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

Deadline for manuscript submissions: closed (30 September 2020) | Viewed by 39736

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Prof. Dr. Yuriy L. Orlov

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The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 119991 Moscow, Russia
Interests: computer genomics; bioinformatics; digital medicine (e-Health); gene expression regulation; ChIP-seq
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Prof. Dr. Ancha Baranova

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Guest Editor

School of Systems Biology, George Mason University, Fairfax, VA 22030, USA
Interests: biomedicine; bioinformatics; medical genomics; genetics; molecular network analysis; personalized medicine
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Prof. Dr. Vadim Klimontov

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Laboratory of Endocrinology, Research Institute of Clinical and Experimental Lymphology – Branch of the Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
Interests: diabetes; obesity; chronic kidney disease; metabolism; biomedicine; e-health
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue collects papers on medical genomics, human population genetics, and computational biology applications in biomedicine, providing a continuation of an earlier MDPI IJMS Special Issue entitled “Medical Genetics, Genomics and Bioinformatics” https://www.mdpi.com/journal/ijms/special_issues/Medical_Genetics_Bioinformatics

Based on the readers’ interest in medical genetics and genomics we are continuing our publication in this area based on novel technological approaches, gene networks, and metabolic pathways analysis. Here, we focus on bioinformatics and systems biology approaches to medical genetics problems.

Topics of interest to this Special Issue include:

Bioinformatics approaches for medical genomics;
Bioinformatics approaches for omics-based technologies;
Medical applications of genetics research;
Genotyping and personalized medicine;
Research of gene pools in populations;
Systems biology and network medicine;
Interdisciplinary research in genetics and biomedicine;
Molecular biology in human health and diseases;
New biomarkers and molecular targets;
E-health and digital medicine tools;

The current collection continues the series of post-conference Special Journal Issues presenting the highlights from the set of meetings on genetics and systems biology held in Russia last and this year. We welcome novel materials beyond the conference discussion.

Prof. Dr. Yuriy L Orlov
Prof. Dr. Ancha Baranova
Prof. Dr. Vadim Klimontov
Guest Editors

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

Medical genetics
Population genetics
Medical genomics
Bioinformatics
Computational biology
Molecular mechanisms of diseases
Systems biology for medicine
E-health

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Related Special Issue

Medical Genetics, Genomics and Bioinformatics – 2021 in International Journal of Molecular Sciences (32 articles)

Published Papers (11 papers)

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Editorial

Jump to: Research, Review

6 pages, 200 KiB

Open AccessEditorial

Medical Genetics, Genomics and Bioinformatics Aid in Understanding Molecular Mechanisms of Human Diseases

by Yuriy L. Orlov, Anastasia A. Anashkina, Vadim V. Klimontov and Ancha V. Baranova

Int. J. Mol. Sci. 2021, 22(18), 9962; https://doi.org/10.3390/ijms22189962 - 15 Sep 2021

Cited by 25 | Viewed by 3140

Abstract

Molecular mechanisms of human disease progression often have complex genetic underpinnings, and sophisticated sequencing approaches coupled with advanced analytics [...] Full article

(This article belongs to the Special Issue Medical Genetics, Genomics and Bioinformatics – 2020)

Research

Jump to: Editorial, Review

20 pages, 1263 KiB

Open AccessArticle

Bioinformatic Reconstruction and Analysis of Gene Networks Related to Glucose Variability in Diabetes and Its Complications

by Olga V. Saik and Vadim V. Klimontov

Int. J. Mol. Sci. 2020, 21(22), 8691; https://doi.org/10.3390/ijms21228691 - 18 Nov 2020

Cited by 30 | Viewed by 4890

Abstract

Glucose variability (GV) has been recognized recently as a promoter of complications and therapeutic targets in diabetes. The aim of this study was to reconstruct and analyze gene networks related to GV in diabetes and its complications. For network analysis, we used the ANDSystem that provides automatic network reconstruction and analysis based on text mining. The network of GV consisted of 37 genes/proteins associated with both hyperglycemia and hypoglycemia. Cardiovascular system, pancreas, adipose and muscle tissues, gastrointestinal tract, and kidney were recognized as the loci with the highest expression of GV-related genes. According to Gene Ontology enrichment analysis, these genes are associated with insulin secretion, glucose metabolism, glycogen biosynthesis, gluconeogenesis, MAPK and JAK-STAT cascades, protein kinase B signaling, cell proliferation, nitric oxide biosynthesis, etc. GV-related genes were found to occupy central positions in the networks of diabetes complications (cardiovascular disease, diabetic nephropathy, retinopathy, and neuropathy) and were associated with response to hypoxia. Gene prioritization analysis identified new gene candidates (THBS1, FN1, HSP90AA1, EGFR, MAPK1, STAT3, TP53, EGF, GSK3B, and PTEN) potentially involved in GV. The results expand the understanding of the molecular mechanisms of the GV phenomenon in diabetes and provide molecular markers and therapeutic targets for future research. Full article

(This article belongs to the Special Issue Medical Genetics, Genomics and Bioinformatics – 2020)

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15 pages, 10395 KiB

Open AccessArticle

New Model for Stacking Monomers in Filamentous Actin from Skeletal Muscles of Oryctolagus cuniculus

by Anna V. Glyakina, Alexey K. Surin, Sergei Yu. Grishin, Olga M. Selivanova, Mariya Yu. Suvorina, Liya G. Bobyleva, Ivan M. Vikhlyantsev and Oxana V. Galzitskaya

Int. J. Mol. Sci. 2020, 21(21), 8319; https://doi.org/10.3390/ijms21218319 - 6 Nov 2020

Cited by 5 | Viewed by 2837

Abstract

To date, some scientific evidence (limited proteolysis, mass spectrometry analysis, electron microscopy (EM)) has accumulated, which indicates that the generally accepted model of double-stranded of filamentous actin (F-actin) organization in eukaryotic cells is not the only one. This entails an ambiguous understanding of many of the key cellular processes in which F-actin is involved. For a detailed understanding of the mechanism of F-actin assembly and actin interaction with its partners, it is necessary to take into account the polymorphism of the structural organization of F-actin at the molecular level. Using electron microscopy, limited proteolysis, mass spectrometry, X-ray diffraction, and structural modeling we demonstrated that F-actin presented in the EM images has no double-stranded organization, the regions of protease resistance are accessible for action of proteases in F-actin models. Based on all data, a new spatial model of filamentous actin is proposed, and the F-actin polymorphism is discussed. Full article

(This article belongs to the Special Issue Medical Genetics, Genomics and Bioinformatics – 2020)

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12 pages, 713 KiB

Open AccessArticle

Prediction of Protein–ligand Interaction Based on Sequence Similarity and Ligand Structural Features

by Dmitry Karasev, Boris Sobolev, Alexey Lagunin, Dmitry Filimonov and Vladimir Poroikov

Int. J. Mol. Sci. 2020, 21(21), 8152; https://doi.org/10.3390/ijms21218152 - 31 Oct 2020

Cited by 7 | Viewed by 2434

Abstract

Computationally predicting the interaction of proteins and ligands presents three main directions: the search of new target proteins for ligands, the search of new ligands for targets, and predicting the interaction of new proteins and new ligands. We proposed an approach providing the fuzzy classification of protein sequences based on the ligand structural features to analyze the latter most complicated case. We tested our approach on five protein groups, which represented promised targets for drug-like ligands and differed in functional peculiarities. The training sets were built with the original procedure overcoming the data ambiguity. Our study showed the effective prediction of new targets for ligands with an average accuracy of 0.96. The prediction of new ligands for targets displayed the average accuracy 0.95; accuracy estimates were close to our previous results, comparable in accuracy to those of other methods or exceeded them. Using the fuzzy coefficients reflecting the target-to-ligand specificity, we provided predicting interactions for new proteins and new ligands; the obtained accuracy values from 0.89 to 0.99 were acceptable for such a sophisticated task. The protein kinase family case demonstrated the ability to account for subtle features of proteins and ligands required for the specificity of protein–ligand interaction. Full article

(This article belongs to the Special Issue Medical Genetics, Genomics and Bioinformatics – 2020)

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17 pages, 2812 KiB

Open AccessArticle

Gene Expression Regulation and Secretory Activity of Mesenchymal Stem Cells upon In Vitro Contact with Microarc Calcium Phosphate Coating

by Larisa Litvinova, Kristina Yurova, Valeria Shupletsova, Olga Khaziakhmatova, Vladimir Malashchenko, Egor Shunkin, Elena Melashchenko, Natalia Todosenko, Marina Khlusova, Yurii Sharkeev, Ekaterina Komarova, Maria Sedelnikova and Igor Khlusov

Int. J. Mol. Sci. 2020, 21(20), 7682; https://doi.org/10.3390/ijms21207682 - 16 Oct 2020

Cited by 9 | Viewed by 2888

Abstract

The manufacture of biomaterial surfaces with desired physical and chemical properties that can directly induce osteogenic differentiation without the need for biochemical additives is an excellent strategy for controlling the behavior of mesenchymal stem cells (MSCs) in vivo. We studied the cellular and molecular reactions of MSCs to samples with a double-sided calcium phosphate (CaP) coating and an average roughness index (Ra) of 2.4–4.6 µm. The study aimed to evaluate the effect of a three-dimensional matrix on the relative mRNA expression levels of genes associated with the differentiation and maturation of MSCs toward osteogenesis (RUNX2, BMP2, BMP6, BGLAP, and ALPL) under conditions of distant interaction in vitro. Correlations were revealed between the mRNA expression of some osteogenic and cytokine/chemokine genes and the secretion of cytokines and chemokines that may potentiate the differentiation of cells into osteoblasts, which indicates the formation of humoral components of the extracellular matrix and the creation of conditions supporting the establishment of hematopoietic niches. Full article

(This article belongs to the Special Issue Medical Genetics, Genomics and Bioinformatics – 2020)

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25 pages, 3387 KiB

Open AccessArticle

Natural Catalytic IgGs Hydrolyzing Histones in Schizophrenia: Are They the Link between Humoral Immunity and Inflammation?

by Evgeny A. Ermakov, Daria A. Parshukova, Georgy A. Nevinsky and Valentina N. Buneva

Int. J. Mol. Sci. 2020, 21(19), 7238; https://doi.org/10.3390/ijms21197238 - 30 Sep 2020

Cited by 12 | Viewed by 2526

Abstract

Schizophrenia is known to be accompanied not only with an imbalance in the neurotransmitter systems but also with immune system dysregulation and chronic low-grade inflammation. Extracellular histones and nucleosomes as damage-associated molecular patterns (DAMPs) trigger systemic inflammatory and toxic reactions by activating Toll-like receptors. In this work, we obtained the first evidence that polyclonal IgGs of patients with schizophrenia effectively hydrolyze five histones (H1, H2a, H2b, H3, and H4). Several strict criteria were used to demonstrate that histone-hydrolyzing activity is a property of the analyzed IgGs. The IgGs histone-hydrolyzing activity level, depending on the type of histone (H1–H4), was statistically significantly 6.1–20.2 times higher than that of conditionally healthy donors. The investigated biochemical properties (pH and metal ion dependences, kinetic characteristics) of these natural catalytic IgGs differed markedly from canonical proteases. It was previously established that the generation of natural catalytic antibodies is an early and clear sign of impaired humoral immunity. One cannot, however, exclude that histone-hydrolyzing antibodies may play a positive role in schizophrenia pathogenesis because histone removal from circulation or the inflamed area minimizes the inflammatory responses. Thus, it can be assumed that histone-hydrolyzing antibodies are a link between humoral immunity and inflammatory responses in schizophrenia. Full article

(This article belongs to the Special Issue Medical Genetics, Genomics and Bioinformatics – 2020)

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13 pages, 810 KiB

Open AccessArticle

Immunohistochemistry and Mutation Analysis of SDHx Genes in Carotid Paragangliomas

by Anastasiya V. Snezhkina, Dmitry V. Kalinin, Vladislav S. Pavlov, Elena N. Lukyanova, Alexander L. Golovyuk, Maria S. Fedorova, Elena A. Pudova, Maria V. Savvateeva, Oleg A. Stepanov, Andrey A. Poloznikov, Tatiana B. Demidova, Nataliya V. Melnikova, Alexey A. Dmitriev, George S. Krasnov and Anna V. Kudryavtseva

Int. J. Mol. Sci. 2020, 21(18), 6950; https://doi.org/10.3390/ijms21186950 - 22 Sep 2020

Cited by 15 | Viewed by 3434

Abstract

Carotid paragangliomas (CPGLs) are rare neuroendocrine tumors often associated with mutations in SDHx genes. The immunohistochemistry of succinate dehydrogenase (SDH) subunits has been considered a useful instrument for the prediction of SDHx mutations in paragangliomas/pheochromocytomas. We compared the mutation status of SDHx genes with the immunohistochemical (IHC) staining of SDH subunits in CPGLs. To identify pathogenic/likely pathogenic variants in SDHx genes, exome sequencing data analysis among 42 CPGL patients was performed. IHC staining of SDH subunits was carried out for all CPGLs studied. We encountered SDHx variants in 38% (16/42) of the cases in SDHx genes. IHC showed negative (5/15) or weak diffuse (10/15) SDHB staining in most tumors with variants in any of SDHx (94%, 15/16). In SDHA-mutated CPGL, SDHA expression was completely absent and weak diffuse SDHB staining was detected. Positive immunoreactivity for all SDH subunits was found in one case with a variant in SDHD. Notably, CPGL samples without variants in SDHx also demonstrated negative (2/11) or weak diffuse (9/11) SDHB staining (42%, 11/26). Obtained results indicate that SDH immunohistochemistry does not fully reflect the presence of mutations in the genes; diagnostic effectiveness of this method was 71%. However, given the high sensitivity of SDHB immunohistochemistry, it could be used for initial identifications of patients potentially carrying SDHx mutations for recommendation of genetic testing. Full article

(This article belongs to the Special Issue Medical Genetics, Genomics and Bioinformatics – 2020)

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32 pages, 1378 KiB

Open AccessArticle

Gene Expression Changes in the Ventral Tegmental Area of Male Mice with Alternative Social Behavior Experience in Chronic Agonistic Interactions

by Olga Redina, Vladimir Babenko, Dmitry Smagin, Irina Kovalenko, Anna Galyamina, Vadim Efimov and Natalia Kudryavtseva

Int. J. Mol. Sci. 2020, 21(18), 6599; https://doi.org/10.3390/ijms21186599 - 9 Sep 2020

Cited by 9 | Viewed by 2681

Abstract

Daily agonistic interactions of mice are an effective experimental approach to elucidate the molecular mechanisms underlying the excitation of the brain neurons and the formation of alternative social behavior patterns. An RNA-Seq analysis was used to compare the ventral tegmental area (VTA) transcriptome profiles for three groups of male C57BL/6J mice: winners, a group of chronically winning mice, losers, a group of chronically defeated mice, and controls. The data obtained show that both winners and defeated mice experience stress, which however, has a more drastic effect on defeated animals causing more significant changes in the levels of gene transcription. Four genes (Nrgn, Ercc2, Otx2, and Six3) changed their VTA expression profiles in opposite directions in winners and defeated mice. It was first shown that Nrgn (neurogranin) expression was highly correlated with the expression of the genes involved in dopamine synthesis and transport (Th, Ddc, Slc6a3, and Drd2) in the VTA of defeated mice but not in winners. The obtained network of 31 coregulated genes, encoding proteins associated with nervous system development (including 24 genes associated with the generation of neurons), may be potentially useful for studying their role in the VTA dopaminergic neurons maturation under the influence of social stress. Full article

(This article belongs to the Special Issue Medical Genetics, Genomics and Bioinformatics – 2020)

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24 pages, 2189 KiB

Open AccessArticle

Potential Associations Among Alteration of Salivary miRNAs, Saliva Microbiome Structure, and Cognitive Impairments in Autistic Children

by Marco Ragusa, Maria Santagati, Federica Mirabella, Giovanni Lauretta, Matilde Cirnigliaro, Duilia Brex, Cristina Barbagallo, Carla Noemi Domini, Mariangela Gulisano, Rita Barone, Laura Trovato, Salvatore Oliveri, Gino Mongelli, Ambra Spitale, Davide Barbagallo, Cinzia Di Pietro, Stefania Stefani, Renata Rizzo and Michele Purrello

Int. J. Mol. Sci. 2020, 21(17), 6203; https://doi.org/10.3390/ijms21176203 - 27 Aug 2020

Cited by 29 | Viewed by 5464

Abstract

Recent evidence has demonstrated that salivary molecules, as well as bacterial populations, can be perturbed by several pathological conditions, including neuro-psychiatric diseases. This relationship between brain functionality and saliva composition could be exploited to unveil new pathological mechanisms of elusive diseases, such as Autistic Spectrum Disorder (ASD). We performed a combined approach of miRNA expression profiling by NanoString technology, followed by validation experiments in qPCR, and 16S rRNA microbiome analysis on saliva from 53 ASD and 27 neurologically unaffected control (NUC) children. MiR-29a-3p and miR-141-3p were upregulated, while miR-16-5p, let-7b-5p, and miR-451a were downregulated in ASD compared to NUCs. Microbiome analysis on the same subjects revealed that Rothia, Filifactor, Actinobacillus, Weeksellaceae, Ralstonia, Pasteurellaceae, and Aggregatibacter increased their abundance in ASD patients, while Tannerella, Moryella and TM7-3 decreased. Variations of both miRNAs and microbes were statistically associated to different neuropsychological scores related to anomalies in social interaction and communication. Among miRNA/bacteria associations, the most relevant was the negative correlation between salivary miR-141-3p expression and Tannerella abundance. MiRNA and microbiome dysregulations found in the saliva of ASD children are potentially associated with cognitive impairments of the subjects. Furthermore, a potential cross-talking between circulating miRNAs and resident bacteria could occur in saliva of ASD. Full article

(This article belongs to the Special Issue Medical Genetics, Genomics and Bioinformatics – 2020)

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Review

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16 pages, 1013 KiB

Open AccessReview

Current Insights in Elucidation of Possible Molecular Mechanisms of the Juvenile Form of Batten Disease

by Elena K. Shematorova and George V. Shpakovski

Int. J. Mol. Sci. 2020, 21(21), 8055; https://doi.org/10.3390/ijms21218055 - 29 Oct 2020

Cited by 6 | Viewed by 4297

Abstract

The neuronal ceroid lipofuscinoses (NCLs) collectively constitute one of the most common forms of inherited childhood-onset neurodegenerative disorders. They form a heterogeneous group of incurable lysosomal storage diseases that lead to blindness, motor deterioration, epilepsy, and dementia. Traditionally the NCL diseases were classified according to the age of disease onset (infantile, late-infantile, juvenile, and adult forms), with at least 13 different NCL varieties having been described at present. The current review focuses on classic juvenile NCL (JNCL) or the so-called Batten (Batten-Spielmeyer-Vogt; Spielmeyer-Sjogren) disease, which represents the most common and the most studied form of NCL, and is caused by mutations in the CLN3 gene located on human chromosome 16. Most JNCL patients carry the same 1.02-kb deletion in this gene, encoding an unusual transmembrane protein, CLN3, or battenin. Accordingly, the names CLN3-related neuronal ceroid lipofuscinosis or CLN3-disease sometimes have been used for this malady. Despite excessive in vitro and in vivo studies, the precise functions of the CLN3 protein and the JNCL disease mechanisms remain elusive and are the main subject of this review. Although the CLN3 gene is highly conserved in evolution of all mammalian species, detailed analysis of recent genomic and transcriptomic data indicates the presence of human-specific features of its expression, which are also under discussion. The main recorded to date changes in cell metabolism, to some extent contributing to the emergence and progression of JNCL disease, and human-specific molecular features of CLN3 gene expression are summarized and critically discussed with an emphasis on the possible molecular mechanisms of the malady appearance and progression. Full article

(This article belongs to the Special Issue Medical Genetics, Genomics and Bioinformatics – 2020)

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26 pages, 744 KiB

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Multiple Endocrine Neoplasia Type 1: The Potential Role of microRNAs in the Management of the Syndrome

by Simone Donati, Simone Ciuffi, Francesca Marini, Gaia Palmini, Francesca Miglietta, Cinzia Aurilia and Maria Luisa Brandi

Int. J. Mol. Sci. 2020, 21(20), 7592; https://doi.org/10.3390/ijms21207592 - 14 Oct 2020

Cited by 10 | Viewed by 3044

Abstract

Multiple endocrine neoplasia type 1 (MEN1) is a rare inherited tumor syndrome, characterized by the development of multiple neuroendocrine tumors (NETs) in a single patient. Major manifestations include primary hyperparathyroidism, gastro-entero-pancreatic neuroendocrine tumors, and pituitary adenomas. In addition to these main NETs, various combinations of more than 20 endocrine and non-endocrine tumors have been described in MEN1 patients. Despite advances in diagnostic techniques and treatment options, which are generally similar to those of sporadic tumors, patients with MEN1 have a poor life expectancy, and the need for targeted therapies is strongly felt. MEN1 is caused by germline heterozygous inactivating mutations of the MEN1 gene, which encodes menin, a tumor suppressor protein. The lack of a direct genotype–phenotype correlation does not permit the determination of the exact clinical course of the syndrome. One of the possible causes of this lack of association could be ascribed to epigenetic factors, including microRNAs (miRNAs), single-stranded non-coding small RNAs that negatively regulate post-transcriptional gene expression. Some miRNAs, and their deregulation, have been associated with MEN1 tumorigenesis. Recently, an extracellular class of miRNAs has also been identified (c-miRNAs); variations in their levels showed association with various human diseases, including tumors. The aim of this review is to provide a general overview on the involvement of miRNAs in MEN1 tumor development, to be used as possible targets for novel molecular therapies. The potential role of c-miRNAs as future non-invasive diagnostic and prognostic biomarkers of MEN1 will be discussed as well. Full article

(This article belongs to the Special Issue Medical Genetics, Genomics and Bioinformatics – 2020)

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