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Disease Biomarkers in the Precision Medicine Era: A Comprehensive Multi-Omics...
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Disease Biomarkers in the Precision Medicine Era: A Comprehensive Multi-Omics Analysis

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Molecular and Translational Medicine".

Deadline for manuscript submissions: closed (31 January 2025) | Viewed by 9347

Special Issue Editor

Dr. Chia-Jung Li

E-Mail Website
Guest Editor
Department of Obstetrics and Gynecology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
Interests: mitochondrial medicine; free radical biology; reproduction; cancer biology; chronic diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Late-stage diagnosis often leads to advanced tumors, resulting in unfavorable survival outcomes despite continuous research and advancements in treatment modalities. Precision medicine efforts in disease have been prominent due to a comprehensive understanding of the impact of genetic mutations on disease initiation and progression. The recent surge in precision medicine techniques represents a groundbreaking era, where advancements in measurement technologies enable the sequencing of thousands of exomes, whole genomes, and the exploration of entire genomes, transcriptomes, proteomes, and metabolites at the single-cell level. Precision medicine, currently undergoing a multi-omics revolution, leverages insights from both germline and somatic cell differences to tailor treatments for individual disease patients. Molecular characterization, enabled by the diverse assessment of multi-omics, offers clinicians valuable information for personalized treatment planning.

This Special Issue aims to achieve precision in disease medicine through a multi-omics approach, emphasizing the fundamental understanding of disease biology. We welcome submissions that utilize multi-omics methodologies to uncover novel findings or identify new targets in disease research. The focus is on effectively generating, analyzing, and interpreting multi-omics data to inform decisions based on precision medicine. Authors are encouraged to submit research and review papers covering various aspects of the field, such as the basic understanding of genomics and signaling pathways, diagnostic and prognostic biomarkers, pharmacogenomic biomarkers, molecular diagnosis through gene expression profiling, molecular targets driving disease progression, drug development against these targets, clinical trials of new drugs, and investigations into disease epigenetics.

Dr. Chia-Jung Li
Guest Editor

Manuscript Submission Information

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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. Biomedicines is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

  • personalized medicine
  • disease biomarkers: screening and diagnosis
  • multi-omics analysis
  • epidemiology

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Published Papers (5 papers)

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Research

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19 pages, 3367 KiB  
Article
Role of miRNA–mRNA Interactome in Pathophysiology of Arrhythmogenic Cardiomyopathy
by Fernando Bonet, Oscar Campuzano, José Córdoba-Caballero, Mireia Alcalde, Georgia Sarquella-Brugada, Aitana Braza-Boïls, Ramon Brugada, Francisco Hernández-Torres, Maribel Quezada-Feijoo, Monica Ramos, Alipio Mangas, Juan A. G. Ranea and Rocío Toro
Biomedicines 2024, 12(8), 1807; https://doi.org/10.3390/biomedicines12081807 - 9 Aug 2024
Viewed by 1522
Abstract
Arrhythmogenic cardiomyopathy is an inherited entity characterized by irregular cell–cell adhesion, cardiomyocyte death and fibro-fatty replacement of ventricular myocytes, leading to malignant ventricular arrythmias, contractile dysfunction and sudden cardiac death. Pathogenic variants in genes that encode desmosome are the predominant cause of arrhythmogenic [...] Read more.
Arrhythmogenic cardiomyopathy is an inherited entity characterized by irregular cell–cell adhesion, cardiomyocyte death and fibro-fatty replacement of ventricular myocytes, leading to malignant ventricular arrythmias, contractile dysfunction and sudden cardiac death. Pathogenic variants in genes that encode desmosome are the predominant cause of arrhythmogenic cardiomyopathy. Moreover, signalling pathways such as Wnt/ß-catenin and transforming growth factor-β have been involved in the disease progression. However, still little is known about the molecular pathophysiological mechanisms that underlie arrhythmogenic cardiomyopathy pathogenesis. We used mRNA and small RNA sequencing to analyse the transcriptome of health and arrhythmogenic cardiomyopathy of autopsied human hearts. Our results showed 697 differentially expressed genes and eight differentially expressed miRNAs. Functional enrichment revealed mitochondrial respiratory-related pathways, impaired response to oxidative stress, apoptotic signalling pathways and inflammatory response-related and extracellular matrix response pathways. Furthermore, analysis of the miRNA–mRNA interactome identified eleven negatively correlated miRNA-target pairs for arrhythmogenic cardiomyopathy. Our finding revealed novel arrhythmogenic cardiomyopathy-related miRNAs with important regulatory function in disease pathogenesis, highlighting their value as potential key targets for therapeutic approaches. Full article
(This article belongs to the Special Issue Disease Biomarkers in the Precision Medicine Era: A Comprehensive Multi-Omics Analysis)
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17 pages, 4071 KiB  
Article
Resistant Starch-Encapsulated Probiotics Attenuate Colorectal Cancer Cachexia and 5-Fluorouracil-Induced Microbial Dysbiosis
by Jui-Ling Wang, Yu-Siang Chen, Kuo-Chin Huang, Chin-Hsing Yeh, Miles Chih-Ming Chen, Lawrence Shih-Hsin Wu and Yi-Han Chiu
Biomedicines 2024, 12(7), 1450; https://doi.org/10.3390/biomedicines12071450 - 28 Jun 2024
Cited by 1 | Viewed by 2091
Abstract
5-Fluorouracil (5-FU) is commonly used as the primary chemotherapy for colorectal cancer (CRC). However, it can lead to unwanted chemoresistance. Resistant starch (RS), which functions similarly to fermentable dietary fiber, has the potential to reduce the risk of CRC. The effects of RS [...] Read more.
5-Fluorouracil (5-FU) is commonly used as the primary chemotherapy for colorectal cancer (CRC). However, it can lead to unwanted chemoresistance. Resistant starch (RS), which functions similarly to fermentable dietary fiber, has the potential to reduce the risk of CRC. The effects of RS on improving CRC-associated cachectic symptoms and 5-FU chemotherapy-induced microbial dysbiosis remain unknown. Female BALB/cByJNarl mice were randomly divided into four groups: one tumor group (with CT26 colonic carcinoma but no treatment) and three CT26 colonic carcinoma-bearing groups that were administered 20 mg/kg 5-FU (T+5-FU group), a probiotic cocktail (4 × 108 CFUs) plus chemotherapy (T+5-FU+Pro), or resistant-starch-encapsulated probiotics plus chemotherapy (T+5-FU+RS-Pro). T+5-FU and T+5-FU+RS-Pro administration significantly suppressed tumor growth and activated apoptotic cell death in CT26-bearing mice. 5-FU-induced increases in inflammatory cytokines and NF-κB signaling were mitigated by the Pro or RS-Pro supplementation. A gut microbial composition comparison indicated that the abundance of intestinal bacteria in the T and T+5-FU groups decreased significantly, while the groups receiving Pro or RS-Pro maintained a greater abundance and healthy gut microbiota composition, suggesting that RS can reduce the microbial dysbiosis that occurs during 5-FU chemotherapy. The use of RS-Pro before chemotherapy should be considered for the regulation of chemotherapy-associated cachectic symptoms, inflammation, and chemotherapy-induced microbial dysbiosis. Full article
(This article belongs to the Special Issue Disease Biomarkers in the Precision Medicine Era: A Comprehensive Multi-Omics Analysis)
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13 pages, 1675 KiB  
Article
IFN-γ, IL-17A, IL-4, and IL-13: Potential Biomarkers for Prediction of the Effectiveness of Biologics in Psoriasis Patients
by Ching-Liang Hsieh, Sheng-Jie Yu, Kuo-Lung Lai, Wei-Ting Chao and Chung-Yang Yen
Biomedicines 2024, 12(5), 1115; https://doi.org/10.3390/biomedicines12051115 - 17 May 2024
Cited by 1 | Viewed by 2127
Abstract
Biologics are widely used to treat moderate-to-severe psoriasis. However, we have unmet needs for predicting individual patient responses to biologics before starting psoriasis treatment. We investigate a reliable platform and biomarkers for predicting individual patient responses to biologics. In a cohort study between [...] Read more.
Biologics are widely used to treat moderate-to-severe psoriasis. However, we have unmet needs for predicting individual patient responses to biologics before starting psoriasis treatment. We investigate a reliable platform and biomarkers for predicting individual patient responses to biologics. In a cohort study between 2018 and 2023 from a referral center in Taiwan, twenty psoriasis patients with or without psoriatic arthritis who had ever experienced two or more biologics were enrolled. Peripheral blood mononuclear cells obtained from these patients were treated with Streptococcus pyogenes and different biologics. The PASI reduction rate was strongly correlated with the reduction rate in the IL-13 level (p = 0.001) and the ratios of IFN-γ to IL-13 (p < 0.001), IFN-γ to IL-4 (p = 0.019), and IL-17A to IL-13 (p = 0.001). The PASI reduction difference was strongly correlated with the difference in the IFN-γ level (p = 0.002), the difference in the ratios of IFN-γ to IL-4 (p = 0.041), the difference in the ratios of IFN-γ to IL-13 (p = 0.006), the difference in the ratios of IL-17A to IL-4 (p = 0.011), and the difference in the ratios of IL-17A to IL-13 (p = 0.029). The biomarkers IFN-γ, IL-13, IFN-γ/IL4, IFN-γ/IL13, IL-17A/IL-4, and IL-17A/IL-13 are representative of the effectiveness of psoriasis treatment. Full article
(This article belongs to the Special Issue Disease Biomarkers in the Precision Medicine Era: A Comprehensive Multi-Omics Analysis)
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14 pages, 3345 KiB  
Article
Tumors Established in a Defective Immune Environment Reprogram the Oncogenic Signaling Pathways to Escalate Tumor Antigenicity
by Chiao-Hsu Ke, Hsin-Yi Wu, Yu-Shan Wang, Wei-Hsiang Huang and Chen-Si Lin
Biomedicines 2024, 12(4), 846; https://doi.org/10.3390/biomedicines12040846 - 11 Apr 2024
Viewed by 1544
Abstract
Tumors developed in immunocompromised hosts are more immunogenic. However, few studies have addressed the potential mechanisms underlying the high immunogenicity of tumors found in a suppressed immune system. Therefore, we aimed to elucidate the impacts of the immune system on tumor behaviors and [...] Read more.
Tumors developed in immunocompromised hosts are more immunogenic. However, few studies have addressed the potential mechanisms underlying the high immunogenicity of tumors found in a suppressed immune system. Therefore, we aimed to elucidate the impacts of the immune system on tumor behaviors and immunogenicity sculpting. A murine colorectal adenocarcinoma cell line, CT26wt, was administrated into immunocompetent (BALB/c) and immunocompromised (NOD.SCID) mice, respectively. On day 11, the CT26 cells slowly progressed in the NOD.SCID mice compared to the BALB/c mice. We then performed liquid chromatography–tandem mass spectrometry (LC-MS/MS) and analyzed the differentially expressed proteins (DEPs). The DEPs participated in numerous oncogenic pathways, PI3K/AKT/mTOR cell signaling, and the silencing of several tumor suppressors, such as PTEN and RBL1, during tumorigenesis. On day 34, the CT26/SCID tumors inversely became malignant counterparts; then the CT26/SCID tumors were harvested and re-inoculated into immunocompetent mice (CT26/SCID-Re tumors) to determine the immunogenicity. The CT26/SCID-Re tumor growth rate significantly decreased. Furthermore, increased infiltrations of dendritic cells and tumor-infiltrating T lymphocytes were found in the CT26/SCID-Re tumors. These findings suggest that immunogenic tumors might express multiple tumor rejection antigens, unlike wild-type tumors, and attract more immune cells, therefore decreasing the growth rate. Collectively, our study first revealed that in immunodeficient hosts, tumor suppressors were silenced and oncogenic signaling pathways were changed during the initial phase of tumor development. With tumor progression, the tumor antigens were overexpressed, exhibiting elevated immunogenicity. This study offers a hint on the mechanisms of tumorigenesis and provides a niche for investigating the interaction between host immunity and cancer development. Full article
(This article belongs to the Special Issue Disease Biomarkers in the Precision Medicine Era: A Comprehensive Multi-Omics Analysis)
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Review

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18 pages, 690 KiB  
Review
Application of Omics Analyses in Pediatric B-Cell Acute Lymphoblastic Leukemia
by Megi Vllahu, Maria Savarese, Immacolata Cantiello, Carmen Munno, Rosalba Sarcina, Pio Stellato, Ornella Leone and Mariaevelina Alfieri
Biomedicines 2025, 13(2), 424; https://doi.org/10.3390/biomedicines13020424 - 10 Feb 2025
Viewed by 1289
Abstract
Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer, comprising almost 25% of all malignancies diagnosed in children younger than 20 years, and its incidence is still increasing. ALL is a blood cancer arising from the unregulated proliferation of clonal lymphoid progenitor [...] Read more.
Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer, comprising almost 25% of all malignancies diagnosed in children younger than 20 years, and its incidence is still increasing. ALL is a blood cancer arising from the unregulated proliferation of clonal lymphoid progenitor cells. To make a diagnosis of B-cell ALL, bone marrow morphology and immunophenotyping are needed; cerebrospinal fluid examination, and chromosomal analysis are currently used as stratification exams. Currently, almost 70% of children affected by B-cell ALL are characterized by well-known cytogenetic abnormalities. However, the integration of results with “omic” techniques (genomics, transcriptomics, proteomics, and metabolomics, both individually and integrated) able to analyze simultaneously thousands of molecules, has enabled a deeper definition of the molecular scenario of B-cell ALL and the identification of new genetic alterations. Studies based on omics have greatly deepened our knowledge of ALL, expanding the horizon from the traditional morphologic and cytogenetic point of view. In this review, we focus our attention on the “omic” approaches mainly used to improve the understanding and management of B-cell ALL, crucial for the diagnosis, prognosis, and treatment of the disease, offering a pathway toward more precise and personalized therapeutic interventions. Full article
(This article belongs to the Special Issue Disease Biomarkers in the Precision Medicine Era: A Comprehensive Multi-Omics Analysis)
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