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25th Anniversary of IJMS: Updates and Advances in Molecular Genetics and Genomics

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: 31 December 2025 | Viewed by 5694

Special Issue Editors

Dr. Francesco Sessa

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Guest Editor
Department of Medical, Surgical and Advanced Technologies “G.F. Ingrassia”, University of Catania, 95121 Catania, Italy
Interests: genetics and molecular biology; forensic and biological sciences; forensic genetics; genomic physiology; aging and genetics; pharmacology; toxicology; health professions; translational pharmacology; biochemistry
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Lasse Lindahl

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Guest Editor
Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
Interests: ribosome formation and function; RNA processing; protein-RNA complexes
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Apostolos Zaravinos

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Guest Editor
Cancer Genetics, Genomics and Systems Biology Laboratory, Basic and Translational Cancer Research Center (BTCRC), Nicosia 1516, Cyprus
Interests: cancer genomics; precision medicine; data science in genomics; next-generation sequencing; translational oncology; tumor immunology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

As we celebrate the 25th anniversary of the International Journal of Molecular Sciences, this special issue is dedicated to showcasing recent advances in the understanding of fundamental biological processes and their transformative impact on molecular genetics and genomics across the biomedical landscape. Over recent decades, this has revolutionized our understanding of human biology, enabling unprecedented advances in disease diagnosis, prognosis, and therapy.

Molecular genetics and genomics now underpin precision medicine from identifying pathogenic variants in rare genetic disorders to guiding targeted therapies in oncology. Moreover, high-throughput sequencing technologies and bioinformatics tools have accelerated discoveries in gene regulation, epigenetics, and transcriptomics, offering new insights into complex diseases such as neurodegenerative disorders, cardiovascular conditions, and autoimmune syndromes.

Beyond traditional medical applications, molecular genetics and genomics are also increasingly pivotal in interdisciplinary fields such as forensic science, pharmacogenomics, and optimizing drug efficacy.

This special issue welcomes a broad spectrum of contributions—including original research articles, reviews, and methodological papers—that align with the journal’s aims in molecular genetics and genomics and their broader implications. We also invite submissions that highlight novel discoveries, technological innovations, and translational applications that reflect the dynamic and interdisciplinary nature of this field. 

Dr. Francesco Sessa
Prof. Dr. Lasse Lindahl
Prof. Dr. Apostolos Zaravinos
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 250 words) can be sent to the Editorial Office for assessment.

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

  • molecular genetics
  • genomics
  • precision medicine
  • genetic diagnostics
  • gene therapy
  • next-generation sequencing (NGS)
  • pharmacogenomics
  • epigenetics
  • forensic genomics
  • translational genomics
  • genome replication
  • gene expression
  • cell stress
  • cell cycle
  • cell signaling
  • macromolecular surveillance and turnover
  • molecular evolution

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (5 papers)

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Research

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24 pages, 3439 KB  
Article
Mitogenome of Medicago lupulina L. Cultivar-Population VIK32, Line MlS-1: Dynamic Structural Organization and Foreign Sequences
by Maria E. Vladimirova, Marina L. Roumiantseva, Alla S. Saksaganskaia, Alexandra P. Kozlova, Victoria S. Muntyan, Sergey P. Gaponov, Andrey P. Yurkov, Vladimir A. Zhukov and Mikhail P. Grudinin
Int. J. Mol. Sci. 2025, 26(24), 11830; https://doi.org/10.3390/ijms262411830 - 7 Dec 2025
Viewed by 190
Abstract
This study presents the complete assembly and analysis of the mitochondrial genome (mitogenome) of Medicago lupulina L. var. vulgaris Koch, cultivar-population VIK32, line MlS-1, which forms an effective symbiosis not only with arbuscular mycorrhiza but also with the root nodule bacteria Sinorhizobium meliloti [...] Read more.
This study presents the complete assembly and analysis of the mitochondrial genome (mitogenome) of Medicago lupulina L. var. vulgaris Koch, cultivar-population VIK32, line MlS-1, which forms an effective symbiosis not only with arbuscular mycorrhiza but also with the root nodule bacteria Sinorhizobium meliloti. The assembly, generated using a hybrid sequencing approach, revealed sequences of putative horizontal origin. These include a highly conserved open reading frame (ORF), orf279, encoding a protein structurally homologous to maturase K, yet bearing remote similarity to bacterial reverse transcriptases and CRISPR-associated proteins. We also identified sequences homologous to mitovirus RNA-dependent RNA polymerases and a fragment of the chloroplast 23S ribosomal RNA (rRNA), suggesting historical gene transfers from viruses and plastids. This work establishes a foundation for investigating the role of mitochondrial genome variation in key plant’s phenotypic traits, such as the enhanced responsiveness to arbuscular mycorrhiza observed in this agronomically valuable line. Full article
(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Genetics and Genomics)
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10 pages, 256 KB  
Communication
Association of DPP4 Gene Variants with Classic and DPP4 Inhibitor-Associated Bullous Pemphigoid
by Charoula Achilla, Christina Foutsitzidou, Parthena Meltzanidou, Aikaterini Patsatsi, Elizabeth Lazaridou, Glykeria Tzatzagou, Alexandros Lambropoulos and Anthoula Chatzikyriakidou
Int. J. Mol. Sci. 2025, 26(23), 11698; https://doi.org/10.3390/ijms262311698 - 3 Dec 2025
Viewed by 196
Abstract
Bullous pemphigoid (BP), the most prevalent autoimmune blistering skin disorder, has been associated with dipeptidyl peptidase-4 inhibitor (DPP4i) treatment in type 2 diabetic patients. This study aimed to investigate the association of DPP4 gene variants, rs3788979 and rs12617656, with classic BP (cBP)- and [...] Read more.
Bullous pemphigoid (BP), the most prevalent autoimmune blistering skin disorder, has been associated with dipeptidyl peptidase-4 inhibitor (DPP4i) treatment in type 2 diabetic patients. This study aimed to investigate the association of DPP4 gene variants, rs3788979 and rs12617656, with classic BP (cBP)- and DPP4i-associated BP predisposition. Fifty-six (56) unrelated patients with cBP, 32 DPP4i-associated BP patients, 60 healthy controls, and 49 diabetic patients receiving DPP4i were included. Genotyping was performed using polymerase chain reaction-restriction fragment length polymorphism assay (PCR-RFLP). Statistical analyses were conducted using SPSS software. For rs3788979, the CT+TT genotypes were significantly associated with increased risk of DPP4i-associated BP compared with cBP [(Odds Ratio (OR) = 2.80, 95% Confidence Interval (CI) = 1.07–7.35; p-value = 0.034] and healthy controls (OR = 0.30, 95% CI = 0.13–0.86; p-value = 0.020). The T allele was also enriched in DPP4i-associated BP (OR = 2.57, 95% CI = 1.09–6.07; p-value = 0.027). Additionally, the TC genotype of rs12617656 (OR = 2.29, 95% CI = 1.04–5.03, p-value = 0.039) showed significant association with cBP susceptibility. These findings highlight DPP4 variants as potential BP risk factors, supporting personalized risk assessment prior to initiating gliptin therapy. Large-scale studies are warranted to validate these associations. Full article
(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Genetics and Genomics)
19 pages, 3843 KB  
Article
Mitochondrial Gene Regulation and Pain Susceptibility: A Multi-Omics Causal Inference Study
by Chien-Cheng Liu
Int. J. Mol. Sci. 2025, 26(17), 8690; https://doi.org/10.3390/ijms26178690 - 6 Sep 2025
Viewed by 1515
Abstract
The causal contributions of specific mitochondrial genes to common pain phenotypes remain unclear. We employed a multi-omics Mendelian randomization (SMR) approach, integrating QTL data (expression, methylation, protein) for mitochondrial genes with GWAS summary statistics for seven pain phenotypes. We identified 18 candidate genes [...] Read more.
The causal contributions of specific mitochondrial genes to common pain phenotypes remain unclear. We employed a multi-omics Mendelian randomization (SMR) approach, integrating QTL data (expression, methylation, protein) for mitochondrial genes with GWAS summary statistics for seven pain phenotypes. We identified 18 candidate genes with robust SMR associations across omics layers. However, strong colocalization evidence (PP.H4 > 0.7) was largely absent, pointing towards complex genetic architectures. A notable exception was a strong signal for a shared causal variant found at the methylation level for the MCL1 gene in hip pain (PP.H4 = 0.962), nominating it as a high-confidence candidate. Additionally, genetically predicted higher protein levels of Glycine amidinotransferase (GATM) showed consistent protective associations with neck or shoulder, back, and knee pain. This study provides novel evidence for mitochondrial gene regulation in pain, highlighting the GATM pathway as protective and identifying MCL1 methylation as a potential causal mechanism in hip pain. Full article
(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Genetics and Genomics)
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23 pages, 4531 KB  
Article
Examining the Roles of Genomic Context and Endogenous Regulatory Elements on IS1 Transposition Within the Escherichia coli Genome
by Sofia Smith, Zhongge Zhang, Allyson Ho, Tusha Karnani, Jack Ord and Milton H. Saier, Jr.
Int. J. Mol. Sci. 2025, 26(17), 8375; https://doi.org/10.3390/ijms26178375 - 28 Aug 2025
Viewed by 1249
Abstract
Insertion sequence (IS) elements are key drivers of bacterial genome plasticity, yet the overall regulation of their transposition remains poorly understood. This is especially true for the multiple-layer regulation at the donor site, which has been largely overlooked. Using multiple mutation assays, genetic [...] Read more.
Insertion sequence (IS) elements are key drivers of bacterial genome plasticity, yet the overall regulation of their transposition remains poorly understood. This is especially true for the multiple-layer regulation at the donor site, which has been largely overlooked. Using multiple mutation assays, genetic manipulations and reporter genes, this study focuses on characterizing how endogenous DNA sequences, transcriptional and translational factors, and genomic context regulate IS1 transposition from its donor site. Out of six elements within the chromosome of E. coli strain BW25113, IS1A and IS1E (both with the consensus sequence) contribute to over 99.9% of the overall IS1 transposition within the genome while the other four elements without the non-consensus sequence are essentially incapable of transposing. Inducing a ribosomal -1 frameshift at the A6C motif increases transposition over 1000-fold, but this enhancement is largely reversed by restoring InsA-mediated transcriptional regulation. Strikingly, genomic sequences flanking IS1 elements appreciably modulate transposition by promoting transcription or facilitating formation of transpososomes, a phenomenon that remains under-studied. Finally, IS1 was confirmed to undergo replicative transposition intramolecularly, a mechanism shown here to be independent of transposase levels in the cell. These findings contribute to our understanding of mobile genetic element regulation and potentially offer strategies for mitigating their potentially harmful effects. Full article
(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Genetics and Genomics)
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Review

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29 pages, 2053 KB  
Review
Targeting Granulin Haploinsufficiency in Frontotemporal Dementia: From Genetic Mechanisms to Therapeutics
by Eva Bagyinszky and Seong Soo A. An
Int. J. Mol. Sci. 2025, 26(20), 9960; https://doi.org/10.3390/ijms26209960 - 13 Oct 2025
Viewed by 1800
Abstract
Frontotemporal dementia (FTD) is the second most common early-onset dementia after Alzheimer’s disease, characterized by progressive neurodegeneration primarily in the frontal and temporal lobes. Granulin (GRN) gene for encoding the progranulin (PGRN) protein was a key genetic contributor to FTD. PGRN [...] Read more.
Frontotemporal dementia (FTD) is the second most common early-onset dementia after Alzheimer’s disease, characterized by progressive neurodegeneration primarily in the frontal and temporal lobes. Granulin (GRN) gene for encoding the progranulin (PGRN) protein was a key genetic contributor to FTD. PGRN was a multifunctional protein involved in lysosomal function, neuroinflammation, and neuronal survival. This review discusses the contributions of GRN haploinsufficiency to FTD pathogenesis with an emphasis on genetic mutations, downstream cellular consequences, relevant animal and cellular models, and emerging therapeutic strategies. Loss-of-function mutations in GRN were responsible up to ~50% reduction in PGRN levels, resulting in lysosomal dysfunction, TDP-43 aggregation, impaired microglial homeostasis, and enhanced neuroinflammation. Multiple in vitro and in vivo models recapitulated these pathological features. Novel therapeutic approaches, such as AAV-mediated gene therapy, stop codon readthrough compounds, SORT1 inhibitors, and antisense oligonucleotides, were investigated to restore PGRN levels and to mitigate disease progressions. However, challenges included the oncogenic risks of overexpression and the limited translational success in clinical trials to date. Targeting GRN haploinsufficiency became a promising avenue for FTD therapy. Improved models and refined delivery systems would be essential to develop safe and effective treatments. Future work should also focus on biomarker-guided interventions in presymptomatic mutation carriers. Full article
(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Genetics and Genomics)
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