Emanuela Leonardi

@article{Aspromonte2024D434,

title = {DisProt in 2024: improving function annotation of intrinsically disordered proteins},

author = { Maria Cristina Aspromonte and Maria Victoria Nugnes and Federica Quaglia and Adel Bouharoua and Silvio C.E. Tosatto and Damiano Piovesan and Vasileios Sagris and Vasilis J. Promponas and Anastasia Chasapi and Erzs\'{e}bet Fich\'{o} and Galo E. Balatti and Gustavo Parisi and Mart\'{i}n Gonz\'{a}lez Buitr\'{o}n and Gabor Erdos and Matyas Pajkos and Zsuzsanna Doszt\'{a}nyi and Laszlo Dobson and Alessio Del Conte and Damiano Clementel and Edoardo Salladini and Emanuela Leonardi and Fatemeh Kordevani and Hamidreza Ghafouri and Luiggi G. Tenorio Ku and Alexander Miguel Monzon and Carlo Ferrari and Zs\'{o}fia K\'{a}lm\'{a}n and Juliet F. Nilsson and Jaime Santos and Carlos Pintado-Grima and Salvador Ventura and Veronika \'{A}cs and Rita Pancsa and Mariane Goncalves Kulik and Miguel A. Andrade-Navarro and Pedro Jos\'{e} Barbosa Pereira and Sonia Longhi and Philippe Le Mercier and Julian Bergier and Peter Tompa and Tamas Lazar},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85176208048\&doi=10.1093%2fnar%2fgkad928\&partnerID=40\&md5=fc34ce08667ff42029fdb54d5142c08f},

doi = {10.1093/nar/gkad928},

issn = {03051048},

year  = {2024},

date = {2024-01-01},

abstract = {DisProt (URL: https://disprot.org) is the gold standard database for intrinsically disordered proteins and regions, providing valuable information about their functions. The latest version of DisProt brings significant advancements, including a broader representation of functions and an enhanced curation process. These improvements aim to increase both the quality of annotations and their coverage at the sequence level. Higher coverage has been achieved by adopting additional evidence codes. Quality of annotations has been improved by systematically applying Minimum Information About Disorder Experiments (MIADE) principles and reporting all the details of the experimental setup that could potentially influence the structural state of a protein. The DisProt database now includes new thematic datasets and has expanded the adoption of Gene Ontology terms, resulting in an extensive functional repertoire which is automatically propagated to UniProtKB. Finally, we show that DisProt’s curated annotations strongly correlate with disorder predictions inferred from AlphaFold2 pLDDT (predicted Local Distance Difference Test) confidence scores. This comparison highlights the utility of DisProt in explaining apparent uncertainty of certain well-defined predicted structures, which often correspond to folding-upon-binding fragments. Overall, DisProt serves as a comprehensive resource, combining experimental evidence of disorder information to enhance our understanding of intrinsically disordered proteins and their functional implications. © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.},

note = {Cited by: 10; All Open Access, Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ghafouri2024D536,

title = {PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins},

author = { Hamidreza Ghafouri and Tamas Lazar and Alessio Del Conte and Luiggi G. Tenorio Ku and Peter Tompa and Silvio C.E. Tosatto and Alexander Miguel Monzon and Maria C. Aspromonte and Pau Bernad\'{o} and Bel\'{e}n Chaves-Arquero and Lucia Beatriz Chemes and Damiano Clementel and Tiago N. Cordeiro and Carlos A. Elena-Real and Michael Feig and Isabella C. Felli and Carlo Ferrari and Julie D. Forman-Kay and Tiago Gomes and Frank Gondelaud and Claudiu C. Gradinaru and T\^{a}p Ha-Duong and Teresa Head-Gordon and P\'{e}tur O. Heidarsson and Giacomo Janson and Gunnar Jeschke and Emanuela Leonardi and Zi Hao Liu and Sonia Longhi and Xamuel L. Lund and Maria J. Macias and Pau Martin-Malpartida and Davide Mercadante and Assia Mouhand and Gabor Nagy and Mar\'{i}a Victoria Nugnes and Jos\'{e} Manuel P\'{e}rez-Ca\~{n}adillas and Giulia Pesce and Roberta Pierattelli and Damiano Piovesan and Federica Quaglia and Sylvie Ricard-Blum and Paul Robustelli and Amin Sagar and Edoardo Salladini and Lucile S\'{e}nicourt and Nathalie Sibille and Jo\~{a}o M.C. Teixeira and Thomas E. Tsangaris and Mihaly Varadi},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85181761325\&doi=10.1093%2fnar%2fgkad947\&partnerID=40\&md5=0ad51562357f3e5f603d744e02f8729a},

doi = {10.1093/nar/gkad947},

issn = {03051048},

year  = {2024},

date = {2024-01-01},

abstract = {The Protein Ensemble Database (PED) (URL: https://proteinensemble.org) is the primary resource for depositing structural ensembles of intrinsically disordered proteins. This updated version of PED reflects advancements in the field, denoting a continual expansion with a total of 461 entries and 538 ensembles, including those generated without explicit experimental data through novel machine learning (ML) techniques. With this significant increment in the number of ensembles, a few yet-unprecedented new entries entered the database, including those also determined or refined by electron paramagnetic resonance or circular dichroism data. In addition, PED was enriched with several new features, including a novel deposition service, improved user interface, new database cross-referencing options and integration with the 3D-Beacons network\textemdashall representing efforts to improve the FAIRness of the database. Foreseeably, PED will keep growing in size and expanding with new types of ensembles generated by accurate and fast ML-based generative models and coarse-grained simulations. Therefore, among future efforts, priority will be given to further develop the database to be compatible with ensembles modeled at a coarse-grained level. © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.},

note = {Cited by: 10; All Open Access, Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Quaglia2024,

title = {Best practices for the manual curation of intrinsically disordered proteins in DisProt},

author = { Federica Quaglia and Anastasia Chasapi and Maria Victoria Nugnes and Maria Cristina Aspromonte and Emanuela Leonardi and Damiano Piovesan and Silvio C.E. Tosatto},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85188297172\&doi=10.1093%2fdatabase%2fbaae009\&partnerID=40\&md5=df4fca19479789139b3fd19bb35c817f},

doi = {10.1093/database/baae009},

issn = {17580463},

year  = {2024},

date = {2024-01-01},

abstract = {The DisProt database is a resource containing manually curated data on experimentally validated intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) from the literature. Developed in 2005, its primary goal was to collect structural and functional information into proteins that lack a fixed three-dimensional structure.Today, DisProt has evolved into a major repository that not only collects experimental data but also contributes to our understanding of the IDPs/IDRs roles in various biological processes, such as autophagy or the life cycle mechanisms in viruses or their involvement in diseases (such as cancer and neurodevelopmental disorders). DisProt offers detailed information on the structural states of IDPs/IDRs, including state transitions, interactions and their functions, all provided as curated annotations. One of the central activities of DisProt is the meticulous curation of experimental data from the literature. For this reason, to ensure that every expert and volunteer curator possesses the requisite knowledge for data evaluation, collection and integration, training courses and curation materials are available. However, biocuration guidelines concur on the importance of developing robust guidelines that not only provide critical information about data consistency but also ensure data acquisition.This guideline aims to provide both biocurators and external users with best practices for manually curating IDPs and IDRs in DisProt. It describes every step of the literature curation process and provides use cases of IDP curation within DisProt. © The Author(s) 2024. Published by Oxford University Press.},

note = {Cited by: 1; All Open Access, Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gehin2023,

title = {CERT1 mutations perturb human development by disrupting sphingolipid homeostasis},

author = { Charlotte Gehin and Museer A. Lone and Winston Lee and Laura Capolupo and Sylvia Ho and Adekemi M. Adeyemi and Erica H. Gerkes and Alexander P.A. Stegmann and Estrella L\'{o}pez-Mart\'{i}n and Eva Bermejo-S\'{a}nchez and Beatriz Mart\'{i}nez-Delgado and Christiane Zweier and Cornelia Kraus and Bernt Popp and Vincent Strehlow and Daniel Gr\"{a}fe and Ina Knerr and Eppie R. Jones and Stefano Zamuner and Luciano A. Abriata and Vidya Kunnathully and Brandon E. Moeller and Anthony Vocat and Samuel Rommelaere and Jean-Philippe Bocquete and Evelyne Ruchti and Greta Limoni and Marine Van Campenhoudt and Samuel Bourgeat and Petra Henklein and Christian Gilissen and Bregje W. van Bon and Rolph Pfundt and Marjolein H. Willemsen and Jolanda H. Schieving and Emanuela Leonardi and Fiorenza Soli and Alessandra Murgia and Hui Guo and Qiumeng Zhang and Kun Xia and Christina R. Fagerberg and Christoph P. Beier and Martin J. Larsen and Irene Valenzuela and Paula Fern\'{a}ndez-\'{A}lvarez and Shiyi Xiong and Robert \'{S}migiel and Vanesa L\'{o}pez-Gonz\'{a}lez and Llu\'{i}s Armengol and Manuela Morleo and Angelo Selicorni and Annalaura Torella and Moira Blyth and Nicola S. Cooper and Valerie Wilson and Renske Oegema and Yvan Herenger and Aurore Garde and Ange-Line Bruel and Frederic Tran Mau-Them and Alexis B.R. Maddocks and Jennifer M. Bain and Musadiq A. Bhat and Gregory Costain and Peter Kannu and Ashish Marwaha and Neena L. Champaigne and Michael J. Friez and Ellen B. Richardson and Vykuntaraju K. Gowda and Varunvenkat M. Srinivasan and Yask Gupta and Tze Y. Lim and Simone Sanna-Cherchi and Bruno Lemaitre and Toshiyuki Yamaji and Kentaro Hanada and John E. Burke and Ana Marjia Jak\v{s}i\'{c} and Brian D. McCabe and Paolo De Los Rios and Thorsten Hornemann and Giovanni D’Angelo and Vincenzo A. Gennarino},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85159733545\&doi=10.1172%2fJCI165019\&partnerID=40\&md5=0f32fc96f0219379d9b830efbbbbefb6},

doi = {10.1172/JCI165019},

issn = {00219738},

year  = {2023},

date = {2023-01-01},

abstract = {Neural differentiation, synaptic transmission, and action potential propagation depend on membrane sphingolipids, whose metabolism is tightly regulated. Mutations in the ceramide transporter CERT (CERT1), which is involved in sphingolipid biosynthesis, are associated with intellectual disability, but the pathogenic mechanism remains obscure. Here, we characterize 31 individuals with de novo missense variants in CERT1. Several variants fall into a previously uncharacterized dimeric helical domain that enables CERT homeostatic inactivation, without which sphingolipid production goes unchecked. The clinical severity reflects the degree to which CERT autoregulation is disrupted, and inhibiting CERT pharmacologically corrects morphological and motor abnormalities in a Drosophila model of the disease, which we call ceramide transporter (CerTra) syndrome. These findings uncover a central role for CERT autoregulation in the control of sphingolipid biosynthetic flux, provide unexpected insight into the structural organization of CERT, and suggest a possible therapeutic approach for patients with CerTra syndrome. © 2023, Gehin et al.},

note = {Cited by: 11; All Open Access, Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Leonardi2023202,

title = {Expanding the genetics and phenotypic spectrum of Lysine-specific demethylase 5C (KDM5C): a report of 13 novel variants},

author = { Emanuela Leonardi and Maria Cristina Aspromonte and Denise Drongitis and Elisa Bettella and Lucia Verrillo and Roberta Polli and Meriel McEntagart and Laura Licchetta and Robertino Dilena and Stefano D’Arrigo and Claudia Ciaccio and Silvia Esposito and Vincenzo Leuzzi and Annalaura Torella and Demetrio Baldo and Fortunato Lonardo and Giulia Bonato and Serena Pellegrin and Franco Stanzial and Renata Posmyk and Ewa Kaczorowska and Miryam Carecchio and Monika Gos and Sylwia Rzo\'{n}ca-Niewczas and Maria Giuseppina Miano and Alessandra Murgia},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85142646250\&doi=10.1038%2fs41431-022-01233-4\&partnerID=40\&md5=56692e2c9b3994a0703776134808e698},

doi = {10.1038/s41431-022-01233-4},

issn = {10184813},

year  = {2023},

date = {2023-01-01},

abstract = {Lysine-specific demethylase 5C (KDM5C) has been identified as an important chromatin remodeling gene, contributing to X-linked neurodevelopmental disorders (NDDs). The KDM5C gene, located in the Xp22 chromosomal region, encodes the H3K4me3-me2 eraser involved in neuronal plasticity and dendritic growth. Here we report 30 individuals carrying 13 novel and one previously identified KDM5C variants. Our cohort includes the first reported case of somatic mosaicism in a male carrying a KDM5C nucleotide substitution, and a dual molecular finding in a female carrying a homozygous truncating FUCA1 alteration together with a de novo KDM5C variant. With the use of next generation sequencing strategies, we detected 1 frameshift, 1 stop codon, 2 splice-site and 10 missense variants, which pathogenic role was carefully investigated by a thorough bioinformatic analysis. The pattern of X-chromosome inactivation was found to have an impact on KDM5C phenotypic expression in females of our cohort. The affected individuals of our case series manifested a neurodevelopmental condition characterized by psychomotor delay, intellectual disability with speech disorders, and behavioral features with particular disturbed sleep pattern; other observed clinical manifestations were short stature, obesity and hypertrichosis. Collectively, these findings expand the current knowledge about the pathogenic mechanisms leading to dysfunction of this important chromatin remodeling gene and contribute to a refinement of the KDM5C phenotypic spectrum. © 2022, This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.},

note = {Cited by: 5; All Open Access, Green Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vos2023351,

title = {DNA methylation episignatures are sensitive and specific biomarkers for detection of patients with KAT6A/KAT6B variants},

author = { Niels Vos and Jack Reilly and Mariet W Elting and Philippe M Campeau and David Coman and Zornitza Stark and Tiong Yang Tan and David J Amor and Simran Kaur and Miya Stjohn and Angela T Morgan and Benjamin A Kamien and Chirag Patel and Matthew L Tedder and Giuseppe Merla and Paolo Prontera and Marco Castori and Kai Muru and Felicity Collins and John Christodoulou and Janine Smith and Bruria Ben Zeev and Alessandra Murgia and Emanuela Leonardi and Natacha Esber and Antonio Martinez-Monseny and Didac Casas-Alba and Matthew Wallis and Marcel Mannens and Michael A Levy and Raissa Relator and Marielle Alders and Bekim Sadikovic},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85160965403\&doi=10.2217%2fepi-2023-0079\&partnerID=40\&md5=5fb586acb83064545e1a62385bf47b83},

doi = {10.2217/epi-2023-0079},

issn = {17501911},

year  = {2023},

date = {2023-01-01},

abstract = {Accurate diagnosis for patients living with neurodevelopmental disorders is often met with numerous challenges, related to the ambiguity of findings and lack of specificity in genetic variants leading to pathology. Genome-wide DNA methylation analysis has been used to develop highly sensitive and specific 'episignatures' as biomarkers capable of differentiating and classifying complex neurodevelopmental disorders. In this study we describe distinct episignatures for KAT6A syndrome, caused by pathogenic variants in the lysine acetyltransferase A gene (KAT6A), and for the two neurodevelopmental disorders associated with lysine acetyl transferase B (KAT6B). We demonstrate the ability of our models to differentiate between highly overlapping episignatures, increasing the ability to effectively identify and diagnose these conditions. © 2023 Future Medicine Ltd.},

note = {Cited by: 2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Godler2022,

title = {Feasibility of Screening for Chromosome 15 Imprinting Disorders in 16579 Newborns by Using a Novel Genomic Workflow},

author = { David E. Godler and Ling Ling and Dinusha Gamage and Emma K. Baker and Minh Bui and Michael J. Field and Carolyn Rogers and Merlin G. Butler and Alessandra Murgia and Emanuela Leonardi and Roberta Polli and Charles E. Schwartz and Cindy D. Skinner and Angelica M. Alliende and Lorena Santa Maria and James Pitt and Ronda Greaves and David Francis and Ralph Oertel and Min Wang and Cas Simons and David J. Amor},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85122738953\&doi=10.1001%2fjamanetworkopen.2021.41911\&partnerID=40\&md5=32c9ffb6cf9d94db2d9f3bd72f534d93},

doi = {10.1001/jamanetworkopen.2021.41911},

issn = {25743805},

year  = {2022},

date = {2022-01-01},

abstract = {Importance: Newborn screening for Angelman syndrome (AS), Prader-Willi syndrome (PWS), and chromosome 15 duplication syndrome (Dup15q) may lead to benefit from early diagnosis and treatment. Objective: To examine the feasibility of newborn screening for these chromosome 15 imprinting disorders at population scale. Design, Setting, and Participants: In this diagnostic study, the validation data set for the first-tier SNRPN test, called methylation-specific quantitative melt analysis (MS-QMA), included 109 PWS, 48 AS, 9 Dup15q, and 1190 population control newborn blood spots (NBS) and peripheral tissue samples from participants recruited from January 2000 to December 2016. The test data set included NBS samples from 16579 infants born in 2011. Infants with an NBS identified as positive for PWS, AS, or Dup15q by the first-tier test were referred for droplet digital polymerase chain reaction, real-time polymerase chain reaction, and low-coverage whole-genome sequencing for confirmatory testing. Data analyses were conducted between February 12, 2015, and August 15, 2020. Results: In the validation data set, the median age for the 77 patients with PWS was 3.00 years (IQR, 0.01-44.50 years); for the 46 patients with AS, 2.76 years (IQR, 0.028 to 49.00 years); and for the 9 patients with Dup15q, 4.00 years (IQR, 1.00 to 28.00 years). Thirty-eight patients (51.4%) in the PWS group, 20 patients (45.5%) in the AS group, and 6 patients (66.7%) in the Dup15q group who had sex reported were male. The validation data set showed MS-QMA sensitivity of 99.0% for PWS, 93.8% for AS, and 77.8% for Dup15q; specificity of 100% for PWS, AS, and Dup15q; positive predictive and negative predictive values of 100% for PWS and AS; and a positive predictive value of 87.5% and negative predictive value of 100% for Dup15q. In the test data set of NBS samples from 16579 infants, 92 had a positive test result using a methylation ratio cut-off of 3 standard deviations from the mean. Of these patients, 2 were confirmed to have PWS; 2, AS; and 1, maternal Dup15q. With the use of more conservative PWS- and AS-specific thresholds for positive calls from the validation data set, 9 positive NBS results were identified by MS-QMA in this cohort. The 2 PWS and 2 AS calls were confirmed by second-tier testing, but the 1 Dup15q case was not confirmed. Together, these results provided prevalence estimates of 1 in 8290 for both AS and PWS and 1 in 16579 for maternal Dup15q, with positive predictive values for first-tier testing at 67.0% for AS, 33.0% for PWS, and 44.0% for combined detection of chromosome 15 imprinting disorders for the validation data set. Conclusions and Relevance: The findings of this diagnostic study suggest that it is feasible to screen for all chromosome 15 imprinting disorders using SNRPN methylation analysis, with 5 individuals identified with these disorders out of 16579 infants screened.. © 2022 American Medical Association. All rights reserved.},

note = {Cited by: 16; All Open Access, Gold Open Access, Green Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Quaglia2022D480,

title = {DisProt in 2022: Improved quality and accessibility of protein intrinsic disorder annotation},

author = { Federica Quaglia and B\'{a}lint Mesz\'{a}ros and Edoardo Salladini and Andr\'{a}s Hatos and Rita Pancsa and Luc\'{i}a B. Chemes and M\'{a}ty\'{a}s Pajkos and Tamas Lazar and Samuel Pe\~{n}a-D\'{i}az and Jaime Santos and Veronika \'{A}cs and Nazanin Farahi and Erzsebet Fich\'{o} and Maria Cristina Aspromonte and Claudio Bassot and Anastasia Chasapi and Norman E. Davey and Radoslav Davidovi\'{c} and Laszlo Dobson and Arne Elofsson and G\'{a}bor Erdos and Pascale Gaudet and Michelle Giglio and Juliana Glavina and Javier Iserte and Valent\'{i}n Iglesias and Zs\'{o}fia K\'{a}lm\'{a}n and Matteo Lambrughi and Emanuela Leonardi and Sonia Longhi and Sandra Macedo-Ribeiro and Emiliano Maiani and Julia Marchetti and Cristina Marino-Buslje and Attila Mesz\'{a}ros and Alexander Miguel Monzon and Giovanni Minervini and Suvarna Nadendla and Juliet F. Nilsson and Marian Novotn\'{y} and Christos A. Ouzounis and Nicol\'{a}s Palopoli and Elena Papaleo and Pedro Jose Barbosa Pereira and Gabriele Pozzati and Vasilis J. Promponas and Jordi Pujols and Alma Carolina Sanchez Rocha and Martin Salas and Luciana Rodriguez Sawicki and Eva Schad and Aditi Shenoy and Tam\'{a}s Szaniszl\'{o} and Konstantinos D. Tsirigos and Nevena Veljkovic and Gustavo Parisi and Salvador Ventura and Zsuzsanna Doszt\'{a}nyi and Peter Tompa and Silvio C. E. Tosatto and Damiano Piovesan},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85125157608\&doi=10.1093%2fnar%2fgkab1082\&partnerID=40\&md5=270bf5618598238b9e614e8070e3723a},

doi = {10.1093/nar/gkab1082},

issn = {03051048},

year  = {2022},

date = {2022-01-01},

abstract = {The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure. © 2022 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.},

note = {Cited by: 107; All Open Access, Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cousin2022,

title = {Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome},

author = { Margot A. Cousin and Emma L. Veale and Nikita R. Dsouza and Swarnendu Tripathi and Robyn G. Holden and Maria Arelin and Geoffrey Beek and Mir Reza Bekheirnia and Jasmin Beygo and Vikas Bhambhani and Martin Bialer and Stefania Bigoni and Cyrus Boelman and Jenny Carmichael and Thomas Courtin and Benjamin Cogne and Ivana Dabaj and Diane Doummar and Laura Fazilleau and Alessandra Ferlini and Ralitza H. Gavrilova and John M. Graham and Tobias B. Haack and Jane Juusola and Sarina G. Kant and Saima Kayani and Boris Keren and Petra Ketteler and Chiara Kl\"{o}ckner and Tamara T. Koopmann and Teresa M. Kruisselbrink and Alma Kuechler and La\"{e}titia Lambert and X\'{e}nia Latypova and Robert Roger Lebel and Magalie S. Leduc and Emanuela Leonardi and Andrea M. Lewis and Wendy Liew and Keren Machol and Samir Mardini and Kirsty McWalter and Cyril Mignot and Julie McLaughlin and Alessandra Murgia and Vinodh Narayanan and Caroline Nava and Sonja Neuser and Mathilde Nizon and Davide Ognibene and Joohyun Park and Konrad Platzer and C\'{e}line Poirsier and Maximilian Radtke and Keri Ramsey and Cassandra K. Runke and Maria J. Guillen Sacoto and Fernando Scaglia and Marwan Shinawi and Stephanie Spranger and Ee Shien Tan and John Taylor and Anne-Sophie Trentesaux and Filippo Vairo and Rebecca Willaert and Neda Zadeh and Raul Urrutia and Dusica Babovic-Vuksanovic and Michael T. Zimmermann and Alistair Mathie and Eric W. Klee},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85131795908\&doi=10.1186%2fs13073-022-01064-4\&partnerID=40\&md5=81531c1a0244ddf38e75235cde81e258},

doi = {10.1186/s13073-022-01064-4},

issn = {1756994X},

year  = {2022},

date = {2022-01-01},

abstract = {Background: Genomics enables individualized diagnosis and treatment, but large challenges remain to functionally interpret rare variants. To date, only one causative variant has been described for KCNK9 imprinting syndrome (KIS). The genotypic and phenotypic spectrum of KIS has yet to be described and the precise mechanism of disease fully understood. Methods: This study discovers mechanisms underlying KCNK9 imprinting syndrome (KIS) by describing 15 novel KCNK9 alterations from 47 KIS-affected individuals. We use clinical genetics and computer-assisted facial phenotyping to describe the phenotypic spectrum of KIS. We then interrogate the functional effects of the variants in the encoded TASK3 channel using sequence-based analysis, 3D molecular mechanic and dynamic protein modeling, and in vitro electrophysiological and functional methodologies. Results: We describe the broader genetic and phenotypic variability for KIS in a cohort of individuals identifying an additional mutational hotspot at p.Arg131 and demonstrating the common features of this neurodevelopmental disorder to include motor and speech delay, intellectual disability, early feeding difficulties, muscular hypotonia, behavioral abnormalities, and dysmorphic features. The computational protein modeling and in vitro electrophysiological studies discover variability of the impact of KCNK9 variants on TASK3 channel function identifying variants causing gain and others causing loss of conductance. The most consistent functional impact of KCNK9 genetic variants, however, was altered channel regulation. Conclusions: This study extends our understanding of KIS mechanisms demonstrating its complex etiology including gain and loss of channel function and consistent loss of channel regulation. These data are rapidly applicable to diagnostic strategies, as KIS is not identifiable from clinical features alone and thus should be molecularly diagnosed. Furthermore, our data suggests unique therapeutic strategies may be needed to address the specific functional consequences of KCNK9 variation on channel function and regulation. © 2022, The Author(s).},

note = {Cited by: 7; All Open Access, Gold Open Access, Green Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Necci2021472,

title = {Critical assessment of protein intrinsic disorder prediction},

author = { Marco Necci and Damiano Piovesan and Md Tamjidul Hoque and Ian Walsh and Sumaiya Iqbal and Michele Vendruscolo and Pietro Sormanni and Chen Wang and Daniele Raimondi and Ronesh Sharma and Yaoqi Zhou and Thomas Litfin and Oxana Valerianovna Galzitskaya and Michail Yu. Lobanov and Wim Vranken and Bj\"{o}rn Wallner and Claudio Mirabello and Nawar Malhis and Zsuzsanna Doszt\'{a}nyi and G\'{a}bor Erd\H{o}s and B\'{a}lint M\'{e}sz\'{a}ros and Jianzhao Gao and Kui Wang and Gang Hu and Zhonghua Wu and Alok Sharma and Jack Hanson and Kuldip Paliwal and Isabelle Callebaut and Tristan Bitard-Feildel and Gabriele Orlando and Zhenling Peng and Jinbo Xu and Sheng Wang and David T. Jones and Domenico Cozzetto and Fanchi Meng and Jing Yan and J\"{o}rg Gsponer and Jianlin Cheng and Tianqi Wu and Lukasz Kurgan and Vasilis J. Promponas and Stella Tamana and Cristina Marino-Buslje and Elizabeth Mart\'{i}nez-P\'{e}rez and Anastasia Chasapi and Christos Ouzounis and A. Keith Dunker and Andrey V. Kajava and Jeremy Y. Leclercq and Burcu Aykac-Fas and Matteo Lambrughi and Emiliano Maiani and Elena Papaleo and Lucia Beatriz Chemes and Luc\'{i}a \'{A}lvarez and Nicol\'{a}s S. Gonz\'{a}lez-Foutel and Valentin Iglesias and Jordi Pujols and Salvador Ventura and Nicol\'{a}s Palopoli and Guillermo Ignacio Ben\'{i}tez and Gustavo Parisi and Claudio Bassot and Arne Elofsson and Sudha Govindarajan and John Lamb and Marco Salvatore and Andr\'{a}s Hatos and Alexander Miguel Monzon and Martina Bevilacqua and Ivan Mi\v{c}eti\'{c} and Giovanni Minervini and Lisanna Paladin and Federica Quaglia and Emanuela Leonardi and Norman Davey and Tamas Horvath and Orsolya Panna Kovacs and Nikoletta Murvai and Rita Pancsa and Eva Schad and Beata Szabo and Agnes Tantos and Sandra Macedo-Ribeiro and Jose Antonio Manso and Pedro Jos\'{e} Barbosa Pereira and Radoslav Davidovi\'{c} and Nevena Veljkovic and Borb\'{a}la Hajdu-Solt\'{e}sz and M\'{a}ty\'{a}s Pajkos and Tam\'{a}s Szaniszl\'{o} and Mainak Guharoy and Tamas Lazar and Mauricio Macossay-Castillo and Peter Tompa and Silvio C. E. Tosatto},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85104988931\&doi=10.1038%2fs41592-021-01117-3\&partnerID=40\&md5=de0effc341a3dba548f76a749640b858},

doi = {10.1038/s41592-021-01117-3},

issn = {15487091},

year  = {2021},

date = {2021-01-01},

abstract = {Intrinsically disordered proteins, defying the traditional protein structure\textendashfunction paradigm, are a challenge to study experimentally. Because a large part of our knowledge rests on computational predictions, it is crucial that their accuracy is high. The Critical Assessment of protein Intrinsic Disorder prediction (CAID) experiment was established as a community-based blind test to determine the state of the art in prediction of intrinsically disordered regions and the subset of residues involved in binding. A total of 43 methods were evaluated on a dataset of 646 proteins from DisProt. The best methods use deep learning techniques and notably outperform physicochemical methods. The top disorder predictor has Fmax = 0.483 on the full dataset and Fmax = 0.792 following filtering out of bona fide structured regions. Disordered binding regions remain hard to predict, with Fmax = 0.231. Interestingly, computing times among methods can vary by up to four orders of magnitude. © 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.},

note = {Cited by: 181; All Open Access, Hybrid Gold Open Access},

keywords = {},

pubstate = {published},

tppubtype = {article}

}