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Herrera-Orozco H, García-Castillo V, López-Urrutia E, Martinez-Gutierrez AD, Pérez-Yepez E, Millán-Catalán O, Cantú de León D, López-Camarillo C, Jacobo-Herrera NJ, Rodríguez-Dorantes M, Ramos-Payán R, Pérez-Plasencia C. Somatic Copy Number Alterations in Colorectal Cancer Lead to a Differentially Expressed ceRNA Network (ceRNet). Curr Issues Mol Biol 2023; 45:9549-9565. [PMID: 38132443 PMCID: PMC10742218 DOI: 10.3390/cimb45120597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/14/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
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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Affiliation(s)
- Héctor Herrera-Orozco
- Laboratorio de Genómica, FES-Iztacala, Universidad Nacional Autónoma de México. Av. De los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico; (H.H.-O.); (V.G.-C.); (E.L.-U.)
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Edificio D. Circuito de Posgrados, Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico
| | - Verónica García-Castillo
- Laboratorio de Genómica, FES-Iztacala, Universidad Nacional Autónoma de México. Av. De los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico; (H.H.-O.); (V.G.-C.); (E.L.-U.)
| | - Eduardo López-Urrutia
- Laboratorio de Genómica, FES-Iztacala, Universidad Nacional Autónoma de México. Av. De los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico; (H.H.-O.); (V.G.-C.); (E.L.-U.)
| | - Antonio Daniel Martinez-Gutierrez
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Tlalpan, Mexico City 14080, Mexico; (A.D.M.-G.); (E.P.-Y.); (O.M.-C.); (D.C.d.L.)
| | - Eloy Pérez-Yepez
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Tlalpan, Mexico City 14080, Mexico; (A.D.M.-G.); (E.P.-Y.); (O.M.-C.); (D.C.d.L.)
| | - Oliver Millán-Catalán
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Tlalpan, Mexico City 14080, Mexico; (A.D.M.-G.); (E.P.-Y.); (O.M.-C.); (D.C.d.L.)
| | - David Cantú de León
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Tlalpan, Mexico City 14080, Mexico; (A.D.M.-G.); (E.P.-Y.); (O.M.-C.); (D.C.d.L.)
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Calle Dr. García Diego 168, Cuauhtémoc, Mexico City 06720, Mexico;
| | - Nadia J. Jacobo-Herrera
- Unidad de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Av. Vasco de Quiroga 15, Tlalpan, Mexico City 14080, Mexico;
| | | | - Rosalío Ramos-Payán
- Faculty of Chemical and Biological Sciences, Autonomous University of Sinaloa, Culiacan 80030, Mexico;
| | - Carlos Pérez-Plasencia
- Laboratorio de Genómica, FES-Iztacala, Universidad Nacional Autónoma de México. Av. De los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico; (H.H.-O.); (V.G.-C.); (E.L.-U.)
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Tlalpan, Mexico City 14080, Mexico; (A.D.M.-G.); (E.P.-Y.); (O.M.-C.); (D.C.d.L.)
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Xiong L, He X, Wang L, Dai P, Zhao J, Zhou X, Tang H. Hypoxia-associated prognostic markers and competing endogenous RNA coexpression networks in lung adenocarcinoma. Sci Rep 2022; 12:21340. [PMID: 36494419 PMCID: PMC9734750 DOI: 10.1038/s41598-022-25745-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common form of non-small cell lung cancer (NSCLC). Hypoxia has been found in 50-60% of locally advanced solid tumors and is associated with poor prognosis in various tumors, including NSCLC. This study focused on hypoxia-associated molecular hallmarks in LUAD. Fifteen hypoxia-related genes were selected to define the hypoxia status of LUAD by ConsensusClusterPlus based on data from The Cancer Genome Atlas (TCGA). Then, we investigated the immune status under different hypoxia statuses. Subsequently, we constructed prognostic models based on hypoxia-related differentially expressed genes (DEGs), identified hypoxia-related microRNAs, lncRNAs and mRNAs, and built a network based on the competing endogenous RNA (ceRNA) theory. Two clusters (Cluster 1 and Cluster 2) were identified with different hypoxia statuses. Cluster 1 was defined as the hypoxia subgroup, in which all 15 hypoxia-associated genes were upregulated. The infiltration of CD4+ T cells and Tfh cells was lower, while the infiltration of regulatory T (Treg) cells, the expression of PD-1/PD-L1 and TMB scores were higher in Cluster 1, indicating an immunosuppressive status. Based on the DEGs, a risk signature containing 7 genes was established. Furthermore, three differentially expressed microRNAs (hsa-miR-9, hsa-miR-31, hsa-miR-196b) associated with prognosis under different hypoxia clusters and their related mRNAs and lncRNAs were identified, and a ceRNA network was built. This study showed that hypoxia was associated with poor prognosis in LUAD and explored the potential mechanism from the perspective of the gene signature and ceRNA theory.
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Affiliation(s)
- Lecai Xiong
- grid.413247.70000 0004 1808 0969Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Xueyu He
- grid.413247.70000 0004 1808 0969Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Le Wang
- grid.413247.70000 0004 1808 0969Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Peng Dai
- grid.413247.70000 0004 1808 0969Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Jinping Zhao
- grid.413247.70000 0004 1808 0969Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Xuefeng Zhou
- grid.413247.70000 0004 1808 0969Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Hexiao Tang
- grid.413247.70000 0004 1808 0969Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
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