GBCdb: RNA Expression Landscapes and NcRNA-mRNA Interactions in Gallbladder Carcinoma

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2023 Jan 9

PMID 36624399

Authors

Li Guo

Yangyang Xiang

Yuyang Dou

Zibo Yin

Xinru Xu

Lihua Tang

Jiafeng Yu

Jun Wang

Tingming Liang

Affiliations

Soon will be listed here.

Abstract

Gallbladder carcinoma (GBC), an aggressive malignant tumor of the biliary system, is characterized by high cellular heterogeneity and poor prognosis. Fewer data have been reported in GBC than other common cancer types. Multi-omics data will contribute to the understanding of the molecular mechanisms of cancer, cancer diagnosis and prognosis. Herein, to provide better understanding of the molecular events in GBC pathogenesis, we developed GBCdb ( http://tmliang.cn/gbc/ ), a user-friendly interface for the query and browsing of GBC-associated genes and RNA interaction networks using published multi-omics data, which also included experimentally supported data from different molecular levels. GBCdb will help to elucidate the potential biological roles of different RNAs and allow for the exploration of RNA interactions in GBC. These resources will provide an opportunity for unraveling the potential molecular features of Gallbladder carcinoma.

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References

Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z . clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation (Camb). 2021; 2(3):100141. PMC: 8454663. DOI: 10.1016/j.xinn.2021.100141. View

Li Y, Li L, Wang Z, Pan T, Sahni N, Jin X . LncMAP: Pan-cancer atlas of long noncoding RNA-mediated transcriptional network perturbations. Nucleic Acids Res. 2018; 46(3):1113-1123. PMC: 5815097. DOI: 10.1093/nar/gkx1311. View

Albrecht T, Rausch M, Roessler S, Geissler V, Albrecht M, Halske C . HER2 gene (ERBB2) amplification is a low-frequency driver with potential predictive value in gallbladder carcinoma. Virchows Arch. 2019; 476(6):871-880. DOI: 10.1007/s00428-019-02706-6. View

Mao W, Deng F, Wang D, Gao L, Shi X . Treatment of advanced gallbladder cancer: A SEER-based study. Cancer Med. 2019; 9(1):141-150. PMC: 6943088. DOI: 10.1002/cam4.2679. View

Varshney S, Butturini G, Buttirini G, Gupta R . Incidental carcinoma of the gallbladder. Eur J Surg Oncol. 2002; 28(1):4-10. DOI: 10.1053/ejso.2001.1175. View

Roa E I, Lantadilla H S, Ibacache S G, de Aretxabala U X . [p53 and p27 gene expression in subserosal gallbladder carcinoma]. Rev Med Chil. 2009; 137(8):1017-22. DOI: /S0034-98872009000800003. View

Yan X, Yang P, Liu H, Zhao Y, Wu Z, Zhang B . miR-4461 inhibits the progression of Gallbladder carcinoma via regulating EGFR/AKT signaling. Cell Cycle. 2022; 21(11):1166-1177. PMC: 9103642. DOI: 10.1080/15384101.2022.2042775. View

Sui Z, Sui X . Long non-coding RNA TMPO-AS1 promotes cell proliferation, migration, invasion and epithelial-to-mesenchymal transition in gallbladder carcinoma by regulating the microRNA-1179/E2F2 axis. Oncol Lett. 2021; 22(6):855. PMC: 8581476. DOI: 10.3892/ol.2021.13116. View

Shannon P, Markiel A, Ozier O, Baliga N, Wang J, Ramage D . Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498-504. PMC: 403769. DOI: 10.1101/gr.1239303. View

10.

Zhu G, Chen X, Wang X, Li X, Du Q, Hong H . Expression of the RIP-1 gene and its role in growth and invasion of human gallbladder carcinoma. Cell Physiol Biochem. 2014; 34(4):1152-65. DOI: 10.1159/000366328. View

11.

Xu S, Zhan M, Jiang C, He M, Yang L, Shen H . Genome-wide CRISPR screen identifies ELP5 as a determinant of gemcitabine sensitivity in gallbladder cancer. Nat Commun. 2019; 10(1):5492. PMC: 6889377. DOI: 10.1038/s41467-019-13420-x. View

12.

Chen P, Wang Y, Li J, Bo X, Wang J, Nan L . Diversity and intratumoral heterogeneity in human gallbladder cancer progression revealed by single-cell RNA sequencing. Clin Transl Med. 2021; 11(6):e462. PMC: 8236117. DOI: 10.1002/ctm2.462. View

13.

Liu M, Wang Q, Shen J, Yang B, Ding X . Circbank: a comprehensive database for circRNA with standard nomenclature. RNA Biol. 2019; 16(7):899-905. PMC: 6546381. DOI: 10.1080/15476286.2019.1600395. View

14.

Li M, Liu F, Zhang F, Zhou W, Jiang X, Yang Y . Genomic / mutations promote PD-L1-mediated immune escape in gallbladder cancer: a whole-exome sequencing analysis. Gut. 2018; 68(6):1024-1033. DOI: 10.1136/gutjnl-2018-316039. View

15.

Li H, Hu Y, Jin Y, Zhu Y, Hao Y, Liu F . Long noncoding RNA lncGALM increases risk of liver metastasis in gallbladder cancer through facilitating N-cadherin and IL-1β-dependent liver arrest and tumor extravasation. Clin Transl Med. 2020; 10(7):e201. PMC: 7653798. DOI: 10.1002/ctm2.201. View

16.

Goeppert B, Truckenmueller F, Ori A, Fritz V, Albrecht T, Fraas A . Profiling of gallbladder carcinoma reveals distinct miRNA profiles and activation of STAT1 by the tumor suppressive miRNA-145-5p. Sci Rep. 2019; 9(1):4796. PMC: 6423323. DOI: 10.1038/s41598-019-40857-3. View

17.

Leek J, Johnson W, Parker H, Jaffe A, Storey J . The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012; 28(6):882-3. PMC: 3307112. DOI: 10.1093/bioinformatics/bts034. View

18.

Shukla S, Singh G, Shahi K, Bhuvan , Pant P . Genetic Changes of P and Kras in Gallbladder Carcinoma in Kumaon Region of Uttarakhand. J Gastrointest Cancer. 2019; 51(2):552-559. DOI: 10.1007/s12029-019-00283-0. View

19.

Hu X, Zhang J, Bu J, Yang K, Xu S, Pan M . MiR-4733-5p promotes gallbladder carcinoma progression via directly targeting kruppel like factor 7. Bioengineered. 2022; 13(4):10691-10706. PMC: 9161844. DOI: 10.1080/21655979.2022.2065951. View

20.

Wistuba I, Gazdar A . Gallbladder cancer: lessons from a rare tumour. Nat Rev Cancer. 2004; 4(9):695-706. DOI: 10.1038/nrc1429. View