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Omics Era: From Principles to Applications in Disease Diagnosis and Treatment

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 (20 May 2025) | Viewed by 13827

Special Issue Editor

Dr. Kieu The Loan Trinh

E-Mail Website
Guest Editor
Bionano Applications Research Center, Gachon University, Seongnam-si 13120, Republic of Korea
Interests: lab-on-a-chip; system integration; nucleic acid detection
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The recent advent of technologies has revolutionized different methods for mining the DNA, RNA and protein data of various organisms. These enormous data enabled the exploration of various pathways in living organisms through the assistance of a variety of bioinformatics tools. Diseases in plants, animals and human beings can be caused by abiotic and biotic factors. Emergence of the “Omics” era has allowed for the discovery of biotic factors (i.e., bacteria and viruses) and the process of different pathways in the host. Therefore, “Omics” tools are essential to disease diagnosis and finding effective treatments for various diseases. Alongside applications of “Omics” in disease diagnosis, various bioinformatic tools have been developed for interpreting and mining “Omics” data from different organisms. The development of bioinformatic tools strengthens the reliability of research results and shortens the time of study.

This Special Issue welcomes the submission of review and original research papers or short communications on the following topics: genomics, comparative genomics, metagenomics, transcriptomics and metabolomics research; functional genomics and metagenomics; the discovery of new pathways; application of omics for disease diagnostics and treatments; and bioinformatic tools.

Dr. Kieu The Loan Trinh
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

  • genomics
  • metagenomics
  • transcriptomics
  • proteomics
  • metabolomics
  • functional genomics
  • functional metagenomics
  • omics-based diagnostics

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Published Papers (6 papers)

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Research

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21 pages, 5172 KiB  
Article
Characterizing the Ovarian Cytogenetic Dynamics of Sichuan Bream (Sinibrama taeniatus) During Vitellogenesis at a Single-Cell Resolution
by Zhe Zhao, Shixia Huang, Qilin Feng, Li Peng, Qiang Zhao and Zhijian Wang
Int. J. Mol. Sci. 2025, 26(5), 2265; https://doi.org/10.3390/ijms26052265 - 4 Mar 2025
Viewed by 639
Abstract
Vitellogenesis in fish represents a critical phase of oogenesis, significantly influencing the nutritional provisioning for oocyte maturation and subsequent offspring development. However, research on the physiological mechanisms governing vitellogenesis at the single-cell level remains limited. In this study, we performed single-nucleus RNA sequencing [...] Read more.
Vitellogenesis in fish represents a critical phase of oogenesis, significantly influencing the nutritional provisioning for oocyte maturation and subsequent offspring development. However, research on the physiological mechanisms governing vitellogenesis at the single-cell level remains limited. In this study, we performed single-nucleus RNA sequencing (snRNA-seq) on the ovaries of Sichuan bream (Sinibrama taeniatus). We first identified six distinct cell types (germ cells, follicular cells, immune cells, stromal cells, endothelial cells, and epithelial cells) in the ovaries based on typical functional marker genes. Subsequently, we reconstructed the developmental trajectory of germ cells using pseudotime analysis, which describes the transcriptional dynamics of germ cells at various developmental stages. Additionally, we identified transcription factors (TFs) specific to germ cells that exhibit high activity at each developmental stage. Furthermore, we analyzed the genetic functional heterogeneity of germ cells and follicular cells at different developmental stages to elucidate their contributions to vitellogenesis. Finally, cell interaction analysis revealed that germ cells communicate with somatic cells or with each other via multiple receptors and ligands to regulate growth, development, and yolk acquisition. These findings enhance our understanding of the physiological mechanisms underlying vitellogenesis in fish, providing a theoretical foundation for regulating ovarian development in farmed fish. Full article
(This article belongs to the Special Issue Omics Era: From Principles to Applications in Disease Diagnosis and Treatment)
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13 pages, 1827 KiB  
Article
Serum Lipoprotein Profiling by NMR Spectroscopy Reveals Alterations in HDL-1 and HDL-2 Apo-A2 Subfractions in Alzheimer’s Disease
by Jonas Ellegaard Mortensen, Trygve Andreassen, Dorte Aalund Olsen, Karsten Vestergaard, Jonna Skov Madsen, Søren Risom Kristensen and Shona Pedersen
Int. J. Mol. Sci. 2024, 25(21), 11701; https://doi.org/10.3390/ijms252111701 - 31 Oct 2024
Cited by 1 | Viewed by 1216
Abstract
Identifying biomarkers for Alzheimer’s disease (AD) is crucial, due to its complex pathology, which involves dysfunction in lipid transport, contributing to neuroinflammation, synaptic loss, and impaired amyloid-β clearance. Nuclear magnetic resonance (NMR) is able to quantify and stratify lipoproteins. The study investigated lipoproteins [...] Read more.
Identifying biomarkers for Alzheimer’s disease (AD) is crucial, due to its complex pathology, which involves dysfunction in lipid transport, contributing to neuroinflammation, synaptic loss, and impaired amyloid-β clearance. Nuclear magnetic resonance (NMR) is able to quantify and stratify lipoproteins. The study investigated lipoproteins in blood from AD patients, aiming to evaluate their diagnostic potential. Serum and plasma were collected from AD patients (n = 25) and healthy individuals (n = 25). We conducted a comprehensive lipoprotein profiling on serum samples using NMR spectroscopy, analysing 112 lipoprotein subfractions. In plasma, we measured unspecific markers of neuronal damage and AD hallmark proteins using single molecule array technology. Additionally, clinical data and cerebrospinal fluid biomarker levels were also collected to enrich our data. Our findings, after adjusting for age and sex differences, highlight significant alterations in two specific lipoproteins; high-density lipoprotein (HDL)-1 Apo-A2 (H1A2) and HDL-2 Apo-A2 (H2A2), both with area under the curve (AUC) values of 0.67, 95% confidence interval (CI) = 0.52–0.82). These results indicate that these lipoprotein subfractions may have potential as indicators of AD-related metabolic changes. Full article
(This article belongs to the Special Issue Omics Era: From Principles to Applications in Disease Diagnosis and Treatment)
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20 pages, 8996 KiB  
Article
Platelet Proteomics and Tissue Metabolomics Investigation for the Mechanism of Aspirin Eugenol Ester on Preventive Thrombosis Mechanism in a Rat Thrombosis Model
by Qi Tao, Li-Ping Fan, Ji Feng, Zhi-Jie Zhang, Xi-Wang Liu, Zhe Qin, Jian-Yong Li and Ya-Jun Yang
Int. J. Mol. Sci. 2024, 25(19), 10747; https://doi.org/10.3390/ijms251910747 - 6 Oct 2024
Viewed by 1271
Abstract
Platelet activation is closely related to thrombosis. Aspirin eugenol ester (AEE) is a novel medicinal compound synthesized by esterifying aspirin with eugenol using the pro-drug principle. Pharmacological and pharmacodynamic experiments showed that AEE has excellent anti-inflammatory, antioxidant, and inhibitory platelet activation effects, preventing [...] Read more.
Platelet activation is closely related to thrombosis. Aspirin eugenol ester (AEE) is a novel medicinal compound synthesized by esterifying aspirin with eugenol using the pro-drug principle. Pharmacological and pharmacodynamic experiments showed that AEE has excellent anti-inflammatory, antioxidant, and inhibitory platelet activation effects, preventing thrombosis. However, the regulatory network and action target of AEE in inhibiting platelet activation remain unknown. This study aimed to investigate the effects of AEE on platelets of thrombosed rats to reveal its regulatory mechanism via a multi-omics approach. The platelet proteomic results showed that 348 DEPs were identified in the AEE group compared with the model group, of which 87 were up- and 261 down-regulated. The pathways in this result were different from previous results, including mTOR signaling and ADP signaling at P2Y purinoceptor 12. The metabolomics of heart and abdominal aortic tissue results showed that the differential metabolites were mainly involved in steroid biosynthesis, the citric acid cycle, phenylalanine metabolism, phenylalanine, tyrosine, and tryptophan biosynthesis, and glutathione metabolism. Molecular docking results showed that AEE had a better binding force to both the COX-1 and P2Y12 protein. AEE could effectively inhibit platelet activation by inhibiting COX-1 protein and P2Y12 protein activity, thereby inhibiting platelet aggregation. Therefore, AEE can have a positive effect on inhibiting platelet activation. Full article
(This article belongs to the Special Issue Omics Era: From Principles to Applications in Disease Diagnosis and Treatment)
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Review

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22 pages, 3871 KiB  
Review
Emerging Biomarkers in Metabolomics: Advancements in Precision Health and Disease Diagnosis
by Dang-Khoa Vo and Kieu The Loan Trinh
Int. J. Mol. Sci. 2024, 25(23), 13190; https://doi.org/10.3390/ijms252313190 - 8 Dec 2024
Cited by 4 | Viewed by 4438
Abstract
Metabolomics has come to the fore as an efficient tool in the search for biomarkers that are critical for precision health approaches and improved diagnostics. This review will outline recent advances in biomarker discovery based on metabolomics, focusing on metabolomics biomarkers reported in [...] Read more.
Metabolomics has come to the fore as an efficient tool in the search for biomarkers that are critical for precision health approaches and improved diagnostics. This review will outline recent advances in biomarker discovery based on metabolomics, focusing on metabolomics biomarkers reported in cancer, neurodegenerative disorders, cardiovascular diseases, and metabolic health. In cancer, metabolomics provides evidence for unique oncometabolites that are important for early disease detection and monitoring of treatment responses. Metabolite profiling for conditions such as neurodegenerative and mental health disorders can offer early diagnosis and mechanisms into the disease especially in Alzheimer’s and Parkinson’s diseases. In addition to these, lipid biomarkers and other metabolites relating to cardiovascular and metabolic disorders are promising for patient stratification and personalized treatment. The gut microbiome and environmental exposure also feature among the influential factors in biomarker discovery because they sculpt individual metabolic profiles, impacting overall health. Further, we discuss technological advances in metabolomics, current clinical applications, and the challenges faced by metabolomics biomarker validation toward precision medicine. Finally, this review discusses future opportunities regarding the integration of metabolomics into routine healthcare to enable preventive and personalized approaches. Full article
(This article belongs to the Special Issue Omics Era: From Principles to Applications in Disease Diagnosis and Treatment)
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24 pages, 2635 KiB  
Review
Functional Bidirectionality of ERV-Derived Long Non-Coding RNAs in Humans
by Yanmei Song, Hongling Wen, Xiuli Zhai, Lei Jia and Lin Li
Int. J. Mol. Sci. 2024, 25(19), 10481; https://doi.org/10.3390/ijms251910481 - 29 Sep 2024
Viewed by 1850
Abstract
Human endogenous retroviruses (HERVs) are widely recognized as the result of exogenous retroviruses infecting the ancestral germline, stabilizing integration and vertical transmission during human genetic evolution. To date, endogenous retroviruses (ERVs) appear to have been selected for human physiological functions with the loss [...] Read more.
Human endogenous retroviruses (HERVs) are widely recognized as the result of exogenous retroviruses infecting the ancestral germline, stabilizing integration and vertical transmission during human genetic evolution. To date, endogenous retroviruses (ERVs) appear to have been selected for human physiological functions with the loss of retrotransposable capabilities. ERV elements were previously regarded as junk DNA for a long time. Since then, the aberrant activation and expression of ERVs have been observed in the development of many kinds of human diseases, and their role has been explored in a variety of human disorders such as cancer. The results show that specific ERV elements play respective crucial roles. Among them, long non-coding RNAs (lncRNAs) transcribed from specific long-terminal repeat regions of ERVs are often key factors. lncRNAs are over 200 nucleotides in size and typically bind to DNA, RNA, and proteins to perform biological functions. Dysregulated lncRNAs have been implicated in a variety of diseases. In particular, studies have shown that the aberrant expression of some ERV-derived lncRNAs has a tumor-suppressive or oncogenic effect, displaying significant functional bidirectionality. Therefore, theses lncRNAs have a promising future as novel biomarkers and therapeutic targets to explore the concise relationship between ERVs and cancers. In this review, we first summarize the role of ERV-derived lncRNAs in physiological regulation, mainly including immunomodulation, the maintenance of pluripotency, and erythropoiesis. In addition, pathological regulation examples of their aberrant activation and expression leading to carcinogenesis are highlighted, and specific mechanisms of occurrence are discussed. Full article
(This article belongs to the Special Issue Omics Era: From Principles to Applications in Disease Diagnosis and Treatment)
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61 pages, 3156 KiB  
Review
Omics Studies of Specialized Cells and Stem Cells under Microgravity Conditions
by Fatima Abdelfattah, Herbert Schulz, Markus Wehland, Thomas J. Corydon, Jayashree Sahana, Armin Kraus, Marcus Krüger, Luis Fernando González-Torres, José Luis Cortés-Sánchez, Petra M. Wise, Ashwini Mushunuri, Ruth Hemmersbach, Christian Liemersdorf, Manfred Infanger and Daniela Grimm
Int. J. Mol. Sci. 2024, 25(18), 10014; https://doi.org/10.3390/ijms251810014 - 17 Sep 2024
Cited by 5 | Viewed by 3068
Abstract
The primary objective of omics in space with focus on the human organism is to characterize and quantify biological factors that alter structure, morphology, function, and dynamics of human cells exposed to microgravity. This review discusses exciting data regarding genomics, transcriptomics, epigenomics, metabolomics, [...] Read more.
The primary objective of omics in space with focus on the human organism is to characterize and quantify biological factors that alter structure, morphology, function, and dynamics of human cells exposed to microgravity. This review discusses exciting data regarding genomics, transcriptomics, epigenomics, metabolomics, and proteomics of human cells and individuals in space, as well as cells cultured under simulated microgravity. The NASA Twins Study significantly heightened interest in applying omics technologies and bioinformatics in space and terrestrial environments. Here, we present the available publications in this field with a focus on specialized cells and stem cells exposed to real and simulated microgravity conditions. We summarize current knowledge of the following topics: (i) omics studies on stem cells, (ii) omics studies on benign specialized different cell types of the human organism, (iii) discussing the advantages of this knowledge for space commercialization and exploration, and (iv) summarizing the emerging opportunities for translational regenerative medicine for space travelers and human patients on Earth. Full article
(This article belongs to the Special Issue Omics Era: From Principles to Applications in Disease Diagnosis and Treatment)
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