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Transcriptomics and Diseases
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Transcriptomics and Diseases

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 (30 June 2023) | Viewed by 17814

Special Issue Editor

Dr. Giancarlo Russo

E-Mail Website
Guest Editor
EMBL Partner Institute for Gene Editing, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
Interests: CRISPR-Cas; microbiology; next-generation sequencing; bioinformatics data analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

It has been known for a long time that alterations in gene expression can induce pronounced consequences on the function of a protein and ultimately hijack several signalling pathways, producing physiologically adverse effects. However, until recently, most of the research based on quantifying gene expression was limited by either the size of the gene pool (targeted panels) or the measurable dynamic range of the levels of expression (microarrays). Only in the past decade RNA sequencing has become cheap enough to enable scientists to routinely perform whole-transcriptome studies with high number of groups and replicates, therefore leading to an unprecedented detective power, also in the case of genes present at low abundances. Moreover, long read technologies have unlocked the potential of sequencing full-length transcripts, greatly expanding the isoform repertoires in model and non-model organisms, as well as robustly interrogating alternative splicing-driven phenotypic associations and exploring RNA modifications through direct RNA sequencing.

This special issue will focus on the effect of a malfunctioning transcription machinery on human health and aims to include original articles on how RNA sequencing can help understanding the molecular mechanisms behind onset and progression of diseases and selecting potential targets for therapies. Suggested topics include altered gene expression, preferential splicing, expanded/reduced isoform repertoire, RNA editing, microRNA, allele-specific expression, RNA modifications, identification of targeted gene therapies.

Dr. Giancarlo Russo
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

  • RNA sequencing
  • alternative splicing
  • gene therapy
  • RNA editing
  • microRNA
  • small RNA
  • transcriptomics
  • single cell RNA sequencing
  • direct RNA sequencing
  • RNA modifications

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Published Papers (5 papers)

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Research

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12 pages, 2119 KiB  
Article
A Protocol for Low-Input RNA-Sequencing of Patients with Febrile Neutropenia Captures Relevant Immunological Information
by Victoria Probst, Lotte Møller Smedegaard, Arman Simonyan, Yuliu Guo, Olga Østrup, Kia Hee Schultz Dungu, Nadja Hawwa Vissing, Ulrikka Nygaard and Frederik Otzen Bagger
Int. J. Mol. Sci. 2023, 24(12), 10251; https://doi.org/10.3390/ijms241210251 - 16 Jun 2023
Viewed by 1732
Abstract
Improved methods are needed for diagnosing infectious diseases in children with cancer. Most children have fever for other reasons than bacterial infection and are exposed to unnecessary antibiotics and hospital admission. Recent research has shown that host whole blood RNA transcriptomic signatures can [...] Read more.
Improved methods are needed for diagnosing infectious diseases in children with cancer. Most children have fever for other reasons than bacterial infection and are exposed to unnecessary antibiotics and hospital admission. Recent research has shown that host whole blood RNA transcriptomic signatures can distinguish bacterial infection from other causes of fever. Implementation of this method in clinics could change the diagnostic approach for children with cancer and suspected infection. However, extracting sufficient mRNA to perform transcriptome profiling by standard methods is challenging due to the patient’s low white blood cell (WBC) counts. In this prospective cohort study, we succeeded in sequencing 95% of samples from children with leukaemia and suspected infection by using a low-input protocol. This could be a solution to the issue of obtaining sufficient RNA for sequencing from patients with low white blood cell counts. Further studies are required to determine whether the captured immune gene signatures are clinically valid and thus useful to clinicians as a diagnostic tool for patients with cancer and suspected infection. Full article
(This article belongs to the Special Issue Transcriptomics and Diseases)
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20 pages, 16076 KiB  
Article
Acss2 Deletion Reveals Functional Versatility via Tissue-Specific Roles in Transcriptional Regulation
by Narayanan Puthillathu Vasudevan, Dharmendra K. Soni, John R. Moffett, Jishnu K. S. Krishnan, Abhilash P. Appu, Sarani Ghoshal, Peethambaran Arun, John M. Denu, Thomas P. Flagg, Roopa Biswas and Aryan M. Namboodiri
Int. J. Mol. Sci. 2023, 24(4), 3673; https://doi.org/10.3390/ijms24043673 - 12 Feb 2023
Cited by 1 | Viewed by 3454
Abstract
The coordination of cellular biological processes is regulated in part via metabolic enzymes acting to match cellular metabolism to current conditions. The acetate activating enzyme, acyl-coenzyme A synthetase short-chain family member 2 (Acss2), has long been considered to have a predominantly lipogenic function. [...] Read more.
The coordination of cellular biological processes is regulated in part via metabolic enzymes acting to match cellular metabolism to current conditions. The acetate activating enzyme, acyl-coenzyme A synthetase short-chain family member 2 (Acss2), has long been considered to have a predominantly lipogenic function. More recent evidence suggests that this enzyme has regulatory functions in addition to its role in providing acetyl-CoA for lipid synthesis. We used Acss2 knockout mice (Acss2−/−) to further investigate the roles this enzyme plays in three physiologically distinct organ systems that make extensive use of lipid synthesis and storage, including the liver, brain, and adipose tissue. We examined the resulting transcriptomic changes resulting from Acss2 deletion and assessed these changes in relation to fatty acid constitution. We find that loss of Acss2 leads to dysregulation of numerous canonical signaling pathways, upstream transcriptional regulatory molecules, cellular processes, and biological functions, which were distinct in the liver, brain, and mesenteric adipose tissues. The detected organ-specific transcriptional regulatory patterns reflect the complementary functional roles of these organ systems within the context of systemic physiology. While alterations in transcriptional states were evident, the loss of Acss2 resulted in few changes in fatty acid constitution in all three organ systems. Overall, we demonstrate that Acss2 loss institutes organ-specific transcriptional regulatory patterns reflecting the complementary functional roles of these organ systems. Collectively, these findings provide further confirmation that Acss2 regulates key transcription factors and pathways under well-fed, non-stressed conditions and acts as a transcriptional regulatory enzyme. Full article
(This article belongs to the Special Issue Transcriptomics and Diseases)
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17 pages, 3149 KiB  
Article
Prediction of Metabolic Profiles from Transcriptomics Data in Human Cancer Cell Lines
by Maria Vittoria Cavicchioli, Mariangela Santorsola, Nicola Balboni, Daniele Mercatelli and Federico Manuel Giorgi
Int. J. Mol. Sci. 2022, 23(7), 3867; https://doi.org/10.3390/ijms23073867 - 31 Mar 2022
Cited by 9 | Viewed by 4645
Abstract
The Metabolome and Transcriptome are mutually communicating within cancer cells, and this interplay is translated into the existence of quantifiable correlation structures between gene expression and metabolite abundance levels. Studying these correlations could provide a novel venue of understanding cancer and the discovery [...] Read more.
The Metabolome and Transcriptome are mutually communicating within cancer cells, and this interplay is translated into the existence of quantifiable correlation structures between gene expression and metabolite abundance levels. Studying these correlations could provide a novel venue of understanding cancer and the discovery of novel biomarkers and pharmacological strategies, as well as laying the foundation for the prediction of metabolite quantities by leveraging information from the more widespread transcriptomics data. In the current paper, we investigate the correlation between gene expression and metabolite levels in the Cancer Cell Line Encyclopedia dataset, building a direct correlation network between the two molecular ensembles. We show that a metabolite/transcript correlation network can be used to predict metabolite levels in different samples and datasets, such as the NCI-60 cancer cell line dataset, both on a sample-by-sample basis and in differential contrasts. We also show that metabolite levels can be predicted in principle on any sample and dataset for which transcriptomics data are available, such as the Cancer Genome Atlas (TCGA). Full article
(This article belongs to the Special Issue Transcriptomics and Diseases)
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Review

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23 pages, 3406 KiB  
Review
Microbiomes, Their Function, and Cancer: How Metatranscriptomics Can Close the Knowledge Gap
by Lina Aitmanaitė, Karolis Širmonaitis and Giancarlo Russo
Int. J. Mol. Sci. 2023, 24(18), 13786; https://doi.org/10.3390/ijms241813786 - 7 Sep 2023
Cited by 9 | Viewed by 2948
Abstract
The interaction between the microbial communities in the human body and the onset and progression of cancer has not been investigated until recently. The vast majority of the metagenomics research in this area has concentrated on the composition of microbiomes, attempting to link [...] Read more.
The interaction between the microbial communities in the human body and the onset and progression of cancer has not been investigated until recently. The vast majority of the metagenomics research in this area has concentrated on the composition of microbiomes, attempting to link the overabundance or depletion of certain microorganisms to cancer proliferation, metastatic behaviour, and its resistance to therapies. However, studies elucidating the functional implications of the microbiome activity in cancer patients are still scarce; in particular, there is an overwhelming lack of studies assessing such implications directly, through analysis of the transcriptome of the bacterial community. This review summarises the contributions of metagenomics and metatranscriptomics to the knowledge of the microbial environment associated with several cancers; most importantly, it highlights all the advantages that metatranscriptomics has over metagenomics and suggests how such an approach can be leveraged to advance the knowledge of the cancer bacterial environment. Full article
(This article belongs to the Special Issue Transcriptomics and Diseases)
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29 pages, 1429 KiB  
Review
A Comprehensive Exploration of the Transcriptomic Landscape in Multiple Sclerosis: A Systematic Review
by Luigi Chiricosta, Santino Blando, Simone D’Angiolini, Agnese Gugliandolo and Emanuela Mazzon
Int. J. Mol. Sci. 2023, 24(2), 1448; https://doi.org/10.3390/ijms24021448 - 11 Jan 2023
Cited by 9 | Viewed by 3758
Abstract
Multiple Sclerosis (MS) is, to date, an incurable disease of the nervous system characterized by demyelination. Several genetic mutations are associated with the disease but they are not able to explain all the diagnosticated cases. Thus, it is suggested that altered gene expression [...] Read more.
Multiple Sclerosis (MS) is, to date, an incurable disease of the nervous system characterized by demyelination. Several genetic mutations are associated with the disease but they are not able to explain all the diagnosticated cases. Thus, it is suggested that altered gene expression may play a role in human pathologies. In this review, we explored the role of the transcriptomic profile in MS to investigate the main altered biological processes and pathways involved in the disease. Herein, we focused our attention on RNA-seq methods that in recent years are producing a huge amount of data rapidly replacing microarrays, both with bulk and single-cells. The studies evidenced that different MS stages have specific molecular signatures and non-coding RNAs may play a key role in the disease. Sex-dependence was observed before and after treatments used to alleviate symptomatology activating different biological processes in a drug-dependent manner. New pathways, such as neddylation, were found deregulated in MS and inflammation was linked to neuron degeneration areas through spatial transcriptomics. It is evident that the use of RNA-seq in the study of complex pathologies, such as MS, is a valid strategy to shed light on new involved mechanisms. Full article
(This article belongs to the Special Issue Transcriptomics and Diseases)
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