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Molecular Research on Rare Cancers and Metabolic Diseases
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Molecular Research on Rare Cancers and Metabolic Diseases

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Endocrinology and Metabolism".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 5161

Special Issue Editor

Prof. Dr. Andrea Bernini

E-Mail Website
Guest Editor
Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
Interests: structural biology; rare diseases; metabolomics; nuclear magnetic resonance; protein dynamics; protein core & surface; transient pockets
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Rare diseases are life-threatening or chronically debilitating disorders uncommon in the general population. Rare diseases typically exhibit a high level of symptom complexity leading to diagnostic delays and requiring regular, ongoing multidisciplinary care and treatment. Omics techniques hold the key to new diagnoses and therapies for rare diseases, but constant advances in molecular research are needed to support these techniques at an increasing scale.

We are seeking papers that investigate the molecular basis of rare cancers and rare metabolic diseases by observation of dysregulated metabolites, tumor-derived circulating nucleic acids (cell-free circulating tumor DNA - ctDNA, microRNA - miRNA, non-coding RNAs - ncRNAs), cancer-associated proteins (CAPs), as well as emerging biomarkers such as exosomes Papers proposing innovative, multi-omics approaches and integration with bioinformatics, artificial intelligence, big data, and structural biology are warmly welcomed, Innovative applications of liquid biopsy for molecular research in rare diseases are desired as well.

Prof. Dr. Andrea Bernini
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • rare cancers
  • rare metabolic diseases
  • -omics research
  • integrated omics approaches
  • metabolomics
  • proteomics
  • transcriptomics
  • genomics
  • exosomes
  • liquid biopsy
  • structural biology

Published Papers (3 papers)

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Research

12 pages, 1829 KiB  
Article
Small Molecule Pytren-4QMn Metal Complex Slows down Huntington’s Disease Progression in Male zQ175 Transgenic Mice
by Marián Merino, Sonia González, Mª Carmen Tronch, Ana Virginia Sánchez-Sánchez, Mª Paz Clares, Antonio García-España, Enrique García-España and José L. Mullor
Int. J. Mol. Sci. 2023, 24(20), 15153; https://doi.org/10.3390/ijms242015153 - 13 Oct 2023
Viewed by 875
Abstract
Huntington’s disease (HD) is an inherited neurodegenerative disorder considered a rare disease with a prevalence of 5.7 per 100,000 people. It is caused by an autosomal dominant mutation consisting of expansions of trinucleotide repeats that translate into poly-glutamine enlarged mutant huntingtin proteins (mHTT), [...] Read more.
Huntington’s disease (HD) is an inherited neurodegenerative disorder considered a rare disease with a prevalence of 5.7 per 100,000 people. It is caused by an autosomal dominant mutation consisting of expansions of trinucleotide repeats that translate into poly-glutamine enlarged mutant huntingtin proteins (mHTT), which are particularly deleterious in brain tissues. Since there is no cure for this progressive fatal disease, searches for new therapeutic approaches are much needed. The small molecule pytren-4QMn (4QMn), a highly water-soluble mimic of the enzyme superoxide dismutase, has shown in vivo beneficial anti-inflammatory activity in mice and was able to remove mHTT deposits in a C. elegans model of HD. In this study, we assessed 4QMn therapeutic potential in zQ175 neo-deleted knock-in mice, a model of HD that closely mimics the heterozygosity, genetic injury, and progressive nature of the human disease. We provide evidence that 4QMn has good acute and chronic tolerability, and can cross the blood–brain barrier, and in male, but not female, zQ175 mice moderately ameliorate HD-altered gene expression, mHtt aggregation, and HD disease phenotype. Our data highlight the importance of considering sex-specific differences when testing new therapies using animal models and postulate 4QMn as a potential novel type of small water-soluble metal complex that could be worth further investigating for its therapeutic potential in HD, as well as in other polyglutamine diseases. Full article
(This article belongs to the Special Issue Molecular Research on Rare Cancers and Metabolic Diseases)
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15 pages, 1507 KiB  
Article
Molecular Signature of Biological Aggressiveness in Clear Cell Sarcoma of the Kidney (CCSK)
by Michele Fiore, Alberto Taddia, Valentina Indio, Salvatore Nicola Bertuccio, Daria Messelodi, Salvatore Serravalle, Jessica Bandini, Filippo Spreafico, Daniela Perotti, Paola Collini, Andrea Di Cataldo, Gianandrea Pasquinelli, Francesca Chiarini, Maura Fois, Fraia Melchionda, Andrea Pession and Annalisa Astolfi
Int. J. Mol. Sci. 2023, 24(4), 3743; https://doi.org/10.3390/ijms24043743 - 13 Feb 2023
Cited by 2 | Viewed by 2049
Abstract
Clear cell sarcoma of the kidney (CCSK) is a rare pediatric renal tumor with a worse prognosis than Wilms’ tumor. Although recently, BCOR internal tandem duplication (ITD) has been found as a driver mutation in more than 80% of cases, a deep molecular [...] Read more.
Clear cell sarcoma of the kidney (CCSK) is a rare pediatric renal tumor with a worse prognosis than Wilms’ tumor. Although recently, BCOR internal tandem duplication (ITD) has been found as a driver mutation in more than 80% of cases, a deep molecular characterization of this tumor is still lacking, as well as its correlation with the clinical course. The aim of this study was to investigate the differential molecular signature between metastatic and localized BCOR-ITD-positive CCSK at diagnosis. Whole-exome sequencing (WES) and whole-transcriptome sequencing (WTS) were performed on six localized and three metastatic BCOR-ITD-positive CCSKs, confirming that this tumor carries a low mutational burden. No significant recurrences of somatic or germline mutations other than BCOR-ITD were identified among the evaluated samples. Supervised analysis of gene expression data showed enrichment of hundreds of genes, with a significant overrepresentation of the MAPK signaling pathway in metastatic cases (p < 0.0001). Within the molecular signature of metastatic CCSK, five genes were highly and significantly over-expressed: FGF3, VEGFA, SPP1, ADM, and JUND. The role of FGF3 in the acquisition of a more aggressive phenotype was investigated in a cell model system obtained by introducing the ITD into the last exon of BCOR by Crispr/Cas9 gene editing of the HEK-293 cell line. Treatment with FGF3 of BCOR-ITD HEK-293 cell line induced a significant increase in cell migration versus both untreated and scramble cell clone. The identification of over-expressed genes in metastatic CCSKs, with a particular focus on FGF3, could offer new prognostic and therapeutic targets in more aggressive cases. Full article
(This article belongs to the Special Issue Molecular Research on Rare Cancers and Metabolic Diseases)
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12 pages, 1642 KiB  
Article
Untargeted NMR Metabolomics Reveals Alternative Biomarkers and Pathways in Alkaptonuria
by Daniela Grasso, Michela Geminiani, Silvia Galderisi, Gabriella Iacomelli, Luana Peruzzi, Barbara Marzocchi, Annalisa Santucci and Andrea Bernini
Int. J. Mol. Sci. 2022, 23(24), 15805; https://doi.org/10.3390/ijms232415805 - 13 Dec 2022
Cited by 3 | Viewed by 1879
Abstract
Alkaptonuria (AKU) is an ultra-rare metabolic disease caused by the accumulation of homogentisic acid (HGA), an intermediate product of phenylalanine and tyrosine degradation. AKU patients carry variants within the gene coding for homogentisate-1,2-dioxygenase (HGD), which are responsible for reducing the enzyme catalytic activity [...] Read more.
Alkaptonuria (AKU) is an ultra-rare metabolic disease caused by the accumulation of homogentisic acid (HGA), an intermediate product of phenylalanine and tyrosine degradation. AKU patients carry variants within the gene coding for homogentisate-1,2-dioxygenase (HGD), which are responsible for reducing the enzyme catalytic activity and the consequent accumulation of HGA and formation of a dark pigment called the ochronotic pigment. In individuals with alkaptonuria, ochronotic pigmentation of connective tissues occurs, leading to inflammation, degeneration, and eventually osteoarthritis. The molecular mechanisms underlying the multisystemic development of the disease severity are still not fully understood and are mostly limited to the metabolic pathway segment involving HGA. In this view, untargeted metabolomics of biofluids in metabolic diseases allows the direct investigation of molecular species involved in pathways alterations and their interplay. Here, we present the untargeted metabolomics study of AKU through the nuclear magnetic resonance of urine from a cohort of Italian patients; the study aims to unravel molecular species and mechanisms underlying the AKU metabolic disorder. Dysregulation of metabolic pathways other than the HGD route and new potential biomarkers beyond homogentisate are suggested, contributing to a more comprehensive molecular signature definition for AKU and the development of future adjuvant treatment. Full article
(This article belongs to the Special Issue Molecular Research on Rare Cancers and Metabolic Diseases)
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