@article{%a1.%Yb_47,

title = {TGS1 impacts snRNA 3'-end processing, ameliorates survival motor neuron-dependent neurological phenotypes in vivo and prevents neurodegeneration},

author = {Chen L and Roake CM and Maccallini P and Bavasso F and Dehghannasiri R and Santonicola P and Mendoza-Ferreira N and Scatolini L and Rizzuti L and Esposito A and Gallotta I and Francia S and Cacchione S and Galati A and Palumbo V and Kobin MA and Tartaglia GG and Colantoni A and Proietti G and Wu Y and Hammerschmidt M and De Pittà C and Sales G and Salzman J and Pellizzoni L and Wirth B and Schiavi ED and Gatti M and Artandi SE and Raffa GD},

url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac659/6659874?login=true},

doi = {10.1093/nar/gkac659},

year  = {2022},

date = {2022-03-31},

journal = {Nucleic acids research},

volume = {50},

number = {12400},

issue = {21},

pages = {12424},

abstract = {Trimethylguanosine synthase 1 (TGS1) is a highly conserved enzyme that converts the 5'-monomethylguanosine cap of small nuclear RNAs (snRNAs) to a trimethylguanosine cap. Here, we show that loss of TGS1 in Caenorhabditis elegans, Drosophila melanogaster and Danio rerio results in neurological phenotypes similar to those caused by survival motor neuron (SMN) deficiency. Importantly, expression of human TGS1 ameliorates the SMN-dependent neurological phenotypes in both flies and worms, revealing that TGS1 can partly counteract the effects of SMN deficiency. TGS1 loss in HeLa cells leads to the accumulation of immature U2 and U4atac snRNAs with long 3' tails that are often uridylated. snRNAs with defective 3' terminations also accumulate in Drosophila Tgs1 mutants. Consistent with defective snRNA maturation, TGS1 and SMN mutant cells also exhibit partially overlapping transcriptome alterations that include aberrantly spliced and readthrough transcripts. Together, these results identify a neuroprotective function for TGS1 and reinforce the view that defective snRNA maturation affects neuronal viability and function.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_44,

title = {The role of prelamin A post-translational maturation in stress response and 53BP1 recruitment},

author = {Capanni C and Schena E and Di Giampietro ML and Montecucco A and Mattioli E and Lattanzi G},

url = {https://www.frontiersin.org/articles/10.3389/fcell.2022.1018102/full},

doi = {10.3389/fcell.2022.1018102},

year  = {2022},

date = {2022-03-31},

journal = {Frontiers in cell and developmental biology},

volume = {10},

abstract = {Lamin A is a main constituent of the nuclear lamina and contributes to nuclear shaping, mechano-signaling transduction and gene regulation, thus affecting major cellular processes such as cell cycle progression and entry into senescence, cellular differentiation and stress response. The role of lamin A in stress response is particularly intriguing, yet not fully elucidated, and involves prelamin A post-translational processing. Here, we propose prelamin A as the tool that allows lamin A plasticity during oxidative stress response and permits timely 53BP1 recruitment to DNA damage foci. We show that while PCNA ubiquitination, p21 decrease and H2AX phosphorylation occur soon after stress induction in the absence of prelamin A, accumulation of non-farnesylated prelamin A follows and triggers recruitment of 53BP1 to lamin A/C complexes. Then, the following prelamin A processing steps causing transient accumulation of farnesylated prelamin A and maturation to lamin A reduce lamin A affinity for 53BP1 and favor its release and localization to DNA damage sites. Consistent with these observations, accumulation of prelamin A forms in cells under basal conditions impairs histone H2AX phosphorylation, PCNA ubiquitination and p21 degradation, thus affecting the early stages of stress response. As a whole, our results are consistent with a physiological function of prelamin A modulation during stress response aimed at timely recruitment/release of 53BP1 and other molecules required for DNA damage repair. In this context, it becomes more obvious how farnesylated prelamin A accumulation to toxic levels alters timing of DNA damage signaling and 53BP1 recruitment, thus contributing to cellular senescence and accelerated organismal aging as observed in progeroid laminopathies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_66,

title = {Collagen VI ablation in zebrafish causes neuromuscular defects during developmental and adult stages},

author = {Tonelotto V and Consorti C and Facchinello N and Trapani V and Sabatelli P and Giraudo C and Spizzotin M and Cescon M and Bertolucci C and Bonaldo P},

url = {https://www.sciencedirect.com/science/article/pii/S0945053X22000981?via%3Dihub},

doi = {10.1016/j.matbio.2022.08.004},

year  = {2022},

date = {2022-03-30},

urldate = {2022-03-30},

journal = {Matrix biology},

volume = {112},

pages = {39-61},

abstract = {Collagen VI (COL6) is an extracellular matrix protein exerting multiple functions in different tissues. In humans, mutations of COL6 genes cause rare inherited congenital disorders, primarily affecting skeletal muscles and collectively known as COL6-related myopathies, for which no cure is available yet. In order to get insights into the pathogenic mechanisms underlying COL6-related diseases, diverse animal models were produced. However, the roles exerted by COL6 during embryogenesis remain largely unknown. Here, we generated the first zebrafish COL6 knockout line through CRISPR/Cas9 site-specific mutagenesis of the col6a1 gene. Phenotypic characterization during embryonic and larval development revealed that lack of COL6 leads to neuromuscular defects and motor dysfunctions, together with distinctive alterations in the three-dimensional architecture of craniofacial cartilages. These phenotypic features were maintained in adult col6a1 null fish, which displayed defective muscle organization and impaired swimming capabilities. Moreover, col6a1 null fish showed autophagy defects and organelle abnormalities at both embryonic and adult stages, thus recapitulating the main features of patients affected by COL6-related myopathies. Mechanistically, lack of COL6 led to increased BMP signaling, and direct inhibition of BMP activity ameliorated the locomotor col6a1 null embryos. Finally performance of, treatment with salbutamol, a beta2-adrenergic receptor agonist, elicited a significant amelioration of the neuromuscular and motility defects of col6a1 null fish embryos. Altogether, these findings indicate that this newly generated zebrafish col6a1 null line is a valuable in vivo tool to model COL6-related myopathies and suitable for drug screenings aimed at addressing the quest for effective therapeutic strategies for these disorders.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_53,

title = {Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis},

author = {Kanoni S and Graham SE and Wang Y and Surakka I and …. and Biino G and ….. and Deloukas P and Willer CJ and Assimes TL and Peloso GM},

url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02837-1},

doi = {10.1186/s13059-022-02837-1},

year  = {2022},

date = {2022-03-30},

urldate = {2022-03-30},

journal = {Genome biology},

volume = {23},

issue = {1},

pages = {268},

abstract = {Background: Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results: To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions: Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_50,

title = {Novel pyrazolo[3,4-d]pyrimidines as dual Src/Bcr-Abl kinase inhibitors: Synthesis and biological evaluation for chronic myeloid leukemia treatment. },

author = {Di Maria S and Picarazzi F and Mori M and Cianciusi A and Carbone A and Crespan E and Perini C and Sabetta S and Deplano S and Poggialini F and Molinari A and Aronne R and Maccioni E and Maga G and Angelucci A and Schenone S and Musumeci F and Dreassi E},

url = {https://www.sciencedirect.com/science/article/pii/S0045206822004771?via%3Dihub},

doi = {10.1016/j.bioorg.2022.106071},

year  = {2022},

date = {2022-03-30},

journal = {Bioorganic chemistry},

volume = {128},

pages = {106071},

abstract = {The Bcr-Abl tyrosine kinase (TK) is the molecular hallmark of chronic myeloid leukemia (CML). Src is another TK kinase whose involvement in CML was widely demonstrated. Small molecules active as dual Src/Bcr-Abl inhibitors emerged as effective targeted therapies for CML and a few compounds are currently in clinical use. In this study, we applied a target-oriented approach to identify a family of pyrazolo[3,4-d]pyrimidines as dual Src/Bcr-Abl inhibitors as anti-leukemia agents. Considering the high homology between Src and Bcr-Abl, in-house Src inhibitors 8a-l and new analogue compounds 9a-n were screened as dual Src/Bcr-Abl inhibitors. The antiproliferative activity on K562 CML cells and the ADME profile were determined for the most promising compounds. Molecular modeling studies elucidated the binding mode of the inhibitors into the Bcr-Abl (wt) catalytic pocket. Compounds 8j and 8k showed nanomolar activities in enzymatic and cellular assays, together with favorable ADME properties, emerging as promising candidates for CML therapy. Finally, derivatives 9j and 9k, emerging as valuable inhibitors of the most aggressive Bcr-Abl mutation, T315I, constitute a good starting point in the search for compounds able to treat drug-resistant forms of CML. Overall, this study allowed us to identify more potent compounds than those previously reported by the group, marking a step forward in searching for new antileukemic agents.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_67,

title = {Differential and shared genetic effects on kidney function between diabetic and non-diabetic individuals},

author = {Winkler TW and Rasheed H and Teumer A and Gorski M and Rowan BX and Stanzick KJ and Thomas LF and Tin A and Hoppmann A and Chu AY and Tayo B and Thio CHL and Cusi D and Chai JF and Sieber KB and Horn K and Li M and Scholz M and Cocca M and Wuttke M and van der Most PJ and Yang Q and Ghasemi S and Nutile T and Li Y and ……. and Biino G and ……. {et al}},

url = {https://www.nature.com/articles/s42003-022-03448-z},

doi = {Communications biology},

year  = {2022},

date = {2022-03-26},

journal = {Communications biology},

volume = {5},

issue = {1},

pages = {580},

abstract = {Reduced glomerular filtration rate (GFR) can progress to kidney failure. Risk factors include genetics and diabetes mellitus (DM), but little is known about their interaction. We conducted genome-wide association meta-analyses for estimated GFR based on serum creatinine (eGFR), separately for individuals with or without DM (nDM = 178,691, nnoDM = 1,296,113). Our genome-wide searches identified (i) seven eGFR loci with significant DM/noDM-difference, (ii) four additional novel loci with suggestive difference and (iii) 28 further novel loci (including CUBN) by allowing for potential difference. GWAS on eGFR among DM individuals identified 2 known and 27 potentially responsible loci for diabetic kidney disease. Gene prioritization highlighted 18 genes that may inform reno-protective drug development. We highlight the existence of DM-only and noDM-only effects, which can inform about the target group, if respective genes are advanced as drug targets. Largely shared effects suggest that most drug interventions to alter eGFR should be effective in DM and noDM.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_56,

title = {TFIIH stabilization recovers the DNA repair and transcription dysfunctions in thermo-sensitive trichothiodystrophy},

author = {Lanzafame M and Nardo T and Ricotti R and Pantaleoni C and D'Arrigo S and Stanzial F and Benedicenti F and Thomas MA and Stefanini M and Orioli D and Botta E},

url = {https://onlinelibrary.wiley.com/doi/10.1002/humu.24488},

doi = {10.1002/humu.24488},

year  = {2022},

date = {2022-03-25},

journal = {Human mutation},

volume = {43},

issue = {12},

pages = {2222},

abstract = {Trichothiodystrophy (TTD) is a rare hereditary disease whose prominent feature is brittle hair. Additional clinical signs are physical and neurodevelopmental abnormalities and in about half of the cases hypersensitivity to UV radiation. The photosensitive form of TTD (PS-TTD) is most commonly caused by mutations in the ERCC2/XPD gene encoding a subunit of the transcription/DNA repair complex TFIIH. Here we report novel ERCC2/XPD mutations affecting proper protein folding, which generate thermo-labile forms of XPD associated with thermo-sensitive phenotypes characterized by reversible aggravation of TTD clinical signs during episodes of fever. In patient cells, the newly identified XPD variants result in thermo-instability of the whole TFIIH complex and consequent temperature-dependent defects in DNA repair and transcription. Improving the protein folding process by exposing patient cells to low temperature or to the chemical chaperone glycerol allowed rescue of TFIIH thermo-instability and a concomitant recovery of the complex activities. Besides providing a rationale for the peculiar thermo-sensitive clinical features of these new cases, the present findings demonstrate how variations in the cellular concentration of mutated TFIIH impact the cellular functions of the complex and underlie how both quantitative and qualitative TFIIH alterations contribute to TTD clinical features.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_46,

title = {Privileged Scaffold Decoration for the Identification of the First Trisubstituted Triazine with Anti-SARS-CoV-2 Activity},

author = {Cesarini S and Vicenti I and Poggialini F and Secchi M and Giammarino F and Varasi I and Lodola C and Zazzi M and Dreassi E and Maga G and Botta L and Saladino R},

url = {https://www.mdpi.com/1420-3049/27/24/8829},

doi = {10.3390/molecules27248829},

year  = {2022},

date = {2022-03-25},

journal = {Molecules},

volume = {27},

issue = {24},

pages = {8829},

abstract = {Current therapy against severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) are based on the use of Remdesivir 1, Molnupiravir 2, and the recently identified Nirmatrelvir 3. Unfortunately, these three drugs showed some limitations regarding potency and possible drug-drug interactions. A series of derivatives coming from a decoration approach of the privileged scaffold s-triazines were synthesized and evaluated against SAR-CoV-2. One derivative emerged as the hit of the series for its micromolar antiviral activity and low cytotoxicity. Mode of action and pharmacokinetic in vitro preliminary studies further confirm the role as candidates for a future optimization campaign of the most active derivative identified with this work.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_43,

title = {Screening Questionnaire for Vitamin D Insufficiency in Children with Obesity},

author = {Calcaterra V and Cena H and Biino G and Grazi R and Bortoni G and Braschi V and Tomasinelli CE and Schneider L and Zuccotti G},

url = {https://www.mdpi.com/2227-9067/9/11/1685},

doi = {https://www.mdpi.com/2227-9067/9/11/1685},

year  = {2022},

date = {2022-03-25},

urldate = {2022-03-25},

journal = {Children (Basel)},

volume = {9},

issue = {11},

pages = {1685},

abstract = {"Non-invasive screening tools to identify children at high risk of vitamin D (VitD) deficiency are proactive measures in preventive care. Recently, a validated questionnaire (Evaluation dEficieNCy Questionnaire, EVIDENCe-Q) for identifying newly diagnosed VitD-insufficient adults has been developed. We tested the EVIDENCe-Q modified for children with obesity and evaluated the correlation between VitD and questionnaire scores to adapt this tool to the pediatric population. We enrolled 120 children with obesity (BMI ≥ 2). Clinical evaluation and VitD levels were considered. The modified EVIDENCe-Q included information regarding factors affecting control of VitD, with scores ranging between 0 (best) and 36 (worst). VitD and adiposity indices were inversely correlated. The threshold values for identifying severe deficiency (<10 mg/dL), deficiency (<20 mg/dL) and insufficiency (<30 mg/dL) were scores of 21, 19 and 23, respectively. According to those thresholds, the prevalence of severe deficiency, deficiency and insufficiency was 47.5%, 69.2% and 23.3%, respectively; the best accuracy was obtained with a questionnaire score cut-off of 19 for the VitD deficiency level. A novel simple screening tool such as the modified EVIDENCe-Q would be useful in clinical practice to identify potential cases of hypovitaminosis D and select at-risk patients. Considering the limited accuracy and specificity of our results, for the pediatric population a dedicated tool should be created. Phases of childhood and the role of adipose tissue could be considered in the definition of a questionnaire intended for pediatric patients with obesity.

"},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_66,

title = {A saturated map of common genetic variants associated with human height},

author = {Yengo L and Vedantam S and Marouli E and Sidorenko J and Bartell E and Sakaue S and Graff M and Eliasen AU and Jiang Y and Raghavan S and Miao J and Arias JD and Graham SE and Mukamel RE and Spracklen CN and Yin X and Chen SH and Ferreira T and Highland HH and Ji Y and Karaderi T and Lin K and Lüll K and Malden DE and Medina-Gomez C and Machado and ……. and Biino G and ….. and {et al}},

url = {https://www.nature.com/articles/s41586-022-05275-y},

doi = {10.1038/s41586-022-05275-y.},

year  = {2022},

date = {2022-03-24},

journal = {Nature},

volume = {610},

issue = {7933},

pages = {704-712},

abstract = {Common single-nucleotide polymorphisms (SNPs) are predicted to collectively explain 40-50% of phenotypic variation in human height, but identifying the specific variants and associated regions requires huge sample sizes1. Here, using data from a genome-wide association study of 5.4 million individuals of diverse ancestries, we show that 12,111 independent SNPs that are significantly associated with height account for nearly all of the common SNP-based heritability. These SNPs are clustered within 7,209 non-overlapping genomic segments with a mean size of around 90 kb, covering about 21% of the genome. The density of independent associations varies across the genome and the regions of increased density are enriched for biologically relevant genes. In out-of-sample estimation and prediction, the 12,111 SNPs (or all SNPs in the HapMap 3 panel2) account for 40% (45%) of phenotypic variance in populations of European ancestry but only around 10-20% (14-24%) in populations of other ancestries. Effect sizes, associated regions and gene prioritization are similar across ancestries, indicating that reduced prediction accuracy is likely to be explained by linkage disequilibrium and differences in allele frequency within associated regions. Finally, we show that the relevant biological pathways are detectable with smaller sample sizes than are needed to implicate causal genes and variants. Overall, this study provides a comprehensive map of specific genomic regions that contain the vast majority of common height-associated variants. Although this map is saturated for populations of European ancestry, further research is needed to achieve equivalent saturation in other ancestries.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_57,

title = {Cell-Autonomous Processes That Impair Xenograft Survival into the Cerebellum},

author = {Magrassi L and Nato G and Delia D and Buffo A},

url = {https://link.springer.com/article/10.1007/s12311-022-01414-3},

doi = {10.1007/s12311-022-01414-3},

year  = {2022},

date = {2022-03-24},

journal = {Cerebellum},

volume = {21},

issue = {5},

abstract = {In immunocompetent animals, numerous factors including the immune system of the host regulate the survival of neuro-glial precursors transplanted into the cerebellum. We transplanted human neuro-glial precursors derived in vitro from partial differentiation of IPS cells into the developing cerebellum of mice and rats before maturation of the host immune system. These approaches should facilitate the development of immune-tolerance for the transplanted cells. However, we found that human cells survived the engraftment and integrated into the host cerebellum and brain stem up to about 1 month postnatally when they were rejected in both species. On the contrary, when we transplanted the same cells in NOD-SCID mice, they survived indefinitely. Our findings are consistent with the hypothesis that the slower pace of differentiation of human neural precursors compared to that of rodents restricts the induction of immune-tolerance to human antigens expressed before completion of the maturation of the immune system. As predicted by our hypothesis, when we engrafted the human neuro-glial precursor cells either in a more mature state or mixed with extracts from adult cerebellum, we prolonged the survival of the graft.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_55,

title = {Combined alteration of lamin and nuclear morphology influences the localization of the tumor-associated factor AKTIP},

author = {{La Torre M} and Merigliano C and Maccaroni K and Chojnowski A and Goh WI and Giubettini M and Vernì F and Capanni C and Rhodes D and Wright G and Burke B and Soddu S and Burla R and Saggio I},

url = {https://jeccr.biomedcentral.com/articles/10.1186/s13046-022-02480-5},

doi = {10.1186/s13046-022-02480-5},

year  = {2022},

date = {2022-03-24},

journal = {Journal of experimental & clinical cancer research},

volume = {41},

issue = {1},

pages = {273},

abstract = {Background: Lamins, key nuclear lamina components, have been proposed as candidate risk biomarkers in different types of cancer but their accuracy is still debated. AKTIP is a telomeric protein with the property of being enriched at the nuclear lamina. AKTIP has similarity with the tumor susceptibility gene TSG101. AKTIP deficiency generates genome instability and, in p53-/- mice, the reduction of the mouse counterpart of AKTIP induces the exacerbation of lymphomas. Here, we asked whether the distribution of AKTIP is altered in cancer cells and whether this is associated with alterations of lamins. Methods: We performed super-resolution imaging, quantification of lamin expression and nuclear morphology on HeLa, MCF7, and A549 tumor cells, and on non-transformed fibroblasts from healthy donor and HGPS (LMNA c.1824C > T p.Gly608Gly) and EDMD2 (LMNA c.775 T > G) patients. As proof of principle model combining a defined lamin alteration with a tumor cell setting, we produced HeLa cells exogenously expressing the HGPS lamin mutant progerin that alters nuclear morphology. Results: In HeLa cells, AKTIP locates at less than 0.5 µm from the nuclear rim and co-localizes with lamin A/C. As compared to HeLa, there is a reduced co-localization of AKTIP with lamin A/C in both MCF7 and A549. Additionally, MCF7 display lower amounts of AKTIP at the rim. The analyses in non-transformed fibroblasts show that AKTIP mislocalizes in HGPS cells but not in EDMD2. The integrated analysis of lamin expression, nuclear morphology, and AKTIP topology shows that positioning of AKTIP is influenced not only by lamin expression, but also by nuclear morphology. This conclusion is validated by progerin-expressing HeLa cells in which nuclei are morphologically altered and AKTIP is mislocalized. Conclusions: Our data show that the combined alteration of lamin and nuclear morphology influences the localization of the tumor-associated factor AKTIP. The results also point to the fact that lamin alterations per se are not predictive of AKTIP mislocalization, in both non-transformed and tumor cells. In more general terms, this study supports the thesis that a combined analytical approach should be preferred to predict lamin-associated changes in tumor cells. This paves the way of next translational evaluation to validate the use of this combined analytical approach as risk biomarker.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_54,

title = {CHD8 suppression impacts on histone H3 lysine 36 trimethylation and alters RNA alternative splicing},

author = {Kerschbamer E and Arnoldi M and Tripathi T and Pellegrini M and Maturi S and Erdin S and Salviato E and Di Leva F and Sebestyén E and Dassi E and Zarantonello G and Benelli M and Campos E and Basson MA and Gusella JF and Gustincich S and Piazza S and Demichelis F and Talkowski ME and Ferrari F and Biagioli M},

url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1134/6947080?login=false},

doi = {10.1093/nar/gkac1134},

year  = {2022},

date = {2022-03-24},

journal = {Nucleic acids research},

volume = {50},

issue = {22},

pages = {12809-12828},

abstract = {Disruptive mutations in the chromodomain helicase DNA-binding protein 8 gene (CHD8) have been recurrently associated with autism spectrum disorders (ASDs). Here we investigated how chromatin reacts to CHD8 suppression by analyzing a panel of histone modifications in induced pluripotent stem cell-derived neural progenitors. CHD8 suppression led to significant reduction (47.82%) in histone H3K36me3 peaks at gene bodies, particularly impacting on transcriptional elongation chromatin states. H3K36me3 reduction specifically affects highly expressed, CHD8-bound genes and correlates with altered alternative splicing patterns of 462 genes implicated in 'regulation of RNA splicing' and 'mRNA catabolic process'. Mass spectrometry analysis uncovered a novel interaction between CHD8 and the splicing regulator heterogeneous nuclear ribonucleoprotein L (hnRNPL), providing the first mechanistic insights to explain the CHD8 suppression-derived splicing phenotype, partly implicating SETD2, a H3K36me3 methyltransferase. In summary, our results point toward broad molecular consequences of CHD8 suppression, entailing altered histone deposition/maintenance and RNA processing regulation as important regulatory processes in ASD.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_45,

title = {3D ECM-rich environment sustains the identity of naive human iPSCs},

author = {Cesare E and Urciuolo A and Stuart HT and Torchio E and Gesualdo A and Laterza C and Gagliano O and Martewicz S and Cui M and Manfredi A and Di Filippo L and Sabatelli P and Squarzoni S and Zorzan I and Betto RM and Martello G and Cacchiarelli D and Luni C and Elvassore N},

url = {https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(22)00458-1?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1934590922004581%3Fshowall%3Dtrue},

doi = {10.1016/j.stem.2022.11.011},

year  = {2022},

date = {2022-03-24},

urldate = {2022-03-24},

journal = {Cell stem cell},

volume = {29},

issue = {12},

pages = {1703-1717},

abstract = {The establishment of in vitro naive human pluripotent stem cell cultures opened new perspectives for the study of early events in human development. The role of several transcription factors and signaling pathways have been characterized during maintenance of human naive pluripotency. However, little is known about the role exerted by the extracellular matrix (ECM) and its three-dimensional (3D) organization. Here, using an unbiased and integrated approach combining microfluidic cultures with transcriptional, proteomic, and secretome analyses, we found that naive, but not primed, hiPSC colonies are characterized by a self-organized ECM-rich microenvironment. Based on this, we developed a 3D culture system that supports robust long-term feeder-free self-renewal of naive hiPSCs and also allows direct and timely developmental morphogenesis simply by modulating the signaling environment. Our study opens new perspectives for future applications of naive hiPSCs to study critical stages of human development in 3D starting from a single cell.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_64,

title = {Imaging and spectral analysis of autofluorescence patterns in larval head structures of mosquito vectors},

author = {Scolari F and Girella A and Croce AC},

url = {https://www.ejh.it/index.php/ejh/article/view/3462},

doi = {10.4081/ejh.2022.3462},

year  = {2022},

date = {2022-03-23},

journal = {European journal of histochemistry},

volume = {66},

issue = {4},

pages = {3462},

abstract = {Autofluorescence (AF) in mosquitoes is currently poorly explored, despite its great potential as a marker of body structures and biological functions. Here, for the first time AF in larval heads of two mosquitoes of key public health importance, Aedes albopictus and Culex pipiens, is studied using fluorescence imaging and spectrofluorometry, similarly to a label-free histochemical approach. In generally conserved distribution patterns, AF shows differences between mouth brushes and antennae of the two species. The blue AF ascribable to resilin at the antennal bases, more extended in Cx. pipiens, suggests a potential need to support different antennal movements. The AF spectra larger in Cx. pipiens indicate a variability in material composition and properties likely relatable to mosquito biology, including diverse feeding and locomotion behaviours with implications for vector control.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_58,

title = {Clinical Significance and Regulation of ERK5 Expression and Function in Cancer},

author = {Monti M and Celli J and Missale F and Cersosimo F and Russo M and Belloni E and {Di Matteo A} and Lonardi S and Vermi W and Ghigna C and Giurisato E},

url = {https://www.mdpi.com/2072-6694/14/2/348},

doi = {10.3390/cancers14020348},

year  = {2022},

date = {2022-03-23},

urldate = {2022-03-23},

journal = {Cancers (Basel)},

volume = {14},

issue = {2},

pages = {348},

abstract = {Extracellular signal-regulated kinase 5 (ERK5) is a unique kinase among MAPKs family members, given its large structure characterized by the presence of a unique C-terminal domain. Despite increasing data demonstrating the relevance of the ERK5 pathway in the growth, survival, and differentiation of normal cells, ERK5 has recently attracted the attention of several research groups given its relevance in inflammatory disorders and cancer. Accumulating evidence reported its role in tumor initiation and progression. In this review, we explore the gene expression profile of ERK5 among cancers correlated with its clinical impact, as well as the prognostic value of ERK5 and pERK5 expression levels in tumors. We also summarize the importance of ERK5 in the maintenance of a cancer stem-like phenotype and explore the major known contributions of ERK5 in the tumor-associated microenvironment. Moreover, although several questions are still open concerning ERK5 molecular regulation, different ERK5 isoforms derived from the alternative splicing process are also described, highlighting the potential clinical relevance of targeting ERK5 pathways.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Ybm,

title = {Novel Perceptions on Chemical Profile and Biopharmaceutical Properties of Mentha spicata Extracts: Adding Missing Pieces to the Scientific Puzzle},

author = {Zengin G and Ak G and Ceylan R and Uysal S and Llorent-Martínez E and Di Simone SC and Rapino M and Acquaviva A and Libero ML and Chiavaroli A and Recinella L and Leone S and Brunetti L and Cataldi A and Orlando G and Menghini L and Ferrante C and Balaha M and di Giacomo V},

url = {https://www.mdpi.com/2223-7747/11/2/233},

doi = {10.3390/plants11020233},

year  = {2022},

date = {2022-03-21},

journal = {Plants (Basel)},

volume = {11},

issue = {2},

pages = {233},

abstract = {Mentha spicata is one of the most popular species in the genus, and it is of great interest as a gastrointestinal and sedative agent in the folk medicine system. In this study, different M. spicata extracts, obtained by the use of four solvents (hexane, chloroform, acetone and acetone/water) were chemically characterized using HPLC-ESI-MS n, which allowed for identification of 27 phenolic compounds. The extracts' antioxidant and enzyme inhibitory properties were investigated. In addition, neuroprotective effects were evaluated in hypothalamic HypoE22 cells, and the ability of the extracts to prevent the hydrogen peroxide-induced degradation of dopamine and serotonin was observed. The best antioxidant effect was achieved for all the extraction methods using acetone/water as a solvent. These extracts were the richest in acacetin, eriodictyol, hesperidin, sagerinic acid, naringenin, luteolin, chlorogenic acid, chrysoeriol and apigenin. The intrinsic antioxidant and enzyme inhibition properties of the acetone/water extract could also explain, albeit partially, its efficacy in preventing prostaglandin E2 overproduction and dopamine depletion (82.9% turnover reduction) in HypoE22 cells exposed to hydrogen peroxide. Thus, our observations can provide a scientific confirmation of the neuromodulatory and neuroprotective effects of M. spicata.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Ybl,

title = {Early Morphological Changes of the Rectus Femoris Muscle and Deep Fascia in Ullrich Congenital Muscular Dystrophy},

author = {Sabatelli P and Merlini L and Di Martino A and Cenni V and Faldini C},

url = {https://www.mdpi.com/1660-4601/19/3/1252},

doi = {International journal of environmental research and public health},

year  = {2022},

date = {2022-03-21},

journal = {International journal of environmental research and public health},

volume = {19},

issue = {3},

pages = {1252},

abstract = {Ullrich congenital muscular dystrophy (UCMD) is a severe form of muscular dystrophy caused by the loss of function of collagen VI, a critical component of the muscle-tendon matrix. Magnetic resonance imaging of UCMD patients' muscles shows a peculiar rim of abnormal signal at the periphery of each muscle, and a relative sparing of the internal part. The mechanism/s involved in the early fat substitution of muscle fiber at the periphery of muscles remain elusive. We studied a muscle biopsy of the rectus femoris/deep fascia (DF) of a 3-year-old UCMD patient, with a homozygous mutation in the COL6A2 gene. By immunohistochemical and ultrastructural analysis, we found a marked fatty infiltration at the interface of the muscle with the epimysium/DF and an atrophic phenotype, primarily in fast-twitch fibers, which has never been reported before. An unexpected finding was the widespread increase of interstitial cells with long cytoplasmic processes, consistent with the telocyte phenotype. Our study documents for the first time in a muscle biopsy the peculiar pattern of outside-in muscle degeneration followed by fat substitution as already shown by muscle imaging, and an increase of telocytes in the interstitium of the deep fascia, which highlights a potential involvement of this structure in the pathogenesis of UCMD.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Ybk,

title = {Telomere dysfunction in ageing and age-related diseases},

author = {Rossiello F and Jurk D and Passos JF and {d'Adda di Fagagna F}},

url = {https://www.nature.com/articles/s41556-022-00842-x},

doi = {10.1038/s41556-022-00842-x},

year  = {2022},

date = {2022-03-21},

volume = {24},

issue = {2},

pages = {135-147},

abstract = {Ageing organisms accumulate senescent cells that are thought to contribute to body dysfunction. Telomere shortening and damage are recognized causes of cellular senescence and ageing. Several human conditions associated with normal ageing are precipitated by accelerated telomere dysfunction. Here, we systematize a large body of evidence and propose a coherent perspective to recognize the broad contribution of telomeric dysfunction to human pathologies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Ybj,

title = {Exosomes Recovered From the Plasma of COVID-19 Patients Expose SARS-CoV-2 Spike-Derived Fragments and Contribute to the Adaptive Immune Response},

author = {Pesce E and Manfrini N and Cordiglieri C and Santi S and Bandera A and Gobbini A and Gruarin P and Favalli A and Bombaci M and Cuomo A and Collino F and Cricri' G and Ungaro R and Lombardi A and Mangioni D and Muscatello A and Aliberti S and Blasi F and Gori A and Abrignani S and De Francesco R and Biffo S and Grifantini R},

url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-85123854300&partnerID=q2rCbXpz},

doi = {10.3389/fimmu.2021.785941},

year  = {2022},

date = {2022-03-21},

journal = {Frontiers in immunology},

volume = {12},

pages = {7859},

abstract = {Coronavirus disease 2019 (COVID-19) is an infectious disease caused by beta-coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has rapidly spread across the globe starting from February 2020. It is well established that during viral infection, extracellular vesicles become delivery/presenting vectors of viral material. However, studies regarding extracellular vesicle function in COVID-19 pathology are still scanty. Here, we performed a comparative study on exosomes recovered from the plasma of either MILD or SEVERE COVID-19 patients. We show that although both types of vesicles efficiently display SARS-CoV-2 spike-derived peptides and carry immunomodulatory molecules, only those of MILD patients are capable of efficiently regulating antigen-specific CD4+ T-cell responses. Accordingly, by mass spectrometry, we show that the proteome of exosomes of MILD patients correlates with a proper functioning of the immune system, while that of SEVERE patients is associated with increased and chronic inflammation. Overall, we show that exosomes recovered from the plasma of COVID-19 patients possess SARS-CoV-2-derived protein material, have an active role in enhancing the immune response, and possess a cargo that reflects the pathological state of patients in the acute phase of the disease.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Ybi,

title = {Mutation in senataxin alters the mechanism of R-loop resolution in amyotrophic lateral sclerosis 4},

author = {Kannan A and Cuartas J and Gangwani P and Branzei D and Gangwani L},

url = {https://academic.oup.com/brain/advance-article/doi/10.1093/brain/awab464/6511590},

doi = {10.1093/brain/awab464},

year  = {2022},

date = {2022-03-21},

journal = {Brain},

abstract = {Mutation in the Senataxin (SETX) gene causes an autosomal dominant neuromuscular disorder, amyotrophic lateral sclerosis 4 (ALS4), characterized by degeneration of motor neurons, muscle weakness and atrophy. SETX is an RNA-DNA helicase that mediates resolution of co-transcriptional RNA-DNA hybrids (R-loops). The process of R-loop resolution is essential for the normal functioning of cells, including neurons. The molecular basis of ALS4 pathogenesis and the mechanism of R-loop resolution are unclear. We report that the zinc finger protein ZPR1 binds to RNA-DNA hybrids, recruits SETX onto R-loops and is critical for R-loop resolution. ZPR1 deficiency disrupts the integrity of R-loop resolution complexes (RLRC) containing SETX and causes increased R-loop accumulation throughout gene transcription. We uncover that SETX is a downstream target of ZPR1 and that overexpression of ZPR1 can rescue RLRC assembly in SETX-deficient cells but not vice versa. To uncover the mechanism of R-loop resolution, we examined the function of SETX-ZPR1 complexes using two genetic motor neuron disease models with altered R-loop resolution. Notably, chronic low levels of SETX-ZPR1 complexes onto R-loops result in a decrease of R-loop resolution activity causing an increase in R-loop levels in spinal muscular atrophy (SMA). ZPR1 overexpression increases recruitment of SETX onto R-loops, decreases R-loops and rescues the SMA phenotype in motor neurons and patient cells. Strikingly, interaction of SETX with ZPR1 is disrupted in ALS4 patients that have heterozygous SETX (L389S) mutation. ZPR1 fails to recruit the mutant SETX homodimer but recruits the heterodimer with partially disrupted interaction between SETX and ZPR1. Interestingly, disruption of SETX-ZPR1 complexes causes increase in R-loop resolution activity leading to fewer R-loops in ALS4. Modulation of ZPR1 levels regulates R-loop accumulation and rescues the pathogenic R-loop phenotype in ALS4 patient cells. These findings originate a new concept, "opposite alterations in a cell biological activity (R-loop resolution) result in similar pathogenesis (neurodegeneration) in different genetic motor neuron disorders". We propose that ZPR1 collaborates with SETX and may function as a molecular brake to regulate SETX-dependent R-loop resolution activity critical for the normal functioning of motor neurons.},

keywords = {},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{%a1.%Ybh,

title = {The wide and growing range of lamin B-related diseases: from laminopathies to cancer. },

author = {Evangelisti C and Rusciano I and Mongiorgi S and Ramazzotti G and Lattanzi G and Manzoli L and Cocco L and Ratti S and},

url = {https://link.springer.com/article/10.1007/s00018-021-04084-2},

doi = {10.1007/s00018-021-04084-2},

year  = {2022},

date = {2022-03-21},

journal = {Cellular and molecular life sciences},

volume = {79},

number = {126},

issue = {2},

abstract = {B-type lamins are fundamental components of the nuclear lamina, a complex structure that acts as a scaffold for organization and function of the nucleus. Lamin B1 and B2, the most represented isoforms, are encoded by LMNB1 and LMNB2 gene, respectively. All B-type lamins are synthesized as precursors and undergo sequential post-translational modifications to generate the mature protein. B-type lamins are involved in a wide range of nuclear functions, including DNA replication and repair, regulation of chromatin and nuclear stiffness. Moreover, lamins B1 and B2 regulate several cellular processes, such as tissue development, cell cycle, cellular proliferation, senescence, and DNA damage response. During embryogenesis, B-type lamins are essential for organogenesis, in particular for brain development. As expected from the numerous and pivotal functions of B-type lamins, mutations in their genes or fluctuations in their expression levels are critical for the onset of several diseases. Indeed, a growing range of human disorders have been linked to lamin B1 or B2, increasing the complexity of the group of diseases collectively known as laminopathies. This review highlights the recent findings on the biological role of B-type lamins under physiological or pathological conditions, with a particular emphasis on brain disorders and cancer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Ybg,

title = {Parental histone deposition on the replicated strands promotes error-free DNA damage tolerance and regulates drug resistance},

author = {Dolce V and Dusi S and Giannattasio M and Joseph CR and Fumasoni M and Branzei D},

url = {http://genesdev.cshlp.org/content/early/2022/02/01/gad.349207.121.long},

doi = {10.1101/gad.349207.121},

year  = {2022},

date = {2022-03-21},

urldate = {2022-03-21},

journal = {Genes & development},

volume = {36},

issue = {1-4},

pages = {167-179},

abstract = {Ctf4 is a conserved replisome component with multiple roles in DNA metabolism. To investigate connections between Ctf4-mediated processes involved in drug resistance, we conducted a suppressor screen of ctf4delta sensitivity to the methylating agent MMS. We uncovered that mutations in Dpb3 and Dpb4 components of polymerase ε result in the development of drug resistance in ctf4Δ via their histone-binding function. Alleviated sensitivity to MMS of the double mutants was not associated with rescue of ctf4delta defects in sister chromatid cohesion, replication fork architecture, or template switching, which ensures error-free replication in the presence of genotoxic stress. Strikingly, the improved viability depended on translesion synthesis (TLS) polymerase-mediated mutagenesis, which was drastically increased in ctf4 dpb3 double mutants. Importantly, mutations in Mcm2-Ctf4-Polα and Dpb3-Dpb4 axes of parental (H3-H4)2 deposition on lagging and leading strands invariably resulted in reduced error-free DNA damage tolerance through gap filling by template switch recombination. Overall, we uncovered a chromatin-based drug resistance mechanism in which defects in parental histone transfer after replication fork passage impair error-free recombination bypass and lead to up-regulation of TLS-mediated mutagenesis and drug resistance.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb,

title = {Three dimensional spheroid cell culture of human MSC-derived neuron-like cells: new in vitro model to assess magnetite nanoparticle-induced neurotoxicity effects},

author = {{De Simone U} and Croce AC and Pignatti P and Buscaglia E and Caloni F and Coccini T},

url = {https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/jat.4292},

doi = {10.1002/jat.4292},

year  = {2022},

date = {2022-03-21},

urldate = {2022-03-21},

journal = {Journal of applied toxicology},

volume = {42},

issue = {7},

pages = {1230-1252},

abstract = {As nanoparticles (NPs) can access the brain and impact on CNS function, novel in vitro models for the evaluation of NPs-induced neurotoxicity are advocated. 3D-spheroids of primary neuron-like cells (hNLCs) of human origin have been generated, from differentiation of human umbilical cord mesenchymal stem cells (MSCs). The study evaluated Fe3 O4 NP impact on the differentiation process by applying the challenge at complete 3D hNLC spheroid formation (after 4 days-T4) or at beginning of neurogenic induction/simultaneously 3D forming (T0). Different endpoints were monitored over time (up to 10 days): spheroid growth, size, morphology, ATP, cell death, neuronal markers (β-Tub III, MAP-2, NSE), NP-uptake. At T0-application, a marked concentration- and time-dependent cell mortality occurred: effect started early (day 2) and low concentration (1 μg/ml) and exacerbated (80% mortality) after prolonged time (day 6) and increased concentrations (50 μg/ml). ATP was strikingly affected. All neuronal markers were downregulated and spheroid morphology altered in a concentration-dependent manner (from ≥ 5μg/ml) after day 2. Fe3 O4 NPs applied at complete 3D formation (T4) still induced adverse effects although less severe: cell mortality (20-60%) and ATP content decrease (10-40%) were observed in a concentration-dependent manner (from ≥ 5 μg/ml). A neuronal-specific marker effect and spheroid size reduction from 25 μg/ml without morphology alteration were evidenced. This finding provides additional information on neurotoxic effects of Fe3 O4 NPs in a new 3D hNLC spheroid model derived from MSCs, that could find a consistent application as in a testing strategy serving in first step hazard identification for correct risk assessment.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Ybd,

title = {Genomic loci mispositioning in Tmem120a knockout mice yields latent lipodystrophy},

author = {Czapiewski R and Batrakou DG and de Las Heras JI and Carter RN and Sivakumar A and Sliwinska M and Dixon CR and Webb S and Lattanzi G and Morton NM and Schirmer EC},

url = {https://www.nature.com/articles/s41467-021-27869-2},

doi = {10.1038/s41467-021-27869-2},

year  = {2022},

date = {2022-02-25},

urldate = {2022-02-25},

journal = {Nature communications},

volume = {13},

number = {321},

issue = {1},

abstract = {Little is known about how the observed fat-specific pattern of 3D-spatial genome organisation is established. Here we report that adipocyte-specific knockout of the gene encoding nuclear envelope transmembrane protein Tmem120a disrupts fat genome organisation, thus causing a lipodystrophy syndrome. Tmem120a deficiency broadly suppresses lipid metabolism pathway gene expression and induces myogenic gene expression by repositioning genes, enhancers and miRNA-encoding loci between the nuclear periphery and interior. Tmem120a-/- mice, particularly females, exhibit a lipodystrophy syndrome similar to human familial partial lipodystrophy FPLD2, with profound insulin resistance and metabolic defects that manifest upon exposure to an obesogenic diet. Interestingly, similar genome organisation defects occurred in cells from FPLD2 patients that harbour nuclear envelope protein encoding LMNA mutations. Our data indicate TMEM120A genome organisation functions affect many adipose functions and its loss may yield adiposity spectrum disorders, including a miRNA-based mechanism that could explain muscle hypertrophy in human lipodystrophy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Ybc,

title = {The Bright Side of the Tiger: Autofluorescence Patterns in Aedes albopictus (Diptera, Culicidae) Male and Female Mosquitoes. },

author = {Croce AC and Scolari F},

url = {https://www.mdpi.com/1420-3049/27/3/713},

doi = {10.3390/molecules27030713},

year  = {2022},

date = {2022-02-25},

journal = {Molecules},

volume = {27},

issue = {3},

pages = {713},

abstract = {Light-based events in insects deserve increasing attention for various reasons. Besides their roles in inter- and intra-specific visual communication, with biological, ecological and taxonomical implications, optical properties are also promising tools for the monitoring of insect pests and disease vectors. Among these is the Asian tiger mosquito, Aedes albopictus, a global arbovirus vector. Here we have focused on the autofluorescence characterization of Ae. albopictus adults using a combined imaging and spectrofluorometric approach. Imaging has evidenced that autofluorescence rises from specific body compartments, such as the head appendages, and the abdominal and leg scales. Spectrofluorometry has demonstrated that emission consists of a main band in the 410-600 nm region. The changes in the maximum peak position, between 430 nm and 500 nm, and in the spectral width, dependent on the target structure, indicate the presence, at variable degrees, of different fluorophores, likely resilin, chitin and melanins. The aim of this work has been to provide initial evidence on the so far largely unexplored autofluorescence of Ae. albopictus, to furnish new perspectives for the set-up of species- and sex-specific investigation of biological functions as well as of strategies for in-flight direct detection and surveillance of mosquito vectors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Ybb,

title = {BRCA1 deficiency specific base substitution mutagenesis is dependent on translesion synthesis and regulated by 53BP1},

author = {Chen D and Gervai JZ and Poti A and Nemeth E and Szeltner Z and Szikriszt B and Gyure Z and Zamborszky J and Ceccon M and {d'Adda di Fagagna F} and Szallasi Z and Richardson AL and Szuts D},

url = {https://www.nature.com/articles/s41467-021-27872-7},

doi = {10.1038/s41467-021-27872-7},

year  = {2022},

date = {2022-02-25},

journal = {Nature communications},

volume = {13},

issue = {1},

pages = {226},

abstract = {Defects in BRCA1, BRCA2 and other genes of the homology-dependent DNA repair (HR) pathway cause an elevated rate of mutagenesis, eliciting specific mutation patterns including COSMIC signature SBS3. Using genome sequencing of knock-out cell lines we show that Y family translesion synthesis (TLS) polymerases contribute to the spontaneous generation of base substitution and short insertion/deletion mutations in BRCA1 deficient cells, and that TLS on DNA adducts is increased in BRCA1 and BRCA2 mutants. The inactivation of 53BP1 in BRCA1 mutant cells markedly reduces TLS-specific mutagenesis, and rescues the deficiency of template switch-mediated gene conversions in the immunoglobulin V locus of BRCA1 mutant chicken DT40 cells. 53BP1 also promotes TLS in human cellular extracts in vitro. Our results show that HR deficiency-specific mutagenesis is largely caused by TLS, and suggest a function for 53BP1 in regulating the choice between TLS and error-free template switching in replicative DNA damage bypass.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb,

title = {Validation of a Cleanroom Compliant Sonication-Based Decellularization Technique: A New Concept in Nerve Allograft Production},

author = {Bolognesi F and Fazio N and Boriani F and Fabbri VP and Gravina D and Pedrini FA and Zini N and Greco M and Paolucci M and Re MC and Asioli S and Foschini MP and D'Errico A and Baldini N and Marchetti C},

url = {https://www.mdpi.com/1422-0067/23/3/1530},

doi = {10.3390/ijms23031530},

year  = {2022},

date = {2022-02-25},

urldate = {2022-02-25},

journal = {International journal of molecular sciences},

volume = {23},

issue = {2},

pages = {1530},

abstract = {Defects of the peripheral nervous system are extremely frequent in trauma and surgeries and have high socioeconomic costs. If the direct suture of a lesion is not possible, i.e., nerve gap > 2 cm, it is necessary to use grafts. While the gold standard is the autograft, it has disadvantages related to its harvesting, with an inevitable functional deficit and further morbidity. An alternative to autografting is represented by the acellular nerve allograft (ANA), which avoids disadvantages of autograft harvesting and fresh allograft rejection. In this research, the authors intend to transfer to human nerves a novel technique, previously implemented in animal models, to decellularize nerves. The new method is based on soaking the nerve tissues in decellularizing solutions while associating ultrasounds and freeze-thaw cycles. It is performed without interrupting the sterility chain, so that the new graft may not require post-production γ-ray irradiation, which is suspected to affect the structural and functional quality of tissues. The new method is rapid, safe, and inexpensive if compared with available commercial ANAs. Histology and immunohistochemistry have been adopted to evaluate the new decellularized nerves. The study shows that the new method can be applied to human nerve samples, obtaining similar, and, sometimes better, results compared with the chosen control method, the Hudson technique.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb_62,

title = {DNA damage response at telomeres boosts the transcription of SARS-CoV-2 receptor ACE2 during aging.},

author = {Sepe S and Rossiello F and Cancila V and Iannelli F and Matti V and Cicio G and Cabrini M and Marinelli E and Alabi BR and di Lillo A and Di Napoli A and Shay JW and Tripodo C and {d'Adda di Fagagna F}},

url = {https://www.embopress.org/doi/full/10.15252/embr.202153658},

doi = {10.15252/embr.202153658},

year  = {2022},

date = {2022-02-04},

urldate = {2021-12-06},

journal = {EMBO Reports},

abstract = {The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID-19), known to be more common in the elderly, who also show more severe symptoms and are at higher risk of hospitalization and death. Here, we show that the expression of the angiotensin converting enzyme 2 (ACE2), the SARS-CoV-2 cell receptor, increases during aging in mouse and human lungs. ACE2 expression increases upon telomere shortening or dysfunction in both cultured mammalian cells and in vivo in mice. This increase is controlled at the transcriptional level, and Ace2 promoter activity is DNA damage response (DDR)-dependent. Both pharmacological global DDR inhibition of ATM kinase activity and selective telomeric DDR inhibition by the use of antisense oligonucleotides prevent Ace2 upregulation following telomere damage in cultured cells and in mice. We propose that during aging telomere dysfunction due to telomeric shortening or damage triggers DDR activation and this causes the upregulation of ACE2, the SARS-CoV-2 cell receptor, thus contributing to make the elderly more susceptible to the infection.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb_71,

title = {Retrotransposons Down- and Up-Regulation in Aging Somatic Tissue},

author = {Giordani G and Cavaliere V and Gargiulo G and Lattanzi G and Andrenacci D},

url = {https://www.mdpi.com/2073-4409/11/1/79},

doi = {10.3390/cells11010079},

year  = {2021},

date = {2021-12-30},

journal = {Cells},

volume = {11},

number = {1},

pages = {79},

abstract = {The transposon theory of aging hypothesizes the activation of transposable elements (TEs) in somatic tissues with age, leading to a shortening of the lifespan. It is thought that TE activation in aging produces an increase in DNA double-strand breaks, contributing to genome instability and promoting the activation of inflammatory responses. To investigate how TE regulation changes in somatic tissues during aging, we analyzed the expression of some TEs, as well as a source of small RNAs that specifically silence the analyzed TEs; the Drosophila cluster named flamenco. We found significant variations in the expression levels of all the analyzed TEs during aging, with a trend toward reduction in middle-aged adults and reactivation in older individuals that suggests dynamic regulation during the lifespan.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb_70,

title = {Elongating RNA polymerase II and RNA:DNA hybrids hinder fork progression and gene expression at sites of head-on replication-transcription collisions},

author = {Zardoni L and Nardini E and Brambati A and Lucca C and Choudhary R and Loperfido F and Sabbioneda S and Liberi G},

url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab1146/6456226},

doi = {10.1093/nar/gkab1146},

year  = {2021},

date = {2021-12-14},

urldate = {2021-12-14},

journal = {Nucleic acids research},

volume = {49},

number = {22},

pages = {12769-12784},

abstract = {Uncoordinated clashes between replication forks and transcription cause replication stress and genome instability, which are hallmarks of cancer and neurodegeneration. Here, we investigate the outcomes of head-on replication-transcription collisions, using as a model system budding yeast mutants for the helicase Sen1, the ortholog of human Senataxin. We found that RNA Polymerase II accumulates together with RNA:DNA hybrids at sites of head-on collisions. The replication fork and RNA Polymerase II are both arrested during the clash, leading to DNA damage and, in the long run, the inhibition of gene expression. The inactivation of RNA Polymerase II elongation factors, such as the HMG-like protein Spt2 and the DISF and PAF complexes, but not alterations in chromatin structure, allows replication fork progression through transcribed regions. Attenuation of RNA Polymerase II elongation rescues RNA:DNA hybrid accumulation and DNA damage sensitivity caused by the absence of Sen1, but not of RNase H proteins, suggesting that such enzymes counteract toxic RNA:DNA hybrids at different stages of the cell cycle with Sen1 mainly acting in replication. We suggest that the main obstacle to replication fork progression is the elongating RNA Polymerase II engaged in an R-loop, rather than RNA:DNA hybrids per se or hybrid-associated chromatin modifications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb_69,

title = {Proliferation Pattern of Pediatric Tumor-Derived Mesenchymal Stromal Cells and Role in Cancer Dormancy: A Perspective of Study for Surgical Strategy},

author = {Pelizzo G and Riva F and Croce S and Avanzini MA and Acquafredda G and de Silvestri A and Mazzon E and Bramanti P and Zuccotti G and Mazzini G and Calcaterra V},

editor = {Pelizzo G and Riva F and Croce S and Avanzini MA and Acquafredda G and de Silvestri A and Mazzon E and Bramanti P and Zuccotti G and Mazzini G and Calcaterra V},

url = {https://www.frontiersin.org/articles/10.3389/fped.2021.766610/full},

doi = {10.3389/fped.2021.766610},

year  = {2021},

date = {2021-12-14},

urldate = {2021-12-14},

journal = {Frontiers in pediatrics},

volume = {9},

pages = {766610},

abstract = {The explanation for cancer recurrence still remains to be fully elucidated. Moreover, tumor dormancy, which is a process whereby cells enter reversible G0 cell cycle arrest, appears to be a critical step in this phenomenon. We evaluated the cell cycle proliferation pattern in pediatric tumor-derived mesenchymal stromal cells (MSCs), in order to provide a better understanding of the complex mechanisms underlying cancer dormancy. Specimens were obtained from 14 pediatric patients diagnosed with solid tumors and submitted to surgery. Morphology, phenotype, differentiation, immunological capacity, and proliferative growth of tumor MSCs were studied. Flow cytometric analysis was performed to evaluate the cell percentage of each cell cycle phase. Healthy donor bone marrow-derived mesenchymal stromal cells (BM-MSCs) were employed as controls. It was noted that the DNA profile of proliferating BM-MSC was different from that of tumor MSCs. All BM-MSCs expressed the typical DNA profile of proliferating cells, while in all tumor MSC samples, ≥70% of the cells were detected in the G0/G1 phase. In particular, seven tumor MSC samples displayed intermediate cell cycle behavior, and the other seven tumor MSC samples exhibited a slow cell cycle. The increased number of tumor MSCs in the G0-G1 phase compared with BM-MSCs supports a role for quiescent MSCs in tumor dormancy regulation. Understanding the mechanisms that promote dormant cell cycle arrest is essential in identifying predictive markers of recurrence and to promote a dedicated surgical planning.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb_68,

title = {Epistasis, aneuploidy, and functional mutations underlie evolution of resistance to induced microtubule depolymerization},

author = {Pavani M and Bonaiuti P and Chiroli E and Gross F and Natali F and Macaluso F and Poti A and Pasqualato S and Farkas Z and Pompei S and Cosentino Lagomarsino M and Rancati G and Szüts D and Ciliberto A},

url = {https://www.embopress.org/doi/abs/10.15252/embj.2021108225},

doi = {10.15252/embj.2021108225},

year  = {2021},

date = {2021-12-14},

journal = {EMBO Journal},

volume = {40},

number = {22},

pages = {e108225},

abstract = {Cells with blocked microtubule polymerization are delayed in mitosis, but eventually manage to proliferate despite substantial chromosome missegregation. While several studies have analyzed the first cell division after microtubule depolymerization, we have asked how cells cope long-term with microtubule impairment. We allowed 24 clonal populations of yeast cells with beta-tubulin mutations preventing proper microtubule polymerization, to evolve for  about 150 generations. At the end of the laboratory evolution experiment, cells had regained the ability to form microtubules and were less sensitive to microtubule-depolymerizing drugs. Whole-genome sequencing identified recurrently mutated genes, in particular for tubulins and kinesins, as well as pervasive duplication of chromosome VIII. Recreating these mutations and chromosome VIII disomy prior to evolution confirmed that they allow cells to compensate for the original mutation in beta-tubulin. Most of the identified mutations did not abolish function, but rather restored microtubule functionality. Analysis of the temporal order of resistance development in independent populations repeatedly revealed the same series of events: disomy of chromosome VIII followed by a single additional adaptive mutation in either tubulins or kinesins. Since tubulins are highly conserved among eukaryotes, our results have implications for understanding resistance to microtubule-targeting drugs widely used in cancer therapy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb_67,

title = {The Combination of AHCC and ETAS Decreases Migration of Colorectal Cancer Cells, and Reduces the Expression of LGR5 and Notch1 Genes in Cancer Stem Cells: A Novel Potential Approach for Integrative Medicine},

author = {Paganelli F and Chiarini F and Palmieri A and Martinelli M and Sena P and Bertacchini J and Roncucci L and Cappellini A and Martelli AM and Bonucci M and Fiorentini C and Hammarberg Ferri I},

doi = {10.3390/ph14121325},

year  = {2021},

date = {2021-12-14},

journal = {Pharmaceuticals},

volume = {14},

number = {12},

pages = {1325},

abstract = {The AHCC standardized extract of cultured Lentinula edodes mycelia, and the standardized extract of Asparagus officinalis stem, trademarked as ETAS, are well known supplements with immunomodulatory and anticancer potential. Several reports have described their therapeutic effects, including antioxidant and anticancer activity and improvement of immune response. In this study we aimed at investigating the effects of a combination of AHCC and ETAS on colorectal cancer cells and biopsies from healthy donors to assess the possible use in patients with colorectal cancer. Our results showed that the combination of AHCC and ETAS was synergistic in inducing a significant decrease in cancer cell growth, compared with single agents. Moreover, the combined treatment induced a significant increase in apoptosis, sparing colonocytes from healthy donors, and was able to induce a strong reduction in migration potential, accompanied by a significant modulation of proteins involved in invasiveness. Finally, combined treatment was able to significantly downregulate LGR5 and Notch1 in SW620 cancer stem cell (CSC) colonospheres. Overall, these findings support the potential therapeutic benefits of the AHCC and ETAS combinatorial treatment for patients with colorectal cancer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb_66,

title = {The prolyl-isomerase PIN1 is essential for nuclear Lamin-B structure and function and protects heterochromatin under mechanical stress},

author = {Napoletano F and Ferrari Bravo G and Voto IAP and Santin A and Celora L and Campaner E and Dezi C and Bertossi A and Valentino E and Santorsola M and Rustighi A and Fajner V and Maspero E and Ansaloni F and Cancila V and Valenti CF and Santo M and Artimagnella OB and Finaurini S and Gioia U and Polo S and Sanges R and Tripodo C and Mallamaci A and Gustincich S and {d'Adda di Fagagna F} and Mantovani F and Specchia V and Del Sal G},

url = {https://www.cell.com/cell-reports/fulltext/S2211-1247(21)01141-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124721011414%3Fshowall%3Dtrue#%20},

doi = {10.1016/j.celrep.2021.109694},

year  = {2021},

date = {2021-12-14},

journal = {Cell reports},

volume = {36},

number = {11},

pages = {109694},

abstract = {Chromatin organization plays a crucial role in tissue homeostasis. Heterochromatin relaxation and consequent unscheduled mobilization of transposable elements (TEs) are emerging as key contributors of aging and aging-related pathologies, including Alzheimer's disease (AD) and cancer. However, the mechanisms governing heterochromatin maintenance or its relaxation in pathological conditions remain poorly understood. Here we show that PIN1, the only phosphorylation-specific cis/trans prolyl isomerase, whose loss is associated with premature aging and AD, is essential to preserve heterochromatin. We demonstrate that this PIN1 function is conserved from Drosophila to humans and prevents TE mobilization-dependent neurodegeneration and cognitive defects. Mechanistically, PIN1 maintains nuclear type-B Lamin structure and anchoring function for heterochromatin protein 1α (HP1α). This mechanism prevents nuclear envelope alterations and heterochromatin relaxation under mechanical stress, which is a key contributor to aging-related pathologies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb_65,

title = {Computed structures of core eukaryotic protein complexes.},

author = {Humphreys IR and Pei J and Baek M and Krishnakumar A and Anishchenko I and Ovchinnikov S and Zhang J and Ness TJ and Banjade S and Bagde SR and Stancheva VG and Li XH and Liu K and Zheng Z and Barrero DJ and Roy U and Kuper J and Fernández IS and Szakal B and Branzei D and Rizo J and Kisker C and Greene EC and Biggins S and Keeney S and Miller EA and Fromme JC and Hendrickson TL and Cong Q and Baker D},

url = {https://www.science.org/doi/10.1126/science.abm4805?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed},

doi = {10.1126/science.abm4805},

year  = {2021},

date = {2021-12-14},

journal = {Science},

volume = {374},

number = {6573},

abstract = {Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions not yet identified. We take advantage of advances in proteome-wide amino acid coevolution analysis and deep-learning–based structure modeling to systematically identify and build accurate models of core eukaryotic protein complexes within the Saccharomyces cerevisiae proteome. We use a combination of RoseTTAFold and AlphaFold to screen through paired multiple sequence alignments for 8.3 million pairs of yeast proteins, identify 1505 likely to interact, and build structure models for 106 previously unidentified assemblies and 806 that have not been structurally characterized. These complexes, which have as many as five subunits, play roles in almost all key processes in eukaryotic cells and provide broad insights into biological function.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb_64,

title = {The power of genetic diversity in genome-wide association studies of lipids.},

author = {Graham SE and Clarke SL and Wu KH and Kanoni S and Zajac GJM ...... and Biino G and et al.},

url = {https://www.nature.com/articles/s41586-021-04064-3},

doi = {10.1038/s41586-021-04064-3},

year  = {2021},

date = {2021-12-14},

urldate = {2021-12-14},

journal = {Nature},

volume = {600},

number = {7890},

pages = {675-679},

abstract = {Increased blood lipid levels are heritable risk factors of cardiovascular disease with varied prevalence worldwide owing to different dietary patterns and medication use1. Despite advances in prevention and treatment, in particular through reducing low-density lipoprotein cholesterol levels2, heart disease remains the leading cause of death worldwide3. Genome-wideassociation studies (GWAS) of blood lipid levels have led to important biological and clinical insights, as well as new drug targets, for cardiovascular disease. However, most previous GWAS4-23 have been conducted in European ancestry populations and may have missed genetic variants that contribute to lipid-level variation in other ancestry groups. These include differences in allele frequencies, effect sizes and linkage-disequilibrium patterns24. Here we conduct a multi-ancestry, genome-wide genetic discovery meta-analysis of lipid levels in approximately 1.65 million individuals, including 350,000 of non-European ancestries. We quantify the gain in studying non-European ancestries and provide evidence to support the expansion of recruitment of additional ancestries, even with relatively small sample sizes. We find that increasing diversity rather than studying additional individuals of European ancestry results in substantial improvements in fine-mapping functional variants and portability of polygenic prediction (evaluated in approximately 295,000 individuals from 7 ancestry groupings). Modest gains in the number of discovered loci and ancestry-specific variants were also achieved. As GWAS expand emphasis beyond the identification of genes and fundamental biology towards the use of genetic variants for preventive and precision medicine25, we anticipate that increased diversity of participants will lead to more accurate and equitable26 application of polygenic scores in clinical practice.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb_61,

title = {Revisiting the Role of GSK3, A Modulator of Innate Immunity, in Idiopathic Inclusion Body Myositis.},

author = {Piazzi M and Bavelloni A and Cenni V and Faenza I and Blalock WL},

url = {https://www.mdpi.com/2073-4409/10/11/3255},

doi = {10.3390/cells10113255},

year  = {2021},

date = {2021-12-06},

journal = {Cells},

volume = {10},

number = {11},

pages = {3255},

abstract = {Idiopathic or sporadic inclusion body myositis (IBM) is the leading age-related (onset >50 years of age) autoimmune muscular pathology, resulting in significant debilitation in affected individuals. Once viewed as primarily a degenerative disorder, it is now evident that much like several other neuro-muscular degenerative disorders, IBM has a major autoinflammatory component resulting in chronic inflammation-induced muscle destruction. Thus, IBM is now considered primarily an inflammatory pathology. To date, there is no effective treatment for sporadic inclusion body myositis, and little is understood about the pathology at the molecular level, which would offer the best hopes of at least slowing down the degenerative process. Among the previously examined potential molecular players in IBM is glycogen synthase kinase (GSK)-3, whose role in promoting TAU phosphorylation and inclusion bodies in Alzheimer's disease is well known. This review looks to re-examine the role of GSK3 in IBM, not strictly as a promoter of TAU and Abeta inclusions, but as a novel player in the innate immune system, discussing some of the recent roles discovered for this well-studied kinase in inflammatory-mediated pathology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb_60,

title = {Targeting DDX3X Helicase Activity with BA103 Shows Promising Therapeutic Effects in Preclinical Glioblastoma Models},

author = {Brai A and Riva V and Clementi L and Falsitta L and Zamperini C and Sinigiani V and Festuccia C and Sabetta S and Aiello D and Roselli C and Garbelli A and Trivisani CI and Maccari L and Bugli F and Sanguinetti M and Calandro P and Chiariello M and Quaranta P and Botta L and Angelucci A and Maga G and Botta M},

url = {https://www.mdpi.com/2072-6694/13/21/5569},

doi = {10.3390/cancers13215569},

year  = {2021},

date = {2021-12-06},

journal = {Cancers (Basel)},

volume = {13},

number = {21},

pages = {5569},

abstract = {DDX3X is an ATP-dependent RNA helicase that has recently attracted interest for its involvement in viral replication and oncogenic progression. Starting from hit compounds previously identified by our group, we have designed and synthesized a new series of DDX3X inhibitors that effectively blocked its helicase activity. These new compounds were able to inhibit the proliferation of cell lines from different cancer types, also in DDX3X low-expressing cancer cell lines. According to the absorption, distribution, metabolism, elimination properties, and antitumoral activity, compound BA103 was chosen to be further investigated in glioblastoma models. BA103 determined a significant reduction in the proliferation and migration of U87 and U251 cells, downregulating the oncogenic protein β-catenin. An in vivo evaluation demonstrated that BA103 was able to reach the brain and reduce the tumor growth in xenograft and orthotopic models without evident side effects. This study represents the first demonstration that DDX3X-targeted small molecules are feasible and promising drugs also in glioblastoma.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}