@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:%Y__512,

title = {Expansion of the clinical and molecular spectrum of an XPD-related disorder linked to biallelic mutations in ERCC2 gene},

author = {Agolini E and Botta E and Lodi M and Digilio MC and Rinelli M and Bellacchio E and Alesi V and Nardo T and Zambruno G and Orioli D and Alessi I and Boccuto L and Rossi S and Carai A and Colafati GS and Cacchione A and Dallapiccola B and Novelli A and Mastronuzzi A.},

url = {https://onlinelibrary.wiley.com/doi/10.1111/cge.13957},

doi = {10.1111/cge.13957},

year  = {2021},

date = {2021-04-14},

journal = {Clinical genetics},

volume = {99},

number = {6},

pages = {842-848},

abstract = {Bi-allelic inactivation of XPD protein, a nucleotide excision repair (NER) signaling pathway component encoded by ERCC2 gene, has been associated with several defective DNA repair phenotypes, including xeroderma pigmentosum, photosensitive trichothiodystrophy, and cerebro-oculo-facio-skeletal syndrome. We report a pediatric patient harboring two compound heterozygous variants in ERCC2 gene, c.361-1G > A and c.2125A > C (p.Thr709Pro), affected by severe postnatal growth deficiency, microcephaly, facial dysmorphisms and pilocytic astrocytoma of the brainstem. Some of these features point to a DNA repair syndrome, and altogether delineate a phenotype differentiating from disorders known to be associated with ERCC2 mutations. The DNA repair efficiency following UV irradiation in the proband's skin fibroblasts was defective indicating that the new set of ERCC2 alleles impacts on NER efficiency. Sequencing analysis on tumor DNA did not reveal any somatic deleterious point variant in cancer-related genes, while SNP-array analysis disclosed a 2 Mb microduplication involving the 7q34 region, spanning from KIAA1549 to BRAF, and resulting in the KIAA1549:BRAF fusion protein, a marker of pilocytic astrocytoma. In conclusion, this report expands the clinical and mutational spectrum of ERCC2-related disorders.},

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},

urldate = {2021-05-14},

journal = {Human molecular genetics},

volume = {30},

number = {1711},

issue = {18},

pages = {1720},

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 = {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:%Y_451,

title = {Heterogeneity and overlaps in nucleotide excision repair disorders.},

author = {Ferri D and Orioli D and Botta E},

url = {https://onlinelibrary.wiley.com/doi/full/10.1111/cge.13545},

doi = {10.1111/cge.13545},

year  = {2020},

date = {2020-01-01},

journal = {Clinical Genetics},

volume = {97},

number = {1},

pages = {12-24},

abstract = {Nucleotide excision repair (NER) is an essential DNA repair pathway devoted to the removal of bulky lesions such as photoproducts induced by the ultraviolet (UV) component of solar radiation. Deficiencies in NER typically result in a group of heterogeneous distinct disorders ranging from the mild UV sensitive syndrome to the cancer-prone xeroderma pigmentosum and the neurodevelopmental/progeroid conditions trichothiodystrophy, Cockayne syndrome and cerebro-oculo-facio-skeletal-syndrome. A complicated genetic scenario underlines these disorders with the same gene linked to different clinical entities as well as different genes associated with the same disease. Overlap syndromes with combined hallmark features of different NER disorders can occur and sporadic presentations showing extra features of the hematological disorder Fanconi Anemia or neurological manifestations mimicking Hungtinton disease-like syndromes have been described. Here, we discuss the multiple functions of the five major pleiotropic NER genes (ERCC3/XPB, ERCC2/XPD, ERCC5/XPG, ERCC1 and ERCC4/XPF) and their relevance in phenotypic complexity. We provide an update of mutational spectra and examine genotype-phenotype relationships. Finally, the molecular defects that could explain the puzzling overlap syndromes are discussed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y%_49,

title = {Bi-allelic TARS Mutations Are Associated with Brittle Hair Phenotype.},

author = {Theil AF and Botta E and Raams A and Smith DEC and Mendes MI and Caligiuri G and Giachetti S and Bione S and Carriero R and Liberi G and Zardoni L and Swagemakers SMA and Salomons GS and Sarasin A and Lehmann A and van der Spek PJ and Ogi T and Hoeijmakers JHJ and Vermeulen W and Orioli D},

url = {https://www.sciencedirect.com/science/article/abs/pii/S0002929719302423?via%3Dihub},

doi = {10.1016/j.ajhg.2019.06.017},

year  = {2019},

date = {2019-02-13},

journal = {American Journal of Human Genetics},

volume = {105},

number = {2},

pages = {434-440},

abstract = {Brittle and "tiger-tail" hair is the diagnostic hallmark of trichothiodystrophy (TTD), a rare recessive disease associated with a wide spectrum of clinical features including ichthyosis, intellectual disability, decreased fertility, and short stature. As a result of premature abrogation of terminal differentiation, the hair is brittle and fragile and contains reduced cysteine content. Hypersensitivity to UV light is found in about half of individuals with TTD; all of these individuals harbor bi-allelic mutations in components of the basal transcription factor TFIIH, and these mutations lead to impaired nucleotide excision repair and basal transcription. Different genes have been found to be associated with non-photosensitive TTD (NPS-TTD); these include MPLKIP (also called TTDN1), GTF2E2 (also called TFIIEβ), and RNF113A. However, a relatively large group of these individuals with NPS-TTD have remained genetically uncharacterized. Here we present the identification of an NPS-TTD-associated gene, threonyl-tRNA synthetase (TARS), found by next-generation sequencing of a group of uncharacterized individuals with NPS-TTD. One individual has compound heterozygous TARS variants, c.826A>G (p.Lys276Glu) and c.1912C>T (p.Arg638∗), whereas a second individual is homozygous for the TARS variant: c.680T>C (p.Leu227Pro). We showed that these variants have a profound effect on TARS protein stability and enzymatic function. Our results expand the spectrum of genes involved in TTD to include genes implicated in amino acid charging of tRNA, which is required for the last step in gene expression, namely protein translation. We previously proposed that some of the TTD-specific features derive from subtle transcription defects as a consequence of unstable transcription factors. We now extend the definition of TTD from a transcription syndrome to a "gene-expression" syndrome.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_122,

title = {Functional and clinical relevance of novel mutations in a large cohort of patients with Cockayne syndrome.},

author = {Calmels N and Botta E and Jia N and Fawcett H and Nardo T and Nakazawa Y and Lanzafame M and Moriwaki S and Sugita K and Kubota M and Obringer C and Spitz MA and Stefanini M and Laugel V and Orioli D and Ogi T and Lehmann AR},

url = {https://jmg.bmj.com/content/55/5/329.long},

doi = {10.1136/jmedgenet-2017-104877},

year  = {2018},

date = {2018-05-31},

journal = {Journal of medical genetics},

volume = {55},

number = {5},

pages = {329-343},

abstract = {BACKGROUND: Cockayne syndrome (CS) is a rare, autosomal recessive multisystem disorder characterised by prenatal or postnatal growth failure, progressive neurological dysfunction, ocular and skeletal abnormalities and premature ageing. About half of the patients with symptoms diagnostic for CS show cutaneous photosensitivity and an abnormal cellular response to UV light due to mutations in either the ERCC8/CSA or ERCC6/CSB gene. Studies performed thus far have failed to delineate clear genotype-phenotype relationships. We have carried out a four-centre clinical, molecular and cellular analysis of 124 patients with CS. METHODS AND RESULTS: We assigned 39 patients to the ERCC8/CSA and 85 to the ERCC6/CSB genes. Most of the genetic variants were truncations. The missense variants were distributed non-randomly with concentrations in relatively short regions of the respective proteins. Our analyses revealed several hotspots and founder mutations in ERCC6/CSB. Although no unequivocal genotype-phenotype relationships could be made, patients were more likely to have severe clinical features if the mutation was downstream of the PiggyBac insertion in intron 5 of ERCC6/CSB than if it was upstream. Also a higher proportion of severely affected patients was found with mutations in ERCC6/CSB than in ERCC8/CSA. CONCLUSION: By identifying >70 novel homozygous or compound heterozygous genetic variants in 124 patients with CS with different disease severity and ethnic backgrounds, we considerably broaden the CSA and CSB mutation spectrum responsible for CS. Besides providing information relevant for diagnosis of and genetic counselling for this devastating disorder, this study improves the definition of the puzzling genotype-phenotype relationships in patients with CS.

Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_173,

title = {Phenotypic variability in xeroderma pigmentosum group G: An uncommon case with severe prenatal-onset Cockayne syndrome features.},

author = {Ricotti R and Nardo T and Striano P and Stefanini M and Orioli D and Botta E},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cge.13364},

doi = {10.1111/cge.13364.},

year  = {2018},

date = {2018-10-25},

journal = {Clinical Genetics},

volume = {94},

number = {3-4},

pages = {386-388},

abstract = {not available LETTER TO EDITOR},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_278,

title = {Deep phenotyping of 89 xeroderma pigmentosum patients reveals unexpected heterogeneity dependent on the precise molecular defect.},

author = {Fassihi H and Sethi M and Fawcett H and Wing J and Chandler N and Mohammed S and Craythorne E and Morley AM and Lim R and Turner S and Henshaw T and Garrood I and Giunti P and Hedderly T and Abiona A and Naik H and Harrop G and McGibbon D and Jaspers NG and Botta E and Nardo T and Stefanini M and Young AR and Sarkany RP and Lehmann AR},

url = {http://www.pnas.org/content/113/9/E1236.long},

doi = {10.1073/pnas.1519444113},

year  = {2016},

date = {2016-02-25},

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

volume = {113},

number = {9},

pages = {1236-1245},

abstract = {Xeroderma pigmentosum (XP) is a rare DNA repair disorder characterized by increased susceptibility to UV radiation (UVR)-induced skin pigmentation, skin cancers, ocular surface disease, and, in some patients, sunburn and neurological degeneration. Genetically, it is assigned to eight complementation groups (XP-A to -G and variant). For the last 5 y, the UK national multidisciplinary XP service has provided follow-up for 89 XP patients, representing most of the XP patients in the United Kingdom. Causative mutations, DNA repair levels, and more than 60 clinical variables relating to dermatology, ophthalmology, and neurology have been measured, using scoring systems to categorize disease severity. This deep phenotyping has revealed unanticipated heterogeneity of clinical features, between and within complementation groups. Skin cancer is most common in XP-C, XP-E, and XP-V patients, previously considered to be the milder groups based on cellular analyses. These patients have normal sunburn reactions and are therefore diagnosed later and are less likely to adhere to UVR protection. XP-C patients are specifically hypersensitive to ocular damage, and XP-F and XP-G patients appear to be much less susceptible to skin cancer than other XP groups. Within XP groups, different mutations confer susceptibility or resistance to neurological damage. Our findings on this large cohort of XP patients under long-term follow-up reveal that XP is more heterogeneous than has previously been appreciated. Our data now enable provision of personalized prognostic information and management advice for each XP patient, as well as providing new insights into the functions of the XP proteins.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_290,

title = {GTF2E2 Mutations Destabilize the General Transcription Factor Complex TFIIE in Individuals with DNA Repair-Proficient Trichothiodystrophy.},

author = {Kuschal C and Botta E and Orioli D and Digiovanna JJ and Seneca S and Keymolen K and Tamura D and Heller E and Khan SG and Caligiuri G and Lanzafame M and Nardo T and Ricotti R and Peverali FA and Stephens R and Zhao Y and Lehmann AR and Baranello L and Levens D and Kraemer KH and Stefanini M},

url = {http://www.sciencedirect.com/science/article/pii/S0002929716000598},

doi = {10.1016/j.ajhg.2016.02.008},

year  = {2016},

date = {2016-04-16},

journal = {American Journal of Human Genetics},

volume = {98},

number = {4},

pages = {627-642},

abstract = {The general transcription factor IIE (TFIIE) is essential for transcription initiation by RNA polymerase II (RNA pol II) via direct interaction with the basal transcription/DNA repair factor IIH (TFIIH). TFIIH harbors mutations in two rare genetic disorders, the cancer-prone xeroderma pigmentosum (XP) and the cancer-free, multisystem developmental disorder trichothiodystrophy (TTD). The phenotypic complexity resulting from mutations affecting TFIIH has been attributed to the nucleotide excision repair (NER) defect as well as to impaired transcription. Here, we report two unrelated children showing clinical features typical of TTD who harbor different homozygous missense mutations in GTF2E2 (c.448G>C [p.Ala150Pro] and c.559G>T [p.Asp187Tyr]) encoding the beta subunit of transcription factor IIE (TFIIEbeta). Repair of ultraviolet-induced DNA damage was normal in the GTF2E2 mutated cells, indicating that TFIIE was not involved in NER. We found decreased protein levels of the two TFIIE subunits (TFIIEalpha and TFIIEbeta) as well as decreased phosphorylation of TFIIEalpha in cells from both children. Interestingly, decreased phosphorylation of TFIIEalpha was also seen in TTD cells with mutations in ERCC2, which encodes the XPD subunit of TFIIH, but not in XP cells with ERCC2 mutations. Our findings support the theory that TTD is caused by transcriptional impairments that are distinct from the NER disorder XP. Copyright  2016 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_329,

title = {A novel X-linked trichothiodystrophy associated with a nonsense mutation in RNF113A.},

author = {Corbett MA and Dudding-Byth T and Crock PA and Botta E and Christie LM and Nardo T and Caligiuri G and Hobson L and Boyle J and Mansour A and Friend KL and Crawford J and Jackson G and Vandeleur L and Hackett A and Tarpey P and Stratton MR and Turner G and Gécz J and Field M},

url = {https://jmg.bmj.com/content/52/4/269.long},

doi = {10.1136/jmedgenet-2014-102418},

year  = {2015},

date = {2015-02-17},

journal = {Journal of Medical Genetics},

volume = {52},

number = {4},

pages = {269-274},

abstract = {Trichothiodystrophy (TTD) is a group of rare autosomal recessive disorders that variably affect a wide range of organs derived from the neuroectoderm. The key diagnostic feature is sparse, brittle, sulfur deficient hair that has a 'tiger-tail' banding pattern under polarising light microscopy. PATIENTS AND METHODS: We describe two male cousins affected by TTD associated with microcephaly, profound intellectual disability, sparse brittle hair, aged appearance, short stature, facial dysmorphism, seizures, an immunoglobulin deficiency, multiple endocrine abnormalities, cerebellar hypoplasia and partial absence of the corpus callosum, in the absence of cellular photosensitivity and ichthyosis. Obligate female carriers showed 100% skewed X-chromosome inactivation. Linkage analysis and Sanger sequencing of 737 X-chromosome exons and whole exome sequencing was used to find the responsible gene and mutation. RESULTS: Linkage analysis localised the disease allele to a 7.75 Mb interval from Xq23-q25. We identified a nonsense mutation in the highly conserved RNF113A gene (c.901 C>T, p.Q301*). The mutation segregated with the disease in the family and was not observed in over 100,000 control X chromosomes. The mutation markedly reduced RNF113A protein expression in extracts from lymphoblastoid cell lines derived from the affected individuals. CONCLUSIONS: The association of RNF113A mutation with non-photosensitive TTD identifies a new locus for these disorders on the X chromosome. The extended phenotype within this family includes panhypopituitarism, cutis marmorata and congenital short oesophagus. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_400,

title = {Reference genes for gene expression analysis in proliferating and differentiating human keratinocytes.},

author = {Lanzafame M and Botta E and Teson M and Fortugno P and Zambruno G and Stefanini M and Orioli D},

url = {https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/iub.1366},

doi = {10.1002/iub.1366},

year  = {2015},

date = {2015-04-07},

journal = {Experimental Dermatology},

volume = {24},

number = {4},

abstract = {Abnormalities in keratinocyte growth and differentiation have a pathogenic significance in many skin disorders and result in gene expression alterations detectable by quantitative real-time RT-PCR (qRT-PCR). Relative quantification based on endogenous control (EC) genes is the commonly adopted approach, and the use of multiple reference genes from independent pathways is considered a best practice guideline, unless fully validated EC genes are available. The literature on optimal reference genes during in vitro calcium-induced differentiation of normal human epidermal keratinocytes (NHEK) is inconsistent. In many studies, the expression of target genes is compared to that of housekeeping genes whose expression, however, significantly varies during keratinocyte differentiation. Here, we report the results of our investigations on the expression stability of 15 candidate EC genes, including those commonly used as reference in expression analysis by qRT-PCR, during NHEK calcium-induced differentiation. We demonstrate that YWHAZ and UBC are extremely stable genes, and therefore, they represent optimal EC genes for expression studies in proliferating and calcium-induced differentiating NHEK. Furthermore, we demonstrate that YWHAZ/14-3-3-zeta is a suitable reference for quantitative comparison of both transcript and protein levels. 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}