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High-Throughput
Volume 9
Issue 1
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High-Throughput, Volume 9, Issue 1 (March 2020) – 6 articles

Cover Story (view full-size image): The challenge of modern medicine is to respond appropriately to oncological diseases by referring to a targeted vision in which the therapy is traced in the molecular profile of the tumor. The comparative use of two methods for the detection of somatic cancer variants, at different depths of evaluation, allows assuring an absolute accuracy of molecular investigation even in small neoplastic clones. In this perspective of innovation, it is essential to provide all the information so that “therapy can be sewn on the patient's skin”, to maximize the potential for response to treatment. View this paper.
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6 pages, 220 KiB  
Review
Factors Influencing Epigenetic Mechanisms: Is There A Role for Bariatric Surgery?
by Alessio Metere and Claire E. Graves
High-Throughput 2020, 9(1), 6; https://doi.org/10.3390/ht9010006 - 20 Mar 2020
Cited by 11 | Viewed by 4251
Abstract
Epigenetics is the interaction between the genome and environmental stimuli capable of influencing gene expression during development and aging. A large number of studies have shown that metabolic diseases are highly associated with epigenetic alterations, suggesting that epigenetic factors may play a central [...] Read more.
Epigenetics is the interaction between the genome and environmental stimuli capable of influencing gene expression during development and aging. A large number of studies have shown that metabolic diseases are highly associated with epigenetic alterations, suggesting that epigenetic factors may play a central role in obesity. To investigate these relationships, we focus our attention on the most common epigenetic modifications that occur in obesity, including DNA methylation and post-translational modifications of histones. We also consider bariatric surgery as an epigenetic factor, evaluating how the anatomic and physiologic modifications induced by these surgical techniques can change gene expression. Here we discuss the importance of epigenetic mechanisms in chronic disease and cancer, and the role of epigenetic disturbances in obesity, with a focus on the role of bariatric surgery. Full article
15 pages, 1953 KiB  
Article
Rational Engineering of the Substrate Specificity of a Thermostable D-Hydantoinase (Dihydropyrimidinase)
by Hovsep Aganyants, Pierre Weigel, Yeranuhi Hovhannisyan, Michèle Lecocq, Haykanush Koloyan, Artur Hambardzumyan, Anichka Hovsepyan, Jean-Noël Hallet and Vehary Sakanyan
High-Throughput 2020, 9(1), 5; https://doi.org/10.3390/ht9010005 - 12 Feb 2020
Cited by 4 | Viewed by 4186
Abstract
D-hydantoinases catalyze an enantioselective opening of 5- and 6-membered cyclic structures and therefore can be used for the production of optically pure precursors for biomedical applications. The thermostable D-hydantoinase from Geobacillus stearothermophilus ATCC 31783 is a manganese-dependent enzyme and exhibits low activity towards [...] Read more.
D-hydantoinases catalyze an enantioselective opening of 5- and 6-membered cyclic structures and therefore can be used for the production of optically pure precursors for biomedical applications. The thermostable D-hydantoinase from Geobacillus stearothermophilus ATCC 31783 is a manganese-dependent enzyme and exhibits low activity towards bulky hydantoin derivatives. Homology modeling with a known 3D structure (PDB code: 1K1D) allowed us to identify the amino acids to be mutated at the substrate binding site and in its immediate vicinity to modulate the substrate specificity. Both single and double substituted mutants were generated by site-directed mutagenesis at appropriate sites located inside and outside of the stereochemistry gate loops (SGL) involved in the substrate binding. Substrate specificity and kinetic constant data demonstrate that the replacement of Phe159 and Trp287 with alanine leads to an increase in the enzyme activity towards D,L-5-benzyl and D,L-5-indolylmethyl hydantoins. The length of the side chain and the hydrophobicity of substrates are essential parameters to consider when designing the substrate binding pocket for bulky hydantoins. Our data highlight that D-hydantoinase is the authentic dihydropyrimidinase involved in the pyrimidine reductive catabolic pathway in moderate thermophiles. Full article
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12 pages, 669 KiB  
Article
Comparative Study of NGS Platform Ion Torrent Personal Genome Machine and Therascreen Rotor-Gene Q for the Detection of Somatic Variants in Cancer
by Angela Lombardi, Margherita Russo, Amalia Luce, Floriana Morgillo, Virginia Tirino, Gabriella Misso, Erika Martinelli, Teresa Troiani, Vincenzo Desiderio, Gianpaolo Papaccio, Francesco Iovino, Giuseppe Argenziano, Elvira Moscarella, Pasquale Sperlongano, Gennaro Galizia, Raffaele Addeo, Alois Necas, Andrea Necasova, Fortunato Ciardiello, Andrea Ronchi, Michele Caraglia and Anna Grimaldiadd Show full author list remove Hide full author list
High-Throughput 2020, 9(1), 4; https://doi.org/10.3390/ht9010004 - 11 Feb 2020
Cited by 2 | Viewed by 8265
Abstract
Molecular profiling of a tumor allows the opportunity to design specific therapies which are able to interact only with cancer cells characterized by the accumulation of several genomic aberrations. This study investigates the usefulness of next-generation sequencing (NGS) and mutation-specific analysis methods for [...] Read more.
Molecular profiling of a tumor allows the opportunity to design specific therapies which are able to interact only with cancer cells characterized by the accumulation of several genomic aberrations. This study investigates the usefulness of next-generation sequencing (NGS) and mutation-specific analysis methods for the detection of target genes for current therapies in non-small-cell lung cancer (NSCLC), metastatic colorectal cancer (mCRC), and melanoma patients. We focused our attention on EGFR, BRAF, KRAS, and BRAF genes for NSCLC, melanoma, and mCRC samples, respectively. Our study demonstrated that in about 2% of analyzed cases, the two techniques did not show the same or overlapping results. Two patients affected by mCRC resulted in wild-type (WT) for BRAF and two cases with NSCLC were WT for EGFR according to PGM analysis. In contrast, these samples were mutated for the evaluated genes using the therascreen test on Rotor-Gene Q. In conclusion, our experience suggests that it would be appropriate to confirm the WT status of the genes of interest with a more sensitive analysis method to avoid the presence of a small neoplastic clone and drive the clinician to correct patient monitoring. Full article
(This article belongs to the Special Issue Selected Papers from 1st International and 32nd Annual Conference of Italian Association of Cell Culture)
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9 pages, 970 KiB  
Commentary
Precision Medicine in Non-Communicable Diseases
by Giuseppe Novelli, Michela Biancolella, Andrea Latini, Aldo Spallone, Paola Borgiani and Marisa Papaluca
High-Throughput 2020, 9(1), 3; https://doi.org/10.3390/ht9010003 - 7 Feb 2020
Cited by 6 | Viewed by 5405
Abstract
The increase in life expectancy during the 20th century ranks as one of society’s greatest achievements, with massive growth in the numbers and proportion of the elderly, virtually occurring in every country of the world. The burden of chronic diseases is one of [...] Read more.
The increase in life expectancy during the 20th century ranks as one of society’s greatest achievements, with massive growth in the numbers and proportion of the elderly, virtually occurring in every country of the world. The burden of chronic diseases is one of the main consequences of this phenomenon, severely hampering the quality of life of elderly people and challenging the efficiency and sustainability of healthcare systems. Non-communicable diseases (NCDs) are considered a global emergency responsible for over 70% of deaths worldwide. NCDs are also the basis for complex and multifactorial diseases such as hypertension, diabetes, and obesity. The epidemics of NCDs are a consequence of a complex interaction between health, economic growth, and development. This interaction includes the individual genome, the microbiome, the metabolome, the immune status, and environmental factors such as nutritional and chemical exposure. To counteract NCDs, it is therefore essential to develop an innovative, personalized, preventative, early care model through the integration of different molecular profiles of individuals to identify both the critical biomarkers of NCD susceptibility and to discover novel therapeutic targets. Full article
(This article belongs to the Special Issue Selected Papers from 1st International and 32nd Annual Conference of Italian Association of Cell Culture)
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2 pages, 221 KiB  
Editorial
Acknowledgement to Reviewers of High-Throughput in 2019
by High-Throughput Editorial Office
High-Throughput 2020, 9(1), 2; https://doi.org/10.3390/ht9010002 - 16 Jan 2020
Viewed by 2657
Abstract
The editorial team greatly appreciates the reviewers who have dedicated their considerable time and expertise to the journal’s rigorous editorial process over the past 12 months, regardless of whether the papers are finally published or not [...] Full article
16 pages, 314 KiB  
Review
Applications of Next Generation Sequencing to the Analysis of Familial Breast/Ovarian Cancer
by Veronica Zelli, Chiara Compagnoni, Katia Cannita, Roberta Capelli, Carlo Capalbo, Mauro Di Vito Nolfi, Edoardo Alesse, Francesca Zazzeroni and Alessandra Tessitore
High-Throughput 2020, 9(1), 1; https://doi.org/10.3390/ht9010001 - 10 Jan 2020
Cited by 23 | Viewed by 7479
Abstract
Next generation sequencing (NGS) provides a powerful tool in the field of medical genetics, allowing one to perform multi-gene analysis and to sequence entire exomes (WES), transcriptomes or genomes (WGS). The generated high-throughput data are particularly suitable for enhancing the understanding of the [...] Read more.
Next generation sequencing (NGS) provides a powerful tool in the field of medical genetics, allowing one to perform multi-gene analysis and to sequence entire exomes (WES), transcriptomes or genomes (WGS). The generated high-throughput data are particularly suitable for enhancing the understanding of the genetic bases of complex, multi-gene diseases, such as cancer. Among the various types of tumors, those with a familial predisposition are of great interest for the isolation of novel genes or gene variants, detectable at the germline level and involved in cancer pathogenesis. The identification of novel genetic factors would have great translational value, helping clinicians in defining risk and prevention strategies. In this regard, it is known that the majority of breast/ovarian cases with familial predisposition, lacking variants in the highly penetrant BRCA1 and BRCA2 genes (non-BRCA), remains unexplained, although several less penetrant genes (e.g., ATM, PALB2) have been identified. In this scenario, NGS technologies offer a powerful tool for the discovery of novel factors involved in familial breast/ovarian cancer. In this review, we summarize and discuss the state of the art applications of NGS gene panels, WES and WGS in the context of familial breast/ovarian cancer. Full article
(This article belongs to the Special Issue Selected Papers from 1st International and 32nd Annual Conference of Italian Association of Cell Culture)
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