Super-Enhancer-Driven Long Non-Coding RNA LINC01503, Regulated by TP63, Is Over-Expressed and Oncogenic in Squamous Cell Carcinoma
Authors: Li-Yan Xu
Jian-Jun Xie
Wei Yang
Chun Sun
Ling-Wen Ding
De-Chen Lin
Le-Hang Lin
Stephen J Meltzer
Chun-Quan Li
Omer An
Jian-Yi Wu
Qi Cao
Lin Long
Henry Yang
Melissa Fullwood
Li Chen
Zhi-Yong Wu
Yuan Jiang
Harmik Soukiasian
Anand Mayakonda
Yan-Yi Jiang
H Phillip Koeffler
En-Min Li
Wang-Kai Fang
Mei-Chee Lim
Journal: Gastroenterology (2018)
Discipline: CLINICAL MEDICINE
Keywords: Epigenetic Regulation; Gene Regulation; Oncongenesis; Signal Transduction.
Affiliations: Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China; Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California. Electronic address: ., Cancer Science Institute of Singapore, National University of Singapore, Singapore., School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China., Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China., Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California., Department of Oncologic Surgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-Sen University, Shantou, China., Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California., Division of Thoracic Surgery, Cedars-Sinai Medical Center, Los Angeles, California., Departments of Medicine and Oncology, the Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland., Cancer Science Institute of Singapore, National University of Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore., Institute of Oncologic Pathology, Medical College of Shantou University, Shantou, China. Electronic address: ., Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China. Electronic address: ., Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California. Electronic address: ., Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California; Cancer Science Institute of Singapore, National University of Singapore, Singapore; National University Cancer Institute, National University Hospital Singapore, Singapore.

Abstract:  Background &amp; aims: Long non-coding RNAs (lncRNAs) are expressed in tissue-specific pattern, but it is not clear how these are regulated. We aimed to identify squamous cell carcinoma (SCC)-specific lncRNAs and investigate mechanisms that control their expression and function. Methods: We studied expression patterns and functions of 4 SCC-specific lncRNAs. We obtained 113 esophageal SCC (ESCC) and matched non-tumor esophageal tissues from a hospital in Shantou City, China, and performed quantitative reverse transcription polymerase chain reaction assays to measure expression levels of LINC01503. We collected clinical data from patients and compared expression levels with survival times. LINC01503 was knocked down using small interfering RNAs and oligonucleotides in TE7, TE5, and KYSE510 cell lines and overexpressed in KYSE30 cells. Cells were analyzed by chromatin immunoprecipitation sequencing, luciferase reporter assays, colony formation, migration and invasion, and mass spectrometry analyses. Cells were injected into nude mice and growth of xenograft tumors was measured. LINC01503 interaction with proteins was studied using fluorescence in situ hybridization, RNA pulldown, and RNA immunoprecipitation analyses. Results: We identified a lncRNA, LINC01503, which is regulated by a super enhancer and is expressed at significantly higher levels in esophageal and head and neck SCCs than in non-tumor tissues. High levels in SCCs correlated with shorter survival times of patients. The transcription factor TP63 bound to the super enhancer at the LINC01503 locus and activated its transcription. Expression of LINC01503 in ESCC cell lines increased their proliferation, colony formation, migration, and invasion. Knockdown of LINC01503 in SCC cells reduced their proliferation, colony formation, migration, and invasion, and the growth of xenograft tumors in nude mice. Expression of LINC01503 in ESCC cell lines reduced ERK2 dephosphorylation by DUSP6, leading to activation of ERK signaling via MAPK. LINC01503 disrupted the interaction between EBP1 and the p85 subunit of PI3K, increasing AKT signaling. Conclusions: We identified an lncRNA, LINC01503, which is increased in SCC cells compared with non-tumor cells. Increased expression of LINC01503 promotes ESCC cell proliferation, migration, invasion, and growth of xenograft tumors. It might be developed as a biomarker of aggressive SCCs in patients. 

Retracted: No

PubPeer comments:
 Figure 4D appears to have a repeated image. *** Closeup ![file] *** ![file] , 
 #1 Dear Dr. Actinopolyspora Biskrensis, We truly appreciate you for pointing out the error in our publication. We had carefully checked the raw data, and found that in Figure 4D, the representative figure of the LINC01503 knock-down KYSE510 cells in migration assay was inadvertently pasted as a repetitive figure of TE7 cells. We apologize for this mistake that had occurred during figure preparation. We will contact the publisher to correct the figure with the repeated raw images immediately, and we believe that it does not affect the conclusion of our study. Attached please find the original data of triplicate experiments for the effect of LINC01503 on the migration of KYSE510 cells. We thank you again for your attention! Best regards, Jianjun Xie ![file] , 
 Figure 6B. Much more similar than expected. https: imgur.com OwijMcu , 
 Figures 6C and 6D. Much more similar than expected. https: imgur.com iwBwSL8 , 
 #4 Hi Gulyaevia Longivaginata, We appreciate that your brought this up to our attention, and we have immediately started investigating these issues. We also began discussion with our institution for their advice. We will perform a comprehensive investigation of these issues. Sincerely, Jianjun Xie , 
 #3 Hi Gulyaevia Longivaginata We appreciate that your brought this up to our attention, and we have immediately started investigating these issues. We also began discussion with our institution for their advice. We will perform a comprehensive investigation of these issues. Sincerely, Jianjun Xie , 
 ![file] Figure 6A. Similar bands are obvious, only under different exposure time? , 
 #7 Indicated bands are not similar. , 
 #8 Hoya, maybe the ones marked with red and green have the same origin, but Iu2019m confused why an author of this paper would suggest there are additional problems. #7 Dr. Li, are you saying youu2019ve done an investigation and these bands in Figure 6A are also problematic? , 
 #9 This is En-Min Li. There has been a serious fraud use of my ID on Pubpeer. Specifically, someone hacked my email address and registered under my name and made the above comment. This conduct is not only a fraudulent behavior using my name, but also a clear attempt to defame our paper. We are working with Pubpeer to look into this matter. Best Regards, En-Min Li , 
 More duplicate images in Fig. 4, S15, S16, S17 ![file] , 
 #11 This is Jianjun Xie, the first author and co-corresponding author of this paper. These aforementioned experiments were performed by me and I also made these figures. I am now working with our institution to investigate the nature of these issues and will keep you posted. Regards, Jianjun Xie , 
 Is there an update from the authors? I didn t see any correction at the journal website for this paper. , 
 Figure 4D and 4E seem to have another issue (green boxes). *** ![file] , 
 #14 Dear Actinopolyspora Biskrensis, This is Jianjun Xie, the first author and co-corresponding author of this paper. For the issues mentioned above, our institution has conducted and completed a full investigation last year. Subsequently, we reported the institutional investigation to the editorial office of Gastroenterology. After review of the investigational report, the Journal has then decided to publish an erratum for the article. Last month, we communicated with the Journal to follow up on the process of the erratum and we were informed that the erratum has been arranged for publication in the coming issues. We will keep you posted once the final version of the corrections is published. Regards, Jianjun Xie , 
 Correction Published: September 21, 2021 In the above article, Figure 4 included an inadvertently duplicated image in panel D that has been corrected. Figure 6 included duplicated images used in error in panels B, C and D that have been corrected. Additionally, densitometry was added to quantitate the results at the request of the editors. The updated figures are shown here. ![file] ![file] *** These corrections do not address all of the issues raised by readers above. For example the issues with the overlapping images of the supplemental figures is not mentioned. ,