Group Publications

@article{bensaoud_quantitative_2022,

title = {Quantitative proteomics analysis reveals core and variable tick salivary proteins at the tick-vertebrate host interface},

author = {Chaima Bensaoud and Stefan Tenzer and Alicia Poplawski and José María Medina and Mohamed Amine Jmel and Hanne Voet and Imen Mekki and Ernesto Aparicio-Puerta and Brent Cuveele and Ute Distler and Federico Marini and Michael Hackenberg and Michalis Kotsyfakis},

doi = {10.1111/mec.16561},

issn = {1365-294X},

year  = {2022},

date = {2022-08-01},

journal = {Molecular Ecology},

volume = {31},

number = {15},

pages = {4162–4175},

abstract = {Few studies have examined tick proteomes, how they adapt to their environment, and their roles in the parasite-host interactions that drive tick infestation and pathogen transmission. Here we used a proteomics approach to screen for biologically and immunologically relevant proteins acting at the tick-host interface during tick feeding and, as proof of principle, measured host antibody responses to some of the discovered candidates. We used a label-free quantitative proteomic workflow to study salivary proteomes of (i) wild Ixodes ricinus ticks fed on different hosts, (ii) wild or laboratory ticks fed on the same host, and (iii) adult ticks cofed with nymphs. Our results reveal high and stable expression of several protease inhibitors and other tick-specific proteins under different feeding conditions. Most pathways functionally enriched in sialoproteomes were related to proteolysis, endopeptidase, and amine-binding activities. The generated catalogue of tick salivary proteins enabled the selection of six candidate secreted immunogenic peptides for rabbit immunizations, three of which induced strong and durable antigen-specific antibody responses in rabbits. Furthermore, rabbits exposed to ticks mounted immune responses against the candidate peptides/proteins, confirming their expression at the tick-vertebrate interface. Our approach provides insights into tick adaptation strategies to different feeding conditions and promising candidates for developing antitick vaccines or markers of exposure of vertebrate hosts to tick bites.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fortunato_selective_2022,

title = {Selective isolation of extracellular vesicles from minimally processed human plasma as a translational strategy for liquid biopsies},

author = {Diogo Fortunato and Stavros Giannoukakos and Ana Giménez-Capitán and Michael Hackenberg and Miguel A. Molina-Vila and Nataša Zarovni},

doi = {10.1186/s40364-022-00404-1},

issn = {2050-7771},

year  = {2022},

date = {2022-08-01},

journal = {Biomarker Research},

volume = {10},

number = {1},

pages = {57},

abstract = {BACKGROUND: Intercellular communication is mediated by extracellular vesicles (EVs), as they enclose selectively packaged biomolecules that can be horizontally transferred from donor to recipient cells. Because all cells constantly generate and recycle EVs, they provide accurate timed snapshots of individual pathophysiological status. Since blood plasma circulates through the whole body, it is often the biofluid of choice for biomarker detection in EVs. Blood collection is easy and minimally invasive, yet reproducible procedures to obtain pure EV samples from circulating biofluids are still lacking. Here, we addressed central aspects of EV immunoaffinity isolation from simple and complex matrices, such as plasma. 

METHODS: Cell-generated EV spike-in models were isolated and purified by size-exclusion chromatography, stained with cellular dyes and characterized by nano flow cytometry. Fluorescently-labelled spike-in EVs emerged as reliable, high-throughput and easily measurable readouts, which were employed to optimize our EV immunoprecipitation strategy and evaluate its performance. Plasma-derived EVs were captured and detected using this straightforward protocol, sequentially combining isolation and staining of specific surface markers, such as CD9 or CD41. Multiplexed digital transcript detection data was generated using the Nanostring nCounter platform and evaluated through a dedicated bioinformatics pipeline. 

RESULTS: Beads with covalently-conjugated antibodies on their surface outperformed streptavidin-conjugated beads, coated with biotinylated antibodies, in EV immunoprecipitation. Fluorescent EV spike recovery evidenced that target EV subpopulations can be efficiently retrieved from plasma, and that their enrichment is dependent not only on complex matrix composition, but also on the EV surface phenotype. Finally, mRNA profiling experiments proved that distinct EV subpopulations can be captured by directly targeting different surface markers. Furthermore, EVs isolated with anti-CD61 beads enclosed mRNA expression patterns that might be associated to early-stage lung cancer, in contrast with EVs captured through CD9, CD63 or CD81. The differential clinical value carried within each distinct EV subset highlights the advantages of selective isolation. 

CONCLUSIONS: This EV isolation protocol facilitated the extraction of clinically useful information from plasma. Compatible with common downstream analytics, it is a readily implementable research tool, tailored to provide a truly translational solution in routine clinical workflows, fostering the inclusion of EVs in novel liquid biopsy settings.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{barturen_whole_2022,

title = {Whole blood DNA methylation analysis reveals respiratory environmental traits involved in COVID-19 severity following SARS-CoV-2 infection},

author = {Guillermo Barturen and Elena Carnero-Montoro and Manuel Martínez-Bueno and Silvia Rojo-Rello and Beatriz Sobrino and Óscar Porras-Perales and Clara Alcántara-Domínguez and David Bernardo and Marta E. Alarcón-Riquelme},

doi = {10.1038/s41467-022-32357-2},

issn = {2041-1723},

year  = {2022},

date = {2022-08-01},

journal = {Nature Communications},

volume = {13},

number = {1},

pages = {4597},

abstract = {SARS-CoV-2 infection can cause an inflammatory syndrome (COVID-19) leading, in many cases, to bilateral pneumonia, severe dyspnea, and in textasciitilde5% of these, death. DNA methylation is known to play an important role in the regulation of the immune processes behind COVID-19 progression, however it has not been studied in depth. In this study, we aim to evaluate the implication of DNA methylation in COVID-19 progression by means of a genome-wide DNA methylation analysis combined with DNA genotyping. The results reveal the existence of epigenomic regulation of functional pathways associated with COVID-19 progression and mediated by genetic loci. We find an environmental trait-related signature that discriminates mild from severe cases and regulates, among other cytokines, IL-6 expression via the transcription factor CEBP. The analyses suggest that an interaction between environmental contribution, genetics, and epigenetics might be playing a role in triggering the cytokine storm described in the most severe cases.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{medina_bioinformatic_2022,

title = {Bioinformatic Analysis of Ixodes ricinus Long Non-Coding RNAs Predicts Their Binding Ability of Host miRNAs},

author = {José María Medina and Muhammad Nadeem Abbas and Chaima Bensaoud and Michael Hackenberg and Michail Kotsyfakis},

doi = {10.3390/ijms23179761},

issn = {1422-0067},

year  = {2022},

date = {2022-08-01},

journal = {International Journal of Molecular Sciences},

volume = {23},

number = {17},

pages = {9761},

abstract = {Ixodes ricinus ticks are distributed across Europe and are a vector of tick-borne diseases. Although I. ricinus transcriptome studies have focused exclusively on protein coding genes, the last decade witnessed a strong increase in long non-coding RNA (lncRNA) research and characterization. Here, we report for the first time an exhaustive analysis of these non-coding molecules in I. ricinus based on 131 RNA-seq datasets from three different BioProjects. Using this data, we obtained a consensus set of lncRNAs and showed that lncRNA expression is stable among different studies. While the length distribution of lncRNAs from the individual data sets is biased toward short length values, implying the existence of technical artefacts, the consensus lncRNAs show a more homogeneous distribution emphasizing the importance to incorporate data from different sources to generate a solid reference set of lncRNAs. KEGG enrichment analysis of host miRNAs putatively targeting lncRNAs upregulated upon feeding showed that these miRNAs are involved in several relevant functions for the tick-host interaction. The possibility that at least some tick lncRNAs act as host miRNA sponges was further explored by identifying lncRNAs with many target regions for a given host miRNA or sets of host miRNAs that consistently target lncRNAs together. Overall, our findings suggest that lncRNAs that may act as sponges have diverse biological roles related to the tick-host interaction in different tissues.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{aparicio-puerta_srnabench_2022,

title = {sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms},

author = {Ernesto Aparicio-Puerta and Cristina Gómez-Martín and Stavros Giannoukakos and José María Medina and Chantal Scheepbouwer and Adrián García-Moreno and Pedro Carmona-Saez and Bastian Fromm and Michiel Pegtel and Andreas Keller and Juan Antonio Marchal and Michael Hackenberg},

doi = {10.1093/nar/gkac363},

issn = {1362-4962},

year  = {2022},

date = {2022-07-01},

journal = {Nucleic Acids Research},

volume = {50},

number = {W1},

pages = {W710–W717},

abstract = {The NCBI Sequence Read Archive currently hosts microRNA sequencing data for over 800 different species, evidencing the existence of a broad taxonomic distribution in the field of small RNA research. Simultaneously, the number of samples per miRNA-seq study continues to increase resulting in a vast amount of data that requires accurate, fast and user-friendly analysis methods. Since the previous release of sRNAtoolbox in 2019, 55 000 sRNAbench jobs have been submitted which has motivated many improvements in its usability and the scope of the underlying annotation database. With this update, users can upload an unlimited number of samples or import them from Google Drive, Dropbox or URLs. Micro- and small RNA profiling can now be carried out using high-confidence Metazoan and plant specific databases, MirGeneDB and PmiREN respectively, together with genome assemblies and libraries from 441 Ensembl species. The new results page includes straightforward sample annotation to allow downstream differential expression analysis with sRNAde. Unassigned reads can also be explored by means of a new tool that performs mapping to microbial references, which can reveal contamination events or biologically meaningful findings as we describe in the example. sRNAtoolbox is available at: https://arn.ugr.es/srnatoolbox/.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zubkovic_virus-induced_2022,

title = {The Virus-Induced Upregulation of the miR-183/96/182 Cluster and the FoxO Family Protein Members Are Not Required for Efficient Replication of HSV-1},

author = {Andreja Zubković and Ines Žarak and Ivana Ratkaj and Filip Rokić and Maja Jekić and Marina Pribanić Matešić and Ricardo Lebrón and Cristina Gómez-Martín and Berislav Lisnić and Vanda Juranić Lisnić and Stipan Jonjić and Dongli Pan and Oliver Vugrek and Michael Hackenberg and Igor Jurak},

doi = {10.3390/v14081661},

issn = {1999-4915},

year  = {2022},

date = {2022-07-01},

journal = {Viruses},

volume = {14},

number = {8},

pages = {1661},

abstract = {Herpes simplex virus 1 (HSV-1) expresses a large number of miRNAs, and their function is still not completely understood. In addition, HSV-1 has been found to deregulate host miRNAs, which adds to the complexity of the regulation of efficient virus replication. In this study, we comprehensively addressed the deregulation of host miRNAs by massive-parallel sequencing. We found that only miRNAs expressed from a single cluster, miR-183/96/182, are reproducibly deregulated during productive infection. These miRNAs are predicted to regulate a great number of potential targets involved in different cellular processes and have only 33 shared targets. Among these, members of the FoxO family of proteins were identified as potential targets for all three miRNAs. However, our study shows that the upregulated miRNAs do not affect the expression of FoxO proteins, moreover, these proteins were upregulated in HSV-1 infection. Furthermore, we show that the individual FoxO proteins are not required for efficient HSV-1 replication. Taken together, our results indicate a complex and redundant response of infected cells to the virus infection that is efficiently inhibited by the virus.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pedraz-valdunciel_digital_2022,

title = {Digital multiplexed analysis of circular RNAs in FFPE and fresh non-small cell lung cancer specimens},

author = {Carlos Pedraz-Valdunciel and Stavros Giannoukakos and Nicolas Potie and Ana Giménez-Capitán and Chung-Ying Huang and Michael Hackenberg and Alberto Fernandez-Hilario and Jill Bracht and Martyna Filipska and Erika Aldeguer and Sonia Rodríguez and Trever G. Bivona and Sarah Warren and Cristina Aguado and Masaoki Ito and Andrés Aguilar-Hernández and Miguel Angel Molina-Vila and Rafael Rosell},

doi = {10.1002/1878-0261.13182},

issn = {1878-0261},

year  = {2022},

date = {2022-06-01},

journal = {Molecular Oncology},

volume = {16},

number = {12},

pages = {2367–2383},

abstract = {Although many studies highlight the implication of circular RNAs (circRNAs) in carcinogenesis and tumor progression, their potential as cancer biomarkers has not yet been fully explored in the clinic due to the limitations of current quantification methods. Here, we report the use of the nCounter platform as a valid technology for the analysis of circRNA expression patterns in non-small cell lung cancer (NSCLC) specimens. Under this context, our custom-made circRNA panel was able to detect circRNA expression both in NSCLC cells and formalin-fixed paraffin-embedded (FFPE) tissues. CircFUT8 was overexpressed in NSCLC, contrasting with circEPB41L2, circBNC2, and circSOX13 downregulation even at the early stages of the disease. Machine learning (ML) approaches from different paradigms allowed discrimination of NSCLC from nontumor controls (NTCs) with an 8-circRNA signature. An additional 4-circRNA signature was able to classify early-stage NSCLC samples from NTC, reaching a maximum area under the ROC curve (AUC) of 0.981. Our results not only present two circRNA signatures with diagnosis potential but also introduce nCounter processing following ML as a feasible protocol for the study and development of circRNA signatures for NSCLC.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fromm_limits_2022,

title = {The limits of human microRNA annotation have been met},

author = {Bastian Fromm and Xiangfu Zhong and Marcel Tarbier and Marc R. Friedländer and Michael Hackenberg},

doi = {10.1261/rna.079098.122},

issn = {1469-9001},

year  = {2022},

date = {2022-06-01},

journal = {RNA},

volume = {28},

number = {6},

pages = {781–785},

address = {New York, N.Y.},

abstract = {Over the last few years, the number of microRNAs in the human genome has become a controversially debated issue. Several publications reported thousands of putative novel microRNAs not included in the curated microRNA gene database MirGeneDB and the repository miRBase. Recently, by using sequencing of ∼300 human tissues and cell lines, the human RNA atlas, an expanded inventory of human RNA annotations, was published, reporting thousands of putative microRNAs. We, the developers of established microRNA prediction tools and hosts of MirGeneDB, raise concerns about the frequently applied prediction and functional validation strategies, briefly discussing the drawbacks of false positive detections. By means of quantifying well-established biogenesis-derived features, we show that the reported novel microRNAs essentially represent false-positives and argue that the human microRNA complement, at about 550 microRNA genes, is already near complete. Output of available tools must be curated as false predictions will misguide scientists looking for biomarkers or therapeutic targets.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{garcia-moreno_functional_2022,

title = {Functional Enrichment Analysis of Regulatory Elements},

author = {Adrian Garcia-Moreno and Raul López-Domínguez and Juan Antonio Villatoro-García and Alberto Ramirez-Mena and Ernesto Aparicio-Puerta and Michael Hackenberg and Alberto Pascual-Montano and Pedro Carmona-Saez},

doi = {10.3390/biomedicines10030590},

issn = {2227-9059},

year  = {2022},

date = {2022-03-01},

journal = {Biomedicines},

volume = {10},

number = {3},

pages = {590},

abstract = {Statistical methods for enrichment analysis are important tools to extract biological information from omics experiments. Although these methods have been widely used for the analysis of gene and protein lists, the development of high-throughput technologies for regulatory elements demands dedicated statistical and bioinformatics tools. Here, we present a set of enrichment analysis methods for regulatory elements, including CpG sites, miRNAs, and transcription factors. Statistical significance is determined via a power weighting function for target genes and tested by the Wallenius noncentral hypergeometric distribution model to avoid selection bias. These new methodologies have been applied to the analysis of a set of miRNAs associated with arrhythmia, showing the potential of this tool to extract biological information from a list of regulatory elements. These new methods are available in GeneCodis 4, a web tool able to perform singular and modular enrichment analysis that allows the integration of heterogeneous information.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fromm_mirgenedb_2022,

title = {MirGeneDB 2.1: toward a complete sampling of all major animal phyla},

author = {Bastian Fromm and Eirik Høye and Diana Domanska and Xiangfu Zhong and Ernesto Aparicio-Puerta and Vladimir Ovchinnikov and Sinan U. Umu and Peter J. Chabot and Wenjing Kang and Morteza Aslanzadeh and Marcel Tarbier and Emilio Mármol-Sánchez and Gianvito Urgese and Morten Johansen and Eivind Hovig and Michael Hackenberg and Marc R. Friedländer and Kevin J. Peterson},

doi = {10.1093/nar/gkab1101},

issn = {1362-4962},

year  = {2022},

date = {2022-01-01},

journal = {Nucleic Acids Research},

volume = {50},

number = {D1},

pages = {D204–D210},

abstract = {We describe an update of MirGeneDB, the manually curated microRNA gene database. Adhering to uniform and consistent criteria for microRNA annotation and nomenclature, we substantially expanded MirGeneDB with 30 additional species representing previously missing metazoan phyla such as sponges, jellyfish, rotifers and flatworms. MirGeneDB 2.1 now consists of 75 species spanning over ∼800 million years of animal evolution, and contains a total number of 16 670 microRNAs from 1549 families. Over 6000 microRNAs were added in this update using ∼550 datasets with ∼7.5 billion sequencing reads. By adding new phylogenetically important species, especially those relevant for the study of whole genome duplication events, and through updating evolutionary nodes of origin for many families and genes, we were able to substantially refine our nomenclature system. All changes are traceable in the specifically developed MirGeneDB version tracker. The performance of read-pages is improved and microRNA expression matrices for all tissues and species are now also downloadable. Altogether, this update represents a significant step toward a complete sampling of all major metazoan phyla, and a widely needed foundation for comparative microRNA genomics and transcriptomics studies. MirGeneDB 2.1 is part of RNAcentral and Elixir Norway, publicly and freely available at http://www.mirgenedb.org/.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fonseca_functional_2022,

title = {Functional characterization of the tomato HAIRPLUS gene reveals the implication of the epigenome in the control of glandular trichome formation},

author = {Rocío Fonseca and Carmen Capel and Fernando J. Yuste-Lisbona and Jorge L. Quispe and Cristina Gómez-Martín and Ricardo Lebrón and Michael Hackenberg and José L. Oliver and Trinidad Angosto and Rafael Lozano and Juan Capel},

doi = {10.1093/hr/uhab015},

issn = {2662-6810},

year  = {2022},

date = {2022-01-01},

journal = {Horticulture Research},

volume = {9},

pages = {uhab015},

abstract = {Trichomes are specialised epidermal cells developed in the aerial surface of almost every terrestrial plant. These structures form physical barriers, which combined with their capability of synthesis of complex molecules, prevent plagues from spreading and confer trichomes a key role in the defence against herbivores. In this work, the tomato gene HAIRPLUS (HAP) that controls glandular trichome density in tomato plants was characterised. HAP belongs to a group of proteins involved in histone tail modifications although some also bind methylated DNA. HAP loss of function promotes epigenomic modifications in the tomato genome reflected in numerous differentially methylated cytosines and causes transcriptomic changes in hap mutant plants. Taken together, these findings demonstrate that HAP links epigenome remodelling with multicellular glandular trichome development and reveal that HAP is a valuable genomic tool for pest resistance in tomato breeding.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{medina_transcriptomic_2022,

title = {Transcriptomic analysis of the tick midgut and salivary gland responses upon repeated blood-feeding on a vertebrate host},

author = {José María Medina and Mohamed Amine Jmel and Brent Cuveele and Cristina Gómez-Martín and Ernesto Aparicio-Puerta and Imen Mekki and Jan Kotál and Larissa Almeida Martins and Michael Hackenberg and Chaima Bensaoud and Michail Kotsyfakis},

doi = {10.3389/fcimb.2022.919786},

issn = {2235-2988},

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in Cellular and Infection Microbiology},

volume = {12},

pages = {919786},

abstract = {Ticks are blood-feeding arthropods that use the components of their salivary glands to counter the host's hemostatic, inflammatory, and immune responses. The tick midgut also plays a crucial role in hematophagy. It is responsible for managing blood meals (storage and digestion) and protecting against host immunity and pathogen infections. Previous transcriptomic studies revealed the complexity of tick sialomes (salivary gland transcriptomes) and mialomes (midgut transcriptomes) which encode for protease inhibitors, lipocalins (histamine-binding proteins), disintegrins, enzymes, and several other tick-specific proteins. Several studies have demonstrated that mammalian hosts acquire tick resistance against repeated tick bites. Consequently, there is an urgent need to uncover how tick sialomes and mialomes respond to resistant hosts, as they may serve to develop novel tick control strategies and applications. Here, we mimicked natural repeated tick bites in a laboratory setting and analyzed gene expression dynamics in the salivary glands and midguts of adult female ticks. Rabbits were subjected to a primary (feeding on a naive host) and a secondary infestation of the same host (we re-exposed the hosts but to other ticks). We used single salivary glands and midguts dissected from individual siblings adult pathogen-free female Ixodes ricinus to reduce genetic variability between individual ticks. The comprehensive analysis of 88 obtained RNA-seq data sets allows us to provide high-quality annotated sialomes and mialomes from individual ticks. Comparisons between fed/unfed, timepoints, and exposures yielded as many as 3000 putative differentially expressed genes (DEG). Interestingly, when classifying the exposure DEGs by means of a clustering approach we observed that the majority of these genes show increased expression at early feeding time-points in the mid-gut of re-exposed ticks. The existence of clearly defined groups of genes with highly similar responses to re-exposure suggests the existence of molecular swiches. In silico functional analysis shows that these early feeding reexposure response genes form a dense interaction network at protein level being related to virtually all aspects of gene expression regulation and glycosylation. The processed data is available through an easy-to-use database-associated webpage (https://arn.ugr.es/IxoriDB/) that can serve as a valuable resource for tick research.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{teruel_integrative_2021,

title = {Integrative epigenomics in Sjögren´s syndrome reveals novel pathways and a strong interaction between the HLA, autoantibodies and the interferon signature},

author = {María Teruel and Guillermo Barturen and Manuel Martínez-Bueno and Olivia Castellini-Pérez and Miguel Barroso-Gil and Elena Povedano and Martin Kerick and Francesc Català-Moll and Zuzanna Makowska and Anne Buttgereit and PRECISESADS Clinical Consortium and PRECISESADS Flow Cytometry Study Group and Jacques-Olivier Pers and Concepción Marañón and Esteban Ballestar and Javier Martin and Elena Carnero-Montoro and Marta E. Alarcón-Riquelme},

doi = {10.1038/s41598-021-01324-0},

issn = {2045-2322},

year  = {2021},

date = {2021-12-01},

journal = {Scientific Reports},

volume = {11},

number = {1},

pages = {23292},

abstract = {Primary Sjögren's syndrome (SS) is a systemic autoimmune disease characterized by lymphocytic infiltration and damage of exocrine salivary and lacrimal glands. The etiology of SS is complex with environmental triggers and genetic factors involved. By conducting an integrated multi-omics study, we confirmed a vast coordinated hypomethylation and overexpression effects in IFN-related genes, what is known as the IFN signature. Stratified and conditional analyses suggest a strong interaction between SS-associated HLA genetic variation and the presence of Anti-Ro/SSA autoantibodies in driving the IFN epigenetic signature and determining SS. We report a novel epigenetic signature characterized by increased DNA methylation levels in a large number of genes enriched in pathways such as collagen metabolism and extracellular matrix organization. We identified potential new genetic variants associated with SS that might mediate their risk by altering DNA methylation or gene expression patterns, as well as disease-interacting genetic variants that exhibit regulatory function only in the SS population. Our study sheds new light on the interaction between genetics, autoantibody profiles, DNA methylation and gene expression in SS, and contributes to elucidate the genetic architecture of gene regulation in an autoimmune population.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{beckmann_downregulation_2021,

title = {Downregulation of exhausted cytotoxic T cells in gene expression networks of multisystem inflammatory syndrome in children},

author = {Noam D. Beckmann and Phillip H. Comella and Esther Cheng and Lauren Lepow and Aviva G. Beckmann and Scott R. Tyler and Konstantinos Mouskas and Nicole W. Simons and Gabriel E. Hoffman and Nancy J. Francoeur and Diane Marie Del Valle and Gurpawan Kang and Anh Do and Emily Moya and Lillian Wilkins and Jessica Le Berichel and Christie Chang and Robert Marvin and Sharlene Calorossi and Alona Lansky and Laura Walker and Nancy Yi and Alex Yu and Jonathan Chung and Matthew Hartnett and Melody Eaton and Sandra Hatem and Hajra Jamal and Alara Akyatan and Alexandra Tabachnikova and Lora E. Liharska and Liam Cotter and Brian Fennessy and Akhil Vaid and Guillermo Barturen and Hardik Shah and Ying-Chih Wang and Shwetha Hara Sridhar and Juan Soto and Swaroop Bose and Kent Madrid and Ethan Ellis and Elyze Merzier and Konstantinos Vlachos and Nataly Fishman and Manying Tin and Melissa Smith and Hui Xie and Manishkumar Patel and Kai Nie and Kimberly Argueta and Jocelyn Harris and Neha Karekar and Craig Batchelor and Jose Lacunza and Mahlet Yishak and Kevin Tuballes and Ieisha Scott and Arvind Kumar and Suraj Jaladanki and Charuta Agashe and Ryan Thompson and Evan Clark and Bojan Losic and Lauren Peters and Mount Sinai COVID-19 Biobank Team and Panagiotis Roussos and Jun Zhu and Wenhui Wang and Andrew Kasarskis and Benjamin S. Glicksberg and Girish Nadkarni and Dusan Bogunovic and Cordelia Elaiho and Sandeep Gangadharan and George Ofori-Amanfo and Kasey Alesso-Carra and Kenan Onel and Karen M. Wilson and Carmen Argmann and Supinda Bunyavanich and Marta E. Alarcón-Riquelme and Thomas U. Marron and Adeeb Rahman and Seunghee Kim-Schulze and Sacha Gnjatic and Bruce D. Gelb and Miriam Merad and Robert Sebra and Eric E. Schadt and Alexander W. Charney},

doi = {10.1038/s41467-021-24981-1},

issn = {2041-1723},

year  = {2021},

date = {2021-08-01},

journal = {Nature Communications},

volume = {12},

number = {1},

pages = {4854},

abstract = {Multisystem inflammatory syndrome in children (MIS-C) presents with fever, inflammation and pathology of multiple organs in individuals under 21 years of age in the weeks following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Although an autoimmune pathogenesis has been proposed, the genes, pathways and cell types causal to this new disease remain unknown. Here we perform RNA sequencing of blood from patients with MIS-C and controls to find disease-associated genes clustered in a co-expression module annotated to CD56dimCD57+ natural killer (NK) cells and exhausted CD8+ T cells. A similar transcriptome signature is replicated in an independent cohort of Kawasaki disease (KD), the related condition after which MIS-C was initially named. Probing a probabilistic causal network previously constructed from over 1,000 blood transcriptomes both validates the structure of this module and reveals nine key regulators, including TBX21, a central coordinator of exhausted CD8+ T cell differentiation. Together, this unbiased, transcriptome-wide survey implicates downregulation of NK cells and cytotoxic T cell exhaustion in the pathogenesis of MIS-C.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kerick_expression_2021,

title = {Expression Quantitative Trait Locus Analysis in Systemic Sclerosis Identifies New Candidate Genes Associated With Multiple Aspects of Disease Pathology},

author = {Martin Kerick and David González-Serna and Elena Carnero-Montoro and Maria Teruel and Marialbert Acosta-Herrera and Zuzanna Makowska and Anne Buttgereit and Sepideh Babaei and Guillermo Barturen and Elena López-Isac and PRECISESADS Clinical Consortium and Ralf Lesche and Lorenzo Beretta and Marta E. Alarcon-Riquelme and Javier Martin},

doi = {10.1002/art.41657},

issn = {2326-5205},

year  = {2021},

date = {2021-07-01},

journal = {Arthritis & Rheumatology},

volume = {73},

number = {7},

pages = {1288–1300},

address = {Hoboken, N.J.},

abstract = {OBJECTIVE: To identify the genetic variants that affect gene expression (expression quantitative trait loci [eQTLs]) in systemic sclerosis (SSc) and to investigate their role in the pathogenesis of the disease. 

METHODS: We performed an eQTL analysis using whole-blood sequencing data from 333 SSc patients and 524 controls and integrated them with SSc genome-wide association study (GWAS) data. We integrated our findings from expression modeling, differential expression analysis, and transcription factor binding site enrichment with key clinical features of SSc. 

RESULTS: We detected 49,123 validated cis-eQTLs from 4,539 SSc-associated single-nucleotide polymorphisms (SNPs) (PGWAS < 10-5 ). A total of 1,436 genes were within 1 Mb of the 4,539 SSc-associated SNPs. Of those 1,436 genes, 565 were detected as having ≥1 eQTL with an SSc-associated SNP. We developed a strategy to prioritize disease-associated genes based on their expression variance explained by SSc eQTLs (r2 > 0.05). As a result, 233 candidates were identified, 134 (58%) of them associated with hallmarks of SSc and 105 (45%) of them differentially expressed in the blood cells, skin, or lung tissue of SSc patients. Transcription factor binding site analysis revealed enriched motifs of 24 transcription factors (5%) among SSc eQTLs, 5 of which were found to be differentially regulated in the blood cells (ELF1 and MGA), skin (KLF4 and ID4), and lungs (TBX4) of SSc patients. Ten candidate genes (4%) can be targeted by approved medications for immune-mediated diseases, of which only 3 have been tested in clinical trials in patients with SSc. 

CONCLUSION: The findings of the present study indicate a new layer to the molecular complexity of SSc, contributing to a better understanding of the pathogenesis of the disease.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{drees_extracellular_2021,

title = {Extracellular vesicle miRNA predict FDG-PET status in patients with classical Hodgkin Lymphoma},

author = {Esther E. E. Drees and Margaretha G. M. Roemer and Nils J. Groenewegen and Jennifer Perez-Boza and Monique A. J. Eijndhoven and Leah I. Prins and Sandra A. W. M. Verkuijlen and Xuan-Mai Tran and Julia Driessen and G. J. C. Zwezerijnen and Phylicia Stathi and Kevin Mol and Joey J. J. P. Karregat and Aikaterini Kalantidou and Andrea Vallés-Martí and T. J. Molenaar and Ernesto Aparicio-Puerta and Erik Dijk and Bauke Ylstra and Catharina G. M. Groothuis-Oudshoorn and Michael Hackenberg and Daphne Jong and Josée M. Zijlstra and D. Michiel Pegtel},

doi = {10.1002/jev2.12121},

issn = {2001-3078},

year  = {2021},

date = {2021-07-01},

journal = {Journal of Extracellular Vesicles},

volume = {10},

number = {9},

pages = {e12121},

abstract = {Minimally-invasive tools to assess tumour presence and burden may improve clinical management. FDG-PET (metabolic) imaging is the current gold standard for interim response assessment in patients with classical Hodgkin Lymphoma (cHL), but this technique cannot be repeated frequently. Here we show that microRNAs (miRNA) associated with tumour-secreted extracellular vesicles (EVs) in the circulation of cHL patients may improve response assessment. Small RNA sequencing and qRT-PCR reveal that the relative abundance of cHL-expressed miRNAs, miR-127-3p, miR-155-5p, miR-21-5p, miR-24-3p and let-7a-5p is up to hundred-fold increased in plasma EVs of cHL patients pre-treatment when compared to complete metabolic responders (CMR). Notably, in partial responders (PR) or treatment-refractory cases (n = 10) the EV-miRNA levels remain elevated. In comparison, tumour specific copy number variations (CNV) were detected in cell-free DNA of 8 out of 10 newly diagnosed cHL patients but not in patients with PR. Combining EV-miR-127-3p and/or EV-let-7a-5p levels, with serum TARC (a validated protein cHL biomarker), increases the accuracy for predicting PET-status (n = 129) to an area under the curve of 0.93 (CI: 0.87-0.99), 93.5% sensitivity, 83.8/85.0% specificity and a negative predictive value of 96%. Thus the level of tumour-associated miRNAs in plasma EVs is predictive of metabolic tumour activity in cHL patients. Our findings suggest that plasma EV-miRNA are useful for detection of small residual lesions and may be applied as serial response prediction tool.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{barturen_integrative_2021,

title = {Integrative Analysis Reveals a Molecular Stratification of Systemic Autoimmune Diseases},

author = {Guillermo Barturen and Sepideh Babaei and Francesc Català-Moll and Manuel Martínez-Bueno and Zuzanna Makowska and Jordi Martorell-Marugán and Pedro Carmona-Sáez and Daniel Toro-Domínguez and Elena Carnero-Montoro and María Teruel and Martin Kerick and Marialbert Acosta-Herrera and Lucas Le Lann and Christophe Jamin and Javier Rodríguez-Ubreva and Antonio García-Gómez and Jorge Kageyama and Anne Buttgereit and Sikander Hayat and Joerg Mueller and Ralf Lesche and Maria Hernandez-Fuentes and Maria Juarez and Tania Rowley and Ian White and Concepción Marañón and Tania Gomes Anjos and Nieves Varela and Rocío Aguilar-Quesada and Francisco Javier Garrancho and Antonio López-Berrio and Manuel Rodriguez Maresca and Héctor Navarro-Linares and Isabel Almeida and Nancy Azevedo and Mariana Brandão and Ana Campar and Raquel Faria and Fátima Farinha and António Marinho and Esmeralda Neves and Ana Tavares and Carlos Vasconcelos and Elena Trombetta and Gaia Montanelli and Barbara Vigone and Damiana Alvarez-Errico and Tianlu Li and Divya Thiagaran and Ricardo Blanco Alonso and Alfonso Corrales Martínez and Fernanda Genre and Raquel López Mejías and Miguel A. Gonzalez-Gay and Sara Remuzgo and Begoña Ubilla Garcia and Ricard Cervera and Gerard Espinosa and Ignasi Rodríguez-Pintó and Ellen De Langhe and Jonathan Cremer and Rik Lories and Doreen Belz and Nicolas Hunzelmann and Niklas Baerlecken and Katja Kniesch and Torsten Witte and Michaela Lehner and Georg Stummvoll and Michael Zauner and Maria Angeles Aguirre-Zamorano and Nuria Barbarroja and Maria Carmen Castro-Villegas and Eduardo Collantes-Estevez and Enrique Ramon and Isabel Díaz Quintero and Alejandro Escudero-Contreras and María Concepción Fernández Roldán and Yolanda Jiménez Gómez and Inmaculada Jiménez Moleón and Rosario Lopez-Pedrera and Rafaela Ortega-Castro and Norberto Ortego and Enrique Raya and Carolina Artusi and Maria Gerosa and Pier Luigi Meroni and Tommaso Schioppo and Aurélie De Groof and Julie Ducreux and Bernard Lauwerys and Anne-Lise Maudoux and Divi Cornec and Valérie Devauchelle-Pensec and Sandrine Jousse-Joulin and Pierre-Emmanuel Jouve and Bénédicte Rouvière and Alain Saraux and Quentin Simon and Montserrat Alvarez and Carlo Chizzolini and Aleksandra Dufour and Donatienne Wynar and Attila Balog and Márta Bocskai and Magdolna Deák and Sonja Dulic and Gabriella Kádár and László Kovács and Qingyu Cheng and Velia Gerl and Falk Hiepe and Laleh Khodadadi and Silvia Thiel and Emanuele Rinaldis and Sambasiva Rao and Robert J. Benschop and Chris Chamberlain and Ernst R. Dow and Yiannis Ioannou and Laurence Laigle and Jacqueline Marovac and Jerome Wojcik and Yves Renaudineau and Maria Orietta Borghi and Johan Frostegård and Javier Martín and Lorenzo Beretta and Esteban Ballestar and Fiona McDonald and Jacques-Olivier Pers and Marta E. Alarcón-Riquelme},

doi = {10.1002/art.41610},

issn = {2326-5205},

year  = {2021},

date = {2021-06-01},

journal = {Arthritis & Rheumatology},

volume = {73},

number = {6},

pages = {1073–1085},

address = {Hoboken, N.J.},

abstract = {OBJECTIVE: Clinical heterogeneity, a hallmark of systemic autoimmune diseases, impedes early diagnosis and effective treatment, issues that may be addressed if patients could be classified into groups defined by molecular pattern. This study was undertaken to identify molecular clusters for reclassifying systemic autoimmune diseases independently of clinical diagnosis. 

METHODS: Unsupervised clustering of integrated whole blood transcriptome and methylome cross-sectional data on 955 patients with 7 systemic autoimmune diseases and 267 healthy controls was undertaken. In addition, an inception cohort was prospectively followed up for 6 or 14 months to validate the results and analyze whether or not cluster assignment changed over time. 

RESULTS: Four clusters were identified and validated. Three were pathologic, representing "inflammatory," "lymphoid," and "interferon" patterns. Each included all diagnoses and was defined by genetic, clinical, serologic, and cellular features. A fourth cluster with no specific molecular pattern was associated with low disease activity and included healthy controls. A longitudinal and independent inception cohort showed a relapse-remission pattern, where patients remained in their pathologic cluster, moving only to the healthy one, thus showing that the molecular clusters remained stable over time and that single pathogenic molecular signatures characterized each individual patient. 

CONCLUSION: Patients with systemic autoimmune diseases can be jointly stratified into 3 stable disease clusters with specific molecular patterns differentiating different molecular disease mechanisms. These results have important implications for future clinical trials and the study of nonresponse to therapy, marking a paradigm shift in our view of systemic autoimmune diseases.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{soret_new_2021,

title = {A new molecular classification to drive precision treatment strategies in primary Sjögren's syndrome},

author = {Perrine Soret and Christelle Le Dantec and Emiko Desvaux and Nathan Foulquier and Bastien Chassagnol and Sandra Hubert and Christophe Jamin and Guillermo Barturen and Guillaume Desachy and Valérie Devauchelle-Pensec and Cheïma Boudjeniba and Divi Cornec and Alain Saraux and Sandrine Jousse-Joulin and Nuria Barbarroja and Ignasi Rodríguez-Pintó and Ellen De Langhe and Lorenzo Beretta and Carlo Chizzolini and László Kovács and Torsten Witte and PRECISESADS Clinical Consortium and PRECISESADS Flow Cytometry Consortium and Eléonore Bettacchioli and Anne Buttgereit and Zuzanna Makowska and Ralf Lesche and Maria Orietta Borghi and Javier Martin and Sophie Courtade-Gaiani and Laura Xuereb and Mickaël Guedj and Philippe Moingeon and Marta E. Alarcón-Riquelme and Laurence Laigle and Jacques-Olivier Pers},

doi = {10.1038/s41467-021-23472-7},

issn = {2041-1723},

year  = {2021},

date = {2021-06-01},

journal = {Nature Communications},

volume = {12},

number = {1},

pages = {3523},

abstract = {There is currently no approved treatment for primary Sjögren's syndrome, a disease that primarily affects adult women. The difficulty in developing effective therapies is -in part- because of the heterogeneity in the clinical manifestation and pathophysiology of the disease. Finding common molecular signatures among patient subgroups could improve our understanding of disease etiology, and facilitate the development of targeted therapeutics. Here, we report, in a cross-sectional cohort, a molecular classification scheme for Sjögren's syndrome patients based on the multi-omic profiling of whole blood samples from a European cohort of over 300 patients, and a similar number of age and gender-matched healthy volunteers. Using transcriptomic, genomic, epigenetic, cytokine expression and flow cytometry data, combined with clinical parameters, we identify four groups of patients with distinct patterns of immune dysregulation. The biomarkers we identify can be used by machine learning classifiers to sort future patients into subgroups, allowing the re-evaluation of response to treatments in clinical trials.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{martorell-marugan_comprehensive_2021,

title = {A comprehensive database for integrated analysis of omics data in autoimmune diseases},

author = {Jordi Martorell-Marugán and Raúl López-Domínguez and Adrián García-Moreno and Daniel Toro-Domínguez and Juan Antonio Villatoro-García and Guillermo Barturen and Adoración Martín-Gómez and Kevin Troule and Gonzalo Gómez-López and Fátima Al-Shahrour and Víctor González-Rumayor and María Peña-Chilet and Joaquín Dopazo and Julio Sáez-Rodríguez and Marta E. Alarcón-Riquelme and Pedro Carmona-Sáez},

doi = {10.1186/s12859-021-04268-4},

issn = {1471-2105},

year  = {2021},

date = {2021-06-01},

journal = {BMC bioinformatics},

volume = {22},

number = {1},

pages = {343},

abstract = {BACKGROUND: Autoimmune diseases are heterogeneous pathologies with difficult diagnosis and few therapeutic options. In the last decade, several omics studies have provided significant insights into the molecular mechanisms of these diseases. Nevertheless, data from different cohorts and pathologies are stored independently in public repositories and a unified resource is imperative to assist researchers in this field. 

RESULTS: Here, we present Autoimmune Diseases Explorer ( https://adex.genyo.es ), a database that integrates 82 curated transcriptomics and methylation studies covering 5609 samples for some of the most common autoimmune diseases. The database provides, in an easy-to-use environment, advanced data analysis and statistical methods for exploring omics datasets, including meta-analysis, differential expression or pathway analysis. 

CONCLUSIONS: This is the first omics database focused on autoimmune diseases. This resource incorporates homogeneously processed data to facilitate integrative analyses among studies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gomez-martin_geno5mc_2021,

title = {geno5mC: A Database to Explore the Association between Genetic Variation (SNPs) and CpG Methylation in the Human Genome},

author = {C. Gómez-Martín and E. Aparicio-Puerta and J. M. Medina and Guillermo Barturen and J. L. Oliver and M. Hackenberg},

doi = {10.1016/j.jmb.2020.11.008},

issn = {1089-8638},

year  = {2021},

date = {2021-05-01},

journal = {Journal of Molecular Biology},

volume = {433},

number = {11},

pages = {166709},

abstract = {Genetic variation, gene expression and DNA methylation influence each other in a complex way. To study the impact of sequence variation and DNA methylation on gene expression, we generated geno5mC, a database that contains statistically significant SNP-CpG associations that are biologically classified either through co-localization with known regulatory regions (promoters and enhancers), or through known correlations with the expression levels of nearby genes. The SNP rs727563 can be used to illustrate the usefulness of this approach. This SNP has been associated with inflammatory bowel disease through GWAS, but it is not located near any gene related to this phenotype. However, geno5mC reveals that rs727563 is associated with the methylation state of several CpGs located in promoter regions of genes reported to be involved in inflammatory processes. This case exemplifies how geno5mC can be used to infer relevant and previously unknown interactions between described disease-associated SNPs and their functional targets.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bettacchioli_elevated_2021,

title = {An elevated polyclonal free light chain level reflects a strong interferon signature in patients with systemic autoimmune diseases},

author = {Eléonore Bettacchioli and Christelle Le Gaffric and Margaux Mazeas and Maria Orietta Borghi and Johan Frostegard and Guillermo Barturen and Zuzanna Makowska and Sepideh Babei and Ralf Lesche and PRECISESADS Clinical Consortium and Pier Luigi Meroni and Marta E. Alarcon-Riquelme and Yves Renaudineau},

doi = {10.1016/j.jtauto.2021.100090},

issn = {2589-9090},

year  = {2021},

date = {2021-01-01},

journal = {Journal of Translational Autoimmunity},

volume = {4},

pages = {100090},

abstract = {High amount of polyclonal free light chains (FLC) are reported in systemic autoimmune diseases (SAD) and we took advantage of the PRECISESADS study to better characterize them. Serum FLC levels were explored in 1979 patients with SAD (RA, SLE, SjS, Scl, APS, UCTD, MCTD) and 614 healthy controls. Information regarding clinical parameters, disease activity, medications, autoantibodies (Ab) and the interferon α and/or γ scores were recorded. Among SAD patients, 28.4% had raised total FLC (from 12% in RA to 30% in SLE and APS) with a normal kappa/lambda ratio. Total FLC levels were significantly higher in SAD with inflammation, active disease in SLE and SjS, and an impaired pulmonary functional capacity in SSc, while independent from kidney impairment, infection, cancer and treatment. Total FLC concentrations were positively correlated among the 10/17 (58.8%) autoantibodies (Ab) tested with anti-RNA binding protein Ab (SSB, SSA-52/60 kDa, Sm, U1-RNP), anti-dsDNA/nucleosome Ab, rheumatoid factor and negatively correlated with complement fractions C3/C4. Finally, examination of interferon (IFN) expression as a potential driver of FLC overexpression was tested showing an elevated level of total FLC among patients with a high IFNα and IFNγ Kirou's score, a strong IFN modular score, and the detection in the sera of B-cell IFN dependent factors, such as TNF-R1/TNFRSF1A and CXCL10/IP10. In conclusion, an elevated level of FLC, in association with a strong IFN signature, defines a subgroup of SAD patients, including those without renal affectation, characterized by increased disease activity, autoreactivity, and complement reduction.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{aparicio-puerta_silico_2021,

title = {In Silico Analysis of Micro-RNA Sequencing Data},

author = {Ernesto Aparicio-Puerta and Bastian Fromm and Michael Hackenberg and Marc K. Halushka},

doi = {10.1007/978-1-0716-1307-8_13},

issn = {1940-6029},

year  = {2021},

date = {2021-01-01},

journal = {Methods in Molecular Biology},

volume = {2284},

pages = {231–251},

address = {Clifton, N.J.},

abstract = {High-throughput sequencing for micro-RNAs (miRNAs) to obtain expression estimates is a central method of molecular biology. Surprisingly, there are a number of different approaches to converting sequencing output into micro-RNA counts. Each has their own strengths and biases that impact on the final data that can be obtained from a sequencing run. This chapter serves to make the reader aware of the trade-offs one must consider in analyzing small RNA sequencing data. It then compares two methods, miRge2.0 and the sRNAbench and the steps utilized to output data from their tools.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{moya_driven_2020,

title = {Driven progressive evolution of genome sequence complexity in Cyanobacteria},

author = {Andrés Moya and José L. Oliver and Miguel Verdú and Luis Delaye and Vicente Arnau and Pedro Bernaola-Galván and Rebeca Fuente and Wladimiro Díaz and Cristina Gómez-Martín and Francisco M. González and Amparo Latorre and Ricardo Lebrón and Ramón Román-Roldán},

doi = {10.1038/s41598-020-76014-4},

issn = {2045-2322},

year  = {2020},

date = {2020-11-01},

journal = {Scientific Reports},

volume = {10},

number = {1},

pages = {19073},

abstract = {Progressive evolution, or the tendency towards increasing complexity, is a controversial issue in biology, which resolution entails a proper measurement of complexity. Genomes are the best entities to address this challenge, as they encode the historical information of a species' biotic and environmental interactions. As a case study, we have measured genome sequence complexity in the ancient phylum Cyanobacteria. To arrive at an appropriate measure of genome sequence complexity, we have chosen metrics that do not decipher biological functionality but that show strong phylogenetic signal. Using a ridge regression of those metrics against root-to-tip distance, we detected positive trends towards higher complexity in three of them. Lastly, we applied three standard tests to detect if progressive evolution is passive or driven-the minimum, ancestor-descendant, and sub-clade tests. These results provide evidence for driven progressive evolution at the genome-level in the phylum Cyanobacteria.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bensaoud_emerging_2020,

title = {Emerging roles of non-coding RNAs in vector-borne infections},

author = {Chaima Bensaoud and Larissa Almeida Martins and Hajer Aounallah and Michael Hackenberg and Michail Kotsyfakis},

doi = {10.1242/jcs.246744},

issn = {1477-9137},

year  = {2020},

date = {2020-11-01},

journal = {Journal of Cell Science},

volume = {134},

number = {5},

pages = {jcs246744},

abstract = {Non-coding RNAs (ncRNAs) are nucleotide sequences that are known to assume regulatory roles previously thought to be reserved for proteins. Their functions include the regulation of protein activity and localization and the organization of subcellular structures. Sequencing studies have now identified thousands of ncRNAs encoded within the prokaryotic and eukaryotic genomes, leading to advances in several fields including parasitology. ncRNAs play major roles in several aspects of vector-host-pathogen interactions. Arthropod vector ncRNAs are secreted through extracellular vesicles into vertebrate hosts to counteract host defense systems and ensure arthropod survival. Conversely, hosts can use specific ncRNAs as one of several strategies to overcome arthropod vector invasion. In addition, pathogens transmitted through vector saliva into vertebrate hosts also possess ncRNAs thought to contribute to their pathogenicity. Recent studies have addressed ncRNAs in vectors or vertebrate hosts, with relatively few studies investigating the role of ncRNAs derived from pathogens and their involvement in establishing infections, especially in the context of vector-borne diseases. This Review summarizes recent data focusing on pathogen-derived ncRNAs and their role in modulating the cellular responses that favor pathogen survival in the vertebrate host and the arthropod vector, as well as host ncRNAs that interact with vector-borne pathogens.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{beretta_genome-wide_2020,

title = {Genome-wide whole blood transcriptome profiling in a large European cohort of systemic sclerosis patients},

author = {Lorenzo Beretta and Guillermo Barturen and Barbara Vigone and Chiara Bellocchi and Nicolas Hunzelmann and Ellen De Langhe and Ricard Cervera and Maria Gerosa and László Kovács and Rafaela Ortega Castro and Isabel Almeida and Divi Cornec and Carlo Chizzolini and Jacques-Olivier Pers and Zuzanna Makowska and Ralf Lesche and Martin Kerick and Marta Eugenia Alarcón-Riquelme and Javier Martin and PRECISESADS SSc group and PRECISESADS Flow Cytometry group},

doi = {10.1136/annrheumdis-2020-217116},

issn = {1468-2060},

year  = {2020},

date = {2020-09-01},

journal = {Annals of the Rheumatic Diseases},

volume = {79},

number = {9},

pages = {1218–1226},

abstract = {OBJECTIVES: The analysis of annotated transcripts from genome-wide expression studies may help to understand the pathogenesis of complex diseases, such as systemic sclerosis (SSc). We performed a whole blood (WB) transcriptome analysis on RNA collected in the context of the European PRECISESADS project, aiming at characterising the pathways that differentiate SSc from controls and that are reproducible in geographically diverse populations. METHODS: Samples from 162 patients and 252 controls were collected in RNA stabilisers. Cases and controls were divided into a discovery (n=79+163; Southern Europe) and validation cohort (n=83+89; Central-Western Europe). RNA sequencing was performed by an Illumina assay. Functional annotations of Reactome pathways were performed with the Functional Analysis of Individual Microarray Expression (FAIME) algorithm. In parallel, immunophenotyping of 28 circulating cell populations was performed. We tested the presence of differentially expressed genes/pathways and the correlation between absolute cell counts and RNA transcripts/FAIME scores in regression models. Results significant in both populations were considered as replicated. 

RESULTS: Overall, 15 224 genes and 1277 functional pathways were available; of these, 99 and 225 were significant in both sets. Among replicated pathways, we found a deregulation in type-I interferon, Toll-like receptor cascade, tumour suppressor p53 protein function, platelet degranulation and activation. RNA transcripts or FAIME scores were jointly correlated with cell subtypes with strong geographical differences; neutrophils were the major determinant of gene expression in SSc-WB samples. 

CONCLUSIONS: We discovered a set of differentially expressed genes/pathways validated in two independent sets of patients with SSc, highlighting a number of deregulated processes that have relevance for the pathogenesis of autoimmunity and SSc.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{aparicio-puerta_mirnaqc_2020,

title = {mirnaQC: a webserver for comparative quality control of miRNA-seq data},

author = {Ernesto Aparicio-Puerta and Cristina Gómez-Martín and Stavros Giannoukakos and José María Medina and Juan Antonio Marchal and Michael Hackenberg},

doi = {10.1093/nar/gkaa452},

issn = {1362-4962},

year  = {2020},

date = {2020-07-01},

journal = {Nucleic Acids Research},

volume = {48},

number = {W1},

pages = {W262–W267},

abstract = {Although miRNA-seq is extensively used in many different fields, its quality control is frequently restricted to a PhredScore-based filter. Other important quality related aspects like microRNA yield, the fraction of putative degradation products (such as rRNA fragments) or the percentage of adapter-dimers are hard to assess using absolute thresholds. Here we present mirnaQC, a webserver that relies on 34 quality parameters to assist in miRNA-seq quality control. To improve their interpretability, quality attributes are ranked using a reference distribution obtained from over 36 000 publicly available miRNA-seq datasets. Accepted input formats include FASTQ and SRA accessions. The results page contains several sections that deal with putative technical artefacts related to library preparation, sequencing, contamination or yield. Different visualisations, including PCA and heatmaps, are available to help users identify underlying issues. Finally, we show the usefulness of this approach by analysing two publicly available datasets and discussing the different quality issues that can be detected using mirnaQC.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gomez-martin_transcriptional_2020,

title = {Transcriptional Dynamics and Candidate Genes Involved in Pod Maturation of Common Bean (Phaseolus vulgaris L.)},

author = {Cristina Gómez-Martín and Carmen Capel and Ana M. González and Ricardo Lebrón and Fernando J. Yuste-Lisbona and Michael Hackenberg and José L. Oliver and Marta Santalla and Rafael Lozano},

doi = {10.3390/plants9040545},

issn = {2223-7747},

year  = {2020},

date = {2020-04-01},

journal = {Plants},

volume = {9},

number = {4},

pages = {545},

address = {Basel, Switzerland},

abstract = {Pod maturation of common bean relies upon complex gene expression changes, which in turn are crucial for seed formation and dispersal. Hence, dissecting the transcriptional regulation of pod maturation would be of great significance for breeding programs. In this study, a comprehensive characterization of expression changes has been performed in two common bean cultivars (ancient and modern) by analyzing the transcriptomes of five developmental pod stages, from fruit setting to maturation. RNA-seq analysis allowed for the identification of key genes shared by both accessions, which in turn were homologous to known Arabidopsis maturation genes and furthermore showed a similar expression pattern along the maturation process. Gene- expression changes suggested a role in promoting an accelerated breakdown of photosynthetic and ribosomal machinery associated with chlorophyll degradation and early activation of alpha-linolenic acid metabolism. A further study of transcription factors and their DNA binding sites revealed three candidate genes whose functions may play a dominant role in regulating pod maturation. Altogether, this research identifies the first maturation gene set reported in common bean so far and contributes to a better understanding of the dynamic mechanisms of pod maturation, providing potentially useful information for genomic-assisted breeding of common bean yield and pod quality attributes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{desvignes_unification_2020,

title = {Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API},

author = {Thomas Desvignes and Phillipe Loher and Karen Eilbeck and Jeffery Ma and Gianvito Urgese and Bastian Fromm and Jason Sydes and Ernesto Aparicio-Puerta and Victor Barrera and Roderic Espín and Florian Thibord and Xavier Bofill-De Ros and Eric Londin and Aristeidis G. Telonis and Elisa Ficarra and Marc R. Friedländer and John H. Postlethwait and Isidore Rigoutsos and Michael Hackenberg and Ioannis S. Vlachos and Marc K. Halushka and Lorena Pantano},

doi = {10.1093/bioinformatics/btz675},

issn = {1367-4811},

year  = {2020},

date = {2020-02-01},

journal = {Bioinformatics},

volume = {36},

number = {3},

pages = {698–703},

address = {Oxford, England},

abstract = {MOTIVATION: MicroRNAs (miRNAs) are small RNA molecules (∼22 nucleotide long) involved in post-transcriptional gene regulation. Advances in high-throughput sequencing technologies led to the discovery of isomiRs, which are miRNA sequence variants. While many miRNA-seq analysis tools exist, the diversity of output formats hinders accurate comparisons between tools and precludes data sharing and the development of common downstream analysis methods. 

RESULTS: To overcome this situation, we present here a community-based project, miRNA Transcriptomic Open Project (miRTOP) working towards the optimization of miRNA analyses. The aim of miRTOP is to promote the development of downstream isomiR analysis tools that are compatible with existing detection and quantification tools. Based on the existing GFF3 format, we first created a new standard format, mirGFF3, for the output of miRNA/isomiR detection and quantification results from small RNA-seq data. Additionally, we developed a command line Python tool, mirtop, to create and manage the mirGFF3 format. Currently, mirtop can convert into mirGFF3 the outputs of commonly used pipelines, such as seqbuster, isomiR-SEA, sRNAbench, Prost! as well as BAM files. Some tools have also incorporated the mirGFF3 format directly into their code, such as, miRge2.0, IsoMIRmap and OptimiR. Its open architecture enables any tool or pipeline to output or convert results into mirGFF3. Collectively, this isomiR categorization system, along with the accompanying mirGFF3 and mirtop API, provide a comprehensive solution for the standardization of miRNA and isomiR annotation, enabling data sharing, reporting, comparative analyses and benchmarking, while promoting the development of common miRNA methods focusing on downstream steps of miRNA detection, annotation and quantification. 

AVAILABILITY AND IMPLEMENTATION: https://github.com/miRTop/mirGFF3/ and https://github.com/miRTop/mirtop. 

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fromm_mirgenedb_2020,

title = {MirGeneDB 2.0: the metazoan microRNA complement},

author = {Bastian Fromm and Diana Domanska and Eirik Høye and Vladimir Ovchinnikov and Wenjing Kang and Ernesto Aparicio-Puerta and Morten Johansen and Kjersti Flatmark and Anthony Mathelier and Eivind Hovig and Michael Hackenberg and Marc R. Friedländer and Kevin J. Peterson},

doi = {10.1093/nar/gkz885},

issn = {1362-4962},

year  = {2020},

date = {2020-01-01},

journal = {Nucleic Acids Research},

volume = {48},

number = {D1},

pages = {D132–D141},

abstract = {Small non-coding RNAs have gained substantial attention due to their roles in animal development and human disorders. Among them, microRNAs are special because individual gene sequences are conserved across the animal kingdom. In addition, unique and mechanistically well understood features can clearly distinguish bona fide miRNAs from the myriad other small RNAs generated by cells. However, making this distinction is not a common practice and, thus, not surprisingly, the heterogeneous quality of available miRNA complements has become a major concern in microRNA research. We addressed this by extensively expanding our curated microRNA gene database - MirGeneDB - to 45 organisms, encompassing a wide phylogenetic swath of animal evolution. By consistently annotating and naming 10,899 microRNA genes in these organisms, we show that previous microRNA annotations contained not only many false positives, but surprisingly lacked >2000 bona fide microRNAs. Indeed, curated microRNA complements of closely related organisms are very similar and can be used to reconstruct ancestral miRNA repertoires. MirGeneDB represents a robust platform for microRNA-based research, providing deeper and more significant insights into the biology and evolution of miRNAs as well as biomedical and biomarker research. MirGeneDB is publicly and freely available at http://mirgenedb.org/.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bensaoud_noncoding_2019,

title = {Noncoding RNAs in Parasite-Vector-Host Interactions},

author = {Chaima Bensaoud and Michael Hackenberg and Michail Kotsyfakis},

doi = {10.1016/j.pt.2019.06.012},

issn = {1471-5007},

year  = {2019},

date = {2019-09-01},

journal = {Trends in Parasitology},

volume = {35},

number = {9},

pages = {715–724},

abstract = {Systems biology approaches, especially in the big data era, have revolutionized modern parasitology. Of the many different molecules participating in parasite-host interactions, noncoding RNAs (ncRNAs) are now known to be (i) transmitted by the vector to possibly modulate vertebrate host responses and favor vector survival and (ii) regulated in the host by parasites to favor parasite survival. Here we provide an overview of the involvement of ncRNAs in the parasite-vector-host triad and their effect on host homeostasis based on recent advances and accumulating knowledge about the role of endogenous vertebrate noncoding RNAs in vertebrate host physiology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{aparicio-puerta_srnabench_2019,

title = {sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression},

author = {Ernesto Aparicio-Puerta and Ricardo Lebrón and Antonio Rueda and Cristina Gómez-Martín and Stavros Giannoukakos and David Jaspez and José María Medina and Andreja Zubkovic and Igor Jurak and Bastian Fromm and Juan Antonio Marchal and José Oliver and Michael Hackenberg},

doi = {10.1093/nar/gkz415},

issn = {1362-4962},

year  = {2019},

date = {2019-07-01},

journal = {Nucleic Acids Research},

volume = {47},

number = {W1},

pages = {W530–W535},

abstract = {Since the original publication of sRNAtoolbox in 2015, small RNA research experienced notable advances in different directions. New protocols for small RNA sequencing have become available to address important issues such as adapter ligation bias, PCR amplification artefacts or to include internal controls such as spike-in sequences. New microRNA reference databases were developed with different foci, either prioritizing accuracy (low number of false positives) or completeness (low number of false negatives). Additionally, other small RNA molecules as well as microRNA sequence and length variants (isomiRs) have continued to gain importance. Finally, the number of microRNA sequencing studies deposited in GEO nearly triplicated from 2014 (280) to 2018 (764). These developments imply that fast and easy-to-use tools for expression profiling and subsequent downstream analysis of miRNA-seq data are essential to many researchers. Key features in this sRNAtoolbox release include addition of all major RNA library preparation protocols to sRNAbench and improvements in sRNAde, a tool that summarizes several aspects of small RNA sequencing studies including the detection of consensus differential expression. A special emphasis was put on the user-friendliness of the tools, for instance sRNAbench now supports parallel launching of several jobs to improve reproducibility and user time efficiency.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{requena_nomeplot_2019,

title = {NOMePlot: analysis of DNA methylation and nucleosome occupancy at the single molecule},

author = {Francisco Requena and Helena G. Asenjo and Guillermo Barturen and Jordi Martorell-Marugán and Pedro Carmona-Sáez and David Landeira},

doi = {10.1038/s41598-019-44597-2},

issn = {2045-2322},

year  = {2019},

date = {2019-05-01},

journal = {Scientific Reports},

volume = {9},

number = {1},

pages = {8140},

abstract = {Recent technical advances highlight that to understand mammalian development and human disease we need to consider transcriptional and epigenetic cell-to-cell differences within cell populations. This is particularly important in key areas of biomedicine like stem cell differentiation and intratumor heterogeneity. The recently developed nucleosome occupancy and methylome (NOMe) assay facilitates the simultaneous study of DNA methylation and nucleosome positioning on the same DNA strand. NOMe-treated DNA can be sequenced by sanger (NOMe-PCR) or high throughput approaches (NOMe-seq). NOMe-PCR provides information for a single locus at the single molecule while NOMe-seq delivers genome-wide data that is usually interrogated to obtain population-averaged measures. Here, we have developed a bioinformatic tool that allow us to easily obtain locus-specific information at the single molecule using genome-wide NOMe-seq datasets obtained from bulk populations. We have used NOMePlot to study mouse embryonic stem cells and found that polycomb-repressed bivalent gene promoters coexist in two different epigenetic states, as defined by the nucleosome binding pattern detected around their transcriptional start site.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{aparicio-puerta_liqdb_2019,

title = {liqDB: a small-RNAseq knowledge discovery database for liquid biopsy studies},

author = {Ernesto Aparicio-Puerta and David Jáspez and Ricardo Lebrón and Danijela Koppers-Lalic and Juan A. Marchal and Michael Hackenberg},

doi = {10.1093/nar/gky981},

issn = {1362-4962},

year  = {2019},

date = {2019-01-01},

journal = {Nucleic Acids Research},

volume = {47},

number = {D1},

pages = {D113–D120},

abstract = {MiRNAs are important regulators of gene expression and are frequently deregulated under pathologic conditions. They are highly stable in bodily fluids which makes them feasible candidates to become minimally invasive biomarkers. In fact, several studies already proposed circulating miRNA-based biomarkers for different types of neoplastic, cardiovascular and degenerative diseases. However, many of these studies rely on small RNA sequencing experiments that are based on different RNA extraction and processing protocols, rendering results incomparable. We generated liqDB, a database for liquid biopsy small RNA sequencing profiles that provides users with meaningful information to guide their small RNA liquid biopsy research and to overcome technical and conceptual problems. By means of a user-friendly web interface, miRNA expression profiles from 1607 manually annotated samples can be queried and explored at different levels. Result pages include downloadable expression matrices, differential expression analysis, most stably expressed miRNAs, cluster analysis and relevant visualizations by means of boxplots and heatmaps. We anticipate that liqDB will be a useful tool in liquid biopsy research as it provides a consistently annotated large compilation of experiments together with tools for reproducible analysis, comparison and hypothesis generation. LiqDB is available at http://bioinfo5.ugr.es/liqdb.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carnero-montoro_epigenome-wide_2019,

title = {Epigenome-Wide Comparative Study Reveals Key Differences Between Mixed Connective Tissue Disease and Related Systemic Autoimmune Diseases},

author = {Elena Carnero-Montoro and Guillermo Barturen and Elena Povedano and Martin Kerick and Manuel Martinez-Bueno and PRECISESADS Clinical Consortium and Esteban Ballestar and Javier Martin and María Teruel and Marta E. Alarcón-Riquelme},

doi = {10.3389/fimmu.2019.01880},

issn = {1664-3224},

year  = {2019},

date = {2019-01-01},

journal = {Frontiers in Immunology},

volume = {10},

pages = {1880},

abstract = {Mixed Connective Tissue Disease (MCTD) is a rare complex systemic autoimmune disease (SAD) characterized by the presence of increased levels of anti-U1 ribonucleoprotein autoantibodies and signs and symptoms that resemble other SADs such as systemic sclerosis (SSc), rheumatoid arthritis (RA), and systemic lupus erythematosus (SLE). Due to its low prevalence, this disease has been very poorly studied at the molecular level. We performed for the first time an epigenome-wide association study interrogating DNA methylation data obtained with the Infinium MethylationEPIC array from whole blood samples in 31 patients diagnosed with MCTD and 255 healthy subjects. We observed a pervasive hypomethylation involving 170 genes enriched for immune-related function such as those involved in type I interferon signaling pathways or in negative regulation of viral genome replication. We mostly identified epigenetic signals at genes previously implicated in other SADs, for example MX1, PARP9, DDX60, or IFI44L, for which we also observed that MCTD patients exhibit higher DNA methylation variability compared with controls, suggesting that these sites might be involved in plastic immune responses that are relevant to the disease. Through methylation quantitative trait locus (meQTL) analysis we identified widespread local genetic effects influencing DNA methylation variability at MCTD-associated sites. Interestingly, for IRF7, IFI44 genes, and the HLA region we have evidence that they could be exerting a genetic risk on MCTD mediated through DNA methylation changes. Comparison of MCTD-associated epigenome with patients diagnosed with SLE, or Sjögren's Syndrome, reveals a common interferon-related epigenetic signature, however we find substantial epigenetic differences when compared with patients diagnosed with rheumatoid arthritis and systemic sclerosis. Furthermore, we show that MCTD-associated CpGs are potential epigenetic biomarkers with high diagnostic value. Our study serves to reveal new genes and pathways involved in MCTD, to illustrate the important role of epigenetic modifications in MCTD pathology, in mediating the interaction between different genetic and environmental MCTD risk factors, and as potential biomarkers of SADs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cokaric_brdovcak_herpes_2018,

title = {Herpes simplex virus 1 miRNA sequence variations in latently infected human trigeminal ganglia},

author = {Maja Cokarić Brdovčak and Andreja Zubković and Antun Ferenčić and Ivan Šoša and Valter Stemberga and Dražen Cuculić and Filip Rokić and Oliver Vugrek and Michael Hackenberg and Igor Jurak},

doi = {10.1016/j.virusres.2018.08.002},

issn = {1872-7492},

year  = {2018},

date = {2018-09-01},

journal = {Virus Research},

volume = {256},

pages = {90–95},

abstract = {Human herpes simplex virus 1 (HSV-1) expresses numerous miRNAs, the function of which is not well understood. Several qualitative and quantitative analyses of HSV-1 miRNAs have been performed on infected cells in culture and animal models, however, there is very limited knowledge of their expression in human samples. We sequenced small-RNA libraries of RNA derived from human trigeminal ganglia latently infected with HSV-1 and Varicella zoster virus (VZV) and detected only a small subset of HSV-1 miRNA. The most abundantly expressed miRNAs are miR-H2, miRNA that regulates the expression of immediate early gene ICP0, and miR-H3 and -H4, both miRNAs expressed antisense to the transcript encoding the major neurovirulence factor ICP34.5. The sequence of many HSV-1 miRNAs detected in human samples was different from the sequences deposited in miRBase, which might significantly affect targeted functional analyses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{jimenez_mesenchymal_2018,

title = {Mesenchymal stem cell's secretome promotes selective enrichment of cancer stem-like cells with specific cytogenetic profile},

author = {Gema Jiménez and Michael Hackenberg and Purificación Catalina and Houria Boulaiz and Carmen Griñán-Lisón and María Ángel García and Macarena Perán and Elena López-Ruiz and Alberto Ramírez and Cynthia Morata-Tarifa and Esther Carrasco and Margarita Aguilera and Juan Antonio Marchal},

doi = {10.1016/j.canlet.2018.04.042},

issn = {1872-7980},

year  = {2018},

date = {2018-08-01},

journal = {Cancer Letters},

volume = {429},

pages = {78–88},

abstract = {Cancer stem cells (CSCs) are responsible for tumor initiation, metastasis and cancer recurrence, however the involvement of microenvironment is crucial. Here, we have analyzed how human mesenchymal stem cells (MSCs)-derived conditioned medium (CM) affect colon and melanoma CSCs enrichment and maintenance. Our results strongly suggest that the secretome of CM-MSCs selects and maintains subpopulations with high expression of CSCs markers and ALDH1 activity, low proliferation rates with G1 phase arrest, and notably retain in vivo these properties. Cytogenetic analyses indicated that CM-cultured cells contain alterations in chromosome 17 (17q25). Subsequent SKY-FISH analyses suggested that genes located in 17q25 might be involved in stem-cell maintenance. The characterization of secreted proteins present in CM-MSCs revealed that four cytokines and seven growth factors are directly linked to the CSCs enrichment reported in this study. Further analyses revealed that the combination of just IL6 and HGF is enough to provide cancer cells with better stemness properties. In conclusion, this study demonstrates how specific chromosomal alterations present in CSCs subpopulations might represent an advantage for their in vitro maintenance and in vivo stemness properties.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zhou_identification_2018,

title = {Identification and characterisation of a previously unknown drought tolerance-associated microRNA in barley},

author = {Hui Zhou and Syed S. Hussain and Michael Hackenberg and Natalia Bazanova and Omid Eini and Jie Li and Perry Gustafson and Bujun Shi},

doi = {10.1111/tpj.13938},

issn = {1365-313X},

year  = {2018},

date = {2018-07-01},

journal = {The Plant Journal: For Cell and Molecular Biology},

volume = {95},

number = {1},

pages = {138–149},

abstract = {Drought is the most serious abiotic stress, and causes crop losses on a worldwide scale. The present study identified a previously unknown microRNA (designated as hvu-miRX) of 21 nucleotides (nt) in length in barley. Its precursor (designated pre-miRX) and primary transcript (designated pri-miRX) were also identified, with lengths of 73 and 559 nt, respectively. The identified upstream sequence of pri-miRX contained both the TATA box and the CAAT box, which are both required for initiation of transcription. Transient promoter activation assays showed that the core promoter region of pri-miRX ranged 500 nt from the transcription start site. In transgenic barley overexpression of the wheat DREB3 transcription factor (TaDREB3) caused hvu-miRX to be highly expressed as compared with the same miRNA in non-transgenic barley. However, the high expression was not directly associated with TaDREB3. Genomic analysis revealed that the hvu-miRX gene was a single copy located on the short arm of chromosome 2 and appeared to be only conserved in Triticeae, but not in other plant species. Notably, transgenic barley that overexpressed hvu-miRX showed drought tolerance. Degradome library analysis and other tests showed that hvu-miRX targeted various genes including transcription factors via the cleavage mode. Our data provides an excellent opportunity to develop drought stress tolerant cereals using hvu-miRX.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hackenberg_exosome-mediated_2018,

title = {Exosome-Mediated Pathogen Transmission by Arthropod Vectors},

author = {Michael Hackenberg and Michail Kotsyfakis},

doi = {10.1016/j.pt.2018.04.001},

issn = {1471-5007},

year  = {2018},

date = {2018-07-01},

journal = {Trends in Parasitology},

volume = {34},

number = {7},

pages = {549–552},

abstract = {Recent molecular and cellular studies have highlighted a potentially important role for tick exosomes in parasite transmission. Here we summarize evolving hypotheses about the largely unknown cellular events that may take place at the tick-host-pathogen interface, focusing on a potential role for arthropod exosomes in this tripartite interaction.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pentimone_identification_2018,

title = {Identification of tomato miRNAs responsive to root colonization by endophytic Pochonia chlamydosporia},

author = {Isabella Pentimone and Ricardo Lebrón and Michael Hackenberg and Laura C. Rosso and Mariantonietta Colagiero and Franco Nigro and Aurelio Ciancio},

doi = {10.1007/s00253-017-8608-7},

issn = {1432-0614},

year  = {2018},

date = {2018-01-01},

journal = {Applied Microbiology and Biotechnology},

volume = {102},

number = {2},

pages = {907–919},

abstract = {The molecular mechanisms active during the endophytic phase of the fungus Pochonia chlamydosporia are still poorly understood. In particular, few data are available on the links between the endophyte and the root response, as modulated by noncoding small RNAs. In this study, we describe the microRNAs (miRNAs) that are differentially expressed (DE) in the roots of tomato, colonized by P. chlamydosporia. A genome-wide NGS expression profiling of small RNAs in roots, either colonized or not by the fungus, showed 26 miRNAs upregulated in inoculated roots. Their predicted target genes are involved in the plant information processing system, which recognizes, percepts, and transmits signals, with higher representations in processes such as apoptosis and plant defense regulation. RNAseq data showed that predicted miRNA target genes were downregulated in tomato roots after 4, 7, 10, and 21 days post P. chlamydosporia inoculation. The differential expression of four miRNAs was further validated using qPCR analysis. The P. chlamydosporia endophytic lifestyle in tomato roots included an intricate network of miRNAs and targets. Data provide a first platform of DE tomato miRNAs after P. chlamydosporia colonization. They indicated that several miRNAs are involved in the host response to the fungus, playing important roles for its recognition as a symbiotic microorganism, allowing endophytism by modulating the host defense reaction. Data also indicated that endophytism affects tRNA fragmentation. This is the first study on miRNAs induced by P. chlamydosporia endophytism and related development regulation effects in Solanum lycopersicum.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{barturen_moving_2018,

title = {Moving towards a molecular taxonomy of autoimmune rheumatic diseases},

author = {Guillermo Barturen and Lorenzo Beretta and Ricard Cervera and Ronald Van Vollenhoven and Marta E. Alarcón-Riquelme},

doi = {10.1038/nrrheum.2017.220},

issn = {1759-4804},

year  = {2018},

date = {2018-01-01},

journal = {Nature Reviews. Rheumatology},

volume = {14},

number = {2},

pages = {75–93},

abstract = {Autoimmune rheumatic diseases pose many problems that have, in general, already been solved in the field of cancer. The heterogeneity of each disease, the clinical similarities and differences between different autoimmune rheumatic diseases and the large number of patients that remain without a diagnosis underline the need to reclassify these diseases via new approaches. Knowledge about the molecular basis of systemic autoimmune diseases, along with the availability of bioinformatics tools capable of handling and integrating large volumes of various types of molecular data at once, offer the possibility of reclassifying these diseases. A new taxonomy could lead to the discovery of new biomarkers for patient stratification and prognosis. Most importantly, this taxonomy might enable important changes in clinical trial design to reach the expected outcomes or the design of molecularly targeted therapies. In this Review, we discuss the basis for a new molecular taxonomy for autoimmune rheumatic diseases. We highlight the evidence surrounding the idea that these diseases share molecular features related to their pathogenesis and development and discuss previous attempts to classify these diseases. We evaluate the tools available to analyse and combine different types of molecular data. Finally, we introduce PRECISESADS, a project aimed at reclassifying the systemic autoimmune diseases.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gomez-martin_prediction_2018,

title = {Prediction of CpG Islands as an Intrinsic Clustering Property Found in Many Eukaryotic DNA Sequences and Its Relation to DNA Methylation},

author = {Cristina Gómez-Martín and Ricardo Lebrón and José L. Oliver and Michael Hackenberg},

doi = {10.1007/978-1-4939-7768-0_3},

issn = {1940-6029},

year  = {2018},

date = {2018-01-01},

journal = {Methods in Molecular Biology},

volume = {1766},

pages = {31–47},

address = {Clifton, N.J.},

abstract = {The promoter region of around 70% of all genes in the human genome is overlapped by a CpG island (CGI). CGIs have known functions in the transcription initiation and outstanding compositional features like high G+C content and CpG ratios when compared to the bulk DNA. We have shown before that CGIs manifest as clusters of CpGs in mammalian genomes and can therefore be detected using clustering methods. These techniques have several advantages over sliding window approaches which apply compositional properties as thresholds. In this protocol we show how to determine local (CpG islands) and global (distance distribution) clustering properties of CG dinucleotides and how to generalize this analysis to any k-mer or combinations of it. In addition, we illustrate how to easily cross the output of a CpG island prediction algorithm with our methylation database to detect differentially methylated CGIs. The analysis is given in a step-by-step protocol and all necessary programs are implemented into a virtual machine or, alternatively, the software can be downloaded and easily installed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hackenberg_silico_2017,

title = {In silico target network analysis of de novo-discovered, tick saliva-specific microRNAs reveals important combinatorial effects in their interference with vertebrate host physiology},

author = {Michael Hackenberg and David Langenberger and Alexandra Schwarz and Jan Erhart and Michail Kotsyfakis},

doi = {10.1261/rna.061168.117},

issn = {1469-9001},

year  = {2017},

date = {2017-08-01},

journal = {RNA},

volume = {23},

number = {8},

pages = {1259–1269},

address = {New York, N.Y.},

abstract = {The hard tick Ixodes ricinus is an important disease vector whose salivary secretions mediate blood-feeding success on vertebrate hosts, including humans. Here we describe the expression profiles and downstream analysis of de novo-discovered microRNAs (miRNAs) expressed in I. ricinus salivary glands and saliva. Eleven tick-derived libraries were sequenced to produce 67,375,557 Illumina reads. De novo prediction yielded 67 bona fide miRNAs out of which 35 are currently not present in miRBase. We report for the first time the presence of microRNAs in tick saliva, obtaining furthermore molecular indicators that those might be of exosomal origin. Ten out of these microRNAs are at least 100 times more represented in saliva. For the four most expressed microRNAs from this subset, we analyzed their combinatorial effects upon their host transcriptome using a novel in silico target network approach. We show that only the inclusion of combinatorial effects reveals the functions in important pathways related to inflammation and pain sensing. A control set of highly abundant microRNAs in both saliva and salivary glands indicates no significant pathways and a far lower number of shared target genes. Therefore, the analysis of miRNAs from pure tick saliva strongly supports the hypothesis that tick saliva miRNAs can modulate vertebrate host homeostasis and represents the first direct evidence of tick miRNA-mediated regulation of vertebrate host gene expression at the tick-host interface. As such, the herein described miRNAs may support future drug discovery and development projects that will also experimentally question their predicted molecular targets in the vertebrate host.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{lutz_viral_2017,

title = {Viral Ubiquitin Ligase Stimulates Selective Host MicroRNA Expression by Targeting ZEB Transcriptional Repressors},

author = {Gabriel Lutz and Igor Jurak and Eui Tae Kim and Ju Youn Kim and Michael Hackenberg and Andrew Leader and Michelle L. Stoller and Donna M. Fekete and Matthew D. Weitzman and Donald M. Coen and Angus C. Wilson},

doi = {10.3390/v9080210},

issn = {1999-4915},

year  = {2017},

date = {2017-08-01},

journal = {Viruses},

volume = {9},

number = {8},

pages = {210},

abstract = {Infection with herpes simplex virus-1 (HSV-1) brings numerous changes in cellular gene expression. Levels of most host mRNAs are reduced, limiting synthesis of host proteins, especially those involved in antiviral defenses. The impact of HSV-1 on host microRNAs (miRNAs), an extensive network of short non-coding RNAs that regulate mRNA stability/translation, remains largely unexplored. Here we show that transcription of the miR-183 cluster (miR-183, miR-96, and miR-182) is selectively induced by HSV-1 during productive infection of primary fibroblasts and neurons. ICP0, a viral E3 ubiquitin ligase expressed as an immediate-early protein, is both necessary and sufficient for this induction. Nuclear exclusion of ICP0 or removal of the RING (really interesting new gene) finger domain that is required for E3 ligase activity prevents induction. ICP0 promotes the degradation of numerous host proteins and for the most part, the downstream consequences are unknown. Induction of the miR-183 cluster can be mimicked by depletion of host transcriptional repressors zinc finger E-box binding homeobox 1 (ZEB1)/-crystallin enhancer binding factor 1 (δEF1) and zinc finger E-box binding homeobox 2 (ZEB2)/Smad-interacting protein 1 (SIP1), which we establish as new substrates for ICP0-mediated degradation. Thus, HSV-1 selectively stimulates expression of the miR-183 cluster by ICP0-mediated degradation of ZEB transcriptional repressors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{barturen_sle_2017,

title = {SLE redefined on the basis of molecular pathways},

author = {Guillermo Barturen and Marta E. Alarcón-Riquelme},

doi = {10.1016/j.berh.2017.09.006},

issn = {1532-1770},

year  = {2017},

date = {2017-06-01},

journal = {Best Practice & Research. Clinical Rheumatology},

volume = {31},

number = {3},

pages = {291–305},

abstract = {The implementation of precision medicine requires the recruiting of patients in statistically enough numbers, the possibility of obtaining enough materials, and the integration of data from various platforms, which are all real limitations. These types of studies have been performed extensively in cancer but barely on systemic lupus erythematosus (SLE) or other rheumatic diseases. To consider the practical use of the information obtained from such studies, we have to take into account the best biological fluid to use, the ease to perform the analysis in clinical practice, and its relevance to clinical practice. Here we review the most relevant studies that have performed analyses that attempt to classify or stratify SLE. We focus on two types of studies: those that stratify individuals diagnosed with SLE and those that compare SLE with other autoimmune diseases, defining differences and similarities that may be clinically relevant in the future.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{srivastava_thiourea_2017,

title = {Thiourea priming enhances salt tolerance through co-ordinated regulation of microRNAs and hormones in Brassica juncea},

author = {Ashish Kumar Srivastava and Gaurav Sablok and Michael Hackenberg and Uday Deshpande and Penna Suprasanna},

doi = {10.1038/srep45490},

issn = {2045-2322},

year  = {2017},

date = {2017-04-01},

journal = {Scientific Reports},

volume = {7},

pages = {45490},

abstract = {Activation of stress tolerance mechanisms demands transcriptional reprogramming. Salt stress, a major threat to plant growth, enhances ROS production and affects transcription through modulation of miRNAs and hormones. The present study delineates salt stress ameliorating action of thiourea (TU, a ROS scavenger) in Brassica juncea and provides mechanistic link between redox, microRNA and hormones. The ameliorative potential of TU towards NaCl stress was related with its ability to decrease ROS accumulation in roots and increase Na+ accumulation in shoots. Small RNA sequencing revealed enrichment of down-regulated miRNAs in NaCl + TU treated roots, indicating transcriptional activation. Ranking analysis identified three key genes including BRX4, CBL10 and PHO1, showing inverse relationship with corresponding miRNA expression, which were responsible for TU mediated stress mitigation. Additionally, ABA level was consistently higher till 24 h in NaCl, while NaCl + TU treated roots showed only transient increase at 4 h suggesting an effective stress management. Jasmonate and auxin levels were also increased, which prioritized defence and facilitated root growth, respectively. Thus, the study highlights redox as one of the "core" components regulating miRNA and hormone levels, and also strengthens the use of TU as a redox priming agent for imparting crop resilience to salt stress.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{barturen_systemic_2017,

title = {Systemic Lupus Erythematosus in 2016: Gene expression profiling comes closer to the clinic},

author = {Guillermo Barturen and Marta E. Alarcón-Riquelme},

doi = {10.1038/nrrheum.2016.211},

issn = {1759-4804},

year  = {2017},

date = {2017-02-01},

journal = {Nature Reviews. Rheumatology},

volume = {13},

number = {2},

pages = {69–70},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{lebron_ngsmethdb_2017,

title = {NGSmethDB 2017: enhanced methylomes and differential methylation},

author = {Ricardo Lebrón and Cristina Gómez-Martín and Pedro Carpena and Pedro Bernaola-Galván and Guillermo Barturen and Michael Hackenberg and José L. Oliver},

doi = {10.1093/nar/gkw996},

issn = {1362-4962},

year  = {2017},

date = {2017-01-01},

journal = {Nucleic Acids Research},

volume = {45},

number = {D1},

pages = {D97–D103},

abstract = {The 2017 update of NGSmethDB stores whole genome methylomes generated from short-read data sets obtained by bisulfite sequencing (WGBS) technology. To generate high-quality methylomes, stringent quality controls were integrated with third-part software, adding also a two-step mapping process to exploit the advantages of the new genome assembly models. The samples were all profiled under constant parameter settings, thus enabling comparative downstream analyses. Besides a significant increase in the number of samples, NGSmethDB now includes two additional data-types, which are a valuable resource for the discovery of methylation epigenetic biomarkers: (i) differentially methylated single-cytosines; and (ii) methylation segments (i.e. genome regions of homogeneous methylation). The NGSmethDB back-end is now based on MongoDB, a NoSQL hierarchical database using JSON-formatted documents and dynamic schemas, thus accelerating sample comparative analyses. Besides conventional database dumps, track hubs were implemented, which improved database access, visualization in genome browsers and comparative analyses to third-part annotations. In addition, the database can be also accessed through a RESTful API. Lastly, a Python client and a multiplatform virtual machine allow for program-driven access from user desktop. This way, private methylation data can be compared to NGSmethDB without the need to upload them to public servers. Database website: http://bioinfo2.ugr.es/NGSmethDB.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gomez-martin_srnatoolboxvm_2017,

title = {sRNAtoolboxVM: Small RNA Analysis in a Virtual Machine},

author = {Cristina Gómez-Martín and Ricardo Lebrón and Antonio Rueda and José L. Oliver and Michael Hackenberg},

doi = {10.1007/978-1-4939-6866-4_12},

issn = {1940-6029},

year  = {2017},

date = {2017-01-01},

journal = {Methods in Molecular Biology},

volume = {1580},

pages = {149–174},

address = {Clifton, N.J.},

abstract = {High-throughput sequencing (HTS) data for small RNAs (noncoding RNA molecules that are 20-250 nucleotides in length) can now be routinely generated by minimally equipped wet laboratories; however, the bottleneck in HTS-based research has shifted now to the analysis of such huge amount of data. One of the reasons is that many analysis types require a Linux environment but computers, system administrators, and bioinformaticians suppose additional costs that often cannot be afforded by small to mid-sized groups or laboratories. Web servers are an alternative that can be used if the data is not subjected to privacy issues (what very often is an important issue with medical data). However, in any case they are less flexible than stand-alone programs limiting the number of workflows and analysis types that can be carried out.We show in this protocol how virtual machines can be used to overcome those problems and limitations. sRNAtoolboxVM is a virtual machine that can be executed on all common operating systems through virtualization programs like VirtualBox or VMware, providing the user with a high number of preinstalled programs like sRNAbench for small RNA analysis without the need to maintain additional servers and/or operating systems.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hackenberg_generation_2016,

title = {Generation of different sizes and classes of small RNAs in barley is locus, chromosome and/or cultivar-dependent},

author = {Michael Hackenberg and Antonio Rueda and Perry Gustafson and Peter Langridge and Bu-Jun Shi},

doi = {10.1186/s12864-016-3023-5},

issn = {1471-2164},

year  = {2016},

date = {2016-09-01},

journal = {BMC genomics},

volume = {17},

number = {1},

pages = {735},

abstract = {BACKGROUND: Various small RNA (sRNA) sizes and varieties have been identified, but their relationship as well as relationship with their origins and allocations have not been well understood or investigated. 

RESULTS: By comparing sRNAs generated from two barley cultivars, Golden Promise (GP) and Pallas, we identified that the generation of different sizes and types of sRNAs in barley was locus-, chromosome- and/or cultivar-dependent. 20-nt sRNAs mainly comprising miRNAs and chloroplast-derived sRNAs were significantly over-expressed in Pallas vs. GP on chromosomes 3H and 6H. MiRNAs-enriched 21-nt sRNAs were significantly over-expressed in Pallas vs. GP only on chromosome 4H. On chromosome 5H this size of sRNAs was significantly under-expressed in Pallas, so were 22-nt sRNAs mainly comprising miRNAs and repeat-derived sRNAs. 24-nt sRNAs mostly derived from repeats were evenly distributed in all chromosomes and expressed similarly between GP and Pallas. Unlike other sizes of sRNAs, 24-nt sRNAs were little conserved in other plant species. Abundant sRNAs were mostly generated from 3' terminal regions of chromosome 1H and 5' terminal regions of chromosome 5H. Over-expressed miRNAs in GP vs. Pallas primarily function in stress responses and iron-binding. 

CONCLUSIONS: Our study indicates that 23-24-nt sRNAs may be linked to repressive chromatin modifications and function in genome stability while 20-21-nt sRNAs may be important for the cultivar specificity. This study provides a novel insight into the mechanism of sRNA expression and function in barley.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{koppers-lalic_noninvasive_2016,

title = {Non‑invasive prostate cancer detection by measuring miRNA variants (isomiRs) in urine extracellular vesicles},

author = {Danijela Koppers-Lalic and Michael Hackenberg and Renee Menezes and Branislav Misovic and Magda Wachalska and Albert Geldof and Nicoletta Zini and Theo Reijke and Thomas Wurdinger and Andre Vis and Jeroen Moorselaar and Michiel Pegtel and Irene Bijnsdorp},

doi = {10.18632/oncotarget.8124},

issn = {1949-2553},

year  = {2016},

date = {2016-04-01},

journal = {Oncotarget},

volume = {7},

number = {16},

pages = {22566–22578},

abstract = {In many cancer types, the expression and function of textasciitilde22 nucleotide-long microRNAs (miRNA) is deregulated. Mature miRNAs can be stably detected in extracellular vesicles (EVs) in biofluids, therefore they are considered to have great potential as biomarkers. In the present study, we investigated whether miRNAs have a distinct expression pattern in urine-EVs of prostate cancer (PCa) patients compared to control males. By next generation sequencing, we determined the miRNA expression in a discovery cohort of 4 control men and 9 PCa patients. miRNAs were validated by using a stemloop RT-PCR in an independent cohort of 74 patients (26 control and 48 PCa-patients). Whereas standard mapping protocols identified > 10 PCa associated miRNAs in urinary EVs, miR-21, miR-375 and miR-204 failed to robustly discriminate for disease in a validation study with RT-PCR-detection of mature miRNA sequences. In contrast, we observed that miRNA isoforms (isomiRs) with 3' end modifications were highly discriminatory between samples from control men and PCa patients. Highly differentially expressed isomiRs of miR-21, miR-204 and miR-375 were subsequently validated in an independent group of 74 patients. Receiver-operating characteristic analysis was performed to evaluate the diagnostic performance of three isomiRs, resulting in a 72.9% sensitivity with a high (88%) specificity and an area under the curve (AUC) of 0.866. In comparison, prostate specific antigen had an AUC of 0.707 and measuring the mature form of these miRNAs yielded a lower 70.8% sensitivity and 72% specificity (AUC 0.766). We propose that isomiRs may carry discriminatory information which is useful to generate stronger biomarkers.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}