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Advances in Cancer-Related Transcriptome and Genome Analyses
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Advances in Cancer-Related Transcriptome and Genome Analyses

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: 20 February 2025 | Viewed by 5310

Special Issue Editor

Dr. Enrico Gaffo

E-Mail Website
Guest Editor
Department of Molecular Medicine, University of Padova, 35121 Padova, Italy
Interests: bioinformatics; RNA-seq; DNA-seq; scRNA-seq; transcriptomics; cancer; blood diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues, 

The advent of high-throughput sequencing technologies opened a new era in molecular medicine and cancer research, allowing the genome-wide study of the molecular characteristics of tumours at the nucleotide level. As a more recent technology, single-cell sequencing allows an even higher resolution for dissecting the tumour environment at the cellular scale, while long-read sequencing improves genome assembly and the detection of transcript isoforms and structural variants.

DNA-seq and RNA-seq experiments generate massive amounts of data, which require the application of advanced interdisciplinary techniques, including bioinformatics, biostatistics, and artificial intelligence, to extract meaningful information. The molecular complexity of tumours, which requires the combination of multiple levels of information, and the difficulties of cancer studies (e.g., scarcity of samples, cost, and time limitations) make transcriptome and genome analysis even more challenging in cancer research.

In this Special Issue, we welcome submissions of original research articles, reviews, short communications, and perspectives on cancer-related transcriptome and genome analyses, with a focus on the analysis of novel or existing cancer omics data sets bringing new knowledge on molecular mechanisms and aberrancies driving tumour biogenesis and progression. We also accept studies presenting newly developed computational methods, software and resources for cancer research or the improvement of existing ones.

Dr. Enrico Gaffo
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

  • cancer
  • genomics
  • transcriptomics
  • omic data integration
  • computational analysis
  • RNA-seq
  • DNA-seq
  • scRNA-seq
  • long-read sequencing

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Published Papers (3 papers)

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Research

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15 pages, 6133 KiB  
Article
Systematic Modeling of Risk-Associated Copy Number Alterations in Cancer
by Alejandra Guardado, Raúl Aguirre-Gamboa and Victor Treviño
Int. J. Mol. Sci. 2024, 25(19), 10455; https://doi.org/10.3390/ijms251910455 - 27 Sep 2024
Viewed by 485
Abstract
The determination of the cancer prognosis is paramount for patients and medical personnel so that they can devise treatment strategies. Transcriptional-based signatures and subtypes derived from cancer biopsy material have been used in clinical practice for several cancer types to aid in setting [...] Read more.
The determination of the cancer prognosis is paramount for patients and medical personnel so that they can devise treatment strategies. Transcriptional-based signatures and subtypes derived from cancer biopsy material have been used in clinical practice for several cancer types to aid in setting the patient prognosis and forming treatment strategies. Other genomic features in cancer biopsies, such as copy number alterations (CNAs), have been underused in clinical practice, and yet they represent a complementary source of molecular information that can add detail to the prognosis, which is supported by recent work in breast, ovarian, and lung cancers. Here, through a systematic strategy, we explored the prognostic power of CNAs in 37 cancer types. In this analysis, we defined two modes of informative features, deep and soft, depending on the number of alleles gained or lost. These informative modes were grouped by amplifications or deletions to form four single-data prognostic models. Finally, the single-data models were summed or combined to generate four additional multidata prognostic models. First, we show that the modes of features are cancer-type dependent, where deep alterations generate better models. Nevertheless, some cancers require soft alterations to generate a feasible model due to the lack of significant deep alterations. Then, we show that the models generated by summing coefficients from amplifications and deletions appear to be more practical for many but not all cancer types. We show that the CNA-derived risk group is independent of other clinical factors. Furthermore, overall, we show that CNA-derived models can define clinically relevant risk groups in 33 of the 37 (90%) cancer types analyzed. Our study highlights the use of CNAs as biomarkers that are potentially clinically relevant to survival in cancer patients. Full article
(This article belongs to the Special Issue Advances in Cancer-Related Transcriptome and Genome Analyses)
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15 pages, 2672 KiB  
Article
A Molecular Characterization of the Allelic Expression of the BRCA1 Founder Δ9–12 Pathogenic Variant and Its Potential Clinical Relevance in Hereditary Cancer
by Julieta Dominguez-Ortiz, Rosa M. Álvarez-Gómez, Rogelio Montiel-Manríquez, Alberto Cedro-Tanda, Nicolás Alcaraz, Clementina Castro-Hernández, Luis Bautista-Hinojosa, Laura Contreras-Espinosa, Leda Torres-Maldonado, Verónica Fragoso-Ontiveros, Yuliana Sánchez-Contreras, Rodrigo González-Barrios, Marcela Angélica De la Fuente-Hernández, María de la Luz Mejía-Aguayo, Ulises Juárez-Figueroa, Alejandra Padua-Bracho, Rodrigo Sosa-León, Gabriela Obregon-Serrano, Silvia Vidal-Millán, Paulina María Núñez-Martínez, Abraham Pedroza-Torres, Sergio Nicasio-Arzeta, Alfredo Rodríguez, Fernando Luna, Fernanda Cisneros-Soberanis, Sara Frías, Cristian Arriaga-Canon and Luis A. Herrera-Montalvoadd Show full author list remove Hide full author list
Int. J. Mol. Sci. 2024, 25(12), 6773; https://doi.org/10.3390/ijms25126773 - 20 Jun 2024
Viewed by 1575
Abstract
Hereditary breast and ovarian cancer (HBOC) syndrome is a genetic condition that increases the risk of breast cancer by 80% and that of ovarian cancer by 40%. The most common pathogenic variants (PVs) causing HBOC occur in the BRCA1 gene, with more than [...] Read more.
Hereditary breast and ovarian cancer (HBOC) syndrome is a genetic condition that increases the risk of breast cancer by 80% and that of ovarian cancer by 40%. The most common pathogenic variants (PVs) causing HBOC occur in the BRCA1 gene, with more than 3850 reported mutations in the gene sequence. The prevalence of specific PVs in BRCA1 has increased across populations due to the effect of founder mutations. Therefore, when a founder mutation is identified, it becomes key to improving cancer risk characterization and effective screening protocols. The only founder mutation described in the Mexican population is the deletion of exons 9 to 12 of BRCA1 (BRCA1Δ9–12), and its description focuses on the gene sequence, but no transcription profiles have been generated for individuals who carry this gene. In this study, we describe the transcription profiles of cancer patients and healthy individuals who were heterozygous for PV BRCA1Δ9–12 by analyzing the differential expression of both alleles compared with the homozygous BRCA1 control group using RT–qPCR, and we describe the isoforms produced by the BRCA1 wild-type and BRCA1Δ9–12 alleles using nanopore long-sequencing. Using the Kruskal–Wallis test, our results showed a similar transcript expression of the wild-type allele between the healthy heterozygous group and the homozygous BRCA1 control group. An association between the recurrence and increased expression of both alleles in HBOC patients was also observed. An analysis of the sequences indicated four wild-type isoforms with diagnostic potential for discerning individuals who carry the PV BRCA1Δ9–12 and identifying which of them has developed cancer. Full article
(This article belongs to the Special Issue Advances in Cancer-Related Transcriptome and Genome Analyses)
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Review

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34 pages, 1604 KiB  
Review
Genomic and Transcriptomic Research in the Discovery and Application of Colorectal Cancer Circulating Markers
by Anastasia A. Ponomaryova, Elena Yu. Rykova, Anastasia I. Solovyova, Anna S. Tarasova, Dmitry N. Kostromitsky, Alexey Yu. Dobrodeev, Sergey A. Afanasiev and Nadezhda V. Cherdyntseva
Int. J. Mol. Sci. 2023, 24(15), 12407; https://doi.org/10.3390/ijms241512407 - 3 Aug 2023
Cited by 4 | Viewed by 2504
Abstract
Colorectal cancer (CRC) is the most frequently occurring malignancy in the world. However, the mortality from CRC can be reduced through early diagnostics, selection of the most effective treatment, observation of the therapy success, and the earliest possible diagnosis of recurrences. A comprehensive [...] Read more.
Colorectal cancer (CRC) is the most frequently occurring malignancy in the world. However, the mortality from CRC can be reduced through early diagnostics, selection of the most effective treatment, observation of the therapy success, and the earliest possible diagnosis of recurrences. A comprehensive analysis of genetic and epigenetic factors contributing to the CRC development is needed to refine diagnostic, therapeutic, and preventive strategies and to ensure appropriate decision making in managing specific CRC cases. The liquid biopsy approach utilizing circulating markers has demonstrated its good performance as a tool to detect the changes in the molecular pathways associated with various cancers. In this review, we attempted to brief the main tendencies in the development of circulating DNA and RNA-based markers in CRC such as cancer-associated DNA mutations, DNA methylation changes, and non-coding RNA expression shifts. Attention is devoted to the existing circulating nucleic acid-based CRC markers, the possibility of their application in clinical practice today, and their future improvement. Approaches to the discovery and verification of new markers are described, and the existing problems and potential solutions for them are highlighted. Full article
(This article belongs to the Special Issue Advances in Cancer-Related Transcriptome and Genome Analyses)
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