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Special Issue "Feature Annual Reviews in Molecular Genetics and Genomics 2021"

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

Deadline for manuscript submissions: closed (31 October 2021).

Special Issue Editors

Dr. Akiko Maeda
E-Mail Website
Guest Editor
1. Laboratory for Retinal Regeneration, BDR, RIKEN Kobe, Hyogo, Japan
2. Retinal Degeneration Research Unit, Kobe City Eye Hospital Kobe, Hyogo, Japan
Interests: inherited retinal dystrophy; gene therapy; pharmacological therapy; stem cell therapy; disease modelling
Prof. Dr. Maria Adelaide Caligo
E-Mail Website
Guest Editor
Molecular Genetics Unit, Azienda Ospedaliera-Universitaria Pisana-Santa Chiara University Hospital, Pisa, Italy
Interests: hereditary cancer; breast ovarian tumor; cancer predisposition genes; BRCA1; BRCA2; splicing mutations; regulatory variants; genetic variant classification

Special Issue Information

Dear Colleagues,

This Special Issue aims to collect high quality review papers in all the fields of molecular genetics and genomics. We encourage researchers from related fields within the journal’s scope to contribute review papers highlighting the latest developments in their research field, or to invite relevant experts and colleagues to do so. This Topical Collection primarily publishes review papers by invitation, but will also publish reviews on topics of particular interest that do not overlap with current or recent Special Issues in our section.

https://www.mdpi.com/journal/ijms/sections/genetics_genomics

In this Special Issue, full length comprehensive reviews and topical reviews will be considered. Reviews provide comprehensive in depth overviews with no length restrictions, whereas topical reviews focus on a concise and precise “at-a-glance” summary of novel developments in the field. Topical reviews should be no more than 4000 words in length, with 2–4 “at-a-glance” figure(s) or a comprehensive table.

Dr. Akiko Maeda
Prof. Dr. Maria Adelaide Caligo
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 papers will be 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

  • Gene regulation, chromatin, and epigenetics
  • Genome integrity, repair, and replication
  • Genes or genomes related to phenotypes and human physiopathology
  • Gene flow and transfer
  • Plant genetic and genomic studies
  • Computational genomics
  • Functional genomics
  • Cancer Genetics, Epigenetics and Oncogenomics
  • Nutrigenomics, Pharmacogenetics and Pharmacogenomics

Published Papers (12 papers)

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Research

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Article
Aloysia Citrodora Essential Oil Inhibits Melanoma Cell Growth and Migration by Targeting HB-EGF-EGFR Signaling
Int. J. Mol. Sci. 2021, 22(15), 8151; https://doi.org/10.3390/ijms22158151 - 29 Jul 2021
Viewed by 852
Abstract
Patients diagnosed with melanoma have a poor prognosis due to regional invasion and metastases. The receptor tyrosine kinase epidermal growth factor receptor (EGFR) is found in a subtype of melanoma with a poor prognosis and contributes to drug resistance. Aloysia citrodora essential oil [...] Read more.
Patients diagnosed with melanoma have a poor prognosis due to regional invasion and metastases. The receptor tyrosine kinase epidermal growth factor receptor (EGFR) is found in a subtype of melanoma with a poor prognosis and contributes to drug resistance. Aloysia citrodora essential oil (ALOC-EO) possesses an antitumor effect. Understanding signaling pathways that contribute to the antitumor of ALOC-EO is important to identify novel tumor types that can be targeted by ALOC-EO. Here, we investigated the effects of ALOC-EO on melanoma growth and tumor cell migration. ALOC-EO blocked melanoma growth in vitro and impaired primary tumor cell growth in vivo. Mechanistically, ALOC-EO blocked heparin-binding-epidermal growth factor (HB-EGF)-induced EGFR signaling and suppressed ERK1/2 phosphorylation. Myelosuppressive drugs upregulated HB-EGF and EGFR expression in melanoma cells. Cotreatment of myelosuppressive drugs with ALOC-EO improved the antitumor activity and inhibited the expression of matrix metalloproteinase-7 and -9 and a disintegrin and metalloproteinase domain-containing protein9. In summary, our study demonstrates that ALOC-EO blocks EGFR and ERK1/2 signaling, with preclinical efficacy as a monotherapy or in combination with myelosuppressive drugs in melanoma. Full article
(This article belongs to the Special Issue Feature Annual Reviews in Molecular Genetics and Genomics 2021)
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Review

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Review
The Complex Interplay between Autophagy and NLRP3 Inflammasome in Renal Diseases
Int. J. Mol. Sci. 2021, 22(23), 12766; https://doi.org/10.3390/ijms222312766 - 25 Nov 2021
Viewed by 210
Abstract
Autophagy is a highly conserved process of the eukaryotic cell cycle. It plays an important role in the survival and maintenance of cells by degrading organelles, proteins, and macromolecules in the cytoplasm and the circulation of degraded products. The dysfunction of autophagy can [...] Read more.
Autophagy is a highly conserved process of the eukaryotic cell cycle. It plays an important role in the survival and maintenance of cells by degrading organelles, proteins, and macromolecules in the cytoplasm and the circulation of degraded products. The dysfunction of autophagy can lead to the pathology of many human diseases. The nucleotide-binding oligomerization domain-like receptor family, pyrin domain-containing 3 (NLRP3) inflammasome belongs to the family of nucleotide-binding and oligomerization domain-like receptors (NLRs) and can induce caspase-1 activation, thus leading to the maturation and secretion of interleukin-1beta (IL-1β) and IL-18. It has been reported that the interplay between autophagy and NLRP3 inflammasome is involved in many diseases, including renal diseases. In this review, the interplay between autophagy and the NLRP3 inflammasome and the mechanisms in renal diseases are explored to provide ideas for relevant basic research in the future. Full article
(This article belongs to the Special Issue Feature Annual Reviews in Molecular Genetics and Genomics 2021)
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Review
Plant-Growth-Promoting Rhizobacteria Emerging as an Effective Bioinoculant to Improve the Growth, Production, and Stress Tolerance of Vegetable Crops
Int. J. Mol. Sci. 2021, 22(22), 12245; https://doi.org/10.3390/ijms222212245 - 12 Nov 2021
Viewed by 430
Abstract
Vegetable cultivation is a promising economic activity, and vegetable consumption is important for human health due to the high nutritional content of vegetables. Vegetables are rich in vitamins, minerals, dietary fiber, and several phytochemical compounds. However, the production of vegetables is insufficient to [...] Read more.
Vegetable cultivation is a promising economic activity, and vegetable consumption is important for human health due to the high nutritional content of vegetables. Vegetables are rich in vitamins, minerals, dietary fiber, and several phytochemical compounds. However, the production of vegetables is insufficient to meet the demand of the ever-increasing population. Plant-growth-promoting rhizobacteria (PGPR) facilitate the growth and production of vegetable crops by acquiring nutrients, producing phytohormones, and protecting them from various detrimental effects. In this review, we highlight well-developed and cutting-edge findings focusing on the role of a PGPR-based bioinoculant formulation in enhancing vegetable crop production. We also discuss the role of PGPR in promoting vegetable crop growth and resisting the adverse effects arising from various abiotic (drought, salinity, heat, heavy metals) and biotic (fungi, bacteria, nematodes, and insect pests) stresses. Full article
(This article belongs to the Special Issue Feature Annual Reviews in Molecular Genetics and Genomics 2021)
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Review
SARS-CoV-2, Cardiovascular Diseases, and Noncoding RNAs: A Connected Triad
Int. J. Mol. Sci. 2021, 22(22), 12243; https://doi.org/10.3390/ijms222212243 - 12 Nov 2021
Viewed by 298
Abstract
Coronavirus Disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is characterized by important respiratory impairments frequently associated with severe cardiovascular damages. Moreover, patients with pre-existing comorbidity for cardiovascular diseases (CVD) often present a dramatic increase in inflammatory cytokines [...] Read more.
Coronavirus Disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is characterized by important respiratory impairments frequently associated with severe cardiovascular damages. Moreover, patients with pre-existing comorbidity for cardiovascular diseases (CVD) often present a dramatic increase in inflammatory cytokines release, which increases the severity and adverse outcomes of the infection and, finally, mortality risk. Despite this evident association at the clinical level, the mechanisms linking CVD and COVID-19 are still blurry and unresolved. Noncoding RNAs (ncRNAs) are functional RNA molecules transcribed from DNA but usually not translated into proteins. They play an important role in the regulation of gene expression, either in relatively stable conditions or as a response to different stimuli, including viral infection, and are therefore considered a possible important target in the design of specific drugs. In this review, we introduce known associations and interactions between COVID-19 and CVD, discussing the role of ncRNAs within SARS-CoV-2 infection from the perspective of the development of efficient pharmacological tools to treat COVID-19 patients and taking into account the equally dramatic associated consequences, such as those affecting the cardiovascular system. Full article
(This article belongs to the Special Issue Feature Annual Reviews in Molecular Genetics and Genomics 2021)
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Review
Pharmacogenetics of Drug-Resistant Epilepsy (Review of Literature)
Int. J. Mol. Sci. 2021, 22(21), 11696; https://doi.org/10.3390/ijms222111696 - 28 Oct 2021
Viewed by 330
Abstract
Pharmacogenomic studies in epilepsy are justified by the high prevalence rate of this disease and the high cost of its treatment, frequent drug resistance, different response to the drug, the possibility of using reliable methods to assess the control of seizures and side [...] Read more.
Pharmacogenomic studies in epilepsy are justified by the high prevalence rate of this disease and the high cost of its treatment, frequent drug resistance, different response to the drug, the possibility of using reliable methods to assess the control of seizures and side effects of antiepileptic drugs. Candidate genes encode proteins involved in pharmacokinetic processes (drug transporters, metabolizing enzymes), pharmacodynamic processes (receptors, ion channels, enzymes, regulatory proteins, secondary messengers) and drug hypersensitivity (immune factors). This article provides an overview of the literature on the influence of genetic factors on treatment in epilepsy. Full article
(This article belongs to the Special Issue Feature Annual Reviews in Molecular Genetics and Genomics 2021)
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Review
Role of microRNAs in Obesity-Related Kidney Disease
Int. J. Mol. Sci. 2021, 22(21), 11416; https://doi.org/10.3390/ijms222111416 - 22 Oct 2021
Viewed by 414
Abstract
Obesity is a major global health problem and is associated with a significant risk of renal function decline. Obesity-related nephropathy, as one of the complications of obesity, is characterized by a structural and functional damage of the kidney and represents one of the [...] Read more.
Obesity is a major global health problem and is associated with a significant risk of renal function decline. Obesity-related nephropathy, as one of the complications of obesity, is characterized by a structural and functional damage of the kidney and represents one of the important contributors to the morbidity and mortality worldwide. Despite increasing data linking hyperlipidemia and lipotoxicity to kidney injury, the apprehension of molecular mechanisms leading to a development of kidney damage is scarce. MicroRNAs (miRNAs) are endogenously produced small noncoding RNA molecules with an important function in post-transcriptional regulation of gene expression. miRNAs have been demonstrated to be important regulators of a vast array of physiological and pathological processes in many organs, kidney being one of them. In this review, we present an overview of miRNAs, focusing on their functional role in the pathogenesis of obesity-associated renal pathologies. We explain novel findings regarding miRNA-mediated signaling in obesity-related nephropathies and highlight advantages and future perspectives of the therapeutic application of miRNAs in renal diseases. Full article
(This article belongs to the Special Issue Feature Annual Reviews in Molecular Genetics and Genomics 2021)
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Review
Editing SOX Genes by CRISPR-Cas: Current Insights and Future Perspectives
Int. J. Mol. Sci. 2021, 22(21), 11321; https://doi.org/10.3390/ijms222111321 - 20 Oct 2021
Viewed by 412
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and its associated proteins (Cas) is an adaptive immune system in archaea and most bacteria. By repurposing these systems for use in eukaryote cells, a substantial revolution has arisen in the genome engineering field. In recent [...] Read more.
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and its associated proteins (Cas) is an adaptive immune system in archaea and most bacteria. By repurposing these systems for use in eukaryote cells, a substantial revolution has arisen in the genome engineering field. In recent years, CRISPR-Cas technology was rapidly developed and different types of DNA or RNA sequence editors, gene activator or repressor, and epigenome modulators established. The versatility and feasibility of CRISPR-Cas technology has introduced this system as the most suitable tool for discovering and studying the mechanism of specific genes and also for generating appropriate cell and animal models. SOX genes play crucial roles in development processes and stemness. To elucidate the exact roles of SOX factors and their partners in tissue hemostasis and cell regeneration, generating appropriate in vitro and in vivo models is crucial. In line with these premises, CRISPR-Cas technology is a promising tool for studying different family members of SOX transcription factors. In this review, we aim to highlight the importance of CRISPR-Cas and summarize the applications of this novel, promising technology in studying and decoding the function of different members of the SOX gene family. Full article
(This article belongs to the Special Issue Feature Annual Reviews in Molecular Genetics and Genomics 2021)
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Review
Applications of Adductomics in Chemically Induced Adverse Outcomes and Major Emphasis on DNA Adductomics: A Pathbreaking Tool in Biomedical Research
Int. J. Mol. Sci. 2021, 22(18), 10141; https://doi.org/10.3390/ijms221810141 - 20 Sep 2021
Viewed by 577
Abstract
Adductomics novel and emerging discipline in the toxicological research emphasizes on adducts formed by reactive chemical agents with biological molecules in living organisms. Development in analytical methods propelled the application and utility of adductomics in interdisciplinary sciences. This review endeavors to add a [...] Read more.
Adductomics novel and emerging discipline in the toxicological research emphasizes on adducts formed by reactive chemical agents with biological molecules in living organisms. Development in analytical methods propelled the application and utility of adductomics in interdisciplinary sciences. This review endeavors to add a new dimension where comprehensive insights into diverse applications of adductomics in addressing some of society’s pressing challenges are provided. Also focuses on diverse applications of adductomics include: forecasting risk of chronic diseases triggered by reactive agents and predicting carcinogenesis induced by tobacco smoking; assessing chemical agents’ toxicity and supplementing genotoxicity studies; designing personalized medication and precision treatment in cancer chemotherapy; appraising environmental quality or extent of pollution using biological systems; crafting tools and techniques for diagnosis of diseases and detecting food contaminants; furnishing exposure profile of the individual to electrophiles; and assisting regulatory agencies in risk assessment of reactive chemical agents. Characterizing adducts that are present in extremely low concentrations is an exigent task and more over absence of dedicated database to identify adducts is further exacerbating the problem of adduct diagnosis. In addition, there is scope of improvement in sample preparation methods and data processing software and algorithms for accurate assessment of adducts. Full article
(This article belongs to the Special Issue Feature Annual Reviews in Molecular Genetics and Genomics 2021)
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Review
From Fighting Critters to Saving Lives: Polyphenols in Plant Defense and Human Health
Int. J. Mol. Sci. 2021, 22(16), 8995; https://doi.org/10.3390/ijms22168995 - 20 Aug 2021
Viewed by 648
Abstract
Polyphenols, such as flavonoids and phenolic acids, are a group of specialized metabolites in plants that largely aid in plant defense by deterring biotic stressors and alleviating abiotic stress. Polyphenols offer a wide range of medical applications, acting as preventative and active treatments [...] Read more.
Polyphenols, such as flavonoids and phenolic acids, are a group of specialized metabolites in plants that largely aid in plant defense by deterring biotic stressors and alleviating abiotic stress. Polyphenols offer a wide range of medical applications, acting as preventative and active treatments for diseases such as cancers and diabetes. Recently, researchers have proposed that polyphenols may contribute to certain applications aimed at tackling challenges related to the COVID-19 pandemic. Understanding the beneficial impacts of phytochemicals, such as polyphenols, could potentially help prepare society for future pandemics. Thus far, most reviews have focused on polyphenols in cancer prevention and treatment. This review aims to provide a comprehensive discussion on the critical roles that polyphenols play in both plant chemical defense and human health based on the most recent studies while highlighting prospective avenues for future research, as well as the implications for phytochemical-based applications in both agricultural and medical fields. Full article
(This article belongs to the Special Issue Feature Annual Reviews in Molecular Genetics and Genomics 2021)
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Review
Molecular Hydrogen as a Novel Antitumor Agent: Possible Mechanisms Underlying Gene Expression
Int. J. Mol. Sci. 2021, 22(16), 8724; https://doi.org/10.3390/ijms22168724 - 13 Aug 2021
Viewed by 1161
Abstract
While many antitumor drugs have yielded unsatisfactory therapeutic results, drugs are one of the most prevalent therapeutic measures for the treatment of cancer. The development of cancer largely results from mutations in nuclear DNA, as well as from those in mitochondrial DNA (mtDNA). [...] Read more.
While many antitumor drugs have yielded unsatisfactory therapeutic results, drugs are one of the most prevalent therapeutic measures for the treatment of cancer. The development of cancer largely results from mutations in nuclear DNA, as well as from those in mitochondrial DNA (mtDNA). Molecular hydrogen (H2), an inert molecule, can scavenge hydroxyl radicals (·OH), which are known to be the strongest oxidizing reactive oxygen species (ROS) in the body that causes these DNA mutations. It has been reported that H2 has no side effects, unlike conventional antitumor drugs, and that it is effective against many diseases caused by oxidative stress and chronic inflammation. Recently, there has been an increasing number of papers on the efficacy of H2 against cancer and its effects in mitigating the side effects of cancer treatment. In this review, we demonstrate the efficacy and safety of H2 as a novel antitumor agent and show that its mechanisms may not only involve the direct scavenging of ·OH, but also other indirect biological defense mechanisms via the regulation of gene expression. Full article
(This article belongs to the Special Issue Feature Annual Reviews in Molecular Genetics and Genomics 2021)
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Review
Genetic Ancestry Inference and Its Application for the Genetic Mapping of Human Diseases
Int. J. Mol. Sci. 2021, 22(13), 6962; https://doi.org/10.3390/ijms22136962 - 28 Jun 2021
Viewed by 897
Abstract
Admixed populations arise when two or more ancestral populations interbreed. As a result of this admixture, the genome of admixed populations is defined by tracts of variable size inherited from these parental groups and has particular genetic features that provide valuable information about [...] Read more.
Admixed populations arise when two or more ancestral populations interbreed. As a result of this admixture, the genome of admixed populations is defined by tracts of variable size inherited from these parental groups and has particular genetic features that provide valuable information about their demographic history. Diverse methods can be used to derive the ancestry apportionment of admixed individuals, and such inferences can be leveraged for the discovery of genetic loci associated with diseases and traits, therefore having important biomedical implications. In this review article, we summarize the most common methods of global and local genetic ancestry estimation and discuss the use of admixture mapping studies in human diseases. Full article
(This article belongs to the Special Issue Feature Annual Reviews in Molecular Genetics and Genomics 2021)
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Review
Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry
Int. J. Mol. Sci. 2021, 22(12), 6184; https://doi.org/10.3390/ijms22126184 - 08 Jun 2021
Cited by 1 | Viewed by 1041
Abstract
With advanced technology and its development, bioinformatics is one of the avant-garde fields that has managed to make amazing progress in the pharmaceutical–medical field by modeling the infrastructural dimensions of healthcare and integrating computing tools in drug innovation, facilitating prevention, detection/more accurate diagnosis, [...] Read more.
With advanced technology and its development, bioinformatics is one of the avant-garde fields that has managed to make amazing progress in the pharmaceutical–medical field by modeling the infrastructural dimensions of healthcare and integrating computing tools in drug innovation, facilitating prevention, detection/more accurate diagnosis, and treatment of disorders, while saving time and money. By association, bioinformatics and pharmacovigilance promoted both sample analyzes and interpretation of drug side effects, also focusing on drug discovery and development (DDD), in which systems biology, a personalized approach, and drug repositioning were considered together with translational medicine. The role of bioinformatics has been highlighted in DDD, proteomics, genetics, modeling, miRNA discovery and assessment, and clinical genome sequencing. The authors have collated significant data from the most known online databases and publishers, also narrowing the diversified applications, in order to target four major areas (tetrad): DDD, anti-microbial research, genomic sequencing, and miRNA research and its significance in the management of current pandemic context. Our analysis aims to provide optimal data in the field by stratification of the information related to the published data in key sectors and to capture the attention of researchers interested in bioinformatics, a field that has succeeded in advancing the healthcare paradigm by introducing developing techniques and multiple database platforms, addressed in the manuscript. Full article
(This article belongs to the Special Issue Feature Annual Reviews in Molecular Genetics and Genomics 2021)
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