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Background Long non-coding RNAs (lncRNAs) are emerging as key molecules in gastric cancer(GC), yet their potential molecular mechanisms are not well understood. The aim of our study is to identify lncRNAs that are up-regulated in gastric cancer tissues and explore their function in gastric cancer metastasis. Methods RNA sequencing of 48 paired gastric tumor and non-tumor tissues in SYSUCC was conducted. The upregulated lncRNAs were selected and overlapped with those in TCGA database. A siRNA library was established using the top 50 lncRNAs highly expressed in GC and used to identify lncRNAs that significantly affected cell migration based on transwell assays. The expression of our focused lncRNA CRCAL-2(ColoRectal Cancer Associated LncRNA-2) was measured using quantitative reverse transcription PCR assays and lncRNA in situ hybridization. In vivo,cell-based and patient-derived xenograft (PDX) models were used to further explore roles of CRCAL-2 in GC metastasis. Then, RNA pull-down, mass spectrometry analyses, western blot and RNA-binding protein immunoprecipitation (RIP) were performed to identify interaction proteins and related mechanisms of CRCAL-2. Results LncRNA CRCAL-2, significantly overexpressed in the tumor tissues, was identified as the key regulator of GC metastasis. Upregulated CRCAL-2 in GC correlated with poor overall survival. Knockdown of CRCAL-2 significantly reduced GC cells migration, invasion, and metastasis of xenograft tumors in nude mice. Mechanistically, CRCAL-2 promoted GC metastasis by directly interacting with and stabilizing the nuclear transport protein RAN, resulting in increasement of nuclear import of beta-catenin and ultimately, activation of downstream targeted EMT(Epithelial-Mesenchymal Transition) genes. Additionally, the transcription factor YY1 could bind to the promoter of CRCAL-2 to upregulate its expression. Conclusions Our results suggest that YY1/CRCAL2/beta-catenin axis play a crucial role in GC metastasis, and the newly identified lncRNA CRCAL-2 might be developed as a biomarker and potential therapeutic target of GC in patients.

Background Rapid proliferation and glucose metabolism remodeling are hallmarks of cancers. Long non-coding RNAs (lncRNAs) are potentially involved in Warburg effect. We aimed to identify oncogenic lncRNAs that significantly affect the development of esophageal squamous cell carcinoma (ESCC) and investigate the metabolism-related mechanisms. Methods Bioinformatics analysis and siRNA library screening were used to pinpoint lncRNAs that significantly affected cell glycolysis and proliferation. RNAScope(R) in situ hybridization and qRT-PCR assays were performed in clinical samples to investigate expression levels and clinical relevance of the lncRNA. RNA interference and CRISPR-Cas9 were used to explore the functional roles of the lncRNA. In vivo, cell-based and patient-derived xenograft (PDX) models were used. Extracellular acidification rate and 13C-labeled intracellular metabolites were determined. RNA pull-down, MS2-Tagged RNA affinity purification, RNA-binding protein immunoprecipitation and cross-linking immunoprecipitation were performed to identify lncRNA associated proteins and related mechanisms. Results The lncRNA LOC148709 was identified as a metabolism-related lncRNA. Increased expression of LOC148709 was observed in ESCC and was correlated with poor prognosis. LOC148709 knockdown significantly decreased cell proliferation and glycolysis. Mechanistically, LOC148709 was directly associated with PFKFB3 and significantly affected PFKFB3 stability. LOC148709 interacted mainly with the C-terminal fragment of PFKFB3 and the T5 (2031–2321) fragment of LOC148709 mediated the interaction with PFKFB3. Through inhibiting K302 ubiquitination, LOC148709 protected PFKFB3 from proteasomal degradation, which subsequently activated glycolytic flux and promoted cell cycle progression by regulating p27 and CDK1. P53 could bind to the LOC148709 promoter and repress its transcription, p53 loss or mutation triggered striking LOC148709 upregulation. Multiple micro-environmental factors, including hypoxia and oncogenic stress, were also involved in the LOC148709 regulatory network via affecting the status of p53. Notably, our patient-derived xenograft (PDX) model studies demonstrated that LOC148709 knockdown dramatically impaired tumor growth. Conclusions The lncRNA LOC148709 plays an essential role in glycolytic reprogramming by binding to and stabilizing PFKFB3. This study identified a novel metabolism-related lncRNA and revealed a novel mechanism underlying lncRNA-mediated cancer metabolism remodeling. Translational studies further implicated that LOC148709 is a promising biomarker for cancer diagnosis and therapy.

Background Duodenum adenocarcinoma is one of the most common small intestinal malignancies, accounting for approximately 50% of small intestinal malignancies. Molecular classification and lncRNA expression profile of duodenum adenocarcinoma were unknown. Methods RNA-seqeuncing of 11 pairs of duodenal adenocarcinoma tissues and adjacent normal tissues was carried out. Biological information analysis and RT-PCR were further carried out. We performed signal pathways enrichment and cluster analysis. We established C1/C2 molecular classification, explored its prognostic value. LncRNA expression profile of duodenum adenocarcinoma was also explored. Function and the RNA-binding protein of the lncRNA were confirmed. Results Cancer hallmark signal pathways enrichment found that the MYC, mTORC1, Notch and G2M signal pathways were significantly enriched. KEGG signal pathways enrichment showed that ribosomal production, IL-17 and P53 signal pathways were significantly enriched. Cluster analysis showed that patients can be divided into two molecular subtypes, C1 and C2 subtypes. In C1 patients, base repair signal pathway was significantly enriched, while in C2 patients, PI3K-AKT, RAS and Hippo signal pathway were significantly enriched. Gastric cancer and colorectal cancer patients could also be automatically divided into C1 and C2 subtypes. C1 and C2 molecular subtypes have prognostic value in predicting the overall survival of 11 duodenum adenocarcinoma patients, gastric cancer and colorectal cancer patients in TCGA database, the prognosis of C2 subtype patients was worse. Tumor mutation burden (TMB) of C2 subtype was significantly lower than that of C1 subtype, Cancer Associated Fibroblast(CAF) cells of C2 subtype were significantly increased, and Myeloid-derived suppressor cells(MDSC) were significantly decreased. Analysis of the expression profile of lncRNAs showed that linc01559 increased most significantly in cancer tissues. We conducted siRNA interference on linc01559 in WDC-1 and Hutu-80 cells. Cell proliferation, invasion and migration were significantly decreased. Apoptosis rate was significantly increased, suggesting that linc01559 can promote proliferation and metastasis of duodenum adenocarcinoma. RNA pulldown and RIP confirmed that the RNA-binding protein of linc01559 is GRSF1(figures 1,2,3, and 4). Conclusions C1 and C2 molecular subtypes were prognostic of overall survival of duodenum adenocarcinoma. Linc01559 is a novel and important lncRNA that can promote the proliferation and metastasis of duodenum adenocarcinoma.

Background Tumour cells often exhibit altered energy metabolism for tumour progression, but whether long noncoding RNAs (lncRNAs) are involved in this process remains elusive. We aimed to identify novel lncRNAs significantly affecting the development of Esophageal Squamous Cell Carcinoma (ESCC) and investigate the metabolism-related mechanisms. Methods A siRNA library was established using top 100 lncRNAs highly expressed in ESCC screened from TCGA database and transfected into ESCC cells to identify lncRNAs that significantly affected cell glucose metabolism and proliferation. RNAscope in situ hybridization, qRT-PCR and RNAi assays were performed to investigate the functional role of lncRNA AGPG (Actin Gamma 1 Pseudogene) and clinical relevance. In vivo, cell-based and patient-derived xenograft (PDX) models were used to further explore roles of AGPG in ESCC tumorigenesis. RNA pull-down, mass spectrometry analyses, western blot and RNA-binding protein immunoprecipitation (RIP) were performed to identify interaction proteins and related mechanisms. Results We identified that lncRNA AGPG was markedly increased in ESCC and correlated with poor prognosis. AGPG depletion significantly repressed ESCC cell proliferation and glycolytic activity including decreased glucose uptake and increased lactate production. In vivo experiments further showed that silencing AGPG decreased tumours growth in cell-based xenografts and PDX models. Mechanistically, AGPG could interact with 6-phosphofructo-2-kinase/fructose-2, 6-biphosphatase 3 (PFKFB3) in the nucleus, thus enhancing PFKFB3 stability via preventing its ubiquitination and proteosomal degradation. Subsequently, AGPG-PFKFB3 promoted glycolysis and dysregulated cell cycle by suppressing p27 and over-activating cyclin-dependent kinase 1(CDK1), thereby leading to G1/S cell cycle progression. Additionally, TP53 could bind to the promoter of AGPG to negatively regulate its expression. Conclusions We first identified that AGPG, which is regulated by TP53, is playing a pivotal role in glucose metabolism remodelling and cell proliferation through enhancing PFKFB3 stability, thus facilitating the development of ESCC. Collectively, our study suggests that TP53-AGPG-PFKFB3 axis might serve as potential biomarkers and therapeutic targets in ESCC.