دورية أكاديمية
Somatic Copy Number Alterations in Colorectal Cancer Lead to a Differentially Expressed ceRNA Network (ceRNet).
| العنوان: | Somatic Copy Number Alterations in Colorectal Cancer Lead to a Differentially Expressed ceRNA Network (ceRNet). |
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| المؤلفون: | Herrera-Orozco H; Laboratorio de Genómica, FES-Iztacala, Universidad Nacional Autónoma de México. Av. De los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico.; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Edificio D. Circuito de Posgrados, Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico., García-Castillo V; Laboratorio de Genómica, FES-Iztacala, Universidad Nacional Autónoma de México. Av. De los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico., López-Urrutia E; Laboratorio de Genómica, FES-Iztacala, Universidad Nacional Autónoma de México. Av. De los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico., Martinez-Gutierrez AD; Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Tlalpan, Mexico City 14080, Mexico., Pérez-Yepez E; Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Tlalpan, Mexico City 14080, Mexico., Millán-Catalán O; Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Tlalpan, Mexico City 14080, Mexico., Cantú de León D; Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Tlalpan, Mexico City 14080, Mexico., López-Camarillo C; Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Calle Dr. García Diego 168, Cuauhtémoc, Mexico City 06720, Mexico., Jacobo-Herrera NJ; Unidad de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Av. Vasco de Quiroga 15, Tlalpan, Mexico City 14080, Mexico., Rodríguez-Dorantes M; Laboratorio de Oncogenómica, Instituto Nacional de Medicina Genómica, Tlalpan, Mexico City 14610, Mexico., Ramos-Payán R; Faculty of Chemical and Biological Sciences, Autonomous University of Sinaloa, Culiacan 80030, Mexico., Pérez-Plasencia C; Laboratorio de Genómica, FES-Iztacala, Universidad Nacional Autónoma de México. Av. De los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico.; Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Tlalpan, Mexico City 14080, Mexico. |
| المصدر: | Current issues in molecular biology [Curr Issues Mol Biol] 2023 Nov 28; Vol. 45 (12), pp. 9549-9565. Date of Electronic Publication: 2023 Nov 28. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: MDPI Country of Publication: Switzerland NLM ID: 100931761 Publication Model: Electronic Cited Medium: Internet ISSN: 1467-3045 (Electronic) Linking ISSN: 14673037 NLM ISO Abbreviation: Curr Issues Mol Biol Subsets: PubMed not MEDLINE |
| أسماء مطبوعة: | Publication: 2021- : Basel, Switzerland : MDPI Original Publication: Wymondham, Norfolk, UK : Caister Academic Press, |
| مستخلص: | Colorectal cancer (CRC) represents the second deadliest malignancy worldwide. Around 75% of CRC patients exhibit high levels of chromosome instability that result in the accumulation of somatic copy number alterations. These alterations are associated with the amplification of oncogenes and deletion of tumor-ppressor genes and contribute to the tumoral phenotype in different malignancies. Even though this relationship is well known, much remains to be investigated regarding the effect of said alterations in long non-coding RNAs (lncRNAs) and, in turn, the impact these alterations have on the tumor phenotype. The present study aimed to evaluate the role of differentially expressed lncRNAs coded in regions with copy number alterations in colorectal cancer patient samples. We downloaded RNA-seq files of the Colorectal Adenocarcinoma Project from the The Cancer Genome Atlas (TCGA) repository (285 sequenced tumor tissues and 41 non-tumor tissues), evaluated differential expression, and mapped them over genome sequencing data with regions presenting copy number alterations. We obtained 78 differentially expressed (LFC > 1|< -1, padj < 0.05) lncRNAs, 410 miRNAs, and 5028 mRNAs and constructed a competing endogenous RNA (ceRNA) network, predicting significant lncRNA-miRNA-mRNA interactions. Said network consisted of 30 lncRNAs, 19 miRNAs, and 77 mRNAs. To understand the role that our ceRNA network played, we performed KEGG and GO analysis and found several oncogenic and anti-oncogenic processes enriched by the molecular players in our network. Finally, to evaluate the clinical relevance of the lncRNA expression, we performed survival analysis and found that C5orf64, HOTAIR, and RRN3P3 correlated with overall patient survival. Our results showed that lncRNAs coded in regions affected by SCNAs form a complex gene regulatory network in CCR. |
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| معلومات مُعتمدة: | Not Sure Instituto Nacional de Cancerología |
| فهرسة مساهمة: | Keywords: colorectal cancer; competitive endogenous RNA (ceRNA) network; long non-coding RNAs; somatic copy number alterations |
| تواريخ الأحداث: | Date Created: 20231222 Latest Revision: 20231224 |
| رمز التحديث: | 20231224 |
| مُعرف محوري في PubMed: | PMC10742218 |
| DOI: | 10.3390/cimb45120597 |
| PMID: | 38132443 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1467-3045 |
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| DOI: | 10.3390/cimb45120597 |