%0 Journal Article %J Br J Dermatol %D 2019 %T Fibroblast activation and abnormal extracellular matrix remodelling as common hallmarks in three cancer-prone genodermatoses. %A Chacón-Solano, E %A León, C %A Díaz, F %A García-García, F %A García, M %A Escámez, M J %A Guerrero-Aspizua, S %A Conti, C J %A Mencía, Á %A Martínez-Santamaría, L %A Llames, S %A Pévida, M %A Carbonell-Caballero, J %A Puig-Butillé, J A %A Maseda, R %A Puig, S %A de Lucas, R %A Baselga, E %A Larcher, F %A Dopazo, J %A Del Rio, M %K Adolescent %K Adult %K Biopsy %K Blister %K Case-Control Studies %K Cells, Cultured %K Child %K Child, Preschool %K Epidermolysis Bullosa %K Epidermolysis Bullosa Dystrophica %K Extracellular Matrix %K Extracellular Matrix Proteins %K Female %K Fibroblasts %K Fibrosis %K Gene Expression Regulation %K Healthy Volunteers %K Humans %K Infant %K Infant, Newborn %K Male %K Middle Aged %K mutation %K Periodontal Diseases %K Photosensitivity Disorders %K Primary Cell Culture %K RNA-seq %K Skin %K Xeroderma Pigmentosum %K Young Adult %X

BACKGROUND: Recessive dystrophic epidermolysis bullosa (RDEB), Kindler syndrome (KS) and xeroderma pigmentosum complementation group C (XPC) are three cancer-prone genodermatoses whose causal genetic mutations cannot fully explain, on their own, the array of associated phenotypic manifestations. Recent evidence highlights the role of the stromal microenvironment in the pathology of these disorders.

OBJECTIVES: To investigate, by means of comparative gene expression analysis, the role played by dermal fibroblasts in the pathogenesis of RDEB, KS and XPC.

METHODS: We conducted RNA-Seq analysis, which included a thorough examination of the differentially expressed genes, a functional enrichment analysis and a description of affected signalling circuits. Transcriptomic data were validated at the protein level in cell cultures, serum samples and skin biopsies.

RESULTS: Interdisease comparisons against control fibroblasts revealed a unifying signature of 186 differentially expressed genes and four signalling pathways in the three genodermatoses. Remarkably, some of the uncovered expression changes suggest a synthetic fibroblast phenotype characterized by the aberrant expression of extracellular matrix (ECM) proteins. Western blot and immunofluorescence in situ analyses validated the RNA-Seq data. In addition, enzyme-linked immunosorbent assay revealed increased circulating levels of periostin in patients with RDEB.

CONCLUSIONS: Our results suggest that the different causal genetic defects converge into common changes in gene expression, possibly due to injury-sensitive events. These, in turn, trigger a cascade of reactions involving abnormal ECM deposition and underexpression of antioxidant enzymes. The elucidated expression signature provides new potential biomarkers and common therapeutic targets in RDEB, XPC and KS. What's already known about this topic? Recessive dystrophic epidermolysis bullosa (RDEB), Kindler syndrome (KS) and xeroderma pigmentosum complementation group C (XPC) are three genodermatoses with high predisposition to cancer development. Although their causal genetic mutations mainly affect epithelia, the dermal microenvironment likely contributes to the physiopathology of these disorders. What does this study add? We disclose a large overlapping transcription profile between XPC, KS and RDEB fibroblasts that points towards an activated phenotype with high matrix-synthetic capacity. This common signature seems to be independent of the primary causal deficiency, but reflects an underlying derangement of the extracellular matrix via transforming growth factor-β signalling activation and oxidative state imbalance. What is the translational message? This study broadens the current knowledge about the pathology of these diseases and highlights new targets and biomarkers for effective therapeutic intervention. It is suggested that high levels of circulating periostin could represent a potential biomarker in RDEB.

%B Br J Dermatol %V 181 %P 512-522 %8 2019 09 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/30693469?dopt=Abstract %R 10.1111/bjd.17698 %0 Journal Article %J Am J Med Genet A %D 2016 %T Screening of CD96 and ASXL1 in 11 patients with Opitz C or Bohring-Opitz syndromes. %A Urreizti, Roser %A Roca-Ayats, Neus %A Trepat, Judith %A Garcia-Garcia, Francisco %A Alemán, Alejandro %A Orteschi, Daniela %A Marangi, Giuseppe %A Neri, Giovanni %A Opitz, John M %A Dopazo, Joaquin %A Cormand, Bru %A Vilageliu, Lluïsa %A Balcells, Susana %A Grinberg, Daniel %K Adolescent %K Antigens, CD %K Child %K Child, Preschool %K Craniosynostoses %K Exome %K Female %K High-Throughput Nucleotide Sequencing %K Humans %K Infant %K Intellectual Disability %K Male %K mutation %K Pedigree %K Phenotype %K Prognosis %K Repressor Proteins %X

Opitz C trigonocephaly (or Opitz C syndrome, OTCS) and Bohring-Opitz syndrome (BOS or C-like syndrome) are two rare genetic disorders with phenotypic overlap. The genetic causes of these diseases are not understood. However, two genes have been associated with OTCS or BOS with dominantly inherited de novo mutations. Whereas CD96 has been related to OTCS (one case) and to BOS (one case), ASXL1 has been related to BOS only (several cases). In this study we analyze CD96 and ASXL1 in a group of 11 affected individuals, including 2 sibs, 10 of them were diagnosed with OTCS, and one had a BOS phenotype. Exome sequences were available on six patients with OTCS and three parent pairs. Thus, we could analyze the CD96 and ASXL1 sequences in these patients bioinformatically. Sanger sequencing of all exons of CD96 and ASXL1 was carried out in the remaining patients. Detailed scrutiny of the sequences and assessment of variants allowed us to exclude putative pathogenic and private mutations in all but one of the patients. In this patient (with BOS) we identified a de novo mutation in ASXL1 (c.2100dupT). By nature and location within the gene, this mutation resembles those previously described in other BOS patients and we conclude that it may be responsible for the condition. Our results indicate that in 10 of 11, the disease (OTCS or BOS) cannot be explained by small changes in CD96 or ASXL1. However, the cohort is too small to make generalizations about the genetic etiology of these diseases.

%B Am J Med Genet A %V 170A %P 24-31 %8 2016 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26768331?dopt=Abstract %R 10.1002/ajmg.a.37418 %0 Journal Article %J Hum Genet %D 2016 %T Whole exome sequencing of Rett syndrome-like patients reveals the mutational diversity of the clinical phenotype. %A Lucariello, Mario %A Vidal, Enrique %A Vidal, Silvia %A Saez, Mauricio %A Roa, Laura %A Huertas, Dori %A Pineda, Mercè %A Dalfó, Esther %A Dopazo, Joaquin %A Jurado, Paola %A Armstrong, Judith %A Esteller, Manel %K Adolescent %K Adult %K Animals %K Caenorhabditis elegans %K Carrier Proteins %K Cell Cycle Proteins %K Child %K Child, Preschool %K DNA Mutational Analysis %K Exome %K Female %K Forkhead Transcription Factors %K Genetic Variation %K High-Throughput Nucleotide Sequencing %K Humans %K Methyl-CpG-Binding Protein 2 %K mutation %K Nerve Tissue Proteins %K Protein Serine-Threonine Kinases %K Receptors, Nicotinic %K Rett Syndrome %X

Classical Rett syndrome (RTT) is a neurodevelopmental disorder where most of cases carry MECP2 mutations. Atypical RTT variants involve mutations in CDKL5 and FOXG1. However, a subset of RTT patients remains that do not carry any mutation in the described genes. Whole exome sequencing was carried out in a cohort of 21 female probands with clinical features overlapping with those of RTT, but without mutations in the customarily studied genes. Candidates were functionally validated by assessing the appearance of a neurological phenotype in Caenorhabditis elegans upon disruption of the corresponding ortholog gene. We detected pathogenic variants that accounted for the RTT-like phenotype in 14 (66.6 %) patients. Five patients were carriers of mutations in genes already known to be associated with other syndromic neurodevelopmental disorders. We determined that the other patients harbored mutations in genes that have not previously been linked to RTT or other neurodevelopmental syndromes, such as the ankyrin repeat containing protein ANKRD31 or the neuronal acetylcholine receptor subunit alpha-5 (CHRNA5). Furthermore, worm assays demonstrated that mutations in the studied candidate genes caused locomotion defects. Our findings indicate that mutations in a variety of genes contribute to the development of RTT-like phenotypes.

%B Hum Genet %V 135 %P 1343-1354 %8 2016 12 %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/27541642?dopt=Abstract %R 10.1007/s00439-016-1721-3 %0 Journal Article %J PLoS One %D 2014 %T Exome sequencing reveals novel and recurrent mutations with clinical significance in inherited retinal dystrophies. %A González-del Pozo, María %A Méndez-Vidal, Cristina %A Bravo-Gil, Nereida %A Vela-Boza, Alicia %A Dopazo, Joaquin %A Borrego, Salud %A Antiňolo, Guillermo %K Adolescent %K Adult %K Amino Acid Sequence %K Base Sequence %K Child %K Chromosome Segregation %K DNA Mutational Analysis %K Exome %K Family %K Female %K Humans %K Inheritance Patterns %K Male %K Middle Aged %K Molecular Sequence Data %K mutation %K Pedigree %K Retinal Dystrophies %K Rhodopsin %X

This study aimed to identify the underlying molecular genetic cause in four Spanish families clinically diagnosed of Retinitis Pigmentosa (RP), comprising one autosomal dominant RP (adRP), two autosomal recessive RP (arRP) and one with two possible modes of inheritance: arRP or X-Linked RP (XLRP). We performed whole exome sequencing (WES) using NimbleGen SeqCap EZ Exome V3 sample preparation kit and SOLID 5500xl platform. All variants passing filter criteria were validated by Sanger sequencing to confirm familial segregation and the absence in local control population. This strategy allowed the detection of: (i) one novel heterozygous splice-site deletion in RHO, c.937-2_944del, (ii) one rare homozygous mutation in C2orf71, c.1795T>C; p.Cys599Arg, not previously associated with the disease, (iii) two heterozygous null mutations in ABCA4, c.2041C>T; p.R681* and c.6088C>T; p.R2030*, and (iv) one mutation, c.2405-2406delAG; p.Glu802Glyfs*31 in the ORF15 of RPGR. The molecular findings for RHO and C2orf71 confirmed the initial diagnosis of adRP and arRP, respectively, while patients with the two ABCA4 mutations, both previously associated with Stargardt disease, presented symptoms of RP with early macular involvement. Finally, the X-Linked inheritance was confirmed for the family with the RPGR mutation. This latter finding allowed the inclusion of carrier sisters in our preimplantational genetic diagnosis program.

%B PLoS One %V 9 %P e116176 %8 2014 %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/25544989?dopt=Abstract %R 10.1371/journal.pone.0116176 %0 Journal Article %J Mol Genet Metab %D 2013 %T Exome sequencing identifies a new mutation in SERAC1 in a patient with 3-methylglutaconic aciduria. %A Tort, Frederic %A García-Silva, María Teresa %A Ferrer-Cortès, Xènia %A Navarro-Sastre, Aleix %A Garcia-Villoria, Judith %A Coll, Maria Josep %A Vidal, Enrique %A Jiménez-Almazán, Jorge %A Dopazo, Joaquin %A Briones, Paz %A Elpeleg, Orly %A Ribes, Antonia %K Adolescent %K Adult %K Carboxylic Ester Hydrolases %K Child %K Exome %K Female %K High-Throughput Nucleotide Sequencing %K Humans %K Infant %K Male %K Metabolism, Inborn Errors %K mutation %X

3-Methylglutaconic aciduria (3-MGA-uria) is a heterogeneous group of syndromes characterized by an increased excretion of 3-methylglutaconic and 3-methylglutaric acids. Five types of 3-MGA-uria (I to V) with different clinical presentations have been described. Causative mutations in TAZ, OPA3, DNAJC19, ATP12, ATP5E, and TMEM70 have been identified. After excluding the known genetic causes of 3-MGA-uria we used exome sequencing to investigate a patient with Leigh syndrome and 3-MGA-uria. We identified a homozygous variant in SERAC1 (c.202C>T; p.Arg68*), that generates a premature stop codon at position 68 of SERAC1 protein. Western blot analysis in patient's fibroblasts showed a complete absence of SERAC1 that was consistent with the prediction of a truncated protein and supports the pathogenic role of the mutation. During the course of this project a parallel study identified mutations in SERAC1 as the genetic cause of the disease in 15 patients with MEGDEL syndrome, which was compatible with the clinical and biochemical phenotypes of the patient described here. In addition, our patient developed microcephaly and optic atrophy, two features not previously reported in MEGDEL syndrome. We highlight the usefulness of exome sequencing to reveal the genetic bases of human rare diseases even if only one affected individual is available.

%B Mol Genet Metab %V 110 %P 73-7 %8 2013 Sep-Oct %G eng %N 1-2 %1 https://www.ncbi.nlm.nih.gov/pubmed/23707711?dopt=Abstract %R 10.1016/j.ymgme.2013.04.021 %0 Journal Article %J Oncogene %D 2008 %T Molecular profiling related to poor prognosis in thyroid carcinoma. Combining gene expression data and biological information. %A Montero-Conde, C %A Martín-Campos, J M %A Lerma, E %A Gimenez, G %A Martínez-Guitarte, J L %A Combalía, N %A Montaner, D %A Matías-Guiu, X %A Dopazo, J %A de Leiva, A %A Robledo, M %A Mauricio, D %K Adenoma %K Adolescent %K Adult %K Aged %K Biomarkers, Tumor %K Carcinoma %K Carcinoma, Papillary %K Cell Differentiation %K Female %K Gene Expression Profiling %K Gene Expression Regulation, Neoplastic %K Humans %K Male %K Middle Aged %K Oligonucleotide Array Sequence Analysis %K Prognosis %K Reverse Transcriptase Polymerase Chain Reaction %K RNA, Neoplasm %K Signal Transduction %K Thyroid Neoplasms %X

Undifferentiated and poorly differentiated thyroid tumors are responsible for more than half of thyroid cancer patient deaths in spite of their low incidence. Conventional treatments do not obtain substantial benefits, and the lack of alternative approaches limits patient survival. Additionally, the absence of prognostic markers for well-differentiated tumors complicates patient-specific treatments and favors the progression of recurrent forms. In order to recognize the molecular basis involved in tumor dedifferentiation and identify potential markers for thyroid cancer prognosis prediction, we analysed the expression profile of 44 thyroid primary tumors with different degrees of dedifferentiation and aggressiveness using cDNA microarrays. Transcriptome comparison of dedifferentiated and well-differentiated thyroid tumors identified 1031 genes with >2-fold difference in absolute values and false discovery rate of <0.15. According to known molecular interaction and reaction networks, the products of these genes were mainly clustered in the MAPkinase signaling pathway, the TGF-beta signaling pathway, focal adhesion and cell motility, activation of actin polymerization and cell cycle. An exhaustive search in several databases allowed us to identify various members of the matrix metalloproteinase, melanoma antigen A and collagen gene families within the upregulated gene set. We also identified a prognosis classifier comprising just 30 transcripts with an overall accuracy of 95%. These findings may clarify the molecular mechanisms involved in thyroid tumor dedifferentiation and provide a potential prognosis predictor as well as targets for new therapies.

%B Oncogene %V 27 %P 1554-61 %8 2008 Mar 06 %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/17873908?dopt=Abstract %R 10.1038/sj.onc.1210792