Epithelial to mesenchymal transition trajectories in developmental and disease

Resumen del trabajo presentado al 19th International Congress of Developmental Biology, celebrado en El Algarve (Portugal) del 16 al 20 de octubre de 2022.The Epithelial to Mesenchymal transition (EMT) triggers cell plasticity during embryonic development and tissue repair, but it can also promote tumor progression and organ degeneration. The reactivation of EMT in the adult promotes cell dedifferentiation and profound remodeling of the epithelial program, leading to multiple phenotypes, observed in response to injury, during organ fibrosis and cancer cell dissemination. Despite recent advances, identifying universal EMT molecular signatures and understanding how EMT can instructs different outcomes have remained elusive due to the intrinsic complexity and heterogeneity of the process. We have dissected how EMT transcription factors (EMT-TFs) orchestrate TGFBinduced EMT including phenotypic and behavioral states. Further, we have combined lineage tracing and single-cell transcriptomics in three EMT contexts, namely the neural crest, renal fibrosis, and breast cancer to reveal conserved EMT transcription factor codes and signaling pathways that discriminate different EMT states. After inferring cellular trajectories, we have reconstructed the evolution of EMT phenotypic and functional states in all these contexts. Finally, multiplex labeling allowed to spatially allocate distinct EMT programs in mouse and human tumor samples. Altogether, this work unveils distinct EMT trajectories in development and disease, which should also help propase improved therapeutic strategies for organ fibrosis and cancer.Peer reviewe

Two distinct epithelial to mesenchymal transition programmes. Control invasion and inflammation in segregated tumour cell populations

Resumen del trabajo presentado al 19th Christmas Meeting del Instituto de Neurociencias (CSIC-UMH) celebrado el 21 de diciembre de 2022.Epithelial plasticity is at the core of crucial processes including embryonic cell migration, cancer progression, organ tibrosis and tissue repair. The epithelial to mesenchymal transition (EMT) triggers cell plasticity in all these contexts, highlighting its pleiotropy and intrinsic complcxity. Seminal studies have classified EMT states in cancer celllines and animal modcls. This varicty ofEMT phenotypes necds further investigation, particularly those relevant to the progression ofprevalent and dcvastating diseases such as cancer. Our objcctive is to analyse at single-cell level how different EMT states are established in tumours and if different EMT states pcrform different functions during tumour progression.Peer reviewe

Evolutionary reconstruction of the DNA Damage Response

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The evolutionary history of Ephs and Ephrins: Toward multicellular organisms

Eph receptor (Eph) and ephrin signaling regulate fundamental developmental processes through both forward and reverse signaling triggered upon cell–cell contact. In vertebrates, they are both classified into classes A and B, and some representatives have been identified in many metazoan groups, where their expression and functions have been well studied. We have extended previous phylogenetic analyses and examined the presence of Eph and ephrins in the tree of life to determine their origin and evolution. We have found that 1) premetazoan choanoflagellates may already have rudimental Eph/ephrin signaling as they have an Eph-/ephrin-like pair and homologs of downstream-signaling genes; 2) both forward- and reverse-downstream signaling might already occur in Porifera since sponges have most genes involved in these types of signaling; 3) the nonvertebrate metazoan Eph is a type-B receptor that can bind ephrins regardless of their membrane-anchoring structure, glycosylphosphatidylinositol, or transmembrane; 4) Eph/ephrin cross-class binding is specific to Gnathostomata; and 5) kinase-dead Eph receptors can be traced back to Gnathostomata. We conclude that Eph/ephrin signaling is of older origin than previously believed. We also examined the presence of protein domains associated with functional characteristics and the appearance and conservation of downstream-signaling pathways to understand the original and derived functions of Ephs and ephrins. We find that the evolutionary history of these gene families points to an ancestral function in cell–cell interactions that could contribute to the emergence of multicellularity and, in particular, to the required segregation of cell populations.This work was supported by grants from the Spanish Ministries of Economy and Competitiveness (BFU2014-53128-R) and of Science, Innovation and Universities (RTI2018-096501-B-I00), Generalitat Valenciana (PROMETEO 2017/150) and the European Research Council (ERC AdG 322694) to M.A.N., who also acknowledges financial support from the Spanish State Research Agency (AEI), through BFU and RTI grants as above plus the “Severo Ochoa” Programme for Centres of Excellence in R&D (SEV-2017-0273). The first three grants (BFU, RTI and PROM) are cofinanced by the European Regional Development Fund, ERDF. D.G.W. was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001217), the UK Medical Research Council (FC001217), and the Wellcome Trust (FC001217).Peer reviewe

Emergence and Evolutionary Analysis of the Human DDR Network: Implications in Comparative Genomics and Downstream Analyses

The DNA damage response (DDR) is a crucial signaling network that preserves the integrity of the genome. This network is an ensemble of distinct but often overlapping subnetworks, where different components fulfill distinct functions in precise spatial and temporal scenarios. To understand how these elements have been assembled together in humans, we performed comparative genomic analyses in 47 selected species to trace back their emergence using systematic phylogenetic analyses and estimated gene ages. The emergence of the contribution of posttranslational modifications to the complex regulation of DDR was also investigated. This is the first time a systematic analysis has focused on the evolution of DDR subnetworks as a whole. Our results indicate that a DDR core, mostly constructed around metabolic activities, appeared soon after the emergence of eukaryotes, and that additional regulatory capacities appeared later through complex evolutionary process. Potential key posttranslational modifications were also in place then, with interacting pairs preferentially appearing at the same evolutionary time, although modifications often led to the subsequent acquisition of new targets afterwards. We also found extensive gene loss in essential modules of the regulatory network in fungi, plants, and arthropods, important for their validation as model organisms for DDR studies.This work was supported by the Spanish Ministry of Science (SAF2011-23753), the Association for International Cancer Research (12-0229), the Howard Hughes Medical Institute, and the European Research Council (ERC-210520) to O.F.-C., and by the Spanish Ministry of Science and Innovation (PS09/02111) to A.M.R. and I.C.Peer reviewe

The DNA Damage Response: Evolution of a Pathway

Trabajo presentado en la 6th Annual DREAM competition, 7th Annual RECOMB Satellite Conference on Systems Biology, 8th Annual RECOMB Satellite Conference on Regulatory Genomics, y la IDIBELL Conference on Cancer Informatics, celebradas en Barcelona del 14 al 19 de octubre de 2011.N

The Dna Damage Response: Domain-based analysis of its components

Trabajo presentado en el XII Symposium on Bioinformatics (XII Jornadas de Bioinformática), celebrado en Sevilla del 21 al 24 de septiembre de 2014.The DNA damage response (DDR) is a crucial signaling network that preserves the integrity of the genome. Although extensive work has been conducted in particular proteins of the DDR, few evolutionary studies have been done to understand the origin of these proteins and to provide insightful clues into how this concerted system of pathways has been acquired in eukaryotes. In this work we study at a domain level the orthologous sequences of 118 human DDR proteins to establish the domain repertoire involved in the DDR, to analyze the conservation of domains in different organisms, and to determine the acquisition of novel functions due to diverse domain architectures reflecting differences at the species level. Also, we intend to identify whether there are domains enriched in DDR-related functions. We have identified DDR orthologous sequences with InParanoid in a comprehensive set of species. The domain composition of the orthologous DDR sequences was analyzed using HMMER and the Pfam database. Also, manual identification of remote homologous domains in orthologous proteins without detected Pfam domains was performed. We constructed phylogenetic protein and domain profiles and clustered them to identify proteins and domains that have appeared consistently in evolution, respectively. Besides, domain enrichment analyses were performed and the distribution of domains in DDR functional tiers was analysed. Our results show that most components of the DDR appear to be specific to the eukaryotic lineage. This specificity is related to the acquisition of novel domains that increase the pathways complexity in terms of fine-tuning and extend the interaction repertoire of DDR proteins to cross-talk with closely related pathways. Also, along evolution lineage-specific and domain rearrangement events may have included novel functions in various organisms, mainly in plants.N

Evolution of the DNA Damage Response

Trabajo presentado en el 10th Spanish Symposium on Bioinformatics (JBI2010), celebrado en Torremolinos-Málaga del 27 al 29 de octubre de 2010.N

Serine/threonine kinases and E2-ubiquitin conjugating enzymes in Planctomycetes: unexpected findings

The regulation of signal transduction by phosphorylation and ubiquitination is essential to ensure the correct behavior of eukaryotic cells. We searched for protein families involved in such signaling in several eukaryotic species and in a limited set of prokaryotes, where two members of the Planctomycetes phylum were included as they exhibit eukaryote-like features (Gemmata obscuriglobus and Pirellula staleyi). We identified sequences homologous to eukaryotic serine/threonine kinases (STKs) and E2-ubiquitin conjugating enzymes in the two Planctomycetes species. To extend these analyses to the Planctomycetes/Verrucomicrobia/Chlamydia super-phylum, we performed comparative analyses using domains from kinases, phosphatases and GTPases that serve as signaling signatures, and we analyzed their distributions. We found substantial differences in kinome densities with regards to other prokaryote clades and among the groups in the Planctomycetes/Verrucomicrobia/Chlamydia super-phylum. In addition, we identified the presence of classic eukaryotic E2-conjugating ubiquitin proteins in prokaryotes, these having previously believed to exist only in eukaryotes. Our phylogenetic analyses of the STKs signature domains and E2-enzymes suggest the existence of horizontal gene transfer.Peer reviewe

An evolutionary view of the DNA Damage Response

Trabajo presentado en la 2nd EMBO Meeting (The European Molecular Biology Organization Meeting), celebrada en Barcelona del 4 al 7 de septiembre de 2010.N