Protein-protein Interaction Network Analyses for Elucidating the Roles of LOXL2-delta72 in Esophageal Squamous Cell Carcinoma

Abstract

Lysyl oxidase-like 2 (LOXL2), a member of the lysyl oxidase (LOX) family, is a copper-dependent enzyme that catalyzes oxidative deamination of lysine residues on protein substrates. LOXL2 was found to be overexpressed in esophageal squamous cell carcinoma (ESCC) in our previous research. We later identified a LOXL2 splicing variant LOXL2-delta72 and we overexpressed LOXL2-delta72 and its wild type counterpart in ESCC cells following microarray analyses. First, the differentially expressed genes (DEGs) of LOXL2 and LOXL2-delta72 compared to empty plasmid were applied to generate protein-protein interaction (PPI) sub-networks. Comparison of these two sub-networks showed hundreds of different proteins. To reveal the potential specific roles of LOXL2-delta72 compared to its wild type, the DEGs of LOXL2-delta72 vs LOXL2 were also applied to construct a PPI sub-network which was annotated by Gene Ontology. The functional annotation map indicated the third PPI sub-network involved hundreds of GO terms, such as "cell cycle arrest", "G1/S transition of mitotic cell cycle", "interphase", "cell-matrix adhesion" and "cell-substrate adhesion", as well as significant "immunity" related terms, such as "innate immune response", "regulation of defense response" and "Toll signaling pathway". These results provide important clues for experimental identification of the specific biological roles and molecular mechanisms of LOXL2-delta72. This study also provided a work flow to test the different roles of a splicing variant with high-throughput data.

Identification of a novel lysyl oxidase-like 2 alternative splicing isoform, LOXL2 Δe13, in esophageal squamous cell carcinoma

“…Recently, another human LOXL2 variant LOXL2-delta 72, with a loss of 72 bp (nucleotides 1234-1305 of LOXL2 WT) resulting in the deletion of 24 amino acids, has been identified in esophageal cancer (Wu et al 2014), but its function and molecular mechanisms in diverse processes and diseases need to further examined. In addition, the predicted LOXL2 ⌬e13 variant from other species such as Eptesicus fuscus (big brown bat, GenBank accession No.…”

A novel splice variant of LOXL2 promotes progression of human papillomavirus–negative head and neck squamous cell carcinoma

“…17 In previous studies, it has been demonstrated that LOXL2 was associated with poor prognosis in a variety of tumors and that overexpression of LOXL2 can promote the invasion and metastatic activity of cancer cells. 19,22 In the current study, we used the loss-of-function and gain-of-function experiments to elucidate the role of the novel LOXL2 variant identified from TCGA HPVnegative HNSCC data. 19,22 In the current study, we used the loss-of-function and gain-of-function experiments to elucidate the role of the novel LOXL2 variant identified from TCGA HPVnegative HNSCC data.…”

“…17,39,40 In addition, several LOXL2 splice variants have been found in esophageal squamous cell carcinoma, such as the variant lacking exon 13 and the variant with a deletion of 72 nucleotides, which contribute to tumor progression by a novel molecular mechanism distinct from canonical-type LOXL2. 19,22 In the current study, we used the loss-of-function and gain-of-function experiments to elucidate the role of the novel LOXL2 variant identified from TCGA HPVnegative HNSCC data. The tumor-specific LOXL2 variant could enhance the proliferative, migratory, and invasive capacities of HPV-negative HNSCC cells in vitro.…”

“…17,18 In patients with esophageal squamous cell carcinoma, several alternative splicing isoforms of LOXL2 also have been discovered to exert cell functions distinct from those of canonical-type LOXL2. [19][20][21][22] In our previous study, a total of 580 significant ASEs related to HPV-negative HNSCC have been identified using outlier analysis, including a novel splice variant of LOXL2 with a unique inserted exon. 16 However, to the best of our knowledge, the function and downstream effects of this specific LOXL2 variant have not been described to date.…”

Construction of a Protein-Protein Interaction Network for Chronic Myelocytic Leukemia and Pathway Prediction of Molecular Complexes

“…In Cytoscape, each protein is represented as a node, and each interaction between two nodes is represented as an edge. To increase the liabilities and define the protein perturbation to a certain level, the network reconstruction was limited to the first protein neighbors (Wu et al, 2014).…”