old, healthy centenarians, and unhealthy centenarians. Two miRs, that is, miR-19a-3p and miR-19b-3p, were found increased at old age but decreased at extreme age, as confirmed by RT-qPCR in 49 donors of validation phase. The significant decrease of those miR levels in healthy compared to unhealthy centenarians appears to be due to the presence of isomiRs, not detectable with RT-qPCR, but only with a high-resolution technique such as deep sequencing. Bioinformatically, three main common targets of miR-19a/b-3p were identified, that is, SMAD4, PTEN, and BCL2L11, converging into the FoxO signaling pathway, known to have a significant role in aging mechanisms. For the first time, this study shows the age-related increase of plasma miR-19a/b-3p in old subjects but a decrease in centenarians. This decrease is more pronounced in healthy centenarians and was confirmed by the modified pattern of isomiRs comparing healthy and unhealthy centenarians. Thus, our study paves the way for functional studies using c-miRs and isomiRs as additional parameter to track the onset of aging and age-related diseases using new potential biomarkers.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)},

author = {Klionsky DJ and Abdel-Aziz AK and Abdelfatah S and .... and Scovassi AI and et al.},

url = {https://www.tandfonline.com/doi/full/10.1080/15548627.2020.1797280},

doi = {10.1080/15548627.2020.1797280},

year  = {2021},

date = {2021-08-30},

journal = {Autophagy},

volume = {17},

number = {1},

pages = {1-382},

abstract = {Not available},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {Asparagine sustains cellular proliferation and c‑Myc expression in glutamine‑starved cancer cells},

author = {Chiodi I and Perini C and Berardi D and Mondello C},

url = {https://www.spandidos-publications.com/or/45/6/96},

doi = {10.3892/or.2021.8047},

year  = {2021},

date = {2021-08-30},

journal = {Oncology reports},

volume = {45},

number = {6},

pages = {96},

abstract = {During tumorigenesis, oncogene activation and metabolism rewiring are interconnected. Activated c‑Myc upregulates several genes involved in glutamine metabolism, making cancer cells dependent on high levels of this amino acid to survive and proliferate. After studying the response to glutamine deprivation in cancer cells, it was found that glutamine starvation not only blocked cellular proliferation, but also altered c‑Myc protein expression, leading to a reduction in the levels of the canonical c‑Myc isoform and an increase in the expression of c‑Myc 1, a c‑Myc isoform translated from an in‑frame 5' CUG codon. In an attempt to identify nutrients able to counteract glutamine deprivation effects, it was shown that, in the absence of glutamine, asparagine permitted cell survival and proliferation, and maintained c‑Myc expression as in glutamine‑fed cells, with high levels of canonical c‑Myc and c‑Myc 1 almost undetectable. In asparagine‑fed cells, global protein translation was higher than in glutamine‑starved cells, and there was an increase in the levels of glutamine synthetase (GS), whose activity was essential for cellular viability and proliferation. In glutamine‑starved asparagine‑fed cells, the inhibition of c‑Myc activity led to a decrease in global protein translation and GS synthesis, suggesting an association between c‑Myc expression, GS levels and cellular proliferation, mediated by asparagine when exogenous glutamine is absent.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {No association between frailty index and epigenetic clocks in Italian semi-supercentenarians},

author = {Bacalini MG and Gentilini D and Monti D and Garagnani P and Mari D and Cesari M and Ogliari G and Passarino G and Franceschi C and Pirazzini C and Arosio B},

url = {https://www.sciencedirect.com/science/article/pii/S0047637421000865?via%3Dihub},

doi = {10.1016/j.mad.2021.111514},

year  = {2021},

date = {2021-08-30},

journal = {Mechanisms of ageing and development},

volume = {197},

pages = {111514},

abstract = {Centenarians experience successful ageing, although they still present high heterogeneity in their health status. The frailty index is a biomarker of biological age, able to capture such heterogeneity, even at extreme old age. At the same time, other biomarkers (e.g., epigenetic clocks) may be informative the biological age of the individual and potentially describe the ageing status in centenarians. In this article, we explore the relationship between epigenetic clocks and frailty index in a cohort of Italian centenarians. No association was reported, suggesting that these two approaches may describe different aspects of the same ageing process.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {T Cells Expressing Receptor Recombination/Revision Machinery Are Detected in the Tumor Microenvironment and Expanded in Genomically Over-unstable Models},

author = {Morello G and Cancila V and La Rosa M and Germano G and Lecis D and Amodio V and Zanardi F and Iannelli F and Greco D and La Paglia L and Fiannaca A and Urso AM and Graziano G and Ferrari F and Pupa SM and Sangaletti S and Chiodoni C and Pruneri G and Bardelli A and Colombo MP and Tripodo C},

url = {https://cancerimmunolres.aacrjournals.org/content/early/2021/06/08/2326-6066.CIR-20-0645.long},

doi = {10.1158/2326-6066.CIR-20-0645},

year  = {2021},

date = {2021-08-25},

journal = {Cancer immunology research},

abstract = {Tumors undergo dynamic immunoediting as part of a process that balances immunologic sensing of emerging neoantigens and evasion from immune responses. Tumor-infiltrating lymphocytes (TIL) comprise heterogeneous subsets of peripheral T cells characterized by diverse functional differentiation states and dependence on T-cell receptor (TCR) specificity gained through recombination events during their development. We hypothesized that within the tumor microenvironment (TME), an antigenic milieu and immunologic interface, tumor-infiltrating peripheral T cells could reexpress key elements of the TCR recombination machinery, namely, Rag1 and Rag2 recombinases and Tdt polymerase, as a potential mechanism involved in the revision of TCR specificity. Using two syngeneic invasive breast cancer transplantable models, 4T1 and TS/A, we observed that Rag1, Rag2, and Dntt in situ mRNA expression characterized rare tumor-infiltrating T cells. In situ expression of the transcripts was increased in coisogenic Mlh1-deficient tumors, characterized by genomic overinstability, and was also modulated by PD-1 immune-checkpoint blockade. Through immunolocalization and mRNA hybridization analyses, we detected the presence of rare TDT+RAG1/2+ cells populating primary tumors and draining lymph nodes in human invasive breast cancer. Analysis of harmonized single-cell RNA-sequencing data sets of human cancers identified a very small fraction of tumor-associated T cells, characterized by the expression of recombination/revision machinery transcripts, which on pseudotemporal ordering corresponded to differentiated effector T cells. We offer thought-provoking evidence of a TIL microniche marked by rare transcripts involved in TCR shaping.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {Transcriptional stress induces chromatin relocation of the nucleotide excision repair factor XPG},

author = {Scalera C and Ticli G and Dutto I and Cazzalini O and Stivala LA and Prosperi E},

url = {http://www.scopus.com/record/display.url?eid=2-s2.0-85108105818&origin=inward},

doi = {10.3390/ijms22126589},

year  = {2021},

date = {2021-08-25},

journal = {International journal of molecular sciences},

volume = {22},

pages = {6589},

abstract = {Endonuclease XPG participates in nucleotide excision repair (NER), in basal transcription, and in the processing of RNA/DNA hybrids (R-loops): the malfunction of these processes may cause genome instability. Here, we investigate the chromatin association of XPG during basal transcription and after transcriptional stress. The inhibition of RNA polymerase II with 5,6-dichloro-l-?-D-ribofuranosyl benzimidazole (DRB), or actinomycin D (AD), and of topoisomerase I with camptothecin (CPT) resulted in an increase in chromatin-bound XPG, with concomitant relocation by forming nuclear clusters. The cotranscriptional activators p300 and CREB-binding protein (CREBBP), endowed with lysine acetyl transferase (KAT) activity, interact with and acetylate XPG. Depletion of both KATs by RNA interference, or chemical inhibition with C646, significantly reduced XPG acetylation. However, the loss of KAT activity also resulted in increased chromatin association and the relocation of XPG, indicating that these processes were induced by transcriptional stress and not by reduced acetylation. Transcription inhibitors, including C646, triggered the R-loop formation and phosphorylation of histone H2AX (?-H2AX). Proximity ligation assay (PLA) showed that XPG colocalized with R-loops, indicating the recruitment of the protein to these structures. These results suggest that transcriptional stress-induced XPG relocation may represent recruitment to sites of R-loop processing.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {TERRA transcription destabilizes telomere integrity to initiate break-induced replication in human ALT cells. },

author = {Silva B and Arora R and Bione S and Azzalin CM},

url = {https://www.nature.com/articles/s41467-021-24097-6},

doi = {10.1038/s41467-021-24097-6},

year  = {2021},

date = {2021-08-25},

journal = {Nature communications},

volume = {12},

number = {1},

pages = {3760},

abstract = {Alternative Lengthening of Telomeres (ALT) is a Break-Induced Replication (BIR)-based mechanism elongating telomeres in a subset of human cancer cells. While the notion that spontaneous DNA damage at telomeres is required to initiate ALT, the molecular triggers of this physiological telomere instability are largely unknown. We previously proposed that the telomeric long noncoding RNA TERRA may represent one such trigger; however, given the lack of tools to suppress TERRA transcription in cells, our hypothesis remained speculative. We have developed Transcription Activator-Like Effectors able to rapidly inhibit TERRA transcription from multiple chromosome ends in an ALT cell line. TERRA transcription inhibition decreases marks of DNA replication stress and DNA damage at telomeres and impairs ALT activity and telomere length maintenance. We conclude that TERRA transcription actively destabilizes telomere integrity in ALT cells, thereby triggering BIR and promoting telomere elongation. Our data point to TERRA transcription manipulation as a potentially useful target for therapy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {Reduced levels of prostaglandin I 2 synthase: a distinctive feature of the cancer-free trichothiodystrophy},

author = {Lombardi A and Arseni L and Carriero R and Compe E and Botta E and Ferri D and Uggè M and Biamonti G and Peverali FA and Bione S and Orioli D},

url = {https://www.pnas.org/content/118/26/e2024502118.long},

doi = {10.1073/pnas.2024502118},

year  = {2021},

date = {2021-08-25},

journal = {Proceedings of the National Academy of Sciences of the United States of America.},

volume = {118},

number = {26},

abstract = {The cancer-free photosensitive trichothiodystrophy (PS-TTD) and the cancer-prone xeroderma pigmentosum (XP) are rare monogenic disorders that can arise from mutations in the same genes, namely ERCC2/XPD or ERCC3/XPB Both XPD and XPB proteins belong to the 10-subunit complex transcription factor IIH (TFIIH) that plays a key role in transcription and nucleotide excision repair, the DNA repair pathway devoted to the removal of ultraviolet-induced DNA lesions. Compelling evidence suggests that mutations affecting the DNA repair activity of TFIIH are responsible for the pathological features of XP, whereas those also impairing transcription give rise to TTD. By adopting a relatives-based whole transcriptome sequencing approach followed by specific gene expression profiling in primary fibroblasts from a large cohort of TTD or XP cases with mutations in ERCC2/XPD gene, we identify the expression alterations specific for TTD primary dermal fibroblasts. While most of these transcription deregulations do not impact on the protein level, very low amounts of prostaglandin I2 synthase (PTGIS) are found in TTD cells. PTGIS catalyzes the last step of prostaglandin I2 synthesis, a potent vasodilator and inhibitor of platelet aggregation. Its reduction characterizes all TTD cases so far investigated, both the PS-TTD with mutations in TFIIH coding genes as well as the nonphotosensitive (NPS)-TTD. A severe impairment of TFIIH and RNA polymerase II recruitment on the PTGIS promoter is found in TTD but not in XP cells. Thus, PTGIS represents a biomarker that combines all PS- and NPS-TTD cases and distinguishes them from XP.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {A functional in vitro cell-free system for studying DNA repair in isolated nuclei},

author = {Guardamagna I and Bassi E and Savio M and Perucca P and Cazzalini O and Prosperi E and Stivala LA},

url = {https://journals.biologists.com/jcs/article/133/11/jcs240010/224737/A-functional-in-vitro-cell-free-system-for},

doi = {10.1242/jcs.240010},

year  = {2021},

date = {2021-08-25},

journal = {Journal of cell science},

volume = {133},

number = {11},

abstract = {Assessment of DNA repair is an important endpoint measurement when studying the biochemical mechanisms of the DNA damage response and when investigating the efficacy of chemotherapy, which often uses DNA-damaging compounds. Numerous in vitro methods to biochemically characterize DNA repair mechanisms have been developed so far. However, such methods have some limitations, which are mainly due to the lack of chromatin organization in the DNA templates used. Here we describe a functional cell-free system to study DNA repair synthesis in vitro, using G1-phase nuclei isolated from human cells treated with different genotoxic agents. Upon incubation in the corresponding damage-activated cytosolic extracts, containing biotinylated dUTP, nuclei were able to initiate DNA repair synthesis. The use of specific DNA synthesis inhibitors markedly decreased biotinylated dUTP incorporation, indicating the specificity of the repair response. Exogenously added human recombinant PCNA protein, but not the sensors of UV-DNA damage DDB2 and DDB1, stimulated UVC-induced dUTP incorporation. In contrast, a DDB2PCNA- mutant protein, unable to associate with PCNA, interfered with DNA repair synthesis. Given its responsiveness to different types of DNA lesions, this system offers an additional tool to study DNA repair mechanisms.This article has an associated First Person interview with the first author of the paper.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {System-oriented optimization of multi-target 2,6-diaminopurine derivatives: Easily accessible broad-spectrum antivirals active against flaviviruses, influenza virus and SARS-CoV-2. },

author = {Vicenti I and Martina MG and Boccuto A and De Angelis M and Giavarini G and Dragoni F and Marchi S and Trombetta CM and Crespan E and Maga G and Eydoux C and Decroly E and Montomoli E and Nencioni L and Zazzi M and Radi M},

url = {https://www.sciencedirect.com/science/article/pii/S0223523421005328?via%3Dihub},

doi = {10.1016/j.ejmech.2021.113683},

year  = {2021},

date = {2021-08-25},

journal = {European journal of medicinal chemistry},

volume = {224},

pages = {113683},

abstract = {he worldwide circulation of different viruses coupled with the increased frequency and diversity of new outbreaks, strongly highlight the need for new antiviral drugs to quickly react against potential pandemic pathogens. Broad-spectrum antiviral agents (BSAAs) represent the ideal option for a prompt response against multiple viruses, new and re-emerging. Starting from previously identified anti-flavivirus hits, we report herein the identification of promising BSAAs by submitting the multi-target 2,6-diaminopurine chemotype to a system-oriented optimization based on phenotypic screening on cell cultures infected with different viruses. Among the synthesized compounds, 6i showed low micromolar potency against Dengue, Zika, West Nile and Influenza A viruses (IC50 = 0.5-5.3 μM) with high selectivity index. Interestingly, 6i also inhibited SARS-CoV-2 replication in different cell lines, with higher potency on Calu-3 cells that better mimic the SARS-CoV-2 infection in vivo (IC50 = 0.5 μM, SI = 240). The multi-target effect of 6i on flavivirus replication was also analyzed in whole cell studies (in vitro selection and immunofluorescence) and against isolated host/viral targets.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {Single-cell profiling reveals the dynamics of cytomegalovirusspecific T-cells in haploidentical hematopoietic stem cell transplantation},

author = {Van Beek JJP and Puccio S and Roberto A and De Paoli F and Graziano G and Salviato E and Alvisi G and Zanon V and Scarpa A and Zaghi E and Calvi M and Di Vito C and Mineri R and Sarina B and De Philippis C and Santoro A and Mariotti J and Bramanti S and Ferrari F and Castagna L and Mavilio D and Lugli E},

url = {https://haematologica.org/article/view/haematol.2020.276352},

doi = {10.3324/haematol.2020.276352},

year  = {2021},

date = {2021-08-25},

journal = {Haematologica},

keywords = {},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer-target gene regulatory interactions},

author = {Salviato E and Djordjilovic V and Hariprakash JM and Tagliaferri I and Pal K and Ferrari F},

url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab547/6312759},

doi = {10.1093/nar/gkab547},

year  = {2021},

date = {2021-08-25},

journal = {Nucleic acids research},

abstract = {A growing amount of evidence in literature suggests that germline sequence variants and somatic mutations in non-coding distal regulatory elements may be crucial for defining disease risk and prognostic stratification of patients, in genetic disorders as well as in cancer. Their functional interpretation is challenging because genome-wide enhancer-target gene (ETG) pairing is an open problem in genomics. The solutions proposed so far do not account for the hierarchy of structural domains which define chromatin three-dimensional (3D) architecture. Here we introduce a change of perspective based on the definition of multi-scale structural chromatin domains, integrated in a statistical framework to define ETG pairs. In this work (i) we develop a computational and statistical framework to reconstruct a comprehensive map of ETG pairs leveraging functional genomics data; (ii) we demonstrate that the incorporation of chromatin 3D architecture information improves ETG pairing accuracy and (iii) we use multiple experimental datasets to extensively benchmark our method against previous solutions for the genome-wide reconstruction of ETG pairs. This solution will facilitate the annotation and interpretation of sequence variants in distal non-coding regulatory elements. We expect this to be especially helpful in clinically oriented applications of whole genome sequencing in cancer and undiagnosed genetic diseases research.},

keywords = {},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {SMC complexes are guarded by the SUMO protease Ulp2 against SUMO-chain-mediated turnover},

author = {Psakhye I and Branzei D},

url = {https://www.sciencedirect.com/science/article/pii/S2211124721009128?via%3Dihub},

doi = {10.1016/j.celrep.2021.109485},

year  = {2021},

date = {2021-08-25},

journal = {Cell reports},

volume = {36},

number = {5},

abstract = {Structural maintenance of chromosomes (SMCs) complexes, cohesin, condensin, and Smc5/6, are essential for viability and participate in multiple processes, including sister chromatid cohesion, chromosome condensation, and DNA repair. Here we show that SUMO chains target all three SMC complexes and are antagonized by the SUMO protease Ulp2 to prevent their turnover. We uncover that the essential role of the cohesin-associated subunit Pds5 is to counteract SUMO chains jointly with Ulp2. Importantly, fusion of Ulp2 to kleisin Scc1 supports viability of PDS5 null cells and protects cohesin from proteasomal degradation mediated by the SUMO-targeted ubiquitin ligase Slx5/Slx8. The lethality of PDS5-deleted cells can also be bypassed by simultaneous loss of the proliferating cell nuclear antigen (PCNA) unloader, Elg1, and the cohesin releaser, Wpl1, but only when Ulp2 is functional. Condensin and Smc5/6 complex are similarly guarded by Ulp2 against unscheduled SUMO chain assembly, which we propose to time the availability of SMC complexes on chromatin.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {A ligand-insensitive UNC5B splicing isoform regulates angiogenesis by promoting apoptosis},

author = {Pradella D and Deflorian G and Pezzotta A and Di Matteo A and Belloni E and Campolungo D and Paradisi A and Bugatti M and Vermi W and Campioni M and Chiapparino A and Scietti L and Forneris F and Giampietro C and Volf N and Rehman M and Zacchigna S and Paronetto MP and Pistocchi A and Eichmann A and Mehlen P and Ghigna C},

url = {https://www.nature.com/articles/s41467-021-24998-6},

doi = {10.1038/s41467-021-24998-6},

year  = {2021},

date = {2021-08-25},

journal = {Nature communications},

volume = {12},

number = {1},

pages = {4872},

abstract = {The Netrin-1 receptor UNC5B is an axon guidance regulator that is also expressed in endothelial cells (ECs), where it finely controls developmental and tumor angiogenesis. In the absence of Netrin-1, UNC5B induces apoptosis that is blocked upon Netrin-1 binding. Here, we identify an UNC5B splicing isoform (called UNC5B-Δ8) expressed exclusively by ECs and generated through exon skipping by NOVA2, an alternative splicing factor regulating vascular development. We show that UNC5B-Δ8 is a constitutively pro-apoptotic splicing isoform insensitive to Netrin-1 and required for specific blood vessel development in an apoptosis-dependent manner. Like NOVA2, UNC5B-Δ8 is aberrantly expressed in colon cancer vasculature where its expression correlates with tumor angiogenesis and poor patient outcome. Collectively, our data identify a mechanism controlling UNC5B's necessary apoptotic function in ECs and suggest that the NOVA2/UNC5B circuit represents a post-transcriptional pathway regulating angiogenesis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {Visualizing and Annotating Hi-C Data},

author = {Pal K and Ferrari F},

url = {https://link.springer.com/protocol/10.1007%2F978-1-0716-1390-0_5},

doi = {10.1007/978-1-0716-1390-0_5},

year  = {2021},

date = {2021-08-25},

journal = {Methods in molecular biology},

volume = {2301},

pages = {97-132},

abstract = {Epigenomics studies require the combined analysis and integration of multiple types of data and annotations to extract biologically relevant information. In this context, sophisticated data visualization techniques are fundamental to identify meaningful patterns in the data in relation to the genomic coordinates. Data visualization for Hi-C contact matrices is even more complex as each data point represents the interaction between two distant genomic loci and their three-dimensional positioning must be considered. In this chapter we illustrate how to obtain sophisticated plots showing Hi-C data along with annotations for other genomic features and epigenomics data. For the example code used in this chapter we rely on a Bioconductor package able to handle even high-resolution Hi-C datasets. The provided examples are explained in details and highly customizable, thus facilitating their extension and adoption by end users for other studies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {Global Alternative Splicing Defects in Human Breast Cancer Cells},

author = {Oh J and Pradella D and Kim Y and Shao C and Li H and Choi N and Ha J and Di Matteo A and Fu XD and Zheng X and Ghigna C and Shen H},

url = {https://www.mdpi.com/2072-6694/13/12/3071},

doi = {10.3390/cancers13123071},

year  = {2021},

date = {2021-08-25},

journal = {Cancers},

volume = {13},

number = {12},

pages = {3071},

abstract = {Breast cancer is the most frequently occurred cancer type and the second cause of death in women worldwide. Alternative splicing (AS) is the process that generates more than one mRNA isoform from a single gene, and it plays a major role in expanding the human protein diversity. Aberrant AS contributes to breast cancer metastasis and resistance to chemotherapeutic interventions. Therefore, identifying cancer-specific isoforms is the prerequisite for therapeutic interventions intended to correct aberrantly expressed AS events. Here, we performed RNA-mediated oligonucleotide annealing, selection, and ligation coupled with next-generation sequencing (RASL-seq) in breast cancer cells, to identify global breast cancer-specific AS defects. By RT-PCR validation, we demonstrate the high accuracy of RASL-seq results. In addition, we analyzed identified AS events using the Cancer Genome Atlas (TCGA) database in a large number of non-pathological and breast tumor specimens and validated them in normal and breast cancer samples. Interestingly, aberrantly regulated AS cassette exons in cancer tissues do not encode for known functional domains but instead encode for amino acids constituting regions of intrinsically disordered protein portions characterized by high flexibility and prone to be subjected to post-translational modifications. Collectively, our results reveal novel AS errors occurring in human breast cancer, potentially affecting breast cancer-related biological processes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {Selective Inhibitors of the Inducible Nitric Oxide Synthase as Modulators of Cell Responses in LPS-Stimulated Human Monocytes},

author = {Gallorini M and Rapino M and Schweikl H and Cataldi A and Amoroso R and Maccallini C},

url = {https://www.mdpi.com/1420-3049/26/15/4419},

doi = {10.3390/molecules26154419},

year  = {2021},

date = {2021-08-25},

journal = {Molecules},

volume = {26},

number = {15},

pages = {4419},

abstract = {Inducible nitric oxide synthase (iNOS) is a crucial enzyme involved in monocyte cell response towards inflammation, and it is responsible for the production of sustained amounts of nitric oxide. This free radical molecule is involved in the defense against pathogens; nevertheless, its continuous and dysregulated production contributes to the development of several pathological conditions, including inflammatory and autoimmune diseases. In the present study, we investigated the effects of two new iNOS inhibitors, i.e., 4-(ethanimidoylamino)-N-(4-fluorophenyl)benzamide hydrobromide (FAB1020) and N-{3-[(ethanimidoylamino)methyl]benzyl}-l-prolinamidedihydrochloride (CM554), on human LPS-stimulated monocytes, using the 1400 W compound as a comparison. Our results show that CM544 and FAB1020 are selective and decrease cytotoxicity, IL-6 secretion and LPS-stimulated monocyte migration. Furthermore, the modulation of iNOS, nitrotyrosine and Nrf2 were analyzed at the protein level. Based on the collected preliminary results, the promising therapeutic value of the investigated compounds emerges, as they appear able to modulate the pro-inflammatory LPS-stimulated response in the low micromolar range in human monocytes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {Post-Translational Modifications Modulate Proteinopathies of TDP-43, FUS and hnRNP-A/B in Amyotrophic Lateral Sclerosis. },

author = {Farina S and Esposito F and Battistoni M and Biamonti G and Francia S},

url = {https://www.frontiersin.org/articles/10.3389/fmolb.2021.693325/full},

doi = {10.3389/fmolb.2021.693325},

year  = {2021},

date = {2021-08-25},

journal = {Frontiers in molecular biosciences},

volume = {8},

abstract = {It has been shown that protein low-sequence complexity domains (LCDs) induce liquid-liquid phase separation (LLPS), which is responsible for the formation of membrane-less organelles including P-granules, stress granules and Cajal bodies. Proteins harbouring LCDs are widely represented among RNA binding proteins often mutated in ALS. Indeed, LCDs predispose proteins to a prion-like behaviour due to their tendency to form amyloid-like structures typical of proteinopathies. Protein post-translational modifications (PTMs) can influence phase transition through two main events: i) destabilizing or augmenting multivalent interactions between phase-separating macromolecules; ii) recruiting or excluding other proteins and/or nucleic acids into/from the condensate. In this manuscript we summarize the existing evidence describing how PTM can modulate LLPS thus favouring or counteracting proteinopathies at the base of neurodegeneration in ALS.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb,

title = {Long-term cold storage preservation does not affect fatty livers from rats fed with a methionine and choline deficient diet},

author = {Di Pasqua LG and Berardo C and Cagna M and Mannucci B and Milanesi G and Croce AC and Ferrigno A and Vairetti M},

url = {https://lipidworld.biomedcentral.com/articles/10.1186/s12944-021-01503-y},

doi = {10.1186/s12944-021-01503-y},

year  = {2021},

date = {2021-08-25},

urldate = {2021-08-25},

journal = {Lipids in health and disease},

volume = {20},

number = {1},

pages = {78},

abstract = {Background: Waiting lists that continue to grow and the lack of organs available for transplantation necessitate the use of marginal livers, such as fatty livers. Since steatotic livers are more susceptible to damage from ischemia and reperfusion, it was investigated whether fatty livers with different lipidomic profiles show a different outcome when subjected to long-term cold storage preservation. Methods: Eight-week-old male Wistar rats fed for 2 weeks by a methionine-choline-deficient (MCD) diet or control diet were employed in this study. Livers were preserved in a University of Wisconsin (UW) solution at 4 °C for 6, 12 or 24 h and, after washout, reperfused for 2 h with a Krebs-Henseleit buffer at 37 °C. Hepatic enzyme release, bile production, O2-uptake, and portal venous pressure (PVP) were evaluated. The liver fatty acid profile was evaluated by a gas chromatography-mass spectrometry (GC/MS). Results: MCD rats showed higher LDH and AST levels with respect to the control group. When comparing MCD livers preserved for 6, 12 or 24 h, no differences in enzyme release were found during both the washout or the reperfusion period. The same trend occurred for O2-uptake, PVP, and bile flow. A general decrease in SFA and MUFA, except for oleic acid, and a decrease in PUFA, except for arachidonic, eicosadienoic, and docosahexanaeoic acids, were found in MCD rats when compared with control rats. Moreover, the ratio between SFA and the various types of unsaturated fatty acids (UFA) was significantly lower in MCD rats. Conclusions: Although prolonged cold ischemia negatively affects the graft outcome, our data suggest that the quality of lipid constituents could influence liver injury during cold storage: the lack of an increased hepatic injury in MCD may be justified by low SFA, which likely reduces the deleterious tendency toward lipid crystallization occurring under cold ischemia.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybu,

title = {Exploring the anticancer effects of standardized extracts of poplar-type propolis: In vitro cytotoxicity toward cancer and normal cell lines},

author = {Campoccia D and Ravaioli S and Santi S and Mariani V and Santarcangelo C and De Filippis A and Montanaro L and Arciola CR and Daglia M},

url = {https://www.sciencedirect.com/science/article/pii/S0753332221006776?via%3Dihub},

doi = {10.1016/j.biopha.2021.111895},

year  = {2021},

date = {2021-08-25},

urldate = {2021-08-25},

journal = {Biomedicine & pharmacotherapy},

volume = {141},

pages = {111895},

abstract = {Propolis was shown to exert antimicrobial, antioxidant, anti-inflammatory, and anticancer activities. Its composition is influenced by seasonal, climatic and phytogeographic conditions. Further variability derives from the extraction methods. Multi Dynamic Extraction Method (MED) has been recently proposed to improve extracts reproducibility. Here, the cytotoxic/anticancer activity of three MED extracts of poplar-type propolis was assayed on human promyelocytic leukaemia HL60, human monocytic leukaemia THP-1, human osteosarcoma MG63, murine fibroblast L929 and human mesenchymal cells (hMSCs). As far as we are aware of, MG63 cells have never been challenged with propolis before, while few studies have so far addressed the effects of propolis on non-tumor cell lines. Consistent results were observed for all propolis preparations. The extracts turned out mildly cytotoxic toward cancer cells, in particular osteosarcoma cells (IC50: 81.9-86.7 µg/ml). Nonetheless, cytotoxicity was observed also in non-tumor L929 cells, with an even lower IC50. hMSCs demonstrated the lowest sensitivity to propolis (IC50: 258.3-287.2 µg/ml). In THP-1 cells, extracts were found to stimulate apoptosis caspase 3/7 activity. The IC50 values observed with osteosarcoma and leukaemia cells do not support a relevant cytotoxicity (as the figures abundantly exceeded 30 µg/ml), despites some selective activity exhibited with HL60 cells. The results confirm the validity of the extraction method, emphasizing the need to assess the selectivity of the interaction with cancer cells when screening for anticancer-drug candidates.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybu,

title = {DNA helicases in homologous recombination repair},

author = {Branzei D and Szakal B},

url = {https://www.sciencedirect.com/science/article/abs/pii/S0959437X21000794?via%3Dihub},

doi = {10.1016/j.gde.2021.06.009},

year  = {2021},

date = {2021-08-25},

urldate = {2021-08-25},

journal = {Current opinion in genetics & development},

volume = {71},

pages = {27-33},

abstract = {Helicases are in the spotlight of DNA metabolism and are critical for DNA repair in all domains of life. At their biochemical core, they bind and hydrolyze ATP, converting this energy to translocate unidirectionally, with different strand polarities and substrate binding specificities, along one strand of a nucleic acid. In doing so, DNA and RNA helicases separate duplex strands or remove nucleoprotein complexes, affecting DNA repair and the architecture of replication forks. In this review, we focus on recent advances on the roles and regulations of DNA helicases in homologous recombination repair, a critical pathway for mending damaged chromosomes and for ensuring genome integrity. Copyright 2021 Elsevier Ltd. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybu,

title = {Comparative Molecular Dynamics Investigation of the Electromotile Hearing Protein Prestin},

author = {Abrusci G and Tarenzi T and Sturlese M and Giachin G and Battistutta R and Lattanzi G},

url = {https://www.mdpi.com/1422-0067/22/15/8318},

doi = {10.3390/ijms22158318},

year  = {2021},

date = {2021-08-25},

urldate = {2021-08-25},

journal = {International journal of molecular sciences},

volume = {22},

number = {15},

pages = {8318},

abstract = {The mammalian protein prestin is expressed in the lateral membrane wall of the cochlear hair outer cells and is responsible for the electromotile response of the basolateral membrane, following hyperpolarisation or depolarisation of the cells. Its impairment marks the onset of severe diseases, like non-syndromic deafness. Several studies have pointed out possible key roles of residues located in the Transmembrane Domain (TMD) that differentiate mammalian prestins as incomplete transporters from the other proteins belonging to the same solute-carrier (SLC) superfamily, which are classified as complete transporters. Here, we exploit the homology of a prototypical incomplete transporter (rat prestin, rPres) and a complete transporter (zebrafish prestin, zPres) with target structures in the outward open and inward open conformations. The resulting models are then embedded in a model membrane and investigated via a rigorous molecular dynamics simulation protocol. The resulting trajectories are analyzed to obtain quantitative descriptors of the equilibration phase and to assess a structural comparison between proteins in different states, and between different proteins in the same state. Our study clearly identifies a network of key residues at the interface between the gate and the core domains of prestin that might be responsible for the conformational change observed in complete transporters and hindered in incomplete transporters. In addition, we study the pathway of Cl- ions in the presence of an applied electric field towards their putative binding site in the gate domain. Based on our simulations, we propose a tilt and shift mechanism of the helices surrounding the ion binding cavity as the working principle of the reported conformational changes in complete transporters.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb,

title = {A new method for the study of biophysical and morphological parameters in 3D cell cultures: Evaluation in LoVo spheroids treated with crizotinib},

author = {Sargenti A and Musmeci F and Cavallo C and Mazzeschi M and Bonetti S and Pasqua S and Bacchi F and Filardo G and Gazzola D and Lauriola M and Santi S},

url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0252907},

doi = {10.1371/journal.pone.0252907},

year  = {2021},

date = {2021-06-10},

journal = {PLoS One},

volume = {16},

number = {6},

pages = {PLoS One},

abstract = {Three-dimensional (3D) culture systems like tumor spheroids represent useful in vitro models for drug screening and more broadly for cancer biology research, but the generation of uniform populations of spheroids remains challenging. The possibility to properly characterize spheroid properties would increase the reliability of these models. To address this issue different analysis were combined: i) a new device and relative analytical method for the accurate, simultaneous, and rapid measurement of mass density, weight, and size of spheroids, ii) confocal imaging, and iii) protein quantification, in a clinically relevant 3D model. The LoVo colon cancer cell line forming spheroids, treated with crizotinib (CZB) an ATP-competitive small-molecule inhibitor of the receptor tyrosine kinases, was employed to study and assess the correlation between biophysical and morphological parameters in both live and fixed cells. The new fluidic-based measurements allowed a robust phenotypical characterization of the spheroids structure, offering insights on the spheroids bulk and an accurate measurement of the tumor density. This analysis helps overcome the technical limits of the imaging that hardly penetrates the thickness of 3D structures. Accordingly, we were able to document that CZB treatment has an impact on mass density, which represents a key marker characterizing cancer cell treatment. Spheroid culture is the ultimate technology in drug discovery and the adoption of such precise measurement of the tumor characteristics can represent a key step forward for the accurate testing of treatment's potential in 3D in vitro models.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb,

title = {Telomere damage promotes vascular smooth muscle cell senescence and immune cell recruitment after vessel injury},

author = {Uryga AK and Grootaert MOJ and Garrido AM and Oc S and Foote K and Chappell J and Finigan A and Rossiello F and {d'Adda di Fagagna F} and Aravani D and Jorgensen HF and Bennett MR},

url = {https://www.nature.com/articles/s42003-021-02123-z},

doi = {10.1038/s42003-021-02123-z},

year  = {2021},

date = {2021-06-08},

journal = {Communications biology},

volume = {4},

number = {1},

pages = {611},

abstract = {Accumulation of vascular smooth muscle cells (VSMCs) is a hallmark of multiple vascular pathologies, including following neointimal formation after injury and atherosclerosis. However, human VSMCs in advanced atherosclerotic lesions show reduced cell proliferation, extensive and persistent DNA damage, and features of premature cell senescence. Here, we report that stress-induced premature senescence (SIPS) and stable expression of a telomeric repeat-binding factor 2 protein mutant (TRF2T188A) induce senescence of human VSMCs, associated with persistent telomeric DNA damage. VSMC senescence is associated with formation of micronuclei, activation of cGAS-STING cytoplasmic sensing, and induction of multiple pro-inflammatory cytokines. VSMC-specific TRF2T188A expression in a multicolor clonal VSMC-tracking mouse model shows no change in VSMC clonal patches after injury, but an increase in neointima formation, outward remodeling, senescence and immune/inflammatory cell infiltration or retention. We suggest that persistent telomere damage in VSMCs inducing cell senescence has a major role in driving persistent inflammation in vascular disease.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb,

title = {Cellular senescence in vascular wall mesenchymal stromal cells, a possible contribution to the development of aortic aneurysm},

author = {Teti G and Chiarini F and Mazzotti E and Ruggeri A and Carano F and Falconi M},

url = {https://www.sciencedirect.com/science/article/pii/S0047637421000877?via%3Dihub},

doi = {10.1016/j.mad.2021.111515},

year  = {2021},

date = {2021-06-08},

journal = {Mechanisms of ageing and development},

volume = {197},

number = {111515},

abstract = {Cellular senescence is a hallmark of ageing and it plays a key role in the development of age-related diseases. Abdominal aortic aneurysm (AAA) is an age related degenerative vascular disorder, characterized by a progressive dilatation of the vascular wall and high risk of rupture over time. Nowadays, no pharmacological therapies are available and the understanding of the molecular mechanisms that lead to AAA onset and development are poorly defined. In this study we investigated the cellular features of senescence in vascular mesenchymal stromal cells, isolated from pathological (AAA - MSCs) and healthy (h - MSCs) segments of human abdominal aorta and their implication in impairing the vascular repair ability of MSCs. Cell proliferation, ROS production, cell surface area, the expression of cyclin dependent kinase inhibitors p21CIP1 and p16INK4a, the activation of the DNA damage response and a dysregulated autophagy showed a senescent state in AAA - MSCs compared to h-MSCs. Moreover, a reduced ability to differentiate toward endothelial cells was observed in AAA - MSCs. All these data suggest that the accumulation of senescent vascular MSCs over time impairs their remodeling ability during ageing. This condition could support the onset and development of AAA.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb,

title = {Polysaccharides on gelatin-based hydrogels differently affect chondrogenic differentiation of human mesenchymal stromal cells},

author = {Sartore L and Manferdini C and Saleh Y and Dey K and Gabusi E and Ramorino G and Zini N and Almici C and Re F and Russo D and Mariani E and Lisignoli G},

url = {https://www.sciencedirect.com/science/article/pii/S0928493121003143?via%3Dihub},

doi = {10.1016/j.msec.2021.112175},

year  = {2021},

date = {2021-06-08},

journal = {Materials science & engineering. C, Materials for biological applications},

volume = {126},

pages = {112175},

abstract = {Selection of feasible hybrid-hydrogels for best chondrogenic differentiation of human mesenchymal stromal cells (hMSCs) represents an important challenge in cartilage regeneration. In this study, three-dimensional hybrid hydrogels obtained by chemical crosslinking of poly (ethylene glycol) diglycidyl ether (PEGDGE), gelatin (G) without or with chitosan (Ch) or dextran (Dx) polysaccharides were developed. The hydrogels, namely G-PEG, G-PEG-Ch and G-PEG-Dx, were prepared with an innovative, versatile and cell-friendly technique that involves two preparation steps specifically chosen to increase the degree of crosslinking and the physical-mechanical stability of the product: a first homogeneous phase reaction followed by directional freezing, freeze-drying and post-curing. Chondrogenic differentiation of human bone marrow mesenchymal stromal cells (hBM-MSC) was tested on these hydrogels to ascertain whether the presence of different polysaccharides could favor the formation of the native cartilage structure. We demonstrated that the hydrogels exhibited an open pore porous morphology with high interconnectivity and the incorporation of Ch and Dx into the G-PEG common backbone determined a slightly reduced stiffness compared to that of G-PEG hydrogels. We demonstrated that G-PEG-Dx showed a significant increase of its anisotropic characteristic and G-PEG-Ch exhibited higher and faster stress relaxation behavior than the other hydrogels. These characteristics were associated to absence of chondrogenic differentiation on G-PEG-Dx scaffold and good chondrogenic differentiation on G-PEG and G-PEG-Ch. Furthermore, G-PEG-Ch induced the minor collagen proteins and the formation of collagen fibrils with a diameter like native cartilage. This study demonstrated that both anisotropic and stress relaxation characteristics of the hybrid hydrogels were important features directly influencing the chondrogenic differentiation potentiality of hBM-MSC.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb,

title = {High Flexibility of RNaseH2 Catalytic Activity with Respect to Non-Canonical DNA Structures},

author = {Dede M and Napolitano S and Melati A and Pirota V and Maga G and Crespan E},

url = {https://www.mdpi.com/1422-0067/22/10/5201},

doi = {10.3390/ijms22105201},

year  = {2021},

date = {2021-06-08},

journal = {International journal of molecular sciences},

volume = {22},

number = {10},

pages = {5201},

abstract = {Ribonucleotides misincorporated in the human genome are the most abundant DNA lesions. The 2'-hydroxyl group makes them prone to spontaneous hydrolysis, potentially resulting in strand breaks. Moreover, their presence may decrease the rate of DNA replication causing replicative fork stalling and collapse. Ribonucleotide removal is initiated by Ribonuclease H2 (RNase H2), the key player in Ribonucleotide Excision Repair (RER). Its absence leads to embryonic lethality in mice, while mutations decreasing its activity cause Aicardi-Goutières syndrome. DNA geometry can be altered by DNA lesions or by peculiar sequences forming secondary structures, like G-quadruplex (G4) and trinucleotide repeats (TNR) hairpins, which significantly differ from canonical B-form. Ribonucleotides pairing to lesioned nucleotides, or incorporated within non-B DNA structures could avoid RNase H2 recognition, potentially contributing to genome instability. In this work, we investigate the ability of RNase H2 to process misincorporated ribonucleotides in a panel of DNA substrates showing different geometrical features. RNase H2 proved to be a flexible enzyme, recognizing as a substrate the majority of the constructs we generated. However, some geometrical features and non-canonical DNA structures severely impaired its activity, suggesting a relevant role of misincorporated ribonucleotides in the physiological instability of specific DNA sequences.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_91,

title = {Alternative splicing in Alzheimer's disease.},

author = {Biamonti G and Amato A and Belloni E and Di Matteo A and Infantino L and Pradella D and Ghigna C},

url = {https://link.springer.com/article/10.1007%2Fs40520-019-01360-x},

doi = {10.1007/s40520-019-01360-x},

year  = {2021},

date = {2021-05-24},

journal = {Aging clinical and experimental research},

volume = {33},

number = {4},

pages = {747-758},

abstract = {Alzheimer's disease (AD) is the most frequent neurodegenerative disorder in the elderly, occurring in approximately 20% of people older than 80. The molecular causes of AD are still poorly understood. However, recent studies have shown that Alternative Splicing (AS) is involved in the gene expression reprogramming associated with the functional changes observed in AD patients. In particular, mutations in cis-acting regulatory sequences as well as alterations in the activity and sub-cellular localization of trans-acting splicing factors and components of the spliceosome machinery are associated with splicing abnormalities in AD tissues, which may influence the onset and progression of the disease. In this review, we discuss the current molecular understanding of how alterations in the AS process contribute to AD pathogenesis. Finally, recent therapeutic approaches targeting aberrant AS regulation in AD are also reviewed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb,

title = {Opposing forces fight over the same ground to regulate interferon signaling.},

author = {Blalock WL},

url = {https://portlandpress.com/biochemj/article/478/10/1853/228676/Opposing-forces-fight-over-the-same-ground-to},

doi = {10.1042/BCJ20210110},

year  = {2021},

date = {2021-05-17},

journal = {Biochemical journal},

volume = {478},

number = {10},

pages = {1853-1859},

abstract = {The current SARS-CoV-2 pandemic has spurred new interest in interferon signaling in response to viral pathogens. Much of what we know about the signaling molecules and associated signal transduction induced during the host cellular response to viral pathogens has been gained from research conducted from the 1990's to the present day, but certain intricacies of the mechanisms involved, still remain unclear. In a recent study by Vaughn et al. the authors examine one of the main mechanisms regulating interferon induction following viral infection, the RIG-I/MAVS/IRF3 pathway, and find that similar to PKR both DICER interacting proteins, PACT and TRBP, regulate RIG-I signaling in an opposing manner. More specifically, the reported findings demonstrate, like others, that PACT stimulates RIG-I-mediated signaling in a manner independent of PACT dsRNA-binding ability or phosphorylation at sites known to be important for PACT-dependent PKR activation. In contrast, they show for the first time that TRBP inhibits RIG-I-mediated signaling. RIG-I inhibition by TRBP did not require phosphorylation of sites shown to be important for inhibiting PKR, nor did it involve PACT or PKR, but it did require the dsRNA-binding ability of TRBP. These findings open the door to a complex co-regulation of RIG-I, PKR, MDA5, miRNA processing, and interferon induction.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb,

title = {Tephritid Fruit Fly Semiochemicals: Current Knowledge and Future Perspectives},

author = {Scolari F and Valerio F and Benelli G and Papadopoulos NT and Vaníckova' L.},

url = {https://www.mdpi.com/2075-4450/12/5/408},

doi = {10.3390/insects12050408},

year  = {2021},

date = {2021-05-17},

journal = {Insects},

volume = {12},

number = {5},

abstract = {The Dipteran family Tephritidae (true fruit flies) comprises more than 5000 species classified in 500 genera distributed worldwide. Tephritidae include devastating agricultural pests and highly invasive species whose spread is currently facilitated by globalization, international trade and human mobility. The ability to identify and exploit a wide range of host plants for oviposition, as well as effective and diversified reproductive strategies, are among the key features supporting tephritid biological success. Intraspecific communication involves the exchange of a complex set of sensory cues that are species- and sex-specific. Chemical signals, which are standing out in tephritid communication, comprise long-distance pheromones emitted by one or both sexes, cuticular hydrocarbons with limited volatility deposited on the surrounding substrate or on the insect body regulating medium- to short-distance communication, and host-marking compounds deposited on the fruit after oviposition. In this review, the current knowledge on tephritid chemical communication was analysed with a special emphasis on fruit fly pest species belonging to the Anastrepha, Bactrocera, Ceratitis, and Rhagoletis genera. The multidisciplinary approaches adopted for characterising tephritid semiochemicals, and the real-world applications and challenges for Integrated Pest Management (IPM) and biological control strategies are critically discussed. Future perspectives for targeted research on fruit fly chemical communication are highlighted.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb,

title = {Evaluation and efficiency of curcumin against periodontal bacteria: an in vitro study},

author = {Pulcini R and Avolio F and Sinjari B and Robuffo I and Flati V and Pignatelli L and Martinotti S and Toniato E},

url = {https://www.biolifesas.org/biolife/2021/03/15/evaluation-and-efficiency-of-curcumin-against-periodontal-bacteria-an-in-vitro-study/},

doi = {10.23812/20-556-L},

year  = {2021},

date = {2021-05-17},

journal = {Journal of biological regulators and homeostatic agents},

volume = {35},

number = {2},

pages = {725-728},

abstract = {No abstract available},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb,

title = {Widespread Alternative Splicing Changes in Metastatic Breast Cancer Cells},

author = {Oh J and Pradella D and Shao C and Li H and Choi N and Ha J and Ruggiero S and Fu XD and Zheng X and Ghigna C and Shen H},

url = {https://www.mdpi.com/2073-4409/10/4/858},

doi = {10.3390/cells10040858},

year  = {2021},

date = {2021-05-17},

journal = {Cells},

volume = {10},

number = {4},

pages = {858},

abstract = {Aberrant alternative splicing (AS) is a hallmark of cancer and a potential target for novel anti-cancer therapeutics. Breast cancer-associated AS events are known to be linked to disease progression, metastasis, and survival of breast cancer patients. To identify altered AS programs occurring in metastatic breast cancer, we perform a global analysis of AS events by using RNA-mediated oligonucleotide annealing, selection, and ligation coupled with next-generation sequencing (RASL-seq). We demonstrate that, relative to low-metastatic, high-metastatic breast cancer cells show different AS choices in genes related to cancer progression. Supporting a global reshape of cancer-related splicing profiles in metastatic breast cancer we found an enrichment of RNA-binding motifs recognized by several splicing regulators, which have aberrant expression levels or activity during breast cancer progression, including SRSF1. Among SRSF1-regulated targets we found DCUN1D5, a gene for which skipping of exon 4 in its pre-mRNA introduces a premature termination codon (PTC), thus generating an unstable transcript degraded by nonsense-mediated mRNA decay (NMD). Significantly, distinct breast cancer subtypes show different DCUN1D5 isoform ratios with metastatic breast cancer expressing the highest level of the NMD-insensitive DCUN1D5 mRNA, thus showing high DCUN1D5 expression levels, which are ultimately associated with poor overall and relapse-free survival in breast cancer patients. Collectively, our results reveal global AS features of metastatic breast tumors, which open new possibilities for the treatment of these aggressive tumor types.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb,

title = {Skeletal and Cardiac Muscle Disorders Caused by Mutations in Genes Encoding Intermediate Filament Proteins},

author = {Maggi L and Mavroidis M and Psarras S and Capetanaki Y and Lattanzi G},

url = {https://www.mdpi.com/1422-0067/22/8/4256},

doi = {10.3390/ijms22084256},

year  = {2021},

date = {2021-05-17},

journal = {International journal of molecular sciences},

volume = {22},

number = {8},

pages = {4256},

abstract = {Intermediate filaments are major components of the cytoskeleton. Desmin and synemin, cytoplasmic intermediate filament proteins and A-type lamins, nuclear intermediate filament proteins, play key roles in skeletal and cardiac muscle. Desmin, encoded by the DES gene (OMIM *125660) and A-type lamins by the LMNA gene (OMIM *150330), have been involved in striated muscle disorders. Diseases include desmin-related myopathy and cardiomyopathy (desminopathy), which can be manifested with dilated, restrictive, hypertrophic, arrhythmogenic, or even left ventricular non-compaction cardiomyopathy, Emery-Dreifuss Muscular Dystrophy (EDMD2 and EDMD3, due to LMNA mutations), LMNA-related congenital Muscular Dystrophy (L-CMD) and LMNA-linked dilated cardiomyopathy with conduction system defects (CMD1A). Recently, mutations in synemin (SYNM gene, OMIM *606087) have been linked to cardiomyopathy. This review will summarize clinical and molecular aspects of desmin-, lamin- and synemin-related striated muscle disorders with focus on LMNA and DES-associated clinical entities and will suggest pathogenetic hypotheses based on the interplay of desmin and lamin A/C. In healthy muscle, such interplay is responsible for the involvement of this network in mechanosignaling, nuclear positioning and mitochondrial homeostasis, while in disease it is disturbed, leading to myocyte death and activation of inflammation and the associated secretome alterations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb,

title = {DDX11 loss causes replication stress and pharmacologically exploitable DNA repair defects.},

author = {Jegadesan NK and Branzei D},

url = {https://www.pnas.org/content/118/17/e2024258118.long},

doi = {10.1073/pnas.2024258118},

year  = {2021},

date = {2021-05-17},

urldate = {2021-05-17},

journal = {Proceedings of the National Academy of Sciences of the United States of America},

volume = {118},

number = {17},

pages = {e2024258118},

abstract = {DDX11 encodes an iron-sulfur cluster DNA helicase required for development, mutated, and overexpressed in cancers. Here, we show that loss of DDX11 causes replication stress and sensitizes cancer cells to DNA damaging agents, including poly ADP ribose polymerase (PARP) inhibitors and platinum drugs. We find that DDX11 helicase activity prevents chemotherapy drug hypersensitivity and accumulation of DNA damage. Mechanistically, DDX11 acts downstream of 53BP1 to mediate homology-directed repair and RAD51 focus formation in manners nonredundant with BRCA1 and BRCA2. As a result, DDX11 down-regulation aggravates the chemotherapeutic sensitivity of BRCA1/2-mutated cancers and resensitizes chemotherapy drug-resistant BRCA1/2-mutated cancer cells that regained homologous recombination proficiency. The results further indicate that DDX11 facilitates recombination repair by assisting double strand break resection and the loading of both RPA and RAD51 on single-stranded DNA substrates. We propose DDX11 as a potential target in cancers by creating pharmacologically exploitable DNA repair vulnerabilities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y,

title = {Protein instability associated with AARS1 and MARS1 mutations causes Trichothiodystrophy},

author = {Botta E and Theil AF and Raams A and Caligiuri G and Giachetti S and Bione S and Accadia M and Lombardi A and Smith DEC and Mendes MI and Swagemakers SMA and van der Spek PJ and Salomons GS and Hoeijmakers JHJ and Yesodharan D and Nampoothiri S and Ogi T and Lehmann AR and Orioli D and Vermeulen W},

url = {https://academic.oup.com/hmg/advance-article/doi/10.1093/hmg/ddab123/6256034},

doi = {10.1093/hmg/ddab123},

year  = {2021},

date = {2021-05-14},

journal = {Human molecular genetics},

abstract = {Trichothiodystrophy (TTD) is a rare hereditary neurodevelopmental disorder defined by sulphur-deficient brittle hair and nails and scaly skin, but with otherwise remarkably variable clinical features. The photosensitive TTD (PS-TTD) form exhibits, in addition, progressive neuropathy and other features of segmental accelerated aging and is associated with impaired genome maintenance and transcription. New factors involved in various steps of gene expression have been identified for the different non-photosensitive forms of TTD (NPS-TTD), which do not appear to show features of premature aging. Here we identify AARS1 and MARS1 variants as new gene defects that cause NPS-TTD. These variants result in instability of the respective gene products alanyl- and methionyl-tRNA synthetase. These findings extend our previous observations that TTD mutations affect the stability of the corresponding proteins and emphasise this phenomenon as a common feature of TTD. Functional studies in skin fibroblasts from affected individuals demonstrate that these new variants also impact on the rate of tRNA charging, the first step in protein translation. The extension of reduced abundance of TTD factors to translation as well as transcription, redefines TTD as a syndrome in which proteins involved in gene expression are unstable.},

keywords = {},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{%a1:%Y__516,

title = {Evaluation of Shared Genetic Susceptibility to High and Low Myopia and Hyperopia},

author = {Tideman JWL and Parssinen O and Haarman AEG and Khawaja AP and Wedenoja J and Williams KM and Biino G and Ding X and Kahonen M and Lehtimaki T and Raitakari OT and Cheng CY and Jonas JB and Young TL and Bailey-Wilson JE and Rahi J and Williams C and He M and Mackey DA and Guggenheim JA and {UK Biobank Eye and Vision Consortium} and {the Consortium for Refractive Error and Myopia} (CREAM Consortium)},

url = {https://jamanetwork.com/journals/jamaophthalmology/article-abstract/2778382},

doi = {10.1001/jamaophthalmol.2021.0497},

year  = {2021},

date = {2021-04-14},

journal = {JAMA ophthalmology},

abstract = {Importance: Uncertainty currently exists about whether the same genetic variants are associated with susceptibility to low myopia (LM) and high myopia (HM) and to myopia and hyperopia. Addressing this question is fundamental to understanding the genetics of refractive error and has clinical relevance for genotype-based prediction of children at risk for HM and for identification of new therapeutic targets. Objective: To assess whether a common set of genetic variants are associated with susceptibility to HM, LM, and hyperopia. Design, setting, and participants: This genetic association study assessed unrelated UK Biobank participants 40 to 69 years of age of European and Asian ancestry. Participants 40 to 69 years of age living in the United Kingdom were recruited from January 1, 2006, to October 31, 2010. Of the total sample of 502 682 participants, 117 279 (23.3%) underwent an ophthalmic assessment. Data analysis was performed from December 12, 2019, to June 23, 2020. Exposures: Four refractive error groups were defined: HM, -6.00 diopters (D) or less; LM, -3.00 to -1.00 D; hyperopia, +2.00 D or greater; and emmetropia, 0.00 to +1.00 D. Four genome-wide association study (GWAS) analyses were performed in participants of European ancestry: (1) HM vs emmetropia, (2) LM vs emmetropia, (3) hyperopia vs emmetropia, and (4) LM vs hyperopia. Polygenic risk scores were generated from GWAS summary statistics, yielding 4 sets of polygenic risk scores. Performance was assessed in independent replication samples of European and Asian ancestry. Main outcomes and measures: Odds ratios (ORs) of polygenic risk scores in replication samples. Results: A total of 51 841 unrelated individuals of European ancestry and 2165 unrelated individuals of Asian ancestry were assigned to a specific refractive error group and included in our analyses. Polygenic risk scores derived from all 4 GWAS analyses were predictive of all categories of refractive error in both European and Asian replication samples. For example, the polygenic risk score derived from the HM vs emmetropia GWAS was predictive in the European sample of HM vs emmetropia (OR, 1.58; 95% CI, 1.41-1.77; P = 1.54 × 10-15) as well as LM vs emmetropia (OR, 1.15; 95% CI, 1.07-1.23; P = 8.14 × 10-5), hyperopia vs emmetropia (OR, 0.83; 95% CI, 0.77-0.89; P = 4.18 × 10-7), and LM vs hyperopia (OR, 1.45; 95% CI, 1.33-1.59; P = 1.43 × 10-16). Conclusions and relevance: Genetic risk variants were shared across HM, LM, and hyperopia and across European and Asian samples. Individuals with HM inherited a higher number of variants from among the same set of myopia-predisposing alleles and not different risk alleles compared with individuals with LM. These findings suggest that treatment interventions targeting common genetic risk variants associated with refractive error could be effective against both LM and HM.},

keywords = {},

pubstate = {forthcoming},

tppubtype = {article}

}