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  • 1.
    Tababi, Mouna
    et al.
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.
    Frikha, Fakher
    Univ Sfax, Tunisia.
    Volpe, Massimiliano
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.
    Gimm, Oliver
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Surgery, Orthopedics and Oncology. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Surgery, Orthopaedics and Cancer Treatment, Department of Surgery in Linköping.
    Söderkvist, Peter
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.
    Domain landscapes of somatic NF1 mutations in pheochromocytoma and paraganglioma2023In: Gene, ISSN 0378-1119, E-ISSN 1879-0038, Vol. 872, article id 147432Article in journal (Refereed)
    Abstract [en]

    Pheochromocytoma and paraganglioma (PPGL), are rare neuroendocrine tumors arising from the adrenal me-dulla and extra-adrenal paraganglia, respectively. Up to about 60% are explained by germline or somatic mu-tations in one of the major known susceptibility genes e.g., in NF1, RET, VHL, SDHx, MAX and HRAS. Targeted Next Generation Sequencing was performed in 14 sporadic tumors using a panel including 26 susceptibility genes to characterize the mutation profile. A total of 6 germline and 8 somatic variants were identified. The most frequent somatic mutations were found in NF1 (36%), four have not been reported earlier in PCC or PGL. Gene expression profile analysis showed that NF1 mutated tumors are classified into RTK3 subtype, cluster 2, with a high expression of genes associated with chromaffin cell differentiation, and into a RTK2 subtype, cluster 2, as well with overexpression of genes associated with cortisol biosynthesis. On the other hand, by analyzing the entire probe set on the array and TCGA data, ALDOC was found as the most significantly down regulated gene in NF1-mutated tumors compared to NF1-wild-type. Differential gene expression analysis showed a significant difference between Nt -and Ct-NF1 domains in mutated tumors probably engaging different cellular pathways. Notably, we had a metastatic PCC with a Ct-NF1 frameshift mutation and when performing protein docking analysis, Ct-NF1 showed an interaction with Nt-FAK suggesting their involvement in cell adhesion and cell growth. These results show that depending on the location of the NF1-mutation different pathways are activated in PPGLs. Further studies are required to clarify their clinical significance.

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  • 2.
    Volpe, Massimiliano
    et al.
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.
    Das, Jyotirmoy
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.
    methylR: a graphical interface for comprehensive DNA methylation array data analysis2023In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 39, no 4, article id btad184Article in journal (Refereed)
    Abstract [en]

    Motivation: DNA methylation analysis using arrays is a widely used method in research and clinical studies to study Epigenetics. Although several packages have been published to incur the results, most of them require a deep computational knowledge to perform the analysis. To resolve the limitation and to offer an easily accessible solution for researchers, we developed methylR a graphical tool that can analyze not only the raw data but also performs different downstream analyses with a few mouse clicks.Results: We used standard and established open-source published packages or pipelines in methylR. We evaluated a publicly available dataset and compared the published results with those obtained with our tool. We implemented eight downstream analysis modules that can perform multidimensional analyses to pathway enrichment. Although the main application is designed for Illumina DNA methylation array data analysis, we made the accessory modules suitable for other kinds of data analysis as well.

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  • 3.
    Petrosino, Giuseppe
    et al.
    Stazione Zool Anton Dohrn, Italy; Inst Mol Biol IMB, Germany.
    Ponte, Giovanna
    Stazione Zool Anton Dohrn, Italy.
    Volpe, Massimiliano
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences. Stazione Zool Anton Dohrn, Italy; Ist Italiano Tecnol IIT, Italy.
    Zarrella, Ilaria
    Stazione Zool Anton Dohrn, Italy.
    Ansaloni, Federico
    Ist Italiano Tecnol IIT, Italy.
    Langella, Concetta
    Stazione Zool Anton Dohrn, Italy.
    Di Cristina, Giulia
    Stazione Zool Anton Dohrn, Italy; Univ Cologne, Germany.
    Finaurini, Sara
    Scuola Int Super Avanzati SISSA, Italy.
    Russo, Monia T.
    Stazione Zool Anton Dohrn, Italy.
    Basu, Swaraj
    Stazione Zool Anton Dohrn, Italy; Strand Life Sci, India.
    Musacchia, Francesco
    Stazione Zool Anton Dohrn, Italy.
    Ristoratore, Filomena
    Stazione Zool Anton Dohrn, Italy.
    Pavlinic, Dinko
    European Mol Biol Lab EMBL, Germany; Inst Mol & Clin Ophthalmol, Switzerland.
    Benes, Vladimir
    European Mol Biol Lab EMBL, Germany.
    Ferrante, Maria I.
    Stazione Zool Anton Dohrn, Italy.
    Albertin, Caroline
    Marine Biol Lab MBL, MA USA.
    Simakov, Oleg
    Grad Univ, Japan; Univ Wien, Austria.
    Gustincich, Stefano
    Ist Italiano Tecnol IIT, Italy; Scuola Int Super Avanzati SISSA, Italy.
    Fiorito, Graziano
    Stazione Zool Anton Dohrn, Italy.
    Sanges, Remo
    Stazione Zool Anton Dohrn, Italy; Ist Italiano Tecnol IIT, Italy; Scuola Int Super Avanzati SISSA, Italy.
    Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain2022In: BMC Biology, E-ISSN 1741-7007, Vol. 20, no 1, article id 116Article in journal (Refereed)
    Abstract [en]

    Background Transposable elements (TEs) widely contribute to the evolution of genomes allowing genomic innovations, generating germinal and somatic heterogeneity, and giving birth to long non-coding RNAs (lncRNAs). These features have been associated to the evolution, functioning, and complexity of the nervous system at such a level that somatic retrotransposition of long interspersed element (LINE) L1 has been proposed to be associated to human cognition. Among invertebrates, octopuses are fascinating animals whose nervous system reaches a high level of complexity achieving sophisticated cognitive abilities. The sequencing of the genome of the Octopus bimaculoides revealed a striking expansion of TEs which were proposed to have contributed to the evolution of its complex nervous system. We recently found a similar expansion also in the genome of Octopus vulgaris. However, a specific search for the existence and the transcription of full-length transpositionally competent TEs has not been performed in this genus. Results Here, we report the identification of LINE elements competent for retrotransposition in Octopus vulgaris and Octopus bimaculoides and show evidence suggesting that they might be transcribed and determine germline and somatic polymorphisms especially in the brain. Transcription and translation measured for one of these elements resulted in specific signals in neurons belonging to areas associated with behavioral plasticity. We also report the transcription of thousands of lncRNAs and the pervasive inclusion of TE fragments in the transcriptomes of both Octopus species, further testifying the crucial activity of TEs in the evolution of the octopus genomes. Conclusions The neural transcriptome of the octopus shows the transcription of thousands of putative lncRNAs and of a full-length LINE element belonging to the RTE class. We speculate that a convergent evolutionary process involving retrotransposons activity in the brain has been important for the evolution of sophisticated cognitive abilities in this genus.

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