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Reported findings include links between hCTR1/CTR1 expression and platinum uptake, gene dosage effects from copy-number aberrations, and pathway-level overexpression signatures, alongside the role of germline variation in 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makes identifying cancer-driving elements in structural variant regions particularly difficult?","Question",{"text":62,"@type":63},"Multiple genes and regulatory elements may be involved, so cancer-relevant coding and non-coding drivers in structural variant regions are hard to pinpoint.","Answer",{"name":65,"@type":60,"acceptedAnswer":66},"How do copy number aberrations influence gene expression in the reported studies?",{"text":67,"@type":63},"Broad copy number gains and losses create dosage transcriptional effects, producing dense upregulated genes on gain chromosomes and downregulated genes on loss chromosomes.",{"name":69,"@type":60,"acceptedAnswer":70},"What therapy-relevant relationships are mentioned regarding copper transporters and platinum drugs?",{"text":71,"@type":63},"Higher hCTR1 expression correlates with higher platinum drug uptake in sensitive cancer cells, and overexpression of the copper transporter CTR1 suggests high CRC sensitivity to platinum 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Therapy”  \nVincenza Barresi   \nCitation: Barresi, V. The Crucial Findings Derived from the Special Issue “Inside Cancer Genomics: From Structure to Therapy”. Cancers 2023, 15, 3488. [https://doi.org/10.3390/](https://doi.org/10.3390/)[ ](https://doi.org/10.3390/)cancers15133488  \nReceived: 25 June 2023  \nAccepted: 28 June 2023  \nPublished: 4 July 2023  \nCopyright: © 2023 by the author. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ([https://](https://)[ ](https://)[creativecommons.org/licenses/by/](creativecommons.org/licenses/by/)[ ](creativecommons.org/licenses/by/)[4.0/](4.0/)) .  \nDepartment of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; [vincenza.barresi@unict.it](vincenza.barresi@unict.it)  \nCancer initiation, growth, and progression are sustained by multiple types of genetic alterations, ranging in size from single point mutations, focal genomic errors to broad chromosomal copy number alterations, gains, and losses [1–3] . The identification of cancerdriving coding and non-coding elements located in structural variant regions is particularly difficult, since many genes and/or regulatory elements could be potentially involved [4–7] . The current extensive knowledge on DNA mutations in cancer genomes, derived from the application of omics technologies characterizing entire cancer genomes at structural and transcriptional levels, provides important insights into cancer's molecular mechanisms, and inspires a vast range of targeted therapies [8–10] . In this sense, the correlation between a higher hCTR1 expression and higher platinum drug uptake in cancer cells sensitive to the drug has been reported [11,12] and the overexpression of copper transporter, CTR1, suggests a high sensitivity of CRC to platinum drugs [13] .  \nThe study of the influence of broad copy number aberrations detected by SNP-arrayson the transcriptome profile, analyzed by microarrays and RNA-seq technologies, revealed a high-density of upregulated genes in the chromosomes affected by gains, or, on the contrary, downregulated genes in the chromosomes affected by losses. Uri Ben-David and Angelika Amon discuss in detail the effect of aneuploidy to promote or suppress tumorigenesis and describe how metabolism, microenvironment, and immune system interactions can determine a fitness advantage for cancer development and progression under celltype-specific conditions [14] . The analysis of gene-dosage transcriptional effects and the overexpression of cancer genes in selected altered recurrent chromosomes, such as Chr20, Chr 8, Chr13, and Chr7, have allowed the identification of crucial genes that cooperate at a functional level as subunits of protein complexes or in the same pathways sustaining cancer cell growth and progression. The authors found an increased expression of two genes encoding the eukaryotic translation initiation factors EIF3E and EIF3H, located in Chr8q, and a gene located in Chr20 and encoding the eukaryotic translation initiation factor EIF2S2, involved in the EIF2 signaling pathway of the initiation phase of mRNA translation [15,16] . Another significant pathway identified through the analysis of over-expressed transcriptsand fitness-overexpressed transcripts (please see papers 15,16 for details) is the “Cleavage and Polyadenylation of Pre-mRNA”, which contains multiple amplified subunits belonging to this pathway. On the other hand, growing evidence indicates the implication of germline variations in cancer predisposition and prognostication.  \nThe Special Issue, comprising 10 research articles and 3 reviews, aims to provide the latest findings on the above topics, with a particular focus on their potential biological relevance, the identification of predictive and prognost","cbCainepMRk2g4q9","https://ap.wps.com/l/cbCainepMRk2g4q9","pdf",229970,"English","# Editorial overview\n## Genetic alterations and structural variant challenges\n## Omics insights and targeted therapy connections\n## Copy-number aberrations, gene dosage, and pathways\n## Germline variation and predictive relevance\n## Special Issue scope and therapeutic implications","[{\"question\":\"What makes identifying cancer-driving elements in structural variant regions particularly difficult?\",\"answer\":\"Multiple genes and regulatory elements may be involved, so cancer-relevant coding and non-coding drivers in structural variant regions are hard to pinpoint.\"},{\"question\":\"How do copy number aberrations influence gene expression in the reported studies?\",\"answer\":\"Broad copy number gains and losses create dosage transcriptional effects, producing dense upregulated genes on gain chromosomes and downregulated genes on loss chromosomes.\"},{\"question\":\"What therapy-relevant relationships are mentioned regarding copper transporters and platinum drugs?\",\"answer\":\"Higher hCTR1 expression correlates with higher platinum drug uptake in sensitive cancer cells, and overexpression of the copper transporter CTR1 suggests high CRC sensitivity to platinum drugs.\"}]","The Crucial Findings Derived from the Special Issue “Inside Cancer Genomics: From Structure to Therapy” | PDF",1790233808,15]