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Integration of Meta-Multi-Omics Data: Unraveling Impact and Therapeutic Potential

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: 20 April 2025 | Viewed by 5181

Special Issue Editor

Special Issue Information

Dear Colleagues,

We are delighted to welcome researchers and scholars to this Special Issue of the International Journal of Molecular Sciences. Here, we delve into the realm of "integrating meta-multi-omics data", where cutting-edge science meets the vast complexity of biology. With the unprecedented merging of diverse omics fields, we are on the cusp of transformative breakthroughs that will redefine our understanding of life and health.

This Issue focuses on exploring the profound impact of meta-multiomics on a variety of domains:

  • Aging and Exercise: Dive deep into the molecular intricacies of aging and the central role of exercise. How does the symphony of genes, proteins, and metabolites play out as we age? How does movement influence this complicated dance?
  • Skeletal muscle and mitochondria: understand the dynamic interactions and changes of skeletal muscle and mitochondria, the critical components that underscore our physical health and energy dynamics.
  • Heart and Cancer: embark on a journey through the molecular pathways of the heart and delve into the multi-faceted world of cancer. How are these vital areas affected by the cascade of molecular interactions? What new therapeutic and preventive insights emerge when viewed through the integrated omics lens?
  • Therapy and prevention: explore the therapeutic potential unlocked by multi-omics data. From proteomics, which reveals protein interactions and functions, to metabolomics, which provides insights into small molecules: How can we better plan treatments and preventive measures?
  • Proteomics, metabolomics, and Omnibus: explore the intricate fields of proteomics and metabolomics. Also appreciate the big data collections like the Omnibus dataset that serve as treasure troves of data and drive metamultiomics.

Our goal with this Special Issue is to provide more than just a collection of research articles. We intend to offer a testament to the power of integrated molecular science—a beacon for researchers, clinicians, and students alike. As you flip through these pages, you will find a tapestry of insights, revelations, and forward-looking discussions that promise to shape the future of molecular science.

We sincerely thank the many authors and reviewers who contributed their expertise and passion to this issue. Their collective efforts have made it possible to illuminate the tremendous possibilities of meta-multiomics data integration.

Join us on this insightful journey and be re-inspired and excited by the molecular world that lies within and around us.

Dr. Rui Vitorino
Guest Editor

Manuscript Submission Information

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Keywords

  • integration meta-multiomics data
  • impact
  • aging
  • exercise
  • skeletal muscle
  • mitochondrial
  • heart
  • cancer
  • therapeutic
  • prevention
  • proteomics
  • omnibus
  • metabolite
  • metabolomic
  • repository dataset
  • public data

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Published Papers (3 papers)

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Research

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19 pages, 1864 KiB  
Article
Effects of Pulsed Electromagnetic Field Treatment on Skeletal Muscle Tissue Recovery in a Rat Model of Collagenase-Induced Tendinopathy: Results from a Proteome Analysis
by Enrica Torretta, Manuela Moriggi, Daniele Capitanio, Carlotta Perucca Orfei, Vincenzo Raffo, Stefania Setti, Ruggero Cadossi, Laura de Girolamo and Cecilia Gelfi
Int. J. Mol. Sci. 2024, 25(16), 8852; https://doi.org/10.3390/ijms25168852 - 14 Aug 2024
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Abstract
Tendon disorders often result in decreased muscle function and atrophy. Pulsed Electromagnetic Fields (PEMFs) have shown potential in improving tendon fiber structure and muscle recovery. However, the molecular effects of PEMF therapy on skeletal muscle, beyond conventional metrics like MRI or markers of [...] Read more.
Tendon disorders often result in decreased muscle function and atrophy. Pulsed Electromagnetic Fields (PEMFs) have shown potential in improving tendon fiber structure and muscle recovery. However, the molecular effects of PEMF therapy on skeletal muscle, beyond conventional metrics like MRI or markers of muscle decline, remain largely unexplored. This study investigates the metabolic and structural changes in PEMF-treated muscle tissue using proteomics in a rat model of Achilles tendinopathy induced by collagenase. Sprague Dawley rats were unilaterally induced for tendinopathy with type I collagenase injection and exposed to PEMFs for 8 h/day. Gastrocnemius extracts from untreated or PEMF-treated rats were analyzed with LC-MS/MS, and proteomics differential analysis was conducted through label-free quantitation. PEMF-treated animals exhibited decreased glycolysis and increased LDHB expression, enhancing NAD signaling and ATP production, which boosted respiratory chain activity and fatty acid beta-oxidation. Antioxidant protein levels increased, controlling ROS production. PEMF therapy restored PGC1alpha and YAP levels, decreased by tendinopathy. Additionally, myosins regulating slow-twitch fibers and proteins involved in fiber alignment and force transmission increased, supporting muscle recovery and contractile function. Our findings show that PEMF treatment modulates NAD signaling and oxidative phosphorylation, aiding muscle recovery through the upregulation of YAP and PGC1alpha and increasing slow myosin isoforms, thus speeding up physiological recovery. Full article
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19 pages, 7927 KiB  
Article
The Deep Proteomics Approach Identified Extracellular Vesicular Proteins Correlated to Extracellular Matrix in Type One and Two Endometrial Cancer
by Valeria Capaci, Feras Kharrat, Andrea Conti, Emanuela Salviati, Manuela Giovanna Basilicata, Pietro Campiglia, Nour Balasan, Danilo Licastro, Federica Caponnetto, Antonio Paolo Beltrami, Lorenzo Monasta, Federico Romano, Giovanni Di Lorenzo, Giuseppe Ricci and Blendi Ura
Int. J. Mol. Sci. 2024, 25(9), 4650; https://doi.org/10.3390/ijms25094650 - 24 Apr 2024
Viewed by 1556
Abstract
Among gynecological cancers, endometrial cancer is the most common in developed countries. Extracellular vesicles (EVs) are cell-derived membrane-surrounded vesicles that contain proteins involved in immune response and apoptosis. A deep proteomic approach can help to identify dysregulated extracellular matrix (ECM) proteins in EVs [...] Read more.
Among gynecological cancers, endometrial cancer is the most common in developed countries. Extracellular vesicles (EVs) are cell-derived membrane-surrounded vesicles that contain proteins involved in immune response and apoptosis. A deep proteomic approach can help to identify dysregulated extracellular matrix (ECM) proteins in EVs correlated to key pathways for tumor development. In this study, we used a proteomics approach correlating the two acquisitions—data-dependent acquisition (DDA) and data-independent acquisition (DIA)—on EVs from the conditioned medium of four cell lines identifying 428 ECM proteins. After protein quantification and statistical analysis, we found significant changes in the abundance (p < 0.05) of 67 proteins. Our bioinformatic analysis identified 26 pathways associated with the ECM. Western blotting analysis on 13 patients with type 1 and type 2 EC and 13 endometrial samples confirmed an altered abundance of MMP2. Our proteomics analysis identified the dysregulated ECM proteins involved in cancer growth. Our data can open the path to other studies for understanding the interaction among cancer cells and the rearrangement of the ECM. Full article
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Review

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24 pages, 2316 KiB  
Review
Unmasking the Metabolite Signature of Bladder Cancer: A Systematic Review
by Francisca Pereira, M. Rosário Domingues, Rui Vitorino, Inês M. S. Guerra, Lúcio Lara Santos, José Alexandre Ferreira and Rita Ferreira
Int. J. Mol. Sci. 2024, 25(6), 3347; https://doi.org/10.3390/ijms25063347 - 15 Mar 2024
Cited by 5 | Viewed by 2072
Abstract
Bladder cancer (BCa) research relying on Omics approaches has increased over the last few decades, improving the understanding of BCa pathology and contributing to a better molecular classification of BCa subtypes. To gain further insight into the molecular profile underlying the development of [...] Read more.
Bladder cancer (BCa) research relying on Omics approaches has increased over the last few decades, improving the understanding of BCa pathology and contributing to a better molecular classification of BCa subtypes. To gain further insight into the molecular profile underlying the development of BCa, a systematic literature search was performed in PubMed until November 2023, following the PRISMA guidelines. This search enabled the identification of 25 experimental studies using mass spectrometry or nuclear magnetic resonance-based approaches to characterize the metabolite signature associated with BCa. A total of 1562 metabolites were identified to be altered by BCa in different types of samples. Urine samples displayed a higher likelihood of containing metabolites that are also present in bladder tumor tissue and cell line cultures. The data from these comparisons suggest that increased concentrations of L-isoleucine, L-carnitine, oleamide, palmitamide, arachidonic acid and glycoursodeoxycholic acid and decreased content of deoxycytidine, 5-aminolevulinic acid and pantothenic acid should be considered components of a BCa metabolome signature. Overall, molecular profiling of biological samples by metabolomics is a promising approach to identifying potential biomarkers for early diagnosis of different BCa subtypes. However, future studies are needed to understand its biological significance in the context of BCa and to validate its clinical application. Full article
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